ModernaTX, Inc. et al v. Pfizer Inc. et al

Filing 1

COMPLAINT against BioNTech US Inc., BioNTech SE, Pfizer Inc., BioNTech Manufacturing GmbH Filing fee: $ 402, receipt number AMADC-9469742 (Fee Status: Filing Fee paid), filed by Moderna US, Inc., ModernaTX, Inc.. (Attachments: #1 Exhibit 1, #2 Exhibit 2, #3 Exhibit 3, #4 Exhibit 4, #5 Exhibit 5, #6 Exhibit 6, #7 Exhibit 7, #8 Exhibit 8, #9 Exhibit 9, #10 Civil Cover Sheet, #11 Category Form)(Lee, William)

EXHIBIT 3

US010933127B2

( 12 ) United States Patent

( 10) Patent No .:

Ciaramella et al .

(45 ) Date of Patent :

2317/76 ( 2013.01 ) ; CI2N 2760/18034

( 54 ) BETACORONAVIRUS MRNA VACCINE
( 71 ) Applicant: Moderna TX , Inc. , Cambridge, MA

(2013.01 ) ; C12N 2760/18334 ( 2013.01 ) ; C12N
2760/18434 ( 2013.01 ) ; CI2N 2760/18534
(2013.01 ) ; CI2N 2760/18634 ( 2013.01 ) ; C12N

(US)

( 72 ) Inventors: Giuseppe Ciaramella , Sudbury, MA
( US ) ; Sunny Himansu , Winchester,
MA (US)
( 73 ) Assignee : ModernaTX, Inc. , Cambridge, MA
( US )

2770/20034 (2013.01 ) ; YO2A 50/30 (2018.01 )

( 58 ) Field of Classification Search
None

See application file for complete search history.
References Cited
U.S. PATENT DOCUMENTS

(56)

Subject to any disclaimer, the term of this
patent is extended or adjusted under 35
U.S.C. 154 ( b ) by 0 days.
( 21 ) Appl. No .: 16 /880,829
May 21 , 2020
( 22 ) Filed :
Prior Publication Data
( 65 )
US 2020/0282046 A1
Sep. 10, 2020

( * ) Notice :

3,906,092 A
4,790,987 A
5,169,628 A

5,427,782
6,225,091
6,500,419
6,514,948
7,001,890
7,208,161

7,531,342 B2
7,671,186 B2

7,704,720
8,217,016
8,252,289
8,710,200
8,722,341
8,734,853
8,754,062
8,822,663
8,841,433
8,889,146
8,927,206
8,999,380
9,192,661

B2
B2
B2
B2
B2
B2
B2
B2
B2
B2
B2
B2
B2
9,221,891 B2

( 60 ) Division of application No. 16 / 805,587 , filed on Feb.
28 , 2020 , now Pat. No. 10,702,600 , which is a
continuation of application No. 16 /368,270 , filed on

A61K 39/215

( 2006.01 )

A61K 39/12

(2006.01 )
( 2006.01 )
( 2006.01 )
( 2006.01 )
( 2006.01 )

A61P 11/00
A61K 39/155
COZK 16/10
A61K 39/00

(52) U.S. CI .
CPC

A61K 39/155 (2013.01 ) ; A61K 39/12
(2013.01 ) ; A61K 39/215 (2013.01 ) ; A61P
11/00 (2018.01 ) ; C07K 16/10 ( 2013.01 ) ; CO7K
16/1027 ( 2013.01 ) ; A6IK 2039/53 ( 2013.01 ) ;
AOIK 2039/55511 (2013.01 ) ; A61K
2039/55555 (2013.01 ) ; A61K 2039/6018
( 2013.01 ) ; A61K 2039/70 ( 2013.01 ) ; CO7K

9/1975 Hilleman et al .

12/1988 Compans et al .
12/1992 Wathen
6/1995 Compans et al .

5/2001 Klein et al .
12/2002 Hone et al .
2/2003 Raz et al .

2/2006 Wagner et al.
4/2007 Murphy et al .

11/2008 Fouchier et al .
5/2009 Fouchier et al .
3/2010 Klein et al .

4/2010 Tang et al .

7/2012 Hoerr et al.

8/2012
4/2014
5/2014
5/2014

Eleouet et al.
Schrum et al.
Fouchier et al .
Sood et al .

6/2014 De Fougerolles et al .

9/2014 Schrum et al .
9/2014 Fouchier et al .
11/2014 Blais et al .

1/2015 De Jong et al .

4/2015 Bancel et al .
11/2015 Jain et al.
12/2015 Bancel et al .

(Continued )
FOREIGN PATENT DOCUMENTS
CA
EP

2473135
1026253

6/2003
8/2000

(Continued )
OTHER PUBLICATIONS

U.S. Appl. No. 16 /048,154 , filed Jul. 27 , 2018 , Ciaramella et al .

(Continued )

22 , 2015 .

( 51 ) Int . Cl .

A
B1
B1
B1
B1
B1

7,449,324 B2

Related U.S. Application Data

Mar. 28 , 2019 , now Pat. No. 10,702,599 , which is a
continuation of application No. 16 /040,981 , filed on
Jul. 20 , 2018 , now Pat . No. 10,272,150 , which is a
continuation of application No. 15 / 674,599 , filed on
Aug. 11 , 2017 , now Pat . No. 10,064,934 , which is a
continuation
of
application
No.
PCT /US2016 / 058327 , filed on Oct. 21 , 2016 .
(60) Provisional application No. 62/ 247,394 , filed on Oct.
28 , 2015, provisional application No. 62 /247,362 ,
filed on Oct. 28 , 2015 , provisional application No.
62 / 247,297 , filed on Oct. 28 , 2015 , provisional
application No. 62 / 247,483 , filed on Oct. 28 , 2015 ,
provisional application No. 62/ 244,802 , filed on Oct.
22 , 2015 , provisional application No. 62 /245,031 ,
filed on Oct. 22 , 2015 , provisional application No.
62/ 244,946 , filed on Oct. 22 , 2015 , provisional
application No. 62 / 244,813 , filed on Oct. 22 , 2015 ,
provisional application No. 62 / 244,837 , filed on Oct.

US 10,933,127 B2
Mar. 2 , 2021

Primary Examiner — Nicole Kinsey White

( 74 ) Attorney, Agent, or Firm - Wolf, Greenfield &

Sacks , P.C.
ABSTRACT

( 57 )

The disclosure relates to respiratory virus ribonucleic acid
(RNA ) vaccines and combination vaccines , as well as meth
ods of using the vaccines and compositions comprising the
vaccines .

21 Claims , 24 Drawing Sheets
Specification includes a Sequence Listing .

US 10,933,127 B2
Page 2

( 56 )

References Cited
U.S. PATENT DOCUMENTS
9,283,287 B2

9,303,079
9,376,726
9,464,124
9,512,456
9,567,653
9,597,380
9,623,095
9,669,089
9,790,531
9,868,691

B2
B2
B2
B2
B2
B2
B2
B2
B2
B2

9,872,900 B2
9,937,196 B2

10,064,934 B2
10,064,935 B2

10,124,055
10,207,010
10,273,269
10,449,244
10,465,190
10,493,143
10,526,629
10,653,712
10,653,767

10,695,419
2003/0092653
2003/0232061
2004/0005545
2004/0096451

B2
B2
B2
B2
B1
B2
B2
B2
B2
B2
A1
A1
Al
Al

2005/0032730 Al
2005/0059624 Al
2005/0250723 A1

2006/0002958 A1
A1
Al
Al

2006/0172003
2006/0228367
2007/0280929
2008/0025944
2008/0171711
2009/0123529
2009/0162395
2010/0203076
2010/0239608

A1
A1
A1
Al
A1
Al

2010/0272747 A1

2010/0291156
2010/0305196
2011/0135645
2011/02 50225
2011/0269950
2012/0009221
2012/0045471

Al
A1
Al
A1
A1
Al
A1

2012/0219573 A1
2013/0022538 A1
2013/0078281 Al
2013/0102034
2013/0121988
2013/0142818
2013/0183355
2013/0195867
2013/0195967
2013/0195969
2013/0202684
2013/0236974

Al
Al
Al
A1
A1
A1
A1
A1
A1

2013/0243848 A1
2013/0245103 A1
2013/0259923 A1
2013/0266640
2013/0295043
2013/0336998
2014/0024076
2014/0037660
2014/0147432
2014/0148502
2014/0193482
2014/0206752
2014/0271829

A1
A1
Al
A1
A1
A1
Al
Al
Al
Al

3/2016 Bancel et al.
4/2016 Bancel et al .

6/2016 Fouchier et al .
10/2016 Bancel et al .

12/2016 Wang et al .
2/2017 Fouchier et al .
3/2017 Chakraborty et al.
4/2017 Kallen et al .
6/2017 Thess et al .

10/2017 Wang et al .
1/2018
1/2018
4/2018
9/2018

Benenato et al .
Ciaramella et al .
Jain et al .
Ciaramella et al .

9/2018 Ciaramella et al .

11/2018
2/2019
4/2019
10/2019
11/2019
12/2019
1/2020

Ciaramella et al .
Besin et al .
Ciaramella
Ciaramella et al .
Chen et al .
Ciaramella et al .
Rabideau et al .

5/2020
6/2020
5/2003
12/2003
1/2004

Ciaramella et al .
Ciaramella et al .
Kisich et al .
Fouchier et al .
Fouchier et al .

5/2020 Hoge

5/2004 Young et al .

2/2005 Von Der Mulbe et al .
3/2005 Hoerr et al .
11/2005 Hoerr et al .

1/2006 Naylor et al.

8/2006 Meers et al .

10/2006 Ulbrandt et al .

12/2007
1/2008
7/2008
5/2009
6/2009
8/2010
9/2010
10/2010
11/2010
12/2010
6/2011

Hoerr et al .
Hoerr et al .
Hoerr et al .
Xiaomao
Crowe et al .
Fotin -Mleczek et al .
Von Der Mulbe et al .
Chow et al .
Barner et al .
Probst et al .
Williamson et al .

10/2011 Fotin -Mleczek et al .
11/2011 Von Der Mulbe et al .
1/2012 Hoerr et al .
2/2012 Haller et al .

8/2012 Baumhof et al .

1/2013 Rossi
3/2013 He et al .
4/2013 Schrum et al.

5/2013 Hoerr et al .

6/2013
7/2013
8/2013
8/2013
8/2013

Baumhof et al .
Jain et al .
Hoerr et al .
Guild et al .
Geall et al .

2014/0370497 A1
2014/0378538 A1
2015/0051268
2015/0093413
2015/0126589
2015/0141499
2015/0307542
2015/0315541
2015/0335728
2016/0024141
2016/0032273
2016/0038612
2016/0039884
2016/0151474
2016/0271272
2016/0317647
2016/0331828
2017/0065675
2017/0130255

A1
A1
Al
Al
Al
A1
Al
A1
Al
A1
Al
Al
Al
A1
A1
Al
Al

2017/0340724
2018/0000953
2018/0002393
2018/0008694
2018/0028645
2018/0028664
2018/0237849
2018/0243225
2018/0243230
2018/0256628
2018/0271970
2018/0273977
2018/0274009
2018/0280496
2018/0289792
2018/0303929
2018/0311336
2018/0311343
2018/0318409
2018/0363019
2018/0371047
2019/0002890
2019/0008938
2019/0085368
2019/0099481
2019/0175517
2019/0192646
2019/0192653
2019/0275170
2019/0298658
2019/0314493
2019/0336595
2019/0351040
2020/0030432
2020/0032274
2020/0038499
2020/0054737
2020/0069793
2020/0069794
2020/0071689
2020/0109420
2020/0129608
2020/0129615
2020/0239869

A1
Al
A1
Al
Al
Al
A1
A1
Al
A1
A1
Al
A1
Al
A1
Al
A1
A1
A1
Al
Al
A1
A1
A1
Al
A1
A1
A1
A1
Al
Al
A1
A1
A1
Al
Al
Al
Al
Al
Al
Al
Al
A1
Al

2017/0202979 Al

12/2014
12/2014
2/2015
4/2015

Fouchier et al .
Bancel
Bancel et al .
Thess et al.

5/2015 Geiger et al.
5/2015 Bancel et al .
10/2015 Roy et al.
11/2015 Bancel et al .

11/2015 Wong et al.
1/2016 Issa et al .

2/2016 Shahrokh et al .

2/2016 Hoge et al .

2/2016 Li et al .

6/2016 Kallen et al .
9/2016 Bancel et al .

11/2016 Ciaramella et al .

11/2016 Ciaramella et al .
3/2017 Bancel et al .

5/2017 Wang et al .
7/2017 Chakraborty et al .

11/2017 Ciaramella et al .
1/2018 Almarsson et al .

1/2018 Bancel et al .
1/2018 Ciaramella et al .
2/2018 Ciaramella et al .
2/2018 Besin et al .

8/2018 Thompson

8/2018 Ciaramella
8/2018 Smith

9/2018 Hoge et al .

9/2018 Ciaramella et al .
9/2018 Mousavi et al.

9/2018 Marquardt et al .

10/2018
10/2018
10/2018
11/2018

Ciaramella et al .
Ciaramella et al .
Ciaramella et al .
Ciaramella et al .

11/2018 Huang et al .
11/2018 Valiante et al .
12/2018 Hoge
12/2018 Ticho et al.

1/2019 Martini et al .

1/2019
3/2019
4/2019
6/2019
6/2019

Ciaramella et al .
Bancel et al .
Ciaramella et al .
Martini et al .
Cohen et al .

6/2019 Hoge et al .

9/2019 Benenato et al .
10/2019 Benenato
10/2019 Ciaramella et al .

11/2019 Ciaramella
11/2019 Valiante et al .
1/2020 Ciaramella et al .

1/2020 Mauger et al.

2/2020 Narayanan et al .

2/2020
3/2020
3/2020
3/2020
4/2020
4/2020
4/2020
7/2020

Ciaramella et al .
Ciaramella
Ciaramella et al .
Miracco
Brito et al .
Ciaramella et al .
Ciaramella et al .
Issa et al .

8/2013 Geall et al .

9/2013 De Fougerolles

FOREIGN PATENT DOCUMENTS

9/2013 Lobovkina et al .

9/2013 de Fougerolles et al .
10/2013 De Fougerolles et al .
10/2013 Bancel et al .
11/2013 Kallen et al .

12/2013 Kallen et al .

1/2014 Tang et al .

2/2014
5/2014
5/2014
7/2014

Folin -Mleczek et al .
Bancel et al.
Bancel et al .
Bancel et al.

7/2014 Afeyan et al .
9/2014 Lilja et al .

EP

EP
EP
WO
WO
WO
WO
WO
WO

WO

WO
WO

1083232
1905844 A2
2548960 A1
WO 1987/005326 A1
WO 1990/11092
WO 1993/14778

WO 1995/24485
WO 1995/26204
WO 1995/33835
WO 1998/058956
WO 1999/33982
WO 2003/072720 A2

2/2005

2/2008

1/2013
9/1987
10/1990
8/1993
9/1995
10/1995
12/1995
12/1998

7/1999

9/2003

US 10,933,127 B2
Page 3

( 56 )

References Cited
FOREIGN PATENT DOCUMENTS

WO
WO
WO
WO
WO
WO

WO
WO

WO

WO

WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO

WO
WO
WO
WO

WO
WO
WO
WO
WO

WO 2004/076645 Al
WO 2005/009346

9/2004
2/2005

WO
WO
WO
WO
WO
WO

3/2005

2005/027963
2006/056027
2006/071903
2006/095259
2007/038862
2007/095976

WO
WO
WO
WO
WO
WO

2008/052770
2009/030254
2009/030481
2009/095226
2009/127230
2010/037408
WO 2010/037539
WO 2010/042877
WO 2010/054406
WO 2010/088927
WO 2010/149743
WO 2011/005799
WO 2011/026641
WO 2011/068810
WO 2011/069529
WO 2011/069586
WO 2011/144358
WO 2012/006369

A2
A1

7/2006
A1
A2
A2
A1
Al
A1
Al
A1
Al
A1
A1
A1
A2
A2
A9
A1
A1
A1
Al
A2

WO 2012/019630 A1

WO 2012/019780
WO 2012/031043
WO 2012/116714
WO 2012/116715
WO 2012/116810
WO 2012/116811
WO 2013/055905
WO 2013/090186
WO 2013/090648
WO 2013/102203
WO 2013/120628
WO 2013/120629
WO 2013/185069
WO 2014/089486
WO 2014/144196
WO 2014/152027
WO 2014/152774
WO 2014/152940
WO 2014/160243
WO 2015/024668
WO 2015/095340
WO 2015/101414
WO 2015/101415

6/2006

A1
A1
Al
A1
Al
Al
A1
Al
A1
Al
A1
Al
Al
Al
A1
Al
Al
A1
A1
A2
A1
A2
Al

9/2006

4/2007
8/2007
5/2008
3/2009

3/2009

8/2009

10/2009
4/2010
4/2010

4/2010
5/2010
8/2010

12/2010
1/2011
3/2011
6/2011

6/2011

6/2011
11/2011
1/2012
2/2012

2/2012

3/2012
9/2012
9/2012
9/2012
9/2012
4/2013
6/2013

6/2013

7/2013
8/2013
8/2013

12/2013
6/2014

9/2014

9/2014
9/2014
9/2014
10/2014
2/2015

6/2015

7/2015
7/2015

WO 2015/130584 A2

9/2015
6/2016

A1
A1
A1
A1
A1
A1
A1
A1
A1
A1
A1
A1
A1
A1
A1
A1
A1
A1

10/2016
12/2016

WO 2017/201349 Al

11/2017

WO
WO
WO
WO

3/2018

WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO
WO

2016/103238
2016/164762
2016/201377
2017/015457
2017/015463
2017/019935
2017/020026
2017/062513
2017/066789
2017/070601
2017/070616
2017/070618
2017/070620
2017/070622
2017/070623
2017/201333
2017/201340
2017/201342
2017/201347

2018/053209
2018/075980
2018/081459
2018/081462

Al
A1
Al
A1

1/2017

1/2017
2/2017
2/2017
4/2017

4/2017
4/2017

4/2017

4/2017
4/2017
4/2017
4/2017
11/2017
11/2017
11/2017
11/2017
4/2018
5/2018
5/2018

WO

WO
WO
WO
WO
WO

WO
WO
WO
WO
WO
WO
WO
WO

WO
WO
WO
WO

WO
WO
WO
WO
WO
WO

WO
WO
WO
WO

WO 2018/089851
WO 2018/107088
WO 2018/111967
WO 2018/144082
WO 2018/144778
WO 2018/151816
WO 2018/170245
WO 2018/170256
WO 2018/170260
WO 2018/170270
WO 2018/170347
WO 2018/175783
WO 2018/187590
WO 2018/200737
WO 2018/232355

A1
A1
A1
A1
A1
A1
A1
Al
A1
A1
A1
A1
A2
A1
A1

WO
WO
WO
WO
WO
WO

A1
A1
A1
A1
A1
Al

12/2018
2/2019
2/2019

WO 2019/148101 Al

8/2019

WO 2020/006242 A1

1/2020
3/2020
3/2020
3/2020
3/2020
5/2020

2018/232357
2019/036670
2019/036682
2019/036683
2019/036685
2019/103993

WO 2020/056370 A1
WO 2020/061284 Al

WO 2020/061295 A1
WO 2020/061367 A1
WO 2020/097291 A1

5/2018
6/2018
6/2018

8/2018

8/2018

8/2018

9/2018
9/2018

9/2018
9/2018

9/2018
9/2018
10/2018
11/2018
12/2018

2/2019

2/2019
5/2019

OTHER PUBLICATIONS

U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.

16 /450,882, filed Jun . 24 , 2019 , Ciaramella .
16 /009,880 , filed Jun . 15 , 2018 , Ciaramella et al.
16 / 582,621 , filed Sep. 25 , 2019 , Chen et al.
16 / 839,278 , filed Apr. 3 , 2020 , Hoge et al .
16 /389,545 , filed Apr. 19 , 2019 , Ciaramella et al.
16 /368,270 , filed Mar. 28 , 2019 , Ciaramella et al .

U.S. Appl. No. 16 / 805,587 , filed Feb. 28 , 2020 , Ciaramella et al .
PCT/US2016 /058327, Jun . 29 , 2017 , International Search Report

and Written Opinion .
[No Author Listed ], “ Messenger RNA ” , Internet: Wikipedia . Jun .
19 , 2013 , XP002699196 , Retrieved from the Internet: URL : http : //
en.wikipedia.org/wiki/Messenger RNA .
Archer, S.J. , Induction of a T -cell specific antigen on bone marrow
lymphocytes with thymus RNA . Immunology. Jan. 1978; 34 ( 1): 123
9.
Ashley, D.M. et al ., Bone marrow - generated dendritic cells pulsed
with tumor extracts or tumor RNA induce antitumor immunity
against central nervous system tumors. J Exp Med . Oct. 6 , 1997 ;
186 ( 7 ) : 1177-82 .
Bettinger, T. et al . , Peptide -mediated RNA delivery: a novel approach
for enhanced transfection of primary and post -mitotic cells . Nucleic
Acids Res. Sep. 15 , 201;29 ( 18 ): 3882-91.
Bogers et al . , Potent immune responses in rhesus macaques induced
by nonviral delivery of a self-amplifying RNA vaccine expressing
HIV type 1 envelope with a cationic nanoemulsion.J Infect Dis .
Mar. 15 , 2015 ; 211 ( 6 ) : 947-55 . doi : 10.1093/ infdis/ jiu522. Epub Sep.
18 , 2014 .
Bonehill , A. , et al . , Single - step antigen loading and activation of
dendritic cells by mRNA electroporation for the purpose of thera
peutic vaccination in melanoma patients. Clin Cancer Res. May
2009 ; 15 ( 10 ) : 3366-3375 .

Bose , S. et al . , Role of nucleolin in human parainfluenza virus type
3 infection of human lung epithelial cells . J Viral . Aug.
2004 ; 78 ( 15 ) : 8146-58 .
Conry, R.M. et al., Characterization of a messenger RNA polynucleotide

vaccine vector. Cancer Res. Apr. 1 , 1995 ; 55 ( 7 ) : 1397-1400 .
Dahlman , James E. et al . , In vivo endothelial siRNA delivery using
polymeric nanoparticles with low molecular weight, Nature Nano
technology, 2014 , No. vol . # , pp . 1-8 .
Diken et al . , Current Developments in Actively Personalized Cancer
Vaccination with a Focus on RNA as the Drug Format. Prog Tumor
Res. 2015 ; 42 : 44-54 . doi: 10.1159 /000437184 . Epub Sep. 4 , 2015 .
Review .

US 10,933,127 B2
Page 4

( 56 )

References Cited
OTHER PUBLICATIONS

Fleeton et al . , Self - replicative RNA vaccines elicit protection against
influenza A virus, respiratory syncytial virus, and a tickborne

encephalitis virus. J Infect Dis . May 1 , 2001 ; 183 ( 9 ) : 1395-8 . Epub
Geall et al ., Nonviral delivery of self -amplifying RNA vaccines .
Proc Natl Acad Sci US A. Sep. 4 , 2012 ; 109 (36 ): 14604-9 . doi: 10 .
1073 /pnas.1209367109. Epub Aug. 20 , 2012 .
GenBank Accession No. AHX22069 . First seen on NCBI on May
14 , 2014
Gilboa , E. et al., Cancer immunotherapy with mRNA - transfected
dendritic cells . Immunol Rev. Jun . 2004 ; 199 : 251-63 .
Greer et al . , Long -term protection in hamsters against human
parainfluenza virus type 3 following mucosal or combinations of
mucosal and systemic immunizations with chimeric alphavirus
based replicon particles. Scand J Immunol. Dec. 2007 ;66 (6 ):645
Mar. 30 , 2001 .

Kozielski et al., Bioreducible cationic polymer -based nanoparticles
for efficient and environmentally triggered cytoplasmic siRNA
delivery to primary human brain cancer cells . ACS Nano . Apr. 22 ,
2014 ; 8 (4 ) : 3232-41 . doi: 10.1021 / nn500704t. Epub Apr. 3 , 2014 .
Kreiter, S. , et al . , Intranodal vaccination with naked antigen
encoding RNA elicits potent prophylactic and therapeutic antitumoral
immunity. Cancer Res. 2010 ; 70 : 9031-9040 .
Kreiter, S. , et al . , Tumor vaccination using messenger RNA : pros
pects of a future therapy. Curr Opinion in Immun . Jun . 2011 ; 23 ( 3 ) :
399-406 .
Kuhn , A.N. , et al ., mRNA as a versatile tool for exogenous protein

expression. Current Gene Therapy. Oct. 2012 ; 12 ( 5 ) : 347-361 .

Leitner, W.W. et al . , DNA and RNA -based vaccines: principles ,
progress and prospects . Vaccine. Dec. 10 , 1999 ; 18 ( 9-10 ) :765-77.

Li , L. et al . , Overcoming obstacles to develop effective and safe
siRNA therapeutics. Expert Opin Biol Ther. May 2009 ; 9 ( 5 ) :

609-19 .

Lorenzi , J.C. , et al . , Intranasal vaccination with messenger RNA as

53. Epub Oct. 17 , 2007 .

a new approach in gene therapy: Use against tuberculosis. BMC

CNS Pre -Operatively for Neuroprotection and Following Neurotrauma.
Molecular Therapy. 2004 ; 9 , S258 - S258 .
Heiser, A. et al . , Induction of polyclonal prostate cancer - specific
CTL using dendritic cells transfected with amplified tumor RNA . J

Mockey et al ., mRNA - based cancer vaccine : prevention of B16

Hecker, J.G. et al ., Non - Viral DNA and mRNA Gene Delivery to the

Immunol. Mar. 1 , 2001 ; 166 ( 5 ) : 2953-60 .

Heyes et al . , Cationic lipid saturation influences intracellular deliv
ery of encapsulated nucleic acids . J Control Release . Oct. 3 ,
2005 ; 107 ( 2 ) : 276-87 .
Hoerr, I. et al . , In vivo application of RNA leads to induction of
specific cytotoxic T lymphocytes and antibodies. EurJ Immunol.
Jan. 2000 ; 30 ( 1 ) : 1-7 .
Hoerr, I. et al . , Stabilized Messenger RNA ( RNActiveTM ) as a Tool
for Innovative Gene Delivery. Tissue Engineering. Apr. 2007 ; 13 (4 ) :
865-925 .
Hoerr, More than a messenger: A new class of drugs-mRNA -based
therapeutics. Genetic Engineering & Biotechnology News. Jun . 18 ,
2013. http://www.genengnews.com/gen-articles/more-than-a-messenger
a -new - class-of -drugs -mrna -based - therapeutics /4916 / [ last accessed
Mar. 25, 2016] .
Holtkamp, S. et al . , Modification of antigen - encoding RNA increases

stability, translational efficacy, and T -cell stimulatory capacity of

dendritic cells . Blood . Dec. 15 , 2006 ; 108 ( 13 ) : 4009-17 .

Jirikowski, G.F. , et al., Reversal of diabetes insipidus in Brattleboro

Rats: Intrahypothalamic injection of vasopressin mRNA . Science .
Feb. 1992 ; 255 (5047) : 996-998 .
Kallen et al . , A development that may evolve into a revolution in

medicine: mRNA as the basis for novel , nucleotide -based vaccines

and drugs. Ther Adv Vaccines . Jan. 2014 ; 2 ( 1 ) : 10-31 . doi: 10.1177 /

2051013613508729 .

Biotechnol. Oct. 2010 ; 10 (77 ): 1-11 .

melanoma progression and metastasis by systemic injection of
MART1 mRNA histidylated lipopolyplexes, Cancer Gene Therapy,
2007 , 14 , pp . 802-814 .
Magini et al . , Self - Amplifying mRNA Vaccines Expressing Mul
tiple Conserved Influenza Antigens Confer Protection against Homolo
gous and Heterosubtypic Viral Challenge. PLoS One . Aug. 15 ,
2016 ; 11 ( 8 ) : e0161193 . doi: 10.1371/ journal.pone.0161193. eCollec
tion 2016
Martinon , F. et al . , Induction of virus- specific cytotoxic T lympho
cytes in vivo by liposome- entrapped mRNA . EurJ Immunol. Jul.
1993 ; 23 ( 7 ) : 1719-22 .
Midoux et al . , Lipid-based mRNA vaccine delivery systems. Expert
Rev Vaccines. Feb. 2015 ; 14 ( 2 ) : 221-34 . doi : 10.1586/ 14760584 .
2015.986104 . Epub Dec. 26 , 2014. Review .

Mitchell , DA et al . , RNA transfected dendritic cells as cancer

vaccines. Curr Opin Mal Ther. Apr. 2000 ; 2 ( 2 ) : 176-81 .

Mitchell , DA et al . , RNA -transfected dendritic cells in cancer
immunotherapy. J Clin Invest . Nov. 2000 ; 106 ( 9 ) : 1065-9 .
Muller, M.R. et al . , Transfection of dendritic cells with RNA

induces CD4- and COB -mediated T cell immunity against breast

carcinomas and reveals the immunodominance of presented T cell
epitopes . J Immunol. Jun . 15 , 2003 ; 170 ( 12 ) : 5892-6 .
Narayanan et al . , Interplay between viruses and host mRNA deg
radation . Biochim Biophys Acta . Jun .- Jul. 2013 ; 1829 ( 6-7 ) : 732-41 .

doi : 10.1016 /j.bbagrm.2012.12.003. Epub Dec. 26 , 2012 .
Petsch et al . , Protective efficacy of in vitro synthesized , specific

mRNA vaccines against influenza A virus infection . Nat Biotechnol.

Dec. 2012 ; 30 ( 12 ) : 1210-6 . doi : 10.1038 /nbt.2436 . Epub Nov. 25 ,

Kallen et al ., A novel , disruptive vaccination technology : self
adjuvanted RNActive( ® ) vaccines . Hum Vaccin Immunother. Oct.
2013 ; 9 ( 10 ) : 2263-76 . doi: 10.4161/hv.25181. Epub Jun . 4 , 2013 .
Review .
Kalra et al . , Virosomes : As a Drug Delivery Carrier. American
Journal of Advanced Drug Delivery . 2013 ; 1 : 29-35 .
Kanapathipillai, et al ., Nanoparticle targeting of anti- cancer drugs
that alter intracellular signaling or influence the tumor microenviron
ment, Adv . Drug Deliv . Rev. ( 2014 ) , pp . 1-12 .
Kariko, K. , et al . , Generating the optimal mRNA for therapy: HPLC
purification eliminates immune activation and improves translation
of nucleoside -modified , protein -encoding mRNA, Nucleic Acids
Research , Oxford University Press , GB , vol . 39 , No. 21 , Sep. 2 ,
2011 (Sep. 2 , 2011 ) , e142 . doi : 10.1093 /nar / gkr695. Epub Sep. 2 ,

e11085 .

Kauffman et al ., Optimization of Lipid Nanoparticle Formulations
for mRNA Delivery in Vivo with Fractional Factorial and Definitive
Screening Designs . Nano Lett . Nov. 11 , 2015 ; 15 ( 11 ) : 7300-6 . doi :
10.1021/ acs.nanolett .5b02497. Epub Oct. 20 , 2015 .
Kisich et al . , Antimycobacterial agent based on mRNA encoding
human beta -defensin 2 enables primary macrophages to restrict

nrd4278 . Epub Sep. 19 , 2014 .
Schmitt, W.E. et al . , In vitro induction of a bladder cancer- specific
T - cell response by mRNA -transfected dendritic cells . J Cancer Res

2011 .

growth of Mycobacterium tuberculosis. Infect Immun . Apr.
2001 ; 69 (4 ) : 2692-9 .

2012 .

Phua et al . , Mesenger RNA (MRNA ) nanoparticle tumour vaccina

tion . Nanoscale. Jul. 21 , 2014 ; 6 ( 14 ) : 7715-29 . dsoi : 10.1039 /
c4nr01346h . Review .
Pulford , B. , et al . , Liposome - siRNA -peptide complexes cross the
blood -brain barrier and significantly decrease PrP'C on neuronal
cells and PrP'RES in infected cell cultures. PLoS ONE . 201 0 ; 5 ( 6 ) :

Rabinovich , P.M., et al . , Synthetic messenger RNA as a tool for

gene therapy. Hum . Gene Ther. Oct. 2006 ; 17 : 1027-1035 .

Rittig et al . , Intradermal vaccinations with RNA coding for TAA
generate CD8 + and CD4 + immune responses and induce clinical
benefit in vaccinated patients. Mol Ther. May 2011 ; 19 ( 5 ) : 990-9 .
doi : 10.1038 /mt.2010.289. Epub Dec. 28 , 2010 .
Sahin et al . , mRNA - based therapeutics developing a new class of
drugs. Nat Rev Drug Discov. Oct. 2014 ; 13 ( 10 ) : 759-80 . doi: 10.1038 /
Clin Oncol. 2001 ; 127 ( 3 ) : 203-6 .

Schott , J.W., et al., Viral and non -viral approaches for transient
delivery of mRNA and proteins . Current Gene Ther. 2011 ; 11 ( 5 ) :
382-398 .

US 10,933,127 B2
Page 5

( 56 )

References Cited
OTHER PUBLICATIONS

Segura, J. , et al . , Monitoring gene therapy by external imaging of

mRNA : Pilot study on murine erythropoietin. Ther Drug Monit .

Oct. 2007 ; 29 ( 5 ) : 612-8 .
Smits, E. , et al . , RNA -based gene transfer for adult stem cells and

T cells . Leukemia . 2004 ; 18 : 1898-1902 .

Sohn , R.L. , et al . , In -vivo particle mediated delivery of mRNA to
mammalian tissues : ballistic and biological effects. Wound Rep and
Regen . Jul. - Aug. 2001 ; 287-296 .

Strong, V.T. et al . , Incorporation of beta - globin untranslated regions
into a Sindbis virus vector for augmentation of heterologous mRNA
expression . Gene Ther. Jun . 1997 ; 4 ( 6 ) : 624-7 .
Sullenger, BA et al . , Emerging clinical applications of RNA . Nature.

Jul. 11 , 2002 ;418 (6894 ): 252-8 .

Tavernier, G. , et al . , mRNA as gene therapeutic: How to control
protein expression. J. of Controlled Release . Mar. 2011 ; 150 ( 3 ) :
238-247 .

Teufel, R. et al ., Human peripheral blood mononuclear cells transfected

with messenger RNA stimulate antigen - specific cytotoxic T-lym
phocytes in vitro. Cell Mol Life Sci . Aug. 2005 ; 62 ( 15 ) : 1755-62 .
Thess et al., Sequence - engineered mRNA WithoutChemical Nucleoside
Modifications Enables an Effective Protein Therapy in Large Ani

mals . Mol Ther. Sep. 2015 ; 23 ( 9 ) : 1456-64 . doi : 10.1038 /mt.2015 .
103. Epub Jun . 8 , 2015 .
Wang et al . , Systemic delivery of modified mRNA encoding herpes
simplex virus 1 thymidine kinase for targeted cancer gene therapy.
Mol Ther. Feb. 2013 ; 21 ( 2 ) : 358-67 . doi : 10.1038 /mt.2012.250 . Epub
Dec. 11 , 2012 .
Wong et al . , An mRNA vaccine for influenza . Nat Biotechnol . Dec.
2012 ; 30 ( 12 ) : 1202-4 . doi: 10.1038/nbt.2439 .
Yamamoto et al . , Current prospects for mRNA gene delivery ,

European Journal ofPharmaceutics and Biopharmaceutics 71 ( 2009 )

484-489 .

Zhou , W.Z. et al . , RNA melanoma vaccine : induction of antitumor

immunity by human glycoprotein 100 mRNA immunization . Hum
Gene Ther. Nov. 1 , 1999 ; 10 ( 16 ): 2719-24 .

U.S. Appl. No. 16 /036,318 , filed Jul. 16 , 2018 , Ciaramella et al .
U.S. Appl. No. 16 / 144,394 , filed Sep. 27 , 2018 , Ciaramella et al .
U.S. Appl. No. 90 /014,395 , filed Oct. 24 , 2019 , Ciaramella et al.
U.S. Appl. No. 15 /748,773 , filed Jan. 30 , 2018 , Ciaramella et al .
U.S. Appl. No. 15 /753,293 , filed Feb. 17 , 2018 , Smith .
U.S. Appl. No. 15 /753,297 , filed Feb. 17 , 2018 , Thompson.
U.S. Appl. No. 15 /748,782 , filed Jan. 30 , 2018 , Mousavi et al .
U.S. Appl. No. 15 /767,587 , filed Apr. 11 , 2018 , Ciaramella .
U.S. Appl. No. 16 / 833,409 , filed Mar. 27 , 2020 , Ciaramella .
U.S. Appl. No. 15 /767,600 , filed Apr. 11 , 2018 , Ciaramella et al.
U.S. Appl. No. 15 /769,710 , filed Apr. 19 , 2018 , Ciaramella et al.
U.S. Appl. No. 15 /767,609 , filed Apr. 11 , 2018 , Ciaramella et al .
U.S. Appl. No. 15 /767,613 , filed Apr. 11 , 2018 , Ciaramella et al.
U.S. Appl. No. 15 /767,618 , filed Apr. 11 , 2018 , Ciaramella et al.
U.S. Appl. No. 16 / 853,973 , filed Apr. 21 , 2020 , Ciaramella et al.

U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.

16 / 850,519 , filed Apr. 16 , 2020 , Ciaramella et al.
15 /746,286 , filed Jan. 19 , 2018 , Ciaramella et al .
16 / 897,859 , filed Jun . 10 , 2020 , Ciaramella et al.
16 / 898,268 , filed Jun . 10 , 2020 , Ciaramella et al.
15 /981,762 , filed May 16 , 2018 , Bancel et al .
16 / 599,661 , filed Oct. 11 , 2019 , Besin et al .
16 /333,330 , filed Mar. 14 , 2019 , Hoge et al .
16 / 864,566 , filed May 1 , 2020 , Ciaramella et al.
16 / 897,734 , filed Jun . 10 , 2020 , Ciaramella et al.
16 / 468,838, filed Jun . 12 , 2019 , Miracco .
16 /001,765 , filed Jun . 6 , 2018 , Marquardt et al .
16 /348,943 , filed May 10 , 2019 , Ciaramella .
16 /467,142, filed Jun . 6 , 2019 , Ciaramella et al .
16 /603,111 , filed Oct. 4 , 2019 , Brito et al .
16 /482,844, filed Aug. 1 , 2019 , Valiante et al .

U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.

16 /494,162, filed Sep. 13 , 2019 , Ciaramella .
16 / 494,988, filed Sep. 17 , 2019 , Ciaramella et al .
16 /639,265 , filed Feb. 14 , 2020 , Issa et al.
16 /639,305 , filed Feb. 14 , 2020 , Issa et al .
16 /765,285 , filed May 19 , 2020 , Ciaramella et al .
16 /302,607 , filed Nov. 16 , 2018 , Benenato et al .
16 /623,069 , filed Dec. 16 , 2019 , Hoge et al .

U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.
U.S. Appl. No.

16 /496,135, filed Sep. 20 , 2019 , Narayanan et al .
16 /483,012, filed Aug. 1 , 2019 , Mauger et al .
16 /657,122 , filed Oct. 18 , 2019 , Rabideau et al .
16 /362,366 , filed Mar. 22 , 2019 , Ciaramella .
16 /493,986 , filed Sep. 13 , 2019 , Ciaramella et al .
16 /494,130 , filed Sep. 13 , 2019 , Ciaramella et al .
16 /494,103, filed Sep. 13 , 2019 , Ciaramella et al .

U.S. Appl. No. 16 /639,403 , filed Feb. 14 , 2020 , Hoge et al .
U.S. Appl. No. 16 / 848,318 , filed Apr. 14 , 2020 , Ciaramella et al .
U.S. Appl. No. 16 /965,589 , filed Jul. 28 , 2020 , Ciaramella et al .
U.S. Appl. No. 16 /608,451 , filed Oct. 25 , 2019 , Ciaramella et al .
U.S. Appl. No. 16 /788,182 , filed Feb. 11 , 2020 , Panther et al .
U.S. Appl. No. 16 /794,318 , filed Feb. 19 , 2020 , Mauger et al .
Byoung - Shik et al . , Intranasal immunization with plasmid DNA
encoding spike protein of SARS -coronavirus/polyethylenimine
nanoparticles elicits antigen -specific humoral and cellular immune
responses.BMC Immunol. Dec. 31 , 2010 ; 11 : 65 . doi : 10.1186 / 1471
2172-11-65 .

Du et al . , Recombinant adeno - associated virus expressing the

receptor-binding domain of severe acute respiratory syndrome
coronavirus S protein elicits neutralizing antibodies: Implication for
developing SARS vaccines. Virology. Sep. 15 , 2006 ; 353 ( 1 ) : 6-16 .
doi : 10.1016 /j.virol.2006.03.049. Epub Jun . 21 , 2006 .
Lu et al . , Bat - to -human : spike features determining ‘ host jump of
coronaviruses SARS - CoV, MERS -CoV, and beyond. Trends Microbiol.
Aug. 2015 ; 23 ( 8 ) : 468-78 . doi: 10.1016 / j.tim.2015.06.003. Epub Jul.
21 , 2015 .
Reichmuth et al . , mRNA Vaccine Delivery Using Lipid Nanoparticles.
Ther Deliv . 2016 ; 7 ( 5 ) : 319-34 . doi : 10.4155 / tde - 2016-0006 .
Yuan et al . , Cryo -EM structures of MERS - CoV and SARS - CoV
spike glycoproteins reveal the dynamic receptor binding domains .
Nat Commun . Apr. 10 , 2017 ; 8 : 15092 . doi: 10.1038 /ncomms15092 .

U.S. Patent

539

C

514489

TM

574
516550

HR2 488
445
386397

6
and
5

US 10,933,127 B2

Sheet 1 of 24

Mar. 2 , 2021

429-47

VI
V
,
IV
Area

389

Areal

26-76

II
area
/
site
A

1
.
Fig

F1

238-45

4

3

177
132152179

HMPV

169

199

HR1

2

102127

FP

Aa
no
.

RSV

109137157
Aa
no
.

Egpritoupe

F2
22

18
SP
N

Egpirtoupe

U.S. Patent

Sheet 2 of 24

Mar. 2 , 2021

US 10,933,127 B2

PBS-10ug2ug

10 0
tsDay14ieratuiomn

DFialcutorn

100

2B
.
Fig
41

3

10

1

A450

PBS

*2ug

-PBSDhe10ugAm2ug

{
]
10ug

10 0

2150 0 DFialcutorn

tsiDayOeratuiomn

tserum
i35
Day
t2C
.
Fig
ration
2A
.
Fig

4

3

100

0
2

1

0

4

A450

2

A450

1

0+ 10

FDialcutorn

U.S. Patent

US 10,933,127 B2

Sheet 3 of 24

Mar. 2 , 2021

D2ugoseD1o0suegPBS
35 Day
28 Day

M-HMPVIFspogeucGisf1iec

. 14 Day
WA

02 Day

3B
.
Fig

2.07

1.5

0.5
21.0
A450

0.0

D2ugoseD1o0sueg PBS

D1o0suegDo2sueg
2.0
35 Day

il

28 Day

Ml-HFspogMeuGcPis2fVeac

1.0
>

/IgG1IgG2a

IgG1
/
1.0Th2

14 Day

0.5

02 Day

3A
.
Fig

2.07

1.5

81.0
1

A450

0.5 0.0

1.5

30
.
Fig 2.07

1.5

1.0

Th1/ IgG2a

0.00.04

U.S. Patent

Sheet 4 of 24

Mar. 2 , 2021

US 10,933,127 B2

Fig . 4
Reciprocal serum neutralizing antibody titers

104
103

Day 0
Day 21
Day 56

DFialcutorn 102
10 1

100

D1o0sueg

Dose2ug

PBS
HMPV B2 TN /91-316

U.S. Patent

Mar. 2 , 2021

hi

IL2

Sheet 5 of 24

D2ug1o0sueg

US 10,933,127 B2

HFpeMpotPiVdle

Moendliay

A
Con

PBS

5B
.
Fig

500 400 30 200 100

0

mL / pg

hh

2ugD1o0sueg

D2ug1o0sueg

IFN
Y

IL12
PBS

PBS

150 10 0 500

0

250 200 150 100
mL/pg

??? d

5A
.
Fig

5C
.
Fig

50

0

U.S. Patent

HFpeMpoPtiVdle

Moendliay

US 10,933,127 B2

Sheet 6 of 24

Mar. 2 , 2021

D2ug1PBSo0sueg

IL6
A
Con

6E
.
Fig

1
60 0 mL40 0 / pg 20 0

0

2ugD1o0sueg

D2ug1o0sueg

TNF
IL5

PBS
6B
.
Fig 400 300 200 100
50 7

0

6D
.
Fig

PBS

50

400 300 200 100

0

D2ug1o0sueg
IL10

Dose2ug10ug
IL4

PBS
6A
. 80 7 600
Fig

40 1 200

PBS
6C
Fig
. 400

300 mL/20pg

100

0

U.S. Patent

Moendliay HviMrPuVs

US 10,933,127 B2

Sheet 7 of 24

Mar. 2 , 2021

A
Con

D2ug1o0sueg
IL2

PBS
7B
.
Fig

50 7

400 300 200 100
mL/ pg

2ugD1o0sueg
IFN
Y
-

7A
.
Fig

PBS

50 7

400
.

300 200 100
mL/pg

0

D2ug1o0sueg

IL12
7C
.
Fig

PBS

250

200 150

10 1

mL/pg

50

0

U.S. Patent

US 10,933,127 B2

Sheet 8 of 24

Mar. 2 , 2021

MoendliayHviMrPuVs Con-A

D2ug1PBSo0sueg

IL6

8E
.
Fig
0

60 0 40mL0 / pg20 0
2ugDose10ug

2ugD1o0sueg

TNF
5
IL

PBS
8B
. 500 400 300 200
Fig

100

0

PBS

8D
.
Fig

???6d

500 400

300 200
mL/pg

10 4

0

2ugD1o0sueg

2ugD1o0sueg

IL10

IL4

PBS
8A
. 80 1 600
Fig

400 200
mL/ pg

0

? PBS

8C
.
Fig

400 300 20 4

???td

100

0

U.S. Patent

Mar. 2 , 2021

Sheet 9 of 24

US 10,933,127 B2

Fig . 9A
HMPV lung viral titers
6

GLog10t(PFU/G)eiotMerans

Placebo

HMPV Vaccine 10ug
N HMPV Vaccine 2ug

5

FI - HMPV

LOQ

2

Fig . 9B
HMPV Nose viral titers

Placebo

GLog10
t(
G
/
PFU
)eiotMerans

5

A HMPV Vaccine 10ug
HMPV Vaccine 2ug
FI - HMPV

4
3
2

LOQ

U.S. Patent

Mar. 2 , 2021

Sheet 10 of 24

US 10,933,127 B2

IPeribonchlts Pnterusmoial Alveoits
PeArivasculti

Baselin
10
.
Fig

FI-HMPV

HMPV ac ine 2ug
HMPV Vac ine 10ug

HvliasMtucopPnihVgloey

Placebo

II
100

80 60 40 20
score pathology .Avg

0

U.S. Patent

US 10,933,127 B2

Sheet 11 of 24

Mar. 2 , 2021

Day
35
Day
A 42

0
Day

LOQ
D2ugose

n
H
a
t
c
in
r
e
u
i
o
M
l
P
e
b
t
z
o
a
r
V
d
s
i
n
y
11
.
Fig

A2sHtMrPaiVn

D1o0sueg

Placebo
104

103

102

titers GeoMean

101

U.S. Patent

US 10,933,127 B2

Sheet 12 of 24

Mar. 2 , 2021

01
06

IMPV - FI

D

Nose

PIV3_15ug/ HMPV

? ?

HMPV_10ug

D

Cratlvc-HhoiaMtlraPeondVlge Lung

0

HMPV_15ug

P

HMPV_30ug

? ?

106
12
.
Fig

105

Placebo

104

103

tissue pfulg

ZOL

101

U.S. Patent

Mar. 2 , 2021

US 10,933,127 B2

Sheet 13 of 24

LOD
I

PIV3-FI

?

PIV3_15ug/ HMPV

Nose

0

PIV3_10ug

Cratlvc-PhoiaItlraVeond3lge Lung

?

15ug PIV3

30ug PIV3

40

106 105
13
.
Fig

104

Placebo

.
103

tissue pfulg

102

107

U.S. Patent

Mar. 2 , 2021

Sheet 14 of 24

US 10,933,127 B2

6

5

11

4

14
.
Fig

h/A2nsateuiMraPlbeiuozrVdmnsyg

)
42
day
(

Groups
3

2

1

10. 0

9.0 8.0 7.0 6.0 5.0 4.0
Log2 PRNT % 60

U.S. Patent

Mar. 2 , 2021

Sheet 15 of 24

US 10,933,127 B2

12

11

10

15
.
Fig

tansPeiuIrVbeluoz3dimsnyg

Groups

)
42
day
(
9

8

7

9.0

8.00

7.0

6.0

Log2 PRNT % 60

5.0

4.0

U.S. Patent

Mar. 2 , 2021

Sheet 16 of 24

US 10,933,127 B2

PB PV IP
12
11

10

8
9

7

6

16
Fig
.

Crlhiostuapnhotgl y

PIV3
hMPV
A2hMPV
A2
/
HMPV

5

4

IL

3

2

1

10. 7 90. 0 80. 0 70. 0 60.0 50. 0 40. 0 30.0+ 20.0 10. -1 0.0
score Pathology .Avg

Groups

U.S. Patent

Day
O
Prime
(
0
)

US 10,933,127 B2

Sheet 17 of 24

Mar. 2 , 2021

21
Day
)
Boost
(

Day
V
42
Day
A 56

v

II

17
.
Fig

vFLMCtnasReiuEcOrapRelbiuoVznScdmsaygl

AZ

80 0

60 0

che

4
0
0
20 0
)Log( EC50

U.S. Patent

US 10,933,127 B2

Sheet 18 of 24

Mar. 2 , 2021

SFLproitekin S2sproitkein

I

18
.
Fig

vCMtnasReiucEOrpRelbiuoVznScdmsaygl

LL

56

42

Day
)
Prime
(
0
Boost
21

10 3

10 0

100

) Log ( EC50

10

U.S. Patent

US 10,933,127 B2

Sheet 19 of 24

Mar. 2 , 2021

MERS_Vacine20ug1D MERS_Vacine20ugD

PBS

LOQ
19A
Fig
.

44

Nose
MERSvNoseload-&TDay4postchiarloaenlgte

Throat
8

2

mL /copies Log10

0

U.S. Patent

US 10,933,127 B2

Sheet 20 of 24

Mar. 2 , 2021

MERS_Vacine20ug1D acine_20ugD

PBS

O

A

LOQ
19B
.
Fig

MvlL-D4pchioEuarlRnsadeSgl-te

L L PLounlg

O

g
10

81

ge
6

4

copieslg Log10

2

U.S. Patent

MERS_Vacine20ug1D MERS_Vacine20ugD
o

US 10,933,127 B2

Sheet 21 of 24

Mar. 2 , 2021

PBS
A

LOQ
19C
.
Fig

PLounlg

lvM-LcD4phiEoaulrRanseSdgtle

sob
g

10
.

8

6

4

g/ copies Log10

2

U.S. Patent

Mar. 2 , 2021

Sheet 22 of 24

US 10,933,127 B2
2

LRPeagCnRed

-5 5-6
3.5
< 3.5

6-7

Sumary

7
>

1b
1a

601 40 201
10 7 80percentage

1aGroup

1bGroup

2Group

20A
Fig
.

drop ed
MCoVRNA-linEouanRdgSs

out

Group

U.S. Patent

Mar. 2 , 2021

nRTLCeaIgnD5e0d egative 2-3 3-4
1-2

Sheet 23 of 24

US 10,933,127 B2
2

Sumary

4
>

1b
1?

801 604 404 201
10 7 percentage

16Group

1aGroup

0

2Group

20B
.
Fig

droped

MCoVr-inlepEuincRatgSiosn

out

su
HA11

IM

IRRI

Group

U.S. Patent

Sheet 24 of 24

Mar. 2 , 2021

US 10,933,127 B2

OMERS_20ug1Dose M-OERS_20ugDose Pylacebo
50

Chaleng

40

21
.
Fig

anMteuiErRlbeozSidrnyg

30

?

Bo st

pre
HIH

20
10

104

103

102

) Log( EC50

101

0

US 10,933,127 B2
1
BETACORONAVIRUS MRNA VACCINE
RELATED APPLICATIONS

2

from primary PIV3 viral infection or a secondary conse

quences, such as bacterial infections. Human parainfluenza
viruses ( hPIV ) types 1 , 2 and 3 (hPIV1 , hPIV2 and hPIV3 ,

respectively ), also like hMPV , are second only to RSV as

This application is a division of U.S. application Ser. No. 5 important causes of viral LRI in young children .

16 / 805,587 , filed Feb. 28 , 2020 , now U.S. Pat . No. 10,702 ,
600 , which is a continuation of U.S. application Ser. No.

16 /368,270 , filed Mar. 28 , 2019 , now U.S. Pat . No. 10,702 ,

599 , which is a continuation of Ser. No. 16 /040,981 , filed

RSV, too , is a negative - sense , single - stranded RNA virus
of the genus Pneumovirinae and of the family Paramyxo

viridae . Symptoms in adults typically resemble a sinus

infection or the common cold , although the infection may be

Jul . 20 , 2018 , now U.S. Pat . No. 10,272,150 , which is a 10 asymptomatic . In older adults ( e.g. , > 60 years ), RSV infec
continuation of U.S. application Ser. No. 157674,599 , filed tion may progress to bronchiolitis or pneumonia. Symptoms
Aug. 11 , 2017 , now U.S. Pat. No. 10,064,934 , which is a in children are often more severe , including bronchiolitis
continuation of International application number PCT/ and pneumonia. It is estimated that in the United States,
US2016 /058327 , filed Oct. 21 , 2016 , which claims the most children are infected with RSV by the age of three . The
benefit under 35 U.S.C. § 119 (e) of U.S. provisional appli- 15 RSV virion consists of an internal nucleocapsid comprised

cation No. 62/ 244,802 , filed Oct. 22 , 2015 , U.S. provisional of the viral RNA bound to nucleoprotein ( N ), phosphopro
application No. 62 /247,297 , filed Oct. 28 , 2015 , U.S. pro- tein (P ) , and large polymerase protein (L ) . The nucleocapsid
visional application No. 62/ 244,946 , filed Oct. 22 , 2015 , is surrounded by matrix protein (M) and is encapsulated by
U.S. provisional application No. 62 / 247,362 , filed Oct. 28 , a lipid bilayer into which the viral fusion (F ) and attachment
2015 , U.S. provisional application No. 62/244,813 , filed 20 (G) proteins as well as the small hydrophobic protein ( SH)
Oct. 22 , 2015 , U.S. provisional application No. 62 /247,394 , are incorporated. The viral genome also encodes two non
filed Oct. 28 , 2015 , U.S. provisional application No. 62/244 , structural proteins (NS1 and NS2 ) , which inhibit type I
837 , filed Oct. 22 , 2015, U.S. provisional application No. interferon activity as well as the M - 2 protein .
62 /247,483 , filed Oct. 28 , 2015 , and U.S. provisional appliThe continuing health problems associated with hMPV ,
cation No. 62 / 245,031 , filed Oct. 22 , 2015, each of which is 25 PIV3 and RSV are of concern internationally, reinforcing the
importance of developing effective and safe vaccine candi
incorporated by reference herein in its entirety.
dates against these virus .
BACKGROUND
Despite decades of research , no vaccines currently exist
( Sato and Wright, Pediatr. Infect. Dis. J. 2008 ; 27 ( 10 Suppl):
Respiratory disease is a medical term that encompasses 30 S123-5 ) . Recombinant technology , however, has been used
pathological conditions affecting the organs and tissues that to target the formation of vaccines for hPIV - 1, 2 and 3
make gas exchange possible in higher organisms, and serotypes, for example, and has taken the form of several
includes conditions of the upper respiratory tract, trachea, live - attenuated intranasal vaccines . Two vaccines in particu
bronchi, bronchioles, alveoli , pleura and pleural cavity, and lar were found to be immunogenic and well tolerated against
the nerves and muscles of breathing. Respiratory diseases 35 hPIV - 3 in phase I trials . hPIV1 and hPIV2 vaccine candi
range from mild and self- limiting, such as the common cold , dates remain less advanced (Durbin and Karron , Clinical
to life - threatening entities like bacterial pneumonia, pulmo- infectious diseases: an official publication of the Infectious
nary embolism , acute asthma and lung cancer . Respiratory Diseases Society of America 2003 ; 37 ( 12 ) : 1668-77 ) .
disease is a common and significant cause of illness and
Measles virus (MeV ), like hMPV , PIV3 and RSV, is a
death around the world . In the US , approximately 1 billion 40 negative-sense, single - stranded RNA virus that is the cause
“ common colds” occur each year. Respiratory conditions are of measles , an infection of the respiratory system . MeV is of
among the most frequent reasons for hospital stays among the genus Morbillivirus within the family Paramyxoviridae .
children .
Humans are the natural hosts of the virus; no animal
The human Metapneumovirus ( hMPV ) is a negative- reservoirs are known to exist . Symptoms of measles include
sense , single - stranded RNA virus of the genus Pneumoviri- 45 fever, cough , runny nose , red eyes and a generalized, macu
nae and of the family Paramyxoviridae and is closely related lopapular, erythematous rash . The virus is highly contagious
to the avian Metapneumovirus (AMPV) subgroup C. It was and is spread by coughing
isolated for the first time in 2001 in the Netherlands by using
In additional to hMPV, PIV , RSV and MeV, Betacorona
the RAP -PCR ( RNA arbitrarily primed PCR) technique for viruses are known to cause respiratory illnesses . Betacoro
identification of unknown viruses growing in cultured cells . 50 naviruses (BetaCoVs) are one of four genera of coronavi
hPMV is second only to RSV as an important cause of viral ruses of the subfamily Coronavirinae in the family
lower respiratory tract illness ( LRI ) in young children . The Coronaviridae , of the order Nidovirales. They are envel
seasonal epidemiology of hMPV appears to be similar to that oped , positive - sense , single -stranded RNA viruses of
of RSV, but the incidence of infection and illness appears to zoonotic origin . The coronavirus genera are each composed
be substantially lower .
55 of varying viral lineages, with the Betacoronavirus genus
Parainfluenza virus type 3 ( PIV3 ) , like hMPV, is also a containing four such lineages . The BetaCoVs of the greatest
negative -sense, single - stranded sense RNA virus of the clinical importance concerning humans are OC43 and
genus Pneumovirinae and of the family Paramyxoviridae HKU1 of the A lineage , SARS - CoV of the B lineage , and
and is a major cause of ubiquitous acute respiratory infec- MERS - CoV of the C lineage. MERS - CoV is the first Beta

tions of infancy and early childhood . Its incidence peaks 60 coronavirus belonging to lineage C that is known to infect
around 4-12 months of age , and the virus is responsible for humans.
3-10 % of hospitalizations, mainly for bronchiolitis and
The Middle East respiratory syndrome coronavirus
pneumonia . PIV3 can be fatal, and in some instances is (MERS - CoV ), or EMC / 2012 ( HCV - EMC / 2012 ) , initially

associated with neurologic diseases, such as febrile seizures. referred to as novel coronavirus 2012 or simply novel
It can also result in airway remodeling, a significant cause of 65 coronavirus, was first reported in 2012 after genome
morbidity. In developing regions of the world , infants and sequencing of a virus isolated from sputum samples from a
young children are at the highest risk of mortality, either person who fell ill during a 2012 outbreak of a new flu . As

US 10,933,127 B2
3

4

of July 2015 , MERS - CoV cases have been reported in over
21 countries. The outbreaks of MERS - CoV have raised
serious concerns world -wide, reinforcing the importance of
developing effective and safe vaccine candidates against

unwanted cellular responses , RNA ( e.g. , mRNA ) vaccines
are presented to the cellular system in a more native fashion .
In some aspects the invention is a respiratory virus
vaccine, comprising at least one RNA polynucleotide having
an open reading frame encoding at least one respiratory
virus antigenic polypeptide , formulated in a cationic lipid
nanoparticle.
Surprisingly, in some aspects it has also been shown that
efficacy of mRNA vaccines can be significantly enhanced
when combined with a flagellin adjuvant, in particular, when
one or more antigen - encoding mRNAs is combined with an
mRNA encoding flagellin .
RNA ( e.g. , mRNA ) vaccines combined with the flagellin
adjuvant (e.g. , mRNA - encoded flagellin adjuvant) have
superior properties in that they may produce much larger
antibody titers and produce responses earlier than commer
cially available vaccine formulations. While not wishing to
be bound by theory, it is believed that the RNA ( e.g. ,
mRNA ) vaccines , for example, as mRNA polynucleotides,
are better designed to produce the appropriate protein con
formation upon translation , for both the antigen and the
adjuvant, as the RNA (e.g. , mRNA ) vaccines co - opt natural
cellular machinery. Unlike traditional vaccines , which are
manufactured ex vivo and may trigger unwanted cellular
responses, RNA (e.g. , mRNA ) vaccines are presented to the
cellular system in a more native fashion .
Some embodiments of the present disclosure provide
RNA ( e.g. , mRNA ) vaccines that include at least one RNA
(e.g. , mRNA ) polynucleotide having an open reading frame
encoding at least one antigenic polypeptide or an immuno
genic fragment thereof ( e.g. , an immunogenic fragment
capable of inducing an immune response to the antigenic
polypeptide) and at least one RNA (e.g. , mRNA polynucle
otide ) having an open reading frame encoding a flagellin
adjuvant.
In some embodiments, at least one flagellin polypeptide
( e.g., encoded flagellin polypeptide ) is a flagellin protein. In
some embodiments, at least one flagellin polypeptide ( e.g. ,
encoded flagellin polypeptide) is an immunogenic flagellin
fragment. In some embodiments, at least one flagellin poly
peptide and at least one antigenic polypeptide are encoded
by a single RNA ( e.g. , mRNA ) polynucleotide. In other
embodiments, at least one flagellin polypeptide and at least
one antigenic polypeptide are each encoded by a different
RNA polynucleotide.
In some embodiments at least one flagellin polypeptide

5

MERS -CoV.

Severe acute respiratory syndrome ( SARS ) emerged in
China in 2002 and spread to other countries before brought

under control. Because of a concern for reemergence or a
deliberate release of the SARS coronavirus, vaccine devel 10
opment was initiated .

Deoxyribonucleic acid (DNA ) vaccination is one tech

nique used to stimulate humoral and cellular immune
responses to foreign antigens, such as hMPV antigens and / or
PIV antigensengineered
and/or RSV
. Theplasmid
direct injection
of 15
genetically
DNAantigens
( e.g. , naked
DNA ) into
a living host results in a small number of its cells directly
producing an antigen, resulting in a protective immunologi
cal response . With this technique, however, comes potential
problems, including the possibility of insertional mutagen- 20
esis , which could lead to the activation of oncogenes or the
inhibition of tumor suppressor genes.
SUMMARY

Provided herein are ribonucleic acid ( RNA ) vaccines that
build on the knowledge that RNA ( e.g. , messenger RNA

(mRNA )) can safely direct the body's cellular machinery to
produce nearly any protein of interest, from native proteins
to antibodies and other entirely novel protein constructs that
can have therapeutic activity inside and outside of cells . The
RNA (e.g. , mRNA ) vaccines of the present disclosure may
be used to induce a balanced immune response against
hMPV, PIV , RSV, MeV, and / or BetaCoV (e.g. , MERS - COV,
SARS -COV, HCOV -OC43, HCOV -229E , HCOV -NL63,
HCOV - NL , HCOV - NH and / or HCOV -HKU1 ), or any combination of two or more of the foregoing viruses, comprising
both cellular and humoral immunity, without risking the
possibility of insertional mutagenesis, for example. hMPV,
PIV, RSV, MeV, BetaCoV (e.g. , MERS - CoV, SARS - CoV,
HCOV - OC43, HCOV -229E , HCOV -NL63, HCOV -NL ,
HCOV - NH and HCOV -HKU1) and combinations thereof are
referred to herein as “ respiratory viruses.” Thus, the term
“ respiratory virus RNA vaccines” encompasses hMPV RNA
vaccines , PIV RNA vaccines, RSV RNA vaccines , MeV
RNA vaccines , BetaCoV RNA vaccines , and any combination of two or more of hMPV RNA vaccines , PIV RNA

vaccines , RSV RNA vaccines , MeV RNA vaccines , and

25

30

35

40

45

has at least 80% , at least 85 % , at least 90 % , or at least 95 %

identity to a flagellin polypeptide having a sequence iden
tified by any one of SEQ ID NO : 54-56 .
The RNA ( e.g. , mRNA ) vaccines may be utilized in 50 Provided herein, in some embodiments, is a ribonucleic
various settings depending on the prevalence of the infection acid (RNA ) (e.g. , mRNA ) vaccine, comprising at least one
or the degree or level of unmet medical need . The RNA (e.g. (e.g. , at least 2 , 3 , 4 or 5 ) RNA ( e.g. , mRNA ) polynucleotide
mRNA ) vaccines may be utilized to treat and /or prevent a having an open reading frame encoding at least one ( e.g. , at
hMPV, PIV, RSV , MeV, a BetaCoV ( e.g. , MERS -COV, least 2 , 3 , 4 or 5 ) MPV, PIV , RSV , MeV, or a BetaCoV ( e.g. ,
SARS -CoV, HCOV -OC43, HCOV - 229E , HCOV -NL63, 55 MERS - CoV, SARS -CoV, HCOV -OC43, HCOV - 229E ,
HCOV - NL , HCOV - NH , HCOV -HKU1), or any combination HCOV - NL63, HCOV - NL , HCOV - NH , HCOV -HKU1) anti
BetaCOV RNA vaccines .

of two or more of the foregoing viruses, of various geno- genic polypeptide, or any combination of two or more of the
types, strains, and isolates. The RNA ( e.g. , mRNA ) vaccines foregoing antigenic polypeptides. Herein , use of the term
have superior properties in that they produce much larger " antigenic polypeptide " encompasses immunogenic frag
antibody titers and produce responses earlier than commer- 60 ments of the antigenic polypeptide (an immunogenic frag
cially available anti - viral therapeutic treatments. While not ment that is induces ( or is capable of inducing) an immune
wishing to be bound by theory , it is believed that the RNA response to hMPV , PIV , RSV, MeV, or a BetaCoV) , unless
( e.g. , mRNA) vaccines , as mRNA polynucleotides, are otherwise stated .
better designed to produce the appropriate protein conforAlso provided herein , in some embodiments, is a RNA
mation upon translation as the RNA ( e.g. , mRNA ) vaccines 65 (e.g. , mRNA ) vaccine comprising at least one (e.g. , at least
co - opt natural cellular machinery. Unlike traditional vac- 2 , 3 , 4 or 5 ) RNA polynucleotide having an open reading
cines , which are manufactured ex vivo and may trigger

frame encoding at least one (e.g. , at least 2 , 3 , 4 or 5 ) hMPV ,

US 10,933,127 B2
5

6

PIV , RSV, MeV, and / or a BetaCoV ( e.g. , MERS -CoV,
SARS - CoV, HCV - OC43 , HCV - 229E , HCOV - N163,
HCOV - NL , HCV -NH , HCV - HKU1 ) antigenic polypeptide or an immunogenic fragment thereof, linked to a signal

In some embodiments , at least one antigenic polypeptide
is obtained from hMPV strain CAN98-75 (CAN75 ) or the
hMPV strain CAN97-83 (CAN83 ).

In some embodiments, at least one PIV3 antigenic poly

5 peptide comprises hemagglutinin -neuraminidase, Fusion ( F )
peptide.
Further provided herein , in some embodiments, is a glycoprotein, matrix protein ( M) , nucleocapsid protein ( N ),

viral replicase (L ) , non - structural V protein , or an immuno
nucleic acid (e.g. , DNA ) encoding at least one (e.g. , at least genic
fragment thereof.
2 , 3 , 4 or 5 ) hMPV, PIV , RSV, MeV, and / or a BetaCoV ( e.g. ,
In
some
embodiments, at least one PIV3 antigenic poly
MERS -CoV, SARS - COV, HCOV -OC43, HCOV - 229E , 10 peptide comprises
acid sequence identified by any
HCOV -NL63, HCOV -NL , HCOV -NH , HCOV -HKU1) RNA one of SEQ ID NOan: amino
12-13
( Table 6 ; see also amino acid
( e.g. , mRNA ) polynucleotide.
sequences
of
Table
7
)
.
In
some
embodiments, the amino acid
Further still , provided herein , in some embodiments, is a sequence of the PIV3 antigenic
polypeptide is , or is a
method of inducing an immune response in a subject, the fragment of, or is a homolog or variant
having at least 80 %
method
comprising
administering
to
the
subject
a
vaccine
15
(
e.g.
,
85
%
,
90
%
,
95
%
,
98
%
,
99
%
)
identity
to, the amino acid
comprising at least one (e.g. , at least 2 , 3 , 4 or 5 ) RNA ( e.g. , sequence identified by any one of SEQ ID NO : 12-13 ( Table
mRNA ) polynucleotide having an open reading frame 6 ; see also amino acid sequences of Table 7 ) .
encoding at least one (e.g. , at least 2 , 3 , 4 or 5 ) hMPV, PIV ,
In some embodiments, at least one PIV3 antigenic poly
RSV, MeV, and / or a BetaCoV ( e.g. , MERS - COV, SARS- peptide is encoded by a nucleic acid sequence identified by
COV, HCOV -OC43 , HC0V -229E , HCOV -NL63, HCOV -NL , 20 any one of SEQ ID NO : 9-12 ( Table 5 ; see also nucleic acid
HCOV -NH , HCOV - HKU1) antigenic polypeptide, or any sequences of Table 7) .
combination of two or more of the foregoing antigenic
In some embodiments, at least one PIV3 RNA ( e.g. ,
polypeptides.
mRNA ) polynucleotide is encoded by a nucleic acid
hMPV /PIV3 /RSV
sequence, or a fragment of a nucleotide sequence , identified
In some embodiments, a RNA (e.g. , mRNA ) vaccine 25 by any one of SEQ ID NO : 9-12 ( Table 5 ; see also nucleic
comprises at least one RNA (e.g. , mRNA ) polynucleotide acid sequences of Table 7 ) . In some embodiments , at least
having an open reading frame encoding at least one hMPV , one PIV3 RNA ( e.g. , mRNA ) polynucleotide comprises a
PIV3 or RSV antigenic polypeptide. In some embodiments , nucleic acid sequence, or a fragment of a nucleotide
at least one antigenic polypeptide is a hMPV , PIV3 or RSV sequence , identified by any one of SEQ ID NO : 61-64 ( Table
polyprotein . In some embodiments , at least one antigenic 30 5) .
polypeptide is major surface glycoprotein G or an immuIn some embodiments, at least one antigenic polypeptide
nogenic fragment thereof. In some embodiments, at least is obtained from PIV3 strain HPIV3/ Homo sapiens/PER /
one antigenic polypeptide is Fusion ( F ) glycoprotein ( e.g. , FLA4815 / 2008 .
Fusion glycoprotein FO , F1 or F2 ) or an immunogenic
In some embodiments, at least one RSV antigenic poly

fragment thereof. In some embodiments, at least one anti- 35 peptide comprises at least one antigenic polypeptide that
genic polypeptide is major surface glycoprotein G or an comprises glycoprotein G , glycoprotein F, or an immuno

immunogenic fragment thereof and F glycoprotein or an
immunogenic fragment thereof. In some embodiments , the
antigenic polypeptide is nucleoprotein ( N ) or an immunogenic fragment thereof, phosphoprotein (P ) or an immuno- 40
genic fragment thereof, large polymerase protein ( L) or an
immunogenic fragment thereof, matrix protein ( M) or an
immunogenic fragment thereof, small hydrophobic protein
( SH ) or an immunogenic fragment thereof nonstructural
protein 1 (NSi) or an immunogenic fragment thereof, or 45
nonstructural protein 2 (NS2) and an immunogenic fragment
thereof.
In some embodiments, at least one hMPV antigenic
polypeptide comprises an amino acid sequence identified by
any one of SEQ ID NO : 5-8 ( Table 3 ; see also amino acid 50
sequences of Table 4 ) . In some embodiments , the amino acid
sequence of the hMPV antigenic polypeptide is , or is a
fragment of, or is a homolog or variant having at least 80 %
( e.g. , 85 % , 90% , 95 % , 98 % , 99 % ) identity to , the amino acid
sequence identified by any one of SEQ ID NO : 5-8 ( Table 55
3 ; see also amino acid sequences of Table 4 ) .
In some embodiments, at least one hMPV antigenic
polypeptide is encoded by a nucleic acid sequence identified
by any one of SEQ ID NO : 1-4 ( Table 2 ) .
In some embodiments, at least one hMPV RNA ( e.g. , 60
mRNA ) polynucleotide is encoded by a nucleic acid
sequence, or a fragment of a nucleotide sequence , identified
by any one of SEQ ID NO : 1-4 ( Table 2 ) . In some embodiments, at least one hMPV RNA ( e.g. , mRNA ) polynucleotide comprises a nucleic acid sequence , or a fragment of a 65
nucleotide sequence, identified by any one of SEQ ID NO :
57-60 ( Table 2 ) .

genic fragment thereof. In some embodiments , at least one
RSV antigenic polypeptide comprises at least one antigenic
polypeptide that comprises glycoprotein F and at least one or
at least two antigenic polypeptide selected from G , M , N , P ,
L , SH , M2 , NS1 and NS2 .
MeV
In some embodiments, a RNA (e.g. , mRNA ) vaccine
comprises at least one RNA ( e.g. , mRNA ) polynucleotide
having an open reading frame encoding at least one MeV
antigenic polypeptide . In some embodiments, at least one
antigenic polypeptide is a hemagglutinin (HA) protein or an
immunogenic fragment thereof. The HÀ protein may be
from MeV strain D3 or B8 , for example. In some embodi
ments, at least one antigenic polypeptide is a Fusion ( F )
protein or an immunogenic fragment thereof. The F protein
may be from MeV strain D3 or B8 , for example. In some
embodiments, a MeV RNA (e.g. , mRNA ) vaccines com
prises a least one RNA polynucleotide encoding a HA

protein and a F protein . The HA and F proteins may be from

MeV strain D3 or B8 , for example.
In some embodiments, at least one MeV antigenic poly
peptide comprises an amino acid sequence identified by any
one of SEQ ID NO : 47-50 ( Table 14 ) . In some embodiments,

the amino acid sequence of the MeV antigenic polypeptide
is , or is a fragment of, or is a homolog or variant having at
least 80% (e.g. , 85 % , 90 % , 95 % , 98 % , 99 % ) identity to , the
amino acid sequence identified by any one of SEQ ID NO :
47-50 ( Table 14 ) .
In some embodiments, at least one MeV antigenic poly
peptide is encoded by a nucleic acid sequence of SEQ ID

NO : 35-46 ( Table 13 ) .

US 10,933,127 B2
7

8

In some embodiments , at least one MeV RNA ( e.g. ,
mRNA ) polynucleotide is encoded by a nucleic acid
sequence, or a fragment of a nucleotide sequence , identified
by any one of SEQ ID NO : 35-46 ( Table 13 ) . In some

MERS -CoV, SARS -CoV, HCOV -OC43, HCOV - 229E ,
HCOV - NL63 , HCOV - NL , HCOV - NH and HCOV -HKU1.
Other Betacoronaviruses are encompassed by the present
disclosure .

embodiments, at least one MeV RNA (e.g. , mRNA ) poly- 5 In some embodiments, at least one antigenic polypeptide
nucleotide comprises a nucleic acid sequence, or a fragment is a MERS - CoV structural protein . For example , a MERS
of a nucleotide sequence , identified by any one of SEQ ID CoV structural protein may be spike protein ( S ) , envelope
protein ( E ) , nucleocapsid protein ( N ), membrane protein
NO : 69-80 ( Table 13 ) .
In some embodiments, at least one antigenic polypeptide (M ) or an immunogenic fragment thereof. In some embodi
is obtained from MeV strain B3 /B3.1 , C2 , D4 , D6 , D7 , D8 , 10 ments, the MERS - CoV structural protein is a spike protein
G3 , H1 , Moraten , Rubeovax, MVi /New Jersey.USA /45.05, ( S ) ( see , e.g. , Coleman C M et al . Vaccine 2014 ; 32 : 3169-74 ,
MVi / Texas.USA / 4.07, AIK - C , MVi/New York.USA / 26.09 / incorporated herein by reference ). In some embodiments,
3 , MVi/California.USA / 16.03or, MVi/Virginia.USA / 15.09, the MERS - CoV structural protein is a Sl subunit or a S2
MVi/California.USA / 8.04 ,

MVi /Pennsylvania.USA /

20.09 .

BetaCoV

In some embodiments, a RNA (e.g. , mRNA ) vaccine

comprises at least one RNA ( e.g. , mRNA polynucleotide
having an open reading frame encoding at least one BetaCoV antigenic polypeptide. In some embodiments, the BetaCOV is MERS - CoV . In some embodiments, the BetaCoV is
SARS - CoV. In some embodiments, the BetaCoV is HCOVOC43 . In some embodiments, the BetaCoV is HCOV - 229E .
In some embodiments, the BetaCoV is HCOV - NL63 . In
some embodiments, the BetaCoV is HCOV - HKU1. In some
embodiments, at least one antigenic polypeptide is a Betacoronavirus structural protein . For example, a Betacoronavirus structural protein may be spike protein ( S ) , envelope

subunit of spike protein ( S ) or an immunogenic fragment
15 thereof (Li J et al . Viral Immunol 2013 ; 26 (2 ) : 126-32 ; He Y
et al . Biochem Biophys Res Commun 2004 ; 324 (2 ) : 773-81 ,
each of which is incorporated herein by reference).
In some embodiments , at least one MERS - CoV antigenic
polypeptide comprises an amino acid sequence identified by
20 any one of SEQ ID NO : 24-28 or 33 ( Table 11 ) . In some
embodiments , the amino acid sequence of the MERS - CoV
antigenic polypeptide is , or is a fragment of, or is a homolog
or variant having at least 80 % (e.g. , 85 % , 90 % , 95 % , 98 % ,
99 % ) identity to , the amino acid sequence identified by any
25 one of SEQ ID NO : 24-28 or 33 ( Table 11 ) .
In some embodiments, at least one MERS - CoV antigenic
polypeptide is encoded by a nucleic acid sequence identified
by any one of SEQ ID NO : 20-23 ( Table 10 ) .

protein ( E ) , nucleocapsid protein ( N ), membrane protein
In some embodiments, at least one MERS - COV RNA
(M) or an immunogenic fragment thereof. In some embodi- 30 (e.g. , mRNA) polynucleotide is encoded by a nucleic acid
ments , a Betacoronavirus structural protein is a spike protein sequence, or a fragment of a nucleotide sequence , identified

( S ) . In some embodiments, a Betacoronavirus structural
protein is a S1 subunit or a S2 subunit of spike protein ( S )
or an immunogenic fragment thereof.

by any one of SEQ ID NO : 20-23 ( Table 10 ) . In some
embodia ents, at least one MERS - CoV RNA ( e.g. , mRNA )

polynucleotide comprises a nucleic acid sequence, or a
cines provided herein may encode viral protein components SEQ ID NO : 65-68 ( Table 10 ) .
of Betacoronaviruses, for example , accessory proteins, repIn some embodiments, at least one antigenic polypeptide
licase proteins and the like are encompassed by the present is obtained from MERS - CoV strain Riyadh_14_2013,
disclosure . RNA ( e.g. , mRNA ) vaccines may include RNA 2cEMC/ 2012 , or Hasa_1_2013 .
polynucleotides encoding at least one accessory protein 40 In some embodiments, at least one antigenic polypeptide
( e.g. , protein 3 , protein 4a , protein 4b , protein 5 ) , at least one is a SARS - CoV structural protein . For example, a SARS
replicase protein ( e.g. , protein 1a , protein 1b ) , or a combi- CoV structural protein may be spike protein ( S ) , envelope
nation of at least one accessory protein and at least one protein (E ) , nucleocapsid protein ( N ), membrane protein
replicase protein . The present disclosure also encompasses (M ) or an immunogenic fragment thereof. In some embodi
RNA (e.g. , mRNA ) vaccines comprising RNA ( e.g. , mRNA ) 45 ments, the SARS - CoV structural protein is a spike protein
polynucleotides encoding an accessory protein and / or a ( S ) . In some embodiments, the SARS - CoV structural protein
replicase protein in combination with at least one structural is a S1 subunit or a S2 subunit of spike protein ( S ) or an
protein . Due to their surface expression properties , vaccines immunogenic fragment thereof.
featuring RNA polynucleotides encoding structural proteins
In some embodiments, at least one SARS - CoV antigenic
are believed to have preferred immunogenic activity and, 50 polypeptide comprises an amino acid sequence identified by

BetaCoV RNA (e.g. , mRNA ) polynucleotides of the vac- 35 fragment of a nucleotide sequence, identified by any one of

hence, may be most suitable for use in the vaccines of the any one of SEQ ID NO : 29 , 32 or 34 ( Table 11 ) . In some
present disclosure.
embodiments , the amino acid sequence of the SARS - CoV
Some embodiments of the present disclosure provide antigenic polypeptide is , or is a fragment of, or is a homolog
Betacoronavirus ( e.g. , MERS - CoV, SARS - COV, HCOV- or variant having at least 80 % (e.g. , 85 % , 90 % , 95 % , 98 % ,
OC43 , HCOV - 229E , HCOV -NL63, HCOV -NL , HCOV - NH , 55 99 % ) identity to , the amino acid sequence identified by any
HCOV -HKU1 or a combination thereof) vaccines that one of SEQ ID NO : 29 , 32 or 34 ( Table 11 ) .
include at least one RNA (e.g. , mRNA ) polynucleotide
In some embodiments , at least one antigenic polypeptide
having an open reading frame encoding at least one Beta- is a HCV- OC43 structural protein . For example, a HCOV
coronavirus ( e.g. , MERS -CoV, SARS - CoV, HCV- OC43 , OC43 structural protein may be spike protein ( S ) , envelope

HCOV- 229E, HCOV -NL63, HCOV-NL, HCOV -NH , HCOV- 60 protein (E) , nucleocapsid protein ( N) , membrane protein
HKU1) antigenic polypeptide. Also provided herein are (M ) or an immunogenic fragment thereof. In some embodi

pan - Betacoronavirus vaccines . Thus, a Betacoronavirus ments, the HCOV -OC43 structural protein is a spike protein
vaccine comprising a RNA ( e.g. , mRNA ) polynucleotide ( S ) . In some embodiments, the HCOV - OC43 structural pro
having an open reading frame encoding any one , two , three tein is a S1 subunit or a S2 subunit of spike protein ( S ) or
or four of MERS - CoV, SARS - CoV, HCV - OC43 , HCOV- 65 an immunogenic fragment thereof.
229E , HCOV -NL63 , and HCOV - HKU1, for example, may be
In some embodiments, at least one HCV- OC43 antigenic
effective against any one of, any combination of, or all of, polypeptide comprises an amino acid sequence identified by

US 10,933,127 B2
9

10

any one of SEQ ID NO : 30 ( Table 11 ) . In some embodi- nucleotide is encoded by a nucleic acid having a sequence
ments, the amino acid sequence of the HCOV -OC43 anti- identified by any one of SEQ ID NO : 1-4 , 9-12 , 20-23 , or
genic polypeptide is , or is a fragment of, or is a homolog or 35-46 ( Tables 2 , 5 , 10 and 13 ; see also nucleic acid
variant having at least 80% ( e.g. , 85 % , 90 % , 95 % , 98 % , sequences of Table 7 ) and having less than 40-90 % , 50-90 % ,
99 % ) identity to , the amino acid sequence identified by any 5 60-90% , 30-90% , 70-90% , 75-90% , 80-90% , or 85-90 %
identity to wild - type mRNA sequence .
one of SEQ ID NO : 30 ( Table 11 ) .
In some embodiments, an antigenic polypeptide is a
In some embodiments, at least one RNA polynucleotide

HCOV -HKU1 structural protein . For example, a HCOV- encodes at least one antigenic polypeptide having an amino
HKU1 structural protein may be spike protein ( S ) , envelope acid sequence identified by any one of SEQ ID NO : 5-8 ,
protein ( E ) , nucleocapsid protein ( N ), membrane protein 10 12-13 , 24-34 , or 47-50 ( Tables 3 , 6 , 11 and 14 ; see also
( M) or an immunogenic fragment thereof. In some embodi- amino acid sequences of Tables 4 , 7 , 12 and 15 ) and having
ments, the HCOV -HKU1 structural protein is a spike protein at least 80% (e.g. , 85 % , 90% , 95 % , 98 % , 99 % ) identity to
( S ) . In some embodiments, the HCOV - HKU1 structural wild - type mRNA sequence, but does not include wild -type
protein is a S1 subunit or a S2 subunit of spike protein ( S ) mRNA sequence .
15
or an immunogenic fragment thereof.
In some embodiments, at least one RNA polynucleotide
In some embodiments, at least one HCOV - HKU1 anti- encodes at least one antigenic polypeptide having an amino
genic polypeptide comprises an amino acid sequence iden- acid sequence identified by any one of SEQ ID NO : 5-8 ,
tified by any one of SEQ ID NO : 31 ( Table 11 ) . In some 12-13 , 24-34 , or 47-50 ( Tables 3 , 6 , 11 and 14 ; see also
embodiments , the amino acid sequence of the HCOV - HKU1 amino acid sequences of Tables 4 , 7 , 12 and 15 ) and has less
antigenic polypeptide is , or is a fragment of, or is a homolog 20 than 95 % , 90 % , 85 % , 80 % or 75 % identity to wild -type
or variant having at least 80 % (e.g. , 85 % , 90 % , 95 % , 98 % , mRNA sequence. In some embodiments, at least one RNA
99 % ) identity to , the amino acid sequence identified by any polynucleotide encodes at least one antigenic polypeptide

having an amino acid sequence identified by any one of SEQ
one of SEQ ID NO : 31 ( Table 11 ) .
In some embodiments, an open reading frame of a RNA ID NO : 5-8 , 12-13 , 24-34 , or 47-50 ( Tables 3 , 6 , 11 and 14 ;
( e.g. , mRNA ) vaccine is codon - optimized . In some embodi- 25 see also amino acid sequences of Tables 4 , 7 , 12 and 15 ) and
ments, at least one RNA polynucleotide encodes at least one has 30-80 % , 40-80 % , 50-80% , 60-80 % , 70-80 % , 75-80% or
antigenic polypeptide having an amino acid sequence iden- 78-80% , 30-85 % , 40-85 % , 50-805 % , 60-85 % , 70-85 % ,
tified by any one of SEQ ID NO : 5-8 , 12-13 , 24-34 , or 47-50 75-85 % or 78-85 % , 30-90% , 40-90% , 50-90 % , 60-90 % ,

( Tables 3 , 6 , 11 and 14 ; see also amino acid sequences of 70-90% , 75-90 % , 80-90 % or 85-90 % identity to wild - type
Tables 4 , 7 , 12 and 15 ) and is codon optimized mRNA . 30 mRNA sequence .
In some embodiments, a RNA (e.g. , mRNA ) vaccine
In some embodiments , at least one RNA polynucleotide
encodes at least one antigenic polypeptide having at least
further comprising an adjuvant.
Tables 4 , 7 , 12 and 15 provide National Center for
0% , least 95 % , at least 96 % , at least 97 % , at least 98 % ,
Biotechnology Information (NCBI) accession numbers of or at least 99 % identity to an amino acid sequence identified
interest. It should be understood that the phrase " an amino 35 by any one of SEQ ID NO : 5-8 , 12-13 , 24-34 , or 47-50
acid sequence of Tables 4 , 7 , 12 and 15 ” refers to an amino ( Tables 3 , 6 , 11 and 14 ; see also amino acid sequences of
acid sequence identified by one or more NCBI accession Tables 4 , 7 , 12 and 15 ) . In some embodiments , at least one
numbers listed in Tables 4 , 7 , 12 and 15. Each of the amino RNA polynucleotide encodes at least one antigenic poly
acid sequences, and variants having greater than 95 % idenpeptide having 95 % -99 % identity to an amino acid sequence
tity or greater than 98 % identity to each of the amino acid 40 identified by any one of SEQ ID NO : 5-8 , 12-13 , 24-34 , or
sequences encompassed by the accession numbers of Tables 47-50 ( Tables 3 , 6 , 11 and 14 ; see also amino acid sequences
4 , 7 , 12 and 15 are included within the constructs (poly- of Tables 4 , 7 , 12 and 15 ) .
nucleotides/polypeptides) of the present disclosure .
In some embodiments, at least one RNA polynucleotide
In some embodiments, at least one mRNA polynucleotide encodes at least one antigenic polypeptide having at least
is encoded by a nucleic acid having a sequence identified by 45 90% , at least 95 % , at least 96 % , at least 97 % , at least 98 % ,
any one of SEQ ID NO : 1-4 , 9-12 , 20-23 , or 35-46 ( Tables or at least 99 % identity to an amino acid sequence identified
2 , 5 , 10 and 13 ; see also nucleic acid sequences of Table 7 ) by any one of SEQ ID NO : 5-8 , 12-13 , 24-34 , or 47-50
and having less than 80 % identity to wild -type mRNA ( Tables 3 , 6 , 11 and 14 ; see also amino acid sequences of
sequence . In some embodiments, at least one mRNA poly- Tables 4 , 7 , 12 and 15 ) and having membrane fusion activity .
nucleotide is encoded by a nucleic acid having a sequence 50 In some embodiments, at least one RNA polynucleotide
identified by any one of SEQ ID NO : 1-4 , 9-12 , 20-23 , or encodes at least one antigenic polypeptide having 95 % -99 %
35-46 ( Tables 2 , 5 , 10 and 13 ; see also nucleic acid identity to an amino acid sequence identified by any one of
sequences of Table 7 ) and having less than 75 % , 85 % or SEQ ID NO : 5-8 , 12-13 , 24-34 , or 47-50 ( Tables 3 , 6 , 11 and
95 % identity to a wild -type mRNA sequence . In some 14 ; see also amino acid sequences of Tables 4 , 7 , 12 and 15 )
embodiments, at least one mRNA polynucleotide is encoded 55 and having membrane fusion activity.
by a nucleic acid having a sequence identified by any one of
In some embodiments, at least one RNA polynucleotide
SEQ ID NO : 1-4 , 9-12 , 20-23 , or 35-46 ( Tables 2 , 5 , 10 and encodes at least one antigenic polypeptide ( e.g. , at least one
13 ; see also nucleic acid sequences of Table 7 ) and having hMPV antigenic polypeptide , at least one PIV3 antigenic
less than 50-80 % , 60-80 % , 40-80 % , 30-80 % , 70-80 % , polypeptide, at least one RSV antigenic polypeptide, at least
75-80% or 78-80 % identity to wild -type mRNA sequence . 60 one MeV antigenic polypeptide , or at least one BetaCoV
In some embodiments, at least one mRNA polynucleotide is antigenic polypeptide, e.g. , selected from MERS - CoV,
encoded by a nucleic acid having a sequence identified by SARS -CoV, HCV - OC43 , HCOV - 229E , HCOV - NL63,
any one of SEQ ID NO : 1-4 , 9-12 , 20-23 , or 35-46 ( Tables HCOV -NL , HCOV - NH and HCOV - HKU1, or any combina
2 , 5 , 10 and 13 ; see also nucleic acid sequences of Table 7 ) tion of two or more of the foregoing antigenic polypeptides)
and having less than 40-85 % , 50-85 % , 60-85 % , 30-85 % , 65 that attaches to cell receptors.
70-85 % , 75-85 % or 80-85 % identity to wild -type mRNA
In some embodiments, at least one RNA polynucleotide
sequence . In some embodiments, at least one mRNA poly- encodes at least one antigenic polypeptide ( e.g. , at least one

US 10,933,127 B2
11

12

hMPV antigenic polypeptide, at least one PIV3 antigenic
polypeptide, at least one RSV antigenic polypeptide, at least
one MeV antigenic polypeptide , or at least one BetaCoV
antigenic polypeptide , e.g. , selected from MERS - CoV,
SARS
-CoV, HCOV-OC43 , HCV-229E, HCOV -NL63 ,
HCOV -NL , HCOV -NH and HCOV -HKU1, or any combina
tion of two or more of the foregoing antigenic polypeptides)
that causes fusion of viral and cellular membranes .
In some embodiments, at least one RNA polynucleotide
encodes at least one antigenic polypeptide ( e.g. , at least one
hMPV antigenic polypeptide, at least one PIV3 antigenic
polypeptide , at least one RSV antigenic polypeptide, at least

ionizable cationic lipid and the non -cationic lipid is a neutral
lipid , and the sterol is a cholesterol. In some embodiments ,

a cationic lipid is selected from the group consisting of
2,2 -dilinoleyl - 4 -dimethylaminoethyl-[ 1,3 ] -dioxolane

5 (DLin -KC2-DMA), dilinoleyl-methyl-4-dimethylaminobu
10

tyrate (DLin -MC3 -DMA ), di ( ( Z )-non - 2 - en - 1 - yl) 9- (4 - di
methylamino )butanoyl )oxy )heptadecanedioate
(L319 ) ,
( 122,152 )—N , N -dimethyl - 2 -nonylhenicosa -12,15 -dien -1
amine ( L608 ) , and N ,N -dimethyl-1 -[( 15,2R )-2 - octylcyclo

propyl ]heptadecan - 8 -amine (L530) .

In some embodiments, the lipid is
(L608 )

one MeV antigenic polypeptide, or at least one BetaCOV 25

antigenic polypeptide , e.g. , selected from MERS - CoV,

SARS - CoV, HCOV -OC43 , HCOV - 229E , HCOV - NL63,
HCOV -NL , HCOV -NH and HCOV -HKU1, or any combina
tion of two or more of the foregoing antigenic polypeptides)

In some embodiments, the lipid is
( L530 )

that is responsible for binding of the virus to a cell being 30
infected .

Some embodiments of the present disclosure provide a
vaccine that includes at least one ribonucleic acid (RNA )

( e.g. , mRNA ) polynucleotide having an open reading frame
encoding at least one antigenic polypeptide (e.g. , at least one
hMPV antigenic polypeptide, at least one PIV3 antigenic
polypeptide, at least one RSV antigenic polypeptide, at least
one MeV antigenic polypeptide, or at least one BetaCov
antigenic polypeptide , e.g. , selected from MERS -CoV,
SARS - CoV, HCOV -OC43 , HCOV - 229E , HCOV -N163 ,
HCOV -NL , HCOV -NH and HCOV -HKU1, or any combination of two or more of the foregoing antigenic polypeptides ),
at least one 5 ' terminal cap and at least one chemical
modification , formulated within a lipid nanoparticle.
In some embodiments, a 5 ' terminal cap is 7mG ( 5 ' )ppp
( 5 ') NlmpNp.
In some embodiments, at least one chemical modification
is selected from pseudouridine, N1-methylpseudouridine,
N1 -ethylpseudouridine, 2 -thiouridine, 4 '-thiouridine,
5 -methylcytosine, 5 -methyluridine, 2 - thio - 1-methyl-1deaza - pseudouridine,
2 - thio - 1 -methyl- pseudouridine,
2 - thio - 5 -aza -uridine, 2 - thio - dihydropseudouridine , 2-thiodihydrouridine, 2 -thio - pseudouridine, 4 -methoxy - 2 - thiopseudouridine, 4 -methoxy -pseudouridine, 4 -thio -1 -methyl
pseudouridine, 4 - thio - pseudouridine, 5 - aza -uridine,
dihydropseudouridine, 5 -methoxyuridine and 2 - O -methyl

35

40
45

50

55

uridine. In some embodiments , the chemical modification is

in the 5 -position of the uracil. In some embodiments, the 60
chemical modification is a N1-methylpseudouridine. In

some embodiments, the chemical modification is a N1-eth
In some embodiments, a lipid nanoparticle comprises a 65

ylpseudouridine.

cationic lipid , a PEG -modified lipid , a sterol and a noncationic lipid . In some embodiments, a cationic lipid is an

In some embodiments, a lipid nanoparticle comprises
compounds of Formula (I ) and /or Formula (II ) , discussed
below .
In some embodiments, a respiratory virus RNA ( e.g. ,
mRNA ) vaccine is formulated in a lipid nanoparticle that
comprises a compound selected from Compounds 3 , 18 , 20 ,
25 , 26 , 29 , 30 , 60 , 108-112 and 122 , described below .
Some embodiments of the present disclosure provide a
vaccine that includes at least one RNA ( e.g. , mRNA ) poly
nucleotide having an open reading frame encoding at least
one antigenic polypeptide (e.g. , at least one hMPV antigenic
polypeptide, at least one PIV3 antigenic polypeptide, at least
one RSV antigenic polypeptide, at least one MeV antigenic
polypeptide, or at least one BetaCoV antigenic polypeptide,
e.g. , selected from MERS -CoV, SARS -CoV, HCOV - OC43 ,
HCOV - 229E, HCOV - NL63, HCOV -NL , HCOV -NH and
HCOV - HKU1, or any combination of two or more of the
foregoing antigenic polypeptides ), wherein at least 80 %
(e.g. , 85 % , 90 % , 95 % , 98 % , 99 % ) of the uracil in the open
reading frame have a chemical modification , optionally
wherein the vaccine is formulated in a lipid nanoparticle
( e.g. , a lipid nanoparticle comprises a cationic lipid , a
PEG -modified lipid, a sterol and a non - cationic lipid ).
In some embodiments , 100 % of the uracil in the open
reading
frame, a chemical
have a chemical
modification
In someof
embodiments
modification
is in the 5 -.position
the uracil. In some embodiments, a chemical modification is
a N1 -methyl pseudouridine. In some embodiments, 100% of
the uracil in the open reading frame have a N1 -methyl
pseudouridine in the 5 -position of the uracil .
In some embodiments , an open reading frame of a RNA
(e.g. , mRNA ) polynucleotide encodes at least two antigenic

US 10,933,127 B2
13

14

polypeptides ( e.g. , at least two hMPV antigenic polypepAlso provided herein is a RNA (e.g. , mRNA ) vaccine of
tides , at least two PIV3 antigenic polypeptides, at least two any one of the foregoing paragraphs ( e.g. , a hMPV vaccine ,
RSV antigenic polypeptides, at least two MeV antigenic a PIV3 vaccine , a RSV vaccine , a MeV vaccine , or a
polypeptides, or at least two BetaCoV antigenic polypep- BetaCoV vaccine , e.g. , selected from MERS - CoV, SARS
tides , e.g. , selected from MERS - CoV, SARS -COV, HCOV- 5 COV, HCV - OC43 , HCOV - 229E , HCOV -NL63, HCOV -NL ,
OC43 , HCOV - 229E , HCOV -NL63, HCOV -NL , HCOV - NH HCOV -NH and HCOV -HKU1, or any combination of two or
and HCOV -HKU1, or any combination of two or more of the more of the foregoing vaccines ), formulated in a nanopar
foregoing antigenic polypeptides ). In some embodiments, ticle ( e.g. , a lipid nanoparticle ).
embodiments , the nanoparticle has a mean diam
the open reading frame encodes at least five or at least ten 10 eterInofsome
50-200 nm . In some embodiments, the nanoparticle
antigenic polypeptides. In some embodiments, the open is a lipid
nanoparticle. In some embodiments, the lipid
reading frame encodes at least 100 antigenic polypeptides.
comprises a cationic lipid, a PEG -modified
In some embodiments, the open reading frame encodes nanoparticle
lipid
,
a
sterol
and a non - cationic lipid . In some embodi
2-100 antigenic polypeptides.
ments, the lipid nanoparticle comprises a molar ratio of
In some embodiments, a vaccine comprises at least two
20-60% cationic lipid , 0.5-15 % PEG -modified lipid ,
RNA ( e.g. , mRNA ) polynucleotides, each having an open 15 about
25-55 % sterol , and 25 % non - cationic lipid . In some embodi
reading frame encoding at least one antigenic polypeptide ments, the cationic lipid is an ionizable cationic lipid and the
( e.g. , at least one hMPV antigenic polypeptide , at least one non - cationic lipid is a neutral lipid , and the sterol is a
PIV3 antigenic polypeptide, at least one RSV antigenic cholesterol. In some embodiments , the cationic lipid is
polypeptide, at least one MeV antigenic polypeptide, or at 20 selected from 2,2 -dilinoleyl-4 -dimethylaminoethyl[ 1,3] -di
least one BetaCoV antigenic polypeptide , e.g. , selected from oxolane (DLin -KC2 -DMA ), dilinoleyl-methyl-4 - dimethyl
MERS -CoV, SARS - CoV, HCOV -OC43, HCOV - 229E , aminobutyrate (DLin -MC3 - DMA ), and di(( Z )-non -2 -en -1
HCOV -NL63 , HCOV -NL , HCOV - NH and HCOV -HKU1, or yl ) 9 - ( [ 4- ( dimethylamino )butanoyl ) oxy )heptadecanedioate

any combination of two or more of the foregoing antigenic ( L319 ) .
polypeptides ) . In some embodiments, the vaccine comprises 25 In some embodiments, a lipid nanoparticle comprises
at least five or at least ten RNA (e.g. , mRNA ) polynucleotides, each having an open reading frame encoding at least
one antigenic polypeptide or an immunogenic fragment

compounds of Formula ( I ) and / or Formula (II ) , as discussed
below .

MERS - CoV, SARS - CoV, HCV - OC43 , HCOV - 229E ,
HCOV -NL63, HCOV - NL , HCOV -NH and HCOV - HKU1, or
any combination of two or more of the foregoing antigenic

effective to produce an antigen -specific immune response . In
some embodiments, the RNA ( e.g. , mRNA ) vaccine is a
hMPV vaccine, a PIV3 vaccine , a RSV vaccine , a MeV

In some embodiments, a lipid nanoparticle comprises
thereof. In some embodiments, the vaccine comprises at Compounds 3 , 18 , 20 , 25 , 26 , 29 , 30 , 60 , 108-112 , or 122 ,
least 100 RNA ( e.g. , mRNA polynucleotides, each having 30 as discussed below.
an open reading frame encoding at least one antigenic
In some embodiments, the nanoparticle has a polydisper
polypeptide . In some embodiments, the vaccine comprises sity value of less than 0.4 ( e.g. , less than 0.3 , 0.2 or 0.1 ) .
2-100 RNA (e.g. , mRNA ) polynucleotides, each having an
In some embodi ts , the nanoparticle has a net neutral
open reading frame encoding at least one antigenic poly- charge at a neutral pH value .
35
peptide.
In some embodiments, the respiratory virus vaccine is
In some embodiments, at least one antigenic polypeptide multivalent.
( e.g. , at least one hMPV antigenic polypeptide , at least one
Some embodiments of the present disclosure provide
PIV3 antigenic polypeptide, at least one RSV antigenic methods of inducing an antigen specific immune response in
polypeptide , at least one MeV antigenic polypeptide, or at a subject, comprising administering to the subject any of the
least one BetaCoV antigenic polypeptide , e.g. , selected from 40 RNA ( e.g. , mRNA ) vaccine as provided herein in an amount

polypeptides ) is fused to a signal peptide. In some embodiments, the signal peptide is selected from : a HulgGk signal
peptide (METPAQLLFLLLLWLPDTTG ; SEQ ID NO : 15 ) ;
IgE heavy chain epsilon - 1 signal peptide (MDWTWILFLVAAATRVHS; SEQ ID NO : 16 ) ; Japanese encephalitis
PRM signal sequence (MLGSNSGQRVVFTILLLLVAPAYS ; SEQ ID NO : 17 ) , VSVg protein signal sequence
( MKCLLYLAFLFIGVNCA ; SEQ ID NO : 18 ) and Japanese
encephalitis JEV signal sequence (MWLVSLAIVTACAGA ; SEQ ID NO : 19 ) .
In some embodiments , the signal peptide is fused to the
N - terminus of at least one antigenic polypeptide. In some
embodiments, a signal peptide is fused to the C - terminus of
at least one antigenic polypeptide.
In some embodiments, at least one antigenic polypeptide
( e.g. , at least one hMPV antigenic polypeptide , at least one
PIV3 antigenic polypeptide, at least one RSV antigenic
polypeptide , at least one MeV antigenic polypeptide, or at
least one BetaCoV antigenic polypeptide , e.g. , selected from
MERS -CoV, SARS -CoV, HCV - OC43 , HCOV - 229E ,
HCOV -NL63 , HCOV -NL , HCOV - NH and HCOV -HKU1, or

vaccine , or a BetaCoV vaccine, e.g. , selected from MERS
45 COV, SARS -CoV, HCV - OC43 , HCOV - 229E , HCOV -NL63,
HCOV -NL , HCOV -NH and HCOV -HKU1 vaccines . In some
embodiments, the RNA ( e.g. , mRNA ) vaccine is a combi
nation vaccine comprising a combination of any two or more
of the foregoing vaccines.
50 In some embodiments, an antigen - specific immune
response comprises a T cell response or a B cell response .
In some embodiments, a method of producing an antigen
specific immune response comprises administering to a
subject a single dose (no booster dose ) of a RNA ( e.g. ,
55 mRNA ) vaccine of the present disclosure . In some embodi
ments, the RNA ( e.g. , mRNA ) vaccine is a hMPV vaccine ,
a PIV3 vaccine , a RSV vaccine , a MeV vaccine , or a
BetaCoV vaccine , e.g. , selected from MERS -COV, SARS
COV, HCV - OC43 , HCOV - 229E , HCOV -NL63, HCOV - NL ,
60 HCOV - NH and HCOV - HKU1 vaccines . In some embodi
ments, the RNA (e.g. , mRNA ) vaccine is a combination
vaccine comprising a combination of any two or more of the
foregoing vaccines .
In some embodiments , a method further comprises

any combination of two or more of the foregoing antigenic 65 administering to the subject a second ( booster ) dose of a
polypeptides) comprises a mutated N - linked glycosylation RNA (e.g. , mRNA ) vaccine . Additional doses of a RNA
site .
(e.g. , mRNA ) vaccine may be administered .

US 10,933,127 B2
15

16

In some embodiments, the subjects exhibit a seroconversion rate of at least 80 % ( e.g. , at least 85 % , at least 90 % , or
at least 95 % ) following the first dose or the second (booster)

recombinant hMPV, PIV3 , RSV, MeV and / or BetaCoV
protein vaccine , wherein the anti-antigenic polypeptide anti
body titer produced in the subject is equivalent to an

dose of the vaccine . Seroconversion is the time period anti - antigenic polypeptide antibody titer produced in a con
during which a specific antibody develops and becomes 5 trol subject administered the standard of care dose of a

detectable in the blood . After seroconversion has occurred, recombinant hMPV , PIV3 , RSV, MeV and / or BetaCoV
a virus can be detected in blood tests for the antibody. protein vaccine, a purified hMPV, PIV3 , RSV, MeV and /or
During an infection or immunization, antigens enter the BetaCoV protein vaccine , a live attenuated hMPV , PIV3 ,
blood, and the immune system begins to produce antibodies RSV, MeV and / or BetaCoV vaccine , an inactivated hMPV,
in response . Before seroconversion, the antigen itself may or 10 PIV3 , RSV, MeV and / or BetaCoV vaccine , or a hMPV,
may not be detectable , but antibodies are considered absent. PIV3 , RSV, MeV and /or BetaCoV VLP vaccine . In some
During seroconversion , antibodies are present but not yet embodiments, the effective amount is a dose equivalent to
detectable. Any time after seroconversion , the antibodies can 2-1000 - fold reduction in the standard of care dose of a
be detected in the blood , indicating a prior or current recombinant hMPV , PIV3 , RSV, MeV and / or BetaCoV
infection .
15 protein vaccine, wherein the anti -antigenic polypeptide anti

In some embodiments, a RNA ( e.g. , mRNA ) vaccine is
administered to a subject by intradermal or intramuscular

body titer produced in the subject is equivalent to an
anti-antigenic polypeptide antibody titer produced in a con
injection .
trol subject administered the standard of care dose of a
Some embodiments, of the present disclosure provide recombinant hMPV , PIV3 , RSV, MeV and / or BetaCoV
methods of inducing an antigen specific immune response in 20 protein vaccine, a purified hMPV, PIV3 , RSV, MeV and / or
a subject, including administering to a subject a RNA ( e.g. , BetaCoV protein vaccine , a live attenuated hMPV , PIV3 ,
mRNA ) vaccine in an effective amount to produce an RSV, MeV and / or BetaCoV vaccine , an inactivated hMPV,

antigen specific immune response in a subject. Antigen- PIV3 , RSV, MeV and /or BetaCoV vaccine , or a hMPV,
specific immune responses in a subject may be determined , PIV3 , RSV, MeV and / or BetaCoV VLP vaccine .
in some embodiments, by assaying for antibody titer ( for 25 In some embodiments, the control is an anti -antigenic
titer of an antibody that binds to a hMPV , PIV3 , RSV, MeV polypeptide antibody titer produced in a subject who has

and / or BetaCoV antigenic polypeptide) following adminis- been administered a virus - like particle (VLP ) vaccine com
tration to the subject of any of the RNA ( e.g. , mRNA ) prising structural proteins of hMPV, PIV3 , RSV, MeV
vaccines of the present disclosure . In some embodiments, and / or BetaCoV .
the anti-antigenic polypeptide antibody titer produced in the 30 In some embodiments, the RNA (e.g. , mRNA ) vaccine is
subject is increased by at least 1 log relative to a control. In formulated in an effective amount to produce an antigen
some embodiments, the anti- antigenic polypeptide antibody specific immune response in a subject.
titer produced in the subject is increased by 1-3 log relative
In some embod its, the effective amount is a total dose
to a control.
of 25 ug to 1000 ug , or 50 ug to 1000 ug. In some
In some embodiments, the anti -antigenic polypeptide 35 embodiments, the effective amount is a total dose of 100 ug .
antibody titer produced in a subject is increased at least 2 In some embodiments, the effective amount is a dose of 25
times relative to a control. In some embodiments, the ug administered to the subject a total of two times . In some
anti - antigenic polypeptide antibody titer produced in the embodiments , the effective amount is a dose of 100 ug
subject is increased at least 5 times relative to a control. In administered to the subject a total of two times . In some
some embodiments, the anti-antigenic polypeptide antibody 40 embodiments , the effective amount is a dose of 400 ug
titer produced in the subject is increased at least 10 times administered to the subject a total of two times . In some
relative to a control. In some embodiments, the anti - anti- embodiments , the effective amount is a dose of 500 ug
genic polypeptide antibody titer produced in the subject is administered to the subject a total of two times .
increased 2-10 times relative to a control.
In some embodiments , the efficacy (or effectiveness ) of a
In some embodiments, the control is an anti -antigenic 45 RNA ( e.g. , mRNA ) vaccine is greater than 60 % . In some
polypeptide antibody titer produced in a subject who has not embodiments, the RNA ( e.g. , mRNA ) polynucleotide of the
been administered a RNA ( e.g. , mRNA ) vaccine of the vaccine at least one hMPV antigenic polypeptide, at least
present disclosure . In some embodiments , the control is an one PIV3 antigenic polypeptide, at least one RSV antigenic
anti -antigenic polypeptide antibody titer produced in a sub- polypeptide, at least one MeV antigenic polypeptide, at least
ject who has been administered a live attenuated or inacti- 50 one BetaCoV antigenic polypeptide, e.g. , selected from
vated hMPV , PIV3 , RSV, MeV and / or BetaCoV vaccine
( see , e.g. , Ren J. et al . J ofGen. Virol. 2015 ; 96 : 1515-1520) ,

MERS - CoV, SARS - CoV , HCOV -OC43, HCV - 229E ,
HCOV -NL63, HCOV -NL , HCOV -NH and HCOV -HKU1, or

or wherein the control is an anti -antigenic polypeptide any combination of two or more of the foregoing antigenic
antibody titer produced in a subject who has been adminis- polypeptides.
tered a recombinant or purified hMPV, PIV3 , RSV, MeV 55 Vaccine efficacy may be assessed using standard analyses
and / or BetaCoV protein vaccine . In some embodiments , the ( see , e.g. , Weinberg et al . , J Infect Dis. 2010 Jun . 1 ;
control is an anti -antigenic polypeptide antibody titer pro- 201 ( 11 ) : 1607-10 ) . For example, vaccine efficacy may be
duced in a subject who has been administered a hMPV, measured by double -blind, randomized, clinical controlled
PIV3 , RSV , MeV and / or BetaCoV virus - like particle (VLP ) trials . Vaccine efficacy may be expressed as a proportionate
vaccine ( see , e.g. , Cox R G et al . , J Virol. 2014 June; 88 ( 11 ) : 60 reduction in disease attack rate (AR) between the unvacci
6368-6379 ) .
nated (ARU ) and vaccinated ( ARV ) study cohorts and can
ARNA (e.g. , mRNA ) vaccine of the present disclosure is be calculated from the relative risk (RR ) of disease among
administered to a subject in an effective amount (an amount the vaccinated group with use of the following formulas:
effective to induce an immune response ). In some embodi
Efficacy = (ARU - ARV )/ARUx100 ; and
ments , the effective amount is a dose equivalent to an at least 65
2 - fold , at least 4 - fold , at least 10 - fold , at least 100 - fold , at
least 1000 - fold reduction in the standard of care dose of a

Efficacy = ( 1 - RR )x100 .

US 10,933,127 B2
18

17

Likewise , vaccine effectiveness may be assessed using
standard analyses ( see , e.g. , Weinberg et al . , J Infect Dis.
2010 Jun . 1 ; 201 ( 11 ) : 1607-10) . Vaccine effectiveness is an
assessment of how a vaccine (which may have already
proven to have high vaccine efficacy ) reduces disease in a 5

population . This measure can assess the net balance of

benefits and adverse effects of a vaccination program , not

mRNA ) vaccines for maternal immunization to improve
mother - to - child transmission of protection against the virus .
In some embodiments, the subject is a young adult
between the ages of about 20 years and about 50 years ( e.g. ,
about 20 , 25 , 30 , 35 , 40 , 45 or 50 years old) .
In some embodiments, the subject is an elderly subject
about 60 years old, about 70 years old , or older ( e.g. , about
60 , 65 , 70 , 75 , 80 , 85 or 90 years old) .
In some embodiments, the subject is has a chronic pul

just the vaccine itself, under natural field conditions rather
than in a controlled clinical trial. Vaccine effectiveness is 10 monary disease ( e.g. , chronic obstructive pulmonary disease
proportional to vaccine efficacy ( potency ) but is also (COPD ) or asthma ). Two forms of COPD include chronic
affected by how well target groups in the population are bronchitis, which involves a long -term cough with mucus ,
immunized , as well as by other non - vaccine - related factors and emphysema, which involves damage to the lungs over
that influence the “ real -world ' outcomes of hospitalizations, time
. Thus, a subject administered a RNA ( e.g. , mRNA )
ambulatory visits , or costs . For example, a retrospective case 15 vaccine
may have chronic bronchitis or emphysema.
control analysis may be used , in which the rates of vacci
In
some
, the subject has been exposed to
nation among a set of infected cases and appropriate controls hMPV, PIV3embodiments
,
RSV
,
MeV
( e.g. , selected from
are compared. Vaccine effectiveness may be expressed as a MERS - CoV, SARS - CoV,, BetaCoV
HCV
OC43
, HCOV -229E,
rate difference, with use of the odds ratio (OR) for devel HCOV -NL63, HCOV -NL , HCOV -NH and HCOV
-HKU1 ), or
oping infection despite vaccination :
20 any combination of two or more of the foregoing viruses; the
subject is infected with hMPV , PIV3 , RSV, MeV, BetaCoV
Effectiveness = ( 1 -OR )x100 .
(e.g. , selected from MERS - CoV, SARS - CoV, HCOV -OC43,
In some embodiments, the efficacy ( or effectiveness ) of a HCOV - 229E , HCOV - NL63, HCOV - NL , HCOV - NH and
RNA ( e.g. , mRNA ) vaccine is at least 65 % , at least 70 % , at HCOV -HKU1), or any combination of two or more of the
least 75 % , at least 80% , at least 85 % , or at least 90 % .
25 foregoing viruses ; or subject is at risk of infection by hMPV,
In some embodiments, the vaccine immunizes the subject PIV3 , RSV, MeV, BetaCoV ( e.g. , selected from MERS - CoV,
against hMPV, PIV3 , RSV, MeV , BetaCoV (e.g. , selected SARS -CoV, HCOV -OC43 , HCOV - 229E , HCOV -NL63,
from MERS -CoV , SARS - COV, HCOV -OC43, HCOV - 229E , HCOV - NL , HCOV - NH and HCOV -HKU1 ), or any combina
HCOV -NL63, HCOV -NL , HCOV -NH and HCOV -HKU1 ), or tion of two or more of the foregoing viruses.
any combination of two or more of the foregoing viruses for 30 In some embodiments, the subject is immunocompro
up to 2 years . In some embodiments, the vaccine immunizes mised (has an impaired immune system , e.g. , has an immune
the subject against hMPV , PIV3 , RSV, MeV , BetaCoV ( e.g. , disorder or autoimmune disorder ).
selected from MERS -CoV, SARS -COV, HCOV -OC43,
In some embodiments the nucleic acid vaccines described
HCOV - 229E , HCOV -NL63, HCOV -NL , HCOV -NH and herein are chemically modified . In other embodiments the
HCOV -HKU1), or any combination of two or more of the 35 nucleic acid vaccines are unmodified .
foregoing viruses for more than 2 years , more than 3 years ,
Yet other aspects provide compositions for and methods
of vaccinating a subject comprising administering to the
more than 4 years, or for 5-10 years .
In some embodiments , the subject is about 5 years old or subject a nucleic acid vaccine comprising one or more RNA
younger. For example, the subject may be between the ages polynucleotides having an open reading frame encoding a

of about 1 year and about 5 years ( e.g. , about 1 , 2 , 3 , 5 or
5 years ) , or between the ages of about 6 months and about
1 year (e.g. , about 6 , 7 , 8 , 9 , 10 , 11 or 12 months ). In some
embodiments, the subject is about 12 months or younger
( e.g. , 12 , 11 , 10 , 9 , 8 , 7 , 6 , 5 , 4 , 3 , 2 months or 1 month ). In
some embodiments, the subject is about 6 months or
younger.
In some embodiments, the subject was born full term
( e.g. , about 37-42 weeks ). In some embodiments, the subject
was born prematurely, for example, at about 36 weeks of
gestation or earlier (e.g. , about 36 , 35 , 34 , 33 , 32 , 31 , 30 , 29 ,
28 , 27 , 26 or 25 weeks). For example, the subject may have
been born at about 32 weeks of gestation or earlier. In some
embodiments, the subject was born prematurely between
about 32 weeks and about 36 weeks of gestation . In such
subjects, a RNA ( e.g. , mRNA ) vaccine may be administered
later in life, for example, at the age of about 6 months to
about 5 years , or older.
In some embodiments, the subject is pregnant (e.g. , in the
first, second or third trimester ) when administered an RNA
( e.g. , mRNA ) vaccine . Viruses such as hMPV, PIV3 and
RSV causes infections of the lower respiratory tract, mainly
in infants and young children . One -third of RSV related
deaths, for example, occur in the first year of life, with 99
percent of these deaths occurring in low -resource countries .
It's so widespread in the United States that nearly all
children become infected with the virus before their second
birthdays. Thus, the present disclosure provides RNA ( e.g. ,

40 first respiratory virus antigenic polypeptide , wherein the
RNA polynucleotide does not include a stabilization ele
ment, and wherein an adjuvant is not coformulated or
co - administered with the vaccine .
In other aspects the invention is a composition for or
45 method ofvaccinating a subject comprising administering to
the subject a nucleic acid vaccine comprising one or more
RNA polynucleotides having an open reading frame encod
ing a first antigenic polypeptide wherein a dosage of
between 10 ug /kg and 400 ug/kg of the nucleic acid vaccine
50 is administered to the subject. In some embodiments the
dosage of the RNA polynucleotide is 1-5 ug , 5-10 ug, 10-15
ug , 15-20 ug , 10-25 ug , 20-25 ug , 20-50 ug , 30-50 ug , 40-50
ug , 40-60 ug , 60-80 ug , 60-100 ug , 50-100 ug, 80-120 ug ,
40-120 ug , 40-150 ug , 50-150 ug , 50-200 ug , 80-200 ug ,
55 100-200 ug , 120-250 ug , 150-250 ug , 180-280 ug , 200-300
ug , 50-300 ug , 80-300 ug , 100-300 ug , 40-300 ug , 50-350
ug , 100-350 ug , 200-350 ug , 300-350 ug , 320-400 ug ,
40-380 ug , 40-100 ug , 100-400 ug , 200-400 ug , or 300-400
ug per dose . In some embodiments, the nucleic acid vaccine
60 is administered to the subject by intradermal or intramus
cular injection . In some embodiments, the nucleic acid
vaccine is administered to the subject on day zero . In some
embodiments, a second dose of the nucleic acid vaccine is
administered to the subject on day twenty one .
65 In some embodiments, a dosage of 25 micrograms of the
RNA polynucleotide is included in the nucleic acid vaccine
administered to the subject. In some embodiments, a dosage

US 10,933,127 B2
19

of 100 micrograms of the RNA polynucleotide is included in

the nucleic acid vaccine administered to the subject. In some
embodiments, a dosage of 50 micrograms of the RNA

polynucleotide is included in the nucleic acid vaccine
administered to the subject. In some embodiments, a dosage
of 75 micrograms of the RNA polynucleotide is included in
the nucleic acid vaccine administered to the subject. In some
embodiments, a dosage of 150 micrograms of the RNA
polynucleotide is included in the nucleic acid vaccine
administered to the subject. In some embodiments, a dosage
of 400 micrograms of the RNA polynucleotide is included in
the nucleic acid vaccine administered to the subject. In some
embodiments, a dosage of 200 micrograms of the RNA
polynucleotide is included in the nucleic acid vaccine
administered to the subject. In some embodiments, the RNA
polynucleotide accumulates at a 100 fold higher level in the
local lymph node in comparison with the distal lymph node .
In other embodiments the nucleic acid vaccine is chemically
modified and in other embodiments the nucleic acid vaccine
is not chemically modified .
Aspects of the invention provide a nucleic acid vaccine
comprising one or more RNA polynucleotides having an
open reading frame encoding a first antigenic polypeptide,
wherein the RNA polynucleotide does not include a stabilization element, and a pharmaceutically acceptable carrier
or excipient, wherein an adjuvant is not included in the
vaccine . In some embodiments, the stabilization element is
a histone stem - loop . In some embodiments, the stabilization
element is a nucleic acid sequence having increased GC
content relative to wild type sequence .
Aspects of the invention provide nucleic acid vaccines
comprising one or more RNA polynucleotides having an
open reading frame encoding a first antigenic polypeptide,
wherein the RNA polynucleotide is present in the formulation for in vivo administration to a host, which confers an
antibody titer superior to the criterion for seroprotection for
the first antigen for an acceptable percentage of human
subjects. In some embodiments, the antibody titer produced
by the mRNA vaccines of the invention is a neutralizing
antibody titer. In some embodiments the neutralizing antibody titer is greater than a protein vaccine . In other embodiments the neutralizing antibody titer produced by the mRNA
vaccines of the invention is greater than an adjuvanted
protein vaccine . In yet other embodiments the neutralizing
antibody titer produced by the mRNA vaccines of the
invention is 1,000-10,000 , 1,200-10,000 , 1,400-10,000 ,
1,500-10,000 , 1,000-5,000 , 1,000-4,000 , 1,800-10,000 ,
2000-10,000 , 2,000-5,000 , 2,000-3,000 , 2,000-4,000 , 3,0005,000 , 3,000-4,000 , or 2,000-2,500 . A neutralization titer is
typically expressed as the highest serum dilution required to
achieve a 50% reduction in the number of plaques.
Also provided are nucleic acid vaccines comprising one
or more RNA polynucleotides having an open reading frame
encoding a first antigenic polypeptide, wherein the RNA
polynucleotide is present in a formulation for in vivo administration to a host for eliciting a longer lasting high antibody
titer than an antibody titer elicited by an mRNA vaccine
having a stabilizing element or formulated with an adjuvant
and encoding the first antigenic polypeptide. In some
embodiments , the RNA polynucleotide is formulated to
produce a neutralizing antibodies within one week of a
single administration . In some embodiments , the adjuvant is
selected from a cationic peptide and an immunostimulatory

20

comprising at least one chemical modification or optionally

no nucleotide modification, the open reading frame encod
ing a first antigenic polypeptide, wherein the RNA poly

nucleotide is present in the formulation for in vivo admin
5 istration to a host such that the level of antigen expression
in the host significantly exceeds a level of antigen expres
sion produced by an mRNA vaccine having a stabilizing
element or formulated with an adjuvant and encoding the
first antigenic polypeptide.
10 Other aspects provide nucleic acid vaccines comprising
one or more RNA polynucleotides having an open reading
frame comprising at least one chemical modification or
optionally no nucleotide modification , the open reading
frame encoding a first antigenic polypeptide, wherein the
15 vaccine has at least 10 fold less RNA polynucleotide than is
required for an unmodified mRNA vaccine to produce an
equivalent antibody titer. In some embodiments, the RNA
polynucleotide is present in a dosage of 25-100 micrograms.
Aspects of the invention also provide a unit of use
20 vaccine , comprising between 10 ug and 400 ug of one or
more RNA polynucleotides having an open reading frame
comprising at least one chemical modification or optionally
no nucleotide modification , the open reading frame encod
ing a first antigenic polypeptide, and a pharmaceutically
25 acceptable carrier or excipient, formulated for delivery to a
human subject. In some embodiments , the vaccine further
comprises a cationic lipid nanoparticle.
Aspects of the invention provide methods of creating,
maintaining or restoring antigenic memory to a respiratory
30 virus strain in an individual or population of individuals
comprising administering to said individual or population an
antigenic memory booster nucleic acid vaccine comprising
(a ) at least one RNA polynucleotide, said polynucleotide
comprising at least one chemical modification or optionally
35 no nucleotide modification and two or more codon -opti
mized open reading frames, said open reading frames encod
ing a set of reference antigenic polypeptides , and ( b ) option
ally a pharmaceutically acceptable carrier or excipient. In
some embodiments , the vaccine is administered to the
40 individual via a route selected from the group consisting of
intramuscular administration , intradermal administration
and subcutaneous administration . In some embodiments, the
administering step comprises contacting a muscle tissue of
the subject with a device suitable for injection of the
45 composition. In some embodiments, the administering step
comprises contacting a muscle tissue of the subject with a
device suitable for injection of the composition in combi
nation with electroporation .
Aspects of the invention provide methods of vaccinating
50 a subject comprising administering to the subject a single

dosage of between 25 ug /kg and 400 ug /kg of a nucleic acid
vaccine comprising one or more RNA polynucleotides hav
ing an open reading frame encoding a first antigenic poly
peptide in an effective amount to vaccinate the subject.
55 Other aspects provide nucleic acid vaccines comprising
one or more RNA polynucleotides having an open reading
frame comprising at least one chemical modification , the
open reading frame encoding a first antigenic polypeptide ,
wherein the vaccine has at least 10 fold less RNA poly
60 nucleotide than is required for an unmodified mRNA vac
cine to produce an equivalent antibody titer. In some
embodiments, the RNA polynucleotide is present in dos
age of 25-100 micrograms.
nucleic
acid
.
In
some
embodiments
,
the
cationic
peptide
is
Other aspects provide nucleic acid vaccines comprising
protamine.
65 an LNP formulated RNA polynucleotide having an open
Aspects provide nucleic acid vaccines comprising one or reading frame comprising no nucleotide modifications (un
more RNA polynucleotides having an open reading frame modified ), the open reading frame encoding a first antigenic

US 10,933,127 B2
21

22

polypeptide , wherein the vaccine has at least 10 fold less

polynucleotide is one of SEQ ID NO : 1-4 , 9-12 , 20-23 ,

RNA polynucleotide than is required for an unmodified
mRNA vaccine not formulated in a LNP to produce an

35-46 , 57-61 , and 64-80 and does not include any nucleotide
modifications, or is unmodified . In yet other embodiments

equivalent antibody titer. In some embodiments, the RNA the at least one RNA polynucleotide encodes an antigenic
polynucleotide is present in a dosage of 25-100 micrograms. 5 protein of any of SEQ ID NO : 5-8 , 12-13 , 24-34 , and 47-50
The data presented in the Examples demonstrate signifi-

and includes at least one chemical modification . In other

cant enhanced immune responses using the formulations of embodiments the RNA polynucleotide encodes an antigenic
the invention . Both chemically modified and unmodified protein of any of SEQ ID NO : 5-8 , 12-13 , 24-34 , and 47-50
RNA vaccines are useful according to the invention . Sur and does not include any nucleotide modifications, or is
prisingly, in contrast to prior art reports that it was preferable 10 unmodified
.
to use chemically unmodified mRNA formulated in a carrier
In
preferred
, vaccines of the invention ( e.g. ,
for the production of vaccines , it is described herein that LNP - encapsulatedaspects
mRNA
) produce prophylacti
chemically modified mRNA -LNP vaccines required a much cally- and / or therapeuticallyvaccines
efficacious
levels , concentra
lower effective mRNA dose than unmodified mRNA , i.e. ,

tenfold less than unmodified mRNA when formulated in 15 tions and /or titers of antigen -specific antibodies in the blood
carriers other than LNP. Both the chemically modified and
unmodified RNA vaccines of the invention produce better
immune responses than mRNA vaccines formulated in a
different lipid carrier.
In other aspects the invention encompasses a method of
treating an elderly subject age 60 years or older comprising
administering to the subject a nucleic acid vaccine comprising one or more RNA polynucleotides having an open
reading frame encoding a respiratory virus antigenic polypeptide in an effective amount to vaccinate the subject.
In other aspects the invention encompasses a method of
treating a young subject age 17 years or younger comprising
administering to the subject a nucleic acid vaccine comprising one or more RNA polynucleotides having an open
reading frame encoding a respiratory virus antigenic polypeptide in an effective amount to vaccinate the subject.
In other aspects the invention encompasses a method of
treating an adult subject comprising administering to the
subject a nucleic acid vaccine comprising one or more RNA
polynucleotides having an open reading frame encoding a
respiratory virus antigenic polypeptide in an effective
amount to vaccinate the subject.
In some aspects the invention is a method of vaccinating
a subject with a combination vaccine including at least two
nucleic acid sequences encoding respiratory antigens
wherein the dosage for the vaccine is a combined therapeutic
dosage wherein the dosage of each individual nucleic acid
encoding an antigen is a sub therapeutic dosage . In some
embodiments, the combined dosage is 25 micrograms of the
RNA polynucleotide in the nucleic acid vaccine administered to the subject. In some embodiments, the combined
dosage is 100 micrograms of the RNA polynucleotide in the
nucleic acid vaccine administered to the subject. In some
embodiments the combined dosage is 50 micrograms of the
RNA polynucleotide in the nucleic acid vaccine administered to the subject. In some embodiments, the combined
dosage is 75 micrograms of the RNA polynucleotide in the
nucleic acid vaccine administered the subject. In some
embodiments, the combined dosage is 150 micrograms of
the RNA polynucleotide in the nucleic acid vaccine administered to the subject. In some embodiments, the combined
dosage is 400 micrograms of the RNA polynucleotide in the
nucleic acid vaccine administered to the subject. In some
embodiments, the sub therapeutic dosage of each individual
nucleic acid encoding an antigen is 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 ,
10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , or 20 micrograms. In
other embodiments the nucleic acid vaccine is chemically
modified and in other embodiments the nucleic acid vaccine
is not chemically modified .
The RNA polynucleotide is one of SEQ ID NO : 1-4 , 9-12 ,
20-23 , 35-46 , 57-61 , and 64-80 and includes at least one
chemical modification . In other embodiments the RNA

or serum of a vaccinated subject. As defined herein , the term
antibody titer refers to the amount of antigen - specific anti
body produces in s subject, e.g. , a human subject. In
exemplary embodiments, antibody titer is expressed as the
20 inverse of the greatest dilution (in a serial dilution ) that still
gives a positive result . In exemplary embodiments, antibody
titer is determined or measured by enzyme -linked immu
nosorbent assay (ELISA) . In exemplary embodiments, anti
body titer is determined or measured by neutralization assay ,
25 e.g. , by microneutralization assay. In certain aspects , anti
body titer measurement is expressed as a ratio, such as 1:40 ,
1 : 100 , etc.
In exemplary embodiments of the invention , an effica
cious vaccine produces an antibody titer of greater than 1:40 ,
30 greater that 1 : 100 , greater than 1 : 400 , greater than 1: 1000 ,
greater than 1 : 2000 , greater than 1 : 3000 , greater than
1 : 4000 , greater than 1 : 500 , greater than 1 : 6000 , greater than
1 : 7500 , greater than 1 : 10000 . In exemplary embodiments,
the antibody titer is produced or reached by 10 days fol

35 lowing vaccination , by 20 days following vaccination , by 30
days following vaccination , by 40 days following vaccina
tion, or by 50 or more days following vaccination . In
exemplary embodiments, the titer is produced or reached
following a single dose of vaccine administered to the
40 subject. In other embodiments, the titer is produced or
reached following multiple doses , e.g. , following a first and
a second dose ( e.g. , a booster dose . )
In exemplary aspects of the invention , antigen -specific
antibodies are measured in units of ug /ml or are measured in

45 units of IU / L (International Units per liter) or mIU /ml (milli
International Units per ml ) . In exemplary embodiments of
the invention, an efficacious vaccine produces >0.5 ug /ml,
>0.1 ug/ml, >0.2 ug /ml, >0.35 ug /ml, >0.5 ug /ml, > 1 ug /ml,
>2 ug /ml, > 5 ug /ml or > 10 ug /ml. In exemplary embodi
50 ments of the invention , an efficacious vaccine produces > 10
mIU /ml, >20 mIU /ml, > 50 mIU /ml, > 100 mIU /ml, >200
mIU /ml, > 500 mIU /ml or > 1000 mlU /ml. In exemplary
embodiments, the antibody level or concentration is pro
duced or reached by 10 days following vaccination , by 20
55 days following vaccination , by 30 days following vaccina
tion , by 40 days following vaccination , or by 50 or more

days following vaccination . In exemplary embodiments, the
level or concentration is produced or reached following a
single dose of vaccine administered to the subject. In other
60 embodiments, the level or concentration is produced or
reached following multiple doses , e.g. , following a first and
a second dose ( e.g. , a booster dose . ) In exemplary embodi
ments, antibody level or concentration is determined or
measured by enzyme- linked immunosorbent assay (ELISA) .
65 In exemplary embodiments, antibody level or concentration
is determined or measured by neutralization assay, e.g. , by
microneutralization assay.

US 10,933,127 B2
23

24

The details of various embodiments of the disclosure are
set forth in the description below. Other features, objects ,
and advantages of the disclosure will be apparent from the
description and from the claims.

lap ) ) in splenocytes isolated from mice immunized with the 45

canavalin A was included . The cytokines tested include
IL - 10 (FIG . 8A) , TNF - a (FIG . 8B ) , IL4 (FIG . 8C ) , IL - 5
(FIG . 8D ) and IL - 6 (FIG . 8E ) .
FIGS . 9A - 9B are graphs showing the results of cotton rat
challenge experiments. Two different doses of the hMPV
mRNA vaccines were used ( 2 ug or 10 ug doses ) to
immunize the cotton rats before challenge. The hMPV
mRNA vaccines reduced the viral titer in the lung and nose
of the cotton rat, with the 10 ug dose being more effective
in reducing viral titer. Use of a 10 ug dose resulted in 100 %
protection in the lung and a 2 log reduction in nose viral titer.
Use of a 2 ug dose resulted in a 1 log reduction in lung vital
titer and no reduction in nose viral titer. The vaccine was
administered on Day 0 , and a boost was administered on
Day 21 .
FIG . 10 is a graph showing the lung histopathology of
cotton rats that received hMPV mRNA vaccines. Pathology
associated with vaccine - enhanced disease was not observed
in immunized groups.
FIG . 11 is a graph showing hMPV neutralization antibody
titers in cotton rats that received hMPV mRNA vaccines (2
ug or 10 ug doses ) on days 35 and 42 post immunization .
FIG . 12 is a graph showing the lung and nose viral load
in cotton rats challenged with a hMPV / A2 strain after
immunization with the indicated mRNA vaccines (hMPV
mRNA vaccine or hMPV /PIV mRNA combination vaccine) .
Vaccinated cotton rats showed reduced lung and nose viral
loads after challenge, compared to control.
FIG . 13 is a graph showing the lung and nose viral load
in cotton rats challenged with PIV3 strain after immuniza
tion with indicated mRNA vaccines ( PIV mRNA vaccine or
hMPV /PIV combination vaccine ) . Vaccinated cotton rats
showed reduced lung and nose viral loads after challenge,
compared to control.
FIG . 14 is a graph showing hMPV neutralizing antibody
titers in cotton rats that received different dosages of hMPV
mRNA vaccines or hMPV /PIV combination mRNA vac
cines on day 42 post immunization. The dosages of the
vaccine are indicated in Table 9 .
FIG . 15 is a graph showing PIV3 neutralizing antibody
titers in cotton rats that received different dosages of PIV
mRNA vaccines or hMPV / PIV combination mRNA vac
cines on day 42 post immunization . The dosages of the
vaccine are indicated in Table 9 .
FIG . 16 is a graph showing the lung histopathology score

hMPV mRNA vaccines . Virus - free media was used as a
negative control and Concanavalin A ( ConA , a positive
control for splenocyte stimulation ) was included . The cyto-

of cotton rats immunized with hMPV mRNA vaccines , PIV
mRNA vaccines or hMPV /PIV combination mRNA vac
cines as indicated in Table 9. Low occurrence of alevolitis

BRIEF DESCRIPTION OF THE DRAWINGS

5

The foregoing and other objects, features and advantages
will be apparent from the following description of particular
embodiments of the disclosure , as illustrated in the accom- 10
panying drawings in which like reference characters refer to
the same parts throughout the different views . The drawings
are not necessarily to scale , emphasis instead being placed
upon illustrating the principles of various embodiments of
the disclosure.
15
FIG . 1 shows a schematic of one example of a RNA (e.g.
mRNA ) vaccine construct of the present disclosure . The

construct depicts a human Metapneumovirus and human
respiratory syncytial virus full length fusion protein obtained
from wild - type strains ( The Journal of General Virology. 20

2008 ; 89 ( Pt 12 ) : 3113-3118 , incorporated herein by reference ).

FIGS . 2A - 2C are graphs showing the levels of anti - hMPV
fusion protein - specific antibodies in the serum of mice
immunized with hMPV mRNA vaccines on day 0 (FIG . 2A) ,
day 14 (FIG . 2B ) and day 35 (FIG . 2C ) post immunization .
The mice were immunized with a single dose (2 ug or 10 ug )
on day 0 and were given a boost dose ( 2 ug or 10 ug) on day
21 , hMPV fusion protein - specific antibodies were detected
at up to 1 : 10000 dilution of serum on day 35 for both doses.
FIGS . 3A - 3C are graphs showing the result of IgG
isotyping in the serum of mice immunized with hMPV
mRNA vaccines. The levels of hMPV fusion protein -specific
IgG2a ( FIG . 3A) and IgG1 ( FIG . 3B ) antibodies in the serum
are measured by ELISA . FIG . 3C shows that hMPV fusion
protein mRNA vaccine induced a mixed Th1 /Th2 cytokine
response with a Thi bias .
FIG . 4 is a graph showing in vitro neutralization of a
hMPV B2 strain ( TN /91-316 ) using the sera of mice immunized with a mRNA vaccine encoding hMPV fusion protein .
Mouse serum obtained from mice receiving a 10 ug or a 2
ug dose contained hMPV -neutralizing antibodies.
FIGS . 5A - 5C are graphs showing a Thl cytokine response
induced by a hMPV fusion peptide pool ( 15 - mers - 50 (over-

kines tested included IFN - Y (FIG . 5A) , IL - 2 ( FIG . 5B ) and

25

30

35

40

and interstitial pneumonia was observed , indicating no anti

IL12 ( FIG . 5C) .
50 body -dependent enhancement (ADE ) of hMPV associated
FIGS . 6A - 6E are graphs showing the Th2 cytokine diseases .
response induced by a hMPV fusion peptide pool (15 -mersFIG . 17 is a graph showing the reciprocal MERS - CoV
50 ) in splenocytes isolated from mice immunized with the neutralizing antibody titers in mice immunized with Beta
hMPV mRNA vaccines . Virus - free media was used as a coronavirus mRNA vaccine encoding the MERS - CoV full

negative control and Concanavalin Awas also included . The 55 length Spike protein , on days 0 , 21 , 42 , and 56 post
cytokines tested included IL - 10 (FIG . 6A) , TNF - a ( FIG . immunization .
6B ) , IL4 (FIG . 6C ) , IL - 5 (FIG . 6D ) and IL - 6 (FIG . 6E ) .
FIG . 18 is a graph showing the reciprocal MERS - CoV
FIGS . 7A - 7C are graphs showing the Thl response neutralizing antibody titers in mice immunized with Beta
induced by inactivated hMPV virus in splenocytes isolated coronavirus mRNA vaccine encoding either the MERS - CoV
from mice immunized with hMPV mRNA vaccines. Virus- 60 full-length Spike protein, or the S2 subunit of the Spike
free media was used as a negative control and Concanavalin protein . The full length spike protein induced a stronger
A was included . The cytokines tested included IFN - Y ( FIG . immune response compared to the S2 subunit alone.
7A) , IL - 2 (FIG . 7B ) and IL12 (FIG . 7C ) .
FIGS . 19A - 19C are graphs showing the viral load in the
FIGS . 8A -8E are graphs showing the Th2 response nose and throat, the bronchoalveolar lavage (BAL ) , or the
induced by inactivated hMPV virus in splenocytes isolated 65 lungs of New Zealand white rabbits 4 days post challenge
from mice immunized with the hMPV mRNA vaccines . with MERS - CoV. The New Zealand white rabbits were
Virus - free media was used as a negative control and Con- immunized with one 20 ug -dose ( on day 0 ) or two 20

US 10,933,127 B2
25

26

ug - doses (on day 0 and 21 ) of MERS - CoV mRNA vaccine
encoding the full -length Spike protein before challenge.

(e.g. , mRNA ) vaccines . In some embodiments , a RNA ( e.g. ,
mRNA ) vaccine comprises an adjuvant, such as a flagellin

FIG . 19A shows that two doses of MERS - CoV mRNA

adjuvant, as provided herein .

vaccine resulted in a 3 log reduction of viral load in the nose
The RNA ( e.g. , mRNA ) vaccines (e.g. , hMPV , PIV3 ,
and led to complete protection in the throat of the New 5 RSV, MeV, BetaCOV RNA vaccines and combinations
Zealand white rabbits. FIG . 19B shows that two doses of thereof ), in some embodiments, may be used to induce a
MERS - CoV mRNA vaccine resulted in a 4 log reduction of balanced immune response , comprising both cellular and

viral load in the BAL of the New Zealand white rabbits . FIG .

19C show one dose of MERS - CoV mRNA vaccine resulted

in a 2 log reduction of viral load, while two doses of
MERS - CoV mRNA vaccine resulted in an over 4 log
reduction of viral load in the lungs of the New Zealand white

humoral immunity, without many of the risks associated

10

rabbits .

with DNA vaccination .

The entire contents of International Application No. PCT/
US2015 /02740 is incorporated herein by reference .
Human Metapneumovirus (HMPV )
hMPV shares substantial homology with respiratory syn

FIGS . 20A - 20B are images and graphs showing viral load 15 cytial virus (RSV) in its surface glycoproteins. hMPV fusion
or replicating virus detected by PCR in the lungs of New protein ( F ) is related to other paramyxovirus fusion proteins
Zealand white rabbits 4 days post challenge with MERS- and appears to have homologous regions that may have

COV. The New Zealand white rabbits were immunized with
a single 20 ug dose (on day 0 , Group la ) of MERS - CoV

similar functions. The hMPV fusion protein amino acid
sequence contains features characteristic of other paramyxo

Zealand white rabbits that received 2 doses of 20 ug MERSCoV mRNA vaccine did not have any detectable replicating
MERS - CoV virus in their lungs .
FIG . 21 is a graph showing the MERS -CoV neutralizing
antibody titers in New Zealand white rabbits immunized
with MERS - CoV mRNA vaccine encoding the full- length

in contrast to the two sites established for RSV F, and only
shares 34 % amino acid sequence identity with RSV F. F2 is

mRNA vaccine encoding the full- length Spike protein , two 20 virus F proteins, including a putative cleavage site and
20 ug doses ( on day 0 and 21 , Group 1b ) of MERS - CoV potential N - linked glycosylation sites . Paramyxovirus
mRNA vaccine encoding the full- length Spike protein , or fusion proteins are synthesized as inactive precursors (FO )
olacebo (Group 2 ) before challenge . FIG . 20A shows that that are cleaved host cell proteases into the biologically
two doses of 20 ug a MERS - CoV mRNA vaccine reduced fusion - active F1 and F2 domains ( see , e.g. , Cseke G. et al .
over 99 % ( 2 log) of viruses in the lungs of New Zealand 25 Journal of Virology 2007 ; 81 (2 ) : 698-707 , incorporated
white rabbits. FIG . 20B shows that the group of New herein by reference ). hMPV has one putative cleavage site ,
extracellular and disulfide linked to F1 . Fusion proteins are
30 type
I glycoproteins existing as trimers, with two 4-3 heptad

Spike protein . Immunization of the in New Zealand white
results show that two doses of 20 ug MERS - CoV mRNA 35
vaccine induced a significant amount of neutralizing anti

rabbits were carried out as described in FIGS . 21A - 21C . The

bodies against MERS - CoV (EC50 between 500-1000 ) . The
MERS - CoV mRNA vaccine induced antibody titer is 3-5
fold better than any other vaccines tested in the same model .

40

DETAILED DESCRIPTION

The present disclosure provides, in some embodiments,
vaccines that comprise RNA ( e.g. , mRNA ) polynucleotides
encoding a human Metapneumovirus (hMPV ) antigenic
polypeptide , a parainfluenza virus type 3 (PIV3 ) antigenic
polypeptide , a respiratory syncytial virus ( RSV ) antigenic
polypeptide , a measles virus (MeV) antigenic polypeptide,
or a Betacoronavirus antigenic polypeptide (e.g. , Middle
East respiratory syndrome coronavirus (MERS - CoV ) ,
SARS - CoV, human coronavirus ( HCOV) -OC43 , HCOV229E , HCOV -NL63, HCOV -NL , HCOV - NH (New Haven)
and HCOV -HKU1) ( see , e.g. , Esper F. et al . Emerging
Infectious Diseases, 12 ( 5 ) , 2006 ; and Pyrc K. et al . Journal
of Virology, 81 (7 ) : 3051-57 , 2007 , the contents of each of
which is here incorporated by reference in their entirety ).
The present disclosure also provides, in some embodiments,
combination vaccines that comprise at least one RNA ( e.g. ,
mRNA ) polynucleotide encoding at least two antigenic
polypeptides selected from hMPV antigenic polypeptides,
PIV3 antigenic polypeptides , RSV antigenic polypeptides,
MeV antigenic polypeptides and BetaCoV antigenic polypeptides. Also provided herein are methods of administering
the RNA ( e.g. , mRNA ) vaccines , methods of producing the
RNA ( e.g. , mRNA ) vaccines, compositions ( e.g. , pharmaceutical compositions ) comprising the RNA ( e.g. , mRNA )
vaccines , and nucleic acids ( e.g. , DNA ) encoding the RNA

45

50

repeat domains at the N- and C - terminal regions of the
protein (HR1 and HR2 ) , which form coiled- coil alpha
helices . These coiled coils become apposed in an antiparallel
fashion when the protein undergoes a conformational
change into the fusogenic state . There is a hydrophobic
fusion peptide N proximal to the N -terminal heptad repeat ,
which is thought to insert into the target cell membrane,
while the association of the heptad repeats brings the trans
membrane domain into close proximity, inducing membrane
fusion ( see , e.g. , Baker, K A et al . Mol. Cell 1999 ; 3: 309
319 ) . This mechanism has been proposed for a number of
different viruses , including RSV, influenza virus, and human
immunodeficiency virus . Fusion proteins are major anti
genic determinants for all known paramyxoviruses and for
other viruses that possess similar fusion proteins such as
human immunodeficiency virus, influenza virus, and Ebola
virus .
In some embodiments, a hMPV vaccine of the present
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide
encoding hMPV fusion protein (F ) . In some embodiments,
a hMPV vaccine of the present disclosure comprises a RNA
( e.g. , mRNA ) polynucleotide encoding a F1 or F2 subunit of
a hMPV F protein. In some embodiments, a hMPV vaccine

55 of the present disclosure comprises a RNA (e.g. , mRNA )
polynucleotide encoding hMPV glycoprotein ( G) . In some
embodiments, a hMPV vaccine of the present disclosure
comprises a RNA (e.g. , mRNA ) polynucleotide encoding
hMPV matrix protein (M) . In some embodiments, a hMPV
60 vaccine of the present disclosure comprises a RNA ( e.g. ,
mRNA ) polynucleotide encoding hMPV phosphoprotein
(P ) . In some embodiments, a hMPV vaccine of the present
disclosure comprises a RNA (e.g. , mRNA) polynucleotide
encoding hMPV nucleoprotein ( N ). In some embodiments,
65 a hMPV vaccine of the present disclosure comprises a RNA
( e.g. , mRNA ) polynucleotide encoding hMPV SH protein
( SH ) .

US 10,933,127 B2
28
27
In some embodiments , a hMPV vaccine of the present Infectious Disease 2002 ; 185 : 1660-63 , incorporated herein
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide by reference ). In some embodiments, at least one antigenic
encoding F protein , G protein , M protein , P protein , N polypeptide is obtained from the CAN98-75 (CAN75 )
protein and SH protein .
hMPV strain . In some embodiments, at least one antigenic
In some embodiments, a hMPV vaccine of the present 5 polypeptide is obtained from the CAN97-83 (CAN83 )
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide hMPV strain . In some embodiments, at least one antigenic

encoding F protein and G protein . In some embodiments, a
hMPV vaccine of the present disclosure comprises a RNA
( e.g. , mRNA ) polynucleotide encoding F protein and M
protein . In some embodiments, a hMPV vaccine of the
present disclosure comprises a RNA ( e.g. , mRNA ) polynucleotide encoding F protein and P protein . In some
embodiments, a hMPV vaccine of the present disclosure
comprises a RNA ( e.g., mRNA ) polynucleotide encoding F
protein and N protein . In some embodiments, a hMPV
vaccine of the present disclosure comprises a RNA ( e.g. ,
mRNA ) polynucleotide encoding F protein and SH protein .
In some embodiments , a hMPV vaccine of the present
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide
encoding G protein and M protein . In some embodiments , a
hMPV vaccine of the present disclosure comprises a RNA
( e.g. , mRNA ) polynucleotide encoding G protein and P
protein . In some embodiments, a hMPV vaccine of the
present disclosure comprises a RNA ( e.g. , mRNA ) polynucleotide encoding G protein and N protein . In some
embodiments , a hMPV vaccine of the present disclosure
comprises a RNA ( e.g. , mRNA ) polynucleotide encoding G
protein and SH protein.
In some embodiments, a hMPV vaccine of the present
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide
encoding F protein , G protein and M protein. In some

10

15

20

25
30

polypeptide is obtained from hMPV isolate TN / 92-4 ( e.g. ,
SEQ ID NO : 1 and 5 ) . In some embodiments, at least one
antigenic polypeptide is obtained from hMPV isolate NL/ 1 /
99 (e.g. , SEQ ID NO : 2 and 6 ) . In some embodiments, at
least one antigenic polypeptide is obtained from hMPV
isolate PER /CF10497 / 2010 / B ( e.g. , SEQ ID NO : 3 and 7 ) .
In some embodiments, hMPV vaccines comprise RNA
(e.g. , mRNA ) polynucleotides encoding a hMPV antigenic
polypeptides having at least 95 % , at least 96 % , at least 97 % ,
at least 98 % or at least 99 % identity with hMPV F protein
and having F protein activity .
A protein is considered to have F protein activity if, for
example , the protein acts to fuse the viral envelope and host
cell plasma membrane, mediates viral entry into a host cell
via an interaction with arginine -glycine-aspartate RGD
binding integrins, or a combination thereof ( see , e.g. , Cox R
G et al . J Virol . 2012 ; 88 ( 22 ) : 12148-60 , incorporated herein
by reference )
In some embodiments, hMPV vaccines comprise RNA
( e.g. , mRNA ) polynucleotides encoding hMPV antigenic
polypeptides having at least 95 % , at least 96 % , at least 97 % ,
at least 98 % or at least 99 % identity with hMPV G protein
and having G protein activity .
A protein is considered to have G protein activity if, for
example , the protein acts to modulate ( e.g. , inhibit) hMPV

embodiments, a hMPV vaccine of the present disclosure induced cellular ( immune) responses ( see , e.g. , Bao X et al .
comprises a RNA (e.g. , mRNA ) polynucleotide encoding F PLoS Pathog. 2008 ; 4 ( 5 ) : e1000077 , incorporated herein by
protein , G protein and P protein . In some embodiments, a reference ).
hMPV vaccine of the present disclosure comprises a RNA 35 Human parainfluenza virus type 3 (PIV3 )
( e.g. , mRNA ) polynucleotide encoding F protein , G protein
Parainfluenza viruses belong to the family Paramyxoviri
and N protein . In some embodiments , a hMPV vaccine of dae . These are enveloped viruses with a negative -sense
the present disclosure comprises a RNA ( e.g. , mRNA ) single - stranded RNA genome. Parainfluenza viruses belong
polynucleotide encoding F protein , G protein and SH pro- to the subfamily Paramyxoviridae , which is subdivided into

40 three genera: Respirovirus ( PIV - 1 , PIV - 3, and Sendai virus
( SeV) ) , Rubulavirus ( PIV - 2, PIV - 4 and mumps virus) and
Morbillivirus (measles virus, rinderpest virus and canine
distemper virus ( CDV) ) . Their genome, a ~ 15 500 nucleo
tide - long negative - sense RNA molecule , encodes two enve
amino acid sequences of Table 4 ) .
45 lope glycoproteins , the hemagglutinin -neuraminidase (HN) ,
A hMPV vaccine may comprise, for example, at least one the fusion protein (F or FO ) , which is cleaved into F1 and F2
RNA (e.g. , mRNA ) polynucleotide encoded by a nucleic subunits , a matrix protein ( M ) , a nucleocapsid protein ( N )
acid (e.g. , DNA ) identified by any one of SEQ ID NO : 1-4 and several nonstructural proteins including the viral repli
( Table 2 ) .
case (L) . All parainfluenza viruses, except for PIV - 1, express
The present disclosure is not limited by a particular strain 50 a non - structural V protein that blocks IFN signaling in the
of hMPV . The strain of hMPV used in a vaccine may be any infected cell and acts therefore as a virulence factor ( see ,
strain of hMPV . Non- limiting examples of strains of hMPV e.g. , Nishio M et al . J Virol. 2008 ; 82 ( 13 ) : 6130-38 ) .
for use as provide herein include the CAN98-75 (CAN75 )
PIV3 hemagglutinin -neuraminidase (HN) , a structural
and the CAN97-83 (CAN83) MPV strains ( Skiadopoulos protein , is found on the viral envelope, where it is necessary
MH et al . J Virol. 20014 ; 78 ( 13 ) 6927-37 , incorporated 55 for attachment and cell entry . It recognizes and binds to
herein by reference ), a hMPV A1 , A2 , B1 or B2 strain ( see , sialic acid -containing receptors on the host cell's surface. As
e.g. , de Graaf M et al . The Journal of General Virology a neuroaminidase , HN removes sialic acid from virus par
2008 ; 89 : 975-83 ; Peret TC T et al . The Journal of Infectious ticles , preventing self-aggregation of the virus, and promot
Disease 2002 ; 185 : 1660-63 , incorporated herein by refer- ing the efficient spread of the virus . Furthermore , HN
ence ), a hMPV isolate TN / 92-4 (e.g. , SEQ ID NO : 1 and 5 ) , 60 promotes the activity of the fusion ( F or FO) protein ,
a hMPV isolate NL/ 1 / 99 ( e.g. , SEQ ID NO : 2 and 6 ) , or a contributing to the penetration of the host cell's surface .
hMPV isolate PER /CFI0497 / 2010 / B ( e.g. , SEQ ID NO : 3
PIV3 fusion protein ( PIV3 F ) is located on the viral
and 7) .
envelope, where it facilitates the viral fusion and cell entry .
tein .

A hMPV vaccine may comprise, for example, at least one
RNA ( e.g. , mRNA ) polynucleotide having an open reading
frame encoding at least one hMPV antigenic polypeptide
identified by any one of SEQ ID NO : 5-8 ( Table 3 ; see also

In some embodiments , at least one hMPV antigenic The F protein is initially inactive , but proteolytic cleavage
polypeptide is obtained from a hMPV A1 , A2 , B1 or B2 65 leads to its active forms, F1 and F2 , which are linked by
strain ( see , e.g. , de Graaf M et al . The Journal of General disulfide bonds . This occurs when the HN protein binds its
Virology 2008 ; 89 : 975-83 ; Peret TC T et al . The Journal of receptor on the host cell's surface . During early phases of

US 10,933,127 B2
29

infection , the F glycoprotein mediates penetration of the
host cell by fusion of the viral envelope to the plasma
membrane . In later stages of the infection, the F protein
facilitates the fusion of the infected cells with neighboring
uninfected cells , which leads to the formation of a syncytium 5
and spread of the infection .
PIV3 matrix protein ( M) is found within the viral envelope and assists with viral assembly. It interacts with the
nucleocapsid and envelope glycoproteins , where it facilitates the budding of progeny viruses through its interactions 10
with specific sites on the cytoplasmic tail of the viral
glycoproteins and nucleocapsid. It also plays a role in
transporting viral components to the budding site .
PIV3 phosphoprotein ( P ) and PIV3 large polymerase
protein (L ) are found in the nucleocapsid where they form 15
part of the RNA polymerase complex. The L protein , a viral
RNA -dependent RNA polymerase, facilitates genomic transcription , while the host cell’s ribosomes translate the viral
mRNA into viral proteins.
PIV3 V is a non -structural protein that blocks IFN sig- 20
naling in the infected cell , therefore acting as a virulence
factor.
PIV3 nucleoprotein ( N ) encapsidates the genome in a
ratio of 1 N per 6 ribonucleotides, protecting it from
nucleases. The nucleocapsid (NC ) has a helical structure . 25
The encapsidated genomic RNA is termed the NC and
serves as template for transcription and replication . During
replication , encapsidation by PIV3 N is coupled to RNA
synthesis and all replicative products are resistant to nucleases . PIV3 N homo -multimerizes to form the nucleocapsid 30
and binds to viral genomic RNA . PIV3 N binds the P protein
and thereby positions the polymerase on the template.
In some embodiment a PIV3 vaccine of the present
disclosure comprises a RNA ( e.g. , mRNA ) polynucleotide
encoding PIV3 fusion protein (F ) . In some embodiments , a 35
PIV3 vaccine of the present disclosure comprises a RNA
( e.g. , mRNA ) polynucleotide encoding a F1 or F2 subunit of
a PIV3 F protein . In some embodiments, a PIV3 vaccine of
the present disclosure comprises a RNA ( e.g. , mRNA )
polynucleotide encoding PIV3 hemagglutinin -neuramini- 40
dase (HN) ( see , e.g. , van Wyke Coelingh K L et al . J Virol.
1987 ; 61 ( 5 ) : 1473-77 , incorporated herein by reference ). In
some embodiments, a PIV3 vaccine of the present disclosure
comprises a RNA ( e.g. , mRNA ) polynucleotide encoding
PIV3 matrix protein (M ) . In some embodiments, a PIV3 45
vaccine of the present disclosure comprises a RNA ( e.g. ,
mRNA ) polynucleotide encoding PIV3 phosphoprotein ( P) .
In some embodiments, a PIV3 vaccine of the present disclosure comprises a RNA ( e.g. , mRNA ) polynucleotide
encoding PIV3 nucleoprotein ( N ) .
50
In some embodiments, a PIV3 vaccine of the present
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide
encoding F protein , HN protein , M protein , P protein , and N
protein .
In some embodiments, a PIV3 vaccine of the present 55
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide
encoding F protein and HN protein. In some embodiments ,
a PIV3 vaccine of the present disclosure comprises a RNA
( e.g. , mRNA ) polynucleotide encoding F protein and M
protein. In some embodiments, a PIV3 vaccine of the 60
present disclosure comprises a RNA ( e.g. , mRNA ) polynucleotide encoding F protein and P protein . In some
embodiments, a PIV3 vaccine of the present disclosure
comprises a RNA ( e.g., mRNA ) polynucleotide encoding F
protein and N protein .
65
In some embodiments, a PIV3 vaccine of the present
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide

30

encoding HN protein and M protein . In some embodiments ,
a PIV3 vaccine of the present disclosure comprises a RNA
(e.g. , mRNA ) polynucleotide encoding HN protein and P
protein . In some embodiments , a PIV3 vaccine of the
present disclosure comprises a RNA ( e.g. , mRNA ) poly
nucleotide encoding HN protein and N protein .
In some embodiments, a PIV3 vaccine of the present
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide
encoding F protein , HN protein and M protein . In some
embodiments, a PIV3 vaccine of the present disclosure
comprises a RNA (e.g. , mRNA ) polynucleotide encoding F
protein , HN protein and P protein . In some embodiments, a
PIV3 vaccine of the present disclosure comprises a RNA
(e.g. , mRNA ) polynucleotide encoding F protein , HN pro
tein and N protein .
A PIV3 vaccine may comprise , for example , at least one
RNA ( e.g. , mRNA) polynucleotide having an open reading
frame encoding at least one PIV3 antigenic polypeptide
identified by any one of SEQ ID NO : 12-13 ( Table 6 ; see
also amino acid sequences of Table 7 ) .
A PIV3 vaccine may comprise , for example , at least one
RNA ( e.g. , mRNA ) polynucleotide encoded by a nucleic
acid (e.g. , DNA ) identified by any one of SEQ ID NO : 9-12
( Table 5 ; see also nucleic acid sequences of Table 7 ) .
The present disclosure is not limited by a particular strain
of PIV3 . The strain of PIV3 used in a vaccine may be any
strain of PIV3 . A non - limiting example of a strain of PIV3
for use as provide herein includes HPIV3 /Homo sapiens/
PER /FLA4815 / 2008 .
In some embodiments , PIV3 vaccines comprise RNA
( e.g. , mRNA ) polynucleotides encoding a PIV3 antigenic
polypeptides having at least 95 % , at least 96 % , at least 97 % ,
at least 98 % or at least 99 % identity with PIV3 F protein and
having F protein activity.
In some embodiments, PIV3 vaccines comprise RNA
(e.g. , mRNA ) polynucleotides encoding PIV3 antigenic
polypeptides having at least 95 % , at least 96 % , at least 97 % ,
at least 98 % or at least 99 % identity with PIV3 hemagglu
tinin -neuraminidase ( HN) and having hemagglutinin
neuraminidase activity.
A protein is considered to have hemagglutinin -neuramini
dase activity if, for example, it is capable of both receptor
binding and receptor cleaving. Such proteins are major
surface glycoproteins that have functional sites for cell
attachment and for neuraminidase activity . They are able to
cause red blood cells to agglutinate and to cleave the
glycosidic linkages of neuraminic acids , so they have the
potential to both bind a potential host cell and then release
the cell if necessary, for example , to prevent self -aggrega
tion of the virus.
In some embodiments, PIV3 vaccines comprise RNA
(e.g. , mRNA ) polynucleotides encoding PIV3 antigenic
polypeptides having at least 95 % , at least 96 % , at least 97 % ,
at least 98 % or at least 99 % identity with PIV3 HN , F ( e.g. ,
F, F1 or F2 ) , M , N , L or V and having HN , F (e.g. , F, F1 or
F2 ) , M , N , L or V activity , respectively.
Respiratory Syncytial Virus (RSV )
RSV is a negative - sense, single - stranded RNA virus of the
genus Pneumovirinae . The virus is present in at least two
antigenic subgroups , known as Group A and Group B ,
primarily resulting from differences in the surface G glyco
proteins. Two RSV surface glycoproteins G and F - me
diate attachment with and attachment to cells of the respi
ratory epithelium . F surface glycoproteins mediate
coalescence of neighboring cells . This results in the forma
tion of syncytial cells . RSV is the most common cause of
bronchiolitis. Most infected adults develop mild cold - like

US 10,933,127 B2
31

32

symptoms such as congestion, low - grade fever, and wheezing . Infants and small children may suffer more severe
symptoms such as bronchiolitis and pneumonia. The disease
may be transmitted among humans via contact with respi-

(e.g. , mRNA ) polynucleotide encoding G protein and M2
protein. In some embodiments , a RSV vaccine of the present
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide
encoding G protein and M protein .
In some embodiments, a RSV vaccine of the present
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide
encoding F protein, G protein and L protein . In some
embodiments, a RSV vaccine of the present disclosure

ratory secretions.

5

The genome of RSV encodes at least three surface glycoproteins , including F, G , and SH , four nucleocapsid proteins , including L , P, N , and M2 , and one matrix protein , M.
Glycoprotein F directs viral penetration by fusion between comprises a RNA ( e.g., mRNA ) polynucleotide encoding F
the virion and the host membrane . Glycoprotein G is a type 10 protein , G protein and P protein . In some embodiments, a

II transmembrane glycoprotein and is the major attachment RSV vaccine of the present disclosure comprises a RNA
protein . SH is a short integral membrane protein . Matrix ( e.g. , mRNA ) polynucleotide encoding F protein , G protein
protein M is found in the inner layer of the lipid bilayer and and N protein . In some embodiments, a RSV vaccine of the
assists virion formation . Nucleocapsid proteins L , P , N , and present disclosure comprises a RNA ( e.g. , mRNA ) poly
M2 modulate replication and transcription of the RSV 15 nucleotide encoding F protein , G protein and M2 protein . In
genome. It is thought that glycoprotein G tethers and stabi- some embodiments, a RSV vaccine of the present disclosure
lizes the virus particle at the surface of bronchial epithelial comprises a RNA (e.g. , mRNA ) polynucleotide encoding F
cells , while glycoprotein F interacts with cellular glycosami- protein , G protein and M protein .
noglycans to mediate fusion and delivery of the RSV virion
The present disclosure is not limited by a particular strain
contents into the host cell (Krzyzaniak M A et al . PLoS 20 of RSV . The strain of RSV used in a vaccine may be any
strain of RSV.
Pathog 2013 ; 9 (4 ) ) .
In some embodiments, a RSV vaccine of the present
In some embodiments , RSV vaccines comprise RNA
disclosure comprises a RNA (e.g. , mRNA polynucleotide ( e.g., mRNA ) polynucleotides encoding a RSV antigenic
encoding F protein . In some embodiments, a PIV3 vaccine polypeptides having at least 95 % , at least 96 % , at least 97 % ,
of the present disclosure comprises a RNA (e.g. , mRNA ) 25 at least 98 % or at least 99 % identity with RSV F protein and
polynucleotide encoding G protein . In some embodiments, a having F protein activity.
PIV3 vaccine of the present disclosure comprises a RNA
In some embodiments, RSV vaccines comprise RNA
( e.g. , mRNA ) polynucleotide encoding L protein . In some ( e.g., mRNA ) polynucleotides encoding RSV antigenic
embodiments, a PIV3 vaccine of the present disclosure polypeptides having at least 95 % , at least 96 % , at least 97 % ,

comprises a RNA (e.g. , mRNA ) polynucleotide encoding P 30 at least 98 % or at least 99 % identity with RSVG protein and
having G protein activity.
present disclosure comprises a RNA ( e.g. , mRNA ) polyA protein is considered to have G protein activity if, for

protein . In some embodiments, a PIV3 vaccine of the

nucleotide encoding N protein . In some embodi ts , a example, the protein acts to modulate ( e.g. , inhibit) hMPV
PIV3 vaccine of the present disclosure comprises a RNA induced cellular ( immune) responses ( see , e.g. , Bao X et al .
( e.g. , mRNA ) polynucleotide encoding M2 protein. In some 35 PLoS Pathog . 2008; 4 ( 5 ):e1000077, incorporated herein by
embodiments, a PIV3 vaccine of the present disclosure reference ).

comprises a RNA ( e.g. , mRNA ) polynucleotide encoding M

protein .

In some embodiments, a RSV vaccine of the present

Measles Virus (MeV)
Molecular epidemiologic investigations and virologic sur

veillance contribute notably to the control and prevention of

disclosure comprises a RNA (e.g. , mRNA ) polynucleotide 40 measles . Nearly half of measles -related deaths worldwide

encoding F protein, G protein , L protein , P protein, N occur in India , yet virologic surveillance data are incomplete
protein, M2 protein and M protein .
for many regions of the country . Previous studies have
In some embodiments, a RSV vaccine of the present documented the presence of measles virus genotypes D4 ,
disclosure comprises a RNA ( e.g. , mRNA ) polynucleotide D7 , and D8 in India, and genotypes D5 , D9 , D11 , H1 , and
encoding F protein and G protein . In some embodiments, a 45 G3 have been detected in neighboring countries. Recently,
RSV vaccine of the present disclosure comprises a RNA MeV genotype B3 was detected in India (Kuttiatt V S et al .
( e.g. , mRNA ) polynucleotide encoding F protein and L Emerg Infect Dis. 2014 ; 20 ( 10 ) : 1764-66 ) .
protein . In some embodiments, a RSV vaccine of the present
The glycoprotein complex of paramyxoviruses mediates

disclosure comprises a RNA ( e.g., mRNA ) polynucleotide receptor binding and membrane fusion . In particular, the
encoding F protein and P protein . In some embodiments, a 50 MeV fusion (F ) protein executes membrane fusion, after
RSV vaccine of the present disclosure comprises a RNA receptor binding by the hemagglutinin ( HA) protein (Muhle
( e.g. , mRNA ) polynucleotide encoding F protein and N
protein . In some embodiments, a RSV vaccine of the present

bach M D et al . Journal of Virology 2008 ; 82 (22 ) : 11437-45 ) .
The MeV P gene codes for three proteins: P , an essential

disclosure comprises a RNA ( e.g., mRNA ) polynucleotide polymerase cofactor, and V and C , which have multiple
encoding F protein and M2 protein . In some embodiments , 55 functions but are not strictly required for viral propagation
a RSV vaccine of the present disclosure comprises a RNA in cultured cells . V shares the amino - terminal domain with
( e.g. , mRNA ) polynucleotide encoding F protein and M P but has a zinc - binding carboxyl- terminal domain, whereas
protein .
C is translated from an overlapping reading frame. The MeV
In some embodiments, a RSV vaccine of the present C protein is an infectivity factor. During replication, the P
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide 60 protein binds incoming monomeric nucleocapsid ( N ) pro
encoding G protein and L protein . In some embodiments, a teins with its amino - terminal domain and positions them for
RSV vaccine of the present disclosure comprises a RNA assembly into the nascent ribonucleocapsid . The P protein
( e.g. , mRNA ) polynucleotide encoding G protein and P amino -terminal domain is natively unfolded (Deveaux P et
protein . In some embodiments, a RSV vaccine of the present al . Journal of Virology 2004 ; 78 (21 ) : 11632-40) .
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide 65 In some embodiments, a MeV vaccine of the present
encoding G protein and N protein . In some embodiments, a disclosure comprises a RNA (e.g. , mRNA ) polynucleotide
RSV vaccine of the present disclosure comprises a RNA encoding HA protein . In some embodiments, a MeV vaccine

US 10,933,127 B2
33

34

of the present disclosure comprises a RNA (e.g. , mRNA )

The present disclosure is not limited by a particular strain

polynucleotide encoding F protein . In some embodiments , a of MeV . The strain of MeV used in a vaccine may be any
MeV vaccine of the present disclosure comprises a RNA strain of MeV. Non - limiting examples of strains of MeV for
( e.g. , mRNA ) polynucleotide encoding P protein . In some use as provide herein include B3 /B3.1 , C2 , D4 , D6 , D7 , D8 ,
embodiments , a MeV vaccine of the present disclosure 5 G3 , H1 , Moraten, Rubeovax , MVi /New Jersey.USA /45.05,
comprises a RNA (e.g. , mRNA ) polynucleotide encoding V MVi/ Texas.USA / 4.07, AIK - C , MVi /New York.USA / 26.09 /
protein . In some embodiments, a MeV vaccine of the present 3 , MVi /California.USA / 16.03 , MVi/Virginia.USA / 15.09,
disclosure comprises a RNA ( e.g. , mRNA ) polynucleotide MVi /California.USA / 8.04, and MVi/Pennsylvania.USA /
20.09 .
encoding C protein .
In some embodiments, a MeV vaccine of the present 10 MeV proteins may be from MeV genotype D4 , D5 , D7 ,
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide D8 , D9 , D11 , H1 , G3 or B3 . In some embodiments, a MeV
encoding HA protein , F protein, P protein, V protein and C HA protein or a MeV F protein is from MeV genotype D8 .
protein .
In some embodiments, a MeV HA protein or a MeV F
In some embodiments, a MeV vaccine of the present protein is from MeV genotype B3 .

disclosure comprises a RNA (e.g. , mRNA ) polynucleotide 15 Betacoronaviruses (BetaCoV)

encoding HA protein and F protein . In some embodiments,
a MeV vaccine of the present disclosure comprises a RNA
( e.g. , mRNA ) polynucleotide encoding HA protein and P
protein . In some embodiments, a MeV vaccine of the present
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide
encoding HA protein and V protein. In some embodiments ,
a MeV vaccine of the present disclosure comprises a RNA
( e.g. , mRNA ) polynucleotide encoding HA protein and C
protein.
some embodiments, a MeV vaccine of the present disclosure comprises a RNA (e.g. , mRNA ) polynucleotide encoding F protein and P protein . In some embodiments, a MeV
vaccine of the present disclosure comprises a RNA ( e.g. ,
mRNA ) polynucleotide encoding F protein and V protein . In
some embodiments, a MeV vaccine of the present disclosure
comprises a RNA ( e.g. , mRNA ) polynucleotide encoding F
protein and C protein .
In some embod ents, a MeV vaccine of the present
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide
encoding HA protein , F protein and P protein. In some
embodiments, a MeV vaccine of the present disclosure
comprises a RNA ( e.g., mRNA ) polynucleotide encoding
HA protein , F protein and V protein . In some embodiments,
a MeV vaccine of the present disclosure comprises a RNA
( e.g. , mRNA ) polynucleotide encoding HA protein, F protein and C protein .
In some embodiments, MeV vaccines comprise RNA
( e.g. , mRNA ) encoding a MeV antigenic polypeptide having
at least 95 % , at least 96 % , at least 97 % , at least 98 % or at
least 99 % identity with MeV HA protein and having MeV
HA protein activity.
In some embodiments, MeV vaccines comprise RNA
( e.g. , mRNA ) encoding a MeV antigenic polypeptide having
at least 95 % , at least 96 % , at least 97 % , at least 98 % or at
least 99 % identity with MeV F protein and having MeV F
protein activity.
A protein is considered to have HA protein activity if the
protein mediates receptor binding and / or membrane fusion .
MeV F protein executes membrane fusion , after receptor
binding by the MeV HA protein .
A MeV vaccine may comprise , for example , at least one
RNA ( e.g. , mRNA ) polynucleotide having an open reading
frame encoding at least one MeV antigenic polypeptide
identified by any one of SEQ ID NO : 47-50 ( Table 14 ; see
also amino acid sequences of Table 15 ) .
A MeV vaccine may comprise , for example , at least one
RNA (e.g. , mRNA ) polynucleotide identified by any one of
SEQ ID NO : 37 , 40 , 43 , 46 ( Table 13 ) .
A MeV vaccine may comprise , for example , at least one
RNA (e.g. , mRNA ) polynucleotide encoded by a nucleic
acid (e.g. , DNA ) identified by any one of SEQ ID NO : 35 ,
36 , 38 , 39 , 41 , 42 , 44 and 45 ( Table 13 ) .

20
25
30
35

40

45

50

MERS - Co V. MERS - CoV is a positive - sense , single
stranded RNA virus of the genus Betacoronavirus. The
genomes are phylogenetically classified into two clades ,
clade A and clade B. It has a strong tropism for non - ciliated
bronchial epithelial cells , evades the innate immune
response and antagonizes interferon ( IFN) production in
infected cells . Dipeptyl peptidase 4 (DDP4 , also known as
CD26 ) has been identified as a functional cellular receptor
for MERS -CoV. Its enzymatic activity is not required for
infection , although its amino acid sequence is highly con
served across species and is expressed in the human bron
chial epithelium and kidneys. Most infected individuals
develop severe acute respiratory illnesses , including fever,
cough, and shortness of breath , and the virus can be fatal.
The disease may be transmitted among humans, generally
among those in close contact.
The genome of MERS - CoV encodes at least four unique
accessory proteins, such as 3 , 4a , 4b and two replicase
proteins ( open reading frame la and 1b ) , and four major
structural proteins, including spike ( S ) , envelope ( E ) ,
nucleocapsid ( N ) , and membrane ( M ) proteins (Almazan F
et al . MBio 2013 ; 4 ( 5 ) : e00650-13 ) . The accessory proteins
play nonessential roles in MERS - CoV replication, but they
are likely structural proteins or interferon antagonists ,
modulating in vivo replication efficiency and / or pathogen
esis , as in the case of SARS - CoV (Almazan F et al . MBio
2013 ; 4 ( 5 ) : e00650-13 ; Totura A L et al . Curr Opin Virol
2012 ; 2 ( 3 ) : 264-75 ; Scobey T et al . Proc Natl Acad Sci USA
2013 ; 110 ( 40 ) : 16157-62 ) . The other proteins of MERS- CoV
maintain different functions in virus replication. The E
protein , for example, involves in virulence, and deleting the
E -coding gene results in replication -competent and propa
gation -defective viruses or attenuated viruses (Almazan F et
al . MBio 2013 ; 4 ( 5 ) : e00650-13 ) . The S protein is particu
larly essential in mediating virus binding to cells expressing
receptor dipeptidyl peptidase - 4 (DPP4 ) through receptor
binding domain (RBD ) in the S1 subunit, whereas the S2
subunit subsequently mediates virus entry via fusion of the
virus and target cell membranes (Li F. J Virol 2015 ; 89 ( 4 ) :

55 1954-64 ; Raj V S et al . Nature 2013 ; 495 ( 7440 ) : 251-4 ) .
In some embodiments, a MERS - CoV vaccine of the

present disclosure comprises a RNA ( e.g. , mRNA ) poly
nucleotide encoding S protein . In some embodiments, a
MERS - CoV vaccine of the present disclosure comprises a
60 RNA ( e.g., mRNA) polynucleotide encoding the S1 subunit
of the S protein . In some embodiments, a MERS - CoV
vaccine of the present disclosure comprises a RNA ( e.g. ,
mRNA ) polynucleotide encoding the S2 subunit of the S
protein . In some embodiments, a MERS - CoV vaccine of the
65 present disclosure comprises a RNA ( e.g. , mRNA ) poly
nucleotide encoding E protein . In some embodiments , a
MERS - CoV vaccine of the present disclosure comprises a

US 10,933,127 B2
36

35

RNA ( e.g. , mRNA ) polynucleotide encoding N protein . In

present disclosure comprises a RNA ( e.g. , mRNA ) poly

some embodiments, a MERS - CoV vaccine of the present
disclosure comprises a RNA (e.g. , mRNA ) polynucleotide

nucleotide encoding S protein ( S , S1 and / or S2 ) and N
protein . In some embodiments, a SARS - CoV vaccine of the

In some embodiments, a MERS - CoV vaccine of the
nucleotide encoding S protein ( S , S1 and / or S2 ) , E protein
and M protein . In some embodiments, a MERS - CoV vaccine of the present disclosure comprises a RNA ( e.g. ,

RNA ( e.g. , mRNA ) polynucleotide encoding E protein , M
A SARS - CoV vaccine may comprise , for example, at
least one RNA (e.g. , mRNA ) polynucleotide having an open
reading frame encoding at least one SARS - CoV antigenic

encoding M protein .
present disclosure comprises a RNA ( e.g. , mRNA ) poly
In some embodiments, a MERS - CoV vaccine of the 5 nucleotide encoding S protein ( S , S1 and / or S2 ) and M
present disclosure comprises a RNA ( e.g. , mRNA ) poly protein .
nucleotide encoding S protein ( S , S1 and / or S2 ) , E protein ,
In some embodiments , a SARS - CoV vaccine of the
N protein and M protein .
present disclosure comprises a RNA ( e.g. , mRNA ) poly
In some embodiments, a MERS - CoV vaccine of the
encoding S protein ( S , S1 and / or S2 ) , E protein
present disclosure comprises a RNA ( e.g. , mRNA ) poly- 10 nucleotide
and
M
protein
some embodiments, a SARS - CoV vaccine
nucleotide encoding S protein ( S , S1 and / or S2 ) and E of the present. Indisclosure
a RNA (e.g. , mRNA )
protein . In some embodiments, a MERS - CoV vaccine of the polynucleotide encoding comprises
S
protein
(
S , S1 and / or S2 ) , E
present disclosure comprises a RNA ( e.g. , mRNA ) poly protein and N protein . In some embodiments
, a SARS - CoV
nucleotide encoding S protein ( S , S1 and / or S2 ) and N
protein . In some embodiments, a MERS -CoV vaccine of the 15 mRNA
vaccine) ofpolynucleotide
the present disclosure
comprises
a RNA (e.g. ,
encoding S protein ( S , S1 and / or
present disclosure comprises a RNA ( e.g. , mRNA ) poly
nucleotide encoding S protein ( S , S1 and / or S2 ) and M S2 ) , M protein and N protein . In some embodiments, a
SARS - CoV vaccine of the present disclosure comprises a
protein .

present disclosure comprises a RNA (e.g. , mRNA ) poly- 20 protein and N protein.

mRNA ) polynucleotide encoding S protein ( S , S1 and /or polypeptide identified by any one of SEQ ID NO : 29 , 32 or
S2 ) , E protein and N protein . In some embodiments, a 25 34 ( Table 11 ; see also amino acid sequences of Table 12 ) .

MERS - CoV vaccine of the present disclosure comprises a
The present disclosure is not limited by a particular strain
RNA (e.g., mRNA ) polynucleotide encoding S protein ( S, of SARS - CoV . The strain of SARS - CoV used in a vaccine
S1 and / or S2 ) , M protein and N protein . In some embodi- may be any strain of SARS -CoV .
ments , a MERS - CoV vaccine of the present disclosure
HCOV- OC43 . Human coronavirus OC43 is an enveloped ,
comprises a RNA ( e.g. , mRNA ) polynucleotide encoding E 30 positive - sense , single - stranded RNA virus in the species
protein , M protein and N protein.
Betacoronavirus - 1 (genus Betacoronavirus, subfamily
A MERS - CoV vaccine may comprise, for example, at Coronavirinae, family Coronaviridae, order Nidovirales ).
least one RNA (e.g. , mRNA ) polynucleotide having an open Four HCV - OC43 genotypes (A to D ) , have been identified
reading frame encoding at least one MERS - CoV antigenic with genotype D most likely arising from recombination .
polypeptide identified by any one of SEQ ID NO : 24-38 or 35 The complete genome sequencing of two genotype C and D
33 ( Table 11 ; see also amino acid sequences of Table 12 ) . strains and bootscan analysis shows recombination events
A MERS - CoV vaccine may comprise, for example, at between genotypes B and C in the generation of genotype D.
least one RNA (e.g. , mRNA ) polynucleotide encoded by a Of 29 strains identified , none belong to the more ancient
nucleic acid (e.g. , DNA ) identified by any one of SEQ ID genotype A. Along with HCOV - 229E , a species in the
40 Alphacoronavirus genus, HCOV - OC43 are among the
NO : 20-23 ( Table 10) .
The present disclosure is not limited by a particular strain
of MERS - CoV. The strain of MERS - CoV used in a vaccine

may be any strain of MERS -CoV. Non - limiting examples of

known viruses that cause the common cold . Both viruses can
cause severe lower respiratory tract infections, including

pneumonia in infants, the elderly, and immunocompromised

strains of MERS - CoV for use as provide herein include individuals such as those undergoing chemotherapy and
Riyadh_14_2013, and 2cEMC/2012 , Hasa_1_2013.
45 those with HIV - AIDS .
SARS - CoV . The genome of SARS - CoV includes of a
HCOV - HKU1. Human coronavirus HKU1 (HCV
single , positive - strand RNA that is approximately 29,700 HKU1) is a positive - sense, single -stranded RNA virus with
nucleotides long . The overall genome organization of the HE gene , which distinguishes it as a group 2, or
SARS - CoV is similar to that of other coronaviruses. The Betacoronavirus. It was discovered in January 2005 in two
reference genome includes 13 genes, which encode at least 50 patients in Hong Kong . The genome of HCOV -HKU1 is a
14 proteins. Two large overlapping reading frames ( ORFs ) 29,926 -nucleotide, polyadenylated RNA . The GC content is
encompass 71 % of the genome. The remainder has 12 32 % , the lowest among all known coronaviruses. The
potential ORFs , including genes for structural proteins S genome organization is the same as that of other group II
( spike ) , E ( small envelope ), M (membrane ), and N (nucleo- coronaviruses , with the characteristic gene order 1a , 1b , HE ,
capsid ) . Other potential ORFs code for unique putative 55 S , E , M, and N. Furthermore , accessory protein genes are
SARS -CoV - specific polypeptides that lack obvious present between the S and E genes (ORF4 ) and at the
sequence similarity to known proteins. A detailed analysis of position of the N gene (ORF8 ) . The TRS is presumably
the SARS - CoV genome has been published in J Mol Biol located within the AAUCUAAAC sequence, which pre
2003 ; 331 : 991-1004 .
cedes each ORF except E. As in sialodacryoadenitis virus
In some embodiments, a SARS - CoV vaccine of the 60 and mouse hepatitis virus ( MHV) , translation of the E
present disclosure comprises a RNA ( e.g. , mRNA ) poly- protein possibly occurs via an internal ribosomal entry site .
nucleotide encoding S protein ( S , S1 and /or S2 ) , E protein , The 3 ' untranslated region contains a predicted stem - loop
N protein and M protein .
structure immediately downstream of the N ORF (nucleotide
In some embodiments , a SARS - CoV vaccine of the position 29647 to 29711 ) . Further downstream , a pseudo
present disclosure comprises a RNA ( e.g. , mRNA ) poly- 65 knot structure is present at nucleotide position 29708 to
nucleotide encoding S protein ( S , S1 and / or S2 ) and E 29760. Both RNA structures are conserved in group II
protein . In some embodiments, a SARS - CoV vaccine of the coronaviruses and are critical for virus replication .

US 10,933,127 B2
37
HCOV -NL63 . The RNA genome of human coronavirus
NL63 (HCOV -NL63) is 27,553 nucleotides, with a poly (A)
tail ( FIG . 1 ) . With a GC content of 34 % , HCOV - NL63 has

38

In some embodiments, a combination RNA (e.g. , mRNA )
vaccine comprises a RNA ( e.g. , mRNA ) polynucleotide
encoding a hMPV antigenic polypeptide, a PIV3 antigenic
polypeptide, a RSV antigenic polypeptide, a MeV antigenic

one of the lowest GC contents of the coronaviruses, for
regions of 286 and 287 nucleotides are present at the 5 ' and selected from MERS -CoV, SARS -COV, HCOV -OC43,
3 ' termini, respectively . Genes predicted to encode the S , E ,
- 229E , HCOV -NL63 , HCOV - NL , HCOV - NH and
M , and N proteins are found in the 3 ' part of the HCOV -NL63 HCOV
HCOV
HKU1).
genome. The HE gene , which is present in some group II
In
some
embodiments, a combination RNA (e.g. , mRNA )
coronaviruses, is absent, and there is only a single, mono- 10 vaccine comprises
a RNA ( e.g. , mRNA ) polynucleotide
cistronic accessory protein ORF ( ORF3 ) located between encoding a hMPV antigenic
polypeptide and a PIV3 anti
the S and E genes . Subgenomic mRNAs are generated for all genic polypeptide.
ORFs ( S , ORF3 , E , M , and N) , and the core sequence of the

which GC content ranges from 32 to 42 % . Untranslated 5 polypeptide, and a BetaCoV antigenic polypeptide (e.g. ,

TRS of HCOV -NL63 is defined as AACUAAA . This

In some embodiments , a combination RNA (e.g. , mRNA )

sequence is situated upstream of every ORF except for the 15 vaccine
comprises a RNA (e.g., mRNA ) polynucleotide
E ORF, which contains the suboptimal core sequence AAC encoding a hMPV antigenic polypeptide and a RSV anti

UAUA . Interestingly, a 13 -nucleotide sequence with perfect genic polypeptide.
In some embodiments , a combination RNA (e.g. , mRNA )
homology to the leader sequence is situated upstream of the
suboptimal E TRS . Annealing of this 13 -nucleotide vaccine comprises a RNA ( e.g. , mRNA ) polynucleotide
sequence to the leader sequence may act as a compensatory 20 encoding a hMPV antigenic polypeptide and a MeV anti
mechanism for the disturbed leader - TRS/body - TRS interac- genic polypeptide.
tion .
In some embodiments, a combination RNA (e.g. , mRNA )
HCOV - 229E . Human coronavirus 229E (HCOV -229E ) is a vaccine comprises a RNA ( e.g. , mRNA ) polynucleotide
single - stranded, positive - sense , RNA virus species in the encoding a hMPV antigenic polypeptide and a BetaCoV
Alphacoronavirus genus of the subfamily Coronavirinae, in 25 antigenic polypeptide.
the family Coronaviridae , of the order Nidovirales . Along
In some embodiments, a combination RNA (e.g. , mRNA )
with Human coronavirus OC43 , it is responsible for the vaccine comprises a RNA ( e.g. , mRNA ) polynucleotide
common cold . HCOV -NL63 and HCOV -229E are two of the
four human coronaviruses that circulate worldwide. These

encoding a PIV3 antigenic polypeptide and a RSV antigenic
polypeptide.

two viruses are unique in their relationship towards each 30 In some embodiments, a combination RNA (e.g. , mRNA )
other. Phylogenetically, the viruses are more closely related vaccine comprises a RNA ( e.g. , mRNA ) polynucleotide
to each other than to any other human coronavirus, yet they encoding a PIV3 antigenic polypeptide and a MeV antigenic

only share 65 % sequence identity . Moreover, the viruses use polypeptide.
different receptors to enter their target cell . HCOV -NL63 is
In some embodiments , a combination RNA (e.g. , mRNA )
associated with croup in children , whereas all signs suggest 35 vaccine comprises a RNA ( e.g. , mRNA ) polynucleotide
that the virus probably causes the common cold in healthy encoding a PIV3 antigenic polypeptide and a BetaCoV
adults . HCOV - 229E is a proven common cold virus in antigenic polypeptide ( e.g. , selected from MERS - CoV,

healthy adults, so it is probable that both viruses induce SARS - CoV, HCOV -OC43, HCOV - 229E , HCOV -NL63,
comparable symptoms in adults , even though their mode of HCOV -NL , HCOV -NH and HCOV -HKU1).
infection differs (HCOV -NL63 and HCOV - 229E are two of 40 In some embodiments, a combination RNA (e.g. , mRNA )
the four human coronaviruses that circulate worldwide. vaccine comprises a RNA ( e.g. , mRNA ) polynucleotide
These two viruses are unique in their relationship towards encoding a RSV antigenic polypeptide and a MeV antigenic
each other. Phylogenetically, the viruses are more closely polypeptide.
related to each other than to any other human coronavirus ,
In some embodiments, a combination RNA (e.g. , mRNA )
yet they only share 65 % sequence identity. Moreover, the 45 vaccine comprises a RNA ( e.g. , mRNA ) polynucleotide
viruses use different receptors to enter their target cell . encoding a RSV antigenic polypeptide and a BetaCoV

HCOV -NL63 is associated with croup in children, whereas antigenic polypeptide ( e.g. , selected from MERS -CoV,
SARS - CoV, HCOV -OC43 , HCOV - 229E , HCOV -NL63,
cold in healthy adults. HCOV - 229E is a proven common cold HCOV -NL , HCOV -NH and HCOV -HKU1).
virus in healthy adults , so it is probable that both viruses 50 In some embodiments, a combination RNA (e.g. , mRNA )
induce comparable symptoms in adults, even though their vaccine comprises a RNA ( e.g. , mRNA ) polynucleotide
mode of infection differs (Dijkman R. et al . J Formos Med encoding a MeV antigenic polypeptide and a BetaCoV
Assoc. 2009 April; 108 (4 ) : 270-9 , the contents of which is antigenic polypeptide ( e.g. , selected from MERS - CoV,
all signs suggest that the virus probably causes the common

incorporated herein by reference in their entirety ).
SARS - CoV, HCV - OC43 , HCOV- 229E , HCOV -NL63,
55 HCOV -NL , HCOV - NH and HCOV -HKU1).
Embodiments of the present disclosure also provide comIn some embodiments, a combination RNA (e.g. , mRNA )
bination RNA ( e.g. , mRNA ) vaccines . A combination RNA vaccine comprises a RNA ( e.g. , mRNA ) polynucleotide
( e.g. , mRNA ) vaccine ” of the present disclosure refers to a encoding a hMPV antigenic polypeptide, a PIV3 antigenic
Combination Vaccines

vaccine comprising at least one (e.g. , at least 2 , 3 , 4 , or 5 ) polypeptide , a RSV antigenic polypeptide and a MeV anti
RNA ( e.g. , mRNA ) polynucleotide having an open reading 60 genic polypeptide.
frame encoding a combination of any two or more ( or all of)
In some embodiments, a combination RNA (e.g. , mRNA )
antigenic polypeptides selected from hMPV antigenic poly- vaccine comprises a RNA ( e.g. , mRNA ) polynucleotide
peptides , PIV3 antigenic polypeptides, RSV antigenic poly- encoding a hMPV antigenic polypeptide, a PIV3 antigenic
peptides , MeV antigenic polypeptides , and BetaCoV anti- polypeptide, a RSV antigenic polypeptide and a BetaCoV
genic polypeptides (e.g. , selected from MERS - CoV, SARS- 65 antigenic polypeptide ( e.g. , selected from MERS -CoV,
COV, HCV- OC43 , HCV - 229E , HCOV - NL63, HCOV -NL ,
HCOV -NH and HCOV -HKU1).

SARS - COV, HCOV - OC43 , HCV - 229E , HCOV -NL63,
HCOV -NL , HCOV - NH and HCOV -HKU1 ).

US 10,933,127 B2
39

40

In some embodiments, a combination RNA (e.g. , mRNA )
vaccine comprises a RNA (e.g. , mRNA ) polynucleotide
encoding a hMPV antigenic polypeptide, a PIV3 antigenic
polypeptide, a MeV antigenic polypeptide and a BetaCoV
antigenic polypeptide ( e.g. , selected from MERS -CoV, 5

encoding a RSV antigenic polypeptide , a MeV antigenic
polypeptide and a BetaCoV antigenic polypeptide ( e.g. ,
selected from MERS - CoV, SARS -CoV, HCV- OC43 ,
HCOV - 229E , HCOV - NL63, HCOV - NL , HCOV - NH and
HCOV -HKUI).
SARS -COV, HCOV -OC43 , HCOV -229E , HCOV -NL63,
Other combination respiratory virus RNA (e.g. , mRNA )
HCOV -NL , HCOV -NH and HCOV -HKU1).
vaccines are encompassed by the present disclosure.
In some embodiments, a combination RNA (e.g. , mRNA )
It has been discovered that the mRNA vaccines described
vaccine comprises a RNA (e.g., mRNA polynucleotide herein are superior to current vaccines in several ways. First ,
encoding a hMPV antigenic polypeptide , a RSV antigenic 10 the lipid nanoparticle (LNP ) delivery is superior to other
polypeptide , a MeV antigenic polypeptide and a BetaCoV formulations including a protamine base approach described
antigenic polypeptide ( e.g. , selected from MERS -CoV, in the literature and no additional adjuvants are to be
SARS -CoV, HCOV -OC43, HCOV - 229E , HCOV -NL63, necessary. The use of LNPs enables the effective delivery of
chemically modified or unmodified mRNA vaccines . Addi
HCOV -NL , HCOV -NH and HCOV -HKU1).
In some embodiments, a combination RNA (e.g. , mRNA ) 15 tionally it has been demonstrated herein that both modified
vaccine comprises a RNA (e.g. , mRNA ) polynucleotide and unmodified LNP formulated mRNA vaccines were
encoding a PIV3 antigenic polypeptide, a RSV antigenic superior to conventional vaccines by a significant degree. In
polypeptide, a MeV antigenic polypeptide and a BetaCoV some embodiments the mRNA vaccines of the invention are
antigenic polypeptide ( e.g. , selected from MERS - CoV, superior to conventional vaccines by a factor of at least 10
SARS - CoV, HCOV -OC43 , HCV - 229E , HCOV - NL63, 20 fold , 20 fold , 40 fold , 50 fold, 100 fold , 500 fold or 1,000

HCOV -NL , HCOV -NH and HCOV -HKU1).

fold .

In some embodiments, a combination RNA (e.g. , mRNA )
Although attempts have been made to produce functional
vaccine comprises a RNA (e.g. , mRNA ) polynucleotide RNA vaccines , including mRNA vaccines and self-replicat
encoding a hMPV antigenic polypeptide , a PIV3 antigenic ing RNA vaccines , the therapeutic efficacy of these RNA
polypeptide and a RSV antigenic polypeptide.
25 vaccines have not yet been fully established . Quite surpris
In some embodiments , a combination RNA (e.g. , mRNA ) ingly, the inventors have discovered , according to aspects of
vaccine comprises a RNA (e.g. , mRNA ) polynucleotide the invention a class of formulations for delivering mRNA
encoding a hMPV antigenic polypeptide, a PIV3 antigenic vaccines in vivo that results in significantly enhanced, and in
many respects synergistic , immune responses including
polypeptide and a MeV antigenic polypeptide.
In some embodiments, a combination RNA (e.g. , mRNA ) 30 enhanced antigen generation and functional antibody pro
vaccine comprises a RNA (e.g. , mRNA ) polynucleotide duction with neutralization capability. These results can be
encoding a hMPV antigenic polypeptide, a PIV3 antigenic achieved even when significantly lower doses of the mRNA
polypeptide and a BetaCoV antigenic polypeptide ( e.g. , are administered in comparison with mRNA doses used in

selected from MERS - CoV, SARS - CoV, HCV- OC43 , other classes of lipid based formulations. The formulations
vivo immune responses sufficient to establish the efficacy of
HCOV -HKU1).
In some embodiments, a combination RNA (e.g. , mRNA ) functional mRNA vaccines as prophylactic and therapeutic
vaccine comprises a RNA (e.g. , mRNA ) polynucleotide agents . Additionally, self - replicating RNA vaccines rely on
encoding a hMPV antigenic polypeptide , a RSV antigenic viral replication pathways to deliver enough RNA to a cell
polypeptide and a MeV antigenic polypeptide .
40 to produce an immunogenic response . The formulations of
In some embodiments, a combination RNA (e.g. , mRNA ) the invention do not require viral replication to produce
vaccine comprises a RNA (e.g. , mRNA ) polynucleotide enough protein to result in a strong immune response. Thus,
encoding a hMPV antigenic polypeptide, a RSV antigenic the mRNA of the invention are not self -replicating RNA and
polypeptide and a BetaCoV antigenic polypeptide ( e.g. , do not include components necessary for viral replication .
selected from MERS - CoV, SARS - CoV, HCV- OC43 , 45 The invention involves, in some aspects , the surprising
HCOV - 229E , HCOV -NL63, HCOV -NL , HCOV -NH and finding that lipid nanoparticle ( LNP ) formulations signifi
HCOV-HKU1).
cantly enhance the effectiveness of mRNA vaccines, includ
In some embodiments, a combination RNA (e.g. , mRNA ) ing chemically modified and unmodified mRNA vaccines .
vaccine comprises a RNA (e.g. , mRNA ) polynucleotide The efficacy of mRNA vaccines formulated in LNP was
encoding a hMPV antigenic polypeptide, a MeV antigenic 50 examined in vivo using several distinct antigens. The results
polypeptide and a BetaCoV antigenic polypeptide ( e.g. , presented herein demonstrate the unexpected superior effi
selected from MERS - CoV, SARS -CoV, HCV- OC43 , cacy of the mRNA vaccines formulated in LNP over other
HCOV - 229E , HCOV - NL63, HCOV -NL , HCOV -NH and commercially available vaccines.

HCOV - 229E , HCOV -NL63, HCOV -NL , HCOV -NH and 35 of the invention have demonstrated significant unexpected in

In addition to providing an enhanced immune response ,
In some embodiments, a combination RNA (e.g. , mRNA ) 55 the formulations of the invention generate a more rapid
vaccine comprises a RNA (e.g. , mRNA ) polynucleotide immune response with fewer doses of antigen than other
encoding a PIV3 antigenic polypeptide, a RSV antigenic vaccines tested . The mRNA - LNP formulations of the inven
polypeptide and a MeV antigenic polypeptide.
tion also produce quantitatively and qualitatively better
In some embodiments, a combination RNA (e.g. , mRNA ) immune responses than vaccines formulated in a different
vaccine comprises a RNA (e.g. , mRNA ) polynucleotide 60 carriers.
encoding a PIV3 antigenic polypeptide, a RSV antigenic
The data described herein demonstrate that the formula
polypeptide and a BetaCoV antigenic polypeptide ( e.g. , tions of the invention produced significant unexpected
HCOV -HKU1).

selected from MERS -CoV, SARS -CoV, HCV- OC43 , improvements over existing antigen vaccines. Additionally,
HCOV - 229E , HCOV -NL63, HCOV -NL , HCOV -NH and the mRNA - LNP formulations of the invention are superior
HCOV - HKU1 ) .
65 to other vaccines even when the dose of mRNA is lower than
In some embodiments , a combination RNA (e.g. , mRNA ) other vaccines . Mice immunized with either 10 ug or 2 ug
vaccine comprises a RNA (e.g. , mRNA ) polynucleotide doses of an hMPV fusion protein mRNA LNP vaccine or a

US 10,933,127 B2
42

41

PIV3 mRNA LNP vaccine produced neutralizing antibodies of the present disclosure may function as mRNA but can be
which for instance , successfully neutralized the hMPV B2 distinguished from wild - type mRNA in their functional
virus. A 10 ug dose of mRNA vaccine protected 100 % of and / or structural design features , which serve to overcome
mice from lethal challenge and drastically reduced the viral existing problems of effective polypeptide expression using
5 nucleic -acid based therapeutics.
titer after challenge (~ 2 log reduction ).
Two 20 ug doses of MERS - CoV mRNA LNP vaccine
In some embodiments, a RNA polynucleotide of an RNA
significantly reduced viral load and induced significant (e.g. , mRNA ) vaccine encodes 2-10 , 2-9,2-8 , 2-7 , 2-6 , 2-5 ,
amount of neutralizing antibodies against MERS - CoV 2-4 , 2-3 , 3-10 , 3-9 , 3-8 , 3-7,3-6 , 3-5,3-4,4-10,4-9 , 4-8 , 4-7 ,
( EC50 between 500-1000) . The MERS - CoV mRNA vaccine 4-6 , 4-5 , 5-10 , 5-9 , 5-8 , 5-7 , 5-6 , 6-10 , 6-9 , 6-8 , 6-7,7-10 ,
induced antibody titer was 3-5 fold better than any other 10 7-9 , 7-8 , 8-10 , 8-9 or 9-10 antigenic polypeptides. In some
vaccines tested in the same model .
embodiments, a RNA (e.g. , mRNA ) polynucleotide of a
The LNP used in the studies described herein has been respiratory virus vaccine encodes at least 10 , 20 , 30 , 40 , 50 ,
used previously to deliver siRNA in various animal models 60 , 70 , 80 , 90 or 100 antigenic polypeptides. In some
as well as in humans. In view of the observations made in embodiments, a RNA (e.g. , mRNA ) polynucleotide of a
association with the siRNA delivery of LNP formulations, 15 respiratory virus vaccine encodes at least 100 or at least 200
the fact that LNP is useful in vaccines is quite surprising. It antigenic polypeptides . In some embodiments, a RNA poly
has been observed that therapeutic delivery of siRNA for- nucleotide of an respiratory virus vaccine encodes 1-10 ,
mulated in LNP causes an undesirable inflammatory 5-15 , 10-20 , 15-25 , 20-30 , 25-35 , 30-40 , 35-45 , 40-50 , 1-50 ,
response associated with a transient IgM response, typically 1-100 , 2-50 or 2-100 antigenic polypeptides .
leading to a reduction in antigen production and a compro- 20 Polynucleotides of the present disclosure , in some
mised immune response . In contrast to the findings observed embodiments, are codon optimized . Codon optimization
with siRNA , the LNP -mRNA formulations of the invention methods are known in the art and may be used as provided
are demonstrated herein to generate enhanced IgG levels , herein . Codon optimization , in some embodiments, may be
sufficient for prophylactic and therapeutic methods rather used to match codon frequencies in target and host organ
than transient IgM responses .
25 isms to ensure proper folding; bias GC content to increase
Nucleic Acids/Polynucleotides
mRNA stability or reduce secondary structures ; minimize
Respiratory virus vaccines , as provided herein , comprise tandem repeat codons or base runs that may impair gene
at least one ( one or more) ribonucleic acid (RNA ) ( e.g. , construction or expression ; customize transcriptional and
mRNA ) polynucleotide having an open reading frame translational control regions; insert or remove protein traf
encoding at least one antigenic polypeptide selected from 30 ficking sequences ; remove / add post translation modification
hMPV, PIV3 , RSV, MeV and BetaCoV (e.g. , selected from
MERS - CoV, SARS- CoV, HCOV -OC43 , HCOV -229E ,
HCOV -NL6 . HC
HCOV -NH and HCOV -HKU1)
antigenic polypeptides. The term “ nucleic acid ” includes

any compound and / or substance that comprises a polymer of
nucleotides (nucleotide monomer) . These polymers are
referred to as polynucleotides. Thus, the terms “ nucleic
acid ” and “ polynucleotide ” are used interchangeably.
Nucleic acids may be or may include, for example,
ribonucleic acids ( RNAs ), deoxyribonucleic acids (DNAs),
threose nucleic acids ( TNAs), glycol nucleic acids (GNAs ),
peptide nucleic acids (PNAs ), locked nucleic acids (LNAS,
including LNA having a B - D -ribo configuration, a -LNA
having an a - L - ribo configuration (a diastereomer of LNA ),
2 '- amino -LNA having a 2 ' - amino functionalization , and
2 ' - amino - a - LNA having a 2 - amino functionalization ), ethylene nucleic acids ( ENA ), cyclohexenyl nucleic acids
( CeNA ) or chimeras or combinations thereof.
In some embodiments, polynucleotides of the present
disclosure function as messenger RNA (mRNA ). “ Messenger RNA ” (mRNA ) refers to any polynucleotide that
encodes a (at least one ) polypeptide ( a naturally occurring,
non -naturally occurring , or modified polymer of amino
acids ) and can be translated to produce the encoded polypeptide in vitro , in vivo , in situ or ex vivo . The skilled artisan
will appreciate that, except where otherwise noted , polynucleotide sequences set forth in the instant application will
recite “ T ”' s in a representative DNA sequence but where the
sequence represents RNA ( e.g. , mRNA ), the “ T ” s would be
substituted for “ U” s . Thus, any of the RNA polynucleotides
encoded by a DNA identified by a particular sequence
identification number may also comprise the corresponding

RNA ( e.g. , mRNA ) sequence encoded by the DNA , where

sites in encoded protein ( e.g. glycosylation sites ) ; add,
remove or shuffle protein domains ; insert or delete restric
tion sites ; modify ribosome binding sites and mRNA deg
radation sites ; adjust translational rates to allow the various

35 domains of the protein to fold properly ; or to reduce or
eliminate problem secondary structures within the poly
nucleotide. Codon optimization tools , algorithms and ser
vices are known in the art — non - limiting examples include
services from GeneArt (Life Technologies ), DNA2.0
40 (Menlo Park Calif.) and / or proprietary methods. In some
embodiments, the open reading frame ( ORF ) sequence is
optimized using optimization algorithms.
In some embodiments, a codon optimized sequence
shares less than 95 % sequence identity, less than 90 %
45 sequence identity, less than 85 % sequence identity , less than
80 % sequence identity, or less than 75 % sequence identity
to a naturally -occurring or wild -type sequence ( e.g. , a natu
rally -occurring or wild - type mRNA sequence encoding a
polypeptide or protein of interest (e.g. , an antigenic protein
50 or antigenic polypeptide )).
In some embodiments, a codon- optimized sequence
shares between 65 % and 85 % ( e.g. , between about 67 % and
about 85 % , or between about 67 % and about 80 % ) sequence
identity to a naturally -occurring sequence or a wild -type
55 sequence ( e.g. , a naturally -occurring or wild -type mRNA
sequence encoding a polypeptide or protein of interest ( e.g. ,
an antigenic protein or polypeptide )). In some embodiments,
a codon- optimized sequence shares between 65 % and 75 % ,
or about 80 % sequence identity to a naturally - occurring
60 sequence or wild -type sequence (e.g. , a naturally -occurring
or wild -type mRNA sequence encoding a polypeptide or

protein of interest (e.g. , an antigenic protein or polypep

tide).

each “ T ” of the DNA sequence is substituted with “ U. ”
In some embodiments a codon- optimized RNA ( e.g. ,
The basic components of an mRNA molecule typically 65 mRNA ) may, for instance , be one in which the levels of G / C
include at least one coding region , a 5 ' untranslated region are enhanced . The G / C - content of nucleic acid molecules
(UTR) , a 3 ' UTR , a 5 ' cap and a poly -A tail . Polynucleotides may influence the stability of the RNA . RNA having an

US 10,933,127 B2
43

44

increased amount of guanine (G) and / or cytosine (C ) resiAs such , polynucleotides encoding peptides or polypep
dues may be functionally more stable than nucleic acids tides containing substitutions, insertions and / or additions ,
containing a large amount of adenine ( A ) and thymine ( T) or deletions and covalent modifications with respect to refer
uracil (U) nucleotides . WO02 /098443 discloses a pharma- ence sequences , in particular the polypeptide sequences
ceutical composition containing an mRNA stabilized by 5 disclosed herein , are included within the scope of this
sequence modifications in the translated region . Due to the disclosure . For example, sequence tags or amino acids , such
degeneracy of the genetic code , the modifications work by as one or more lysines , can be added to peptide sequences
substituting existing codons for those that promote greater (e.g. , at the N - terminal or C - terminal ends ). Sequence tags
RNA stability without changing the resulting amino acid . 10 can be used for peptide detection , purification or localiza
The approach is limited to coding regions of the RNA .
tion . Lysines can be used to increase peptide solubility or to
Antigens/ Antigenic Polypeptides
allow for biotinylation . Alternatively, amino acid residues
In some embodiments, an antigenic polypeptide (e.g. , a located at the carboxy and amino terminal regions of the
hMPV, PIV3 , RSV, MeV or BetaCoV antigenic polypeptide ) amino acid sequence of a peptide or protein may optionally
is longer than 25 amino acids and shorter than 50 amino 15 be deleted providing for truncated sequences. Certain amino
acids . Polypeptides include gene products, naturally occur- acids (e.g. , C - terminal residues or N - terminal residues)
ring polypeptides, synthetic polypeptides, homologs, alternatively may be deleted depending on the use of the
orthologs, paralogs, fragments and other equivalents, vari- sequence , as for example , expression of the sequence as part
ants, and analogs of the foregoing. A polypeptide may be a of a larger sequence that is soluble , or linked to a solid
single molecule or may be a multi - molecular complex such 20 support.

as a dimer, trimer or tetramer . Polypeptides may also com“ Substitutional variants” when referring to polypeptides
are those that have at least one amino acid residue in a native
such as antibodies or insulin, and may be associated or or starting sequence removed and a different amino acid
linked to each other. Most commonly, disulfide linkages are inserted in its place at the same position . Substitutions may
found in multichain polypeptides . The term “ polypeptide ” 25 be single, where only one amino acid in the molecule has
may also apply to amino acid polymers in which at least one been substituted , or they may be multiple, where two or
prise single chain polypeptides or multichain polypeptides,

amino acid residue is an artificial chemical analogue of a

corresponding naturally -occurring amino acid .

A “ polypeptide variant” is a molecule that differs in its

more (e.g. , 3 , 4 or 5 ) amino acids have been substituted in

the same molecule .

As used herein the term " conservative amino acid sub

amino acid sequence relative to a native sequence or a 30 stitution ” refers to the substitution of an amino acid that is
reference sequence . Amino acid sequence variants may normally present in the sequence with a different amino acid
possess substitutions, deletions, insertions, or a combination of similar size , charge, or polarity. Examples of conservative
of any two or three of the foregoing, at certain positions substitutions include the substitution of a non - polar (hydro

within the amino acid sequence , as compared to a native phobic ) residue such as isoleucine , valine and leucine for
sequence or a reference sequence. Ordinarily, variants pos- 35 another non - polar residue. Likewise, examples of conserva
sess at least 50 % identity to a native sequence or a reference tive substitutions include the substitution of one polar (hy
sequence. In some embodiments, variants share at least 80 % drophilic ) residue for another such as between arginine and
identity or at least 90% identity with a native sequence or a lysine , between glutamine and asparagine, and between
glycine and serine. Additionally, the substitution of a basic
reference sequence .
In some embodiments “ variant mimics ” are provided. A 40 residue such as lysine , arginine or histidine for another, or
" variant mimic ” contains at least one amino acid that would the substitution of one acidic residue such as aspartic acid or
mimic an activated sequence . For example, glutamate may glutamic acid for another acidic residue are additional
serve as a mimic for phosphoro - threonine and / or phosphoro- examples of conservative substitutions. Examples of non
serine. Alternatively , variant mimics may result in deacti- conservative substitutions include the substitution of a non
vation or in an inactivated product containing the mimic . For 45 polar (hydrophobic ) amino acid residue such as isoleucine,
example , phenylalanine may act as an inactivating substi- valine , leucine, alanine , methionine for a polar (hydrophilic )
tution for tyrosine, or alanine may act as an inactivating residue such as cysteine , glutamine, glutamic acid or lysine
substitution for serine .
and / or a polar residue for a non - polar residue .
“ Orthologs ” refers to genes in different species that
" Features" when referring to polypeptide or polynucle
evolved from a common ancestral gene by speciation . Nor- 50 otide are defined as distinct amino acid sequence -based or
mally, orthologs retain the same function in the course of nucleotide -based components of a molecule respectively.
evolution . Identification of orthologs is important for reliable prediction of gene function in newly sequenced

Features of the polypeptides encoded by the polynucleotides
include surface manifestations, local conformational shape ,
genomes.
folds, loops , half- loops, domains , half - domains, sites , ter
“ Analogs” is meant to include polypeptide variants that 55 mini and any combination (s) thereof.
differ by one or more amino acid alterations, for example,
As used herein when referring to polypeptides the term

substitutions, additions or deletions of amino acid residues

" domain ” refers to a motif of a polypeptide having one or
or starting polypeptide.
properties ( e.g. , binding capacity, serving as a site for
The present disclosure provides several types of compo- 60 protein -protein interactions ).
sitions that are polynucleotide or polypeptide based, includAs used herein when referring to polypeptides the terms
ing variants and derivatives. These include, for example, “ site ” as it pertains to amino acid based embodiments is used

that still maintain one or more of the properties of the parent

more identifiable structural or functional characteristics or

substitutional, insertional, deletion and covalent variants and synonymously with “ amino acid residue” and “ amino acid
derivatives . The term " derivative ” is synonymous with the side chain .” As used herein when referring to polynucle
term “ variant ” and generally refers to a molecule that has 65 otides the terms “ site ” as it pertains to nucleotide based
been modified and / or changed in any way relative to a embodiments is used synonymously with “ nucleotide .” A
site represents a position within a peptide or polypeptide or
reference molecule or a starting molecule .

US 10,933,127 B2
45

46

polynucleotide that may be modified , manipulated, altered, sary, to achieve the maximum percent identity. Methods and
derivatized or varied within the polypeptide -based or poly- computer programs for the alignment are well known in the
art. Identity depends on a calculation of percent identity but
nucleotide -based molecules .
As used herein the terms “ termini” or “ terminus” when may differ in value due to gaps and penalties introduced in
referring to polypeptides or polynucleotides refers to an 5 the calculation . Generally, variants of a particular polynucle
extremity of a polypeptide or polynucleotide respectively. otide or polypeptide have at least 40 % , 45 % , 50% , 55 % ,

Such extremity is not limited only to the first or final site of
the polypeptide or polynucleotide but may include addi-

tional amino acids or nucleotides in the terminal regions.
Polypeptide -based molecules may be characterized as having both an N - terminus ( terminated by an amino acid with
a free amino group (NH2 )) and a C - terminus ( terminated by
an amino acid with a free carboxyl group (COOH ) ) . Proteins
are in some cases made up of multiple polypeptide chains
brought together by disulfide bonds or by non - covalent
forces (multimers, oligomers ). These proteins have multiple
N- and C -termini.Alternatively, the termini of the polypeptides may be modified such that they begin or end , as the
case may be , with a non -polypeptide based moiety such as
an organic conjugate.
As recognized by those skilled in the art, protein fragments , functional protein domains, and homologous proteins
are also considered to be within the scope of polypeptides of
interest. For example , provided herein is any protein fragment (meaning a polypeptide sequence at least one amino
acid residue shorter than a reference polypeptide sequence
but otherwise identical) of a reference protein having a
length of 10 , 20 , 30 , 40 , 50 , 60 , 70 , 80 , 90 , 100 or longer than
100 amino acids . In another example, any protein that
includes a stretch of 20 , 30 , 40 , 50 , or 100 ( contiguous )
amino acids that are 40 % , 50 % , 60 % , 70 % , 80 % , 90 % , 95 % ,
or 100 % identical to any of the sequences described herein

60% , 65 % , 70 % , 75 % , 80 % , 85 % , 90 % , 91 % , 92 % , 93 % ,
94 % , 95 % , 96 % , 97 % , 98 % , 99 % but less than 100 %

sequence identity to that particular reference polynucleotide
10 or polypeptide as determined by sequence alignment pro

grams and parameters described herein and known to those
skilled in the art. Such tools for alignment include those of
the BLAST suite ( Stephen F. Altschul, et al . ( 1997 ). ”
Gapped BLAST and PSI - BLAST : a new generation of
15 protein database search programs,” Nucleic Acids Res.

25 : 3389-3402 ). Another popular local alignment technique
is based on the Smith - Waterman algorithm ( Smith , T. F. &
Waterman, M. S. ( 1981 ) “ Identification of common molecu
lar subsequences.” J. Mol. Biol. 147 : 195-197 ) . A general
20 global alignment technique based on dynamic programming
is the Needleman -Wunsch algorithm (Needleman , S. B. &
Wunsch, C. D. ( 1970) “ A general method applicable to the
search for similarities in the amino acid sequences of two
proteins . ” J. Mol. Biol. 48 : 443-453 ) . More recently, a Fast
25 Optimal Global Sequence Alignment Algorithm ( FOGSAA )
was developed that purportedly produces global alignment

of nucleotide and protein sequences faster than other optimal
global alignment methods, including the Needleman -Wun
sch algorithm . Other tools are described herein , specifically
30 in the definition of “ identity ” below.
As used herein , the term “ homology ” refers to the overall
relatedness between polymeric molecules , e.g. between
can be utilized in accordance with the disclosure . In some nucleic acid molecules (e.g. DNA molecules and / or RNA
embodiments, a polypeptide includes 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , molecules ) and / or between polypeptide molecules . Poly
or more mutations as shown in any of the sequences pro- 35 meric molecules (e.g. nucleic acid molecules (e.g. DNA
vided herein or referenced herein . In another example, any molecules and / or RNA molecules ) and / or polypeptide mol
protein that includes a stretch of 20 , 30 , 40 , 50 , or 100 amino ecules ) that share a threshold level of similarity or identity
acids that are greater than 80 % , 90 % , 95 % , or 100 % determined by alignment of matching residues are termed

identical to any of the sequences described herein , wherein
acids that are less than 80 % , 75 % , 70 % , 65 % to 60 %
identical to any of the sequences described herein can be
utilized in accordance with the disclosure .
Polypeptide or polynucleotide molecules of the present
disclosure may share a certain degree of sequence similarity 45

homologous . Homology is a qualitative term that describes
quantitative similarity or identity . Similarity or identity is a
quantitative term that defines the degree of sequence match
between two compared sequences. In some embodiments,
polymeric molecules are considered to be “ homologous ” to
one another if their sequences are at least 25 % , 30% , 35 % ,

the protein has a stretch of 5 , 10 , 15 , 20 , 25 , or 30 amino 40 a relationship between molecules and can be based upon the

or identity with the reference molecules ( e.g. , reference
polypeptides or reference polynucleotides ), for example ,
with art - described molecules (e.g. , engineered or designed

40% , 45 % , 50 % , 55 % , 60 % , 65 % , 70 % , 75 % , 80% , 85 % ,
90% , 95 % , or 99 % identical or similar. The term “homolo

gous ” necessarily refers to a comparison between at least
molecules or wild - type molecules ) . The term “ identity,” as two sequences ( polynucleotide or polypeptide sequences ).
known in the art, refers to a relationship between the 50 Two polynucleotide sequences are considered homologous

sequences of two or more polypeptides or polynucleotides , if the polypeptides they encode are at least 50 % , 60% , 70 % ,
as determined by comparing the sequences. In the art, 80% , 90 % , 95 % , or even 99 % for at least one stretch of at
identity also means the degree of sequence relatedness least 20 amino acids . In some embodiments, homologous
between two sequences as determined by the number of polynucleotide sequences are characterized by the ability to
matches between strings of two or more amino acid residues 55 encode a stretch of at least 4-5 uniquely specified amino
or nucleic acid residues . Identity measures the percent of acids . For polynucleotide sequences less than 60 nucleotides
identical matches between the smaller of two or more in length , homology is determined by the ability to encode
sequences with gap alignments (if any ) addressed by a a stretch of at least 4-5 uniquely specified amino acids . Two

particular mathematical model or computer program (e.g. , protein sequences are considered homologous if the proteins
“ algorithms ”) . Identity of related peptides can be readily 60 are at least 50% , 60 % , 70 % , 80 % , or 90 % identical for at
calculated by known methods. “ % identity ” as it applies to least one stretch of at least 20 amino acids .
polypeptide or polynucleotide sequences is defined as the
Homology implies that the compared sequences diverged
percentage of residues (amino acid residues or nucleic acid
residues ) in the candidate amino acid or nucleic acid

in evolution from a common origin . The term “ homolog "
refers to a first amino acid sequence or nucleic acid sequence

sequence that are identical with the residues in the amino 65 (e.g. , gene (DNA or RNA ) or protein sequence) that is
acid sequence or nucleic acid sequence of a second sequence related to a second amino acid sequence or nucleic acid
after aligning the sequences and introducing gaps , if neces- sequence by descent from a common ancestral sequence .

US 10,933,127 B2
47

48

The term “ homolog " may apply to the relationship between

( 1984 ) ) , BLASTP, BLASTN , and FASTA Altschul, S. F. et

genes and / or proteins separated by the event of speciation or al . , J. Molec. Biol., 215 , 403 ( 1990 ) ) .
to the relationship between genes and /or proteins separated Multiprotein and Multicomponent Vaccines
The present disclosure encompasses respiratory virus
by the event of genetic duplication. “ Orthologs” are genes
( or proteins ) in different species that evolved from a com- 5 vaccines comprising multiple RNA ( e.g. , mRNA ) poly
mon ancestral gene ( or protein ) by speciation . Typically, nucleotides, each encoding a single antigenic polypeptide, as
orthologs retain the same function in the course of evolution. well as respiratory virus vaccines comprising a single RNA
“ Paralogs” are genes (or proteins) related by duplication polynucleotide encoding more than one antigenic polypep
(e.g. , as a fusion polypeptide). Thus, a vaccine compo
within a genome. Orthologs retain the same function in the 10 tide
sition comprising a RNA (e.g. , mRNA ) polynucleotide
course of evolution , whereas paralogs evolve new functions, having
an open reading frame encoding a first antigenic
even if these are related to the original one .
polypeptide
and a RNA (e.g. , mRNA ) polynucleotide having
The term “ identity ” refers to the overall relatedness an open reading
frame encoding a second antigenic poly
between polymeric molecules , for example, between poly peptide encompasses
( a) vaccines that comprise a first RNA

nucleotide
molecules (e.g. DNA molecules and/or RNA 15 polynucleotide encoding a first antigenic polypeptide and a
molecules ) and / or between polypeptide molecules . Calcula
second RNA polynucleotide encoding a second antigenic
tion of the percent identity of two polynucleic acid polypeptide, and ( b ) vaccines that comprise a single RNA
sequences, for example, can be performed by aligning the polynucleotide encoding a first and second antigenic poly
two sequences for optimal comparison purposes ( e.g. , gaps peptide ( e.g. , as a fusion polypeptide ). RNA ( e.g. , mRNA )
can be introduced in one or both of a first and a second 20 vaccines of the present disclosure, in some embodiments,
nucleic acid sequences for optimal alignment and non- comprise 2-10 (e.g. , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 or 10 ) , or more , RNA
identical sequences can be disregarded for comparison pur- polynucleotides having an open reading frame, each of
poses ) . In certain embodiments, the length of a sequence which encodes a different antigenic polypeptide (or a single
aligned for comparison purposes is at least 30% , at least RNA polynucleotide encoding 2-10 , or more , different anti
40 % , at least 50 % , at least 60 % , at least 70 % , at least 80 % , 25 genic polypeptides ). The antigenic polypeptides may be

at least 90 % , at least 95 % , or 100 % of the length of the selected from hMPV , PIV3 , RSV, MEV and BetaCoV ( e.g. ,
reference sequence . The nucleotides at corresponding selected from MERS - CoV, SARS - CoV, HCV- OC43 ,
nucleotide positions are then compared. When a position in HCOV - 229E , HCOV -NL63, HCOV -NL , HCOV -NH and
the first sequence is occupied by the same nucleotide as the HCOV -HKU1) antigenic polypeptides.
corresponding position in the second sequence, then the 30 In some embodiments, a respiratory virus vaccine com
molecules are identical at that position . The percent identity prises a RNA ( e.g. , mRNA ) polynucleotide having an open

between the two sequences is a function of the number of
identical positions shared by the sequences , taking into

account the number of gaps, and the length of each gap ,
two sequences. The comparison of sequences and determination of percent identity between two sequences can be
accomplished using a mathematical algorithm . For example,
the percent identity between two nucleic acid sequences can

which needs to be introduced for optimal alignment of the 35
be determined using methods such as those described in 40

Computational Molecular Biology , Lesk , A. M. , ed . , Oxford
University Press, New York , 1988 ; Biocomputing: Informatics and Genome Projects, Smith, D. W., ed . , Academic Press ,
New York , 1993 ; Sequence Analysis in Molecular Biology,
von Heinje, G. , Academic Press , 1987 ; Computer Analysis
of Sequence Data, Part I , Griffin , A. M. , and Griffin , H. G. ,
eds . , Humana Press , New Jersey, 1994 ; and Sequence
Analysis Primer, Gribskov, M. and Devereux , J. , eds . , M
Stockton Press, New York , 1991 ; each of which is incorporated herein by reference . For example , the percent identity
between two nucleic acid sequences can be determined
using the algorithm of Meyers and Miller (CABIOS , 1989 ,
4 : 11-17 ) , which has been incorporated into the ALIGN
program (version 2.0 ) using a PAM120 weight residue table ,
a gap length penalty of 12 and a gap penalty of 4. The
percent identity between two nucleic acid sequences can ,
alternatively, be determined using the GAP program in the
GCG software package using an NWSgapdna.CMP matrix .
Methods commonly employed to determine percent identity
between sequences include, but are not limited to those
disclosed in Carillo , H. , and Lipman, D. , SIAM J Applied
Math ., 48 : 1073 ( 1988 ) ; incorporated herein by reference .
Techniques for determining identity are codified in publicly
available computer programs. Exemplary computer software to determine homology between two sequences
include , but are not limited to , GCG program package ,
Devereux, J. , et al . , Nucleic Acids Research , 12 ( 1 ) , 387

45

50

55

60

65

reading frame encoding a viral capsid protein, a RNA ( e.g. ,
mRNA ) polynucleotide having an open reading frame
encoding a viral premembrane /membrane protein , and a
RNA (e.g. , mRNA ) polynucleotide having an open reading
frame encoding a viral envelope protein . In some embodi
ments, a respiratory virus vaccine comprises a RNA ( e.g. ,
mRNA ) polynucleotide having an open reading frame
encoding a viral fusion ( F ) protein and a RNA polynucle
otide having an open reading frame encoding a viral major
surface glycoprotein ( G protein ). In some embodiments, a
vaccine comprises a RNA ( e.g. , mRNA ) polynucleotide
having an open reading frame encoding a viral F protein . In
some embodiments, a vaccine comprises a RNA ( e.g. ,
mRNA ) polynucleotide having an open reading frame
encoding a viral G protein . In some embodiments, a vaccine
comprises a RNA (e.g. , mRNA ) polynucleotide having an
open reading frame encoding a HN protein .
In some embodiments, a multicomponent vaccine com
prises at least one RNA (e.g. , mRNA ) polynucleotide encod
ing at least one antigenic polypeptide fused to a signal
peptide ( e.g. , any one of SEQ ID NO : 15-19 ) . The signal
peptide may be fused at the N - terminus or the C - terminus of
an antigenic polypeptide . An antigenic polypeptide fused to
a signal peptide may be selected from hMPV, PIV3 , RSV,
MEV and BetaCoV ( e.g. , selected from MERS - CoV, SARS
COV, HCV - OC43 , HCOV - 229E , HCOV -NL63, HCOV - NL ,
HCOV-NH and HCOV - HKU1 ) antigenic polypeptides.
Signal Peptides
In some embodiments, antigenic polypeptides encoded by
respiratory virus RNA (e.g. , mRNA ) polynucleotides com
prise a signal peptide . Signal peptides , comprising the
N -terminal 15-60 amino acids of proteins , are typically
needed for the translocation across the membrane on the
secretory pathway and, thus, universally control the entry of
most proteins both in eukaryotes and prokaryotes to the
secretory pathway. Signal peptides generally include three

US 10,933,127 B2
49
regions : an N - terminal region of differing length , which

50

usually comprises positively charged amino acids; a hydrophobic region ; and a short carboxy -terminal peptide region .

33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 ,
49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , or 60 amino acids .
In some embodiments, a signal peptide has a length of

transport of the growing peptide chain across it for process

endoplasmic reticulum (ER) membrane and initiates the

15-50 , 20-50 , 25-50 , 30-50 , 35-50 , 40-50 , 45-50 , 15-45 ,

signal peptide may also facilitate the targeting of the protein
to the cell membrane. The signal peptide , however, is not
responsible for the final destination of the mature protein .

polypeptide at the cleavage junction during ER processing.
The mature antigenic polypeptide produce by a respiratory
virus RNA ( e.g. , mRNA ) vaccine of the present disclosure

In eukaryotes , the signal peptide of a nascent precursor 20-60 , 25-60 , 30-60 , 35-60 , 40-60 , 45-60 , 50-60 , 55-60 ,
protein (pre - protein ) directs the ribosome to the rough5 15-55 , 20-55 , 25-55 , 30-55 , 35-55 , 40-55 , 45-55 , 50-55 ,

20-45 , 25-45 , 30-45 , 35-45 , 40-45 , 15-40 , 20-40 , 25-40 ,
ing . ER processing produces mature proteins, wherein the 30-40
35-40 , 15-35 , 20-35 , 25-35 , 30-35 , 15-30 , 20-30 ,
signal peptide is cleaved from precursor proteins , typically 25-30 ,, 15-25
, 20-25 , or 15-20 amino acids .
by a ER - resident signal peptidase of the host cell , or they 10 A signal peptide
is typically cleaved from the nascent
remain uncleaved and function as a membrane anchor. A

Secretory proteins devoid of additional address tags in their 15 typically
does not comprise a signal peptide.
Chemical Modifications
sequence are by default secreted to the external environ

Respiratory virus vaccines of the present disclosure, in
some embodiments, comprise at least RNA ( e.g. mRNA )
polynucleotide having an open reading frame encoding at
20 least one antigenic polypeptide that comprises at least one
versatile than previously anticipated .
Respiratory virus vaccines of the present disclosure may chemical modification .
comprise , for example, RNA ( e.g. , mRNA ) polynucleotides
The terms “ chemical modification ” and “ chemically
encoding an artificial signal peptide, wherein the signal modified ” refer to modification with respect to adenosine
peptide coding sequence is operably linked to and is in frame ( A ), guanosine ( G ) , uridine ( U ), thymidine ( T ) or cytidine
with the coding sequence of the antigenic polypeptide. Thus, 25 (C ) ribonucleosides or deoxyribnucleosides in at least one of
respiratory virus vaccines of the present disclosure, in some their position , pattern , percent or population . Generally,
ment. During recent years , a more advanced view of signal
peptides has evolved , showing that the functions and immu
nodominance of certain signal peptides are much more

embodiments, produce an antigenic polypeptide comprising

these terms do not refer to the ribonucleotide modifications

to the C - terminus of the antigenic polypeptide .
In some embodin ents, the signal peptide fused to the
antigenic polypeptide is an artificial signal peptide . In some

a combination of substitutions and insertions.

an antigenic polypeptide ( e.g. , hMPV, PIV3 , RSV, MeV or in naturally occurring 5 '- terminal mRNA cap moieties . With
BetaCoV) fused to a signal peptide. In some embodiments, respect to a polypeptide, the term “modification ” refers to a
a signal peptide is fused to the N -terminus of the antigenic 30 modification relative to the canonical set 20 amino acids .
polypeptide . In some embodiments, a signal peptide is fused Polypeptides , as provided herein , are also considered “ modi

embodiments, an artificial signal peptide fused to the antigenic polypeptide encoded by the RNA (e.g. , mRNA ) vaccine is obtained from an immunoglobulin protein , e.g. , an
IgE signal peptide or an IgG signal peptide. In some
embodiments, a signal peptide fused to the antigenic polypeptide encoded by a RNA (e.g. , mRNA ) vaccine is an Ig
heavy chain epsilon - 1 signal peptide (IgE HC SP ) having the
sequence of: MDWTWILFLVAAATRVHS ( SEQ ID NO :
16 ) . In some embodiments, a signal peptide fused to the
antigenic polypeptide encoded by the ( e.g. , mRNA ) RNA
( e.g. , mRNA ) vaccine is an IgGk chain V - III region HAH
signal peptide ( IgGk SP) having the sequence of METPAQLLFLLLLWLPDTTG ( SEQ ID NO : 15 ) . In some
embodiments, thePRM
signal peptide
is selected from : Japanese
encephalitis
signal
sequence (MLGSNSGQRVVFTILLLLVAPAYS ; SEQ ID NO : 17 ) , VSVg
protein signal sequence (MKCLLYLAFLFIGVNCA ; SEQ
ID NO : 18 ) and Japanese encephalitis JEV signal sequence
(MWLVSLAIVTACAGA ; SEQ ID NO : 19 ) .
In some embodiments , the antigenic polypeptide encoded
by a RNA (e.g. , mRNA ) vaccine comprises an amino acid
sequence identified by any one of SEQ ID NO : 5-8 , 12-13 ,

fied ” of they contain amino acid substitutions, insertions or
Polynucleotides (e.g. , RNA polynucleotides, such as

35 mRNA polynucleotides ), in some embodiments, comprise
various (more than one ) different modifications . In some
embodiments, a particular region of a polynucleotide con
tains one , two or more ( optionally different) nucleoside or
nucleotide modifications. In some embodiments, a modified
40 RNA polynucleotide (e.g. , a modified mRNA polynucle
otide ) , introduced to a cell or organism , exhibits reduced
degradation in the cell or organism , respectively, relative to
an unmodified polynucleotide. In some embodiments, a
modified RNA polynucleotide ( e.g. , a modified mRNA
45 polynucleotide ), introduced into a cell or organism , may
exhibit reduced immunogenicity in the cell or organism ,
respectively ( e.g. , a reduced innate response) .
Modifications of polynucleotides include , without limita
tion , those described herein . Polynucleotides (e.g. , RNA
50 polynucleotides, such as mRNA polynucleotides ) may com
prise modifications that are naturally -occurring, non -natu
rally -occurring or the polynucleotide may comprise a com
bination of naturally occurring and non -naturally -occurring
modifications . Polynucleotides may include any useful
55 modification , for example , of a sugar, a nucleobase, or an
internucleoside linkage (e.g. , to a linking phosphate , to a

24-34 , 47-50 or 54-56 ( Tables 3 , 6 , 11 , 14 or 17 ; see also phosphodiester linkage or to the phosphodiester backbone ).
amino acid sequences of Tables 4 , 7 , 12 or 15 ) fused to a
Polynucleotides ( e.g. , RNA polynucleotides, such as
signal peptide identified by any one of SEQ ID NO : 15-19 mRNA polynucleotides ), in some embodiments, comprise
( Table 8 ) . The examples disclosed herein are not meant to be 60 non - natural modified nucleotides that are introduced during
limiting and any signal peptide that is known in the art to synthesis or post - synthesis of the polynucleotides to achieve
facilitate targeting of a protein to ER for processing and / or desired functions or properties. The modifications may be
targeting of a protein to the cell membrane may be used in present on an internucleotide linkages, purine or pyrimidine
bases , or sugars . The modification may be introduced with
accordance with the present disclosure .
A signal peptide may have a length of 15-60 amino acids . 65 chemical synthesis or with a polymerase enzyme at the
For example, a signal peptide may have a length of 15 , 16 , terminal of a chain or anywhere else in the chain . Any of the
17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , regions of a polynucleotide may be chemically modified .

US 10,933,127 B2
52

51

The present disclosure provides for modified nucleosides Ethynyladenosine TP ; 2 - aminoadenine; 2 - Aminoadenosine
and nucleotides of a polynucleotide (e.g. , RNA polynucle- TP ; 2 - Amino - ATP ; 2 '- a - Trifluoromethyladenosine TP ;
otides, such as mRNA polynucleotides ). A “ nucleoside ” 2 - Azidoadenosine TP ; 2 ' - b - Ethynyladenosine TP ; 2 - Bro
refers to a compound containing a sugar molecule (e.g. , a moadenosine TP ; 2 - b - Trifluoromethyladenosine TP ;
pentose or ribose ) or a derivative thereof in combination 5 2 -Chloroadenosine TP ; 2 -Deoxy - 2 ' , 2 ' -difluoroadenosine
with an organic base (e.g. , a purine or pyrimidine ) or a TP ; 2 -Deoxy - 2 '- a -mercaptoadenosine TP ; 2 -Deoxy - 2'-a
derivative thereof (also referred to herein as “ nucleobase ” ). thiomethoxyadenosine TP ; 2 - Deoxy- 2 ' - b - aminoadenosine
A nucleotide ” refers to a nucleoside, including a phosphate TP ; 2 -Deoxy - 2 '- b -azidoadenosine TP ; 2'-Deoxy -2'-b -bro
group . Modified nucleotides may by synthesized by any moadenosine TP ; 2 '-Deoxy - 2 '- b -chloroadenosine TP ; 2 '-De
useful method , such as , for example, chemically, enzymati- 10 oxy - 2' -b - fluoroadenosine TP ; 2 ' -Deoxy - 2 '- b - iodoadenosine
cally, or recombinantly, to include one or more modified or
non -natural nucleosides. Polynucleotides may comprise a

TP ; 2 ' - Deoxy - 2 - b- mercaptoadenosine TP ; 2'-Deoxy -2'-b
thiomethoxyadenosine TP ; 2 - Fluoroadenosine TP ; 2 -Iodo

region or regions of linked nucleosides . Such regions may adenosine TP ; 2 -Mercaptoadenosine TP ; 2-methoxy -ad
have variable backbone linkages. The linkages may be enine ; 2 -methylthio -adenine; 2 - Trifluoromethyladenosine
standard phosphdioester linkages, in which case the poly- 15 TP ; 3 -Deaza - 3 - bromoadenosine TP ; 3 -Deaza-3 -chloroad
enosine TP ; 3 -Deaza - 3 - fluoroadenosine TP ; 3 -Deaza -3 -io
nucleotides would comprise regions of nucleotides .
Modified nucleotide base pairing encompasses not only doadenosine TP ; 3 - Deazaadenosine TP ; 4 ' - Azidoadenosine
the standard adenosine - thymine, adenosine - uracil, or TP ; 4 '-Carbocyclic adenosine TP ; 4 ' -Ethynyladenosine TP ;
guanosine -cytosine base pairs , but also base pairs formed 5 ' - Homo - adenosine TP ; 8 - Aza - ATP ; 8 -bromo -adenosine
between nucleotides and / or modified nucleotides compris- 20 TP ; 8 - Trifluoromethyladenosine TP ; 9 - Deazaadenosine TP ;
ing non - standard or modified bases , wherein the arrange- 2 -aminopurine ; 7 -deaza -2,6 - diaminopurine; 7 -deaza - 8- aza
ment of hydrogen bond donors and hydrogen bond acceptors 2,6 - diaminopurine ; 7 -deaza - 8 -aza - 2 - aminopurine ; 2,6 -di
permits hydrogen bonding between a non - standard base and aminopurine; 7 -deaza - 8 -aza -adenine, 7 -deaza -2 -aminopu
a standard base or between two complementary non -stan- rine; 2 -thiocytidine; 3 -methylcytidine; 5 - formylcytidine;

dard base structures. One example of such non - standard base 25 5 -hydroxymethylcytidine; 5 -methylcytidine; N4-acetylcyti

pairing is the base pairing between the modified nucleotide
inosine and adenine, cytosine or uracil . Any combination of

base / sugar or linker may be incorporated into polynucle-

dine; 2 - O -methylcytidine; 2 - O -methylcytidine; 5,2-0 -di
methylcytidine; 5 - formyl -2-0 -methylcytidine; Lysidine;

N4,2 - O - dimethylcytidine ; N4 -acetyl- 2 - O -methylcytidine;

N4 -methylcytidine; N4 ,N4 -Dimethyl - 2' -OMe- Cytidine TP ;
otides of the present disclosure.
Modifications of polynucleotides ( e.g. , RNA polynucle- 30 4 -methylcytidine; 5 -aza -cytidine; Pseudo - iso - cytidine; pyr
otides, such as mRNA polynucleotides ) that are useful in the rolo -cytidine; a - thio -cytidine; 2- ( thiocytosine ; 2 -Amino
vaccines of the present disclosure include , but are not 2 ' - deoxy - CTP ; 2 ' -Azido - 2 ' - deoxy - CTP ; 2 '-Deoxy - 2'-a -ami
limited to the following: 2 -methylthio - N6-(cis-hydroxyiso- nocytidine TP ; 2 ' - Deoxy - 2 ' - a - azidocytidine TP ; 3 ( deaza ) 5
pentenyl)adenosine; 2 -methylthio -N6 -methyladenosine; (aza cytosine; 3 (methyl ) cytosine; 3- ( alkyl cytosine ;
2 -methylthio -N6 - threonyl carbamoyladenosine; N6 - glyci- 35 3 - deaza ) 5 (aza cytosine ; 3 - methyl) cytidine; 4,2-0 -dim
nylcarbamoyladenosine;

N6 - isopentenyladenosine;

N6 -methyladenosine; N6 -threonylcarbamoyladenosine;
1,2-0 -dimethyladenosine; 1 -methyladenosine; 2 -O -methyladenosine; 2 - O - ribosyladenosine (phosphate ); 2 -methyladenosine; 2 -methylthio - N6 isopentenyladenosine; 2 -meth- 40
ylthio - N6 -hydroxynorvalyl carbamoyladenosine; 2 ' - 0methyladenosine; 2 - O - ribosyladenosine (phosphate );
Isopentenyladenosine; N6-(cis -hydroxyisopentenyl)adenosine ; N6,2-0 -dimethyladenosine; N6,2-0 -dimethyladenosine ; N6 ,N6,2 - O - trimethyladenosine; N6 ,N6 - dimethylad- 45
N6 -acetyladenosine;
enosine;
N6 -hydroxynorvalylcarbamoyladenosine; N6 -methyl -N6threonylcarbamoyladenosine; 2 -methyladenosine; 2 -methylthio - N6 - isopentenyladenosine;
7 -deaza -adenosine;
N1-methyl-adenosine; N6 , N6 ( dimethyl)adenine; N6 -cis- 50
hydroxy -isopentenyl -adenosine; a - thio -adenosine; 2 ( amino)adenine; 2 ( aminopropyl )adenine; 2 (methylthio ) N6
( isopentenyl )adenine; 2- ( alkyl )adenine; 2 - aminoalkyl)adenine; 2 - aminopropyl )adenine; 2-(halo Jadenine ; 2- (halo )
adenine; 2 - propyl ) adenine; 2 '- Amino - 2'-deoxy -ATP ; 55
2 '-Azido - 2'-deoxy -ATP ; 2 '-Deoxy - 2 ' - a - aminoadenosine TP ;
2 '-Deoxy - 2 '- a -azidoadenosine TP ; 6 ( alkyl )adenine; 6
(methyl) adenine; 6- ( alkyl )adenine; 6-(methyl)adenine; 7
(deaza )adenine ; 8 ( alkenyl )adenine; 8 ( alkynyl )adenine; 8
( amino adenine; 8 (thioalkyl ) adenine ; 8- (alkenyl ) adenine; 60
8-(alkyl )adenine; 8-(alkynyl) adenine; 8-(amino ) adenine ;
8 - Chalo )adenine; 8- (hydroxyl )adenine; 8-(thioalkyl ) adenine;
8- ( thiol )adenine; 8 - azido -adeno sine; aza adenine; deaza
adenine; N6 (methyl)adenine; N6- ( isopentyl)adenine;
7 -deaza - 8 -aza -adenosine; 7 -methyladenine; 1 - Deazaade- 65
nosine TP ; 2'Fluoro - N6 - Bz -deoxyadenosine TP ; 2'-OMe-2Amino - ATP ; 2'O -methyl-N6 - Bz -deoxyadenosine TP ; 2'-a-

ethylcytidine; 5 ( halo ) cytosine; 5 (methyl ) cytosine; 5 (pro

pynyl )cytosine; 5 (trifluoromethyl) cytosine; 5-(alkyl)cyto
sine ; 5- ( alkynyl) cytosine; 5- (halo )cytosine; 5- (propynyl)
cytosine; 5- (trifluoromethyl cytosine; 5 -bromo -cytidine;
5 - iodo -cytidine; 5 -propynyl cytosine; 6- (azo ) cytosine;
6 -aza -cytidine; aza cytosine ; deaza cytosine; N4 ( acetyl)
cytosine ; l -methyl - 1 - deaza -pseudoisocytidine; 1 -methyl
pseudoisocytidine;
2 -methoxy - 5 -methyl -cytidine;
2 -methoxy - cytidine ; 2 - thio - 5 -methyl -cytidine; 4 -methoxy
1 -methyl- pseudoisocytidine; 4 -methoxy -pseudoisocytidine;
4 -thio - 1 -methyl - 1 -deaza -pseudoisocytidine;
4 - thio - 1
methyl-pseudoisocytidine; 4 -thio -pseudoisocytidine; 5 -aza
zebularine; 5 -methyl-zebularine; pyrrolo -pseudoisocytidine;
Zebularine; ( E ) -5- ( 2 - Bromo- vinyl) cytidine TP ; 2,2'-an
hydro -cytidine TP hydrochloride; 2 *Fluor -N4 -BZ-cytidine
TP ; 2'Fluoro -N4 -Acetyl- cytidine TP ; 2 - O -Methyl-N4
Acetyl -cytidine TP ; 20 -methyl -N4 -Bz -cytidine TP ; 2'-a
Ethynylcytidine TP ; 2 '- a - Trifluoromethylcytidine TP ; 2 -b
Ethynyleytidine TP ; 2 - b - Trifluoromethylcytidine TP ;
2 -Deoxy - 2 ', 2 ' - difluorocytidine TP ; 2 -Deoxy - 2'-a -mercap
tocytidine TP ; 2 -Deoxy - 2 - a -thiomethoxycytidine TP ;
2 - Deoxy -2'-b - aminocytidine TP ; 2 - Deoxy -2'-b - azidocyti
dine TP ; 2' -Deoxy - 2 ' - b -bromocytidine TP ; 2'-Deoxy -2'-b
chlorocytidine TP ; 2 ' -Deoxy - 2 '- b - fluorocytidine TP ; 2 -De
oxy - 2' -b - iodocytidine TP ; 2 - Deoxy - 2 - b -mercaptocytidine
TP ; 2 - Deoxy -2 -b - thiomethoxycytidine TP ; 2 -O -Methyl-5
( 1 - propynyl) cytidine TP ; 3 ' -Ethynylcytidine TP ; 4 '-Azido
cytidine TP ; 4 '-Carbocyclic cytidine TP ; 4 -Ethynylcytidine
TP ; 5-( 1 - Propynyl)ara - cytidine TP ; 5-(2 - Chloro -phenyl)-2
thiocytidine TP ; 5- ( 4 - Amino - phenyl)-2 - thiocytidine TP ;
5 - Aminoallyl-CTP; 5 - Cyanocytidine TP ; 5 -Ethynylara -cy
tidine TP ; 5 - Ethynylcytidine TP ; 5 - Homo- cytidine TP ;

US 10,933,127 B2
54

53

5 -Methoxycytidine TP ; 5 - Trifluoromethyl- Cytidine TP ;

N4 - Amino - cytidine TP ; N4 - Benzoyl -cytidine TP ; Pseudoisocytidine; 7 -methylguanosine; N2,2 - O - dimethylguanosine ; N2 -methylguanosine; Wyosine ; 1,2-0 - dimethylguanosine; 1 -methylguanosine; 2 '- O -methylguanosine;
2 - O - ribosylguanosine ( phosphate ); 2 - O -methylguanosine;
2 '- O - ribosylguanosine ( phosphate ); 7 -aminomethyl-7 - deazaguanosine; 7 -cyano - 7 -deazaguanosine; Archaeosine;
Methylwyo sine ; N2,7 -dimethylguanosine; N2 N2,2 - Otrimethylguanosine; N2,N2,7 - trimethylguanosine; N2 , N2dimethylguanosine; N2,7,2 ' - O - trimethylguanosine; 6 - thioguanosine ;
7 - deaza - guanosine;
8 -oxo - guanosine;
N1-methyl - guanosine; a - thio -guanosine; 2 ( propyl)guanine;
2- (alkyl )guanine; 2 ' -Amino - 2 '- deoxy -GTP ; 2'-Azido- 2'-deoxy - GTP ; 2 '-Deoxy- 2' - a - aminoguanosine TP ; 2 ' -Deoxy - 2'a -azidoguanosine TP ; 6 (methyl) guanine; 6- ( alkyl )guanine ;
6-(methyl )guanine; 6 -methyl- guanosine; 7 ( alkyl) guanine; 7
( deaza )guanine; 7 (methyl ) guanine; 7 - alkyl )guanine;
7- ( deaza )guanine; 7- (methyl ) guanine; 8 ( alkyl) guanine; 8
( alkynyl) guanine; 8 (halo )guanine; 8 ( thioalkyl )guanine;
8- (alkenyl ) guanine; 8- (alkyl )guanine; 8- (alkynyl )guanine ;
8- ( amino ) guanine; 8 - Chalo )guanine; 8- (hydroxyl )guanine;
8 - thioalkyl guanine; 8- ( thiol) guanine; aza guanine; deaza
guanine; N (methyl) guanine; N-(methyl) guanine; 1 -methyl6 - thio - guanosine; 6 -methoxy -guanosine; 6 -thio - 7 - deaza - 8aza -guanosine; 6 - thio - 7 - deaza - guanosine; 6 - thio - 7 -methylguanosine; 7 -deaza-8 -aza - guanosine; 7 -methyl-8 -oxoguanosine; N2 N2 - dimethyl -6 - thio -guanosine; N2 -methyl6 - thio -guanosine; 1 - Me - GTP ; 2'Fluoro -N2-isobutylguanosine TP ; 2'O -methyl -N2- isobutyl - guanosine TP ; 2 ' - aEthynylguanosine TP ; 2 '- a - Trifluoromethylguanosine TP ;
2 ' -b -Ethynylguano sine TP ; 2 '- b - Trifluoromethylguanosine
TP ; 2 '-Deoxy - 2 ', 2 '- difluoroguanosine TP ; 2 -Deoxy - 2 '-a-

mercaptoguanosine TP ; 2 -Deoxy - 2'-a -thiomethoxyguanosine TP ; 2 -Deoxy - 2' -b -aminoguanosine TP ; 2 - Deoxy - 2 -bazidoguanosine TP ; 2 '- Deoxy - 2 - b -bromoguanosine TP ;
2 '-Deoxy - 2' -b -chloroguanosine TP ; 2'-Deoxy -2'-b - fluoroguanosine TP ; 2 - Deoxy - 2' -b -iodoguanosine TP ; 2'-Deoxy - 2 ' - b -mercaptoguanosine TP; 2 -Deoxy - 2'-b -thiomethoxyguanosine TP ; 4 '-Azidoguanosine TP ;
4 ' -Carbocyclic guanosine TP ; 4 '-Ethynylguanosine TP ;
5 ' - Homo - guanosine TP ; 8 -bromo - guanosine TP ; 9 -Deazaguanosine TP ; N2- isobutyl -guanosine TP ; 1-methylinosine ; Inosine; 1,2 - O -dimethylinosine; 2 - O -methylinosine ;
7 -methylinosine; 2 '- O -methylinosine; Epoxyqueuosine;
galactosyl -queuosine; Mannosylqueuosine; Queuosine;
allyamino -thymidine; aza thymidine; deaza thymidine;
deoxy - thymidine ; 2 - O -methyluridine; 2 - thiouridine ;
3 -methyluridine; 5 - carboxymethyluridine; 5 -hydroxyuridine ; 5 -methyluridine; 5 -taurinomethyl - 2 -thiouridine; 5 - taurinomethyluridine; Dihydrouridine; Pseudouridine; (3-(3amino - 3 -carboxypropyl )uridine; 1 -methyl-3-(3 -amino -5carboxypropyl)pseudouridine;
1 -methylpseduouridine;
1 -methyl- pseudouridine; 2 - O -methyluridine; 2 -O -methylpseudouridine; 2 '-O -methyluridine; 2 - thio -2 '- O -methyluridine; 3- ( 3 -amino - 3 - carboxypropyl )uridine; 3,2-0 -dimethyluridine ; 3 -Methyl -pseudo -Uridine TP ; 4 - thiouridine ;
5-( carboxyhydroxymethyl Juridine ; 5-(carboxyhydroxymethyl)uridine methyl ester ; 5,2 - O -dimethyluridine; 5,6 -dihydro -uridine; 5 - aminomethyl - 2 -thiouridine; 5 -carbamoylmethyl -2-0 -methyluridine; 5 -carbamoylmethyluridine;
5 -carboxyhydroxymethyluridine; 5 -carboxyhydroxymethyluridine methyl ester ; 5 -carboxymethylaminomethyl-2-0methyluridine ; 5 - carboxymethylaminomethyl- 2 - thiouridine ;
5 -carboxymethylaminomethyl - 2 - thiouridine;
5 -carboxymethylaminomethyluridine; 5 -carboxymethylaminomethyluridine; 5 -Carbamoylmethyluridine TP;

5 -methoxycarbonylmethyl- 2 ' - O -methyluridine; 5-methoxy

5
10
15
20

25

30

carbonylmethyl - 2 - thiouridine ; 5 -methoxycarbonylmethylu
ridine; 5 -methoxyuridine; 5 -methyl - 2 - thiouridine; 5 -meth
ylaminomethyl - 2 - selenouridine; 5 -methylaminomethyl-2
5 -methylaminomethyluridine;
thiouridine;
5 -Methyldihydrouridine; 5 - Oxyacetic acid -Uridine TP ;
5 -Oxyacetic acid -methyl ester -Uridine TP ; N1-methyl
pseudo -uridine; uridine 5 - oxyacetic acid ; uridine 5 -oxy
acetic acid methyl ester ; 3-(3 -Amino -3 -carboxypropyl)-Uri
dine TP ; 5 - iso -Pentenylaminomethyl)-2 -thiouridine TP ;
5- ( iso -Pentenylaminomethyl ) -2-0 -methyluridine
TP ;
5 - iso - Pentenylaminomethyl) uridine TP ; 5 -propynyl uracil;
a -thio -uridine; 1 (aminoalkylamino -carbonylethylenyl )-2
( thio )-pseudouracil; 1 (aminoalkylaminocarbonylethyl
enyl) -2,4- ( dithio )pseudouracil; 1 (aminoalkylaminocarbo1
( thio ) pseudouracil;
nylethylenyl ) -4
( aminoalkylaminocarbonylethylenyl )-pseudouracil; 1 ( ami
nocarbonylethylenyl )-2 (thio )-pseudouracil; 1 (aminocarbo
nylethylenyl)-2,4- ( dithio )pseudouracil; 1 (aminocarbonyl
1
(thio )pseudouracil;
ethylenyl ) -4
(aminocarbonylethylenyl )-pseudouracil; 1 substituted
2 ( thio ) -pseudouracil; 1 substituted 2,4- (dithio )pseudouracil;
1 substituted 4 ( thio )pseudouracil; 1 substituted pseudoura
cil ;
1-( aminoalkylamino -carbonylethylenyl)-2-( thio )
pseudouracil;
1 -Methyl - 3- ( 3 -amino - 3 - carboxypropyl)
pseudouridine TP ; 1 -Methyl -3- ( 3 -amino - 3 -carboxypropyl)
pseudo -UTP ; 1 -Methyl-pseudo -UTP; 2 ( thio )pseudouracil;
2 ' deoxy uridine; 2 ' fluorouridine; 2- (thio )uracil; 2,4- (dithio )
psuedouracil; 2 ' methyl, 2'amino , 2'azido , 2'fluro - guanosine;
2 - Amino - 2 ' -deoxy -UTP ;
2 ' - Azido - 2 '-deoxy -UTP ;
2 '-Azido -deoxyuridine TP ; 2 - O -methylpseudouridine ; 2 '
deoxy uridine; 2 ' fluorouridine ; 2 ' -Deoxy - 2' - a - aminouridine
TP ; 2 '-Deoxy - 2 ' - a -azidouridine TP ; 2 -methylpseudouridine;

3 ( 3 amino - 3 carboxypropyl ) uracil; 4 ( thio )pseudouracil;
35 4-( thio )pseudouracil; 4-(thio Juracil; 4 - thiouracil; 5 (1,3-di
azole - 1 - alkyl )uracil; 5 ( 2 -aminopropyl )uracil; 5 ( aminoal
kyl )uracil; 5 (dimethylaminoalkyl )uracil; 5 ( guanidiniumal
kyl)uracil; 5 (methoxycarbonylmethyl)-2-( thio Juracil ; 5

(methoxycarbonyl -methyl )uracil; 5 (methyl) 2 (thio Juracil ;
40 5 (methyl) 2,4 (dithio Juracil ; 5 (methyl) 4 ( thio Juracil; 5
(methylaminomethyl ) -2 ( thio Juracil; 5 (methylaminom
ethyl )-2,4 ( dithio )uracil; 5 (methylaminomethyl ) -4 ( thio )
uracil; 5 ( propynyl ) uracil; 5 ( trifluoromethyl )uracil; 5-(2
aminopropyl )uracil;
5 - alkyl) -2- ( thio ) pseudouracil;
45 5- ( alkyl) -2,4 ( dithio )pseudouracil; 5- (alkyl)-4 ( thio )
pseudouracil; 5- (alkyl )pseudouracil; 5- (alkyl ) uracil;
5-( alkynyl)uracil; 5-( allylamino Juracil ; 5-(cyanoalkyl)ura
cil ; 5-(dialkylaminoalkyl ) uracil; 5- (dimethylaminoalkyl)
uracil; 5-(guanidiniumalkyluracil; 5 - halo )uracil; 5-( 1,3 -di
5 - methoxy )uracil;
50 azole - 1 - alkyl) uracil;
5-(methoxycarbonylmethyl)-2-(thio Juracil ; 5-(methoxycar
bonyl-methyl)uracil; 5- (methyl) 2 ( thio )uracil; 5- (methyl)
2,4 (dithio Juracil ; 5- (methyl) 4 (thio Juracil ; 5-(methyl)-2
(thio )pseudouracil; 5- (methyl) -2,4 ( dithio pseudouracil;
55 5-(methyl)-4 ( thio )pseudouracil; 5- (methyl )pseudouracil;
5 - methylaminomethyl)-2 (thio )uracil; 5-(methylaminom
ethyl )-2,4 (dithio )uracil; 5-(methylaminomethyl) -4-(thio )
uracil; 5- (propynyl ) uracil; 5- ( trifluoromethyl )uracil; 5 -ami
noallyl -uridine ; 5 - bromo -uridine ; 5 - iodo -uridine; 5 -uracil; 6
60 ( azo ) uracil; 6-(azo Juracil; 6 -aza - uridine; allyamino - uracil;
aza uracil; deaza uracil; N3 (methyl)uracil; Pseudo -UTP - 1
2 - ethanoic acid ; Pseudouracil; 4 - Thio - pseudo -UTP ; 1- car
boxymethyl-pseudouridine; 1 -methyl- 1 -deaza -pseudouri
dine ; 1 -propynyl -uridine; 1 -taurinomethyl- 1-methyl
65 uridine ; 1 -taurinomethyl - 4 - thio -uridine ; 1 -taurinomethyl
pseudouridine; 2 -methoxy -4 -thio -pseudouridine; 2 -thio -1
methyl - 1 - deaza -pseudouridine;
2 - thio -1 -methyl

US 10,933,127 B2
55

56

2 - thio-

UTP ; 1 -Methyl- 6 -cyano -pseudo -UTP ; 1-Methyl-6 -dimeth

pseudo -UTP ; 1- (2 -Amino -2 - carboxyethyl)pseudo -UTP;
1- ( 2 - Amino -ethyl )pseudo -UTP ;
1-2 -Hydroxyethyl)
pseudouridine TP ; 1- ( 2 -Methoxyethyl) pseudouridine TP ;
1- (3,4 -Bis - trifluoromethoxybenzyl)pseudouridine TP ; 1- (3 ,
4 -Dimethoxybenzyl)pseudouridine TP ; 1-(3 - Amino -3 -carboxypropyl)pseudo -UTP ; 1- ( 3 -Amino -propyl)pseudo -UTP ;
1- ( 3 - Cyclopropyl -prop - 2 - ynyl)pseudouridine TP ; 1- (4Amino - 4 - carboxybutyl)pseudo -UTP; 1- ( 4 - Amino -benzyl)
pseudo -UTP ; 1- ( 4 -Amino -butyl)pseudo -UTP ; 1- (4 -Aminophenyl)pseudo -UTP; 1- (4 - Azidobenzyl)pseudouridine TP ;
1- ( 4 -Bromobenzyl )pseudouridine TP ; 1- ( 4 -Chlorobenzyl)
pseudouridine TP ; 1- ( 4 - Fluorobenzyl )pseudouridine TP ;
1- ( 4 - Iodobenzyl) pseudouridine TP ; 1-(4 -Methanesulfonylbenzyl )pseudouridine TP ; 1- (4 -Methoxybenzyl)pseudouridine TP ; 1- ( 4 -Methoxy -benzyl )pseudo -UTP ; 1-(4 -Methoxyphenyl )pseudo -UTP ; 1- ( 4 -Methylbenzyl )pseudouridine TP ;
1- ( 4 -Methyl-benzyl) pseudo -UTP ;
1- (4 -Nitrobenzyl)
pseudouridine TP ; 1- ( 4 - Nitro -benzyl)pseudo -UTP ; 1 (4 -Nitro -phenyl) pseudo -UTP ;
1- ( 4 - Thiomethoxybenzyl)
pseudouridine
1- ( 4 - Trifluoromethoxybenzyl )
TP
;
pseudouridine
TP ;
1-(4 - Trifluoromethylbenzyl)
pseudouridine TP ; 1- ( 5 - Amino -pentyl )pseudo -UTP ; 1- (6Amino -hexyl )pseudo -UTP ; 1,6 -Dimethyl- pseudo -UTP;
1-[3-(2- { 2-[2-(2 - Aminoethoxy ) -ethoxy ]-ethoxy } -ethoxy )propionyl ]pseudouridine TP ; 1- {3-[2-(2 -Aminoethoxy)ethoxyl-propionyl}pseudouridine TP ; 1 - Acetylpseudouridine TP ; 1 - Alkyl - 6- ( 1 -propynyl) -pseudo -UTP; 1- Alkyl-6( 2 - propynyl ) -pseudo -UTP ; 1 - Alkyl - 6 - allyl- pseudo -UTP ;
1 - Alkyl -6 - ethynyl -pseudo -UTP ;
1 - Alkyl-6 -homoallylpseudo -UTP ; 1 - Alkyl - 6 - vinyl -pseudo -UTP ; 1 -Allylpseudouridine TP ; 1 - Aminomethyl-pseudo -UTP ; 1 - Benzo-

15 1 -Propargylpseudouridine TP ; 1 - Propyl-pseudo -UTP ;
1 -propynyl-pseudouridine; 1 -p- tolyl-pseudo -UTP; 1-tert
Butyl -pseudo -UTP ; 1 - Thiomethoxymethylpseudouridine
TP ; 1 - Thiomorpholinomethylpseudouridine TP ; 1- Trifluo
roacetylpseudouridine TP ; 1 - Trifluoromethyl- pseudo -UTP ;
20 1 -Vinylpseudouridine TP ; 2.2 -anhydro -uridine TP ;
2 '- bromo- deoxyuridine TP ; 2 ' - F - 5 -Methyl - 2 '- deoxy -UTP ;
2 - OMe - 5 -Me-UTP ; 2 - OMe -pseudo -UTP ; 2'-a -Ethynyluri
dine TP ; 2 -a - Trifluoromethyluridine TP ; 2 -b -Ethynyluri
dine TP ; 2' - b - Trifluoromethyluridine TP ; 2 -Deoxy -2',2'- di
25 fluorouridine TP ; 2 -Deoxy - 2' - a -mercaptouridine TP ;
2 -Deoxy -2'-a - thiomethoxyuridine TP ; 2'-Deoxy -2'-b -ami
nouridine TP ; 2 -Deoxy - 2 '- b -azidouridine TP ; 2 '- Deoxy - 2'
b -bromouridine TP ; 2 '-Deoxy - 2 - b - chlorouridine TP ; 2'-De
oxy - 2 '- b - fluorouridine TP ; 2 '-Deoxy - 2 '- b - iodouridine TP ;
30 2 -Deoxy - 2' - b -mercaptouridine TP ; 2 -Deoxy - 2'-b -thio
methoxyuridine
TP ;
2 -methoxy - 4 - thio -uridine;
2 -methoxyuridine; 2 '- O -Methyl-5- ( 1 - propynyl )uridine TP ;
3 - Alkyl -pseudo -UTP ; 4 ' - Azidouridine TP ; 4 '- Carbocyclic
uridine TP ; 4 '-Ethynyluridine TP ; 5- ( 1 -Propynyl )ara - uridine
35 TP ; 5- ( 2 -Furanyl Juridine TP ; 5 -Cyanouridine TP ; 5 - Dim
ethylaminouridine TP ; 5 '-Homo - uridine TP ; 5 - iodo - 2'
fluoro -deoxyuridine TP ; 5 -Phenylethynyluridine TP ; 5 - Tri
deuteromethyl- 6 -deuterouridine TP ; 5 - Trifluoromethyl
Uridine TP ; 5 - Vinylarauridine TP ; 6- (2,2,2 - Trifluoroethyl)
40 pseudo -UTP ; 6-( 4 -Morpholino - pseudo -UTP ; 6- (4
Thiomorpholino ) -pseudo - UTP; 6- (Substituted - Phenyl)
pseudo -UTP ; 6 -Amino -pseudo -UTP ; 6 - Azido - pseudo -UTP ;
6 - Bromo -pseudo -UTP ; 6 -Butyl -pseudo -UTP ; 6 -Chloro
pseudo -UTP; 6 -Cyano -pseudo -UTP; 6 -Dimethylamino
45 pseudo -UTP ; 6 -Ethoxy -pseudo -UTP; 6 - Ethylcarboxylate

pseudouridine;

2 -thio - 5 - aza -uridine ;

dihydropseudouridine ; 2 - thio - dihydrouridine; 2 - thio- ylamino -pseudo -UTP ; 1 -Methyl -6 - ethoxy - pseudo -UTP;
pseudouridine;
4 -methoxy - 2 - thio -pseudouridine; 1 -Methyl - 6 - ethylcarboxylate -pseudo -UTP ; 1 -Methyl-6
4 -methoxy -pseudouridine; 4 -thio - 1 -methyl -pseudouridine; ethyl- pseudo -UTP ;
1 -Methyl - 6 - fluoro - pseudo -UTP ;
1 -Methyl-6 -hy
4 -thio -pseudouridine; 5 -aza - uridine; Dihydropseudouridine; 5 1 -Methyl -6 -formyl -pseudo -UTP;
( + ) 1- ( 2 -Hydroxypropyl) pseudouridine TP ; ( 2R )-1- (2 -Hy- droxyamino -pseudo -UTP ; 1-Methyl-6 -hydroxy -pseudo
droxypropyl)pseudouridine TP ; (2S )-1- ( 2 -Hydroxypropyl) UTP ; 1 -Methyl- 6 -iodo -pseudo -UTP ; 1-Methyl-6 -iso - pro
pseudouridine TP ; ( E ) -5- ( 2 -Bromo -vinyl ) ara -uridine TP ; pyl -pseudo - UTP ;
1 -Methyl -6 -methoxy -pseudo -UTP;
( E ) -5- ( 2 -Bromo - vinyl ) uridine TP ; ( Z ) -5-( 2 - Bromo - vinyl) 1 -Methyl - 6 -methylamino - pseudo -UTP; 1-Methyl-6 -phenyl
ara - uridine TP ; ( Z ) -5- ( 2 -Bromo -vinyl ) uridine TP ; 1- ( 2,2,2- 10 pseudo -UTP ; 1 -Methyl -6 -propyl-pseudo -UTP ; 1-Methyl-6
Trifluoroethyl) -pseudo -UTP ; 1-(2,2,3,3,3 -Pentafluoropro- tert -butyl -pseudo -UTP ;
1 -Methyl-6 -trifluoromethoxy
pyl)pseudouridine TP ; 1- (2,2 -Diethoxyethyl )pseudouridine pseudo -UTP ;
1 -Methyl - 6 - trifluoromethyl- pseudo -UTP ;
TP ; 1- ( 2,4,6 - Trimethylbenzyl)pseudouridine TP ; 1- ( 2,4,6- 1 -Morpholinomethylpseudouridine TP ; 1- Pentyl-pseudo
Trimethyl- benzyl )pseudo -UTP ; 1- (2,4,6 - Trimethyl -phenyl) UTP ; 1 -Phenyl- pseudo -UTP; 1 - Pivaloylpseudouridine TP ;

ylpseudouridine TP ; 1 -Benzyloxymethylpseudouridine TP ; pseudo -UTP; 6 - Ethyl -pseudo -UTP; 6 - Fluoro -pseudo -UTP ;
1 - Benzyl-pseudo -UTP ; 1- Biotinyl- PEG2- pseudouridine TP ; 6 - Formyl - pseudo -UTP ; 6 -Hydroxyamino -pseudo -UTP ;
1 -Biotinylpseudouridine TP ; 1 -Butyl -pseudo -UTP ; 1- Cya- 6 -Hydroxy -pseudo -UTP ; 6 - Iodo -pseudo -UTP ; 6 -iso - Pro
nomethylpseudouridine TP ; 1 -Cyclobutylmethyl-pseudo- pyl -pseudo -UTP ; 6 -Methoxy - pseudo -UTP ; 6 -Methyl
UTP ; 1 - Cyclobutyl - pseudo -UTP ; 1 - Cycloheptylmethyl- 50 amino - pseudo -UTP; 6 -Methyl -pseudo -UTP ; 6 -Phenyl
pseudo -UTP ;
1 -Cycloheptyl-pseudo -UTP; pseudo -UTP ; 6 -Phenyl-pseudo -UTP ; 6 -Propyl-pseudo
1 - Cyclohexylmethyl-pseudo -UTP ; 1- Cyclohexyl-pseudo- UTP ; 6 - tert -Butyl -pseudo -UTP ; 6 -Trifluoromethoxy
UTP ; 1 - Cyclooctylmethyl -pseudo -UTP ; 1- Cyclooctyl- pseudo -UTP; 6 - Trifluoromethyl-pseudo -UTP; Alpha - thio
pseudo -UTP; 1 -Cyclopentylmethyl-pseudo -UTP; 1-Cyclo- pseudo -UTP; Pseudouridine 1- ( 4 -methylbenzenesulfonic
pentyl-pseudo -UTP; 1 -Cyclopropylmethyl-pseudo -UTP ; 55 acid ) TP ; Pseudouridine 1- ( 4 -methylbenzoic acid) TP ;
1 - Cyclopropyl-pseudo -UTP;
1 -Ethyl -pseudo -UTP ; Pseudouridine TP 1- [3- ( 2 - ethoxy ) ]propionic acid ; Pseudou
1 -Hexyl - pseudo -UTP ; 1 -Homoallylpseudouridine TP ; ridine ?? 1-[3- {2-(2- [2-( 2- ethoxy )-ethoxy ]-ethoxy )
1 -Hydroxymethylpseudouridine TP ; 1 -iso -propyl- pseudo- ethoxy } ] propionic acid ; Pseudouridine TP 1- [3- {2-( 2-[2- {2

UTP ; 1 -Me - 2 - thio -pseudo -UTP ; 1 -Me - 4 -thio -pseudo -UTP ; ( 2 -ethoxy ) -ethoxy }-ethoxy ] -ethoxy ) -ethoxy } ]propionic
1 -Me- alpha -thio -pseudo -UTP ; 1 -Methanesulfonylmethylp- 60 acid ; Pseudouridine TP 1-[3- { 2-( 2-[ 2-ethoxy )-ethoxy )
seudouridine TP ; 1 - Methoxymethylpseudouridine TP ; ethoxy } ]propionic acid ; Pseudouridine TP 1-[3- {2-(2
1 -Methyl -6- (2,2,2 - Trifluoroethyl) pseudo -UTP ; 1-Methyl -6- ethoxy ) -ethoxy }] propionic acid ; Pseudouridine TP 1 -meth
( 4 -morpholino )-pseudo -UTP;
1 -Methyl -6- (4 - thiomor- ylphosphonic acid ; Pseudouridine TP 1 -methylphosphonic
pholino ) -pseudo -UTP ; 1 -Methyl -6- ( substituted phenyl) acid diethyl ester; Pseudo -UTP -N1-3 - propionic acid ;

pseudo -UTP ; 1 -Methyl -6 -amino -pseudo -UTP ; 1 -Methyl -6- 65 Pseudo -UTP -N1-4 - butanoic acid ; Pseudo -UTP -N1-5-pen
azido - pseudo -UTP ;
1 -Methyl- 6 - bromo -pseudo -UTP ;
1 -Methyl- 6 -butyl -pseudo -UTP ; 1-Methyl-6 - chloro - pseudo-

tanoic acid ; Pseudo -UTP - N1-6 -hexanoic acid ; Pseudo
UTP -N1-7 -heptanoic acid ; Pseudo -UTP -N1-methyl-p -ben

US 10,933,127 B2
58

57

zoic acid ; Pseudo -UTP -N1- p -benzoic acid ; Wybutosine; bination of at least two ( e.g. , 2 , 3 , 4 or more ) of the
Hydroxywybutosine; Isowyosine ; Peroxywybutosine; aforementioned modified nucleobases.
undermodified hydroxywybutosine ; 4 -demethylwyosine;
In some embodiments , modified nucleobases in poly
2,6 - diamino )purine; 1-(aza )-2-(thio )-3-(aza ) -phenoxazin- nucleotides (e.g. , RNA polynucleotides, such as mRNA
1 -yl : 1,3-(diaza ) -2-(oxo ) -phenthiazin - 1 - yl; 1,3 - diaza ) -2- 5 polynucleotides) are selected from the group consisting of
(oxo ) -phenoxazin - 1 - yl; 1,3,5 - triaza -2,6 - dioxa ) -naphtha- pseudouridine ( V ), N1 -methylpseudouridine (m'y ) , N1-eth

lene; 2 ( amino ) purine; 2,4,5 - trimethyl )phenyl; 2 * methyl, ylpseudouridine, 2 - thiouridine , 4 ' - thiouridine, 5 -methylcy
tosine , 2 -thio - 1 -methyl - 1 -deaza -pseudouridine, 2- thio - 1
2'amino, 2'azido , 2'fluro -cytidine; 2 ' methyl, 2'amino , methyl
-pseudouridine, 2 -thio - 5 - aza -uridine , 2 - thio
2'azido , 2'fluro - adenine; 2'methyl, 2'amino, 2'azido , 2'fluro 10 dihydropseudouridine
, 2 - thio -dihydrouridine, 2 -thio
uridine ; 2 '-amino - 2 '- deoxyribose; 2 - amino - 6 - Chloro -purine; pseudouridine,
- 2 -thio -pseudouridine,
2 -aza - inosinyl; 2 '-azido - 2 '-deoxyribose; 2'fluoro - 2'-deoxyri 4 -methoxy -pseudouridine, 4 -methoxy
4
thio
1
methyl
- pseudouridine,
bose ; 2 ' - fluoro -modified bases ; 2 - O -methyl-ribose ; 2- oxo 4 -thio -pseudouridine, 5 - aza -uridine, dihydropseudouridine
7 -aminopyridopyrimidin - 3 -yl; 2 -oxo -pyridopyrimidine- 3 5 -methoxyuridine and 2 - O -methyl uridine . In some,
ylisocarbostyrilyl
; 2 -pyridinone; ; 3-3 (methyl
nitropyrrole
; 3-(methyl; )-7-4-((propynyl
, polynucleotides (e.g., RNA polynucleotides,
) isocarbostyrilyl
fluoro ) -6) is embodiments
such
as
mRNA
polynucleotides ) include a combination of at
(methyl ) benzimidazole ;
4 - methyl ) benzimidazole ; least two (e.g. , 2 , 3 , 4 or more ) of the aforementioned
4- (methyl) indolyl; 4,6- (dimethyl) indolyl; 5 nitroindole; 5 modified nucleobases.
substituted pyrimidines; 5- (methyl )isocarbostyrilyl; 5-niIn some embodiments, modified nucleobases in poly
troindole ; 6- (aza )pyrimidine; 6- (azothymine; 6- (methyl) -7- 20 nucleotides ( e.g. , RNA polynucleotides , such as mRNA
( aza) indolyl ; 6 -chloro -purine; 6 -phenyl-pyrrolo -pyrimidin- polynucleotides ) are selected from the group consisting of
2 - on - 3 -yl ; 7-(aminoalkylhydroxy )-1- (aza )-2-(thio )-3-(aza )- 1 -methyl-pseudouridine (m'y ), 5 -methoxy -uridine (mo®U ),
phenthiazin - 1 - yl; 7-(aminoalkylhydroxy )-1- aza )-2- (thio )- 5 -methyl - cytidine ( mC ) , pseudouridine ( V ) , a -thio - guanos
3 - aza ) -phenoxazin - 1 -yl;
7-( aminoalkylhydroxy )-1,3- ine and a - thio - adenosine . In some embodiments, polynucle
( diaza ) -2- (oxo ) -phenoxazin - 1 - yl; 7- ( aminoalkylhydroxy)-1, 25 otides includes a combination of at least two (e.g. , 2 , 3 , 4 or
more) of the aforementioned modified nucleobases .
3- ( diaza ) -2-(oxo ) -phenthiazin - 1 -yl;
7-(aminoalkylhydroxy )-1,3-(diaza )-2-(oxo )-phenoxazin - 1In some embodiments, polynucleotides (e.g. , RNA poly
yl ; 7 - aza lindolyl; 7-(guanidiniumalkylhydroxy )-1 - aza ) -2- nucleotides, such as mRNA polynucleotides) comprise
( thio )-3- ( aza ) -phenoxazinl-yl;
7-(guanidiniumalkylhy- pseudouridine ( ) and 5 -methyl - cytidine ( m ° C ). In some
droxy ) -1 - aza ) -2- ( thio ) -3- (aza )-phenthiazin - 1 -yl;
30 embodiments, polynucleotides ( e.g. , RNA polynucleotides,
7-(guanidiniumalkylhydroxy )-1- aza )-2-(thio ) -3-(aza ) -phe- such as mRNA polynucleotides) comprise 1 -methyl
noxazin - 1 -yl ; 7-(guanidiniumalkylhydroxy)-1,3-(diaza ) -2- pseudouridine (m y ). In some embodiments, polynucle
( oxo )-phenoxazin - 1 -yl; 7-(guanidiniumalkyl-hydroxy )-1,3- otides ( e.g. , RNA polynucleotides, such as mRNA poly
nucleotides) comprise 1 -methyl-pseudouridine (m'y ) and
( diaza )-2-(oxo ) -phenthiazin - 1 -yl;
7-(guanidiniumalkylhydroxy )-1,3-(diaza )-2-( oxo )-phe35 5 -methyl - cytidine (mºC ) . In some embodiments, polynucle
noxazin - 1 -yl ; 7-(propynyl) isocarbostyrilyl; 7-(propynyl)iso- otides ( e.g. , RNA polynucleotides, such as mRNA poly
carbostyrilyl, propynyl - 7 - aza ) indolyl; 7 -deaza - inosinyl; nucleotides) comprise 2 -thiouridine ( s’U) . In some embodi
7 -substituted 1- (aza )-2- (thio ) -3-(aza ) -phenoxazin - 1 -yl; ments, polynucleotides (e.g. , RNA polynucleotides, such as
7 -substituted
1,3 - diaza )-2- ( oxo ) -phenoxazin- 1 - yl ; mRNA polynucleotides ) comprise 2 - thiouridine and
9- (methyl)-imidizopyridinyl; Aminoindolyl; Anthracenyl; 40 5 -methyl-cytidine (mC). In some embodiments, polynucle
bis - ortho- (aminoalkylhydroxy )-6 - phenyl- pyrrolo -pyrimiotides ( e.g. , RNA polynucleotides , such as mRNA poly
din - 2 - on - 3 - yl ; bis -ortho -substituted -6 -phenyl-pyrrolo -py- nucleotides) comprise methoxy - uridine (mo®U) . In some
rimidin - 2 -on - 3 - yl; Difluorotolyl; Hypoxanthine; Imi- embodiments, polynucleotides ( e.g. , RNA polynucleotides ,

dizopyridinyl; Inosinyl; Isocarbostyrilyl; Isoguanisine; such as mRNA polynucleotides ) comprise 5 -methoxy -uri
N2 -substituted purines; N6 -methyl -2-amino -purine; 45 dine (mo?U ) and 5-methyl-cytidine (m C ) . In some embodi
N6 - substituted purines ; N -alkylated derivative; Napthalenyl ; Nitrobenzimidazolyl; Nitroimidazolyl; Nitroindazolyl;
Nitropyrazolyl; Nubularine; 06 - substituted purines; O -alkylated derivative ; ortho - aminoalkylhydroxy) -6 -phenyl-pyr-

ments, polynucleotides (e.g. , RNA polynucleotides, such as
mRNA polynucleotides ) comprise 2 - O -methyl uridine . In
some embodiments polynucleotides ( e.g. , RNA polynucle
otides , such as mRNA polynucleotides ) comprise 2-0

rolo - pyrimidin - 2 -on - 3 -yl;

embodiments, polynucleotides ( e.g. , RNA polynucleotides ,

rolo-pyrimidin -2 -on -3 - yl; ortho - substituted -6 -phenyl-pyr- 50 methyl uridine and 5 -methyl -cytidine ( mC ) . In some
Oxoformycin

TP ;

para-

(aminoalkylhydroxy ) -6 -phenyl-pyrrolo -pyrimidin -2 -on - 3such as mRNA polynucleotides ) comprise N6 -methyl-ad
yl ; para - substituted - 6 - phenyl -pyrrolo -pyrimidin - 2 - on - 3 -yl; enosine (mºA ). In some embodiments , polynucleotides ( e.g. ,
Pentacenyl; Phenanthracenyl; Phenyl; propynyl- 7-(aza )in- RNA polynucleotides, such as mRNA polynucleotides )
dolyl ; Pyrenyl; pyridopyrimidin - 3 - yl; pyridopyrimidin - 3 -yl, 55 comprise N6 -methyl- adenosine (m?A ) and 5-methyl-cyti
2 -oxo - 7 -amino -pyridopyrimidin - 3 -yl; pyrrolo -pyrimidin -2- dine (mC).
on - 3 - yl ; Pyrrolopyrimidinyl; Pyrrolopyrizinyl; Stilbenzyl;
In some embodiments, polynucleotides (e.g. , RNA poly
substituted 1,2,4 - triazoles; Tetracenyl; Tubercidine; Xan- nucleotides, such as mRNA polynucleotides ) are uniformly
thine; Xanthosine - 5 '- TP ; 2 - thio -zebularine; 5 -aza - 2 -thio -ze- modified ( e.g. , fully modified , modified throughout the
bularine; 7 - deaza - 2 -amino -purine; pyridin - 4 -one ribo- 60 entire sequence) for a particular modification . For example ,
nucleoside; 2 -Amino - riboside- TP ; Formycin A TP ; a polynucleotide can be uniformly modified with 5 -methyl
Formycin B TP ; Pyrrolosine TP ; 2 - OH -ara - adenosine TP ; cytidine (m®C ), meaning that all cytosine residues in the
2 '-OH -ara -cytidine TP ; 2 - OH - ara -uridine TP ; 2 -OH -ara- mRNA sequence are replaced with 5 -methyl -cytidine (mC ).
guanosine TP; 5- ( 2 - carbomethoxyvinyl) uridine TP ; and N6- Similarly, a polynucleotide can be uniformly modified for
( 19 -Amino -pentaoxanonadecyl)adenosine TP .
65 any type of nucleoside residue present in the sequence by
In some embodiments, polynucleotides (e.g. , RNA poly- replacement with a modified residue such as those set forth
nucleotides , such as mRNA polynucleotides ) include a com-

above .

US 10,933,127 B2
60

59

Exemplary nucleobases and nucleosides having a modi-

5 - substituted uracil). The modified uracil can be replaced by

fied cytosine include N4 - acetyl -cytidine ( ac4C ), 5 -methylcytidine (m5C ) , 5 - halo - cytidine (e.g. , 5 - iodo -cytidine ),

a compound having a single unique structure , or can be
replaced by a plurality of compounds having different struc

In some embodiments, a modified nucleobase is a modi

50% , at least 80% , at least 90 % or 100 % of the cytosine in
the polynucleotide is replaced with a modified cytosine ( e.g. ,

5 -hydroxymethyl -cytidine (hm5C ), 1-methyl -pseudoisocy- tures (e.g. , 2 , 3 , 4 or more unique structures ). n some
tidine , 2 - thio -cytidine ( s2C ) , and 2 -thio - 5-methyl-cytidine. 5 embodiments, at least 5 % , at least 10 % , at least 25 % , at least
fied uridine . Exemplary nucleobases and In some embodi
ments, a modified nucleobase is a modified cytosine. nucleo
sides having a modified uridine include 5 - cyano uridine, and
4 '- thio uridine.
In some embodiments, a modified nucleobase is a modi
fied adenine. Exemplary nucleobases and nucleosides hav

10

a 5 - substituted cytosine) . The modified cytosine can be
replaced by a compound having a single unique structure , or

can be replaced by a plurality of compounds having different
structures (e.g. , 2 , 3 , 4 or more unique structures ).
Thus, in some embodiments , the RNA (e.g. , mRNA )

ing a modified adenine include 7 -deaza - adenine, 1-methyl vaccines comprise a 5'UTR element, an optionally codon
adenosine (m1A) , 2 -methyl- adenine (m2A) , and N6 -methyl 15 optimized
open reading frame, and a 3'UTR element, a
adenosine (m6A ).
In some embodiments, a modified nucleobase is a modi-

poly (A) sequence and / or a polyadenylation signal wherein

ethyl - 7 - deaza -guanosine ( preQl ), 7 -methyl- guanosine

(m7G) , 1 -methyl -guanosine (m1G) , 8 -oxo -guanosine,

4 - one ribonucleoside, 5 -aza - uridine, 6 -aza -uridine, 2 - thio
5 - aza -uridine , 2 - thio - uridine ( s - U) , 4 - thio - uridine (s * U ),
4 - thio -pseudouridine, 2 - thio - pseudouridine, 5 - hydroxy -uri

all of A , G , U , C ) may be uniformly modified in a poly-

5 - carboxymethyl-uridine

fied guanine. Exemplary nucleobases and nucleosides hav- the RNA is not chemically modified .
In some embodiments , the modified nucleobase is a
ing a modified guanine include inosine ( 1 ) , 1 -methyl- inosine
(m1I ) , wyosine ( img ), methylwyosine (mimG ), 7 -deaza- modified uracil . Exemplary nucleobases and nucleosides
guanosine, 7 -cyano - 7 -deaza - guanosine ( preQo ), 7 - aminom- 20 having a modified uracil include pseudouridine (V ) , pyridin

7 -methyl- 8 -oxo - guanosine.
The polynucleotides of the present disclosure may be dine ( hoU ) , 5 - aminoallyl -uridine, 5 - halo - uridine ( e.g. ,
partially or fully modified along the entire length of the 25 5 - iodo - uridineor 5 -bromo -uridine), 3 -methyl-uridine ( mºU ) ,
molecule . For example, one or more or all or a given type of 5 -methoxy - uridine (mo?U ), uridine 5 - oxyacetic acid
nucleotide (e.g. , purine or pyrimidine, or any one or more or (cmo U ),uridine 5 - oxyacetic acid methyl ester (mcmo®U ),
(cm®U) ,

1 -carboxymethyl

nucleotide of the disclosure, or in a given predetermined pseudouridine, 5 - carboxyhydroxymethyl-uridine (chmU),
sequence region thereof ( e.g. , in the mRNA including or 30 5 -carboxyhydroxymethyl- uridine methyl ester (mchm?U ),
excluding the polyA tail ) . In some embodiments, all nucleo- 5 -methoxycarbonylmethyl-uridine (mcm U ) , 5 -methoxy
tides X in a polynucleotide of the present disclosure ( or in carbonylmethyl -2 -thio - uridine (memºs ?U) , 5 -aminomethyl
a given sequence region thereof) are modified nucleotides, 2 -thio -uridine (nm s’U) , 5 -methylaminomethyl - uridine

5 -methylaminomethyl - 2 - thio -uridine
wherein X may any one of nucleotides A , G , U , C , or any (mnm U ),
one of the combinations A + G , A +U , A + C , G + U , G + C , U + C , 35 (mnm s?U) ,
5 -methylaminomethyl-2 -seleno - uridine
A + G +U , A + G + C , G +U + C or A + G + C .
(mnm se’U ), 5 -carbamoylmethyl-uridine (ncmU ), 5 -car
The polynucleotide may contain from about 1 % to about boxymethylaminomethyl - uridine (cmnm U ), 5 -carboxym
100% modified nucleotides ( either in relation to overall ethylaminomethyl- 2 -thio -uridine ( cmnmºs - U ), 5-propynyl
nucleotide content, or in relation to one or more types of uridine, 1 -propynyl -pseudouridine, 5 -taurinomethyl- uridine

nucleotide, i.e. , any one or more of A, G, U or C ) or any 40 (Tm U ), 1 - taurinomethyl-pseudouridine, 5 -taurinomethyl-2
intervening percentage (e.g. , from 1 % to 20 % , from 1 % to

25 % , from 1 % to 50 % , from 1 % to 60% , from 1 % to 70 % ,
from 1 % to 80% , from 1 % to 90 % , from 1 % to 95 % , from

thio -uridine (Tm s U ), 1-taurinomethyl-4 -thio -pseudouri

dine, 5 -methyl-uridine ( m®U , i.e. , having the nucleobase
deoxythymine ), 1 -methyl-pseudouridine ( m y ), 5-methyl

10 % to 20 % , from 10 % to 25 % , from 10 % to 50 % , from 2 - thio - uridine (mºs’U) , 1 -methyl- 4 -thio - pseudouridine
10 % to 60 % , from 10 % to 70 % , from 10 % to 80 % , from 45 (m's + y ), 4 - thio - 1 -methyl-pseudouridine, 3 -methyl
10 % to 90 % , from 10 % to 95 % , from 10 % to 100 % , from pseudouridine (my ), 2 - thio - 1 -methyl- pseudouridine,

20 % to 25 % , from 20 % to 50 % , from 20 % to 60 % , from
20 % to 70 % , from 20 % to 80 % , from 20 % to 90 % , from

1 -methyl- 1 - deaza -pseudouridine, 2-thio - 1 -methyl- 1 -deaza
pseudouridine, dihydrouridine (D ) , dihydropseudouridine,

20 % to 95 % , from 20 % to 100 % , from 50 % to 60 % , from 5,6 - dihydrouridine, 5 -methyldihydrouridine ( m®D ) , 2- thio
50 % to 70 % , from 50 % to 80 % , from 50 % to 90 % , from 50 dihydrouridine, 2 -thio -dihydropseudouridine, 2-methoxy
50 % to 95 % , from 50 % to 100 % , from 70 % to 80 % , from uridine, 2 -methoxy - 4 - thio -uridine, 4 -methoxy -pseudouri
70 % to 90 % , from 70 % to 95 % , from 70 % to 100 % , from dine, 4 -methoxy - 2 - thio -pseudouridine, N1-methyl
80 % to 90 % , from 80 % to 95 % , from 80 % to 100 % , from pseudouridine,
3- ( 3 - amino - 3 -carboxypropyl )uridine
90 % to 95 % , from 90 % to 100 % , and from 95 % to 100% ) . (acpU ), 1-methyl-3-(3 -amino -3-carboxypropyl)pseudouri
Any remaining percentage is accounted for by the presence 55 dine (acp3 ) , 5- ( isopentenylaminomethyl ) uridine (inm®U ),
5-(isopentenylaminomethyl)-2-thio -uridine
(inm s U ) ,
of unmodified A , G , U , or C.
The polynucleotides may contain at a minimum 1 % and c - thio - uridine, 2 - O -methyl-uridine (Urn ), 5,2-0 -dimethyl
at maximum 100 % modified nucleotides, or any intervening uridine ( m Um ), 2 - O -methyl -pseudouridine (Um ), 2 - thio
percentage, such as at least 5 % modified nucleotides, at least 2 - O -methyl - uridine ( s Um ), 5 -methoxycarbonylmethyl- 2'
10 % modified nucleotides, at least 25 % modified nucleo - 60 O -methyl- uridine (mcm Um ), 5 -carbamoylmethyl-2 - O
tides , at least 50 % modified nucleotides, at least 80 % methyl-uridine (nem Um ), 5 -carboxymethylaminomethyl

modified nucleotides, or at least 90% modified nucleotides. 2 - O -methyl - uridine (cmnm Um ), 3,2 - O -dimethyl -uridine
For example, the polynucleotides may contain a modified ( m Um ), and 5-( isopentenylaminomethyl) -2 - O -methyl-uri
pyrimidine such as a modified uracil or cytosine . In some dine (inm Um ), 1 -thio -uridine, deoxythymidine, 2 - F -ara
embodiments, at least 5 % , at least 10 % , at least 25 % , at least 65 uridine, 2 ' - F -uridine , 2 -OH -ara - uridine, 5- ( 2 - car
50 % , at least 80% , at least 90% or 100% of the uracil in the bomethoxyvinyl) uridine, and 5- (3- ( 1 - E -propenylamino )]
polynucleotide is replaced with a modified uracil (e.g. , a uridine .

US 10,933,127 B2
62

61

In some embodiments, the modified nucleobase is a N2 -methyl-guanosine ( m²G ) , N2,N2 - dimethyl-guanosine
modified cytosine . Exemplary nucleobases and nucleosides ( m² , G ) , N2,7 -dimethyl-guano sine ( m2,7G ) , N2,N2,7 -dim
having a modified cytosine include 5 -aza -cytidine, 6 -aza- ethyl -guanosine (m2.2,7G ), 8-oxo - guanosine, 7 -methyl-8
cytidine, pseudoisocytidine, 3 -methyl- cytidine (mC ), oxo - guanosine, 1 -methyl- 6 - thio - guanosine, N2-methyl-6
N4 -acetyl -cytidine ( ac + C ), 5 - formylcytidine ( fC ) , 5 thio -guanosine, N2,N2 -dimethyl -6 -thio -guanosine, a -thio
N4 -methyl -cytidine ( m * C ), 5 -methyl -cytidine (mC ), guanosine , 2 - O -methyl -guanosine (Gm ), N2 -methyl-2-0
5 -halo -cytidine ( e.g. , 5 - iodo -cytidine ), 5 -hydroxymethyl- methyl-guanosine ( m?Gm ) , N2,N2-dimethyl-2'-O -methyl
cytidine ( hmC), 1 -methyl- pseudoisocytidine, pyrrolo -cyti- guanosine (m²2 Gm ), 1 -methyl- 2 '- O -methyl - guanosine
dine, pyrrolo -pseudoisocytidine, 2 -thio -cytidine ( s C ) , (m'Gm ), N2,7 - dimethyl - 2 - O -methyl -guanosine (m².7Gm ),
2 - thio - 5 -methyl-cytidine, 4 -thio -pseudoisocytidine, 4 - thio- 10 2 - O -methyl - inosine ( Im ) , 1,2 - O -dimethyl - inosine ( m'Im ) ,
1 -methyl -pseudoisocytidine, 4 -thio - 1-methyl- 1 -deaza -pseu- 2 - O -ribosylguanosine ( phosphate ) (Gr( p ) ), 1- thio -guanos
doisocytidine, 1 -methyl- 1 -deaza -pseudoisocytidine, zebu- ine , 06 -methyl- guanosine, 2 '- F - ara -guanosine, and 2'-F
larine , 5 - aza -zebularine , 5 -methyl-zebularine, 5-aza-2 -thio- guanosine .
zebularine, 2 -thio -zebularine, 2 -methoxy -cytidine, N -Linked Glycosylation Site Mutants
2 -methoxy - 5 -methyl-cytidine, 4 -methoxy -pseudoisocyti- 15 N -linked glycans of viral proteins play important roles in
dine , 4 -methoxy - 1 -methyl-pseudoisocytidine, lysidine modulating the immune response . Glycans can be important
(k2C ), a -thio - cytidine, 2 - O -methyl - cytidine ( Cm) , 5,2-0- for maintaining the appropriate antigenic conformations,
dimethylcytidine mCm
(
), N4-acetyl - 2'- O -methyl -cytidine shielding potential neutralization epitopes , and may alter the
( ac +Cm) , N4,2% -O -dimethylcytidine ( m * Cm ), 5 - formyl - 2'- proteolytic susceptibility of proteins . Some viruses have

O -methyl-cytidine (fCm ) , N4 ,N4,2'- O - trimethyl -cytidine 20 putative N - linked glycosylation sites. Deletion or modifica

( m *, Cm ) , 1 - thio - cytidine, 2 - F -ara -cytidine, 2 - F -cytidine, tion of an N - linked glycosylation site may enhance the
and 2 -OH -ara -cytidine.
immune response . Thus , the present disclosure provides , in
In some embodiments , the modified nucleobase is a some embodiments, RNA ( e.g. , mRNA ) vaccines compris
modified adenine . Exemplary nucleobases and nucleosides ing nucleic acids ( e.g. , mRNA ) encoding antigenic polypep
having a modified adenine include 2 -amino -purine, 2,6- 25 tides that comprise a deletion or modification at one or more
diaminopurine, 2 - amino - 6 -halo -purine ( e.g. , 2- amino -6- N - linked glycosylation sites .
chloro -purine ), 6 -halo -purine ( e.g. , 6 -chloro -purine ), In Vitro Transcription of RNA ( e.g. , mRNA )
2 - amino -6 -methyl -purine, 8 - azido - adenosine, 7 -deaza -adRespiratory virus vaccines of the present disclosure com
enine, 7 - deaza - 8 - aza- adenine , 7 -deaza - 2 -amino -purine, prise at least one RNA polynucleotide, such as a mRNA
7 -deaza - 8 -aza - 2 -amino -purine, 7 - deaza - 2,6 -diaminopurine, 30 (e.g. , modified mRNA ). mRNA , for example, is transcribed
7 -deaza - 8 -aza -2,6 -diaminopurine,

1 -methyl - adenosine

(m - A) , 2 -methyl-adenine (m²A ), N6 -methyl-adenosine

(mºA ), 2 -methylthio -N6 -methyl - adenosine ( ms2 mA ),
N6 -isopentenyl- adenosine ( i?A ) , 2 -methylthio -N6 - isopente-

in vitro from template DNA , referred to as an “ in vitro

transcription template .” In some embodiments, an in vitro

transcription template encodes a 5 ' untranslated (UTR)
region, contains an open reading frame, and encodes a 3 '

nyl -adenosine (ms? i?A ), N6-(cis -hydroxyisopentenyl )ad- 35 UTR and a polyA tail . The particular nucleic acid sequence
enosine (io®A) , 2 -methylthio -N6- ( cis -hydroxyisopentenyl) composition and length of an in vitro transcription template
adenosine (ms? io A ) , N6 -glycinylcarbamoyl-adenosine will depend on the mRNA encoded by the template.
( g?A) , N6 -threonylcarbamoyl-adenosine (t®A ), N6 -methylA “ 5'untranslated region ” ( 5'UTR) refers to a region of an
N6 - threonylcarbamoyl -adenosine mA
(
), 2 -methylthio- mRNA that is directly upstream ( i.e. , 5 ' ) from the start codon
N6 -threonylcarbamoyl -adenosine ( ms²gA ) , N6 , N6 - dim- 40 ( i.e. , the first codon of an mRNA transcript translated by a

ethyl- adenosine (m °2A ), N6 -hydroxynorvalylcarbamoyladenosine
(hn?A ),
2 -methylthio -N6hydroxynorvalylcarbamoyl- adenosine
(ms ? hn®A ),
N6 -acetyl -adenosine ( acºA ), 7 -methyl -adenine, 2 -methylthio -adenine, 2 -methoxy -adenine, a - thio -adenosine, 2-0- 45

ribosome) that does not encode a polypeptide.
A “ 3 ' untranslated region ” (3'UTR) refers to a region of an
mRNA that is directly downstream ( i.e. , 3 ' ) from the stop
codon (i.e. , the codon of an mRNA transcript that signals a
termination of translation ) that does not encode a polypep

O - dimethyl -adenosine (m'Am ), 2' - O - ribosyladenosine

beginning with a start codon (e.g. , methionine ( ATG )), and

methyl-adenosine ( Am ), N6,2 '- O -dimethyl- adenosine
(m?Am ), N6 ,N6,2 ' - O - trimethyl -adenosine ( m® , Am ), 1,2'-

tide .
An “ open reading frame” is a continuous stretch of DNA

(phosphate) ( Ar ( p ) ), 2 - amino -N6 -methyl -purine, 1-thio - ad- ending with a stop codon (e.g. , TAA, TAG or TGA ) and
enosine, 8 - azido -adenosine, 2 ' - F - ara - adenosine, 2 ' - F - ad- 50 encodes a polypeptide .

enosine, 2 -OH - ara - adenosine, and N6- ( 19 - amino -pentaoxanonadecyl ) -adenosine.
In some embodiments , the modified nucleobase is a

A “ polyA tail ” is a region of mRNA that is downstream ,
e.g. , directly downstream (i.e. , 3 ' ) , from the 3 ' UTR that
contains multiple, consecutive adenosine monophosphates.
modified guanine . Exemplary nucleobases and nucleosides A polyA tail may contain 10 to 300 adenosine monophos
having a modified guanine include inosine ( I ) , 1 -methyl- 55 phates. For example , a polyA tail may contain 10 , 20 , 30 , 40 ,
inosine ( m'I ) , wyosine ( img ) , methylwyosine ( mimG ) , 50 , 60 , 70 , 80 , 90 , 100 , 110 , 120 , 130 , 140 , 150 , 160 , 170 ,
4 -demethyl -wyosine (img - 14 ) , isowyosine ( imG2 ) , wybu- 180 , 190 , 200 , 210 , 220 , 230 , 240 , 250 , 260 , 270 , 280 , 290
tosine ( yW ) , peroxywybutosine ( 02yW ) , hydroxywybuto- or 300 adenosine monophosphates. In some embodiments, a

sine (OhyW ), undermodified hydroxywybutosine (OhyW * ), polyA tail contains 50 to 250 adenosine monophosphates. In
7 - deaza - guanosine , queuosine (Q ) , epoxyqueuosine ( oQ ) , 60 a relevant biological setting ( e.g. , in cells , in vivo ) the
galactosyl-queuosine ( galQ ), mannosyl- queuosine (manQ ), poly (A) tail functions to protect mRNA from enzymatic
7 -cyano - 7 -deaza - guanosine ( prelo), 7 -aminomethyl-7- degradation , e.g. , in the cytoplasm , and aids in transcription

deaza - guanosine ( preQ . ), archaeosine ( G + ) , 7 -deaza -8 -aza- termination, export of the mRNA from the nucleus and
guanosine, 6 -thio - guanosine, 6 - thio - 7 - deaza -guanosine , translation .
6 -thio -7 - deaza -8 -aza -guanosine,
7 -methyl- guanosine 65 In some embodiments, a polynucleotide includes 200 to
(m7G ) , 6 -thio - 7 -methyl -guanosine, 7 -methyl - inosine, 3,000 nucleotides. For example, a polynucleotide may
6 -methoxy - guanosine, 1 -methyl- guanosine (m'G) , include 200 to 500 , 200 to 1000 , 200 to 1500 , 200 to 3000 ,

US 10,933,127 B2
64
flagellin include flagellin like sequences that activate TLR5

63

500 to 1000 , 500 to 1500 , 500 to 2000 , 500 to 3000 , 1000

to 1500 , 1000 to 2000 , 1000 to 3000 , 1500 to 3000 , or 2000
to 3000 nucleotides .

and contain a 13 amino acid motif that is 53 % or more

Flagellin Adjuvants

Flagellin is an approximately 500 amino acid monomeric 5
protein that polymerizes to form the flagella associated with
bacterial motion . Flagellin is expressed by a variety of
flagellated bacteria ( Salmonella typhimurium for example )
as well as non - flagellated bacteria ( such as Escherichia coli ).
Sensing of flagellin by cells of the innate immune system 10
(dendritic cells , macrophages, etc. ) is mediated by the Tolllike receptor 5 ( TLR5 ) as well as by Nod - like receptors
(NLRs ) Ipaf and Naip5 . TLRs and NLRs have been identified as playing a role in the activation of innate immune
response and adaptive immune response . As such, flagellin 15
provides an adjuvant effect in a vaccine.
The nucleotide and amino acid sequences encoding
known flagellin polypeptides are publicly available in the
NCBI GenBank database . The flagellin sequences from S.

Typhimurium , H. Pylori, V. Cholera , S. marcesens, S. 20
flexneri, T. Pallidum , L. pneumophila, B. burgdorferei, C.
difficile, R. meliloti , A. tumefaciens, R. lupini, B. clarridgeiae, P. Mirabilis, B. subtilus, L. monocytogenes , P.
aeruginosa , and E. coli , among others are known .
A flagellin polypeptide, as used herein , refers to a full 25
length flagellin protein , immunogenic fragments thereof,
and peptides having at least 50% sequence identify to a
flagellin protein or immunogenic fragments thereof. Exemplary flagellin proteins include flagellin from Salmonella
typhi (UniPro Entry number: Q56086 ) , Salmonella typhimurium
( AOA0C9DG09 ),
Salmonella
enteritidis
( AOA0C9BAB7 ), and Salmonella choleraesuis (Q6V2X8 ) ,
and SEQ ID NO : 54-56 ( Table 17 ) . In some embodiments,
the flagellin polypeptide has at least 60 % , 70 % , 75 % , 80 % ,
90 % , 95 % , 97 % , 98 % , or 99 % sequence identify to a
flagellin protein or immunogenic fragments thereof.
In some embodiments, the flagellin polypeptide is an
immunogenic fragment. An immunogenic fragment is a
portion of a flagellin protein that provokes an immune
response . In some embodiments, the immune response is a
TLR5 immune response . An example of an immunogenic
fragment is a flagellin protein in which all or a portion of a
hinge region has been deleted or replaced with other amino
acids . For example, an antigenic polypeptide may be
inserted in the hinge region. Hinge regions are the hypervariable regions of a flagellin. Hinge regions of a flagellin
are also referred to as “ D3 domain or region, " propeller
domain or region ," " hypervariable domain or region " and
“ variable domain or region .” “ At least a portion of a hinge
region ,” as used herein , refers to any part of the hinge region
of the flagellin , or the entirety of the hinge region . In other
embodiments an immunogenic fragment of flagellin is a 20 ,

30

35

40

45

50

25 , 30 , 35 , or 40 amino acid C - terminal fragment of flagel-

lin.

The flagellin monomer is formed by domains Do through 55
D3 . DO and D1, which form the stem , are composed of

tandem long alpha helices and are highly conserved among
different bacteria . The D1 domain includes several stretches
of amino acids that are useful for TLR5 activation . The

identical to the Salmonella sequence in 88-100 of Flic
(LQRVRELAVQSAN ; SEQ ID NO : 84 ) .
In some embodiments, the RNA ( e.g. , mRNA ) vaccine
includes an RNA that encodes a fusion protein of flagellin
and one or more antigenic polypeptides. A " fusion protein ”
as used herein , refers to a linking of two components of the
construct. In some embodiments, a carboxy - terminus of the
antigenic polypeptide is fused or linked to an amino termi
nus of the flagellin polypeptide. In other embodiments, an
amino - terminus of the antigenic polypeptide is fused or
linked to a carboxy -terminus of the flagellin polypeptide .
The fusion protein may include , for example, one , two ,
three, four, five, six or more flagellin polypeptides linked to
one , two, three , four, five , six or more antigenic polypep
tides . When two or more flagellin polypeptides and / or two or
more antigenic polypeptides are linked such a construct may
be referred to as a "multimer.”
Each of the components of a fusion protein may be
directly linked to one another or they may be connected
through a linker. For instance, the linker may be an amino
acid linker. The amino acid linker encoded for by the RNA
(e.g. , mRNA ) vaccine to link the components of the fusion
protein may include , for instance, at least one member
selected from the group consisting of a lysine residue , a
glutamic acid residue, a serine residue and an arginine
residue . In some embodiments the linker is 1-30 , 1-25 , 1-25 ,
5-10 , 5 , 15 , or 5-20 amino acids in length .
In other embodiments the RNA (e.g. , mRNA ) vaccine
includes at least two separate RNA polynucleotides, one
encoding one or more antigenic polypeptides and the other
encoding the flagellin polypeptide . The at least two RNA
polynucleotides may be co -formulated in a carrier such as a
lipid nanoparticle.
Broad Spectrum RNA ( e.g. , mRNA ) Vaccines
There may be situations where persons are at risk for
infection with more than one strain of hMPV , PIV3 , RSV,
MeV and / or BetaCoV ( including MERS - COV, SARS - CoV,
HCOV - OC43 , HCOV - 229E , HCOV - NL63 , HCOV - NL ,
HCOV -NH and / or HCOV -HKU1). RNA (e.g. , mRNA ) thera
peutic vaccines are particularly amenable to combination
vaccination approaches due to a number of factors includ
ing , but not limited to , speed of manufacture, ability to
rapidly tailor vaccines to accommodate perceived geo
graphical threat, and the like . Moreover, because the vac
cines utilize the human body to produce the antigenic
protein , the vaccines are amenable to the production of
larger, more complex antigenic proteins, allowing for proper
folding, surface expression, antigen presentation , etc. in the
human subject. To protect against more than one strain of
hMPV, PIV3 , RSV, MeV and / or BetaCoV ( including
MERS - CoV , SARS - CoV, HCV -OC43 , HCOV - 229E ,
HCOV - NL63 , HCOV - NL , HCOV -NH and / or HCOV -HKU1),
a combination vaccine can be administered that includes
RNA ( e.g. , mRNA ) encoding at least one antigenic poly
peptide protein ( or antigenic portion thereof) of a first
respiratory virus and further includes RNA encoding at least
one antigenic polypeptide protein ( or antigenic portion

entire D1 domain or one or more of the active regions within 60 thereof) of a second respiratory virus. RNA ( e.g. , mRNA )
the domain are immunogenic fragments of flagellin . can be co - formulated , for example , in a single lipid nan
Examples of immunogenic regions within the D1 domain oparticle (LNP ) or can be formulated in separate LNPs for
include residues 88-114 and residues 411-431 ( in Salmo- co -administration .
nella typhimurium Flic flagellin . Within the 13 amino acids Methods of Treatment
in the 88-100 region, at least 6 substitutions are permitted 65 Provided herein are compositions ( e.g. , pharmaceutical
between Salmonella flagellin and other flagellins that still compositions ), methods, kits and reagents for prevention
preserve TLR5 activation . Thus, immunogenic fragments of and / or treatment of respiratory diseases/ infections in

US 10,933,127 B2
66

65

humans and other mammals. Respiratory virus RNA (e.g. vaccines , killed / inactivated microorganism vaccines, sub
mRNA ) vaccines can be used as therapeutic or prophylactic unit vaccines , protein antigen vaccines , DNA vaccines , VLP
agents, alone or in combination with other vaccine ( s ). They vaccines , etc. In exemplary embodiments, a traditional vac
may be used in medicine to prevent and / or treat respiratory cine is a vaccine that has achieved regulatory approval
disease / infection . In exemplary aspects , the RNA ( e.g. , 5 and / or is registered by a national drug regulatory body, for
mRNA ) vaccines of the present disclosure are used to example the Food and Drug Administration (FDA) in the
provide prophylactic protection from hMPV, PIV3, RSV, United States or the European Medicines Agency ( EMA ).
MeV and / or BetaCoV ( including MERS -COV, SARS - CoV,
In some embodiments the anti -antigenic polypeptide anti
HCV - OC43 , HCOV -229E , HCOV -NL63, HCOV -NL , body titer in the subject is increased 1 log to 10 log following
HCOV-NH and /or HCOV - HKU1). Prophylactic protection 10 vaccination relative to anti -antigenic polypeptide antibody
from hMPV, PIV3 , RSV , MeV and / or BetaCoV ( including titer in a subject vaccinated with a prophylactically effective
MERS - CoV, SARS- CoV, HCOV -OC43 , HC0V - 229E ,
of a traditional vaccine against hMPV , PIV3 , RSV ,
HCOV -NL63, HCOV -NL , HCOV -NH and / or HCOV -HKU1) dose
can be achieved following administration of a RNA ( e.g. , MeV and /or BetaCoV ( including MERS - CoV, SARS - CoV,
HCOV -OC43, HCOV - 229E , HCOV -NL63, HCOV -NL ,
mRNA ) vaccine of the present disclosure . Respiratory virus 15 HCOV
-NH and /or HCOV -HKU1 ).
RNA (e.g. , mRNA ) vaccines of the present disclosure may

be used to treat or prevent viral “ co - infections ” containing

In some embodiments the anti- antigenic polypeptide anti

MERS - CoV, SARS - COV, HCOV -OC43, HCOV - 229E ,
HCOV -NL63, HCOV -NL , HCOV - NH and / or HCOV -HKU1)

MERS -CoV, SARS - CoV, HCOV -OC43, HCOV - 229E ,
HCOV -NL63, HCOV -NL , HCOV - NH and / or HCOV -HKU1)

two or more respiratory infections. Vaccines can be admin- body titer in the subject is increased 1 log , 2 log , 3 log , 5 log
istered once , twice, three times , four times or more , but it is or 10 log following vaccination relative to anti- antigenic
likely sufficient to administer the vaccine once (optionally 20 polypeptide antibody titer in a subject vaccinated with a
followed by a single booster ). It is possible , although less prophylactically effective dose of a traditional vaccine
desirable, to administer the vaccine to an infected individual against hMPV, PIV3 , RSV, MeV and / or BetaCoV ( including
to achieve a therapeutic response . Dosing may need to be MERS - CoV , SARS- CoV, HCV - OC43 , HCOV - 229E ,
adjusted accordingly.
HCOV -NL63, HCOV -NL , HCOV - NH and / or HCOV -HKU1 ).
A method of eliciting an immune response in a subject 25 A method of eliciting an immune response in a subject
against hMPV , PIV3 , RSV, MeV and / or BetaCoV ( including against hMPV , PIV3 , RSV, MeV and / or BetaCoV ( including

is provided in aspects of the present disclosure. The method is provided in other aspects of the disclosure . The method
involves administering to the subject a respiratory virus 30 involves administering to the subject a respiratory virus
RNA ( e.g. , mRNA ) vaccine comprising at least one RNA RNA ( e.g. , mRNA ) vaccine comprising at least one RNA

( e.g. , mRNA ) polynucleotide having an open reading frame

encoding

least one hMPV ,

(e.g. , mRNA ) polynucleotide having an open reading frame

V3 , RSV , MeV and / or

encoding at least one hMPV,

BetaCoV ( including MERS - CoV, SARS - CoV, HCOV-

3 , RSV , MeV and /or

BetaCoV (including MERS - CoV, SARS - CoV, HCOV

OC43 , HCOV - 229E , HCOV -NL63 , HCOV -NL , HCOV -NH 35 OC43 , HCOV - 229E , HCOV - NL63, HCOV -NL , HCOV -NH

and /or HCOV -HKU1) antigenic polypeptide thereof, thereby

inducing in the subject an immune response specific to
hMPV, PIV3 , RSV, MeV and /or BetaCoV ( including
MERS - CoV, SARS- CoV, HCV - OC43 , HC0V - 229E ,
HCOV -NL63, HCOV -NL , HCOV - NH and / or HCOV -HKU1)
antigenic polypeptide or an immunogenic fragment thereof,
wherein anti - antigenic polypeptide antibody titer in the
subject is increased following vaccination relative to antiantigenic polypeptide antibody titer in a subject vaccinated
with a prophylactically effective dose of a traditional vaccine against hMPV, PIV3 , RSV, MeV and / or BetaCoV
( including MERS -CoV, SARS -COV, HCOV - OC43, HCV229E , HCOV -NL63, HCOV - NL , HCOV -NH and / or HCOVHKU1). An “ anti- antigenic polypeptide antibody ” is a serum
antibody the binds specifically to the antigenic polypeptide.
In some embodiments, a RNA (e.g. , mRNA ) vaccine
( e.g. , a hMPV, PIV3 , RSV, MeV and / or BetaCoV ( including
MERS -COV, SARS - CoV, HCV - OC43 , HCOV - 229E ,
HCOV -NL63 , HCOV -NL , HCOV -NH and /or HCOV -HKU1
RNA vaccine) capable of eliciting an immune response is
administered intramuscularly via a composition including a
compound according to Formula ( I ) , ( IA ) , ( II ) , ( IIa ) , ( IIb ) ,
( IIC ) , (IId) or (Ile ) ( e.g. , Compound 3 , 18 , 20 , 25 , 26 , 29 , 30 ,

and / or HCOV -HKU1) antigenic polypeptide or an immuno

40

45

50

55

genic fragment thereof, thereby inducing in the subject an
immune response specific to hMPV, PIV3 , RSV, MeV
and / or BetaCoV ( including MERS - CoV, SARS - CoV,
HCV - OC43 , HCOV - 229E , HCOV -NL63, HCOV - NL ,
HCOV - NH and / or HCOV -HKU1) antigenic polypeptide or
an immunogenic fragment thereof, wherein the immune
response in the subject is equivalent to an immune response
in a subject vaccinated with a traditional vaccine against the
MPV, PIV3 , RSV, MeV and / or BetaCoV ( including
MERS - CoV, SARS - CoV, HCV - OC43 , HCOV - 229E ,
HCOV -NL63 , HCOV -NL , HCOV - NH and /or HCOV -HKU1)
at 2 times to 100 times the dosage level relative to the RNA
(e.g. , mRNA ) vaccine .
In some embodiments, the immune response in the sub
ject is equivalent to an immune response in a subject
vaccinated with a traditional vaccine at 2 , 3 , 4 , 5 , 10 , 50 , 100
times the dosage level relative to the hMPV, PIV3 , RSV,
MeV and /or BetaCoV ( including MERS - CoV, SARS - CoV,
HCOV -OC43, HCOV - 229E , HCOV -NL63, HCOV -NL ,
HCOV - NH and /or HCOV -HKU1) RNA (e.g. , mRNA ) vac
cine .
In some embodiments the immune response in the subject

is equivalent to an immune response in a subject vaccinated
A prophylactically effective dose is a therapeutically 60 with a traditional vaccine at 10-100 times , or 100-1000
effective dose that prevents infection with the virus at a times , the dosage level relative to the hMPV, PIV3 , RSV,
clinically acceptable level. In some embodiments the thera- MeV and / or BetaCoV ( including MERS -COV, SARS - COV,
60 , 108-112 , or 122 ) .

peutically effective dose is a dose listed in a package insert HCOV -OC43, HCOV - 229E , HCOV -NL63, HCOV -NL ,
for the vaccine . A traditional vaccine, as used herein , refers HCOV - NH and / or HCOV -HKU1) RNA (e.g. , mRNA ) vac
to a vaccine other than the RNA (e.g. , mRNA ) vaccines of 65 cine .
the present disclosure. For instance, a traditional vaccine
In some embodiments the immune response is assessed by

includes but is not limited to live/ attenuated microorganism

determining [ protein) antibody titer in the subject.

US 10,933,127 B2
67

Some aspects of the present disclosure provide a method
of eliciting an immune response in a subject against a In
some embodiments the immune response in the subject is
equivalent to an immune response in a subject vaccinated
with a traditional vaccine at 2 , 3 , 4 , 5 , 10 , 50 , 100 times the 5
dosage level relative to the hMPV, PIV3 , RSV , MeV and / or
BetaCoV (including MERS - CoV, SARS - CoV, HCOV
OC43 , HCOV -229E , HCOV -NL63 , HCOV -NL , HCOV -NH
and / or HCOV - HKU1) RNA ( e.g. , mRNA ) vaccine by admin
istering to the subject a respiratory virus RNA (e.g. ,mRNA ) 10
vaccine comprising at least one RNA ( e.g. , mRNA ) poly
nucleotide having an open reading frame encoding at least
one hMPV, PIV3 , RSV, MeV and / or BetaCoV ( including
MERS - CoV, SARS - CoV, HCOV -OC43, HCOV - 229E, 15
HCOV -NL63, HCOV -NL , HCOV - NH and / or HCOV -HKU1)

68

such as a human subject ), and the RNA (e.g. , mRNA )
polynucleotides are translated in vivo to produce an anti
genic polypeptide.
The respiratory virus RNA ( e.g. , mRNA ) vaccines may be
induced for translation of a polypeptide (e.g. , antigen or
immunogen ) in a cell , tissue or organism . In some embodi
ments , such translation occurs in vivo , although such trans

lation may occur ex vivo , in culture or in vitro . In some

embodiments, the cell , tissue or organism is contacted with

antoryeffective
amount of a composition containing a respira
virus RNA (e.g. , mRNA ) vaccine that contains a
polynucleotide that has at least one a translatable region

encoding an antigenic polypeptide .

An “ effective amount of an respiratory virus RNA (e.g.

mRNA ) vaccine is provided based , at least in part, on the
target
, target cell type, means of administration ,
antigenic polypeptide, thereby inducing in the subject an physicaltissue
characteristics of the polynucleotide (e.g. , size , and
immune response specific to the antigenic polypeptide or an extent of modified nucleosides) and other components of the
immunogenic fragment thereof, wherein the immune vaccine , and other determinants. In general, an effective
response in the subject is induced 2 days to 10 weeks earlier 20 amount of the respiratory virus RNA ( e.g. , mRNA ) vaccine
relative to an immune response induced in a subject vacci- composition provides an induced or boosted immune
nated with a prophylactically effective dose of a traditional response as a function of antigen production in the cell ,
vaccine against the hMPV, PIV3 , RSV , MeV and /or Beta- preferably more efficient than a composition containing a
COV (including MERS - CoV, SARS - CoV, HCV- OC43 , corresponding unmodified polynucleotide encoding the
HCOV - 229E , HCOV -NL63, HCOV -NL , HCOV -NH and /or 25 same antigen or a peptide antigen . Increased antigen pro
HCOV -HKU1). In some embodiments, the immune response duction may be demonstrated by increased cell transfection
in the subject is induced in a subject vaccinated with a ( the percentage of cells transfected with the RNA , e.g. ,
prophylactically effective dose of a traditional vaccine at 2 mRNA , vaccine ), increased protein translation from the
times to 100 times the dosage level relative to the RNA ( e.g. , polynucleotide, decreased nucleic acid degradation ( as dem
30 onstrated , for example, by increased duration of protein
mRNA ) vaccine.
In some embodiments, the immune response in the sub- translation from a modified polynucleotide ), or altered anti
ject is induced 2 days earlier, or 3 days earlier, relative to an gen specific immune response of the host cell .
immune response induced in a subject vaccinated with a
In some embodiments, RNA ( e.g. mRNA ) vaccines ( in
prophylactically effective dose of a traditional vaccine.
cluding polynucleotides their encoded polypeptides ) in
In some embodiments the immune response in the subject 35 accordance with the present disclosure may be used for
is induced 1 week, 2 weeks , 3 weeks , 5 weeks , or 10 weeks treatment of hMPV, PIV3 , RSV, MeV and /or BetaCoV
earlier relative to an immune response induced in a subject (including MERS - COV, SARS -COV, HCV- OC43 , HCV
vaccinated with a prophylactically effective dose of a tradi- 229E , HCOV -NL63 , HCOV -NL , HCOV - NH and / or HCOV
tional vaccine .
HKU1).
Also provided herein is a method of eliciting an immune 40 Respiratory RNA (e.g. mRNA ) vaccines may be admin
response in a subject against hMPV, PIV3 , RSV , MeV and /or istered prophylactically or therapeutically as part of an
BetaCoV (including MERS - CoV, SARS -CoV, HCOV- active immunization scheme to healthy individuals or early
OC43 , HCOV - 229E , HCOV -NL63, HCOV -NL , HCOV -NH in infection during the incubation phase or during active

and /or HCOV- HKU1) by administering to the subject a infection after onset of symptoms. In some embodiments,
respiratory virus RNA (e.g. , mRNA ) vaccine having an open 45 the amount of RNA (e.g. , mRNA ) vaccine of the present
reading frame encoding a first antigenic polypeptide, disclosure provided to a cell , a tissue or a subject may be an
wherein the RNA polynucleotide does not include a stabi- amount effective for immune prophylaxis.
lization element, and wherein an adjuvant is not co -formuRespiratory virus RNA (e.g. mRNA ) vaccines may be
administrated with other prophylactic or therapeutic com
lated or co - administered with the vaccine .
Therapeutic and Prophylactic Compositions
50 pounds . As a non - limiting example, a prophylactic or thera
Provided herein are compositions ( e.g. , pharmaceutical peutic compound may be an adjuvant or a booster. As used
compositions ), methods, kits and reagents for prevention, herein , when referring to a prophylactic composition, such
treatment or diagnosis of hMPV , PIV3 , RSV, MeV and /or as a vaccine , the term “booster” refers to an extra adminis
BetaCoV ( including MERS - CoV, SARS -CoV, HCOV- tration of the prophylactic ( vaccine ) composition. A booster

OC43 , HCV - 229E , HCOV -NL63, HCOV - NL , HCOV - NH 55 (or booster vaccine) may be given after an earlier adminis
and / or HCOV -HKU1) in humans and other mammals, for tration of the prophylactic composition . The time of admin
example . Respiratory virus RNA ( e.g. mRNA ) vaccines can istration between the initial administration of the prophy
be used as therapeutic or prophylactic agents. They may be lactic composition and the booster may be , but is not limited
used in medicine to prevent and / or treat infectious disease . to , 1 minute , 2 minutes, 3 minutes, 4 minutes, 5 minutes, 6
In some embodiments, the respiratory RNA ( e.g. , mRNA ) 60 minutes, 7 minutes, 8 minutes , 9 minutes, 10 minutes, 15
vaccines of the present disclosure are used fin the priming of minutes, 20 minutes 35 minutes, 40 minutes, 45 minutes, 50
immune effector cells , for example , to activate peripheral minutes, 55 minutes, 1 hour, 2 hours , 3 hours, 4 hours , 5
blood mononuclear cells ( PBMCs ) ex vivo , which are then hours , 6 hours, 7 hours , 8 hours, 9 hours , 10 hours , 11 hours,
12 hours, 13 hours, 14 hours , 15 hours , 16 hours , 17 hours,
infused ( re - infused ) into a subject.

In some embodiments, respiratory virus vaccine contain- 65 18 hours, 19 hours, 20 hours, 21 hours , 22 hours , 23 hours,
ing RNA ( e.g. , mRNA ) polynucleotides as described herein 1 day, 36 hours , 2 days, 3 days, 4 days , 5 days, 6 days, 1

can be administered to a subject (e.g. , a mammalian subject,

week , 10 days, 2 weeks , 3 weeks, 1 month , 2 months, 3

US 10,933,127 B2
69

70

months, 4 months, 5 months, 6 months, 7 months, 8 months,
9 months, 10 months, 11 months, 1 year, 18 months, 2 years ,
3 years, years , 5 years , 6 years , 7 years , 8 years , 9 years ,
10 years, 11 years, 122 years , 13 years , 14 years , 15 years, 16

able , dividing , shaping and / or packaging the product into a
desired single- or multi- dose unit.
Relative amounts of the active ingredient, the pharma
ceutically acceptable excipient, and / or any additional ingre
years , 17 years , 18 years , 19 years , 20 years , 25 years, 30 5 dients in a pharmaceutical composition in accordance with
years, 35 years , 40 years , 45 years , 50 years , 55 years, 60 the disclosure will vary , depending upon the identity, size ,
years , 65 years , 70 years , 75 years , 80 years , 85 years, 90 and /or condition of the subject treated and further depending
years , 95 years or more than 99 years . In some embodi- upon the route by which the composition is to be adminis
ments, the time of administration between the initial admin tered. By way of example, the composition may comprise
istration of the prophylactic composition and the booster 10 between
0.1 % and 100%, e.g., between 0.5 and 50%,
may be , but is not limited to , 1 week, 2 weeks , 3 weeks , 1 between 1-30 % , between 5-80 % , at least 80% ( w / w ) active
ingredient.

month , 2 months, 3 months, 6 months or 1 year.

In some embodiments, respiratory virus RNA (e.g.
mRNA ) vaccines may be administered intramuscularly or 15
intradermally, similarly to the administration of inactivated
vaccines known in the art.
Respiratory virus RNA (e.g. mRNA ) vaccines may be
utilized in various settings depending on the prevalence of
the infection or the degree or level of unmetmedical need . 20
As a non - limiting example, the RNA (e.g. , mRNA ) vaccines
may be utilized to treat and / or prevent a variety of respiratory infections. RNA (e.g. , mRNA ) vaccines have superior
properties in that they produce much larger antibody titers
and produce responses early than commercially available 25
anti- viral agents / compositions.
Provided herein are pharmaceutical compositions including respiratory virus RNA (e.g. mRNA ) vaccines and RNA
( e.g. mRNA ) vaccine compositions and / or complexes
optionally in combination with one or more pharmaceuti- 30
cally acceptable excipients.
Respiratory virus RNA (e.g. mRNA ) vaccines may be
formulated or administered alone or in conjunction with one
or more other components. For instance, hMPV /PIV3/ RSV
RNA ( e.g. , mRNA ) vaccines ( vaccine compositions) may 35
comprise other components including, but not limited to ,

Respiratory virus RNA (e.g. mRNA ) vaccines can be

formulated using one or more excipients to : ( 1 ) increase
stability ; (2 ) increase cell transfection ; (3 ) permit the sus
tained or delayed release (e.g. , from a depot formulation );
(4 ) alter the biodistribution (e.g. , target to specific tissues or
cell types ); ( 5 ) increase the translation of encoded protein in
vivo ; and / or ( 6 ) alter the release profile of encoded protein
( antigen) in vivo . In addition to traditional excipients such as
any and all solvents, dispersion media , diluents, or other
liquid vehicles, dispersion or suspension aids , surface active
agents, isotonic agents, thickening or emulsifying agents ,
preservatives, excipients can include, without limitation ,
lipidoids , liposomes , lipid nanoparticles, polymers ,
lipoplexes, core -shell nanoparticles, peptides, proteins, cells
transfected with respiratory virus RNA (e.g. mRNA ) vac
cines ( e.g. , for transplantation into a subject ), hyaluronidase,
nanoparticle mimics and combinations thereof.
Stabilizing Elements
Naturally -occurring eukaryotic mRNA molecules have
been found to contain stabilizing elements, including, but
not limited to untranslated regions (UTR) at their 5 '- end
( 5'UTR) and / or at their 3 ' - end ( 3'UTR) , in addition to other
structural features, such as a 5 ' - cap structure or a 3 ' - poly (A)
tail . Both the 5'UTR and the 3'UTR are typically transcribed
adjuvants.
from the genomic DNA and are elements of the premature
In some embodiments, respiratory virus (e.g. mRNA ) mRNA . Characteristic structural features of mature mRNA ,
vaccines do not include an adjuvant ( they are adjuvant free ). such as the 5 ' - cap and the 3 '-poly ( A ) tail are usually added
Respiratory virus RNA (e.g. mRNA ) vaccines may be 40 to the transcribed ( premature ) mRNA during mRNA pro

formulated or administered in combination with one or more
pharmaceutically -acceptable excipients. In some embodi-

ments, vaccine compositions comprise at least one additional active substances , such as , for example, a therapeutically - active substance , a prophylactically -active substance ,
or a combination of both . Vaccine compositions may be
sterile, pyrogen - free or both sterile and pyrogen - free. General considerations in the formulation and / or manufacture of
pharmaceutical agents, such as vaccine compositions , may
be found, for example , in Remington : The Science and
Practice of Pharmacy 21st ed . , Lippincott Williams &
Wilkins, 2005 ( incorporated herein by reference in its
entirety ).
In some embodiments, respiratory virus RNA (e.g.
mRNA ) vaccines are administered to humans, human
patients or subjects. For the purposes of the present disclosure , the phrase “ active ingredient “ generally refers to the
RNA (e.g. , mRNA ) vaccines or the polynucleotides contained therein , for example, RNA polynucleotides ( e.g. ,
mRNA polynucleotides) encoding antigenic polypeptides.
Formulations of the respiratory virus vaccine composi-

cessing. The 3 '-poly ( A ) tail is typically a stretch of adenine
nucleotides added to the 3 ' - end of the transcribed mRNA . It

45

50

55

60

can comprise up to about 400 adenine nucleotides . In some
embodiments the length of the 3 '-poly ( A ) tail may be an
essential element with respect to the stability of the indi
vidual mRNA .
In some embodiments the RNA ( e.g. , mRNA ) vaccine
may include one or more stabilizing elements. Stabilizing
elements may include for instance a histone stem - loop. A
stem - loop binding protein ( SLBP) , a 32 kDa protein has
been identified . It is associated with the histone stem - loop at
the 3 ' - end of the histone messages in both the nucleus and
the cytoplasm . Its expression level is regulated by the cell
cycle ; it peaks during the S -phase , when histone mRNA
levels are also elevated . The protein has been shown to be
essential for efficient 3 ' - end processing of histone pre
mRNA by the U7 snRNP. SLBP continues to be associated
with the stem - loop after processing , and then stimulates the
translation of mature histone mRNAs into histone proteins
in the cytoplasm . The RNA binding domain of SLBP is
conserved through metazoa and protozoa ; its binding to the

tions described herein may be prepared by any method histone stem - loop depends on the structure of the loop . The
known or hereafter developed in the art of pharmacology. In minimum binding site includes at least three nucleotides 54
general, such preparatory methods include the step of bring- and two nucleotides 3 ' relative to the stem - loop .
ing the active ingredient ( e.g. , mRNA polynucleotide) into 65 In some embodiments, the RNA (e.g. , mRNA ) vaccines
association with an excipient and / or one or more other include a coding region, at least one histone stem - loop , and
accessory ingredients, and then , if necessary and /or desir- optionally, a poly ( A ) sequence or polyadenylation signal .

US 10,933,127 B2
71

The poly ( A ) sequence or polyadenylation signal generally
should enhance the expression level of the encoded protein .
The encoded protein, in some embodiments, is not a histone
protein , a reporter protein ( e.g. Luciferase, GFP, EGFP,
B - Galactosidase , EGFP ) , or a marker or selection protein
( e.g. alpha -Globin, Galactokinase and Xanthine :guanine
phosphoribosyl transferase (GPT ) ) .
In some embodiments, the combination of a poly (A)
sequence or polyadenylation signal and at least one histone
stem - loop , even though both represent alternative mechanisms in nature , acts synergistically to increase the protein
expression beyond the level observed with either of the
individual elements . It has been found that the synergistic
effect of the combination of poly ( A ) and at least one histone
stem - loop does not depend on the order of the elements or
the length of the poly( A ) sequence .
In some embodiments, the RNA ( e.g. , mRNA ) vaccine
does not comprise a histone downstream element ( HDE) .
“ Histone downstream element” ( HDE) includes a purinerich polynucleotide stretch of approximately 15 to 20
nucleotides 3 ' of naturally occurring stem - loops , representing the binding site for the U7 snRNA , which is involved in
processing of histone pre -mRNA into mature histone
mRNA . Ideally , the inventive nucleic acid does not include
an intron.
In some embodiments, the RNA ( e.g. , mRNA ) vaccine

may or may not contain a enhancer and / or promoter
sequence , which may be modified or unmodified or which
may be activated or inactivated . In some embodiments, the
histone stem - loop is generally derived from histone genes ,
and includes an intramolecular base pairing of two neighbored partially or entirely reverse complementary sequences
separated by a spacer, including ( e.g. , consisting of) a short
sequence, which forms the loop of the structure. The
unpaired loop region is typically unable to base pair with
either of the stem loop elements . It occurs more often in
RNA , as is a key component of many RNA secondary
structures, but may be present in single -stranded DNA as
well . Stability of the stem - loop structure generally depends
on the length , number of mismatches or bulges , and base
composition of the paired region . In some embodiments,
wobble base pairing ( non - Watson -Crick base pairing) may
result . In some embodiments, the at least one histone stemloop sequence comprises a length of 15 to 45 nucleotides.
In other embodiments the RNA (e.g. , mRNA ) vaccine
may have one or more AU - rich sequences removed . These
sequences , sometimes referred to as AURES are destabilizing sequences found in the 3'UTR . The AURES may be
removed from the RNA (e.g. , mRNA ) vaccines . Alterna-

72

ponent, the degree of cationic lipid saturation, the nature of
the PEGylation , ratio of all components and biophysical
parameters such as size . In one example by Semple et al .
(Nature Biotech . 2010 28 : 172-176 ) , the lipid nanoparticle
5 formulation is composed of 57.1 % cationic lipid, 7.1 %
dipalmitoylphosphatidylcholine, 34.3 % cholesterol, and
1.4 % PEG - C - DMA. As another example, changing the com
position of the cationic lipid can more effectively deliver
siRNA to various antigen presenting cells (Basha et al . Mol
10 Ther . 2011 19 : 2186-2200 ) .
In some embodiments, lipid nanoparticle formulations
may comprise 35 to 45 % cationic lipid , 40 % to 50 % cationic
lipid , 50 % to 60 % cationic lipid and / or 55 % to 65 % cationic
lipid . In some embodiments , the ratio of lipid to RNA ( e.g. ,

15 mRNA ) in lipid nanoparticles may be 5 : 1 to 20 : 1 , 10 : 1 to
25 : 1 , 15 : 1 to 30 : 1 and /or at least 30 : 1 .

20
25

30

35

40

45

In some embodiments, the ratio of PEG in the lipid
nanoparticle formulations may be increased or decreased
and / or the carbon chain length of the PEG lipid may be
modified from C14 to C18 to alter the pharmacokinetics
and / or biodistribution of the lipid nanoparticle formulations .
As a non- limiting example, lipid nanoparticle formulations
may contain 0.5 % to 3.0 % , 1.0 % to 3.5 % , 1.5 % to 4.0% ,
2.0 % to 4.5 % , 2.5 % to 5.0 % and / or 3.0 % to 6.0% of the lipid
molar ratio of PEG - C -DOMG (R -3 -[(0 -methoxy -poly (eth
yleneglycol) 2000 )carbamoyl) ]- 1,2- dimyristyloxypropyl- 3
amine) ( also referred to herein as PEG - DOMG) as compared
to the cationic lipid, DSPC and cholesterol. In some embodi
ments, the PEG - c - DOMG may be replaced with a PEG lipid
such as , but not limited to , PEG - DSG ( 1,2 -Distearoyl-sn
glycerol, methoxypolyethylene glycol ), PEG - DMG (1,2
Dimyristoyl -sn - glycerol) and / or PEG - DPG ( 1,2 -Dipalmi
toyl-sn - glycerol, methoxypolyethylene glycol ) . The cationic
lipid may be selected from any lipid known in the art such
as , but not limited to , DLin -MC3 - DMA, DLin -DMA, C12
200 and DLin -KC2 - DMA .
In some embodiments, an respiratory virus RNA (e.g.
mRNA ) vaccine formulation is a nanoparticle that comprises
at least one lipid . The lipid may be selected from , but is not
limited to , DLin -DMA , DLin - K - DMA , 98N12-5 , C12-200 ,
DLin -MC3 -DMA , DLin -KC2 -DMA, DODMA , PLGA ,
PEG , PEG - DMG , PEGylated lipids and amino alcohol lip
ids . In some embodiments, the lipid may be a cationic lipid
such as , but not limited to , DLin -DMA, DLin - D -DMA ,
DLin -MC3 -DMA , DLin -KC2- DMA, DODMA and amino
alcohol lipids . The amino alcohol cationic lipid may be the
lipids described in and / or made by the methods described in
porated by reference in its entirety. As a non -limiting

U.S. Patent Publication No. US20130150625 , herein incor

tively the AURES may remain in the RNA ( e.g. , mRNA ) 50 example , the cationic lipid may be 2 -amino -3 -[(97,12Z )
vaccine .
octadeca -9,12 -dien - 1-yloxy )-2- {[(97,2Z )-octadeca- 9,12
dien - 1 -yloxy]methyl } propan - 1- ol ( Compound 1 in
Nanoparticle Formulations
In some embodiments , respiratory virus RNA (e.g. US20130150625 ) ; 2 - amino -3 -[( 9Z ) -octadec - 9- en -1 -yloxy]
mRNA ) vaccines are formulated in a nanoparticle. In some 2 - { [ (9Z ) -octadec -9 - en - 1 -yloxy ]methyl}propan - 1 -ol (Com
embodiments, respiratory virus RNA ( e.g. mRNA ) vaccines 55 pound 2 in US20130150625 ) ; 2-amino -3 -[( 9Z , 12Z )-octa
are formulated in a lipid nanoparticle . In some embodi- deca -9,12 -dien - 1 -yloxy ] -2 - [ (octyloxy )methyl]propan - 1 - ol
ments, respiratory virus RNA (e.g. mRNA ) vaccines are ( Compound 3 in US20130150625 ) ; and 2-(dimethylamino)
formulated in a lipid -polycation complex , referred to as a 3 -[( 92,12Z) -octadeca -9,12 -dien -1 -yloxy )-2 - { [(97,12Z )-oc

cationic lipid nanoparticle. As a non- limiting example, the tadeca- 9,12 -dien - 1 - yloxy ]methyl }propan - 1 -ol ( Compound
polycation may include a cationic peptide or a polypeptide 60 4 in US20130150625 ) ; or any pharmaceutically acceptable
such as , but not limited to , polylysine, polyornithine and / or salt or stereoisomer thereof.
polyarginine. In some embodiments, respiratory virus RNA
Lipid nanoparticle formulations typically comprise a

( e.g. , mRNA ) vaccines are formulated in a lipid nanoparticle lipid , in particular, an ionizable cationic lipid, for example,
that includes a non - cationic lipid such as , but not limited to , 2,2 - dilinoleyl -4 -dimethylaminoethyl- ( 1,3 ) -dioxolane
cholesterol or dioleoyl phosphatidylethanolamine (DOPE ). 65 (DLin -KC2 -DMA ), dilinoleyl-methyl-4-dimethylaminobu
A lipid nanoparticle formulation may be influenced by, tyrate (DLin -MC3 -DMA ), or di( ( Z ) -non - 2 - en - 1 -yl) 9-( 4
but not limited to , the selection of the cationic lipid com- ( dimethylamino )butanoyl )oxy )heptadecanedioate (L319 ) ,

US 10,933,127 B2
73

74

and further comprise a neutral lipid , a sterol and a molecule 5-10 % of the neutral lipid , 25-40 % of the sterol, and
capable of reducing particle aggregation , for example a PEG 0.5-10 % of the PEG or PEG -modified lipid on a molar basis .
or PEG -modified lipid .
In some embodiments, lipid nanoparticle formulations
In some embodiments, a lipid nanoparticle formulation include 60 % of a cationic lipid selected from 2,2 -dilinoleyl
consists essentially of ( i ) at least one lipid selected from the 5 4 -dimethylaminoethyl- [ 1,3 ] -dioxolane (DLin -KC2 -DMA ),
group consisting of 2,2 -dilinoleyl- 4 -dimethylaminoethyl- [ 1, dilinoleyl-methyl- 4 -dimethylaminobutyrate (DLin -MC3
3 ] -dioxolane (DLin -KC2 -DMA ), dilinoleyl-methyl-4 -dim- DMA ), and di( ( Z )-non - 2 - en - 1 - yl) 9- (4- (dimethylamino )bu
ethylaminobutyrate ( DLin -MC3- DMA ), and di((Z ) -non -2- tanoyl)oxy )heptadecanedioate (L319 ) , 7.5 % of the neutral
en - 1 - yl)
9- (4- (dimethylamino )butanoyl )oxy ) lipid , 31 % of the sterol, and 1.5 % of the PEG or PEG
heptadecanedioate (L319 ) ; ( ii ) a neutral lipid selected from 10 modified lipid on a molar basis .
DSPC , DPPC , POPC , DOPE and SM ; ( iii ) a sterol, e.g. ,
In some embodiments, lipid nanoparticle formulations
cholesterol; and ( iv ) a PEG - lipid , e.g. , PEG - DMG or PEG- include 50 % of a cationic lipid selected from 2,2 -dilinoleyl
CDMA , in a molar ratio of 20-60 % cationic lipid : 5-25 % 4 -dimethylaminoethyl- [1,3 ]-dioxolane ( DLin -KC2 -DMA ),
dilinoleyl-methyl - 4 -dimethylaminobutyrate (DLin -MC3
neutral lipid : 25-55 % sterol; 0.5-15 % PEG - lipid .
In some embodiments, a lipid nanoparticle formulation 15 DMA ), and di ( (Z ) -non- 2 - en- 1 - yl ) 9-((4-( dimethylamino )bu
includes 25 % to 75 % on a molar basis of a cationic lipid tanoyl)oxy )heptadecanedioate ( L319 ) , 10 % of the neutral
selected from 2,2 -dilinoleyl - 4-dimethylaminoethyl- [ 1,3 ]-di- lipid , 38.5 % of the sterol, and 1.5 % of the PEG or PEG
oxolane (DLin -KC2 -DMA ), dilinoleyl-methyl- 4 - dimethyl- modified lipid on a molar basis .

aminobutyrate ( DLin -MC3 -DMA ), and di((Z )-non-2 -en -1In some embodiments, lipid nanoparticle formulations
yl ) 9- (4- ( dimethylamino )butanoyl )oxy )heptadecanedioate 20 include 50 % of a cationic lipid selected from 2,2 -dilinoleyl
( L319 ) , e.g. , 35 to 65 % , 45 to 65 % , 60% , 57.5 % , 50% or

4 -dimethylaminoethyl- [1,31-dioxolane (DLin -KC2 -DMA ),
dilinoleyl-methyl - 4 - dimethylaminobutyrate (DLin -MC3
In some embodiments, a lipid nanoparticle formulation DMA ), and di( ( Z ) -non - 2 - en - 1 -yl) 9- (4-(dimethylamino )bu
includes 0.5 % to 15 % on a molar basis of the neutral lipid , tanoyl )oxy )heptadecanedioate ( L319 ) , 10 % of the neutral
e.g. , 3 to 12 % , 5 to 10 % or 15 % , 10 % , or 7.5 % on a molar 25 lipid , 35 % of the sterol, 4.5 % or 5 % of the PEG or

40 % on a molar basis .

basis . Examples of neutral lipids include , without limitation ,

PEG -modified lipid, and 0.5 % of the targeting lipid on a

DSPC , POPC , DPPC , DOPE and SM . In some embodiments , the formulation includes 5 % to 50 % on a molar basis

molar basis .
In some embodiments, lipid nanoparticle formulations

PEG or PEG -modified lipid ( e.g. , 0.5 10 % , 0.5 % ,
1.5 % , 0.5 % , 1.5 % , 3.5 % , or 5 % on a molar basis . In some

tanoyl) oxy )heptadecanedioate ( L319 ) , 15 % of the neutral
lipid , 40 % of the sterol, and 5 % of the PEG or PEG -modified

of the sterol (e.g. , 15 to 45 % , 20 to 40 % , 40 % , 38.5 % , 35 % , include 40 % of a cationic lipid selected from 2,2 -dilinoleyl
or 31 % on a molar basis . A non- limiting example of a sterol 30 4 -dimethylaminoethyl- [ 1,3 ] -dioxolane ( DLin -KC2 -DMA ),
is cholesterol. In some embodiments, a lipid nanoparticle dilinoleyl -methyl - 4 - dimethylaminobutyrate (DLin -MC3
formulation includes 0.5 % to 20% on a molar basis of the DMA ), and di ( (Z ) -non- 2 - en- 1 - yl ) 9-((4-(dimethylamino )bu
embodiments, a PEG or PEG modified lipid comprises a
PEG molecule of an average molecular weight of 2,000 Da .
In some embodiments, a PEG or PEG modified lipid comprises a PEG molecule of an average molecular weight of
less than 2,000 , for example around 1,500 Da , around 1,000
Da , or around 500 Da . Non- limiting examples of PEGmodified lipids include PEG -distearoyl glycerol (PEGDMG) (also referred herein as PEG - C14 or C14 - PEG ) ,
PEG - CDMA ( further discussed in Reyes et al . J. Controlled
Release , 107 , 276-287 (2005 ) the contents of which are
herein incorporated by reference in their entirety ).
In some embodiments, lipid nanoparticle formulations
include 25-75 % of a cationic lipid selected from 2,2 -dilinoleyl-4 -dimethylaminoethyl- [1,3] -dioxolane (DLin -KC2DMA ), dilinoleyl-methyl- 4 -dimethylaminobutyrate (DLinMC3 -DMA) , and di ( ( Z ) -non - 2 - en - 1 -yl) 9 - ( (4( dimethylamino )butanoyl )oxy )heptadecanedioate ( L319 ) ,
0.5-15 % of the neutral lipid , 5-50 % of the sterol, and
0.5-20 % of the PEG or PEG -modified lipid on a molar basis .

35 lipid on a molar basis .
In some embodiments, lipid nanoparticle formulations
include 57.2 % of a cationic lipid selected from 2,2 - dilinol
eyl - 4 -dimethylaminoethyl- [ 1,3 ] -dioxolane (DLin -KC2
DMA ), dilinoleyl -methyl - 4 -dimethylaminobutyrate (DLin
40 MC3 - DMA) , and di ( ( Z ) -non - 2 - en - 1 - yl ) 9- (4
(dimethylamino )butanoyl) oxy )heptadecanedioate ( L319 ) ,
7.1 % of the neutral lipid, 34.3 % of the sterol, and 1.4 % of
the PEG or PEG -modified lipid on a molar basis .
In some embodiments, lipid nanoparticle formulations
45 include 57.5 % of a cationic lipid selected from the PEG lipid
is PEG -CDMA ( PEG - CDMA is further discussed in Reyes et
al . ( J. Controlled Release , 107 , 276-287 ( 2005 ) , the contents
of which are herein incorporated by reference in their
entirety ), 7.5 % of the neutral lipid , 31.5 % of the sterol, and
50 3.5 % of the PEG or PEG -modified lipid on a molar basis .
In some embodiments, lipid nanoparticle formulations
consists essentially of a lipid mixture in molar ratios of
20-70% cationic lipid : 5-45 % neutral lipid : 20-55 % choles
In some embodiments, lipid nanoparticle formulations terol: 0.5-15 % PEG modified
lipid . In some embodiments ,
include 35-65 % of a cationic lipid selected from 2,2 -dili- 55 lipid nanoparticle formulations consists essentially of a lipid
noleyl- 4 -dimethylaminoethyl- [ 1,3 ] -dioxolane (DLin -KC2- mixture in a molar ratio of 20-60% cationic lipid : 5-25 %

DMA ), dilinoleyl-methyl-4-dimethylaminobutyrate (DLin- neutral lipid : 25-55 % cholesterol: 0.5-15 % PEG -modified
and di( (Z ) -non - 2 - en - 1 -yl)
9- (4- lipid .
( dimethylamino )butanoyl )oxy )heptadecanedioate ( L319 ) ,
In some embodiments, the molar lipid ratio is 50/ 10/38.5 /
3-12 % of the neutral lipid , 15-45 % of the sterol, and 60 1.5 (mol % cationic lipid /neutral lipid , e.g. , DSPC/Chol /
0.5-10 % of the PEG or PEG -modified lipid on a molar basis . PEG -modified lipid , e.g. , PEG - DMG , PEG - DSG or PEG
In some embodiments, lipid nanoparticle formulations DPG) , 57.2 /7.1134.3 / 1.4 (mol % cationic lipid /neutral lipid ,
include 45-65 % of a cationic lipid selected from 2,2 -dili- e.g. , DPPC /Chol/ PEG -modified lipid , e.g. , PEG -CDMA ),
noleyl - 4 - dimethylaminoethyl- ( 1,3 ) -dioxolane (DLin -KC2- 40/15/40/5 (mol % cationic lipid /neutral lipid, e.g. , DSPC/
MC3 -DMA),

DMA ), dilinoleyl-methyl-4-dimethylaminobutyrate (DLin- 65 Chol/PEG -modified lipid , e.g., PEG-DMG ), 50 / 10 /35 / 4.5/

MC3 -DMA ), and di ( ( Z ) -non - 2 - en - 1 -yl) 9- (4( dimethylamino )butanoyl )oxy )heptadecanedioate ( L319 ) ,

0.5 (mol % cationic lipid /neutral lipid , e.g. , DSPC/Chol /
PEG -modified lipid, e.g. , PEG - DSG) , 50/10/35/5 ( cationic

US 10,933,127 B2
75

76

lipid /neutral lipid , e.g. , DSPC /Chol/PEG -modified lipid , dients in a vaccine composition may vary, depending upon
e.g. , PEG - DMG) , 40/10/40/10 (mol % cationic lipid /neutral the identity , size , and /or condition of the subject being
lipid , e.g. , DSPC /Chol/PEG modified
lipid, e.g. , PEG - DMG treated and further depending upon the route by which the
or PEG - CDMA) , 35/15/40/10 (mol % cationic lipid /neutral composition is to be administered . For example, the com
lipid , e.g. , DSPC /Chol / PEG -modified lipid, e.g. , PEG -DMG 5 position may comprise between 0.1 % and 99 % ( w / w ) of the
or PEG -CDMA ) or 52/13/30/5 (mol % cationic lipid /neutral active ingredient. By way of example, the composition may
lipid , e.g. , DSPC /Chol/PEG modified
lipid, e.g. , PEG - DMG comprise between 0.1 % and 100% , e.g. , between 0.5 and
or PEG - CDMA) .

50% , between 1-30 % , between 5-80% , at least 80 % ( w / w )
Non - limiting examples of lipid nanoparticle compositions active
ingredient.
and methods of making them are described , for example, in 10 In some embodiments, the respiratory virus RNA (e.g.
Semple et al . (2010) Nat. Biotechnol. 28 : 172-176 ; Jayarama
) vaccine composition may comprise the polynucle
et al . ( 2012 ) , Angew . Chem . Int. Ed., 51 : 8529-8533 ; and mRNA
otide
described
, formulated in a lipid nanoparticle
Maier et al . (2013 ) Molecular Therapy 21 , 1570-1578 ( the comprising MC3herein
,
Cholesterol
, DSPC and PEG2000 - DMG ,
contents of each of which are incorporated herein by refer the buffer trisodium citrate, sucrose
and water for injection .
15
ence in their entirety ).
As a non - limiting example , the composition comprises: 2.0
In
some
embodiments
,
lipid
nanoparticle
formulations
may comprise a cationic lipid , a PEG lipid and a structural mg/mL of drug substance ( e.g. , polynucleotides encoding
lipid and optionally comprise a non - cationic lipid . As a H1ONS HMPV) , 21.8 mg /mL of MC3 , 10.1 mg/mL of
non- limiting example, a lipid nanoparticle may comprise cholesterol, 5.4 mg/mL of DSPC , 2.7 mg/mL of PEG2000
40-60% of cationic lipid , 5-15 % of a non -cationic lipid, 20 DMG , 5.16 mg/mL of trisodium citrate , 71 mg/mL of
1-2 % of a PEG lipid and 30-50 % of a structural lipid . As sucrose and 1.0 mL of water for injection .
another non -limiting example, the lipid nanoparticle may
In some embodiments, a nanoparticle ( e.g. , a lipid nan
comprise 50 % cationic lipid , 10 % non - cationic lipid , 1.5 % oparticle) has a mean diameter of 10-500 nm , 20-400 nm ,
PEG lipid and 38.5 % structural lipid . As yet another non- 30-300 nm , 40-200 nm . In some embodiments, a nanopar

limiting example, a lipid nanoparticle may comprise 55 % 25 ticle ( e.g., a lipid nanoparticle ) has a mean diameter of
cationic lipid, 10 % non - cationic lipid, 2.5 % PEG lipid and

50-150 nm , 50-200 nm , 80-100 nm or 80-200 nm .

ceutically acceptable excipient, and / or any additional ingre-

ence in its entirety ) and liposomes which may deliver small

32.5 % structural lipid . In some embodiments , the cationic Liposomes , Lipoplexes, and Lipid Nanoparticles
lipid may be any cationic lipid described herein such as , but
The RNA ( e.g. , mRNA ) vaccines of the disclosure can be
not limited to , DLin -KC2 -DMA, DLin -MC3 -DMA and formulated using one or more liposomes , lipoplexes, or lipid
L319 .
30 nanoparticles. In some embodiments, pharmaceutical com
In some embodiments, the lipid nanoparticle formulations positions of RNA ( e.g. , mRNA ) vaccines include liposomes .
described herein may be 4 component lipid nanoparticles. Liposomes are artificially -prepared vesicles which may pri
The lipid nanoparticle may comprise a cationic lipid , a marily be composed of a lipid bilayer and may be used as a
non- cationic lipid , a PEG lipid and a structural lipid . As a delivery vehicle for the administration of nutrients and
non-limiting example, the lipid nanoparticle may comprise 35 pharmaceutical formulations. Liposomes can be of different
40-60% of cationic lipid , 5-15 % of a non - cationic lipid , sizes such as , but not limited to , a multilamellar vesicle
1-2 % of a PEG lipid and 30-50 % of a structural lipid . As (MLV ) which may be hundreds of nanometers in diameter
another non - limiting example , the lipid nanoparticle may and may contain a series of concentric bilayers separated by
comprise 50 % cationic lipid , 10 % non - cationic lipid , 1.5 % narrow aqueous compartments, a small unicellular vesicle
PEG lipid and 38.5 % structural lipid . As yet another non- 40 (SUV ) which may be smaller than 50 nm in diameter, and a
limiting example, the lipid nanoparticle may comprise 55 % large unilamellar vesicle ( LUV ) which may be between 50
cationic lipid, 10 % non - cationic lipid, 2.5 % PEG lipid and and 500 nm in diameter. Liposome design may include , but
32.5 % structural lipid . In some embodiments, the cationic is not limited to , opsonins or ligands in order to improve the
lipid may be any cationic lipid described herein such as , but attachment of liposomes to unhealthy tissue or to activate
not limited to , DLin -KC2 -DMA, DLin -MC3 -DMA and 45 events such as , but not limited to , endocytosis. Liposomes
L319 .
may contain a low or a high pH in order to improve the
In some embodiments, the lipid nanoparticle formulations delivery of the pharmaceutical formulations.
The formation of liposomes may depend on the physico
described herein may comprise a cationic lipid, a non
cationic lipid , a PEG lipid and a structural lipid . As a chemical characteristics such as , but not limited to , the
non- limiting example , the lipid nanoparticle comprise 50 % 50 pharmaceutical formulation entrapped and the liposomal
of the cationic lipid DLin - KC2 -DMA , 10 % of the non- ingredients, the nature of the medium in which the lipid
cationic lipid DSPC , 1.5 % of the PEG lipid PEG - DOMG vesicles are dispersed , the effective concentration of the
and 38.5 % of the structural lipid cholesterol. As a non- entrapped substance and its potential toxicity, any additional
limiting example, the lipid nanoparticle comprise 50 % of the processes involved during the application and / or delivery of
cationic lipid DLin -MC3- DMA, 10 % of the non - cationic 55 the vesicles , the optimization size , polydispersity and the
lipid DSPC , 1.5 % of the PEG lipid PEG - DOMG and 38.5 % shelf -life of the vesicles for the intended application , and the
of the structural lipid cholesterol. As a non- limiting batch - to -batch reproducibility and possibility of large - scale
example , the lipid nanoparticle comprise 50 % of the cationic production of safe and efficient liposomal products.
lipid DLin -MC3 -DMA, 10 % of the non - cationic lipid
In some embodiments, pharmaceutical compositions
DSPC , 1.5 % of the PEG lipid PEG - DMG and 38.5 % of the 60 described herein may include , without limitation , liposomes
structural lipid cholesterol. As yet another non - limiting such as those formed from 1,2 -dioleyloxy -N , N -dimethyl
example, the lipid nanoparticle comprise 55 % of the cationic aminopropane (DODMA ) liposomes , DiLa2 liposomes
lipid L319 , 10 % of the non - cationic lipid DSPC , 2.5 % of the from Marina Biotech (Bothell, Wash . ), 1,2 -dilinoleyloxy -3
PEG lipid PEG - DMG and 32.5 % of the structural lipid dimethylaminopropane (DLin -DMA ), 2,2- dilinoleyl -4-(2
65 dimethylaminoethyl) - [ 1,3 ] -dioxolane ( DLin -KC2 -DMA ),
cholesterol.
Relative amounts of the active ingredient, the pharma- and MC3 (US20100324120 ; herein incorporated by refer

US 10,933,127 B2
78
tion may include a cationic peptide or a polypeptide such as ,
but not limited to , polylysine , polyornithine and / or polyargi
nine . In some embodiments, the RNA ( e.g. , mRNA ) vac

77

molecule drugs such as , but not limited to , DOXIL® from
Janssen Biotech, Inc. (Horsham , Pa . ) .
In some embodiments, pharmaceutical compositions
described herein may include , without limitation , liposomes cines may be formulated in a lipid -polycation complex ,
such as those formed from the synthesis of stabilized plas- 5 which may further include a non - cationic lipid such as , but
mid- lipid particles ( SPLP ) or stabilized nucleic acid lipid not limited to , cholesterol or dioleoyl phosphatidyletha
particle ( SNALP ) that have been previously described and nolamine (DOPE ).
shown to be suitable for oligonucleotide delivery in vitro
In some embodiments, the ratio of PEG in the lipid
and in vivo ( see Wheeler et al . Gene Therapy. 1999 6 : 271 nanoparticle
) formulations may be increased or
281 ; Zhang et al . Gene Therapy. 1999 6 : 1438-1447 ; Jeffs et 10 decreased and(/LNP
or
the
chain length of the PEG lipid
al . Pharm Res . 2005 22 : 362-372 ; Morrissey et al . , Nat may be modified fromcarbon
C14
to
C18 to alter the pharmaco
Biotechnol. 2005 2 : 1002-1007 ; Zimmermann et al . , Nature .
kinetics
and
/
or
biodistribution
of
the LNP formulations. As
2006 441 : 111-114 ; Heyes et al . J Contr Rel . 2005 107 :276 a non- limiting example, LNP formulations
may contain
287 ; Semple et al . Nature Biotech . 2010 28 : 172-176 ; Judge

et al . J Clin Invest. 2009 119 : 661-673 ; de Fougerolles Hum 15 from
about 0.5% to about 3.0%, from about 1.0% to about
3.5 % , from about 1.5 % to about 4.0 % , from about 2.0% to
Gene Ther. 2008 19 : 125-132 ; U.S. Patent Publication No

US20130122104 ; all of which are incorporated herein in about 4.5 % , from about 2.5 % to about 5.0% and / or from
their entireties ). The original manufacture method by about 3.0% to about 6.0 % of the lipid molar ratio of
Wheeler et al . was a detergent dialysis method, which was PEG - C - DOMG ( R - 3 - [( 0 -methoxy -polyethyleneglycol)
later improved by Jeffs et al . and is referred to as the 20 2000 ) carbamoyl ) ]- 1,2 - dimyristyloxypropyl - 3 -amine) ( also
spontaneous vesicle formation method . The liposome for- referred to herein as PEG - DOMG) as compared to the
mulations are composed of 3 to 4 lipid components in cationic lipid , DSPC and cholesterol. In some embodiments ,
addition to the polynucleotide. As an example a liposome the PEG - C - DOMG may be replaced with a PEG lipid such
can contain , but is not limited to , 55 % cholesterol, 20 % as , but not limited to , PEG - DSG (1,2-Distearoyl-sn -glyc
disteroylphosphatidyl choline ( DSPC ) , 10 % PEG - S - DSG , 25 erol, methoxypolyethylene glycol ) , PEG - DMG ( 1,2
and 15 % 1,2 -dioleyloxy - N , N -dimethylaminopropane
(DODMA ), as described by Jeffs et al . As another example,
certain liposome formulations may contain , but are not
limited to , 48 % cholesterol, 20 % DSPC , 2 % PEG - C -DMA,
and 30 % cationic lipid , where the cationic lipid can be 30
1,2 -distearloxy -N ,N -dimethylaminopropane ( DSDMA ) ,

DODMA , DLin -DMA , or 1,2 -dilinolenyloxy -3-dimethyl-

aminopropane (DLenDMA ), as described by Heyes et al .
In some embodiments , liposome formulations may com-

Dimyristoyl -sn - glycerol) and / or PEG - DPG ( 1,2 -Dipalmi
toyl - sn - glycerol, methoxypolyethylene glycol ) . The cationic
lipid may be selected from any lipid known in the art such
as , but not limited to , DLin -MC3 - DMA, DLin - DMA, C12
200 and DLin -KC2 - DMA .
In some embodiments, the RNA (e.g. , mRNA ) vaccines
may be formulated in a lipid nanoparticle .
In some embodiments, the RNA ( e.g. , mRNA ) vaccine

formulation comprising the polynucleotide is a nanoparticle

prise from about 25.0 % cholesterol to about 40.0 % choles- 35 which may comprise at least one lipid . The lipid may be
terol , from about 30.0 % cholesterol to about 45.0% cholesterol , from about 35.0 % cholesterol to about 50.0 %
cholesterol and / or from about 48.5 % cholesterol to about

selected from , but is not limited to , DLin - DMA , DLin - K
DMA, 98N12-5 , C12-200 , DLin -MC3 -DMA, DLin -KC2
DMA, DODMA , PLGA, PEG , PEG - DMG , PEGylated lip

60 % cholesterol. In some embodiments, formulations may

ids and amino alcohol lipids . In another aspect , the lipid may

consisting of 28.5 % , 31.5 % , 33.5 % , 36.5 % , 37.0% , 38.5 % ,
39.0 % and 43.5 % . In some embodiments , formulations may

DLin - D -DMA, DLin- MC3 - DMA , DLin - KC2 - DMA ,
DODMA and amino alcohol lipids . The amino alcohol

comprise a percentage of cholesterol selected from the group 40 be a cationic lipid such as , but not limited to , DLin - DMA ,
comprise from about 5.0% to about 10.0 % DSPC and / or
from about 7.0 % to about 15.0 % DSPC .
In some embodiments, the RNA ( e.g. , mRNA ) vaccine
pharmaceutical compositions may be formulated in liposomes such as , but not limited to , DiLa2 liposomes (Marina
Biotech, Bothell, Wash . ), SMARTICLES® (Marina Biotech, Bothell, Wash . ), neutral DOPC (1,2 -dioleoyl-sn -glycero - 3 -phosphocholine) based liposomes ( e.g. , siRNA delivery for ovarian cancer (Landen et al . Cancer Biology &
Therapy 2006 5 ( 12 ) 1708-1713 ) ; herein incorporated by reference in its entirety ) and hyaluronan -coated liposomes
( Quiet Therapeutics , Israel ).
In some embodiments , the cationic lipid may be a low
molecular weight cationic lipid such as those described in
U.S. Patent Application No. 20130090372 , the contents of
which are herein incorporated by reference in their entirety.
In some embodiments, the RNA (e.g. , mRNA ) vaccines
may be formulated in a lipid vesicle , which may have
crosslinks between functionalized lipid bilayers .
In some embodiments, the RNA (e.g. , mRNA ) vaccines
may be formulated in a lipid -polycation complex . The
formation of the lipid- polycation complex may be accomplished by methods known in the art and / or as described in
U.S. Pub . No. 20120178702 , herein incorporated by reference in its entirety. As a non -limiting example, the polyca-

cationic lipid may be the lipids described in and / or made by
US20130150625 , herein incorporated by reference in its
entirety. As a non - limiting example, the cationic lipid may
be 2 -amino - 3 - [ (97,12Z ) -octadeca - 9,12 - dien - 1 -yloxy )-2-{
[ (9Z ,2Z ) -octadeca- 9,12 -dien - 1 - yloxy ]methyl }propan - 1 - ol
( Compound 1 in US20130150625 ); 2 -amino - 3 -[(9Z) -octa
dec -9 - en - 1 -yloxy ] -2 - {[(9Z )-octadec - 9 - en - 1 -yloxy]
methyl } propan - 1 -ol (Compound 2 in US20130150625 ) ;
2 -amino - 3 -[ (97,12Z ) -octadeca -9,12 - dien -1 -yloxyl-2 -[(oc
tyloxy )methyl ]propan - 1 -ol
( Compound
3
in
US20130150625 ) ; and 2-(dimethylamino )-3 -[( 92,12Z )-oc
tadeca - 9,12-dien - 1 -yloxy ]-2 - {[ (9Z ,12Z )-octadeca- 9,12
dien - 1 -yloxy ]methyl } propan - 1-ol (Compound 4 in
US20130150625 ) ; or any pharmaceutically acceptable salt
or stereoisomer thereof.
Lipid nanoparticle formulations typically comprise a
lipid , in particular, an ionizable cationic lipid, for example,
2,2 -dilinoleyl-4 -dimethylaminoethyl- [ 1,3 ] -dioxolane
(DLin -KC2 -DMA ), dilinoleyl-methyl-4 -dimethylaminobu
tyrate (DLin -MC3 -DMA ), or di ( (Z ) -non- 2 - en- 1 - yl ) 9 -((4
( dimethylamino )butanoyl )oxy )heptadecanedioate ( L319 ) ,
and further comprise a neutral lipid , a sterol and a molecule
capable of reducing particle aggregation , for example a PEG
or PEG -modified lipid .
the methods described in U.S. Patent Publication No.

45

50

55

60

65

US 10,933,127 B2
79

80

In some embodiments, the lipid nanoparticle formulation ( dimethylamino )butanoyl )oxy )heptadecanedioate ( L319 ) ,
consists essentially of ( i ) at least one lipid selected from the 5-10 % of the neutral lipid , 25-40 % of the sterol, and
group consisting of 2,2 -dilinoleyl - 4 -dimethylaminoethyl- [ 1, 0.5-10 % of the PEG or PEG -modified lipid on a molar basis .
3 ]-dioxolane (DLin -KC2 -DMA ), dilinoleyl-methyl- 4 - dimIn some embodiments, the formulations of the present
ethylaminobutyrate (DLin -MC3 -DMA ), and di ( ( Z ) -non -2- 5 disclosure include about 60 % of a cationic lipid selected
en- 1 -yl )
9 - ( (4-(dimethylamino )butanoyl) oxy ) from 2,2 - dilinoleyl -4 -dimethylaminoethyl- [ 1,3 ] -dioxolane
heptadecanedioate (L319 ) ; ( ii ) a neutral lipid selected from ( DLin -KC2 -DMA ), dilinoleyl-methyl-4 - dimethylaminobu
DSPC , DPPC , POPC , DOPE and SM ; ( iii ) a sterol, e.g. , tyrate (DLin -MC3 -DMA ), and di ( ( Z ) -non - 2 - en - 1 - yl) 9-( 4
cholesterol; and ( iv ) a PEG - lipid , e.g. , PEG - DMG or PEG- (dimethylamino )butanoyl)oxy )heptadecanedioate ( L319 ) ,
CDMA , in a molar ratio of about 20-60% cationic lipid : 5- 10 about 7.5 % of the neutral lipid, about 31 % of the sterol, and
25 % neutral lipid : 25-55 % sterol; 0.5-15 % PEG - lipid .
about 1.5 % of the PEG or PEG -modified lipid on a molar
In some embodiments, the formulation includes from
basis .
about 25 % to about 75 % on a molar basis of a cationic lipid
In some embodiments , the formulations of the present
selected from 2,2 -dilinoleyl- 4 - dimethylaminoethyl-[ 1,3 ] -di- disclosure include about 50 % of a cationic lipid selected
oxolane (DLin -KC2 -DMA ), dilinoleyl-methyl - 4 - dimethyl- 15 from 2,2 - dilinoleyl- 4 -dimethylaminoethyl- [1,3 ] -dioxolane
aminobutyrate (DLin -MC3 - DMA ), and di((Z )-non -2 -en -1- (DLin -KC2 -DMA ), dilinoleyl-methyl-4 -dimethylaminobu
yl ) 9 - ( [4- (dimethylamino )butanoyl)oxy )heptadecanedioate tyrate (DLin -MC3 -DMA ), and di ( ( Z ) -non - 2 - en - 1 -yl) 9- (4
( L319 ) , e.g. , from about 35 to about 65 % , from about 45 to ( dimethylamino )butanoyl)oxy )heptadecanedioate ( L319 ) ,
about 65 % , about 60 % , about 57.5 % , about 50 % or about about 10 % of the neutral lipid, about 38.5 % of the sterol, and
40 % on a molar basis .
20 about 1.5 % of the PEG or PEG -modified lipid on a molar
In some embodiments, the formulation includes from
basis .
about 0.5 % to about 15 % on a molar basis of the neutral lipid
In some embodiments, the formulations of the present
e.g. , from about 3 to about 12 % , from about 5 to about 10 % disclosure include about 50 % of a cationic lipid selected
or about 15 % , about 10 % , or about 7.5 % on a molar basis . from 2,2 -dilinoleyl - 4 - dimethylaminoethyl- [ 1,3 ] -dioxolane
Examples of neutral lipids include, but are not limited to , 25 (DLin - KC2 -DMA ), dilinoleyl-methyl-4 -dimethylaminobu
DSPC , POPC , DPPC , DOPE and SM . In some embodi- tyrate ( DLin -MC3 - DMA ), and di( ( Z )-non - 2 - en - 1 - yl) 9- (4
ments, the formulation includes from about 5 % to about ( dimethylamino )butanoyl )oxy )heptadecanedioate (L319) ,
50 % on a molar basis of the sterol ( e.g. , about 15 to about about 10 % of the neutral lipid , about 35 % of the sterol, about
45 % , about 20 to about 40% , about 40 % , about 38.5 % , about 4.5 % or about 5 % of the PEG or PEG -modified lipid , and
35 % , or about 31 % on a molar basis . An exemplary sterol is 30 about 0.5 % of the targeting lipid on a molar basis .
cholesterol. In some embodiments , the formulation includes
In some embodiments, the formulations of the present
from about 0.5 % to about 20% on a molar basis of the PEG

disclosure include about 40 % of a cationic lipid selected

or PEG -modified lipid ( e.g. , about 0.5 about 10 % , about from 2,2 - dilinoleyl - 4 - dimethylaminoethyl- [ 1,3 ] -dioxolane
0.5 to about 5 % , about 1.5 % , about 0.5 % , about 1.5 % , about (DLin -KC2 -DMA ), dilinoleyl-methyl-4 -dimethylaminobu
3.5 % , or about 5 % on a molar basis . In some embodiments, 35 tyrate (DLin- MC3 - DMA) , and di ( ( Z ) -non - 2 - en - 1 -yl) 9 -((4
the PEG or PEG modified lipid comprises a PEG molecule ( dimethylamino )butanoyl)oxy )heptadecanedioate ( L319 ) ,
of an average molecular weight of 2,000 Da . In other about 15 % of the neutral lipid, about 40 % of the sterol, and
embodiments, the PEG or PEG modified lipid comprises a about 5 % of the PEG or PEG -modified lipid on a molar
PEG molecule of an average molecular weight of less than basis .
2,000 , for example around 1,500 Da , around 1,000 Da , or 40 In some embodiments , the formulations of the present

around 500 Da . Examples of PEG -modified lipids include, disclosure include about 57.2 % of a cationic lipid selected
but are not limited to , PEG -distearoyl glycerol (PEG - DMG) from 2,2 - dilinoleyl- 4 -dimethylaminoethyl- [ 1,3 ] -dioxolane
( also referred herein as PEG - C14 or C14 - PEG) , PEG- (DLin -KC2 -DMA ), dilinoleyl-methyl-4 - dimethylaminobu
cDMA ( further discussed in Reyes et al . J. Controlled tyrate (DLin- MC3 - DMA) , and di ( ( Z ) -non - 2 - en - 1 -yl) 9 -((4
Release, 107 , 276-287 (2005 ) the contents of which are 45 ( dimethylamino )butanoyl)oxy )heptadecanedioate (L319 ),
herein incorporated by reference in their entirety )
about 7.1 % of the neutral lipid , about 34.3 % of the sterol,
In some embodiments, the formulations of the present and about 1.4 % of the PEG or PEG -modified lipid on a
disclosure include 25-75 % of a cationic lipid selected from molar basis .
2,2 -dilinoleyl - 4 -dimethylaminoethyl- [ 1,3 ) -dioxolane
In some embodiments, the formulations of the present

( DLin -KC2-DMA ), dilinoleyl-methyl- 4 -dimethylaminobu- 50 disclosure include about 57.5 % of a cationic lipid selected

tyrate ( DLin - MC3 - DMA) , and di ( ( Z ) -non - 2 -en - 1 -yl) 9 -((4- from the PEG lipid is PEG - CDMA (PEG -CDMA is further
( dimethylamino )butanoyl )oxylheptadecanedioate ( L319 ) , discussed in Reyes et al . (J. Controlled Release , 107 , 276
0.5-15 % of the neutral lipid , 5-50 % of the sterol, and 287 ( 2005 ) , the contents of which are herein incorporated by
0.5-20 % of the PEG or PEG -modified lipid on a molar basis . reference in their entirety ), about 7.5 % of the neutral lipid ,
In some embodiments, the formulations of the present 55 about 31.5 % of the sterol, and about 3.5 % of the PEG or
disclosure include 35-65 % of a cationic lipid selected from PEG -modified lipid on a molar basis .
2,2 - dilinoleyl -4 -dimethylaminoethyl- [ 1,3 ] -dioxolane
In some embodiments, lipid nanoparticle formulation
( DLin -KC2 -DMA ), dilinoleyl-methyl- 4 - dimethylaminobu- consists essentially of a lipid mixture in molar ratios of about
tyrate ( DLin - MC3 - DMA) , and di ( ( Z ) -non - 2 -en - 1 -yl) 9 -((4- 20-70% cationic lipid : 5-45 % neutral lipid : 20-55 % choles
( dimethylamino )butanoyl )oxy )heptadecanedioate ( L319 ) , 60 terol: 0.5-15 % PEG -modified lipid ; more preferably in a
3-12 % of the neutral lipid , 15-45 % of the sterol, and molar ratio of about 20-60% cationic lipid : 5-25 % neutral
0.5-10 % of the PEG or PEG -modified lipid on a molar basis . lipid : 25-55 % cholesterol: 0.5-15 % PEG -modified lipid .
In some embodiments, the formulations of the present
In some embodiments, the molar lipid ratio is approxi
disclosure include 45-65 % of a cationic lipid selected from mately 50 / 10 / 38.5 / 1.5 (mol % cationic lipid /neutral lipid ,
2,2 -dilinoleyl - 4 -dimethylaminoethyl- [ 1,3 ) -dioxolane
65 e.g. , DSPC /Chol/PEG -modified lipid, e.g. , PEG - DMG ,
(DLin -KC2 -DMA ), dilinoleyl-methyl-4 -dimethylaminobu- PEG - DSG or PEG - DPG) , 57.2/ 7.1134.3 / 1.4 (mol % cationic
tyrate ( DLin - MC3 - DMA) , and di? ( Z ) -non - 2 - en - 1 -yl) 9 -( (4- lipid /neutral lipid , e.g. , DPPC /Chol/ PEG -modified lipid ,

US 10,933,127 B2
82

81

e.g. , PEG - CDMA) , 40/15/40/5 (mol % cationic lipid /neutral the structural lipid cholesterol. As yet another non- limiting
example , the lipid nanoparticle comprise about 55 % of the
DMG) , 50/ 10/35 / 4.5 /0.5 (mol % cationic lipid /neutral lipid , cationic lipid L319 , about 10 % of the non- cationic lipid
e.g. , DSPC /Chol /PEG -modified lipid , e.g. , PEG - DSG) , DSPC , about 2.5 % of the PEG lipid PEG - DMG and about
50/10/35/5 (cationic lipid /neutral lipid , e.g. , DSPC/Chol / 5 32.5 % of the structural lipid cholesterol.
PEG -modified lipid , e.g. , PEG - DMG) , 40/10/40/10 (mol %
As a non- limiting example, the cationic lipid may be
cationic lipid /neutral lipid, e.g. , DSPC /Chol/PEG -modified selected from (202,23Z ) N ,N -dimethylnonacosa- 20,23
lipid , e.g. , PEG - DMG or PEG - CDMA ), 35/15/40/10 (mol % dien - 10 - amine, (172,202 )—N ,N - dimemylhexacosa- 17,20
cationic lipid /neutral lipid , e.g. , DSPC /Chol /PEG -modified dien- 9 -amine,
(17,19Z )-N5N -dimethylpentacosa - 16 ,
lipid , e.g. , PEG - DMG or PEG -CDMA ) or 52/13/30/5 (mol % 10 19 - dien - 8 -amine, (132,162 ) — N ,N -dimethyldocosa- 13,16
cationic lipid /neutral lipid , e.g. , DSPC /Chol /PEG -modified dien- 5 - amine , (127,152)—N ,N -dimethylhenicosa -12,15
lipid , e.g. , DSPC /Chol /PEG -modified lipid , e.g. , PEG-

lipid , e.g. , PEG - DMG or PEG - CDMA ).
Examples of lipid nanoparticle compositions and methods

dien- 4 - amine ,

(147,177 ) N , N - dimethyltricosa - 14,17

dien- 6 - amine , (157,18Z ) N ,N - dimethyltetracosa - 15,18
of making same are described, for example, in Semple et al . dien- 7 - amine , (182,21Z ) N ,N -dimethylheptacosa - 18,21
( 2010) Nat . Biotechnol. 28 : 172-176 ; Jayarama et al . ( 2012 ) , 15 dien - 10 - amine, ( 152,18Z )—N, N -dimethyltetracosa - 15,18
Angew. Chem . Int. Ed ., 51 : 8529-8533 ; and Maier et al . dien- 5 -amine,
(147,177 ) N , N - dimethyltricosa - 14,17
( 2013 ) Molecular Therapy 21 , 1570-1578 ( the contents of dien- 4 -amine, ( 197,22Z )-N ,N - dimeihyloctacosa - 19,22
each of which are incorporated herein by reference in their dien- 9 - amine , ( 18Z , 21 Z ) N ,N -dimethylheptacosa- 18,21
entirety ).
dien- 8 amine, (172,20Z ) N ,N -dimethylhexacosa - 17,20

In some embodiments,the lipid nanoparticle formulations 20 dien- 7 -amine, (162,192 ) -N ,N -dimethylpentacosa- 16,19

described herein may comprise a cationic lipid , a PEG lipid

dien- 6 - amine , ( 222,25Z ) N , N -dimethylhentriaconta - 22 ,

the non - cationic lipid DSPC , about 1.5 % of the PEG lipid
PEG - DOMG and about 38.5 % of the structural lipid cho-

[ (5Z )-oct - 5 -en - 1 - yloxylpropan - 2 -amine, 1- { 2 -[( 97,12Z )
octadeca - 9,12 - dien -1 -yloxy ]-1 -[(octyloxy )methyl]

and a structural lipid and optionally comprise a non - cationic 25 - dien - 10 - amine, ( 21 Z ,242 )—N , N -dimethyltriaconta - 21,
lipid . As a non - limiting example, the lipid nanoparticle may 24 -dien - 9 - amine, ( 187 )—N ,N - dimetylheptacos - 18 - en - 10
comprise about 40-60 % of cationic lipid, about 5-15 % of a amine , ( 172 )—N , N - dimethylhexacos- 17 - en - 9 -amine, ( 19Z ,
non- cationic lipid , about 1-2 % of a PEG lipid and about 25 22Z ) N ,N - dimethyloctacosa - 19,22 -dien -7 - amine , N , N
30-50% of a structural lipid . As another non- limiting dimethylheptacosan - 10 -amine, (207,23Z )-N - ethyl- N
example, the lipid nanoparticle may comprise about 50 % methylnonacosa - 20,23 - dien - 10 -amine, 1 - [ ( 11Z , 14Z ) -1
cationic lipid , about 10 % non - cationic lipid, about 1.5 % nonylicosa - 11,14 -dien - 1 - yllpyrrolidine,
(202 )—N, N
PEG lipid and about 38.5 % structural lipid . As yet another dimethylheptacos-20 -en - 10 - amine, (152 ) N ,N -dimethyl
non - limiting example, the lipid nanoparticle may comprise 30 eptacos- 15 -en - 10 -amine, ( 142 ) N , N -dimethylnonacos- 14
about 55 % cationic lipid , about 10 % non - cationic lipid , en - 10 - amine,
( 172 ) N , N - dimethylnonacos- 17 -en - 10
about 2.5 % PEG lipid and about 32.5 % structural lipid . In amine , ( 24Z )—N , N -dimethyltritriacont-24 -en - 10 -amine,
some embodiments, the cationic lipid may be any cationic ( 20Z ) N ,N -dimethylnonacos- 20 - en - 10- ne , ( 22Z )N ,
lipid described herein such as , but not limited to , DLin- N -dimethylhentriacont-22 -en - 10 - amine, ( 162 )—N ,N - dim
35 ethylpentacos - 16 -en - 8 -amine, (122,15Z ) N , N - dimethyl
KC2 - DMA , DLin -MC3 - DMA and L319 .
In some embodiments , the lipid nanoparticle formulations 2 - nonylhenicosa - 12,15 - dien - 1 -amine, ( 132,16Z )—N ,N
described herein may be 4 component lipid nanoparticles . dimethyl - 3 - nonyldocosa - 13,16 - dien -1 amine , N , N
The lipid nanoparticle may comprise a cationic lipid , a dimethyl- 1-[( 18,2R ) -2 -octylcyclopropyl]eptadecan -8
1 -[( 15,2R )-2 - hexylcyclopropyl]-N , N
non- cationic lipid , a PEG lipid and a structural lipid . As a amine ,
non - limiting example, the lipid nanoparticle may comprise 40 dimethylnonadecan - 10 -amine, N ,N -dimethyl- 1-[(15,2R )-2
about 40-60% of cationic lipid, about 5-15 % of a non- octylcyclopropyl ]nonadecan - 10 -amine, N , N -dimethyl- 21
cationic lipid , about 1-2 % of a PEG lipid and about 30-50 % [( 15,2R ) -2 -octylcyclopropyl]henicosan - 10 -amine, N , N
of a structural lipid . As another non - limiting example, the dimethyl- 1- [( 15,2S ) -2 - {[( 1R 2R )-2- pentylcyclopropyl]
lipid nanoparticle may comprise about 50 % cationic lipid , methyl }cyclopropyl]nonadecan - 10 -amine, N ,N -dimethyl-1
about 10 % non - cationic lipid , about 1.5 % PEG lipid and 45 [ ( 18,2R ) -2 -octylcyclopropyl]hexadecan - 8 -amine, N , N
about 38.5 % structural lipid . As yet another non- limiting dimethyl-[ (1R ,2S )-2 -undecylcyclopropyl] tetradecan - 5
example, the lipid nanoparticle may comprise about 55 % amine, N ,N -dimethyl-3-{ 7 - [( 18,2R )-2 -octylcyclopropyl ]
cationic lipid , about 10 % non - cationic lipid, about 2.5 % heptyl } dodecan - 1 -amine, 1 -[ (1R ,2S) -2 -heptylcyclopropyl]
1 -[ ( 15,2R ) -2
PEG lipid and about 32.5 % structural lipid . In some embodi- N , N -dimethyloctadecan - 9 -amine,
ments , the cationic lipid may be any cationic lipid described 50 decylcyclopropyl ] -N , N -dimethylpentadecan - 6 - amine, N , N
herein such as , but not limited to , DLin -KC2 -DMA, DLin- dimethyl-1 -R1S ,2R )-2 -octylcyclopropyllpentadecan -8
MC3 - DMA and L319 .
amine , R?N , N -dimethyl- 1-[( 97,12Z ) -octadeca - 9,12 -dien
In some embodiments, the lipid nanoparticle formulations 1 -yloxy ] -3-( octyloxy )propan - 2 -amine, S?N,N - dimethyl- 1
described herein may comprise a cationic lipid, a non- [ ( 92,12Z ) -octadeca - 9,12 -dien - 1 -yloxy ] -3- (octyloxy )
cationic lipid , a PEG lipid and a structural lipid . As a 55 propan - 2 - amine, 1- {2 - [( 9Z , 12Z ) -octadeca - 9,12 - dien - 1
non - limiting example, the lipid nanoparticle comprise about yloxy ] -1 -[(octyloxy )methyljethyl }pyrrolidine, (2S ) N ,N
50 % of the cationic lipid DLin - KC2 -DMA , about 10 % of dimethyl- 1-[( 92,12Z )-octadeca - 9,12 -dien - 1-yloxy ]-3

lesterol. As a non -limiting example, the lipid nanoparticle 60 ethyl } azetidine, ( 2S ) -1- (hexyloxy ) -N , N -dimethyl - 3 -ROZ ,

comprise about 50% of the cationic lipid DLin -MC3 - DMA, 12Z ) -octadeca - 9,12 - dien - 1 -yloxylpropan - 2 -amine, (2S )-1
about 10 % of the non -cationic lipid DSPC , about 1.5 % of (heptyloxy )-N ,N -dimethyl-3 -R9Z ,12Z ) -octadeca- 9,12
the PEG lipid PEG - DOMG and about 38.5 % of the struc- dien - 1 - yloxylpropan -2 -amine, N ,N -dimethyl-1-(nonyloxy )
tural lipid cholesterol. As a non - limiting example , the lipid 3 -R9Z , 12Z ) -octadeca - 9,12 - dien - 1 -yloxylpropan - 2 - amine,
nanoparticle comprise about 50 % of the cationic lipid DLin- 65 N , N -dimethyl - 1 - [ (9Z ) -octadec - 9 -en - 1 -yloxy )-3-( octyloxy)
MC3 - DMA , about 10% of the non - cationic lipid DSPC , propan - 2 -amine; ( 2S )-N ,N -dimethyl- 1 -[ (6Z, 97,12Z )-octa
about 1.5 % of the PEG lipid PEG - DMG and about 38.5 % of deca -6,9,12 - trien - 1 -yloxy ] -3- (octyloxy )propan - 2 - amine,

US 10,933,127 B2
84

83

(2S )-1-[( 11Z ,14Z )-icosa- 11,14 -dien -1 -yloxy] -N ,N -dimWO2013033438 , the contents of which are herein incorpo
ethyl -3- (pentyloxy )propan - 2 -amine, (2S )-1- (hexyloxy) -3- rated by reference in its entirety.
The nanoparticle formulation may comprise a polymer
[( 112,14Z )-icosa -11,14 -dien -1 -yloxy ] -N ,N -dimethylpro
pan - 2 - amine, 1-[( 117,14Z )-icosa- 11,14 -dien - 1 -yloxy] -N ,N- conjugate . The polymer conjugate may be a water soluble
dimethyl - 3- (octyloxypropan - 2 -amine,
1 - [ ( 132,16Z) - 5 conjugate. The polymer conjugate may have a structure as
docosa - 13,16 -dien - 1 -yloxy ] -N , N -dimethyl -3- (octyloxy )
described in U.S. Patent Application No. 20130059360 , the
propan - 2 - amine, (2S )-1 - [( 132,16Z )-docosa - 13,16 -dien - 1- contents of which are herein incorporated by reference in its
yloxy ] -3-(hexyloxy ) -N , N -dimethylpropan - 2 - amine, (2S )-1- entirety. In some embodiments, polymer conjugates with the
polynucleotides of the present disclosure may be made using
[(13Z ) -docos - 13 - en - 1- yloxy ]-3-(hexyloxy ) -N ,N
dimethylpropan - 2 -amine, 1 - [ ( 13Z ) -docos - 13 - en - 1 -yloxy ]- 10 the methods and / or segmented polymeric reagents described
N , N -dimethyl -3- (octyloxy )propan - 2 - amine,
1 - [( 9Z )- in U.S. Patent Application No. 20130072709 , the contents of
hexadec - 9 -en - 1 -yloxy ]-N ,N -dimethyl-3-( octyloxy )propanwhich are herein incorporated by reference in its entirety. In
2 - amine, ( 2R ) -N , N - dimethyl- H ( 1-metoyloctyl)oxy ] -3 - [(92 , some embodiments, the polymer conjugate may have pen
12Z ) -octadeca - 9,12 - dien - 1 - yloxylpropan - 2 - amine, (2R )-1- dant side groups comprising ring moieties such as , but not
[ (3,7 -dimethyloctyl)oxy ]-N , N -dimethyl-3 -ROZ , 12Z )15 limited to , the polymer conjugates described in U.S. Patent
octadeca - 9,12 -dien - 1 -yloxylpropan - 2 - amine,
N , N- Publication No. US20130196948 , the contents which are
herein incorporated by reference in its entirety.
dimethyl- 1-(octyloxy ) -3-( {8 -R15,25) -2- {[(1R ,2R ) -2
pentylcyclopropyl]methyl} cyclopropyl]octyl}oxy )propanThe nanoparticle formulations may comprise a conjugate
2 - amine , N , N -dimethyl- 1-1 [ 8- ( 2 -oclylcyclopropyl )octyl] to enhance the delivery of nanoparticles of the present
oxy } -3- (octyloxy )propan - 2 -amine and ( 11E ,202,23Z ) N , 20 disclosure in a subject. Further, the conjugate may inhibit
N -dimethylnonacosa - 11,20,2 -trien -10 - amine or a phagocytic clearance of the nanoparticles in a subject. In one
pharmaceutically acceptable salt or stereoisomer thereof.
aspect , the conjugate may be a “ self ” peptide designed from
In some embodiments, the LNP formulations of the RNA the human membrane protein CD47 ( e.g. , the “ self ” particles
( e.g. , mRNA ) vaccines may contain PEG - C - DOMG at 3 % described by Rodriguez et al . ( Science 2013 339 , 971-975 ) ,
lipid molar ratio . In some embodiments, the LNP formula- 25 herein incorporated by reference in its entirety ). As shown
tions of the RNA (e.g. , mRNA ) vaccines may contain by Rodriguez et al . , the self peptides delayed macrophage
mediated clearance of nanoparticles which enhanced deliv
PEG - C - DOMG at 1.5 % lipid molar ratio .
In some embodiments, the pharmaceutical compositions ery of the nanoparticles . In another aspect , the conjugate
of the RNA ( e.g. , mRNA ) vaccines may include at least one may be the membrane protein CD47 (e.g. , see Rodriguez et

of the PEGylated lipids described in International Publicaincorporated by reference in their entirety.
In some embodiments, the LNP formulation may contain
PEG - DMG 2000 ( 1,2 -dimyristoyl-sn - glycero - 3 - phopho(polyethylene glycol ) -2000 ). In
ethanolamine -N- methoxy
[
some embodiments, the LNP formulation may contain PEGDMG 2000 , a cationic lipid known in the art and at least one
other component. In some embodiments, the LNP formulation may contain PEG - DMG 2000 , a cationic lipid known in
the art, DSPC and cholesterol. As a non- limiting example,
the LNP formulation may contain PEG - DMG 2000 , DLinDMA , DSPC and cholesterol. As another non- limiting
example the LNP formulation may contain PEG - DMG
2000 , DLin - DMA, DSPC and cholesterol in a molar ratio of
2 : 40 : 10 : 48 ( see e.g. , Geall et al . , Nonviral delivery of
self - amplifying RNA (e.g. , mRNA ) vaccines , PNAS 2012 ;
PMID : 22908294 , the contents of each of which are herein
incorporated by reference in their entirety ).
The lipid nanoparticles described herein may be made in
a sterile environment.
In some embodiments, the LNP formulation may be
formulated in a nanoparticle such as a nucleic acid- lipid
particle . As a non - limiting example, the lipid particle may
comprise one or more active agents or therapeutic agents;
one or more cationic lipids comprising from about 50 mol %
to about 85 mol % of the total lipid present in the particle;
one or more non - cationic lipids comprising from about 13
mol % to about 49.5 mol % of the total lipid present in the
particle; and one or more conjugated lipids that inhibit
aggregation of particles comprising from about 0.5 mol % to
about 2 mol % of the total lipid present in the particle.
The nanoparticle formulations may comprise a phosphate
conjugate. The phosphate conjugate may increase in vivo
circulation times and / or increase the targeted delivery of the
nanoparticle . As a non - limiting example, the phosphate
tion No. WO2012099755 , the contents of which are herein

conjugates may include a compound of any one of the
formulas described in International Application No.

30 al . Science 2013 339 , 971-975 , herein incorporated by

reference in its entirety ). Rodriguez et al . showed that,

similarly to " self " ' peptides , CD47 can increase the circu
lating particle ratio in a subject as compared to scrambled
peptides and PEG coated nanoparticles.
35 In some embodiments, the RNA (e.g. , mRNA ) vaccines of
the present disclosure are formulated in nanoparticles which
comprise a conjugate to enhance the delivery of the nan
oparticles of the present disclosure in a subject. The conju
gate may be the CD47 membrane or the conjugate may be
40 derived from the CD47 membrane protein , such as the " self "
peptide described previously. In some embodiments, the
nanoparticle may comprise PEG and a conjugate of CD47 or
a derivative thereof. In some embodiments, the nanoparticle
may comprise both the " self " peptide described above and
45 the membrane protein CD47 .

In some embodiments, a “ self " peptide and / or CD47

protein may be conjugated to a virus - like particle or

pseudovirion, as described herein for delivery of the RNA

(e.g. , mRNA ) vaccines of the present disclosure .
In some embodiments, RNA (e.g. , mRNA ) vaccine phar
maceutical compositions comprising the polynucleotides of
the present disclosure and a conjugate that may have a
degradable linkage. Non - limiting examples of conjugates
include an aromatic moiety comprising an ionizable hydro
55 gen atom , a spacer moiety, and a water - soluble polymer. As
a non - limiting example , pharmaceutical compositions com
prising a conjugate with a degradable linkage and methods
for delivering such pharmaceutical compositions are
described in U.S. Patent Publication No. US20130184443 ,
60 the contents of which are herein incorporated by reference in
their entirety.
The nanoparticle formulations may be a carbohydrate
nanoparticle comprising a carbohydrate carrier and a RNA
(e.g. , mRNA ) vaccine . As a non - limiting example, the
65 carbohydrate carrier may include , but is not limited to , an

50

anhydride -modified phytoglycogen or glycogen -type mate
rial, phtoglycogen octenyl succinate, phytoglycogen beta

US 10,933,127 B2
85

86

dextrin , anhydride -modified phytoglycogen beta - dextrin .

10-200 nm which are preferred for higher drug encapsula

( See e.g. , International Publication No. WO2012109121 ; the tion efficiency and the ability to provide the sustained
contents of which are herein incorporated by reference in delivery of a wide array of drugs have been thought to be too
their entirety ).
large to rapidly diffuse through mucosal barriers . Mucus is
Nanoparticle formulations of the present disclosure may 5 continuously secreted , shed , discarded or digested and
be coated with a surfactant or polymer in order to improve recycled so most of the trapped particles may be removed
the delivery of the particle. In some embodiments , the from the mucosa tissue within seconds or within a few
nanoparticle may be coated with a hydrophilic coating such hours . Large polymeric nanoparticles (200 nm -500 nm in
as , but not limited to , PEG coatings and / or coatings that have diameter ) which have been coated densely with a low
a neutral surface charge. The hydrophilic coatings may help 10 molecular weight polyethylene glycol (PEG) diffused
to deliver nanoparticles with larger payloads such as , but not through mucus only 4 to 6 - fold lower than the same particles
limited to , RNA ( e.g. , mRNA ) vaccines within the central diffusing in water (Lai et al . PNAS 2007 104 ( 5 ) : 1482-487 ;
nervous system . As a non - limiting example nanoparticles Lai et al . Adv Drug Deliv Rev. 2009 61 ( 2 ) : 158-171 ; each of
comprising a hydrophilic coating and methods of making which is herein incorporated by reference in their entirety ).
such nanoparticles are described in U.S. Patent Publication 15 The transport of nanoparticles may be determined using
No. US20130183244 , the contents of which are herein rates of permeation and / or fluorescent microscopy tech
incorporated by reference in their entirety.
niques including, but not limited to , fluorescence recovery
In some embodiments, the lipid nanoparticles of the after photobleaching ( FRAP ) and high resolution multiple
present disclosure may be hydrophilic polymer particles. particle tracking ( MPT ) . As a non - limiting example, com

Non - limiting examples of hydrophilic polymer particles and 20 positions which can penetrate a mucosal barrier may be

methods of making hydrophilic polymer particles are

described in U.S. Patent Publication No. US20130210991 ,
the contents of which are herein incorporated by reference in
their entirety.
In some embodiments, the lipid nanoparticles of the
present disclosure may be hydrophobic polymer particles.
Lipid nanoparticle formulations may be improved by
replacing the cationic lipid with a biodegradable cationic
lipid which is known as a rapidly eliminated lipid nanoparticle ( reLNP ). Ionizable cationic lipids , such as , but not
limited to , DLinDMA, DLin -KC2 - DMA, and DLin -MC3DMA, have been shown to accumulate in plasma and tissues
over time and may be a potential source of toxicity. The
rapid metabolism of the rapidly eliminated lipids can
improve the tolerability and therapeutic index of the lipid
nanoparticles by an order of magnitude from a 1 mg/kg dose
to a 10 mg/kg dose in rat. Inclusion of an enzymatically
degraded ester linkage can improve the degradation and
metabolism profile of the cationic component, while still
maintaining the activity of the reLNP formulation . The ester
linkage can be internally located within the lipid chain or it
may be terminally located at the terminal end of the lipid
chain . The internal ester linkage may replace any carbon in
the lipid chain.

made as described in U.S. Pat . No. 8,241,670 or Interna

25

30
35

40

tional Patent Publication No. WO2013110028 , the contents
of each of which are herein incorporated by reference in its
entirety.
The lipid nanoparticle engineered to penetrate mucus may
comprise a polymeric material ( i.e. a polymeric core ) and /or
a polymer - vitamin conjugate and / or a tri - block co -polymer.
The polymeric material may include, but is not limited to ,
polyamines, polyethers, polyamides, polyesters, polycar
bamates, polyureas, polycarbonates, poly (styrenes ), polyim
ides , polysulfones, polyurethanes, polyacetylenes, polyeth
ylenes, polyethyeneimines, polyisocyanates, polyacrylates,
polymethacrylates, polyacrylonitriles, and polyarylates. The
polymeric material may be biodegradable and /or biocom
patible . Non - limiting examples of biocompatible polymers
are described in International Patent Publication No.
WO2013116804 , the contents of which are herein incorpo
rated by reference in their entirety. The polymeric material
may additionally be irradiated . As a non - limiting example,
the polymeric material may be gamma irradiated ( see e.g. ,
International App . No. W0201282165 , herein incorporated
by reference in its entirety ). Non - limiting examples of
specific polymers include poly (caprolactone ) (PCL ) , ethyl

ene vinyl acetate polymer (EVA ), poly (lactic acid) ( PLA ),
In some embodiments, the internal ester linkage may be 45 poly ( L - lactic acid) (PLLA) , poly (glycolic acid ) ( PGA ), poly
located on either side of the saturated carbon .
(lactic acid - co - glycolic acid) ( PLGA ), poly (L - lactic acid
In some embodiments, an immune response may be co - glycolic acid ) (PLLGA ), poly (D , L - lactide ) (PDLA) , poly
elicited by delivering a lipid nanoparticle which may include (L - lactide) ( PLLA) , poly ( D , L -lactide - co -caprolactone ),
a nanospecies , a polymer and an immunogen. (U.S. Publi- poly (D.L - lactide- co - caprolactone -co -glycolide ), poly (D ,L
cation No. 20120189700 and International Publication No. 50 lactide - co - PEO - co - D , L - lactide) , poly (D ,L -lactide-co -PPO

WO2012099805 ; each of which is herein incorporated by
reference in their entirety ). The polymer may encapsulate
the nanospecies or partially encapsulate the nanospecies.
The immunogen may be a recombinant protein , a modified

co - D , L - lactide) , polyalkyl cyanoacralate, polyurethane,
poly - L - lysine (PLL ) , hydroxypropyl methacrylate (HPMA ),
polyethyleneglycol, poly - L - glutamic acid , poly (hydroxy
acids ) , polyanhydrides, polyorthoesters, poly ( ester amides ),

RNA and /or a polynucleotide described herein . In some 55 polyamides, poly (ester ethers ), polycarbonates, polyal

embodiments , the lipid nanoparticle may be formulated for kylenes such as polyethylene and polypropylene , polyal
use in a vaccine such as , but not limited to , against a kylene glycols such as poly ( ethylene glycol ) (PEG) , poly
pathogen.
alkylene oxides ( PEO ) , polyalkylene terephthalates such as
Lipid nanoparticles may be engineered to alter the surface poly ( ethylene terephthalate ), polyvinyl alcohols ( PVA ),
properties of particles so the lipid nanoparticles may pen- 60 polyvinyl ethers, polyvinyl esters such as poly (vinyl
etrate the mucosal barrier. Mucus is located on mucosal acetate ), polyvinyl halides such as poly (vinyl chloride )
tissue such as , but not limited to , oral (e.g. , the buccal and (PVC ) , polyvinylpyrrolidone, polysiloxanes, polystyrene
esophageal membranes and tonsil tissue) , ophthalmic, gas- (PS ) , polyurethanes, derivatized celluloses such as alkyl
trointestinal (e.g. , stomach , small intestine, large intestine , celluloses , hydroxyalkyl celluloses , cellulose ethers, cellu
colon, rectum ), nasal, respiratory ( e.g. , nasal , pharyngeal, 65 lose esters, nitro celluloses , hydroxypropylcellulose, car
tracheal and bronchial membranes ), genital (e.g. , vaginal , boxymethylcellulose , polymers of acrylic acids , such as
cervical and urethral membranes ). Nanoparticles larger than

poly (methyl (meth ) acrylate ) (PMMA) , poly ( ethylmeth )

US 10,933,127 B2
87

acrylate ), poly (butyl(meth )acrylate ), poly ( isobutyl (meth )
acrylate ), poly (hexylmethacrylate ), poly (isodecylmeth )
acrylate ), poly ( lauryl(meth )acrylate ), poly (phenyl (meth )
acrylate ), poly (methyl acrylate ), poly ( isopropyl acrylate ),
polyisobutyl acrylate ), poly (octadecyl acrylate) and copolymers and mixtures thereof, polydioxanone and its copolymers , polyhydroxyalkanoates, polypropylene fumarate,
polyoxymethylene, poloxamers, poly (ortho )esters, poly (butyric acid ) , poly (valeric acid ) , poly (lactide -co -caprolactone ) , PEG -PLGA - PEG and trimethylene carbonate , polyvinylpyrrolidone. The lipid nanoparticle may be coated or
associated with a co -polymer such as , but not limited to , a
block co -polymer ( such as a branched polyether -polyamide
block copolymer described in International Publication No.
W02013012476 , herein incorporated by reference in its
entirety ), and (poly (ethylene glycol )) - (poly (propylene
oxide) ) - (poly ( ethylene glycol ) ) triblock copolymer ( see e.g. ,
U.S. Publication 20120121718 and U.S. Publication
20100003337 and U.S. Pat . No. 8,263,665 , the contents of
each of which is herein incorporated by reference in their
entirety ). The co - polymer may be a polymer that is generally
regarded as safe (GRAS ) and the formation of the lipid
nanoparticle may be in such a way that no new chemical
entities are created . For example, the lipid nanoparticle may
comprise poloxamers coating PLGA nanoparticles without
forming new chemical entities which are still able to rapidly
penetrate human mucus ( Yang et al . Angew . Chem . Int. Ed .
2011 50 : 2597-2600 ; the contents of which are herein incorporated by reference in their entirety ). A non -limiting scal-

88

may interact with the mucus and alter the structural and /or
adhesive properties of the surrounding mucus to decrease
mucoadhesion , which may increase the delivery of the
mucus penetrating lipid nanoparticles to the mucosal tissue .
5 In some embodiments, the mucus penetrating lipid nan
oparticles may be a hypotonic formulation comprising a
mucosal penetration enhancing coating. The formulation
may be hypotonice for the epithelium to which it is being
delivered . Non - limiting examples of hypotonic formulations
10 may be found in International Patent Publication No.
WO2013110028 , the contents of which are herein incorpo
rated by reference in their entirety.
In some embodiments, in order to enhance the delivery
through the mucosal barrier the RNA (e.g. , mRNA ) vaccine

15 formulation may comprise or be a hypotonic solution . Hypo
tonic solutions were found to increase the rate at which
mucoinert particles such as , but not limited to , mucus

penetrating particles, were able to reach the vaginal epithe
lial surface ( see e.g. , Ensign et al . Biomaterials 2013 34 ( 28 ) :
20 6922-9 , the contents of which are herein incorporated by
reference in their entirety ) .
In some embodiments, the RNA (e.g. , mRNA ) vaccine is
formulated as a lipoplex , such as , without limitation , the
ATUPLEXTM system , the DACC system , the DBTC system
25 and other siRNA - lipoplex technology from Silence Thera
peutics (London, United Kingdom ), STEMFECTTM from
STEMGENT® ( Cambridge, Mass . ) , and polyethylenimine
( PEI ) or protamine- based targeted and non -targeted delivery
of nucleic acids acids (Aleku et al . Cancer Res . 2008
able method to produce nanoparticles which can penetrate 30 68 : 9788-9798 ; Strumberg et al . Int J Clin Pharmacol Ther
human mucus is described by Xu et al . ( see , e.g. , J Control 2012 50 : 76-78 ; Santel et al . , Gene Ther 2006 13 : 1222-1234 ;
Release 2013 , 170 (2 ) : 279-86 ; the contents of which are Santel et al . , Gene Ther 2006 13 : 1360-1370 ; Gutbier et al . ,
herein incorporated by reference in their entirety ).
Pulm Pharmacol. Ther. 2010 23 : 334-344 ; Kaufmann et al .
The vitamin of the polymer -vitamin conjugate may be

Microvasc Res 2010 80 : 286-293 Weide et al . J Immunother.

vitamin E. The vitamin portion of the conjugate may be 35 2009 32 : 498-507 ; Weide et al . J Immunother. 2008 31: 180
substituted with other suitable components such as , but not 188 ; Pascolo Expert Opin . Biol . Ther. 4 : 1285-1294 ; Fotin
limited to , vitamin A , vitamin E , other vitamins , cholesterol, Mleczek et al . , 2011 J. Immunother. 34 : 1-15 ; Song et al . ,
a hydrophobic moiety, or a hydrophobic component of other Nature Biotechnol. 2005 , 23 : 709-717 ; Peer et al . , Proc Natl
surfactants (e.g. , sterol chains , fatty acids , hydrocarbon Acad Sci USA . 2007 6 ; 104 : 4095-4100 ; deFougerolles Hum
chains and alkylene oxide chains ) .
40 Gene Ther. 2008 19 : 125-132 , the contents of each of which
The lipid nanoparticle engineered to penetrate mucus may are incorporated herein by reference in their entirety ).
include surface altering agents such as , but not limited to ,
In some embodiments, such formulations may also be
polynucleotides, anionic proteins (e.g. , bovine serum albu- constructed or compositions altered such that they passively
min ), surfactants (e.g. , cationic surfactants such as for or actively are directed to different cell types in vivo ,

example dimethyldioctadecylammonium bromide ), sugars 45 including but not limited to hepatocytes, immune cells,
or sugar derivatives (e.g. , cyclodextrin ), nucleic acids , poly-

tumor cells , endothelial cells , antigen presenting cells , and

dornase alfa , neltenexine, erdosteine) and various DNases
including rhDNase . The surface altering agent may be

Gutbier et al . , Pulm Pharmacol. Ther. 2010 23 : 334-344 ;
Basha et al . , Mol . Ther. 2011 19 : 2186-2200 ; Fenske and

mers ( e.g. , heparin , polyethylene glycol and poloxamer ), leukocytes ( Akinc et al . Mol Ther. 2010 18 : 1357-1364 ;
mucolytic agents (e.g. , N -acetylcysteine, mugwort, brome- Song et al . , Nat Biotechnol. 2005 23 : 709-717 ; Judge et al . ,
lain, papain, clerodendrum , acetylcysteine, bromhexine , car- J Clin Invest. 2009 119 : 661-673 ; Kaufmann et al . , Micro
bocisteine , eprazinone , mesna, ambroxol, sobrerol, domi- 50 vasc Res 2010 80 : 286-293 ; Santel et al., Gene Ther 2006
odol , letosteine, stepronin , tiopronin , gelsolin , thymosin B4 13 : 1222-1234 ; Santel et al . , Gene Ther 2006 13 : 1360-1370 ;

embedded or enmeshed in the particle's surface or disposed Cullis , Expert Opin Drug Deliv. 2008 5 : 25-44 ; Peer et al . ,
( e.g. , by coating, adsorption, covalent linkage, or other 55 Science. 2008 319 : 627-630 ; Peer and Lieberman , Gene
process ) on the surface of the lipid nanoparticle . ( see e.g. , Ther. 2011 18 : 1127-1133 , the contents of each of which are
U.S. Publication 20100215580 and U.S. Publication incorporated herein by reference in their entirety ). One
20080166414 and US20130164343 ; the contents of each of example of passive targeting of formulations to liver cells
which are herein incorporated by reference in their entirety ). includes the DLin -DMA , DLin -KC2 - DMA and DLin -MC3

In some embodiments, the mucus penetrating lipid nan- 60 DMA - based lipid nanoparticle formulations, which have
oparticles may comprise at least one polynucleotide been shown to bind to apolipoprotein E and promote binding
described herein . The polynucleotide may be encapsulated and uptake of these formulations into hepatocytes in vivo
in the lipid nanoparticle and /or disposed on the surface of the ( Akinc et al . Mol Ther. 2010 18 : 1357-1364 , the contents of
particle. The polynucleotide may be covalently coupled to which are incorporated herein by reference in their entirety ).
the lipid nanoparticle. Formulations of mucus penetrating 65 Formulations can also be selectively targeted through
lipid nanoparticles may comprise a plurality of nanopar- expression of different ligands on their surface as exempli

ticles . Further, the formulations may contain particles which

fied by, but not limited by, folate , transferrin , N -acetylga

US 10,933,127 B2
89

90

lactosamine (GalNAc ), and antibody targeted approaches
(Kolhatkar et al . , Curr Drug Discov Technol. 2011 8 :197-

sulation may be determined by measuring the escape or the
activity of the pharmaceutical composition or compound of

Ther. 2010 18 : 1357-1364 ; Srinivasan et al . , Methods Mol

In some embodiments , the controlled release formulation

18 : 1127-1133 , the contents of each of which are incorporated herein by reference in their entirety ).
In some embodiments, the RNA ( e.g. , mRNA ) vaccine is

may be encapsulated into a lipid nanoparticle or a rapidly
eliminated lipid nanoparticle and the lipid nanoparticles or a
rapidly eliminated lipid nanoparticle may then be encapsu

between 10 to 1000 nm . SLN possess a solid lipid core
matrix that can solubilize lipophilic molecules and may be

example, the polymer, hydrogel or surgical sealant may be
PLGA, ethylene vinyl acetate (EVAC ), poloxamer,

206 ; Musacchio and Torchilin , Front Biosci . 2011 16 : 1388- the disclosure using fluorescence and / or electron micro
1412 ; Yu et al . , Mol Membr Biol . 2010 27 : 286-298 ; Patil et graph . For example , at least 1 , 5 , 10 , 20 , 30 , 40 , 50 , 60 , 70 ,
al . , Crit Rev Ther Drug Carrier Syst . 2008 25 : 1-61 ; Benoit 5 80 , 85 , 90 , 95 , 96 , 97 , 98 , 99 , 99.9 , 99.99 or greater than
et al . , Biomacromolecules . 2011 12 : 2708-2714 ; Zhao et al . , 99.99 % of the pharmaceutical composition or compound of
Expert Opin Drug Deliv. 2008 5 : 309-319 ; Akinc et al . , Mol the disclosure are encapsulated in the delivery agent.

Biol . 2012 820 : 105-116 ; Ben - Arie et al . , Methods Mol Biol . may include , but is not limited to , tri -block co - polymers . As
2012 757 : 497-507 ; Peer 2010 J Control Release . 20 : 63-68 ; 10 a non - limiting example, the formulation may include two
Peer et al . , Proc Natl Acad Sci USA . 2007 104 : 4095-4100 ; different types of tri- block co - polymers ( International Pub.
Kim et al . , Methods Mol Biol . 2011 721 : 339-353 ; Subra- No. WO2012131104 and
manya et al . , Mol Ther. 2010 18 : 2028-2037 ; Song et al . , Nat
WO2012131106 , the contents of each of which are incor
Biotechnol. 2005 23 : 709-717 ; Peer et al . , Science . 2008 porated herein by reference in their entirety ).
319 : 627-630 ; Peer and Lieberman , Gene Ther. 2011 15 In some embodiments, the RNA (e.g. , mRNA ) vaccines

formulated as a solid lipid nanoparticle. A solid lipid nan- lated into a polymer, hydrogel and / or surgical sealant
oparticle ( SLN) may be spherical with an average diameter 20 described herein and / or known in the art. As a non - limiting
stabilized with surfactants and /or emulsifiers. In some

GELSITE® (Nanotherapeutics, Inc. Alachua, Fla . ) , HYL

embodiments , the lipid nanoparticle may be a self-assembly ENEX® (Halozyme Therapeutics, San Diego Calif.), surgi
lipid -polymer nanoparticle ( see Zhang et al . , ACS Nano, 25 cal sealants such as fibrinogen polymers (Ethicon Inc. Cor

2008 , 2 ( 8 ) , pp 1696-1702 ; the contents of which are herein
incorporated by reference in their entirety ). As a nonlimiting example , the SLN may be the SLN described in

International Patent Publication No. WO2013105101 , the
contents of which are herein incorporated by reference in
their entirety. As another non -limiting example , the SLN
may be made by the methods or processes described in
International Patent Publication No. WO2013105101 , the
contents of which are herein incorporated by reference in
their entirety.
Liposomes , lipoplexes , or lipid nanoparticles may be used
to improve the efficacy of polynucleotides directed protein
production as these formulations may be able to increase cell
transfection by the RNA (e.g. , mRNA ) vaccine ; and / or
increase the translation of encoded protein . One such
example involves the use of lipid encapsulation to enable the
effective systemic delivery of polyplex plasmid DNA
(Heyes et al . , Mol Ther . 2007 15 : 713-720 ; the contents of
which are incorporated herein by reference in their entirety ).
The liposomes , lipoplexes, or lipid nanoparticles may also
be used to increase the stability of the polynucleotide .
In some embodiments, the RNA ( e.g. , mRNA ) vaccines of
the present disclosure can be formulated for controlled
release and / or targeted delivery. As used herein , “ controlled
release” refers to a pharmaceutical composition or compound release profile that conforms to a particular pattern of
release to effect a therapeutic outcome. In some embodiments, the RNA (e.g. , mRNA ) vaccines may be encapsulated into a delivery agent described herein and / or known in
the art for controlled release and / or targeted delivery. As
used herein , the term “ encapsulate ” means to enclose, surround or encase . As it relates to the formulation of the
compounds of the disclosure , encapsulation may be substantial , complete or partial. The term “ substantially encapsulated ” means that at least greater than 50 , 60 , 70 , 80 , 85 , 90 ,
95 , 96 , 97 , 98 , 99 , 99.9 , 99.9 or greater than 99.999 % of the
pharmaceutical composition or compound of the disclosure
may be enclosed , surrounded or encased within the delivery
agent. “ Partially encapsulation ” means that less than 10 , 10 ,
20 , 30 , 40 50 or less of the pharmaceutical composition or
compound of the disclosure may be enclosed, surrounded or
encased within the delivery agent. Advantageously, encap-

nelia , Ga . ) , TISSELL® (Baxter International, Inc Deerfield ,
I11 . ) , PEG - based sealants , and COSEAL® ( Baxter Interna
tional , Inc Deerfield , Ill . ) .

In some embodiments, the lipid nanoparticle may be
30 encapsulated into any polymer known in the art which may
form a gel when injected into a subject. As another non
limiting example, the lipid nanoparticle may be encapsu
lated into a polymer matrix which may be biodegradable.
In some embodiments, the RNA ( e.g. , mRNA ) vaccine
35 formulation for controlled release and / or targeted delivery
may also include at least one controlled release coating .
Controlled release coatings include, but are not limited to ,
OPADRY® , polyvinylpyrrolidone/ vinyl acetate copolymer,
polyvinylpyrrolidone, hydroxypropyl methylcellulose,
40 hydroxypropyl cellulose , hydroxyethyl cellulose,
EUDRAGIT RL® , EUDRAGIT RS® and cellulose deriva
tives such as ethylcellulose aqueous dispersions (AQUA
COAT® and SURELEASE® ).
In some embodiments, the RNA ( e.g. , mRNA ) vaccine
45 controlled release and / or targeted delivery formulation may
comprise at least one degradable polyester which may
contain polycationic side chains . Degradable polyesters
include , but are not limited to , poly ( serine ester), poly (L
lactide - co - L - lysine ), poly ( 4 -hydroxy - L -proline ester ), and
50 combinations thereof. In some embodiments, the degradable
polyesters may include a PEG conjugation to form a PEGy.
lated polymer.
In some embodiments, the RNA ( e.g. , mRNA ) vaccine
controlled release and / or targeted delivery formulation com
55 prising at least one polynucleotide may comprise at least one
PEG and / or PEG related polymer derivatives as described in
U.S. Pat. No. 8,404,222 , the contents of which are incorpo
rated herein by reference in their entirety.
In some embodiments , the RNA ( e.g. , mRNA ) vaccine
60 controlled release delivery formulation comprising at least
one polynucleotide may be the controlled release polymer
system described in US20130130348 , the contents of which
are incorporated herein by reference in their entirety .
In some embodiments, the RNA (e.g. , mRNA ) vaccines of
65 the present disclosure may be encapsulated in a therapeutic
nanoparticle , referred to herein as " therapeutic nanoparticle
RNA ( e.g. , mRNA ) vaccines . ” Therapeutic nanoparticles

US 10,933,127 B2
91

may be formulated by methods described herein and known
in the art such as , but not limited to , International Pub Nos .
WO2010005740 , WO2010030763 , WO2010005721 ,
WO2010005723 , WO2012054923 , U.S. Publication Nos .
US20110262491 , US20100104645 , US20100087337 ,
US20100068285 , US20110274759 , US20100068286 ,
US20120288541 , US20130123351 and US20130230567
and U.S. Pat . Nos . 8,206,747 , 8,293,276 , 8,318,208 and
8,318,211 ; the contents of each of which are herein incorporated by reference in their entirety. In some embodiments,
therapeutic polymer nanoparticles may be identified by the
methods described in US Pub No. US20120140790 , the
contents of which are herein incorporated by reference in
their entirety.
In some embodiments, the therapeutic nanoparticle RNA
( e.g. , mRNA ) vaccine may be formulated for sustained
release . As used herein , " sustained release” refers to a
pharmaceutical composition or compound that conforms to
a release rate over a specific period of time . The period of
time may include, but is not limited to , hours , days , weeks ,
months and years . As a non -limiting example , the sustained
release nanoparticle may comprise a polymer and a therapeutic agent such as , but not limited to , the polynucleotides
of the present disclosure ( see International Pub No.

92

lates , polyvinyl alcohols, polyurethanes , polyphosphazenes ,

polyacrylates, polymethacrylates, polycyanoacrylates, poly
ureas , polystyrenes, polyamines, polylysine , poly ( ethylene

imine ) , poly ( serine ester ), poly ( L -lactide - co - L - lysine ), poly
5 ( 4 -hydroxy - L -proline ester) or combinations thereof. In yet
another embodiment, the diblock copolymer may be a
high- X diblock copolymer such as those described in Inter
national Patent Publication No. WO2013120052 , the con
tents of which are incorporated herein by reference in their
10 entirety.
As a non- limiting example the therapeutic nanoparticle
comprises a PLGA -PEG block copolymer ( see U.S. Publi
cation No. US20120004293 and U.S. Pat . No. 8,236,330 ,
each of which is herein incorporated by reference in their
15 entirety ). In another non- limiting example, the therapeutic
nanoparticle is a stealth nanoparticle comprising a diblock
copolymer of PEG and PLA or PEG and PLGA ( see U.S.
Pat. No. 8,246,968 and International Publication No.
WO2012166923 , the contents of each of which are herein

20 incorporated by reference in their entirety ). In yet another
non - limiting example, the therapeutic nanoparticle is a
stealth nanoparticle or a target - specific stealth nanoparticle
as
described in U.S. Patent Publication No.
US20130172406 , the contents of which are herein incorpo

2010075072 and US Pub No. US20100216804 , 25 rated by reference in their entirety.
US20110217377 and US20120201859 , the contents of each
In some embodiments, the therapeutic nanoparticle may

of which are incorporated herein by reference in their comprise a multiblock copolymer ( see e.g. , U.S. Pat . Nos .
entirety ). In another non -limiting example, the sustained 8,263,665 and 8,287,910 and U.S. Patent Pub . No.
release formulation may comprise agents which permit US20130195987 , the contents of each of which are herein
persistent bioavailability such as , but not limited to , crystals, 30 incorporated by reference in their entirety ).
macromolecular gels and /or particulate suspensions ( see
In yet another non - limiting example , the lipid nanopar
U.S. Patent Publication No US20130150295 , the contents of ticle comprises the block copolymer PEG -PLGA -PEG ( see
each of which are incorporated herein by reference in their e.g. , the thermosensitive hydrogel (PEG -PLGA -PEG ) was
entirety ).
used as a TGF -betal gene delivery vehicle in Lee et al .
In some embodiments , the therapeutic nanoparticle RNA 35 Thermosensitive Hydrogel as a Tgf-fi Gene Delivery
( e.g. , mRNA ) vaccines may be formulated to be target Vehicle Enhances Diabetic Wound Healing. Pharmaceutical

specific . As a non - limiting example, the therapeutic nan- Research , 2003 20 ( 12 ) : 1995-2000 ; as a controlled gene
oparticles may include a corticosteroid ( see International delivery system in Li et al . Controlled Gene Delivery
Pub . No. WO2011084518 , the contents of which are incor- System Based on Thermosensitive Biodegradable Hydrogel.
porated herein by reference in their entirety ). As a non- 40 Pharmaceutical Research 2003 20 ( 6 ) : 884-888 ; and Chang et
limiting example, the therapeutic nanoparticles may be al . , Non - ionic amphiphilic biodegradable PEG - PLGA -PEG
formulated in nanoparticles described in International Pub copolymer enhances gene delivery efficiency in rat skeletal
No. WO2008121949 , WO2010005726 , WO2010005725 ,

muscle . J Controlled Release . 2007 118 : 245-253 , the con

polyethers , polyesters , poly (orthoesters ), polycyanoacry-

comprise at least one poly ( vinyl ester) polymer. The poly

WO2011084521 and US Pub No. US20100069426 , tents of each of which are herein incorporated by reference
US20120004293 and US20100104655 , the contents of each 45 in their entirety ). The RNA ( e.g. , mRNA ) vaccines of the
of which are incorporated herein by reference in their present disclosure may be formulated in lipid nanoparticles
entirety.
comprising the PEG -PLGA -PEG block copolymer.
In some embodiments , the nanoparticles of the present
In some embodiments, the therapeutic nanoparticle may
disclosure may comprise a polymeric matrix . As a non- comprise a multiblock copolymer ( see e.g. , U.S. Pat . Nos .
limiting example, the nanoparticle may comprise two or 50 8,263,665 and 8,287,910 and U.S. Patent Pub . No.
more polymers such as , but not limited to , polyethylenes , US20130195987 , the contents of each of which are herein
polycarbonates, polyanhydrides, polyhydroxyacids, poly- incorporated by reference in their entirety ).
propylfumerates, polycaprolactones, polyamides , polyacIn some embodiments, the block copolymers described
etals , polyethers, polyesters , poly (orthoesters ), polycyano- herein may be included in a polyion complex comprising a
acrylates,
polyvinyl
alcohols ,
polyurethanes, 55 non -polymeric micelle and the block copolymer. ( see e.g. ,
polyphosphazenes, polyacrylates, polymethacrylates, U.S. Publication No. 20120076836 , the contents of which
polycyanoacrylates, polyureas, polystyrenes, polyamines , are herein incorporated by reference in their entirety ).
polylysine, polyethylene imine ), poly (serine ester ), poly (LIn some embodiments, the therapeutic nanoparticle may
lactide - co - L - lysine ) , poly ( 4 -hydroxy - L -proline ester ) or comprise at least one acrylic polymer. Acrylic polymers
combinations thereof.
60 include but are not limited to , acrylic acid , methacrylic acid ,
In some embodiments, the therapeutic nanoparticle com- acrylic acid and methacrylic acid copolymers, methyl meth
prises a diblock copolymer. In some embodiments, the acrylate copolymers, ethoxyethyl methacrylates, cyanoethyl
diblock copolymer may include PEG in combination with a methacrylate, amino alkyl methacrylate copolymer, poly
polymer such as , but not limited to , polyethylenes, polycar- ( acrylic acid ) , poly (methacrylic acid ) , polycyanoacrylates
bonates, polyanhydrides, polyhydroxyacids, polypropyl- 65 and combinations thereof.
fumerates, polycaprolactones, polyamides, polyacetals ,
In some embodiments , the therapeutic nanoparticles may

US 10,933,127 B2
93

94

( vinyl ester) polymer may be a copolymer such as a random herein and / or as described in International Pub No.
copolymer. As a non - limiting example, the random copoly- WO2010138192 and US Pub No. 20100303850 , each of
mer may have a structure such as those described in Inter- which is herein incorporated by reference in their entirety.
national Application No. WO2013032829 or U.S. Patent
In some embodiments, the RNA ( e.g. , mRNA ) vaccine
Publication No US20130121954 , the contents of each of 5 may be formulated for controlled and / or sustained release
which are herein incorporated by reference in their entirety. wherein the formulation comprises at least one polymer that
In some embodiments, the poly ( vinyl ester) polymers may is a crystalline side chain ( CYSC ) polymer. CYSC polymers
be conjugated to the polynucleotides described herein .
are described in U.S. Pat . No. 8,399,007, herein incorpo
In some embodiments, the therapeutic nanoparticle may rated by reference in its entirety.
comprise at least one diblock copolymer. The diblock copo- 10 In some embodiments, the synthetic nanocarrier may be
lymer may be , but it not limited to , a poly (lactic ) acid- poly formulated for use as a vaccine . In some embodiments, the
( ethylene )glycol copolymer ( see , e.g. , International Patent synthetic nanocarrier may encapsulate at least one poly
Publication No. WO2013044219 , the contents of which are nucleotide which encode at least one antigen . As a non

herein incorporated by reference in their entirety ). As a limiting example, the synthetic nanocarrier may include at
non- limiting example, the therapeutic nanoparticle may be 15 least one antigen and an excipient for a vaccine dosage form
used to treat cancer ( see International publication No. ( see International Publication No. WO2011150264 and U.S.
WO2013044219 , the contents of which are herein incorpo- Publication No. US20110293723 , the contents of each of
rated by reference in their entirety ).
which are herein incorporated by reference in their entirety ).
In some embodiments, the therapeutic nanoparticles may As another non- limiting example, a vaccine dosage form
comprise at least one cationic polymer described herein 20 may include at least two synthetic nanocarriers with the
and / or known in the art .
same or different antigens and an excipient ( see International
In some embodiments , the therapeutic nanoparticles may Publication No. WO2011150249 and U.S. Publication No.
comprise at least one amine - containing polymer such as , but US20110293701 , the contents of each of which are herein
not limited to polylysine, polyethylene imine , polyamido- incorporated by reference in their entirety ). The vaccine
amine ) dendrimers, poly (beta - amino esters ) ( see , e.g. , U.S. 25 dosage form may be selected by methods described herein ,
Pat . No. 8,287,849 , the contents of which are herein incor-

porated by reference in their entirety ) and combinations
thereof.

known in the art and / or described in International Publica

tion No. WO2011150258 and U.S. Publication No.
US20120027806 , the contents of each of which are herein

In some embodiments, the nanoparticles described herein incorporated by reference in their entirety ).
may comprise an amine cationic lipid such as those 30 In some embodiments, the synthetic nanocarrier may
described in International Patent Application No. comprise at least one polynucleotide which encodes at least
WO2013059496 , the contents of which are herein incorpo- one adjuvant. As non- limiting example, the adjuvant may
rated by reference in their entirety . In some embodiments , comprise dimethyldioctadecylammonium -bromide, dimeth
the cationic lipids may have an amino - amine or an amino- yldioctadecylammonium - chloride, dimethyldioctadecylam
35 monium -phosphate or dimethyldioctadecylammonium -ac
amide moiety.
In some embodiments , the therapeutic nanoparticles may etate ( DDA) and an apolar fraction or part of said apolar
comprise at least one degradable polyester which may fraction of a total lipid extract of a mycobacterium ( see , e.g. ,
contain polycationic side chains . Degradeable polyesters U.S. Pat . No. 8,241,610 , the content of which is herein
include , but are not limited to , poly ( serine ester) , poly (L- incorporated by reference in its entirety ). In some embodi
lactide -co - L -lysine ), poly ( 4 - hydroxy - L -proline ester ), and 40 ments, the synthetic nanocarrier may comprise at least one
combinations thereof. In some embodiments, the degradable polynucleotide and an adjuvant. As a non - limiting example ,
polyesters may include a PEG conjugation to form a PEGy- the synthetic nanocarrier comprising and adjuvant may be
lated polymer.
formulated by the methods described in International Pub
In some embodiments , the synthetic nanocarriers may lication No. WO2011150240 and U.S. Publication No.
contain an immunostimulatory agent to enhance the immune 45 US20110293700 , the contents of each of which are herein
response from delivery of the synthetic nanocarrier. As a incorporated by reference in their entirety.
non- limiting example, the synthetic nanocarrier may comIn some embodiments, the synthetic nanocarrier may
prise a Thl immunostimulatory agent, which may enhance encapsulate at least one polynucleotide that encodes a pep
a Th1 - based response of the immune system ( see Interna- tide, fragment or region from a virus. As a non - limiting
tional Pub No. W02010123569 and U.S. Publication No. 50 example, the synthetic nanocarrier may include, but is not

US20110223201 , the contents of each of which are herein limited to , any of the nanocarriers described in International
incorporated by reference in their entirety ).
Publication No. WO2012024621 , WO201202629 ,
In some embodiments, the synthetic nanocarriers may be WO2012024632 and U.S. Publication No. US20120064110 ,
formulated for targeted release. In some embodiments, the US20120058153 and US20120058154 , the contents of each
synthetic nanocarrier is formulated to release the polynucle- 55 of which are herein incorporated by reference in their
otides at a specified pH and / or after a desired time interval. entirety.
As a non -limiting example, the synthetic nanoparticle may
In some embodiments, the synthetic nanocarrier may be
be formulated to release the RNA (e.g. , mRNA ) vaccines coupled to a polynucleotide which may be able to trigger a
after 24 hours and / or at a pH of 4.5 ( see International humoral and/or cytotoxic T lymphocyte ( CTL ) response
Publication Nos . WO2010138193 and WO2010138194 and 60 ( see , e.g. , International Publication No. WO2013019669 ,
US Pub Nos . US20110020388 and US20110027217 , each of the contents of which are herein incorporated by reference in
which is herein incorporated by reference in their entireties ). their entirety).
In some embodiments, the synthetic nanocarriers may be
In some embodiments, the RNA ( e.g. , mRNA ) vaccine
formulated for controlled and / or sustained release of the may be encapsulated in , linked to and / or associated with
polynucleotides described herein . As a non- limiting 65 zwitterionic lipids . Non - limiting examples of zwitterionic
example, the synthetic nanocarriers for sustained release lipids and methods of using zwitterionic lipids are described
may be formulated by methods known in the art, described in U.S. Patent Publication No. US20130216607 , the con

US 10,933,127 B2
95

96
40 to about 70 nm , from about 50 to about 70 nm , from about

tents of which are herein incorporated by reference in their
entirety. In some aspects , the zwitterionic lipids may be used 60 to about 70 nm , from about 20 to about 80 nm , from about
in the liposomes and lipid nanoparticles described herein .
30 to about 80 nm , from about 40 to about 80 nm , from about
In some embodiments, the RNA ( e.g. , mRNA ) vaccine 50 to about 80 nm , from about 60 to about 80 nm , from about
may be formulated in colloid nanocarriers as described in 5 20 to about 90 nm , from about 30 to about 90 nm , from about
U.S. Patent Publication No. US20130197100 , the contents 40 to about 90 nm , from about 50 to about 90 nm , from about
of which are herein incorporated by reference in their 60 to about 90 nm and / or from about 70 to about 90 nm .
entirety.
In some embodiments, such LNPs are synthesized using
In some embodiments, the nanoparticle may be optimized methods comprising microfluidic mixers . Examples of
for oral administration . The nanoparticle may comprise at 10 microfluidic mixers may include , but are not limited to , a slit
least one cationic biopolymer such as , but not limited to , interdigital micromixer including , but not limited to those
chitosan or a derivative thereof. As a non -limiting example, manufactured by Microinnova ( Allerheiligen bei Wildon ,
the nanoparticle may be formulated by the methods Austria ) and / or a staggered herringbone micromixer ( SHM)
described in U.S. Publication No. 20120282343 , the con- ( Zhigaltsev, I. V. et al . , Bottom -up design and synthesis of
tents of which are herein incorporated by reference in their 15 limit size lipid nanoparticle systems with aqueous and
entirety.
triglyceride cores using millisecond microfluidic mixing

In some embodiments, LNPs comprise the lipid KL52 ( an
amino - lipid disclosed in U.S. Application Publication No.
2012/0295832 , the contents of which are herein incorporated by reference in their entirety. Activity and / or safety (as 20

have been published (Langmuir. 2012. 28 : 3633-40 ; Bel
liveau , N. M. et al . , Microfluidic synthesis of highly potent
limit - size lipid nanoparticles for in vivo delivery of siRNA .
Molecular Therapy -Nucleic Acids . 2012. 1 : e37 ; Chen, D. et
measured by examining one or more of ALT /AST, white al . , Rapid discovery of potent siRNA - containing lipid nan
blood cell count and cytokine induction , for example) of oparticles enabled by controlled microfluidic formulation . J
LNP administration may be improved by incorporation of Am Chem Soc . 2012. 134 ( 16 ) : 6948-51 , the contents of each
such lipids . LNPs comprising KL52 may be administered of which are herein incorporated by reference in their
intravenously and / or in one or more doses . In some embodi- 25 entirety ). In some embodiments, methods of LNP generation
ments, administration of LNPs comprising KL52 results in comprising SHM , further comprise the mixing of at least
equal or improved mRNA and / or protein expression as two input streams wherein mixing occurs by microstructure
compared to LNPs comprising MC3 .
induced chaotic advection (MICA) . According to this
In some embodiments, RNA (e.g. , mRNA ) vaccine may method , fluid streams flow through channels present in a
be delivered using smaller LNPs . Such particles may com- 30 herringbone pattern causing rotational flow and folding the
prise a diameter from below 0.1 um up to 100 nm such as , fluids around each other. This method may also comprise a
but not limited to , less than 0.1 um , less than 1.0 um , less surface for fluid mixing wherein the surface changes orien

than 5 um , less than 10 um , less than 15 um , less than 20 um , tations during fluid cycling. Methods of generating LNPs
less than 25 um , less than 30 um , less than 35 um , less than using SHM include those disclosed in U.S. Application
40 um , less than 50 um , less than 55 um , less than 60 um , 35 Publication Nos . 2004/0262223 and 2012/0276209 , the con
less than 65 um , less than 70 um , less than 75 um , less than tents of each of which are herein incorporated by reference
80 um , less than 85 um , less than 90 um , less than 95 um , in their entirety.
less than 100 um , less than 125 um , less than 150 um , less
In some embodiments, the RNA ( e.g. , mRNA ) vaccine of
than 175 um , less than 200 um , less than 225 um , less than the present disclosure may be formulated in lipid nanopar
250 um , less than 275 um , less than 300 um , less than 325 40 ticles created using a micromixer such as , but not limited to ,
um , less than 350 um , less than 375 um , less than 400 um , a Slit Interdigital Microstructured Mixer ( SIMM - V2 ) or a
less than 425 um , less than 450 um , less than 475 um , less Standard Slit Interdigital Micro Mixer ( SSIMM) or Cater
than 500 um , less than 525 um , less than 550 um , less than pillar (CPMM) or Impinging - jet ( IJMM ) from the Institut
575 um , less than 600 um , less than 625 um , less than 650 für Mikrotechnik Mainz GmbH , Mainz Germany ).
um , less than 675 um , less than 700 um , less than 725 um , 45 In some embodiments, the RNA (e.g. , mRNA ) vaccines of
less than 750 um , less than 775 um , less than 800 um , less the present disclosure may be formulated in lipid nanopar
than 825 um , less than 850 um , less than 875 um , less than ticles created using microfluidic technology ( see , e.g. , Whi
900 um , less than 925 um , less than 950 um , less than 975 tesides , George M. The Origins and the Future of Micro
um , or less than 1000 um .
fluidics . Nature, 2006 442 : 368-373 ; and Abraham et al .
??

In some embodiments, RNA ( e.g. , mRNA ) vaccines may 50 Chaotic Mixer for Microchannels . Science , 2002 295 : 647
be delivered using smaller LNPs , which may comprise a 651 ; each of which is herein incorporated by reference in its
diameter from about 1 nm to about 100 nm , from about 1 nm entirety ). As a non- limiting example, controlled microfluidic
to about 10 nm , about 1 nm to about 20 nm , from about 1 formulation includes a passive method for mixing streams of
nm to about 30 nm , from about 1 nm to about 40 nm , from steady pressure -driven flows in micro channels at a low

about 1 nm to about 50 nm , from about 1 nm to about 60 nm , 55 Reynolds number ( see , e.g. , Abraham et al . Chaotic Mixer
from about 1 nm to about 70 nm , from about 1 nm to about for Microchannels . Science , 2002 295 : 647-651 , the con
80 nm , from about 1 nm to about 90 nm , from about 5 nm tents of which are herein incorporated by reference in their
to about from 100 nm , from about 5 nm to about 10 nm , entirety ).
about 5 nm to about 20 nm , from about 5 nm to about 30 nm ,
In some embodiments, the RNA (e.g. , mRNA ) vaccines of
from about 5 nm to about 40 nm , from about 5 nm to about 60 the present disclosure may be formulated in lipid nanopar
50 nm , from about 5 nm to about 60 nm , from about 5 nm ticles created using a micromixer chip such as , but not
to about 70 nm , from about 5 nm to about 80 nm , from about limited to , those from Harvard Apparatus (Holliston , Mass . )
5 nm to about 90 nm , about 10 to about 50 nm , from about or Dolomite Microfluidics ( Royston, UK) . A micromixer
20 to about 50 nm , from about 30 to about 50 nm , from about chip can be used for rapid mixing of two or more fluid
40 to about 50 nm , from about 20 to about 60 nm , from about 65 streams with a split and recombine mechanism .
30 to about 60 nm , from about 40 to about 60 nm , from about
In some embodiments, the RNA (e.g. , mRNA ) vaccines of
20 to about 70 nm , from about 30 to about 70 nm , from about the disclosure may be formulated for delivery using the drug

US 10,933,127 B2
97

98

encapsulating microspheres described in International Pat-

ent Publication No. WO2013063468 or U.S. Pat. No. 8,440 ,
614 , the contents of each of which are herein incorporated
by reference in their entirety. The microspheres may comprise a compound of the formula (I ) , (II ) , (III ) , (IV) , (V) or
(VI ) as described in International Patent Publication No.
WO2013063468 , the contents of which are herein incorporated by reference in their entirety. In some embodiments,
the amino acid , peptide, polypeptide, lipids ( APPL ) are
useful in delivering the RNA ( e.g. , mRNA ) vaccines of the
disclosure to cells ( see International Patent Publication No.
WO2013063468 , the contents of which are herein incorporated by reference in their entirety ).
In some embodiments, the RNA ( e.g. , mRNA ) vaccines of
the disclosure may be formulated in lipid nanoparticles
having a diameter from about 10 to about 100 nm such as ,
but not limited to , about 10 to about 20 nm , about 10 to about
30 nm , about 10 to about 40 nm , about 10 to about 50 nm ,
about 10 to about 60 nm , about 10 to about 70 nm , about 10
to about 80 nm , about 10 to about 90 nm , about 20 to about
30 nm , about 20 to about 40 nm , about 20 to about 50 nm ,
about 20 to about 60 nm , about 20 to about 70 nm , about 20
to about 80 nm , about 20 to about 90 nm , about 20 to about
100 nm , about 30 to about 40 nm , about 30 to about 50 nm ,
about 30 to about 60 nm , about 30 to about 70 nm , about 30
to about 80 nm , about 30 to about 90 nm , about 30 to about
100 nm , about 40 to about 50 nm , about 40 to about 60 nm ,
about 40 to about 70 nm , about 40 to about 80 nm , about 40
to about 90 nm , about 40 to about 100 nm , about 50 to about

entirety. As a non - limiting example , a subject may be

5

10

15

20

25

administered an empty polymeric particle prior to , simulta
neously with or after delivering the RNA (e.g. , mRNA )
vaccines to the subject. The empty polymeric particle under
goes a change in volume once in contact with the subject and
becomes lodged, embedded , immobilized or entrapped at a
specific location in the subject.
In some embodiments, the RNA (e.g. , mRNA ) vaccines
may be formulated in an active substance release system
( see , e.g. , U.S. Patent Publication No. US20130102545 , the
contents of which are herein incorporated by reference in
their entirety ). The active substance release system may
comprise 1 ) at least one nanoparticle bonded to an oligo
nucleotide inhibitor strand which is hybridized with a cata
lytically active nucleic acid and 2 ) a compound bonded to at
least one substrate molecule bonded to a therapeutically
active substance (e.g. , polynucleotides described herein ),
where the therapeutically active substance is released by the
cleavage of the substrate molecule by the catalytically active
nucleic acid .
In some embodiments, the RNA (e.g. , mRNA ) vaccines
may be formulated in a nanoparticle comprising an inner
core comprising a non - cellular material and an outer surface
comprising a cellular membrane . The cellular membrane
may be derived from a cell or a membrane derived from a
virus. As a non - limiting example, the nanoparticle may be
made by the methods described in International Patent
Publication No. WO2013052167 , the contents of which are
herein incorporated by reference in their entirety . As another

60 nm , about 50 to about 70 nm about 50 to about 80 nm , 30 non - limiting example , the nanoparticle described in Inter

about 50 to about 90 nm , about 50 to about 100 nm , about
60 to about 70 nm , about 60 to about 80 nm , about 60 to
about 90 nm , about 60 to about 100 nm , about 70 to about
80 nm , about 70 to about 90 nm , about 70 to about 100 nm ,
about 80 to about 90 nm , about 80 to about 100 nm and /or 35

national Patent Publication No. WO2013052167 , the con
tents of which are herein incorporated by reference in their
entirety, may be used to deliver the RNA ( e.g. , mRNA )
vaccines described herein .
In some embodiments, the RNA (e.g. , mRNA ) vaccines

may be formulated in porous nanoparticle - supported lipid
In some embodiments, the lipid nanoparticles may have a bilayers ( protocells ). Protocells are described in Interna
diameter from about 10 to 500 nm .
tional Patent Publication No. WO2013056132 , the contents
In some embodiments, the lipid nanoparticle may have a of which are herein incorporated by reference in their
diameter greater than 100 nm , greater than 150 nm , greater 40 entirety .
than 200 nm , greater than 250 nm , greater than 300 nm ,
In some embodiments, the RNA (e.g. , mRNA ) vaccines
greater than 350 nm , greater than 400 nm , greater than 450 described herein may be formulated in polymeric nanopar
about 90 to about 100 nm .

nm , greater than 500 nm , greater than 550 nm , greater than ticles as described in or made by the methods described in
600 nm , greater than 650 nm , greater than 700 nm , greater U.S. Pat. Nos . 8,420,123 and 8,518,963 and European Patent
than 750 nm , greater than 800 nm , greater than 850 nm , 45 No. EP2073848B1 , the contents of each of which are herein
greater than 900 nm , greater than 950 nm or greater than incorporated by reference in their entirety. As a non- limiting
1000 nm .
example , the polymeric nanoparticle may have a high glass
In some embodiments, the lipid nanoparticle may be a transition temperature such as the nanoparticles described in
limit size lipid nanoparticle described in International Patent or nanoparticles made by the methods described in U.S. Pat.
Publication No. WO2013059922 , the contents of which are 50 No. 8,518,963 , the contents ofwhich are herein incorporated
herein incorporated by reference in their entirety. The limit by reference in their entirety. As another non -limiting
size lipid nanoparticle may comprise a lipid bilayer sur- example , the polymer nanoparticle for oral and parenteral
rounding an aqueous core or a hydrophobic core ; where the formulations may be made by the methods described in
lipid bilayer may comprise a phospholipid such as , but not European Patent No. EP2073848B1 , the contents of which

limited to , diacylphosphatidylcholine, a diacylphosphatidy- 55 are herein incorporated by reference in their entirety.
lethanolamine, a ceramide, a sphingomyelin , a dihyIn some embodiments, the RNA (e.g. , mRNA ) vaccines
drosphingomyelin, a cephalin , a cerebroside, a C8 - C20 fatty described herein may be formulated in nanoparticles used in
acid diacylphophatidylcholine, and l -palmitoyl- 2 - oleoyl imaging. The nanoparticles may be liposome nanoparticles
phosphatidylcholine (POPC ) . In some embodiments, the such as those described in U.S. Patent Publication No
limit size lipid nanoparticle may comprise a polyethylene 60 US20130129636 , herein incorporated by reference in its
glycol - lipid such as , but not limited to , DLPE - PEG , DMPE- entirety . As a non - limiting example, the liposome may
comprise gadolinium (III )2- {4,7 -bis -carboxymethyl -10 - [( N ,
PEG , DPPC - PEG and DSPE - PEG .
In some embodiments, the RNA (e.g. , mRNA ) vaccines N -distearylamidomethyl-N -amido -methyl) -1,4,7,10 -tetra
may be delivered , localized and / or concentrated in a specific azacyclododec - 1 -yl} -acetic acid and a neutral, fully satu
location using the delivery methods described in Interna- 65 rated phospholipid component ( see , e.g. , U.S. Patent
tional Patent Publication No. WO2013063530 , the contents Publication No US20130129636 , the contents of which are
of which are herein incorporated by reference in their herein incorporated by reference in their entirety ).

US 10,933,127 B2
99

100

In some embodiments, the nanoparticles which may be

used in the present disclosure are formed by the methods
described in U.S. Patent Application No. US20130130348 ,
the contents of which are herein incorporated by reference in
their entirety.
The nanoparticles of the present disclosure may further
include nutrients such as , but not limited to , those which

entirety . The nanoparticles of the present disclosure may be

5

deficiencies can lead to health hazards from anemia to neural

made by the methods described in U.S. Patent Publication
No. US20130172406 , the contents of which are herein
incorporated by reference in their entirety .
In some embodiments , the stealth or target -specific stealth
nanoparticles may comprise a polymeric matrix . The poly
meric matrix may comprise two or more polymers such as ,
but not limited to , polyethylenes, polycarbonates, polyan

tube defects ( see , e.g. , the nanoparticles described in Inter-

hydrides, polyhydroxyacids, polypropylfumerates, poly

tents of which are herein incorporated by reference in their
entirety ). As a non - limiting example, the nutrient may be
iron in the form of ferrous, ferric salts or elemental iron ,

ters , poly (orthoesters ), polycyanoacrylates, polyvinyl
alcohols, polyurethanes, polyphosphazenes, polyacrylates,
polymethacrylates, polycyanoacrylates, polyureas, polysty
renes , polyamines, polyesters, polyanhydrides, polyethers ,
polyurethanes, polymethacrylates, polyacrylates, polycya
noacrylates or combinations thereof.
In some embodiments, the nanoparticle may be a nan
oparticle -nucleic acid hybrid structure having a high density
nucleic acid layer. As a non - limiting example, the nanopar
ticle -nucleic acid hybrid structure may made by the methods
described in U.S. Patent Publication No. US20130171646 ,
the contents of which are herein incorporated by reference in
their entirety. The nanoparticle may comprise a nucleic acid
such as , but not limited to , polynucleotides described herein
and / or known in the art .
At least one of the nanoparticles of the present disclosure
may be embedded in in the core a nanostructure or coated
with a low density porous 3 - D structure or coating which is
capable of carrying or associating with at least one payload
within or on the surface of the nanostructure. Non- limiting
examples of the nanostructures comprising at least one
nanoparticle are described in International Patent Publica
tion No. WO2013123523 , the contents of which are herein
incorporated by reference in their entirety.
In some embodiments the RNA ( e.g. , mRNA ) vaccine
may be associated with cationic or polycationic com
pounds , including protamine , nucleoline, spermine or sper
midine, or other cationic peptides or proteins, such as
poly - L - lysine (PLL ) , polyarginine, basic polypeptides , cell
penetrating peptides (CPPs ) , including HIV -binding pep
tides, HIV - 1 Tat (HIV) , Tat - derived peptides, Penetratin ,
VP22 derived or analog peptides , Pestivirus Ems , HSV, VP22
(Herpes simplex ), MAP, KALA or protein transduction

national Patent Publication No W02013072929 , the con- 10 caprolactones, polyamides, polyacetals, polyethers, polyes
iodine , folic acid , vitamins or micronutrients.
In some embodiments, the RNA (e.g. , mRNA ) vaccines of
the present disclosure may be formulated in a swellable

15

nanoparticle . The swellable nanoparticle may be , but is not
limited to , those described in U.S. Pat. No. 8,440,231 , the
contents of which are herein incorporated by reference in
their entirety. As a non -limiting embodiment, the swellable 20
nanoparticle may be used for delivery of the RNA ( e.g. ,
mRNA ) vaccines of the present disclosure to the pulmonary
system ( see , e.g. , U.S. Pat . No. 8,440,231 , the contents of
which are herein incorporated by reference in their entirety ).
The RNA (e.g. , mRNA ) vaccines of the present disclosure 25

may be formulated in polyanhydride nanoparticles such as ,
but not limited to , those described in U.S. Pat . No. 8,449 ,
916 , the contents of which are herein incorporated by
reference in their entirety.
The nanoparticles and microparticles of the present dis- 30
closure may be geometrically engineered to modulate macrophage and / or the immune response . In some embodiments,
the geometrically engineered particles may have varied

shapes , sizes and / or surface charges in order to incorporated
the polynucleotides of the present disclosure for targeted 35
delivery such as , but not limited to , pulmonary delivery ( see ,
e.g. , International Publication No WO2013082111 , the contents of which are herein incorporated by reference in their
entirety ). Other physical features the geometrically engineering particles may have include , but are not limited to , 40
fenestrations, angled arms, asymmetry and surface rough-

ness , charge which can alter the interactions with cells and
tissues . As a non - limiting example, nanoparticles of the
present disclosure may be made by the methods described in domains ( PTDs), PpT620, prolin -rich peptides, arginine - rich
International Publication No WO2013082111 , the contents 45 peptides, lysine -rich peptides , MPG-peptide( s) , Pep - 1 ,
of which are herein incorporated by reference in their L - oligomers , Calcitonin peptide ( s ) , Antennapedia -derived
entirety.
peptides ( particularly from Drosophila antennapedia ),
In some embodiments, the nanoparticles of the present pAntp , plsl , FGF, Lactoferrin , Transportan , Buforin - 2 ,
disclosure may be water soluble nanoparticles such as , but Bac715-24 , SynB , SynB ( 1 ) , pVEC , ACT -derived peptides,
not limited to , those described in International Publication 50 SAP, histones , cationic polysaccharides, for example chito

No. WO2013090601 , the contents of which are herein san , polybrene, cationic polymers, e.g. polyethyleneimine
incorporated by reference in their entirety. The nanoparticles ( PEI ) , cationic lipids , e.g. DOTMA : [ 1- (2,3 - sioleyloxy )
may be inorganic nanoparticles which have a compact and propyl) ] - N , N , N - trimethylammonium chloride , DMRIE ,
zwitterionic ligand in order to exhibit good water solubility. di - C14 -amidine, DOTIM , SAINT, DC - Chol , BGTC , CTAP,
The nanoparticles may also have small hydrodynamic diam- 55 DOPC , DODAP, DOPE : Dioleyl phosphatidylethanol
eters ( HD ) , stability with respect to time , pH , and salinity amine , DOSPA , DODAB , DOIC , DMEPC , DOGS : Diocta
and a low level of non -specific protein binding.
decylamidoglicylspermin , DIMRI : Dimyristooxypropyl
In some embodiments the nanoparticles of the present dimethyl hydroxyethyl ammonium bromide, DOTAP : dio

disclosure may be developed by the methods described in

leoyloxy -3-(trimethylammonio )propane, DC - 6-14 : 0,0

U.S.
Patent Publication No. US20130172406 , the contents 60 ditetradecanoyl-N -.alpha.-trimethylammonioacetyl)dietha
of which are herein incorporated by reference in their nolamine chloride, CLIP 1 : rac - [( 2,3 -dioctadecyloxypropyl)
entirety.

( 2 -hydroxyethyl ) ] -dimethylammonium chloride, CLIP :
In some embodiments, the nanoparticles of the present rac-[2 ( 2,3- dihexadecyloxypropyloxymethyloxy ) ethyl]
disclosure are stealth nanoparticles or target- specific stealth trimethylammonium , CLIPO : rac-[2 ( 2,3 - dihexadecyloxy
nanoparticles such as , but not limited to , those described in 65 propyloxysuccinyloxy Jethyl] -trimethylammonium , oligo
U.S. Patent Publication No. US20130172406 , the contents fectamine , or cationic or polycationic polymers , e.g.
of which are herein incorporated by reference in their modified polyaminoacids, such as beta - aminoacid -polymers

US 10,933,127 B2
101

102

or reversed polyamides , etc., modified polyethylenes , such
R, is selected from the group consisting of H , CN , NO2 ,
as PVP ( poly ( N - ethyl - 4 - vinylpyridinium bromide) ) , etc. , C1-6 alkyl, OR , -S(O ) R , -S ( O ) , N ( R ) 2 , C2-6 alkenyl,
modified acrylates, such as PDMAEMA (poly ( dimethylami- C3-6 carbocycle and heterocycle;
noethyl methylacrylate ) ), etc. , modified amidoamines such
each R is independently selected from the group consist
as PAMAM ( polyamidoamine ) , etc., modified polybetami- 5 ing of C1-3 alkyl , C2-3 alkenyl , and H ;
noester (PBAE ) , such as diamine end modified 1,4 butaneeach R' is independently selected from the group consist
diol diacrylate -co - 5 - amino - 1 -pentanol polymers, etc., den ing of C1-18 alkyl, C2-18 alkenyl, R * YR " , —YR " , and H ;
each R " is independently selected from the group con
drimers , such as polypropylamine dendrimers or PAMAM sisting
alkyl and C3-14 alkenyl;
based dendrimers , etc., polyimine ( s ), such as PEI : poly 10 each ofR *C3-14
is independently selected from the group con
( ethyleneimine ), poly ( propyleneimine ), etc., polyallylam sisting of C1-12
alkyl and C2-12 alkenyl;
ine , sugar backbone based polymers, such as cyclodextrin
each
Y
is
independently
a C3-6 carbocycle;
based polymers , dextran based polymers , chitosan, etc. ,
each
X
is
independently
selected
from the group consist
silan backbone based polymers, such as PMOXA - PDMS ing of F, C1 , Br, and I ; and
copolymers , etc., blockpolymers consisting of a combina 15 m is selected from 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , and 13 .
tion of one or more cationic blocks (e.g. selected from a
In some embodiments, a subset of compounds of Formula
cationic polymer as mentioned above ) and of one or more ( I ) includes those in which when R4 is- ( CH2 ) , Q , (CH )
hydrophilic or hydrophobic blocks (e.g. polyethylenegly- „ CHQR , CHQR , or CQ ( R ) , then ( i ) Q is not —N ( R )2
cole) , etc.
when n is 1 , 2 , 3 , 4 or 5 , or (ii ) Q is not 5 , 6 , or 7 -membered
In other embodiments the RNA (e.g. , mRNA ) vaccine is 20 heterocycloalkyl when n is 1 or 2 .
not associated with a cationic or polycationic compounds .
In some embodiments, another subset of compounds of
In some embodiments, a nanoparticle comprises com- Formula ( I ) includes those in which
pounds of Formula (I ) :
R , is selected from the group consisting of C5-30 alkyl,
C5-20 alkenyl, -R *YR " , —YR " , and --R " M'R ';
25
R2 and Rz are independently selected from the group
consisting
of H , C1-14 alkyl , C2-14 alkenyl, -R * YR ",
RA N Ri R2
-YR " , and —R * OR " , or R2 and R3 , together with the atom
to which they are attached , form a heterocycle or carbocycle;
R7
R5
R4 is selected from the group consisting of a C3-6 carbo
M
R3 ,
30 cycle, (CH2) ,Q, ((CH
CH2) , CHQR, CHQR , CQ ( R) 2 ,
R6
and unsubstituted C1-6 alkyl, where Q is selected from a C3-6
carbocycle , a 5- to 14 -membered heteroaryl having one or
171

or a salt or isomer

wherein :

R? is selected from the group consisting of C5-30 alkyl,

more heteroatoms selected from N , O , and S ,

OR ,

-O ( CH2 ) , N ( R ) , C ( O )OR , -OC ( O ) R , CX3 ,
35 CX H , — CXH
CXH2, CN , C ( O ) N (R ) ,, -N ( R ) C ( O ) R ,
C5-20 alkenyl, -R *YR " , —YR " , and —R " M'R ';
R2 and R3 are independently selected from the group
-N ( R ) S ( O ) R , —N (R ) C ( O ) N ( R ) 2, N (R) C ( S )N ( R) 2 ,
CRN ( R ) , C ( O )OR , N ( R ) Rg , O ( CH2) , OR , -N ( R ) C
consisting of H , C1-14 alkyl, C2-14 alkenyl, R * YR ",
-YR " , and R *OR " , or R and R3 , together with the atom ENR, ) N (R) 2 , N ( R ) C ( = CHR , ) N ( R ) 2, OC ( O ) N ( R ) ,
to which they are attached , form a heterocycle or carbocycle ; -N (R ) C (O ) OR -N ( OR)C ( O )R , -N (OR ) S ( O ) 2R ,

(OR )C ( S ) N
R4 is selected from the group consisting of a Cz. carbo- 40 -N
(OR—N)C ((OOR)OR) ,C ( =NOR
)N C((R O))2, N(RN)2,(OR )NCECHR
,)N
(
R
)
2
,
NR
,
)
cycle , (CH ),, (CH ) , CHQR , CHOR , CQ ( R ) ,

(R ) CNR , ) N ( R ) , CNR ) R , C ( O ) N ( R ) O R ,
and unsubstituted C1-6 alkyl, where Q is selected from a and
5- to 14 -membered heterocycloalkyl having one or
carbocycle, heterocycle , OR
,
OR , O (CH2 ), N (R) 2 , C ( O ) morea heteroatoms
from N , O , and S which is
OR , OC ( O ) R , CX3 , -CX H , CXH2 , CN, —N 45 substituted with oneselected
or more substituents selected from oxo
( R)2, -C ( O ) N ( R ) 2, -N ( R ) C (O )R , N( R)S(O) R, -N ( R ) FO) , OH , amino, mono- or di-alkylamino, and C1-3 alkyl,
C ( O ) N ( R ) 2 , -N ( R ) C ( S ) N ( R ) 2, —N ( RRg , -O (CH2 ) , OR , and
each n is independently selected from 1 , 2 , 3 , 4 , and 5 ;

-N (R )CENR , ) N ( R ) ,, -N ( R )CECHR , ) N ( R ) ,, _OC
N ( R ) C ( O )OR , NOR ) C ( O ) R , —N (OR ) S
( O ) N ( R ) 2, —N

each Rz is independently selected from the group consist
ing of C -3 alkyl , C2-3 alkenyl, and H ;
( O ) , R , -N (OR ) C (O )OR , NOR ) C (O ) N (R ) 2, -N (OR ) 50 each R is independently selected from the group consist

C ( S )N ( R ) ,
-N (OR )CONR ,) N ( R )2
-N (OR )C
SCHR , N (R ) , _CCNR , N ( R ) 2 , -CNR , R ,

ing of C1-3 alkyl, C2-3 alkenyl, and H ;
M and M' are independently selected from C ( O ) O
C ( O ) N ( R ) O R , and C ( R )N (R ) C (O )OR , and each n is
OC ( O ) C ( O )N ( R' ) —, -N(R ' ) C ( O) , C ( 0 ) ,
independently selected from 1 , 2 , 3 , 4 , and 5 ;
C ( S ) , C (S ) S , SC ( S ) , CH (OH ) , —P ( O )
each R, is independently selected from the group consist- 55 heteroaryl
(OR' ) O-, group
-S (;O )2- -S -S—, an aryl group , and a
ing of C1-3 alkyl, C2-3 alkenyl, and H ;
each R is independently selected from the group consistR, is selected from the group consisting of C1-3 alkyl, C2-3
alkenyl, and H ;
ing of C1-3 alkyl, C2-3 alkenyl, and H ;
M and M' are independently selected from -C (O ) O-,
R , is selected from the group consisting of C3-6 carbo

60 cycle and heterocycle;
OC ( O ) - , -C ( O ) N ( R ') — ,
N ( R ) C ( O ) - , -C
-C (S ))S , SC
C ( O ) - , -CC ( S ), C
R, is selected from the group consisting of H , CN , NO2 ,
( S ) CH (OH ) , P (O ) (OR' ) O- , -S ( O ) 2-, S
C -6 alkyl, OR , -S ( O ) 2R , -S ( O ) , N ( R ) 2, C2-6 alkenyl,
C3-6 carbocycle and heterocycle;
S an aryl group , and a heteroaryl group ;
R , is selected from the group consisting of C -3 alkyl, C2-3
each R is independently selected from the group consist
alkenyl, and H ;
65 ing of C1-3 alkyl, C2-3 alkenyl, and H ;
R, is selected from the group consisting of C3-6 carboeach R' is independently selected from the group consist
cycle and heterocycle;
ing of C1-18 alkyl, C2-18 alkenyl, -R *YR " , —YR " , and H ;

US 10,933,127 B2
103

104

each R " is independently selected from the group consisting of C3-14 alkyl and C3-14 alkenyl;
each R * is independently selected from the group consisting of C1-12 alkyl and C2-12 alkenyl;
each Y is independently a C3-6 carbocycle;

In some embodiments, another subset of compounds of
R , is selected from the group consisting of C5-30 alkyl,
C5-20 alkenyl, R * YR " , —YR " , and R " M'R ';
R2 and Rz are independently selected from the group
consisting of H , C1-14 alkyl, C2-14 alkenyl, R * YR " ,
-YR ", and R * OR ", or R2 and Rz , together with the atom
to which they are attached, form a heterocycle or carbocycle;
R4 is selected from the group consisting of a C3-6
carbocycle
, (CH2), Q.C1-6(alkyl
CH ),,where
CHQR ,Q isCHOR
(R) 2 , and unsubstituted
selected,CQ
from
Formula ( 1 ) includes those in which

5

each X is independently selected from the group consist
ing of F , C1 , Br, and I ; and
m is selected from 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , and 13 ,
or salts or isomers thereof.

In some embodiments, another subset of compounds of 10

Formula ( I ) includes those in which
R , is selected from the group consisting of C5-30 alkyl,
C5-20 alkenyl, —R *YR " , —YR " , and —R " M'R ';

a C3-6 carbocycle, a 5- to 14 -membered heteroaryl having
one or more heteroatoms selected from N , O , and S , OR ,
( CH2 ) ,N ( R) 2 , C ( O )OR , OC (OR , CX ,
R2 and Rz are independently selected from the group 15 O
CX , H , CXH , CN
C ( O ))NN( R( )R 2) , -N ( R ) C (O ) R ,
CN, C
consisting of H , C1-14 alkyl, C2-14 alkenyl, -R * YR ",
N ( R )S ( O ) , R , -N ( R ) C ( O ) N ( R ) , -N (R ) C (S )N (R ) 2,
YR " , and -R * OR " , or R2 and R3 , together with the atom
CRN ( R )2C ( O )OR , — N (R )Rg, O (CH2) , OR , -N (R ) C
to which they are attached, form a heterocycle or carbocycle;
NR , ) N ( R ) , -N (R )C (= CHR , )N (R ) OC ( O ) N ( R ) ,
R4 is selected from the group consisting of a C3-6 carboN ( R) C ( O ) OR ,
-N (OR ) C ( O ) R , -N (OR ) S ( O )2R ,
cycle, (CH2), Q , ( CH2) , CHQR , —CHQR , CQ ( R) 2 , 20 N (OR ) C ( O )OR , N (OR ) C ( O ) N (R ) , N (OR ) C ( S ) N
and unsubstituted C1-6 alkyl, where Q is selected from a C3-6 ( R ) —N (OR ) CEONR , N ( R ) 2, -N (OR ) C ( = CHR , ) N
carbocycle , a 5- to 14 -membered heterocycle having one or (R ) 2 , -CE NR , ) R , -C (O ) N (R ) OR , and CONR, )N
more heteroatoms selected from N , O , and S , OR, (R) 2 , and each n is independently selected from 1 , 2 , 3 , 4 ,
O (CH2), N ( R )
C ( O ) OR , VOC ( O ) R , CX3, and 5 ;

CX H , CXH , CN
CN , C ( O )N ( R) 2 , —N ( R ) C (O ) R , 25 each R, is independently selected from the group consist
N (R )S ( O ), R , -N ( R ) C ( O ) N ( R ) , -N (R ) C ( S ) N (R ) , ing of C1-3 alkyl, C2-3 alkenyl, and H ;

CRN ( R) 2C (O ) OR , -N ( R ) R ,, O (CH2 ), OR , -N ( R ) C
each Ro is independently selected from the group consist
ENR , ) N ( R ) ,, -N ( R )CECHR , ) N ( R ) , OC ( O ) N ( R ) , ing of C1-3 alkyl, C2-3 alkenyl, and H ;
-N (R )C (O )OR, -N (OR ) C ( O ) R ,
-N (OR ) S ( O )2R ,
M and M' are independently selected from C (O )O
-N (OR ) C ( O )OR , —N ( OR ) C ( O ) N ( R ) 2, N (OR) C ( S )N 30 OC ( O )- , -C ( O ) N ( R ') — , -N ( R ') C ( O ) - , -C ( O)
( R ) , -N (OR ) CENR , ) N ( R ) , -N (OR ) C ( = CHR , ) N
C ( S ) -C ( S ) S— , -SC ( S ) —, -CH (OH ) —, -P ( O )
(OR ' ) 0 , S (O )2
S — 5— , an aryl group , and a
( R) 2 , CENR , ) R , C ( O ) N ( R )OR ,
and -CNR , ) N ( R ) 2, and each n is independently selected heteroaryl group ;
from 1 , 2 , 3 , 4 , and 5 ; and when Q is a 5- to 14 -membered
R, is selected from the group consisting of C1-3 alkyl , C2-3
.

heterocycle and ( i ) R4 is (CH2) Q in which n is 1 or 2 , or 35 alkenyl, and H ;
( ii ) R4 is – (CH2 ), CHQR in which n is 1 , or (iii ) R4 is
Rg is selected from the group consisting of C3-6 carbo
CHQR , andCQ ( R) 2 , then Q is either a 5- to 14 -mem- cycle and heterocycle;
bered heteroaryl or 8- to 14 -membered heterocycloalkyl;
R, is selected from the group consisting of H , CN , NO2 ,
each R? is independently selected from the group consist- C1-6 alkyl, OR , -S ( O ) 2R , -S ( O ), N ( R ) 2, C2-6 alkenyl,
ing of C -3 alkyl, C2. alkenyl, and H ;
40 C3-6 carbocycle and heterocycle;
each Ro is independently selected from the group consisteach R is independently selected from the group consist
ing of C1-3 alkyl, C2-3 alkenyl, and H ;
ing of C1-3 alkyl, C2-3 alkenyl, and H ;
M and M' are independently selected from C ( O )O- ,
each R' is independently selected from the group consist
OC ( O ) - , C ( O )N ( R' )—, -N ( R ') C ( O ) - , -C ( O ) , ing of C -18 alkyl , C2-18 alkenyl, -R * YR ", -YR" , and H ;

C ( S ) , C ( S ) S , SC ( S ) , CH (OH ) , -P ( O ) 45 each R " is independently selected from the group con
( OR' ) O-, -S ( O ) 2-, SS an aryl group , and a sisting of C3-14 alkyl and C3-14 alkenyl;
heteroaryl group ;
each R * is independently selected from the group con
R , is selected from the group consisting of C1-3 alkyl, C2-3 sisting of C1-12 alkyl and C2-12 alkenyl;
each Y is independently a Cz . carbocycle;
alkenyl, and H ;
R, is selected from the group consisting of C3-6 carbo- 50 each X is independently selected from the group consist
cycle and heterocycle;
ing of F, C1 , Br, and l ; and
R , is selected from the group consisting of H , CN , NO2 ,
m is selected from 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , and 13 ,
C1-6 alkyl, OR , S ( O )2R , S ( O )2N ( R ) 2, C2-6 alkenyl,
or salts or isomers thereof.
C3-6 carbocycle and heterocycle;
In some embodiments, another subset of compounds of

each R is independently selected from the group consist- 55 Formula ( 1 ) includes those in which
R , is selected from the group consisting of C5-30 alkyl,
ing of C1-3 alkyl, C2-3 alkenyl, and H ;
each R' is independently selected from the group consist- C5-20 alkenyl, -R *YR " , —YR " , and —R " M'R' ;
ing of C1-18 alkyl, C2-18 alkenyl, —R * YR " , —YR " , and H ;
R2 and Rz are independently selected from the group
each R " is independently selected from the group con- consisting of H , C2-14 alkyl, C2-14 alkenyl, —R * YR " ,
60 -YR " , and R * OR ", or R2 and R3 , together with the atom
sisting of C3-14 alkyl and C3-14 alkenyl;
each R * is independently selected from the group con- to which they are attached, form a heterocycle or carbocycle;
sisting of C1-12 alkyl and C2-12 alkenyl;
R4 is – (CH ) or ( CH ) , CHQR , where Q is —N
each Y is independently a C2-6 carbocycle ;
(R ) 2 , and n is selected from 3 , 4 , and 5 ;
each X is independently selected from the group consisteach R is independently selected from the group consist
ing of F, C1 , Br , and l ; and
65 ing of C1-3 alkyl, C2-3 alkenyl, and H ;
m is selected from 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , and 13 ,
each Ro is independently selected from the group consist
or salts or isomers thereof.
ing of C1-3 alkyl, C2-3 alkenyl, and H ;

US 10,933,127 B2
105

106

M and M ' are independently selected from CO ) O- ,
OC ( O ) - , C (O )N (R ') ; -N ( R ') C ( O ) , C (O ) ,
SC ( S )
CH (OH ) — —P ( O )
C (S ) , C ( S ) S
(OR ) O
S ( O )2
S S , an aryl group , and a
heteroaryl group ;
R , is selected from the group consisting of C1-3 alkyl, C2-3
alkenyl, and H ;
each R is independently selected from the group consist
ing of C1-3 alkyl, C2-3 alkenyl, and H ;
each R' is independently selected from the group consist
ing of C1.18 alkyl , C2.13 alkenyl, -R * YR ", —YR " , and H ;
each R " is independently selected from the group consisting of C3-14 alkyl and C3-14 alkenyl;
each R * is independently selected from the group consisting of C1-12 alkyl and C1-12 alkenyl;
each Y is independently a C3-6 carbocycle;
each X is independently selected from the group consist

or a salt or isomer thereof, wherein 1 is selected from 1 ,
2 , 3 , 4 , and 5 ; m is selected from 5 , 6 , 7 , 8 , and 9 ; M , is a

bond or M' ; R4 is unsubstituted C1-3alkyl, or - (CH ), Q , in
5

which is OH , - NHC (S )N (R )2, - NHC(O )N (R )2, -N ( R )
C (O ) R , —N (R ) S ( O )2R , —N ( R ) R ,, - NHC NR ,)N (R )2,
- NHCOCHR , N ( R ) 2 , OC ( O ) N ( R ) , -N (R ) C (O )OR ,
heteroaryl or heterocycloalkyl; M and M ' are independently
selected

10

15

C ( 004 OC ( O ) - , -C ( O ) N ( R ') — —P ( O )
( OR )O- , S S— , an aryl group , and a heteroaryl group ;
and R2 and Rz are independently selected from the group
consisting of H , C1-14 alkyl, and C2-14 alkenyl.
In some embodiments, a subset of compounds of Formula
(I ) includes those of Formula ( II ) :
from

ing of F , C1 , Br, and I ; and
m is selected from 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , and 13 ,

MIR

or salts or isomers thereof.

In some embodiments , another subset of compounds of
Formula ( I ) includes those in which
R , is selected from the group consisting of C5-30 alkyl,
C5-20 alkenyl, RR * YR ", —YR " , and R " M'R ';
R2 and Rz are independently selected from the group
consisting of C1-14 alkyl, C2-14 alkenyl, R * YR " , —YR " ,
and R * OR ", or R2 and R3 , together with the atom to which
they are attached , form a heterocycle or carbocycle ;
R4 is selected from the group consisting of — ( CH2) Q ,
(CH2) , CHQR , CHQR , and CQ (R)2 , where Q is
-N ( R ) 2, and n is selected from 1 , 2 , 3 , 4 , and 5 ;
each R, is independently selected from the group consisting of C1-3 alkyl, C2-3 alkenyl , and H ;
each Rg is independently selected from the group consisting of C1-3 alkyl, C2-3 alkenyl, and H ;
M and M' are independently selected from C (O )OOC ( O ) , C ( O ) N ( R ') , -N ( R ') C ( O ) - , -C (O )- ,
C (S ) , C ( S ) S— SC ( S ) , CH (OH ) — , -P ( O )
(OR )O- , -S ( O )2
S S— , an aryl group , and a

20

R4

R3
25

30

35

S

heteroaryl group;
R , is selected from the group consisting of C1-3 alkyl , C2-3

R2
M

40

or a salt or isomer thereof, wherein 1 is selected from 1 , 2 ,
3,4 , and 5 ; M is a bond or M' ; R4 is unsubstituted C1-3 alkyl,
or
(CH2) Q , in which n is 2 , 3 , or 4 , and Q is
?? , NHC ( S ) N ( R ) , NHC ( O ) N ( R ) , N ( R ) C ( O ) R ,
-N ( R ) S ( O )2R , —N ( R )RE, — NHCENR ,)N (R )2, - NHC
ECHR , ) N ( R ) 23 OC ( O ) N ( R ) , —N (R ) C ( O )OR , het
eroaryl or heterocycloalkyl; M and M ' are independently
selected
from C ( O )O
OC ( O )- , -C ( O ) N (R ') — , —P ( O )
(OR ') O ,
S— , an aryl group , and a heteroaryl group ;
and R2 and R3 are independently selected from the group
consisting of H , C1-14 alkyl, and C2-14 alkenyl.
In some embodiments, a subset of compounds of Formula

( I ) includes those of Formula ( IIa) , (IIb ) , (Ilc ) , or (Ile ) :

alkenyl, and H ;
each R is independently selected from the group consist
ing of C1-3 alkyl , C. alkenyl, and H ;

( IIa )

each R' is independently selected from the group consist 45

ing of C1.18 alkyl , C2.18 alkenyl, R * YR ", —YR " , and H ;

each R " is independently selected from the group con

sisting of C3-14 alkyl and C3-14 alkenyl;
each R * is independently selected from the group con

sisting of C1-12 alkyl and C1-12 alkenyl;
each Y is independently a C3-6 carbocycle;
each X is independently selected from the group consist

R4
50

(IIb )

ing of F, C1 , Br, and I ; and

m is selected from 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , and 13 ,
or salts or isomers thereof.

In some embodiments, a subset of compounds of Formula

55

R4

( I ) includes those of Formula ( IA) :
M1-RS

( IA )

( IIC )
60

R2,

R4

R4

177

R3

65

or

US 10,933,127 B2
107

108

-continued

-continued
(Ile)

( IIb )
5

R4

R4
10

or a salt or isomer thereof, wherein R4 is as described
herein .
In some embodiments, a subset of compounds of Formula
( I ) includes those of Formula ( IId ):

( IIC )

15

R4
or

(Ile)

(IId) 20
R'

R"
HO

R5

25 R4

R3 ,

R6

R2

or a salt or isomer thereof, wherein n is 2 , 3 , or 4 ; and m ,

30

R' , R " , and R, through Ro are as described herein . For
example, each of R, and Rz may be independently selected

from the group consisting of C5-14 alkyl and C5-14 alkenyl.
In some embodiments, a subset of compounds of Formula
( I ) includes those of Formula ( IIa) , (IIb ) , (IIc ) , or (Ile ) :

or a salt or isomer thereof, wherein R4 is as described

herein .

In some embodiments , a subset of compounds of Formula

(I ) includes those of Formula ( IId ):
35

(IId)
R
R"
40

HO

R5
R6

( IIa)

R3,

R2
45

or a salt or isomer thereof, wherein n is 2 , 3 , or 4 ; and m ,
R' , R " , and R, through Ro are as described herein . For
example, each of R2 and R3 may be independently selected
50 from the group consisting of C5-14 alkyl and C5-14 alkenyl.
In some embodiments, the compound of Formula ( I ) is
selected from the group consisting of :

R4

( Compound 1 )

HO

US 10,933,127 B2
110

109
-continued

(Compound 2 )

HO

(Compound 3 )

HO

(Compound 4 )

HO

( Compound 5 )

HO

( Compound 6 )

HO1

( Compound 7 )
HO .

( Compound 8 )
N

( Compound 9 )

US 10,933,127 B2
112

111
-continued

( Compound 10 )

HO

(Compound 11 )

HO

(Compound 12 )

MOI...(
(Compound 13 )

??

HO

no

??

( Compound 14)

( Compound 15 )

( Compound 16 )

US 10,933,127 B2
114

113
-continued

( Compound 17 )

( Compound 18 )

HO

( Compound 19 )

?? .

( Compound 20 )

HO

( Compound 21 )

NC

( Compound 22 )

OH

( Compound 23 )

HO

US 10,933,127 B2
116

115
-continued

( Compound 24)

HO

(Compound 25 )

HO

( Compound 26 )

HO

( Compound 27 )

??

( Compound 28 )

HO

( Compound 29 )

HO

( Compound 30 )

HO

US 10,933,127 B2
118

117
-continued

(Compound 31 )

HO

( Compound 32 )

HO

(Compound 33 )

HO

(Compound 34 )

HO

( Compound 35 )

HO

(Compound 36 )

HO

( Compound 37 )

US 10,933,127 B2
120

119
-continued

( Compound 38 )

??

( Compound 39 )

???
????
???
????

(Compound 40 )

N.

( Compound 41 )

( Compound 42 )

( Compound 43 )

HN

( Compound 44)
H2N .

w

US 10,933,127 B2
122

121
-continued

(Compound 45 )
H?N

( Compound 46 )

NH2

(Compound 47 )

HO

~

(Compound 48 )

HO

(Compound 49 )

HO

(Compound 50 )

HO

(Compound 51 )

HO

US 10,933,127 B2
124

123
-continued

(Compound 52 )

HO

( Compound 53 )

HO

( Compound 54 )

HO

( Compound 55 )

HO

( Compound 56 )

HO

( Compound 57 )

.na
HO

( Compound 58 )

US 10,933,127 B2
125

126
-continued

( Compound 59 )

HO

( Compound 60 )

HO

and

(Compound 61 )

HO

30

In further embodiments, the compound of Formula ( I ) is
selected from the group consisting of:
(Compound 62 )

O

HO

( Compound 63 )

HO
and

(Compound 64)

HO

US 10,933,127 B2
127

128

In some embodiments, the compound of Formula ( I ) is
selected from the group consisting of:
( Compound 65 )

?? .
N

(Compound 66 )

?? .
N

( Compound 67 )
HO .

( Compound 68 )
HO

?? .

( Compound 69 )

HO

( Compound 70 )
HO .

US 10,933,127 B2
130

129
-continued

( Compound 71 )
?? ,

( Compound 72 )
HO .

(Compound 73 )
?? .

( Compound 74 )
?? .

( Compound 75 )

HO .
N

?? ,

( Compound 76 )

US 10,933,127 B2
132

131
-continued

( Compound 77 )

?? ,
N

( Compound 78 )

?? .

( Compound 79 )

?? .

a
?? .

(Compound 80 )

'N

(Compound 81 )

?? ,
N

( Compound 82 )

?? ,
N

US 10,933,127 B2
134

133
-continued

( Compound 83 )

?? ,

(Compound 84)

HO.

( Compound 85 )

HO

N

?? .

?? .

HO .

( Compound 86 )

( Compound 87 )

(Compound 88 )

US 10,933,127 B2
136

135
-continued

( Compound 89 )

?? ,

( Compound 90 )

??,
N

( Compound 91 )

HO .

( Compound 92 )

HO .
N

( Compound 93 )

?? .

N

( Compound 94)

US 10,933,127 B2
137

138
-continued
( Compound 95 )

N

Meo

( Compound 96 )
?? .

(Compound 97 )
?? ,

( Compound 98 )
HO .
N

(Compound 99 )
?? .

w

US 10,933,127 B2
140

139
-continued

( Compound 100 )

N

( Compound 101 )

( Compound 102 )

Me01

N

( Compound 103 )

(Compound 104)

?? ,
N

US 10,933,127 B2
142

141
-continued

( Compound 105 )
?? ,
N

you
NH2

( Compound 106 )

OH

( Compound 107 )

F

( Compound 108 )

(Compound 109 )

??????

(Compound 110 )