Controlled modulation of amino acid side chain length of peptide antigens

Abstract

The invention provides a method for the creation of peptide antigens comprising epitopes with at least a first modification comprising a shortened or lengthened amino acid side chain. By extension or shortening of the side chain with CH3/CH2 groups, for example, made by computer assisted modeling of the tumor antigen (peptide) bound in the MHC-I-groove, immunogenicity can be improved with minimal modification of adjacent tertiary structure, thereby avoiding cross-reactivity. Provided by the invention are methods of creating such antigens, as well as methods for therapeutic or prophylactic treatment of various conditions comprising administration of the antigens.

1 . A method for preparing a peptide antigen with modulated immunogenicity comprising substituting at least a first amino acid located in a CTL epitope with a first substitute amino acid having an extended or shortened side chain as compared to the first amino acid. 
     
     
         2 . The method of  claim 1 , wherein the first substitute amino acid:
 has the same base residue as the first amino acid;   b) is a non-natural amino acid;   c) extends the side chain of the first amino acid;   d) adds a —CH 2 /CH 3  group to the side chain of the first amino acid;   e) adds two —CH 2 /CH 3  groups to the side chain of the first amino acid;   f) shortens the side chain of the first amino acid;   g) reduces one —CH 2 /CH 3  group on the side chain of the first amino acid;   h) acid reduces two —CH 2 /CH 3  groups on the side chain of the first amino acid;   i) eliminates an —OH group from the side chain of the first amino acid;   j) eliminates an —NH 2  group from the side chain of the first amino acid; or   k) adds an —NH 2  group to the side chain of the first amino acid.   
     
     
         3 . (canceled) 
     
     
         4 . The method of  claim 1 , wherein the side chain of the first substituted amino acid is an aliphatic side chain. 
     
     
         5 .- 13 . (canceled) 
     
     
         14 . The method of  claim 1 , further comprising determining the CTL epitope of the antigen. 
     
     
         15 . The method of  claim 1 , further comprising modeling the CTL epitope while bound in the MHC-1 groove or the MHCII groove. 
     
     
         16 . (canceled) 
     
     
         17 . The method of  claim 1 , further comprising
 a) substituting a second amino acid located in the CTL epitope with a second substitute amino acid having an extended or shortened side chain as compared to the second amino acid in the CTL epitope;   b) substituting a second and third amino acid located in the CTL epitope with a second and third substitute amino acid each having an extended or shortened side chain as compared to the second and third amino acid of the CTL epitope; or   c) substituting a second, third and fourth amino acid located in the CTL epitope with a second, third and fourth substitute amino acid each having an extended or shortened side chain as compared to the second, third and fourth amino acid of the CTL epitope.   
     
     
         18 .- 19 . (canceled) 
     
     
         20 . The method of  claim 1 , wherein the antigen is a tumor antigen. 
     
     
         21 . The method of  claim 20 , wherein the tumor antigen is derived from breast cancer, ovarian cancer, prostate cancer, blood cancer, skin cancer, uterine cancer, cervical cancer, liver cancer, colon cancer, lung cancer brain cancer, head & neck cancer, stomach cancer, esophageal cancer, pancreatic cancer, or testicular cancer. 
     
     
         22 . The method of  claim 21 , wherein the tumor antigen is HER-2. 
     
     
         23 . The method of  claim 1 , wherein the antigen is a viral antigen bacterial antigen or a parasitic antigen. 
     
     
         24 .- 25 . (canceled) 
     
     
         26 . The method of  claim 1 , wherein modulated immunogenicity of the peptide antigen comprises an increase in the antigen's ability to selectively activate high-avidity or low-avidity CTL precursors. 
     
     
         27 . (canceled) 
     
     
         28 . The method of  claim 1 , wherein the modulated immunogenicity of the peptide antigen comprises a) an increase in the antigen's ability to protect CTLs from activation induced cell death, b) an increase in the antigen's ability to selectively activate cytokine production, c) an increase in the antigen's ability to induce CTL proliferation, d) increases the affinity of the antigen for a T cell receptor or e) reduces interactions that interference with T cell receptor binding. 
     
     
         29 .- 32 . (canceled) 
     
     
         33 . A method of inducing immunity in a subject comprising administering to said subject a modified peptide antigen comprising a CTL epitope, wherein said modified peptide antigen has at least one amino acid with a length-modified side chain, as compared to the amino acid in same position, within the naturally occurring CTL epitope. 
     
     
         34 . The method of  claim 33 , wherein the subject is a human. 
     
     
         35 . The method of  claim 33 , wherein said modified peptide antigen is a modified tumor peptide antigen. 
     
     
         36 . The method of  claim 33 , wherein the length-modified side chain of the modified peptide antigen a) is extended as compared to the amino acid in the same position in the natural CTL epitope, or b) is shortened as compared to the amino acid in the same position in the natural CTL epitope. 
     
     
         37 .- 40 . (canceled) 
     
     
         41 . The method of treating a HER-2 related cancer comprising administering to said subject a modified E75 peptide, wherein said modified E75 peptide has at least one amino acid with a length-modified side chain, as compared to the amino acid in the same position in the natural E75 peptide. 
     
     
         42 . The method of  claim 41 , wherein the HER-2 related cancer is breast or ovarian cancer. 
     
     
         43 . A peptide antigen with modulated immunogenicity comprising at least a first substituted amino acid having an extended or shortened side chain as compared to the amino acid amino acid in same position in the natural CTL epitope. 
     
     
         44 . The method of  claim 33 , wherein the modified peptide antigen further comprises
 a) a second amino acid with a length-modified side chain,   b) a second and third amino acid with a length-modified side chain, or   c) a second, third and fourth amino acid with a length-modified side chain.