IP Library › Granted Patent US 12,275,757
Granted Patent B2
US 12,275,757 · App. 18/337,881 · Granted Apr 15, 2025

Self-assembling protein nanostructures displaying paramyxovirus and/or pneumovirus F proteins and their use

Inventors: Neil P. King (Seattle, WA); David Baker (Seattle, WA); Brooke Fiala (Seattle, WA); Lance Joseph Stewart (Seattle, WA); Laurent Perez (Bellinzona, CH); Antonio Lanzavecchia (Bellinzona, CH); Jessica Marcandalli (Bellinzona, CH); Jorge Fallas (Seattle, WA); Yang Hsia (Seattle, WA)
Assignees: UNIVERSITY OF WASHINGTON; INSTITUTE FOR RESEARCH IN BIOMEDICINE
C07K14/005A61K39/12A61P31/14B82Y5/00C12N7/00A61K2039/575C07K2319/735C12N2760/18022C12N2760/18322C12N2760/18522
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Quick Facts
Patent No.
US 12,275,757
App. No.
18/337,881
Granted
Apr 15, 2025
Kind
B2
Abstract

Disclosed herein are nanostructures and their use, where the nanostructures include (a) a plurality of first assemblies, each first assembly comprising a plurality of identical first polypeptides; (b) a plurality of second assemblies, each second assembly comprising a plurality of identical second polypeptides, wherein the second polypeptide differs from the first polypeptide; wherein the plurality of first assemblies non-covalently interact with the plurality of second assemblies to form a nanostructure; and wherein the nanostructure displays multiple copies of one or more paramyxovirus and/or pneumovirus F proteins or antigenic fragments thereof, on an exterior of the nanostructure.

Claims (110)

1. A nanostructure, comprising:

(a) a plurality of first assemblies, each first assembly comprising a plurality of identical first polypeptides;

(b) a plurality of second assemblies, each second assembly comprising a plurality of identical second polypeptides, wherein the second polypeptide differs from the first polypeptide;

wherein the plurality of first assemblies non-covalently interact with the plurality of second assemblies to form a nanostructure; and

wherein the nanostructure displays multiple copies of one or more paramyxovirus and/or pneumovirus F proteins, or antigenic fragments thereof, on an exterior of the nanostructure.

2. The nanostructure of claim 1 , wherein:

(a) the first polypeptides comprise polypeptides having at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity along their full length to the amino acid sequence of a polypeptide selected from the group consisting of SEQ ID NOS: 1-51; and

(b) the second polypeptides comprise polypeptides having at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity along their full length to the amino acid sequence of a polypeptide selected from the group consisting of SEQ ID NOS: 1-51.

3. The nanostructure of claim 1 , wherein the one or more paramyxovirus and/or pneumovirus F proteins, or antigenic fragments thereof, comprise a polypeptide having at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity along its full length to a polypeptide selected from the group consisting of SEQ ID NOS: 53, 61-68, and 101.

4. The nanostructure of claim 1 , wherein the one or more paramyxovirus and/or pneumovirus F proteins, or antigenic fragments thereof, comprise a polypeptide having at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity along its full length to an RSV F protein or mutant thereof selected from the group consisting of SEQ ID NO:53 and 61-64, wherein the polypeptide includes one or more of the following residues: 67I, 149C, 458C, 46G, 465Q, 215P, 92D, and 487Q.

5. The nanostructure of claim 1 , wherein the one or more paramyxovirus and/or pneumovirus F proteins, or antigenic fragments thereof, comprise a polypeptide having at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity along its full length to an MPV F protein or mutant thereof selected from the group consisting of SEQ ID NO:65-68 and 101, wherein the polypeptide includes one or more of the following residues: 113C, 120C, 339C, 160F, 177L, 185P, and 426C.

6. The nanostructure of claim 1 , wherein the first polypeptides and the second polypeptides comprise polypeptides having at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity along their full length to the amino acid sequences selected from the following pairs:

SEQ ID NO:1 and SEQ ID NO:2 (153-34A and I53-34B);

SEQ ID NO:3 and SEQ ID NO:4 (153-40A and I53-40B);

SEQ ID NO:3 and SEQ ID NO:24 (153-40A and I53-40B.1);

SEQ ID NO:23 and SEQ ID NO:4 (153-40A.1 and 153-40B);

SEQ ID NO:35 and SEQ ID NO:36 (153-40A genus and I53-40B genus);

SEQ ID NO:5 and SEQ ID NO:6 (153-47A and I53-47B);

SEQ ID NO:5 and SEQ ID NO:27 (153-47A and I53-47B.1);

SEQ ID NO:5 and SEQ ID NO:28 (153-47A and I53-47B.1NegT2);

SEQ ID NO:25 and SEQ ID NO:6 (153-47A.1 and 153-47B);

SEQ ID NO:25 and SEQ ID NO:27 (153-47A.1 and 153-47B.1);

SEQ ID NO:25 and SEQ ID NO:28 (153-47A.1 and 153-47B.1NegT2);

SEQ ID NO:26 and SEQ ID NO:6 (153-47A.1NegT2 and 153-47B);

SEQ ID NO:26 and SEQ ID NO:27 (153-47A.1NegT2 and 153-47B.1);

SEQ ID NO:26 and SEQ ID NO:28 (153-47A.1NegT2 and I53-47B.1NegT2);

SEQ ID NO:37 and SEQ ID NO:38 (153-47A genus and 153-47B genus);

SEQ ID NO:7 and SEQ ID NO:8 (153-50A and I53-50B);

SEQ ID NO:7 and SEQ ID NO:32 (153-50A and I53-50B.1);

SEQ ID NO:7 and SEQ ID NO:33 (153-50A and I53-50B.1NegT2);

SEQ ID NO:7 and SEQ ID NO:34 (153-50A and 153-50B.4PosT1);

SEQ ID NO:29 and SEQ ID NO:8 (153-50A.1 and 153-50B);

SEQ ID NO:29 and SEQ ID NO:32 (153-50A.1 and 153-50B.1);

SEQ ID NO:29 and SEQ ID NO:33 (153-50A.1 and 153-50B.1NegT2);

SEQ ID NO:29 and SEQ ID NO:34 (153-50A.1 and 153-50B.4PosT1);

SEQ ID NO:30 and SEQ ID NO:8 (153-50A.1NegT2 and I53-50B);

SEQ ID NO:30 and SEQ ID NO:32 (153-50A.1NegT2 and I53-50B.1);

SEQ ID NO:30 and SEQ ID NO:33 (153-50A.1NegT2 and I53-50B.1NegT2);

SEQ ID NO:30 and SEQ ID NO:34 (153-50A.1NegT2 and I53-50B.4PosT1);

SEQ ID NO:31 and SEQ ID NO:8 (153-50A.1PosT1 and 153-50B);

SEQ ID NO:31 and SEQ ID NO:32 (153-50A.1PosT1 and 153-50B.1);

SEQ ID NO:31 and SEQ ID NO:33 (153-50A.1PosT1 and 153-50B.1NegT2);

SEQ ID NO:31 and SEQ ID NO:34 (153-50A.1PosT1 and 153-50B.4PosT1);

SEQ ID NO:39 and SEQ ID NO:40 (153-50A genus and I53-50B genus);

SEQ ID NO:9 and SEQ ID NO:10 (153-51A and 153-51B);

SEQ ID NO:11 and SEQ ID NO:12 (152-03A and I52-03B);

SEQ ID NO:13 and SEQ ID NO:14 (152-32A and I52-32B);

SEQ ID NO:15 and SEQ ID NO: 16 (152-33A and I52-33B);

SEQ ID NO:17 and SEQ ID NO:18 (132-06A and I32-06B);

SEQ ID NO:19 and SEQ ID NO:20 (132-19A and I32-19B);

SEQ ID NO:21 and SEQ ID NO:22 (132-28A and I32-28B);

SEQ ID NO:23 and SEQ ID NO:24 (153-40A.1 and 153-40B.1);

SEQ ID NO:41 and SEQ ID NO:42 (T32-28A and T32-28B);

SEQ ID NO:43 and SEQ ID NO:44 (T33-09A and T33-09B);

SEQ ID NO:45 and SEQ ID NO:46 (T33-15A and T33-15B);

SEQ ID NO:47 and SEQ ID NO:48 (T33-21A and T33-21B);

SEQ ID NO:49 and SEQ ID NO:50 (T33-28A and T32-28B); and

SEQ ID NO:51 and SEQ ID NO:44 (T33-31B and T33-09B (also referred to as T33-31B)).

7. The nanostructure of claim 1 , wherein the first polypeptides comprise polypeptides having at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity along their full length to the amino acid sequence of T33-31A (SEQ ID NO: 51) and the second polypeptides comprise polypeptides having at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity along their full length to the amino acid sequence of T33-09B/T33-31B (SEQ ID NO:44).

8. The nanostructure of claim 1 , wherein the first polypeptides comprise polypeptides having at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity along their full length to the amino acid sequence of T33-15B (SEQ ID NO: 46) and the second polypeptides comprise polypeptides having at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity along their full length to the amino acid sequence of T33-15A (SEQ ID NO:45).

9. The nanostructure of claim 1 , wherein the first polypeptides comprise polypeptides having at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity along their full length to the amino acid sequence selected from the group consisting of 153-50A (SEQ ID NO:7), 153-50A.1 (SEQ ID NO:29), 153-50A.1NegT2 (SEQ ID NO: 30), and I53-50A.1PosT1 (SEQ ID NO:31), and the second polypeptides comprise polypeptides having at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity along their full length to the amino acid sequence selected from the group consisting of 153-50B (SEQ ID NO:8), 153-50B.1 (SEQ ID NO:32), 153-50B.1NegT2 (SEQ ID NO: 33), and I53-50B.4PosT1 (SEQ ID NO:34).

10. The nanostructure of claim 1 , wherein the first polypeptides comprise polypeptides having at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity along their full length to the amino acid sequence of 132-28A (SEQ ID NO: 21) and the second polypeptides comprise polypeptides having at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity along their full length to the amino acid sequence of 132-28B (SEQ ID NO:22).

11. The nanostructure of claim 1 , wherein the one or more paramyxovirus and/or pneumovirus F proteins, or antigenic fragments thereof, are expressed as a fusion protein with the first polypeptides.

12. The nanostructure of claim 11 , wherein the plurality of first assemblies each comprise identical fusion proteins.

13. The nanostructure of claim 11 , wherein the plurality of first assemblies in total comprise two or more paramyxovirus and/or pneumovirus F proteins, or antigenic fragments thereof.

14. The nanostructure of claim 11 , wherein only a subset of the first polypeptides comprises a fusion protein with an F protein or antigenic fragment thereof.

15. The nanostructure of claim 1 , wherein each first assembly comprises a homotrimer of the first polypeptide.

16. The nanostructure of claim 1 , wherein the one or more paramyxovirus and/or pneumovirus F proteins, or antigenic fragments thereof comprises polypeptides having at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity along their full length to the amino acid sequence the amino acid sequence of DS-Cav1 (SEQ ID NO: 53).

17. The nanostructure of claim 11 , wherein each fusion protein comprises an amino acid linker positioned between the first polypeptide and the one or more paramyxovirus and/or pneumovirus F proteins, or antigenic fragment thereof.

18. The nanostructure of claim 17 , wherein the amino acid linker sequence comprises one or more trimerization domain.

19. The nanostructure of claim 17 , wherein the amino acid linker sequence comprises the amino acid sequence GYIPEAPRDGQAYVRKDGEWVLLSTFL (SEQ ID NO: 54).

20. The nanostructure of claim 17 , wherein the amino acid linker sequence comprises a Gly-Ser linker.

21. The nanostructure of claim 11 , wherein the fusion protein comprises polypeptides having at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity along their full length to the amino acid sequence selected from the group consisting of SEQ ID NOS: 69-100.

22. The nanostructure of claim 21 , wherein:

(a) when each fusion protein is DS-Cav1-foldon-T33-31A (SEQ ID NO:69) or DS-Cav1-T33-31A (SEQ ID NO:70), each second polypeptide is T33-31B (SEQ ID NO:44);

(b) when each fusion protein is DS-Cav1-foldon-T33-15B (SEQ ID NO:71) or DS-Cav1-T33-15B (SEQ ID NO:72), each second polypeptide is T33-15A (SEQ ID NO:45);

(c) when each fusion protein is DS-Cav1-foldon-153-50A (SEQ ID NO:73) or DS-Cav1-153-50A (SEQ ID NO:74), each second polypeptide is 153-50B (SEQ ID NO:8), 153-50B.1 (SEQ ID NO: 32), 153-50B.1NegT2 (SEQ ID NO:33), or 153-50B.4PosT1 (SEQ ID NO:34); or

(d) when each fusion protein is DS-Cav1-132-28A (SEQ ID NO:75), each second polypeptide is I32-28B (SEQ ID NO:22).

23. The nanostructure of claim 16 , wherein each first polypeptide comprises a fusion protein of DS-Cav1 (SEQ ID NO:53) linked to SEQ ID NO:7 (153-50A) via an amino acid linker.

24. The nanostructure of claim 23 , wherein the amino acid linker comprises a Gly-Ser linker and/or a helical extension domain.

25. The nanostructure of claim 11 , wherein each fusion protein comprises the amino acid sequence selected from the group consisting of SEQ ID NOS: 69-77 and 81-90.

26. The nanostructure of claim 23 , wherein each fusion protein comprises the amino acid sequence of SEQ ID NO:76 (F10).

27. The nanostructure of claim 23 , wherein each second polypeptide comprises the amino acid sequence selected from the group consisting of 153-50B (SEQ ID NO:8), 153-50B.1 (SEQ ID NO:32), 153-50B.1NegT2 (SEQ ID NO:33), or 153-50B.4PosT1 (SEQ ID NO: 34).

28. The nanostructure of claim 23 , wherein each second polypeptide comprises the amino acid sequence of 153-50B.4PosT1 (SEQ ID NO:34).

29. The nanostructure of claim 1 , wherein the nanostructure:

(a) binds prefusion F-specific antibodies including but not limited to monoclonal antibody D25;

(b) forms a symmetrical structure, including but not limited to an icosahedral structure;

(c) is stable at 50° C.; and/or

(d) is stable in 2.25M guanidine hydrochloride.

30. A recombinant nucleic acid encoding the first polypeptide fusion protein as recited in claim 11 .

31. A recombinant expression vector comprising the recombinant nucleic acid of claim 30 operatively linked to a promoter.

32. A recombinant host cell, comprising the recombinant expression vector of claim 31 .

33. A recombinant host cell, comprising one or more recombinant expression vectors capable of expressing the first polypeptides and the second polypeptides of claim 1 .

34. An immunogenic composition comprising the nanostructure of claim 1 , and a pharmaceutically acceptable carrier.

35. The immunogenic composition of claim 34 , further comprising an adjuvant.

36. A method for generating an immune response to paramyxovirus and/or pneumovirus F protein in a subject, comprising administering to the subject in need thereof an effective amount of the nanostructure of claim 1 to generate the immune response.

37. A method for treating or limiting a paramyxovirus and/or pneumovirus infection in a subject, comprising administering to the subject in need thereof an effective amount of the nanostructure of claim 1 , thereby treating or preventing paramyxovirus and/or pneumovirus infection in the subject.

38. The method of claim 36 , wherein the administering results in production of paramyxovirus and/or pneumovirus neutralizing antibodies in the subject.

39. The method of claim 38 , wherein the neutralizing antibodies are present in sera of the subject at a titer (1/ID 50 ) of at least 9,400.

40. A process for assembling the nanostructures of claim 1 in vitro, comprising mixing two or more nanostructure components in aqueous conditions to drive spontaneous assembly of the desired nanostructure.

41. The process of claim 40 , wherein the mixing comprises mixing first assemblies comprising first polypeptides each comprising an F protein or antigenic fragment thereof with second assemblies comprising second polypeptides in an approximately 1:1 molar first polypeptide: second polypeptide ratio under conditions and for a time suitable to permit interaction of the first assemblies and the second assemblies to form the nanostructure.

42. The process of claim 40 , wherein the mixing comprises mixing first assemblies comprising first polypeptides, wherein fewer than all first polypeptides comprise an F protein with second assemblies comprising second polypeptides in an approximately 1:1 first polypeptide: second polypeptide molar ratio under conditions and for a time suitable to permit interaction of the first assemblies and the second assemblies to form the nanostructure.

43. The process of claim 40 , wherein the mixing comprises mixing first assemblies comprising first polypeptides each comprising an F protein, wherein in total the first polypeptides comprise multiple different F proteins with second assemblies comprising second polypeptides in an approximately 1:1 molar first polypeptide: second polypeptide ratio under conditions and for a time suitable to permit interaction of the first assemblies and the second assemblies to form the nanostructure comprising multiple F proteins, or antigenic fragments thereof.

44. A method for generating an immune response to paramyxovirus and/or pneumovirus F protein in a subject, comprising administering to the subject in need thereof an effective amount of the immunogenic composition of claim 34 to generate the immune response.

45. A method for treating or limiting a paramyxovirus and/or pneumovirus infection in a subject, comprising administering to the subject in need thereof an effective amount of the immunogenic composition of claim 34 , thereby treating or preventing paramyxovirus and/or pneumovirus infection in the subject.

46. The process of claim 41 , wherein the first polypeptides are trimeric first polypeptides.

47. The process of claim 42 , wherein the first polypeptides are trimeric first polypeptides.

48. The process of claim 42 , wherein fewer than 75% of the first polypeptides comprise an F protein.

49. The process of claim 43 , wherein the first polypeptides are trimeric first polypeptides.

50. The process of claim 43 , wherein the multiple different F proteins comprises 3, 4, or more different F proteins.

Assignments (4)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jun 21, 2023
From: KING, NEIL P.; NICKERSON, BROOKE; STEWART, LANCE JOSEPH
To: UNIVERSITY OF WASHINGTON
Reel/Frame 064021/0859 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jun 21, 2023
From: PEREZ, LAURENT; LANZAVECCHIA, ANTONIO; MARCANDALLI, JESSICA
To: INSTITUTE FOR RESEARCH IN BIOMEDICINE
Reel/Frame 064021/0881 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jun 21, 2023
From: BAKER, DAVID
To: HOWARD HUGHES MEDICAL INSTITUTE
Reel/Frame 064021/0899 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jun 21, 2023
From: HOWARD HUGHES MEDICAL INSTITUTE
To: UNIVERSITY OF WASHINGTON
Reel/Frame 064021/0902 →
Continuity (4)
Continuation 17523174 · Nov 10, 2021
Division 16500331
Provisional Application 62481331 · Apr 4, 2017
Related Publication 20240150411A1 · May 9, 2024
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