# US 2021/0241854 A1 · Method for predicting the off-target biding of a peptide which binds to a target peptide presented by a major histocompatibility complex

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- Number: US 2021/0241854 A1
- Document ID: US20210241854A1
- Status: Published application
- Kind: A1
- Application number: 17/158,940
- Filed: 2021-01-26
- Published: 2021-08-05
- Earliest claimed: 2012-12-21
- Assignees: Immunocore Limited; Adaptimmune Limited
- Applicants: Immunocore Limited; Adaptimmune Limited
- Inventors: Brian John CAMERON; Annelise Brigitte VUIDEPOT; Bent Karsten JAKOBSEN
- Web page: https://patentgrep.com/patent/US20210241854A1

## CPC

- G16B 35/20: Screening of libraries
- G01N 33/505: {involving T-cells}
- G01N 33/6866: {Interferon}
- G01N 33/6878: {in epitope analysis}
- G16B 35/00: ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
- G16C 20/60: In silico combinatorial chemistry
- G01N 2333/57: IFN-gamma
- G01N 2333/70539: MHC-molecules, e.g. HLA-molecules
- G01N 2500/04: Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)
- G16C: COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE

## Abstract

The invention provides a method for predicting whether a binding peptide, which binds to a target peptide presented by a Major Histocompatibility Complex (MHC) and is for administration to a subject, has the potential to cross react with another peptide in the subject in vivo. The method comprises the steps of identifying at least one binding motif in the target peptide to which the binding peptide binds; and searching for peptides that are present in the subject that comprise the at least one binding motif and that are not the target peptide. The presence of one or more such peptides indicates that the binding peptide has the potential to cross react in vivo.

## Claims

### Claim 1

A method for predicting whether a binding peptide, which binds to a target peptide presented by a Major Histocompatibility Complex (MHC) and is for administration to a subject, has the potential to cross react with another peptide in the subject in vivo, the method comprising:
identifying at least one binding motif in the target peptide to which the binding peptide binds; and
searching for peptides that are present in the subject that comprise the at least one binding motif and that are not the target peptide,
wherein the presence of one or more such peptides indicates that the binding peptide has the potential to cross react in vivo.

### Claim 2 (depends on 1)

The method of claim 1, wherein the at least one binding motif is identified by:
creating a series of mutants of the target peptide, each mutant having the amino acid residue at one position in the binding sequence thereof that is involved in binding to the binding peptide substituted for an alternative amino acid, such that over the series of mutants the amino acid residue in each position in the binding sequence is substituted for an alternative amino acid; and
testing each mutant in the series for its activity relative to the wild type target peptide,
wherein an amino acid residue at a position within the binding sequence is identified as being part of the binding motif if the mutant in which the amino acid at that position is mutated to an alternative amino acid has a substantial loss of activity relative to the wild type target peptide.

### Claim 3 (depends on 2)

The method of claim 2, further comprising, where an amino acid residue at a position in the binding sequence is not identified as being part of the binding motif, substituting this position with at least one additional amino acid and testing for activity relative to the wild type peptide,
wherein amino acid substitutions which result in a substantial loss of activity relative to the wild type target peptide are considered to be non-tolerated amino acids and not part of the binding motif and/or amino acid substitutions which do not result in a substantial loss of activity relative to the wild type target peptide are considered as part of the binding motif.

### Claim 4 (depends on 2)

The method of claim 2, further comprising creating a series of mutants, each mutant having the amino acid residue at one position in the binding sequence substituted for an alternative amino acid, such that over the series of mutants the amino acid residue in each position in the binding sequence is substituted for all alternative amino acids, and testing each mutant in the series for activity relative to the wild type peptide,
wherein amino acid substitutions which result in a substantial loss of activity relative to the wild type target peptide are considered to be non-tolerated amino acids and not part of the binding motif and/or amino acids substitutions which do not result in a substantial loss of activity relative to the wild type target peptide are considered as part of the binding motif.

### Claim 5 (depends on 2)

The method of claim 2, wherein the activity that is tested is the ability of the mutant to bind to the binding peptide and/or to elicit the biological response caused by binding to the binding peptide.

### Claim 6 (depends on 2)

The method of claim 2, wherein the alternative amino acid has a different side chain to that of the amino acid for which it is being substituted.

### Claim 7 (depends on 2)

The method of claim 2, wherein the alternative amino acid is one that does not appear in the sequence that is involved in binding to the target peptide.

### Claim 8 (depends on 7)

The method of claim 7, wherein the alternative amino acid is alanine or glycine.

### Claim 9 (depends on 1)

The method of claim 1, wherein the subject is a human and the search is carried out for peptides that are of human origin or of organisms which are commonly present in humans.

### Claim 10 (depends on 1)

The method of claim 1, wherein the search is carried out for peptides that are expressed in selected tissue(s) and/or accessible to the binding peptide.

### Claim 11 (depends on 1)

The method of claim 1, further comprising testing binding to the target peptide of any peptide that is present in the subject that comprises the at least one binding motif.

### Claim 12 (depends on 1)

The method of claim 1, further comprising, if no peptides that are present in the subject that comprise the at least one binding motif are found, using the binding peptide for preventing or treating a disease or condition which is ameliorated by administration of the binding peptide.

### Claim 13 (depends on 1)

The method of claim 1, wherein the binding peptide is an immune binding peptide.

### Claim 14 (depends on 11)

The method of claim 11, wherein the immune binding peptide is a T cell receptor or an antibody.