Epitope focusing by variable effective antigen surface concentration
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.
1. A computing device comprising a processor; and data storage, storing instructions that, upon execution by the processor, cause the computing device to perform functions comprising:
a. obtaining a target antigen protein sequence and one or more antigen homolog sequences;
b. obtaining structural models of the target antigen protein sequence and the one or more antigen homolog sequences and identifying a plurality of surface-exposed amino acid residues;
c. generating, in silico, a library of a plurality of antigen variants using the structural models, wherein such generation comprises:
i. diversifying non-target epitope surface exposed amino acid residues for each antigen variant based on the structural models;
ii. performing comparisons between each of a plurality of non-target epitope surface exposed regions comprising a commonly defined area between antigen variants of the library,
wherein antigen variants of the library share at least 30% sequence identity in non surface exposed amino acid residues, and wherein antigen variants of the library share at most 90% sequence identity in non target epitope surface exposed amino acid residues; and
d. selecting six or more antigen variants generated in (c).
2. The device of claim 1 , wherein the functions further comprise, following step (b), aligning the structural models of the target antigen and the one or more antigen homolog sequences to create an alignment.
3. The device of claim 2 , following the step of claim 2 , wherein the functions further comprise extracting a weighted score for each amino acid residue frequency of the target antigen protein sequences using the alignment.
4. The device of claim 3 , wherein the weighted score is a positional weight matrix.
5. The device of claim 4 , wherein the positional weight matrix comprises an identity and a frequency of each amino acid permitted at each structurally conserved position in all known variants of the antigen.
6. The device of claim 3 , wherein the functions further comprise, following the step of claim 3 , identifying surface exposed amino acid residues using the weighted score.
7. The device of claim 5 , wherein the functions further comprise, following the step of claim 5 , identifying amino acid residues of one or more target epitopes using the weighted score.
8. The device of claim 5 , wherein the functions further comprise, following the step of claim 5 , identifying one or more target epitopes using the weighted score.
9. The device of claim 7 , wherein the functions further comprise, following the step of claim 7 , identifying one or more target epitopes using the weighted score.
10. The device of claim 1 , wherein the target antigen protein sequence comprises the sequence of a: pneumococcal antigen, tuberculosis antigen, anthrax antigen, HIV antigen, seasonal or epidemic flu antigen, Meningococcal antigen, Haemophilus antigen, or a HPV antigen.
11. The device of claim 1 , wherein the library of a plurality of antigen variants comprises at least 1×10 5 antigen variants.
12. The device of claim 1 , wherein the library of a plurality of antigen variants comprises at least 1×10 6 antigen variants.
13. The device of claim 1 , wherein the library of a plurality of antigen variants comprises at least 1×10 7 antigen variants.
14. The device of claim 1 , wherein the data storage is further configured to store at least some of the sequences of the antigens.
15. The device of claim 1 , wherein one or more peripheral devices are in communication with the processor.
16. The device of claim 1 , wherein the device is operatively coupled to a network.
17. The device of claim 16 , wherein the network is an internet, an intranet, an extranet, a telecommunication network, or a data network.