# US 2010/0168398 A1 · Method, computing routine, device for predicting properties of MHC/peptide complexes, and data and peptides produced therefrom.

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- Number: US 2010/0168398 A1
- Document ID: US20100168398A1
- Status: Published application
- Kind: A1
- Application number: 12/660,774
- Filed: 2010-03-04
- Published: 2010-07-01
- Earliest claimed: 2002-06-10
- Inventors: Ignace Lasters; Johan Desmet
- Web page: https://patentgrep.com/patent/US20100168398A1

## CPC

- G16B 15/20: Protein or domain folding
- G16B 15/00: ICT specially adapted for analysing two-dimensional [2D] or three-dimensional [3D] molecular structures, e.g. structural or functional relations or structure alignment
- G16B 20/00: ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

## Abstract

The present invention relates to a method for structure-based prediction of properties of peptides and peptide analogs in complex with major histocompatibility (MHC) class I and class II molecules. The said properties mainly relate to the three-dimensional structure of an MHC/peptide complex and the binding affinity of a peptide for an MHC receptor. The invention further relates to a computer program and a device therefor. The invention further relates to data produced by a method of the invention. The invention further relates to peptides and peptide analogs predicted to bind to target-MHC molecules. The present invention thus relates to the field of immunology, with possible applications in manufacture of vaccinates, de-immunization of proteins, and manufacture of therapeutic agents, especially immunotherapeutic agents.

## Claims

### Claim at position 1

1-15. (canceled)

### Claim 16

A method for producing an immunogenic peptide comprising an MHC class I or class II restricted T cell epitope that binds to an MHC class I or class II molecule and induces an MHC class I or II-restricted cytotoxic T cell response, said method comprising the steps of:
(a) providing an amino acid sequence of a polypeptide of interest;
(b) preparing one or more overlapping putative immunogenic peptide fragments of said polypeptide of interest;
(c) receiving a representation of a complete or partial three-dimensional structure of said MHC class I or class II molecule;
(d) obtaining an ensemble of conformational representations of peptide backbone structures of said putative immunogenic peptides, said conformational representations located within the binding site of said MHC molecule;
(e) modeling the side chains of said peptide backbone structures of said ensemble in relation to said MHC molecule, thereby obtaining an ensemble of modeled MHC/peptide complexes;
(f) evaluating the binding properties of said putative immunogenic peptides for said MHC molecule, by using a scoring function which combines at least:
f1) average binding energy component obtained by evaluating one or more components of the potential energy of each complex of the ensemble of step (e);
f2) conformational entropy component obtained by evaluating the conformational entropy for the complete ensemble of each modeled MHC/peptide complex of step (e);
(g) inferring from the results obtained in (f), one or more putative immunogenic peptides that bind to said MHC molecule;
(h) optionally preparing one or more of said putative immunogenic peptides of said polypeptide of interest;
(i) optionally testing complexes of said one or more putative immunogenic peptides said MHC molecule for an ability to be recognized by a MHC cytotoxic T cells, and to thereby induce a cytotoxic T cell response to the epitope; and
(e) selecting said one or more putative immunogenic fragments comprising an MHC class I or class II binding site that induce an MHC class I or class II cytotoxic T cell response to the epitope.

### Claim 17 (depends on 16)

The method according to claim 16 wherein said conformational representation of step (c) is obtained from one of the following:
one or more experimentally determined structures obtained by for example X-ray crystallography, nuclear magnetic resonance spectroscopy, scanning microscopy; or
one or more models derived from an experimentally determined structure, whereby said experimentally determined structure has a high sequence identity to said MHC molecule.

### Claim 18 (depends on 16)

The method according to claim 16 wherein said conformational representation of step (d) is generated by a computer modeling method, said method being able to generate multiple energetically favorable backbone configurations in relation to said MHC molecule.

### Claim 19 (depends on 16)

The method according to claim 16 wherein said conformational representation of step (d) is retrieved from a library of peptide structures pre-oriented in relation to said MHC molecule.

### Claim 20 (depends on 16)

The method according to claim 16 wherein a complex within said ensemble of step (e) is obtained from a side-chain placement algorithm.

### Claim 21 (depends on 16)

The method according to claim 16 wherein the side-chain placement of step (e) not only involves placing the side-chains of the peptide itself, but also involves placing at least one side-chain of said MHC molecule that are in contact with said peptide.

### Claim 22 (depends on 16)

The method according to claim 16 wherein a complex within said ensemble of step (e) is obtained from a side-chain placement algorithm suited for global side-chain optimization.

### Claim 23 (depends on 20)

The method according to claim 20 wherein the side-chain placement algorithm is a dead-end elimination (DEE) algorithm, characterized in that said DEE algorithm eliminates rotameric conformations on the basis of a mathematical criterion that allows the detection of conformations that are not compatible with the globally optimal conformation.

### Claim 24 (depends on 20)

The method according to claim 20 wherein the side-chain placement algorithm is a FASTER algorithm, said algorithm being characterized by a repeated perturbation, relaxation and evaluation step.

### Claim 25 (depends on 16)

The method according to claim 16 wherein the binding affinity of step (f) is represented by a single scoring value for the whole ensemble of MHC/peptide complexes, said scoring value comprising the sum of the conformational entropy for the complete ensemble of MHC/peptide complexes, and the average of the said energetical components of each of the complexes of said ensemble.

### Claim 26 (depends on 16)

The method according to claim 16 wherein the binding affinity of step (f) is evaluated for the global complex, thereby accounting for interactions between pairs of residues from the peptide, the MHC molecule and both the peptide and the MHC molecule.

### Claim 27 (depends on 16)

The method according to claim 16 wherein the entropical component reflects the overall conformational flexibility of the peptide.

### Claim 28 (depends on 16)

The method according to claim 16 wherein the conformational representations of said peptide contained in said library are derived from experimentally determined structures.

### Claim 29 (depends on 18)

The method according to claim 18 wherein the conformational representations of said peptide contained in said library are derived from computer-generated structures, said structures generated by said computer modeling method.

### Claim 30 (depends on 16)

The method according to claim 16 wherein said peptide comprises one or more non-naturally occurring amino acids.

### Claim 31 (depends on 16)

The method according to claim 16 wherein said MHC class I molecule comprises an HLA antigen selected from any of the HLA-A, HLA-B, HLA-C. HLA-E, HLA-F and HLA-G alleles.

### Claim 32 (depends on 16)

The method according to claim 16 wherein said MHC class II molecule comprises an HLA antigen selected from any of the HLA.-DR, HLA-DQ and HLA-DP gene products.

### Claim 33

Data comprising
conformational representations of one or more peptide backbone structures, each peptide demonstrating an interaction with an MHC class I or class II molecule, and
an indication of the MHC molecule associated with said conformational representation.

### Claim 34

A computer program comprising computing routines, stored on a computer readable medium for evaluating the binding affinity of a peptide for an MHC class I or class II molecule, said routines comprising:
receiving an ensemble of conformational representations of structures of the complex between said MHC molecule and said peptide,
evaluating one or more components of the potential energy of each complex of the ensemble,
evaluating the conformational entropy for the complete ensemble.

### Claim 35 (depends on 34)

The computer program according to claim 34 further comprising modeling for each peptide backbone structure of said ensemble in relation to said MHC molecule, at least the side-chains of said peptide.

### Claim 36 (depends on 34)

The computer program according to claim 34 wherein said peptide backbone structures are obtained by computer modeling or by retrieval from a database.

### Claim 37

A device for evaluating the binding affinity of a peptide for an MHC class I or class II molecule, comprising:
receiving an ensemble of conformational representations of structures of the complex between said MHC molecule and said peptide,
evaluating one or more components of the potential energy of each complex of the ensemble,
evaluating the conformational entropy for the complete ensemble.

### Claim 38 (depends on 16)

A peptide which binds MHC class I or class II molecules, said peptide being obtainable by using the method of claim 16.

### Claim 39

(canceled)

### Claim 40 (depends on 38)

A nucleic acid encoding a peptide as defined in claim 38.

### Claim 41 (depends on 40)

A nucleic acid of at least 15 nucleotides in length specifically hybridizing with the nucleic acid of claim 40.

### Claim 42 (depends on 38)

An antibody specifically recognizing a peptide according to claim 38.

### Claim 43 (depends on 40)

An antibody specifically recognizing a nucleic acid according to claim 40.

### Claim 44 (depends on 38)

A method for producing a peptide according to claim 38 comprising:
(a) culturing host cells comprising a nucleic acid encoding the peptide under conditions allowing the expression of the peptide, and,
(b) recovering the produced peptide from the culture.

### Claim 45 (depends on 38)

The peptide according to claim 38 for use as a medicament.

### Claim 46 (depends on 40)

The nucleic acid according to claim 40 for use as a medicament.