SARS-CoV-2 antigens and uses thereof

Patent metadata

Field	Value
Publication number	US-11872279-B2
Application number	US-202117512902-A
Country	US
Kind code	B2
Filing date	Oct 28, 2021
Priority date	Oct 30, 2020
Publication date	Jan 16, 2024
Grant date	Jan 16, 2024

Abstract

The present disclosure relates to, inter alia, variants of the receptor binding domain of a coronavirus (e.g., SARS-CoV-2) having increased immunogenicity and reduced aggregation, and the use of the RBD variants in methods for preventing infection of the coronavirus.

First claim

What is claimed is:

1. A SARS-CoV-2 Spike (S) glycoprotein variant, wherein the S glycoprotein variant comprises a receptor binding domain (RBD) having a mutation of at least one amino acid residue in an angiostensin-converting enzyme 2 (ACE2) receptor binding motif (RBM) relative to a wild-type RBD, wherein the residue is (i) hydrophobic; and (ii) within an aggregation-prone region of about 3-15 amino acid residues, wherein the mutation is a substitution of the hydrophobic residue with a different amino acid residue.

2. The SARS-CoV-2 S glycoprotein variant of claim 1 , wherein (a) the hydrophobic residue has a positive AggScore, (b) the substitution of the hydrophobic residue reduces the overall aggregation score of the aggregation prone region by about 5-50% relative to the aggregation prone region without the substitution, and/or (c) the substitution of the hydrophobic residue reduces the overall aggregation score of the S glycoprotein variant by about 5-50% relative to the S glycoprotein variant without the substitution.

3. A SARS-CoV-2 Spike (S) glycoprotein variant, wherein the S glycoprotein variant comprises an RBD having a mutation of at least one amino acid residue in a first and/or second aggregation-prone region relative to a wild-type RBD comprising the amino acid sequence of SEQ ID NO: 1, wherein the first aggregation-prone region comprises amino acid residues 122-126 of SEQ ID NO: 1, and the second aggregation-prone region comprises amino acid residues 158-162 of SEQ ID NO: 1, and wherein the mutation is a substitution with a different amino acid residue.

4. The SARS-CoV-2 S glycoprotein variant of claim 3 , wherein
(a) the at least one amino acid residue is selected from: L122, L125, F126, Y159, F160, and any combination thereof;
(b) the S glycoprotein variant comprises an amino acid substitution at L122 with a different amino acid residue;
(c) the S glycoprotein variant comprises an amino acid substitution at L122 and F160 with a different amino acid residue; or
(d) the S glycoprotein variant comprises an amino acid substitution at L122, L125, F126 and F160 with a different amino acid residue.

5. The SARS-CoV-2 S glycoprotein variant of claim 3 , wherein the substitution is selected from the group: L122K, L122F, L122Y, L122S, L125Y, L125S, L125W, L125N, F126L, F126H, F126V, F126K, Y159V, Y159A, F160W, F160M, F160R, F160N, F160Y, and any combination thereof.

6. The SARS-CoV-2 S glycoprotein variant of claim 5 , wherein
(a) the S glycoprotein variant comprises L122K;
(b) the S glycoprotein variant comprises L122K and F160W; or
(c) the S glycoprotein variant comprises L122K, L125Y, F126L and F160W.

7. The SARS-CoV-2 S glycoprotein variant of claim 3 , wherein the RBD comprises a mutation of at least one asparagine-linked glycosylation site relative to the wild-type RBD.

8. The SARS-CoV-2 S glycoprotein variant of claim 7 , wherein the mutation is selected from:
(i) a substitution or deletion of the asparagine-linked glycosylation site at amino acid residue 1 of SEQ ID NO: 1;
(ii) a substitution or deletion of the asparagine-linked glycosylation site at amino acid residue 13 of SEQ ID NO: 1; or
(iii) a combination of (i)-(ii).

9. The SARS-CoV-2 S glycoprotein variant of claim 3 , comprising an amino acid sequence selected from: SEQ ID NO: 8, 9, 11, 15, and 16.

10. The SARS-CoV-2 S glycoprotein variant of claim 3 , wherein the S glycoprotein variant comprises a mutation of at least one amino acid residue in a first and/or second aggregation-prone region of 3-15 amino acid residues that is not part of the ACE2 RBM, wherein the mutation is a substitution with a different amino acid residue, optionally wherein the different amino acid residue is less hydrophobic, found at the same position in a genetic background of at least one species of SARS-CoV, or both.

11. The SARS-CoV-2 S glycoprotein variant of claim 3 , comprising at least one additional amino acid residue substitution selected from: P7D, V11I, A18P, N24E, R27K, Y35W, V37F, K48R, S53D, L60Y, F62W, I72V, R78D, Q84A, K87V, D98N, L111I, L125N, Q168D, Y178H, L188D, V194R, and any combination thereof.

12. A SARS-CoV-2 S glycoprotein variant, wherein the S glycoprotein variant comprises a RBD comprising a mutation of at least one amino acid residue in an ACE2 RBM relative to a wild-type RBD comprising the amino acid sequence of SEQ ID NO: 1, wherein the amino acid residue is L122 of SEQ ID NO: 1, and optionally F160 of SEQ ID NO: 1, and wherein the mutation is a substitution with a different amino acid residue.

13. The SARS-CoV-2 S glycoprotein variant of claim 12 , wherein the mutation of L122 of SEQ ID NO: 1 is a substitution of leucine with lysine (L122K), phenylalanine (L122F), tyrosine (L122Y), or serine (L122S).

14. The SARS-CoV-2 S glycoprotein variant of claim 12 , wherein the S glycoprotein variant comprises a mutation of F160 of SEQ ID NO: 1, wherein the mutation is a substitution with a different amino acid residue, optionally wherein the different amino acid residue is less hydrophobic, found at the same position in a genetic background of at least one species of SARS-CoV, or both.

15. A nucleic acid comprising a nucleotide sequence encoding the SARS-CoV-2 S glycoprotein variant of claim 1 .

16. An expression vector comprising the nucleic acid of claim 15 .

17. A cell transformed with an expression vector of claim 16 .

18. A method for producing an SARS-CoV-2 S glycoprotein variant, the method comprising maintaining the cell of claim 17 under conditions permitting expression of the S glycoprotein variant.

19. A composition comprising:
(a) the SARS-CoV-2 S glycoprotein variant of claim 1 , and
(b) a pharmaceutically acceptable carrier, adjuvant, or package insert comprising instructions for administration of the composition to a subject for inducing an immune response against the S glycoprotein variant.

20. A method of inducing an immune response in a subject or preventing infection of SARS-CoV-2 in a subject comprising, administering to the subject the SARS-CoV-2 S glycoprotein variant of claim 1 .

Assignees

• Massachusetts Inst Technology

Inventors

• Love J Christopher
• Rodriguez Aponte Sergio Andre
• Dalvie Neil Chandra

Classifications

• A61K39/215 Primary

  Coronaviridae, e.g. avian infectious bronchitis virus · CPC title

• A61P31/14 Primary

  for RNA viruses · CPC title

• C07K14/165

  Coronaviridae, e.g. avian infectious bronchitis virus · CPC title

• C12N7/00

  Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof (preparing medicinal viral antigen or antibody compositions, e.g. virus vaccines, A61K39/00) · CPC title

• C07K14/005

  from viruses · CPC title