# US 12,005,116 B2 · Hepatitis C virus immunogenic compositions and methods of use thereof

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- Number: US 12,005,116 B2
- Document ID: US12005116B2
- Status: Granted
- Kind: B2
- Application number: 18/099,044
- Filed: 2023-01-19
- Published: 2023-10-05
- Granted: 2024-06-11
- Earliest claimed: 2015-07-07
- Assignees: The Governors of the University of Alberta
- Applicants: The Governors of the University of Alberta
- Inventors: Michael Houghton; John L. Law; Michael Logan; Darren Hockman; Abdolamir Landi
- Web page: https://patentgrep.com/patent/US12005116B2

## CPC

- A61K 39/29: Hepatitis virus
- A61K 39/12: Viral antigens
- A61K 39/295: Polyvalent viral antigens (vaccinia virus or variola virus A61K39/285); Mixtures of viral and bacterial antigens
- A61P 31/04: Antibacterial agents
- A61P 31/14: for RNA viruses
- A61P 37/04: Immunostimulants
- C12N 15/861: Adenoviral vectors
- A61K 2039/55544: {Bacterial toxins}
- C07K 2319/00: Fusion polypeptide
- C12N 2770/24234: Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
- A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00)

## Abstract

The present disclosure provides heterodimeric polypeptides comprising: 1) a variant hepatitis C virus (HCV) E2 polypeptide and an HCV E1 polypeptide; 2) a variant HCV E1 polypeptide and an HCV E2 polypeptide; or 3) a variant HCV E1 polypeptide and a variant HCV E2 polypeptide, where the variant HCV E2 polypeptide and/or the HCV E1 polypeptide comprises one or more T cell epitopes, present in an HCV polypeptide other than an HCV E1 polypeptide or an HCV E2 polypeptide. The present disclosure provides nucleic acids encoding a polyprotein that includes E1 and variant E2, E2 and variant E1, or variant E2 and variant E1. The present disclosure provides a method of producing an E1/E2 heterodimer of the present disclosure. The present disclosure provides a method of inducing an immune response in an individual. The present disclosure provides variant E2 polypeptides and variant E1 polypeptides; and nucleic acids encoding same.

## Claims

### Claim 1

A heterodimeric polypeptide comprising:
a) a variant hepatitis C virus (HCV) E2 polypeptide comprising:
i) an HCV E2 polypeptide; and
ii) a heterologous polypeptide comprising a T-cell epitope present in an HCV protein other than E1 and E2,
wherein the heterologous polypeptide:
i) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP29 amino acid sequence set forth in SEQ ID NO:1, wherein the heterologous polypeptide has a length of from 29 amino acids to 32 amino acids;
ii) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP50 amino acid sequence set forth in SEQ ID NO:11, wherein the heterologous polypeptide has a length of from 50 amino acids to 55 amino acids;
iii) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP52 amino acid sequence set forth in SEQ ID NO:2, wherein the heterologous polypeptide has a length of from 52 amino acids to 55 amino acids;
iv) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP70 amino acid sequence set forth in SEQ ID NO:3, wherein the heterologous polypeptide has a length of from 70 amino acids to 75 amino acids;
v) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP100 amino acid sequence set forth in SEQ ID NO:4, wherein the heterologous polypeptide has a length of from 100 amino acids to 105 amino acids;
vi) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP171 amino acid sequence set forth in SEQ ID NO:63, wherein the heterologous polypeptide has a length of from 171 amino acids to 175 amino acids;
vii) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP228 amino acid sequence set forth in SEQ ID NO:10, wherein the heterologous polypeptide has a length of from 228 amino acids to 232 amino acids;
viii) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP553 amino acid sequence set forth in SEQ ID NO:12, wherein the heterologous polypeptide has a length of from 553 amino acids to 560 amino acids;
ix) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP778 amino acid sequence set forth in SEQ ID NO:64, wherein the heterologous polypeptide has a length of about 778 amino acids; or
x) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP1985 amino acid sequence set forth in SEQ ID NO:13, wherein the heterologous polypeptide has a length of about 1985 amino acids; and
b) an HCV E1 polypeptide.

### Claim 2 (depends on 1)

The heterodimeric polypeptide of claim 1, wherein:
a) the HCV E2 polypeptide is derived from an HCV of genotype 1, 2, 3, or 7; and
b) the HCV E1 polypeptide is derived from an HCV of genotype 1, 2, 3, or 7.

### Claim 3 (depends on 1)

The heterodimeric polypeptide of claim 1, wherein the HCV E2 polypeptide comprises an amino acid sequence having at least 20% amino acid sequence identity to an E2 polypeptide depicted in one of FIGS. 1A-1C, FIGS. 2A-2C, FIGS. 3A-3C, and FIGS. 4A-4B.

### Claim 4 (depends on 1)

The heterodimeric polypeptide of claim 1, wherein the HCV E2 polypeptide comprises an amino acid sequence having at least 50% amino acid sequence identity to an E2 polypeptide depicted in one of FIGS. 1A-1C, FIGS. 2A-2C, FIGS. 3A-3C, and FIGS. 4A-4B.

### Claim 5 (depends on 1)

The heterodimeric polypeptide of claim 1, wherein the HCV E1 polypeptide comprises an amino acid sequence having at least 20% amino acid sequence identity to an E1 polypeptide depicted in FIGS. 1A-1C, FIGS. 2A-2C, FIGS. 3A-3C, and FIGS. 4A-4B.

### Claim 6 (depends on 1)

The heterodimeric polypeptide of claim 1, wherein the HCV E1 polypeptide comprises an amino acid sequence having at least 50% amino acid sequence identity to an E1 polypeptide depicted in FIGS. 1A-1C, FIGS. 2A-2C, FIGS. 3A-3C, and FIGS. 4A-4B.

### Claim 7 (depends on 1)

The heterodimeric polypeptide of claim 1, wherein the modified HCV E2 polypeptide and the HCV E1 polypeptide are derived from an HCV of the same genotype.

### Claim 8 (depends on 1)

The heterodimeric polypeptide of claim 1, wherein the modified HCV E2 polypeptide and the HCV E1 polypeptide are derived from an HCV of different genotypes.

### Claim 9

A heterodimeric polypeptide comprising:
a) a variant hepatitis C virus (HCV) E1 polypeptide comprising:
i) an HCV E1 polypeptide; and
ii) a heterologous polypeptide comprising a T-cell epitope present in an HCV protein other than E1 and E2,
wherein the heterologous polypeptide:
i) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP29 amino acid sequence set forth in SEQ ID NO:1, wherein the heterologous polypeptide has a length of from 29 amino acids to 32 amino acids;
ii) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP50 amino acid sequence set forth in SEQ ID NO:11, wherein the heterologous polypeptide has a length of from 50 amino acids to 55 amino acids;
iii) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP52 amino acid sequence set forth in SEQ ID NO:2, wherein the heterologous polypeptide has a length of from 52 amino acids to 55 amino acids;
iv) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP70 amino acid sequence set forth in SEQ ID NO:3, wherein the heterologous polypeptide has a length of from 70 amino acids to 75 amino acids;
v) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP100 amino acid sequence set forth in SEQ ID NO:4, wherein the heterologous polypeptide has a length of from 100 amino acids to 105 amino acids;
vi) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP171 amino acid sequence set forth in SEQ ID NO:63, wherein the heterologous polypeptide has a length of from 171 amino acids to 175 amino acids;
vii) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP228 amino acid sequence set forth in SEQ ID NO:10, wherein the heterologous polypeptide has a length of from 228 amino acids to 232 amino acids;
viii) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP553 amino acid sequence set forth in SEQ ID NO:12, wherein the heterologous polypeptide has a length of from 553 amino acids to 560 amino acids;
ix) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP778 amino acid sequence set forth in SEQ ID NO:64, wherein the heterologous polypeptide has a length of about 778 amino acids; or
x) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP1985 amino acid sequence set forth in SEQ ID NO:13, wherein the heterologous polypeptide has a length of about 1985 amino acids; and
b) an HCV E2 polypeptide.

### Claim 10 (depends on 9)

The heterodimeric polypeptide of claim 9, wherein:
a) the HCV E2 polypeptide is derived from an HCV of genotype 1, 2, 3, or 7; and
b) the HCV E1 polypeptide is derived from an HCV of genotype 1, 2, 3, or 7.

### Claim 11 (depends on 9)

The heterodimeric polypeptide of claim 9, wherein the HCV E2 polypeptide comprises an amino acid sequence having at least 20% amino acid sequence identity to an E2 polypeptide depicted in one of FIGS. 1A-1C, FIGS. 2A-2C, FIGS. 3A-3C, and FIGS. 4A-4B.

### Claim 12 (depends on 9)

The heterodimeric polypeptide of claim 9, wherein the HCV E2 polypeptide comprises an amino acid sequence having at least 50% amino acid sequence identity to an E2 polypeptide depicted in one of FIGS. 1A-1C, FIGS. 2A-2C, FIGS. 3A-3C, and FIGS. 4A-4B.

### Claim 13 (depends on 9)

The heterodimeric polypeptide of claim 9, wherein the HCV E1 polypeptide comprises an amino acid sequence having at least 20% amino acid sequence identity to an E1 polypeptide depicted in FIGS. 1A-1C, FIGS. 2A-2C, FIGS. 3A-3C, and FIGS. 4A-4B.

### Claim 14 (depends on 9)

The heterodimeric polypeptide of claim 9, wherein the HCV E1 polypeptide comprises an amino acid sequence having at least 50% amino acid sequence identity to an E1 polypeptide depicted in FIGS. 1A-1C, FIGS. 2A-2C, FIGS. 3A-3C, and FIGS. 4A-4B.

### Claim 15 (depends on 9)

The heterodimeric polypeptide of claim 9, wherein the variant HCV E1 polypeptide and the HCV E2 polypeptide are derived from an HCV of the same genotype.

### Claim 16 (depends on 9)

The heterodimeric polypeptide of claim 9, wherein the variant HCV E1 polypeptide and the HCV E2 polypeptide are derived from an HCV of different genotypes.

### Claim 17

A heterodimeric polypeptide comprising:
a) a variant hepatitis C virus (HCV) E1 polypeptide comprising:
i) an HCV E1 polypeptide; and
ii) a heterologous polypeptide comprising a T-cell epitope present in an HCV protein other than E1 and E2,
wherein the heterologous polypeptide:
i) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP29 amino acid sequence set forth in SEQ ID NO:1, wherein the heterologous polypeptide has a length of from 29 amino acids to 32 amino acids;
ii) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP50 amino acid sequence set forth in SEQ ID NO:11, wherein the heterologous polypeptide has a length of from 50 amino acids to 55 amino acids;
iii) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP52 amino acid sequence set forth in SEQ ID NO:2, wherein the heterologous polypeptide has a length of from 52 amino acids to 55 amino acids;
iv) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP70 amino acid sequence set forth in SEQ ID NO:3, wherein the heterologous polypeptide has a length of from 70 amino acids to 75 amino acids;
v) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP100 amino acid sequence set forth in SEQ ID NO:4, wherein the heterologous polypeptide has a length of from 100 amino acids to 105 amino acids;
vi) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP171 amino acid sequence set forth in SEQ ID NO:63, wherein the heterologous polypeptide has a length of from 171 amino acids to 175 amino acids;
vii) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP228 amino acid sequence set forth in SEQ ID NO:10, wherein the heterologous polypeptide has a length of from 228 amino acids to 232 amino acids;
viii) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP553 amino acid sequence set forth in SEQ ID NO:12, wherein the heterologous polypeptide has a length of from 553 amino acids to 560 amino acids;
ix) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP778 amino acid sequence set forth in SEQ ID NO:64, wherein the heterologous polypeptide has a length of about 778 amino acids; or
x) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP1985 amino acid sequence set forth in SEQ ID NO:13, wherein the heterologous polypeptide has a length of about 1985 amino acids; and
b) a variant HCV E2 polypeptide comprising:
i) an HCV E2 polypeptide; and
ii) a heterologous polypeptide comprising a T-cell epitope present in an HCV protein other than E1 and E2,
wherein the heterologous polypeptide:
i) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP29 amino acid sequence set forth in SEQ ID NO:1, wherein the heterologous polypeptide has a length of from 29 amino acids to 32 amino acids;
ii) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP50 amino acid sequence set forth in SEQ ID NO:11, wherein the heterologous polypeptide has a length of from 50 amino acids to 55 amino acids;
iii) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP52 amino acid sequence set forth in SEQ ID NO:2, wherein the heterologous polypeptide has a length of from 52 amino acids to 55 amino acids;
iv) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP70 amino acid sequence set forth in SEQ ID NO:3, wherein the heterologous polypeptide has a length of from 70 amino acids to 75 amino acids;
v) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP100 amino acid sequence set forth in SEQ ID NO:4, wherein the heterologous polypeptide has a length of from 100 amino acids to 105 amino acids;
vi) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP171 amino acid sequence set forth in SEQ ID NO:63, wherein the heterologous polypeptide has a length of from 171 amino acids to 175 amino acids;
vii) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP228 amino acid sequence set forth in SEQ ID NO:10, wherein the heterologous polypeptide has a length of from 228 amino acids to 232 amino acids;
viii) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP553 amino acid sequence set forth in SEQ ID NO:12, wherein the heterologous polypeptide has a length of from 553 amino acids to 560 amino acids;
ix) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP778 amino acid sequence set forth in SEQ ID NO:64, wherein the heterologous polypeptide has a length of about 778 amino acids; or
x) comprises an amino acid sequence having at least 20% amino acid sequence identity to the TP1985 amino acid sequence set forth in SEQ ID NO:13, wherein the heterologous polypeptide has a length of about 1985 amino acids.

### Claim 18 (depends on 17)

The heterodimeric polypeptide of claim 17, wherein:
a) the HCV E2 polypeptide is derived from an HCV of genotype 1, 2, 3, or 7; and
b) the HCV E1 polypeptide is derived from an HCV of genotype 1, 2, 3, or 7.

### Claim 19 (depends on 17)

The heterodimeric polypeptide of claim 17, wherein the HCV E2 polypeptide comprises an amino acid sequence having at least 20% amino acid sequence identity to an E2 polypeptide depicted in one of FIGS. 1A-1C, FIGS. 2A-2C, FIGS. 3A-3C, and FIGS. 4A-4B.

### Claim 20 (depends on 17)

The heterodimeric polypeptide of claim 17, wherein the HCV E2 polypeptide comprises an amino acid sequence having at least 50% amino acid sequence identity to an E2 polypeptide depicted in one of FIGS. 1A-1C, FIGS. 2A-2C, FIGS. 3A-3C, and FIGS. 4A-4B.

### Claim 21 (depends on 17)

The heterodimeric polypeptide of claim 17, wherein the HCV E1 polypeptide comprises an amino acid sequence having at least 20% amino acid sequence identity to an E1 polypeptide depicted in FIGS. 1A-1C, FIGS. 2A-2C, FIGS. 3A-3C, and FIGS. 4A-4B.

### Claim 22 (depends on 17)

The heterodimeric polypeptide of claim 17, wherein the HCV E1 polypeptide comprises an amino acid sequence having at least 50% amino acid sequence identity to an E1 polypeptide depicted in FIGS. 1A-1C, FIGS. 2A-2C, FIGS. 3A-3C, and FIGS. 4A-4B.

### Claim 23 (depends on 17)

The heterodimeric polypeptide of claim 17, wherein the modified HCV E2 polypeptide and the variant HCV E1 polypeptide are derived from an HCV of the same genotype.

### Claim 24 (depends on 17)

The heterodimeric polypeptide of claim 17, wherein the modified HCV E2 polypeptide and the variant HCV E1 polypeptide are derived from an HCV of different genotypes.