Competitive inhibitors of invariant chain expression and/or ectopic clip binding

Abstract

The invention relates to methods for modulating the immune function through targeting of CLIP molecules. The result is wide range of new therapeutic regimens for treating, inhibiting the development of, or otherwise dealing with, a multitude of illnesses and conditions, including autoimmune disease, cancer, Alzheimer's disease, allergic disease, transplant and cell graft rejection, HIV infection and other viral, bacterial, and parasitic infection, and AIDS. Methods are also provided for preparing a peptide having the property of being able to displace CLIP by feeding one or more peptide sequences into software that predicts MHC Class II binding regions in an antigen sequence and related products.

What is claimed is: 
     
         1 .- 30 . (canceled) 
     
     
         31 . A method for treating a viral infection comprising administering to a subject infected with a virus or at risk of a viral infection a composition comprising a CLIP inhibitor and a pharmaceutically acceptable carrier. 
     
     
         32 . The method of  claim 31 , wherein CLIP inhibitor is a MHC class II CLIP inhibitor. 
     
     
         33 . The method of  claim 32  wherein the subject is infected with  Borrelia burgdorferi.    
     
     
         34 . The method of  claim 32  wherein the subject is infected with hepatitis virus. 
     
     
         35 . The method of  claim 32  wherein the subject is infected with herpes virus, CMV or EBV. 
     
     
         36 . The method of  claim 32  wherein the subject is infected with HIV. 
     
     
         37 .- 40 . (canceled) 
     
     
         41 . A method for treating a bacterial infection comprising administering to a subject infected with a bacteria or at risk of bacterial infection a composition comprising a CLIP inhibitor and a pharmaceutically acceptable carrier. 
     
     
         42 . The method of  claim 41 , wherein CLIP inhibitor is a MHC class I CLIP inhibitor. 
     
     
         43 . A method for treating a cancer comprising administering to a subject having a cancer a composition comprising a CLIP inhibitor and a pharmaceutically acceptable carrier. 
     
     
         44 . The method of  claim 43 , wherein CLIP inhibitor is a MHC class I CLIP inhibitor. 
     
     
         45 . The method of  claim 43 , further comprising administering a cancer antigen. 
     
     
         46 . The method according to  claim 43 , wherein the administration is bi-weekly. 
     
     
         47 . The method according to  claim 46 , wherein the bi-weekly administration is on consecutive days. 
     
     
         48 . The method according to  claim 47 , wherein the administration is at least one of oral, parenteral, subcutaneous, intravenous, intranasal, pulmonary, intramuscular and mucosal administration. 
     
     
         49 .- 62 . (canceled) 
     
     
         63 . A method for identifying a CLIP inhibitor, comprising
 analyzing an amino acid prediction matrix of an MHC class II HLA-DR allele for binding to a peptide to produce a predicted peptide binding score, comparing the predicted peptide binding score with a predicted CLIP binding score, wherein if the predicted peptide binding score is higher than or equivalent to the predicted CLIP binding score then the peptide is a CLIP inhibitor.   
     
     
         64 . The method of  claim 63 , wherein the method is a method for identifying an MHC specific CLIP inhibitor and a single amino acid prediction matrix is used for a single MHC class II HLA-DR. 
     
     
         65 . The method of  claim 63 , wherein the method is performed for a set of prediction matrices for multiple MHC class II HLA-DRs and an average predicted peptide score is generated. 
     
     
         66 . A method for identifying a subject specific CLIP inhibitor, comprising
 determining an MHC class II allele of a subject and determining a peptide that is a CLIP inhibitor based on the MHC class II allele in order to identify the subject specific CLIP inhibitor.   
     
     
         67 . The method of  claim 66 , wherein the peptide is determined based on a predetermined association of the peptide with the MHC class II allele. 
     
     
         68 . The method of  claim 66 , wherein the peptide is determined by analyzing a prediction matrix of the MHC class II allele for binding to a peptide to produce a predicted peptide binding score, comparing the predicted peptide binding score with a predicted CLIP binding score, wherein if the predicted peptide binding score is higher than or equivalent to the predicted CLIP binding score then the peptide is identified as the subject specific CLIP inhibitor. 
     
     
         69 .- 81 . (canceled)