	US 11,673,936 B2
	Method of compact peptide vaccines using residue optimization
David Kenneth Gifford, Newton, MA (US); and Brandon Carter, Cambridge, MA (US)
Assigned to Think Therapeutics, Inc., Newton, MA (US)
Filed by Think Therapeutics, Inc., Newton, MA (US)
Filed on Jul. 13, 2022, as Appl. No. 17/863,603.
Application 17/863,603 is a continuation of application No. 17/389,875, filed on Jul. 30, 2021, granted, now 11,421,015.
Application 17/389,875 is a continuation of application No. 17/114,237, filed on Dec. 7, 2020, granted, now 11,161,892, issued on Nov. 2, 2021.
Prior Publication US 2023/0041112 A1, Feb. 9, 2023
Int. Cl. A61K 39/00 (2006.01); A61K 38/00 (2006.01); C07K 14/74 (2006.01); C07K 14/435 (2006.01); A61K 38/17 (2006.01); G01N 33/569 (2006.01); G16B 20/30 (2019.01); G16B 5/20 (2019.01); G16B 30/00 (2019.01); G16B 20/40 (2019.01); G16B 35/10 (2019.01); G16B 15/20 (2019.01); G16B 5/00 (2019.01)

CPC C07K 14/70539 (2013.01) [A61K 39/0011 (2013.01); G01N 33/56977 (2013.01); G16B 5/00 (2019.02); G16B 5/20 (2019.02); G16B 15/20 (2019.02); G16B 20/30 (2019.02); G16B 20/40 (2019.02); G16B 30/00 (2019.02); G16B 35/10 (2019.02); A61K 38/00 (2013.01)]

30 Claims

1. A method of forming an immunogenic peptide composition, the method comprising:

using a processor to perform the steps of:

determining a plurality of peptide-HLA binding scores for a first peptide sequence, wherein the first peptide sequence is associated with a tumor neoantigen, a pathogen proteome, or a self-protein;

determining whether the first peptide sequence has a peptide-HLA binding score that passes a threshold with respect to at least one HLA allele;

creating a first peptide set comprising at least two modified peptide sequences that each comprise a substitution of at least one amino acid residue of the first peptide sequence;

determining a plurality of peptide-HLA binding scores for each peptide sequence in the first peptide set; and

creating a second peptide set by selecting a subset of the first peptide set, wherein the selecting comprises excluding a peptide-HLA binding score with respect to a first HLA allele for a modified peptide sequence of the at least two modified peptide sequences if a peptide-HLA binding score for the first peptide sequence does not pass the threshold with respect to the first HLA allele;

performing an experimental assay to obtain a peptide-HLA immunogenicity metric for at least one peptide sequence of the second peptide set; and

forming an immunogenic peptide composition comprising the at least one peptide sequence of the second peptide set for which the experimental assay was performed.