Epitope focusing by variable effective antigen surface concentration

• US 10,196,427 B2
• Filed: 12/06/2017
• Issued: 02/05/2019
• Est. Priority Date: 05/21/2012
• Status: Active Grant

• Current Assignee: Centivax Incorporated
• Original Assignee: Distributed Bio, Inc.
• Inventors: Glanville, Jacob E.
• Primary Examiner(s): Chestnut, Barry A
• Application Number:
  US15/833,365
• Publication Number:
  US 20180222944A1
• Time in Patent Office: 426 Days
• CPC Class Codes: A61K 2039/515 Animal cells
• CPC Class Codes: A61K 2039/5154 Antigen presenting cells [APCs], e.g. dendritic cells or macrophages
• CPC Class Codes: A61K 2039/53 DNA (RNA) vaccination
• CPC Class Codes: A61K 2039/575 humoral response
• CPC Class Codes: A61K 2039/70 Multivalent vaccine
• CPC Class Codes: A61K 38/46 Hydrolases (3)
• CPC Class Codes: A61K 39/0011 Cancer antigens
• CPC Class Codes: A61K 39/12 Viral antigens
• CPC Class Codes: A61K 39/145 Orthomyxoviridae, e.g. influenza virus
• CPC Class Codes: A61K 39/21 Retroviridae, e.g. equine infectious anemia virus
• CPC Class Codes: C07K 14/005 from viruses
• CPC Class Codes: C12N 2740/16034 Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
• CPC Class Codes: C12N 2740/16071 Demonstrated in vivo effect
• CPC Class Codes: C12N 2740/16122 New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12N 2740/16134 Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
• CPC Class Codes: C12N 2760/16122 New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12N 2760/16134 Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
• CPC Class Codes: C12N 7/00 Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof preparing medicinal viral antigen or antibody compositions, e.g. virus vaccines, A61K39/00
• CPC Class Codes: C12Y 306/05002 Small monomeric GTPase (3.6.5.2)
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/30 : Detection of binding sites or motifs
• CPC Class Codes: G16B 30/00 : ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 : Sequence alignment; Homology search
• CPC Class Codes: G16B 35/00 : ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16B 35/10 : Design of libraries
• CPC Class Codes: G16C 20/60 : In silico combinatorial chemistry

Abstract

The present disclosure provides compositions and methods for the generation of an antibody or immunogenic composition, such as a vaccine, through epitope focusing by variable effective antigen surface concentration. Generally, the composition and methods of the disclosure comprise three steps: a “design process” comprising one or more in silico bioinformatics steps to select and generate a library of potential antigens for use in the immunogenic composition; a “formulation process”, comprising in vitro testing of potential antigens, using various biochemical assays, and further combining two or more antigens to generate one or more immunogenic compositions; and an “administering” step, whereby the immunogenic composition is administered to a host animal, immune cell, subject or patient. Further steps may also be included, such as the isolation and production of antibodies raised by host immune response to the immunogenic composition.

Claims

1. A method for eliciting an immune response in a human subject, the method comprising:

delivering at least six antigens to the human subject, wherein each of the at least six antigens comprises;

a target epitope that is common to each of the at least six antigens; and

one or more non-conserved regions that are outside of the target epitope;

wherein the at least six antigens are delivered such that each individual antigen of the at least six antigens is delivered in an amount that is insufficient to be immunogenic to the human subject on its own, while the at least six antigens are delivered in a combined amount that is sufficient to generate an immune response to the target epitope in the human subject.

2. The method of claim 1, wherein the at least six antigens are delivered as a single composition.

3. The method of claim 1, wherein each of the at least six antigens comprises a peptide backbone.

4. The method of claim 1, wherein, for each of the at least six antigens, the target epitope comprises a plurality of surface-exposed amino acids that are adjacent to one another in tertiary space, but discontinuous from one another in a primary sequence of the antigen.

5. The method of claim 4, wherein the surface-exposed amino acids that are adjacent to one another in tertiary space have a surface-exposed surface area of at least 25 Å

².

6. The method of claim 4, wherein the surface-exposed amino acids that are adjacent to one another in tertiary space have a surface-exposed surface area of at most 2000 Å

².

7. The method of claim 4, wherein the surface-exposed amino acids that are adjacent to one another in tertiary space have a surface-exposed surface area of between 100 Å

² and 1500 Å

².

8. The method of claim 1, wherein each of the at least six antigens share a common protein fold.

9. The method of claim 1, wherein each of the at least six antigens comprises at least 100 amino acid residues.

10. The method of claim 1, wherein each of the at least six antigens is from about 5 kDa to about 1000 kDa in size.

11. The method of claim 1, wherein the common target epitope is at least 90% identical across each of the at least six antigens.

12. The method of claim 1, wherein no antigen of the at least six antigens has more than 90% of its surface-exposed amino acids in common with any of the remaining at least six antigens.

13. The method of claim 1, wherein the immune response comprises an interaction of a CD4+ T-cell with an antigen-class II WIC molecule complex presenting the common target epitope.

14. The method of claim 1, wherein the subject has a disease selected from the group consisting of infectious disease, autoimmune disease, inflammatory disease, neurological disease, addiction, cardiovascular disease, endocrine disease and cancer.

15. The method of claim 1, wherein a first antigen protein of any of the at least six antigens is immunologically cross reactive with an antibody raised against a second antigen protein of any of the at least six antigens.

16. The method of claim 1, wherein the at least six antigens comprises at least 10 different antigens.

17. The method of claim 1, wherein each of the at least six antigens have a binding equilibrium dissociation constant to an antibody produced by the subject that is less than 10⁻

7 M.

18. The method of claim 1, wherein delivering at least six antigens to the human subject comprises delivering one or more nucleic acids that encode each of the at least six antigens.

19. The method of claim 18, wherein delivering the at least six antigens to the human subject comprises further comprises delivery of the one or more nucleic acids via a viral victor or a lipid-containing complex.

20. The method of claim 1, wherein delivering the at least six antigens comprises delivery of antigens via one or more or parenteral delivery, topical delivery, pulmonary delivery, intranasal delivery, vaginal delivery, enteral delivery, rectal delivery, oral delivery, or sublingual delivery.