Compositions comprising a tn3 scaffold and methods of using the same

Abstract

The present invention provides Tenascin-3 FnIII domain-based scaffolds that specifically bind to CD40L. The invention further provides engineered variants with increased affinity for the target. The present invention is also related to engineered scaffolds as prophylactic, diagnostic, or therapeutic agents, in particular for therapeutic uses against SLE and other autoimmune diseases and conditions.

1 .- 121 . (canceled) 
     
     
         122 . A method of reducing binding of CD40 ligand (CD40L) to CD40 receptor comprising administering an effective amount of a composition comprising a Tn3 scaffold to a subject in need, wherein the Tn3 scaffold comprises at least one CD40L-specific monomer subunit, wherein the monomer subunit comprises seven beta strands designated A, B, C, D, E, F, and G, and six loop regions designated AB, BC, CD, DE, EF, and FG, wherein the AB loop comprises SEQ ID NO: 4, the BC loop comprises a sequence selected from the group consisting of SEQ ID NOS: 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, and 168, the CD loop comprises SEQ ID NO: 6, the DE loop comprises a sequence selected from the group consisting of SEQ ID NOs: 94, 95, 96, 97, 98, and 169, the EF loop comprises SEQ ID NO: 8, and the FG loop comprises a sequence selected from the group consisting of SEQ ID NOS: 9, 99, 139, and 170. 
     
     
         123 . The method of  claim 122 , wherein the CD40L-specific monomer subunit comprises seven beta strands designated A, B, C, D, E, F, and G, wherein the A beta strand consists of SEQ IID NO:11, the B beta strand consists of SEQ ID NO:12, the C beta strand consists of SEQ ID NO:13 or SEQ ID NO:14, the D beta strand consists of SEQ ID NO:15, the E beta strand consists of SEQ ID NO:16, the F beta strand consists of SEQ ID NO:17, and the G beta strand consists of SEQ ID NO:18, and six loop regions designated AB, BC, CD, DE, EF, and FG. 
     
     
         124 . The method of  claim 122 , wherein the AB loop consists of SEQ ID NO: 4, the BC loop consists of SEQ ID NO: 86, the CD loop consists of SEQ ID NO: 6, the DE loop consists of SEQ ID NO: 96, the EF loop consists of SEQ ID NO: 8, and the FG loop consists of SEQ ID NO: 139. 
     
     
         125 . The method of  claim 122 , wherein the CD40L-specific monomer subunit comprises SEQ ID NO: 146. 
     
     
         126 . The method of  claim 122 , wherein the Tn3 scaffold comprises SEQ ID NO: 145. 
     
     
         127 . The method of  claim 122 , wherein the subject in need has cancer, an autoimmune disease, an infectious disease, or an inflammatory disease. 
     
     
         128 . The method of  claim 127 , wherein the subject in need has an autoimmune disease, and the autoimmune disease is selected from the group consisting of: alopecia areata, ankylosing spondylitis, antiphospholipid syndrome, autoimmune Addison's disease, autoimmune diseases of the adrenal gland, autoimmune hemolytic anemia, autoimmune hepatitis, autoimmune oophoritis and orchitis, Sjogren's syndrome, atherosclerosis, a retinopathy, retrolental fibroplasia, age-related macular degeneration, neovascular glaucoma, hemangiomas, Grave's disease, sepsis, arthritis, peritonitis, Crohn's disease, reperfusion injury, septicemia, endotoxic shock, cystic fibrosis, endocarditis, psoriasis, anaphylactic shock, organ ischemia, spinal cord injury and allograft rejection, autoimmune thrombocytopenia, Behçet's disease, bullous pemphigoid, cardiomyopathy, celiac sprue-dermatitis, chronic fatigue immune dysfunction syndrome (CFIDS), chronic inflammatory demyelinating polyneuropathy, Churg-Strauss syndrome, cicatricial pemphigoid, CREST syndrome, cold agglutinin disease, discoid lupus, essential mixed cryoglobulinemia, fibromyalgia-, glomerulonephritis, Guillain-Barre syndrome, Hashimoto's thyroiditis, idiopathic pulmonary fibrosis, idiopathic thrombocytopenia purpura (ITP), IgA neuropathy, lichen planus, Meniere's disease, mixed connective tissue disease, multiple sclerosis, type 1 diabetes mellitus, myasthenia gravis, pemphigus vulgaris, pernicious anemia, polyarteritis nodosa, polychondritis, polyglandular syndromes, polymyalgia rheumatica, polymyositis and dermatomyositis, primary agammaglobulinemia, primary biliary cirrhosis, Raynaud's phenomenon, Reiter's syndrome, sarcoidosis, scleroderma, stiff-man syndrome, systemic lupus erythematosus, lupus erythematosus, Takayasu arteritis, temporal arteritis/giant cell arteritis, ulcerative colitis, uveitis, vasculitis, vitiligo, and Wegener's granulomatosis. 
     
     
         129 . The method of  claim 128 , wherein the autoimmune disease is Sjogren's syndrome. 
     
     
         130 . The method of  claim 128 , wherein the autoimmune disease is arthritis. 
     
     
         131 . The method of  claim 130 , wherein the arthritis is juvenile arthritis. 
     
     
         132 . The method of  claim 130 , wherein the arthritis is rheumatoid arthritis. 
     
     
         133 . The method of  claim 128 , wherein the autoimmune disease is systemic lupus erythematosus. 
     
     
         134 . The method of  claim 122 , wherein the subject in need is a transplant recipient. 
     
     
         135 . The method of  claim 134 , wherein the method is effective in reducing graft-vs-host disease in the subject. 
     
     
         136 . A treatment regimen, comprising administering to a subject in need:
 a) a Tn3 scaffold that comprises at least one CD40L-specific monomer subunit, wherein the monomer subunit comprises seven beta strands designated A, B, C, D, E, F, and G, and six loop regions designated AB, BC, CD, DE, EF, and FG, wherein the AB loop comprises SEQ ID NO: 4, the BC loop comprises a sequence selected from the group consisting of SEQ ID NOS: 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, and 168, the CD loop comprises SEQ ID NO: 6, the DE loop comprises a sequence selected from the group consisting of SEQ ID NOs: 94, 95, 96, 97, 98, and 169, the EF loop comprises SEQ ID NO: 8, and the FG loop comprises a sequence selected from the group consisting of SEQ ID NOS: 9, 99, 139, and 170; and   b) a conventional therapy selected from the group consisting of: surgery, immunotherapy, chemotherapy, radiation therapy, and a small molecule.   
     
     
         137 . The method of  claim 136 , wherein the conventional therapy is administered concurrent with the Tn3 scaffold. 
     
     
         138 . The method of  claim 137 , wherein the conventional therapy is non-concurrently administered. 
     
     
         139 . The method of  claim 136 , wherein the conventional therapy is surgery, and comprises a transplant. 
     
     
         140 . The method of  claim 136 , wherein the conventional therapy is immunotherapy and comprises an antibody or portion thereof. 
     
     
         141 . The method of  claim 136 , wherein the CD40L-specific monomer subunit comprises SEQ ID NO: 146. 
     
     
         142 . The method of  claim 136 , wherein the Tn3 scaffold comprises SEQ ID NO: 145.