Granted Patent B2

US 12,612,621 · App. 18/402,273 · Granted Apr 28, 2026

Inventor: Parag Mallick (San Mateo, CA)

Assignee: Nautilus Subsidiary, Inc.

C12N15/1055G01N33/6845

Abstract

Claims (31)

1 . A method for characterizing an affinity reagent which binds a desired peptide epitope in a plurality of proteins, the method comprising:

obtaining a peptide library comprising a variety of sequence contexts, each peptide of the peptide library comprising the sequence αXβ, wherein X is the desired peptide epitope, wherein X is a sequence of two to seven amino acids, wherein each of α and β comprises at least one amino acid, and wherein each of α and β varies amongst the variety of sequence contexts within the peptide library;

screening a library of different affinity reagents against the peptide library to obtain the affinity reagent from the library of different affinity reagents which binds the desired peptide epitope X in at least 10% of the variety of the sequence contexts;

obtaining binding measurements between the affinity reagent from the library of affinity reagents and a plurality of known protein sequences; and

based upon the binding measurements of the affinity reagent from the library of affinity reagents to the plurality of known protein sequences, determining a model for the affinity reagent, wherein the model infers a binding probability of the affinity reagent from the library of affinity reagents to any protein given a sequence of the protein.

2 . The method of claim 1 , wherein at least one of α and β further comprises a linker.

3 . The method of claim 2 , wherein the linker is attached to a detection moiety.

4 . The method of claim 2 , wherein the linker is attached to a solid support.

5 . The method of claim 1 , wherein α comprises at least two amino acids.

6 . The method of claim 1 , wherein α comprises at least three amino acids.

7 . The method of claim 1 , wherein β comprises at least two amino acids.

8 . The method of claim 1 , wherein β comprises at least three amino acids.

9 . The method of claim 1 , wherein X is a sequence of three amino acids.

10 . The method of claim 1 , wherein the affinity reagent comprises an antibody or antibody fragment.

11 . The method of claim 1 , wherein the affinity reagent comprises an aptamer.

12 . The method of claim 1 , wherein the affinity reagent comprises a peptide.

13 . The method of claim 1 , further comprising screening the affinity reagent from the library of affinity reagents for binding to a library of n-mer peptide sequences, wherein the n-mer peptide sequences comprise two to ten amino acids.

14 . The method of claim 13 , wherein peptides of the library of n-mer peptide sequences comprise the sequence αXβ.

15 . The method of claim 1 , wherein a protein sequence of the plurality of known sequences contains the desired peptide epitope X.

16 . The method of claim 1 , wherein a protein sequence of the plurality of known protein sequences does not contain the desired peptide epitope X.

17 . The method of claim 1 , wherein the variety of sequence contexts comprises at least 400 sequence contexts.

18 . The method of claim 1 , wherein the affinity reagent from the library of affinity reagents binds the desired peptide epitope X in at least 10% of all longer peptides containing the desired peptide epitope X of the variety of the sequence contexts.

19 . The method of claim 1 , wherein the affinity reagent from the library of affinity reagents binds the desired peptide epitope X in at least 15% of the variety of the sequence contexts.

20 . The method of claim 1 , wherein individual affinity reagents of the library of different affinity reagents are immobilized to one or more substrates.

21 . The method of claim 1 , wherein at least one of α and β further comprises a modification selected from the group consisting of a N-terminal modification, a C-terminal modification, a positively-charged group, a negatively-charged group, a hydrophobic group, a sugar, and a nonnaturally occurring amino acid.

22 . The method of claim 1 , wherein the plurality of known protein sequences comprises at least 50 different protein sequences.

23 . The method of claim 1 , wherein the plurality of known protein sequences is provided on an array.

24 . The method of claim 23 , wherein a location of the array contains multiple copies of a protein sequence of the plurality of known protein sequences.

25 . The method of claim 23 , wherein a protein sequence of the plurality of known protein sequences is present at multiple locations of the array.

26 . The method of claim 1 , wherein determining the model for the affinity reagent comprises: (i) providing detected presence or absence of binding of the affinity reagent from the library of affinity reagents to the plurality of known protein sequences to a training algorithm; and (ii) calculating with the training algorithm for a plurality of protein sequences a probability of the affinity reagent from the library of affinity reagents binding to each protein sequence of the plurality of protein sequences.

27 . The method of claim 26 , wherein the plurality of protein sequences comprises known protein sequences of a proteome.

Assignments (1)

Continuity (4)

References Cited (205)