Methods for making HLA binding peptides and their uses

Claim 1

A method for making an immunogenic peptide comprising an HLA-A24.1-restricted T cell epitope consisting of about 8-11 amino acid residues that binds to an HLA-A4.1 molecule and induces an HLA-A24.1-restricted cytotoxic T cell response, said method comprising steps of: (a) providing an amino acid sequence of an antigen of interest; (b) identifying within said sequence a putative T cell epitope, wherein said putative epitope consists of about 8-11 amino acid residues and is identified by the presence of a structural motif associated with peptide binding to HLA-A24.1, said structural motif comprising a first amino acid anchor residue at position two from the epitope's N-terminal residue, said first anchor residue selected from the group consisting of Y, F, and W, and a second anchor residue selected from the group consisting of F, I, L, and W as the epitope's carboxyl-terminal amino acid residue (SEQ ID NOS:1231-1234); (c) preparing one or more peptide fragments of said antigen of interest that comprise a structural motif of step (b); (d) testing complexes of said one or more peptide fragments and an HLA-A24.1 molecule for an ability to be recognized by HLA-A24.1 cytotoxic T cells, and to thereby induce a cytotoxic T cell response to the epitope; and (e) selecting said one or more peptide fragments comprising an HLA-A24.1 structural motif of step (b) that induce an HLA-A24.1 cytotoxic T cell response to the epitope.

Claim 2

A method for making an immunogenic peptide comprising an HLA-A24.1-restricted T cell epitope consisting of about 8-11 amino acid residues that binds to an HLA-A4.1 molecule and induces an HLA-A24.1-restricted cytotoxic T cell response, said method comprising steps of: (a) providing an amino acid sequence of an antigen of interest; (b) identifying within said sequence a putative T cell epitope, wherein said putative epitope consists of about 8-11 amino acid residues and is identified by the presence of a structural motif associated with peptide binding to HLA-A24.1, said structural motif comprising a first amino acid anchor residue at position two from the epitope's N-terminal residue, said first anchor residue selected from the group consisting of Y, F, and W, and a second anchor residue selected from the group consisting of F, I, L, and W as the epitope's carboxyl-terminal amino acid residue (SEQ ID NOS:1231-1234); (c) preparing one or more peptide fragments of said antigen of interest that comprise a structural motif of step (b); (d) testing complexes of said one or more peptide fragments and an HLA-A24.1 molecule for an ability to be recognized by HLA-A24.1 cytotoxic T cells, and to thereby induce a cytotoxic T cell response to the epitope; and (e) selecting said one or more peptide fragments comprising an HLA-A24.1 structural motif of step (b) that induce an HLA-A24.1 cytotoxic T cell response to the epitope.

Claim 15

A method of making a peptide that binds to an HLA-A24.1 molecule at a dissociation constant less than 500 nM, the method comprising steps of: (a) providing an amino acid sequence of an antigen of interest; (b) identifying within said sequence a putative T cell epitope from the provided amino acid sequence, wherein said putative epitope consists of about 8-11 amino acid residues and is identified by the presence of a structural motif associated with peptide binding to HLA-A24.1, said structural motif comprising a first amino acid anchor residue at position two from the epitope's N-terminal residue, said first anchor residue selected from the group consisting of Y, F, and W, and a second amino acid anchor residue selected from the group consisting of F, I, L, and W as the epitope's carboxyl-terminal amino acid residue (SEQ ID NOS:1231-1234); (c) preparing one or more peptide fragments of said antigen of interest that comprise a structural motif of step (b); (d) contacting said one or more peptide fragments of step (c) with an HLA-A24.1 molecule; and, (e) selecting said one or more peptide fragments comprising an HLA-A24.1 structural motif of step (b) that bind to an HLA-A24.1 molecule at a dissociation constant of less than 500 nM.

Claim 16

A method of making a peptide that binds to an HLA-A24.1 molecule at a dissociation constant less than 500 nM, the method comprising steps of: (a) providing an amino acid sequence of an antigen of interest; (b) identifying within said sequence a putative T cell epitope from the provided amino acid sequence, wherein said putative epitope consists of about 8-11 amino acid residues and is identified by the presence of a structural motif associated with peptide binding to HLA-A24.1, said structural motif comprising a first amino acid anchor residue at position two from the epitope's N-terminal residue, said first anchor residue selected from the group consisting of Y, F, and W, and a second amino acid anchor residue selected from the group consisting of F, I, L, and W as the epitope's carboxyl-terminal amino acid residue (SEQ ID NOS:1231-1234); (c) preparing one or more peptide fragments of said antigen of interest that comprise a structural motif of step (b); (d) contacting said one or more peptide fragments of step (c) with an HLA-A24.1 molecule; and, (e) selecting said one or more peptide fragments comprising an HLA-A24.1 structural motif of step (b) that bind to an HLA-A24.1 molecule at a dissociation constant of less than 500 nM.

Claim 20

A method for making an immunogenic peptide comprising an HLA-A1-restricted T cell epitope consisting of about 8-11 amino acid residues that binds to an HLA-A1 molecule and induces an HLA-A1-restricted cytotoxic T cell response, said method comprising steps of: (a) providing an amino acid sequence of an antigen of interest; (b) identifying within said sequence a putative T cell epitope, wherein said putative epitope consists of about 8-11 amino acid residues and is identified by the presence of a structural motif associated with peptide binding to HLA-A1, said structural motif is selected from the group consisting of: (i) a first structural motif having a first amino acid anchor residue at position two from the epitope's N-terminal amino acid residue, said first anchor residue selected from the group consisting of T, S, and M, and a second amino acid anchor residue of Y as the epitope's carboxyl-terminal amino acid residue (SEQ ID NOS:1235-1238); and (ii) a second structural motif having a first amino acid anchor residue at position three from the epitope's N-terminal amino acid residue, said first anchor residue selected from the group consisting of D, E, A, and S, and a second amino acid anchor residue of Y as the epitope's carboxyl-terminal amino acid (SEQ ID NOS:1239-1242); (c) preparing one or more peptide fragments of said antigen of interest that comprise a structural motif of step (b); (d) testing complexes of said one or more peptide fragments and an HLA-A1 molecule for an ability to be recognized by HLA-A1 cytotoxic T cells, and to thereby induce a cytotoxic T cell response to the epitope; and (e) selecting said one or more peptide fragments comprising an HLA-A1 structural motif of step (b) that induce an HLA-A1 cytotoxic T cell response to the epitope.

Claim 21

A method for making an immunogenic peptide comprising an HLA-A1-restricted T cell epitope consisting of about 8-11 amino acid residues that binds to an HLA-A1 molecule and induces an HLA-A1-restricted cytotoxic T cell response, said method comprising steps of: (a) providing an amino acid sequence of an antigen of interest; (b) identifying within said sequence a putative T cell epitope, wherein said putative epitope consists of about 8-11 amino acid residues and is identified by the presence of a structural motif associated with peptide binding to HLA-A1, said structural motif is selected from the group consisting of: (i) a first structural motif having a first amino acid anchor residue at position two from the epitope's N-terminal amino acid residue, said first anchor residue selected from the group consisting of T, S, and M, and a second amino acid anchor residue of Y as the epitope's carboxyl-terminal amino acid residue (SEQ ID NOS:1235-1238); and (ii) a second structural motif having a first amino acid anchor residue at position three from the epitope's N-terminal amino acid residue, said first anchor residue selected from the group consisting of D, E, A, and S, and a second amino acid anchor residue of Y as the epitope's carboxyl-terminal amino acid (SEQ ID NOS:1239-1242); (c) preparing one or more peptide fragments of said antigen of interest that comprise a structural motif of step (b); (d) testing complexes of said one or more peptide fragments and an HLA-A1 molecule for an ability to be recognized by HLA-A1 cytotoxic T cells, and to thereby induce a cytotoxic T cell response to the epitope; and (e) selecting said one or more peptide fragments comprising an HLA-A1 structural motif of step (b) that induce an HLA-A1 cytotoxic T cell response to the epitope.

Claim 34

A method of making a peptide that binds to an HLA-A1 molecule at a dissociation constant less than 500 nM, the method comprising steps of: (a) providing an amino acid sequence of an antigen of interest; (b) identifying within said sequence a putative T cell epitope from the provided amino acid sequence, wherein said putative epitope consists of about 8-11 amino acid residues and is identified by the presence of a structural motif associated with peptide binding to HLA-A1, said structural motif wherein the motif is selected from the group consisting of: (i) a first structural motif having a first amino acid anchor residue at position two from the epitope's N-terminal amino acid residue, said first anchor residue selected from the group consisting of T, S, and M, and a second amino acid anchor residue of Y as the epitope's carboxyl-terminal amino acid residue (SEQ ID NOS:1235-1238); and (ii) a second structural motif having a first amino acid anchor residue at position three from the epitope's N-terminal amino acid residue, said first anchor residue selected from the group consisting of D, E, A, and S, and a second amino acid anchor residue of Y as the epitope's carboxyl-terminal amino acid (SEQ ID NOS:1239-1242); (c) preparing one or more peptide fragments of said antigen of interest that comprise a structural motif of step (b); (d) contacting said one or more peptide fragments of step (c) with an HLA-A1 molecule; and, (e) selecting said one or more peptide fragments comprising an HLA-A1 structural motif of step (b) that bind to an HLA-A1 molecule at a dissociation constant of less than 500 nM.

Claim 35

A method of making a peptide that binds to an HLA-A1 molecule at a dissociation constant less than 500 nM, the method comprising steps of: (a) providing an amino acid sequence of an antigen of interest; (b) identifying within said sequence a putative T cell epitope from the provided amino acid sequence, wherein said putative epitope consists of about 8-11 amino acid residues and is identified by the presence of a structural motif associated with peptide binding to HLA-A1, said structural motif wherein the motif is selected from the group consisting of: (i) a first structural motif having a first amino acid anchor residue at position two from the epitope's N-terminal amino acid residue, said first anchor residue selected from the group consisting of T, S, and M, and a second amino acid anchor residue of Y as the epitope's carboxyl-terminal amino acid residue (SEQ ID NOS:1235-1238); and (ii) a second structural motif having a first amino acid anchor residue at position three from the epitope's N-terminal amino acid residue, said first anchor residue selected from the group consisting of D, E, A, and S, and a second amino acid anchor residue of Y as the epitope's carboxyl-terminal amino acid (SEQ ID NOS:1239-1242); (c) preparing one or more peptide fragments of said antigen of interest that comprise a structural motif of step (b); (d) contacting said one or more peptide fragments of step (c) with an HLA-A1 molecule; and, (e) selecting said one or more peptide fragments comprising an HLA-A1 structural motif of step (b) that bind to an HLA-A1 molecule at a dissociation constant of less than 500 nM.

Claim 39

A method for making an immunogenic peptide comprising an HLA-A11-restricted T cell epitope consisting of about 8-11 amino acid residues that binds to an HLA-A11 molecule and induces an HLA-A11-restricted cytotoxic T cell response, said method comprising steps of: (a) providing the amino acid sequence of an antigen of interest; (b) identifying within said sequence a putative T cell epitope, wherein said putative epitope consists of about 8-11 amino acid residues and is identified by the presence of a structural motif associated with peptide binding to HLA-A11, said structural motif comprising a first amino acid anchor residue at position two from the epitope's N-terminal amino acid residue, said first anchor residue selected from the group consisting of L, M, I, V, A, S, T. G, N, C, F, and D, and a second amino acid anchor residue selected from the group consisting of K, R, and H at the epitope's carboxyl-terminal amino acid residue (SEQ ID NOS:1243-1246); (c) preparing one or more peptide fragments of said antigen of interest that comp se a structural motif of step (b); (d) testing complexes of said one or more peptide fragments and an HLA-A11 molecule for an ability to be recognized by HLA-A11 cytotoxic T cells, and to thereby induce a cytotoxic T cell response to the epitope; and (e) selecting said one or more peptide fragments comprising an HLA-A11 structural motif of step (b) that induce an HLA-A11 cytotoxic T cell response to the epitope.

Claim 40

A method for making an immunogenic peptide comprising an HLA-A11-restricted T cell epitope consisting of about 8-11 amino acid residues that binds to an HLA-A11 molecule and induces an HLA-A11-restricted cytotoxic T cell response, said method comprising steps of: (a) providing the amino acid sequence of an antigen of interest; (b) identifying within said sequence a putative T cell epitope, wherein said putative epitope consists of about 8-11 amino acid residues and is identified by the presence of a structural motif associated with peptide binding to HLA-A11, said structural motif comprising a first amino acid anchor residue at position two from the epitope's N-terminal amino acid residue, said first anchor residue selected from the group consisting of L, M, I, V, A, S, T. G, N, C, F, and D, and a second amino acid anchor residue selected from the group consisting of K, R, and H at the epitope's carboxyl-terminal amino acid residue (SEQ ID NOS:1243-1246); (c) preparing one or more peptide fragments of said antigen of interest that comp se a structural motif of step (b); (d) testing complexes of said one or more peptide fragments and an HLA-A11 molecule for an ability to be recognized by HLA-A11 cytotoxic T cells, and to thereby induce a cytotoxic T cell response to the epitope; and (e) selecting said one or more peptide fragments comprising an HLA-A11 structural motif of step (b) that induce an HLA-A11 cytotoxic T cell response to the epitope.

Claim 53

A method of making a peptide that binds to an HLA-A11 molecule at a dissociation constant less than 500 nM, the method comprising steps of: (a) providing an amino acid sequence of an antigen of interest; (b) identifying within said sequence a putative T cell epitope from the provided amino acid sequence, wherein said putative epitope consists of about 8-11 amino acid residues and is identified by the presence of a structural motif associated with peptide binding to HLA-A11, said structural motif comprising a first amino acid anchor residue at position two from the epitope's N-terminal amino acid residue, said first anchor residue selected from the group consisting of L, M, I, V, A, S, T, G, N, C, F, and D, and a second amino acid anchor residue selected from the group consisting of K, R, and H at the epitope's carboxyl-terminal amino acid residue (SEQ ID NOS:1247-1250); (c) preparing one or more peptide fragments of said antigen of interest that comprise a structural motif of step (b); (d) contacting said one or more peptide fragments of step (c) with an HLA-A11 molecule; and, (e) selecting said one or more peptide fragments comprising an HLA-A11 structural motif of step (b) that bind to an HLA-A11 molecule at a dissociation constant of less than 500 nM.

Claim 54

A method of making a peptide that binds to an HLA-A11 molecule at a dissociation constant less than 500 nM, the method comprising steps of: (a) providing an amino acid sequence of an antigen of interest; (b) identifying within said sequence a putative T cell epitope from the provided amino acid sequence, wherein said putative epitope consists of about 8-11 amino acid residues and is identified by the presence of a structural motif associated with peptide binding to HLA-A11, said structural motif comprising a first amino acid anchor residue at position two from the epitope's N-terminal amino acid residue, said first anchor residue selected from the group consisting of L, M, I, V, A, S, T, G, N, C, F, and D, and a second amino acid anchor residue selected from the group consisting of K, R, and H at the epitope's carboxyl-terminal amino acid residue (SEQ ID NOS:1247-1250); (c) preparing one or more peptide fragments of said antigen of interest that comprise a structural motif of step (b); (d) contacting said one or more peptide fragments of step (c) with an HLA-A11 molecule; and, (e) selecting said one or more peptide fragments comprising an HLA-A11 structural motif of step (b) that bind to an HLA-A11 molecule at a dissociation constant of less than 500 nM.

Claim 58

A method for making an immunogenic peptide comprising an HLA-A3.2-restricted T cell epitope consisting of about 8-11 amino acid residues that binds to an HLA-A3.2 molecule and induces an HLA-A3.2-restricted cytotoxic T cell response, said method comprising steps of: (a) providing the amino acid sequence of an antigen of interest; (b) identifying within said sequence a putative T cell epitope, wherein said putative epitope consists of about 8-11 amino acid residues and is identified by the presence of a structural motif associated with peptide binding to HLA-A3.2, said structural motif comprising a first amino acid anchor residue at position two from the epitope's N-terminal amino acid residue, said first anchor residue selected from the group consisting of L, M, I, V, S, A, T, F, C, G, and D, and a second amino acid anchor residue selected from the group consisting of K, R, Y, H, and F at the epitope's carboxyl-terminal amino acid residue (SEQ ID NOS:1251-1254); (c) preparing one or more peptide fragments of said antigen of interest that comprise a structural motif of step (b); (d) testing complexes of said one or more peptide fragments and an HLA-A3.2 molecule for an ability to be recognized by HLA-A3.2 cytotoxic T cells, and to thereby induce a cytotoxic T cell response to the epitope; and (e) selecting said one or more peptide fragments comprising an HLA-A3.2 structural motif of step (b) that induce an HLA-A3.2 cytotoxic T cell response to the epitope.

Claim 59

A method for making an immunogenic peptide comprising an HLA-A3.2-restricted T cell epitope consisting of about 8-11 amino acid residues that binds to an HLA-A3.2 molecule and induces an HLA-A3.2-restricted cytotoxic T cell response, said method comprising steps of: (a) providing the amino acid sequence of an antigen of interest; (b) identifying within said sequence a putative T cell epitope, wherein said putative epitope consists of about 8-11 amino acid residues and is identified by the presence of a structural motif associated with peptide binding to HLA-A3.2, said structural motif comprising a first amino acid anchor residue at position two from the epitope's N-terminal amino acid residue, said first anchor residue selected from the group consisting of L, M, I, V, S, A, T, F, C, G, and D, and a second amino acid anchor residue selected from the group consisting of K, R, Y, H, and F at the epitope's carboxyl-terminal amino acid residue (SEQ ID NOS:1251-1254); (c) preparing one or more peptide fragments of said antigen of interest that comprise a structural motif of step (b); (d) testing complexes of said one or more peptide fragments and an HLA-A3.2 molecule for an ability to be recognized by HLA-A3.2 cytotoxic T cells, and to thereby induce a cytotoxic T cell response to the epitope; and (e) selecting said one or more peptide fragments comprising an HLA-A3.2 structural motif of step (b) that induce an HLA-A3.2 cytotoxic T cell response to the epitope.

Claim 72

A method of making a peptide that binds to an HLA-A3.2 molecule at a dissociation constant less than 500 nM, the method comprising steps of: (a) providing an amino acid sequence of an antigen of interest; (b) identifying within said sequence a putative T cell epitope from the provided amino acid sequence, wherein said putative epitope consists of about 8-11 amino acid residues and is identified by the presence of a structural motif associated with peptide binding to HLA-A3.2, wherein the motif has a first amino acid anchor residue at position two from the epitope's N-terminal amino acid residue, said first anchor residue selected from the group consisting of L, M, I, V, S, A, T, F, C, G, and D, and a second amino acid residue selected from the group consisting of K, R, Y, H, and F at the epitope's carboxyl-terminal amino acid residue (SEQ ID NOS:1251-1254); (c) preparing one or more peptide fragments of said antigen of interest that comprise a structural motif of step (b); (d) contacting said one or more peptide fragments of step (c) with an HLA-A3.2 molecule; and, (e) selecting said one or more peptide fragments comprising an HLA-A3.2 structural motif of step (b) that bind to an HLA-A3.2 molecule at a dissociation constant of less than 500 nM.

Claim 73

A method of making a peptide that binds to an HLA-A3.2 molecule at a dissociation constant less than 500 nM, the method comprising steps of: (a) providing an amino acid sequence of an antigen of interest; (b) identifying within said sequence a putative T cell epitope from the provided amino acid sequence, wherein said putative epitope consists of about 8-11 amino acid residues and is identified by the presence of a structural motif associated with peptide binding to HLA-A3.2, wherein the motif has a first amino acid anchor residue at position two from the epitope's N-terminal amino acid residue, said first anchor residue selected from the group consisting of L, M, I, V, S, A, T, F, C, G, and D, and a second amino acid residue selected from the group consisting of K, R, Y, H, and F at the epitope's carboxyl-terminal amino acid residue (SEQ ID NOS:1251-1254); (c) preparing one or more peptide fragments of said antigen of interest that comprise a structural motif of step (b); (d) contacting said one or more peptide fragments of step (c) with an HLA-A3.2 molecule; and, (e) selecting said one or more peptide fragments comprising an HLA-A3.2 structural motif of step (b) that bind to an HLA-A3.2 molecule at a dissociation constant of less than 500 nM.