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 . An isolated peptide comprising X 1 RX 2 X 3 X 4 X 5 LX 6 X 7 (SEQ ID NO: 3), wherein each X is an amino acid, wherein R is Arginine, L is Leucine and wherein at least one of X 2  and X 3  is Methionine, wherein the peptide is not N-MRMATPLLM-C, and wherein the peptide is a CLIP displacer. 
     
     
         2 - 23 . (canceled) 
     
     
         24 . A composition comprising a peptide of  claim 1  and a carrier. 
     
     
         25 - 26 . (canceled) 
     
     
         27 . The composition of  claim 24 , wherein the carrier is a particle. 
     
     
         28 . The composition of  claim 27 , wherein the particle is a nanoparticle. 
     
     
         29 - 30 . (canceled) 
     
     
         31 . A method for treating a disease in a subject comprising administering to the subject 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 31  wherein the subject is infected with  Borrelia burgdorferi.    
     
     
         34 . The method of  claim 31 , wherein the subject is infected with hepatitis virus. 
     
     
         35 . The method of  claim 31 , wherein the subject is infected with herpes virus, CMV or EBV. 
     
     
         36 . The method of  claim 31 , wherein the subject is infected with HIV. 
     
     
         37 - 42 . (canceled) 
     
     
         43 . The method of  claim 31 , wherein the subject has a cancer. 
     
     
         44 . (canceled) 
     
     
         45 . The method of  claim 43 , further comprising administering a cancer antigen. 
     
     
         46 - 48 . (canceled) 
     
     
         49 . The method of  claim 31 , wherein the subject has an autoimmune disease. 
     
     
         50 . (canceled) 
     
     
         51 . The method of  claim 49 , wherein the autoimmune disease is multiple sclerosis, systemic lupus erythematosus, inflammatory bowel disease, rheumatoid arthritis, Graves' disease, autoimmune thyroiditis, autoimmune myositis, discoid lupus erythematosus, Crohns disease, Sjogren's syndrome, Reiter's syndrome, Rheumatoid arthritis, myasthenia gravis, Kawasaki's disease, Celiac disease, Goodpasture's syndrome, or aplastic anemia. 
     
     
         52 - 78 . (canceled) 
     
     
         79 . A computer implemented method for identifying a target protein binding peptide comprising:
 computing an average score for each data point in a set of amino acid prediction matrices for at least two target proteins having similar binding sites, wherein the prediction matrices have a first axis representing amino acids and a second axis representing a binding site position number, wherein each data point represents a score for the amino acid at the binding site position number, and   determining a binding peptide based on the average score for each data point by selecting an amino acid for each site of the binding peptide having a score of zero or greater.   
     
     
         80 - 81 . (canceled)