Epitope focusing by variable effective antigen surface concentration

• US 9,884,893 B2
• Filed: 05/21/2013
• Issued: 02/06/2018
• 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:
  US14/398,084
• Publication Number:
  US 20150110836A1
• Time in Patent Office: 1,722 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. An immunogenic composition for eliciting an immune response in a subject comprising

at least six antigen proteins,

wherein each of the at least six antigen proteins comprises a common target epitope of surface exposed residues adjacent in tertiary space, the common target epitope having an effective concentration that is greater than the individual concentrations of the at least six antigen proteins, and

wherein the individual concentrations of each of the at least six antigen proteins is insufficient to be immunogenic in the subject on its own, while the immunogenic composition has an effective concentration of the common target epitope to elicit an immune response to the common target epitope in the subject.

2. The immunogenic composition of claim 1, wherein each of the at least six antigen proteins of the immunogenic composition comprises at least 100 amino acid residues.

3. The immunogenic composition of claim 1, wherein the immunogenic composition is in a unit dose.

5. A virus like particle (VLP) comprising the immunogenic composition of claim 1.

6. The immunogenic composition of claim 1, wherein the immunogenic composition elicits an antibody in a B-cell of the subject.

7. The immunogenic composition of claim 1, wherein the immunogenic composition elicits, in the subject, the production of antibodies to the common target epitope.

8. The immunogenic composition of claim 1, wherein the immunogenic composition elicits an adaptive immune response, humoral immune response or an innate immune response from the subject.

9. The composition 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.

10. A method for treating or reducing the likelihood of a disease in a human subject, the method comprising:

administering an immunogenic composition of claim 1 to a human subject in need thereof.

11. The method of claim 10, wherein the disease is selected from the group consisting of:

infectious disease, autoimmune disease, inflammatory disease, neurological disease, addiction, cardiovascular disease, endocrine disease and cancer.

12. The immunogenic composition of claim 1, wherein at least one of the antigen proteins is selected from the group consisting of:

pneumococcal antigens, tuberculosis antigens, anthrax antigens, HIV antigens, seasonal or epidemic flu antigens, influenza antigens, Pertussis antigens, Staphylococcus aureus antigens, Meningococcal antigens, Haemophilus antigens, HPV antigens, or combinations thereof.

13. A recombinant expression vector comprising at least one nucleic acid encoding a plurality of antigen proteins of the immunogenic composition of claim 1.

14. The immunogenic composition of claim 1, wherein the subject is a human.

15. The immunogenic composition of claim 1, wherein the common target epitope is located in a common protein fold of the at least six antigen proteins.

16. The immunogenic composition of claim 1, wherein the immunogenic composition comprises an agent selected from the following group consisting of:

B-cell targeting moiety, T-cell targeting moiety, anti-viral agent, chemotherapeutic agent, a toxin, immunostimulatory agent, adjuvant, and hapten.

17. The immunogenic composition of claim 1, wherein the surface exposed residues adjacent in tertiary space has an area of at least 25 Å

².

18. The immunogenic composition of claim 1, wherein the surface exposed residues adjacent in tertiary space has an area of at most 2000 Å

².

19. The immunogenic composition of claim 1, wherein the surface exposed residues adjacent in tertiary space has an area of about 100 Å

² to about 1500 Å

².

20. The immunogenic composition of claim 1, wherein the common target epitope is at least 50% identity across the at least six antigen proteins of the immunogenic compositions.

21. The immunogenic composition of claim 1, wherein the common target epitope is at least 90% identity across the at least six antigen proteins of the immunogenic compositions.

22. The immunogenic composition of claim 21, wherein the common target epitope is at least 75% identical between any two antigen proteins of the six antigens.

23. The immunogenic composition of claim 22, wherein the at least 75% identity of the common target epitope between any two antigen proteins of the six antigen proteins and the not more than 90% identity between the remainder of the residues that are surface exposed and not part of the common target epitope can be determined by aligning respective residues for maximal correspondence over a comparison window, wherein the comparison window is for viewing residues adjacent in tertiary space.

24. The immunogenic composition of claim 1, wherein the common target epitope residues are discontinuous in primary sequence.

25. The immunogenic composition of claim 1, wherein the common target epitope residues are continuous in primary sequence.

26. The immunogenic composition of claim 1, wherein a maximum solvent exposed surface of the common target epitope circumference distance is about 100 Å

² to about 1500 Å

².

27. The immunogenic composition of claim 1, wherein a first antigen protein of any of the six antigen proteins is immunologically cross reactive with an antibody raised against a second antigen protein of any of the six antigen proteins.

28. The immunogenic composition of claim 1, wherein each of the at least six antigen proteins comprises a non-common target epitope sequence that is at least 30% different from wild type.

29. The immunogenic composition of claim 1, wherein each of the at least six antigen proteins comprises a non-common target epitope sequence that is at most 50% identical.

30. The immunogenic composition of claim 1, wherein each of the at least six antigen proteins is from about 5 kDa to about 1000 kDa in size.

31. The immunogenic composition of claim 1, wherein each of the at least six antigen proteins is at least 100 amino acids in length.

32. The immunogenic composition of claim 1, wherein the composition comprises at least 10 different antigen proteins.

33. The immunogenic composition of claim 1, wherein each of the six antigen proteins have a binding equilibrium dissociation constant to an antibody produced by the subject that is less than 10⁻

7M.

4. A method for generating an immunogenic composition, the method comprising:

a) introducing into a cell, at least one nucleic acid encoding at least six antigen proteins, wherein each antigen protein comprises a common target epitope of surface exposed residues adjacent in tertiary space;

b) optionally, isolating the plurality of antigen proteins;

c) generating an immunogenic composition comprising the at least six antigen proteins, the common target epitope having an effective concentration that is greater than the individual concentrations of the at least six antigen proteins, wherein the individual concentrations of each of the at least six-antigen proteins is insufficient to be immunogenic in a subject on its own, while the immunogenic composition has an effective concentration of the common target epitope to elicit an immune response to the common target epitope in the subject.