Method of Providing Disease-Specific Binding Molecules and Targets

Abstract

Provided are novel specific binding molecules, particularly human antibodies as well as fragments, derivatives and variants thereof that recognize neoepitopes of disease-associated proteins which derive from native endogenous proteins but are prevalent in the body of a patient in a variant form and/or out of their normal physiological context. In addition, pharmaceutical compositions comprising such binding molecules, antibodies and mimics thereof and methods of screening for novel binding molecules, which may or may not be antibodies as well as targets in the treatment of neurological disorders such as Alzheimer's disease are described.

1 . A method of treating a neurological disorder characterized by abnormal accumulation and/or deposition of a disorder-associated protein in the brain, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising a binding molecule which can selectively recognize a neoepitope of a disorder-associated protein, and which does not substantially recognize the protein in its non-disorder-associated form, a polynucleotide encoding the binding molecule or a subunit of the binding molecule, or a combination thereof. 
     
     
         2 . The method of  claim 1 , wherein the disorder is selected from the group consisting of Alzheimer's disease, Down's syndrome, mild cognitive impairment, cerebral amyloid angiopathy, vascular dementia, multi-infarct dementia, Parkinson's disease, Huntington's disease, Creutzfeldt-Jakob disease, cystic fibrosis, and Gaucher's disease. 
     
     
         3 . A method of diagnosing and/or treating a disorder related to Alzheimer's disease and Abeta deposition, respectively, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising a binding molecule which can selectively recognize a neoepitope of a disorder-associated protein, and which does not substantially recognize the protein in its non-disorder-associated form, a polynucleotide encoding the binding molecule or a subunit of the binding molecule, or a combination thereof. 
     
     
         4 . The method of  claim 1 , wherein the binding molecule is an antibody or antigen-binding, fragment thereof. 
     
     
         5 . The method of  claim 4 , wherein the antibody is a human antibody. 
     
     
         6 . The method of  claim 1 , wherein the binding molecule can bind to beta-amyloid plaques, cerebrovascular amyloid, diffuse Abeta deposits, neurofibrillary tangles, hyperphosphorylated tau, alpha-synuclein positive Lewy-bodies or protein aggregates associated with dystrophic neurites. 
     
     
         7 . The method of  claim 1 , wherein the binding molecule is an antibody or antigen-binding fragment thereof comprising in its variable region at least one complementarity determining region (CDR) selected from the group consisting of: the heavy chain CDR1 of SEQ ID NO: 17, SEQ ID NO: 20, SEQ ID NO: 26, or SEQ ID NO: 32, the heavy chain CDR2 of SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 27 or SEQ ID NO: 33, and the heavy chain CDR3 of SEQ ID NO: 19, SEQ ID NO: 22, SEQ ID NO: 28 or SEQ ID NO: 34, the light chain CDR1 of SEQ ID NO: 23, SEQ ID NO: 29, SEQ ID NO: 35, SEQ ID NO: 46, or SEQ ID NO: 49, the light chain CDR2 of SEQ ID NO: 24, SEQ ID NO: 30, SEQ ID NO: 36, SEQ ID NO: 47, or SEQ ID NO: 50, and the light chain CDR3 of SEQ ID NO: 25, SEQ ID NO: 31, SEQ ID NO: 37, SEQ ID NO: 48, or SEQ ID NO: 51. 
     
     
         8 . The method of  claim 7 , wherein the antibody or antigen-binding fragment thereof comprises the amino acid sequence of a heavy chain variable region (VH) selected from the group consisting of: SEQ ID NO: 4; SEQ ID NO: 6; SEQ ID NO: 10; SEQ ID NO: 14; SEQ ID NO: 39; SEQ ID NO: 42; and SEQ ID NO: 43 and/or a light chain variable region (VL) selected from the group consisting of: SEQ ID NO: 8; SEQ ID NO: 12; SEQ ID NO: 16; SEQ ID NO: 41; SEQ ID NO: 44; and SEQ ID NO: 45. 
     
     
         9 . The method of  claim 1 , wherein the composition further comprises an additional agent useful for treating Alzheimer's disease, wherein the agent can be small organic molecules, anti-Abeta antibodies, or any combination thereof. 
     
     
         10 . The method of  claim 1 , wherein the binding molecule comprises an isolated antibody or antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof specifically binds to the same neoepitope of a disorder-associated protein as a reference antibody, wherein the reference antibody comprises in its variable region at least one complementarity determining region (CDR) selected from the group consisting of: the heavy chain CDR1 of SEQ ID NO: 17, SEQ ID NO: 20, SEQ ID NO: 26, or SEQ ID NO: 32, the heavy chain CDR2 of SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 27 or SEQ ID NO: 33, and the heavy chain CDR3 of SEQ ID NO: 19, SEQ ID NO: 22, SEQ ID NO: 28 or SEQ ID NO: 34, the light chain CDR1 of SEQ ID NO: 23, SEQ ID NO: 29, SEQ ID NO: 35, SEQ ID NO: 46, or SEQ ID NO: 49, the light chain CDR2 of SEQ ID NO: 24, SEQ ID NO: 30, SEQ ID NO: 36, SEQ ID NO: 47, or SEQ ID NO: 50, and the light chain CDR3 of SEQ ID NO: 25, SEQ ID NO: 31, SEQ ID NO: 37, SEQ ID NO: 48, or SEQ ID NO: 51. 
     
     
         11 . The method of  claim 1 , wherein the binding molecule comprises an isolated antibody or antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof competitively inhibits a reference antibody from binding to a neoepitope of a disorder-associated protein, wherein the reference antibody comprises, in its variable region at least one complementarity determining region (CDR) selected from the group consisting of: the heavy chain CDR1 of SEQ ID NO: 17, SEQ ID NO: 20, SEQ ID NO: 26, or SEQ ID NO: 32, the heavy chain CDR2 of SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 27 or SEQ ID NO: 33, and the heavy chain CDR3 of SEQ ID NO: 19, SEQ ID NO: 22, SEQ ID NO: 28 or SEQ ID NO: 34, the light chain CDR1 of SEQ ID NO: 23, SEQ ID NO: 29, SEQ ID NO: 35, SEQ ID NO: 46, or SEQ ID NO: 49, the light chain CDR2 of SEQ ID NO: 24, SEQ ID NO: 30, SEQ ID NO: 36, SEQ ID NO: 47, or SEQ ID NO: 50, and the light chain CDR3 of SEQ ID NO: 25, SEQ ID NO: 31, SEQ ID NO: 37, SEQ ID NO: 48, or SEQ ID NO: 51. 
     
     
         12 . The method of  claim 1 , wherein the binding molecule comprises an isolated antibody or antigen-binding fragment thereof, wherein the antibody comprises an antigen binding domain identical to that of an antibody or antigen-binding fragment thereof which comprises in its variable region at least one complementarity determining region (CDR) selected from the group consisting of the heavy chain CDR1 of SEQ ID NO: 17, SEQ ID NO: 20, SEQ ID NO: 26, or SEQ ID NO: 32, the heavy chain CDR2 of SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 27 or SEQ ID NO: 33, and the heavy chain CDR3 of SEQ ID NO: 19, SEQ ID NO: 22, SEQ ID NO: 28 or SEQ ID NO: 34, the light chain CDR1 of SEQ ID NO: 23, SEQ ID NO: 29, SEQ ID NO: 35, SEQ ID NO: 46, or SEQ ID NO: 49, the light chain CDR2 of SEQ ID NO: 24, SEQ ID NO: 30, SEQ ID NO: 36, SEQ ID NO: 47, or SEQ ID NO: 50, and the light chain CDR3 of SEQ ID NO: 25, SEQ ID NO: 31, SEQ ID NO: 37, SEQ ID NO: 48, or SEQ ID NO: 51. 
     
     
         13 . The method of  claim 4 , wherein the disorder-associated protein is beta amyloid, and wherein said antibody or antigen-binding fragment thereof comprises a VH and a VL, wherein the VH comprises a first complementarity determining region (VHCDR1) with the amino acid sequence SEQ ID NO: 20, a VHCDR2 with the amino acid sequence SEQ ID NO: 21, and a VHCDR3 with the amino acid sequence SEQ ID NO: 22, and wherein the VL comprises a VLCDR1 with the amino acid sequence SEQ ID NO: 23, a VLCDR2 with the amino acid sequence SEQ ID NO: 24, and a VLCDR3 with the amino acid sequence SEQ ID NO: 25. 
     
     
         14 . The method of  claim 3 , wherein the binding molecule is an antibody or antigen-binding fragment thereof. 
     
     
         15 . The method of  claim 14 , wherein the antibody is a human antibody. 
     
     
         16 . The method of  claim 3 , wherein the binding molecule can bind to beta-amyloid plaques, cerebrovascular amyloid, diffuse Abeta deposits, neurofibrillary tangles, hyperphosphorylated tau, alpha-synuclein positive Lewy-bodies or protein aggregates associated with dystrophic neurites. 
     
     
         17 . The method of  claim 3 , wherein the binding molecule is an antibody or antigen-binding fragment thereof comprising in its variable region at least one complementarity determining region (CDR) selected from the group consisting of: the heavy chain CDR1 of SEQ ID NO: 17, SEQ ID NO: 20, SEQ ID NO: 26, or SEQ ID NO: 32, the heavy chain CDR2 of SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 27 or SEQ ID NO: 33, and the heavy chain CDR3 of SEQ ID NO: 19, SEQ ID NO: 22, SEQ ID NO: 28 or SEQ ID NO: 34, the light chain CDR1 of SEQ ID NO: 23, SEQ ID NO: 29, SEQ ID NO: 35, SEQ ID NO: 46, or SEQ ID NO: 49, the light chain CDR2 of SEQ ID NO: 24, SEQ ID NO: 30, SEQ ID NO: 36, SEQ ID NO: 47, or SEQ ID NO: 50, and the light chain CDR3 of SEQ ID NO: 25, SEQ ID NO: 31, SEQ ID NO: 37, SEQ ID NO: 48, or SEQ ID NO: 51. 
     
     
         18 . The method of  claim 17 , wherein the antibody or antigen-binding fragment thereof comprises the amino acid sequence of a heavy chain variable region (VII) selected from the group consisting of: SEQ ID NO: 4; SEQ ID NO: 6; SEQ ID NO: 10; SEQ ID NO: 14; SEQ ID NO: 39; SEQ ID NO: 42; and SEQ ID NO: 43 and/or a light chain variable region (VL) selected from the group consisting of SEQ ID NO: 8; SEQ ID NO: 12; SEQ ID NO: 16; SEQ ID NO: 41; SEQ ID NO: 44; and SEQ ID NO: 45. 
     
     
         19 . The method of  claim 3 , wherein the composition further comprises an additional agent useful for treating Alzheimer's disease, wherein the agent can be small organic molecules, anti-Abeta antibodies, or any combination thereof. 
     
     
         20 . The method of  claim 3 , wherein the binding molecule comprises an isolated antibody or antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof specifically binds to the same neoepitope of a disorder-associated protein as a reference antibody, wherein the reference antibody comprises in its variable region at least one complementarity determining region (CDR) selected from the group consisting of: the heavy chain CDR1 of SEQ ID NO: 17, SEQ ID NO: 20, SEQ ID NO: 26, or SEQ ID NO: 32, the heavy chain CDR2 of SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 27 or SEQ ID NO: 33, and the heavy chain CDR3 of SEQ ID NO: 19, SEQ ID NO: 22, SEQ ID NO: 28 or SEQ ID NO: 34, the light chain CDR1 of SEQ ID NO: 23, SEQ ID NO: 29, SEQ ID NO: 35, SEQ ID NO: 46, or SEQ ID NO: 49, the light chain CDR2 of SEQ ID NO: 24, SEQ ID NO: 30, SEQ ID NO: 36, SEQ ID NO: 47, or SEQ ID NO: 50, and the light chain CDR3 of SEQ ID NO: 25, SEQ ID NO: 31, SEQ ID NO: 37, SEQ ID NO: 48, or SEQ ID NO: 51. 
     
     
         21 . The method of  claim 3 , wherein the binding molecule comprises an isolated antibody or antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof competitively inhibits a reference antibody from binding to a neoepitope of a disorder-associated protein, wherein the reference antibody comprises in its variable region at least one complementarity determining region (CDR) selected from the group consisting of: the heavy chain CDR1 of SEQ ID NO: 17, SEQ ID NO: 20, SEQ ID NO: 26, or SEQ ID NO: 32, the heavy chain CDR2 of SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 27 or SEQ ID NO: 33, and the heavy chain CDR3 of SEQ ID NO: 19, SEQ ID NO: 22, SEQ ID NO: 28 or SEQ ID NO: 34, the light chain CDR1 of SEQ ID NO: 23, SEQ ID NO: 29, SEQ ID NO: 35, SEQ ID NO: 46, or SEQ ID NO: 49, the light chain CDR2 of SEQ ID NO: 24, SEQ ID NO: 30, SEQ ID NO: 36, SEQ ID NO: 47, or SEQ ID NO: 50, and the light chain CDR3 of SEQ ID NO: 25, SEQ ID NO: 31, SEQ ID NO: 37, SEQ ID NO: 48, or SEQ ID NO: 51. 
     
     
         22 . The method of  claim 3 , wherein the binding molecule comprises an isolated antibody or antigen-binding fragment thereof, wherein the antibody comprises an antigen binding domain identical to that of an antibody or antigen-binding fragment thereof which comprises in its variable region at least one complementarity determining region (CDR) selected from the group consisting of: the heavy chain CDR1 of SEQ ID NO: 17, SEQ ID NO: 20, SEQ ID NO: 26, or SEQ ID NO: 32, the heavy chain CDR2 of SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 27 or SEQ ID NO: 33, and the heavy chain CDR3 of SEQ ID NO: 19, SEQ ID NO: 22, SEQ ID NO: 28 or SEQ ID NO: 34, the light chain CDR1 of SEQ ID NO: 23, SEQ ID NO: 29, SEQ ID NO: 35, SEQ ID NO: 46, or SEQ ID NO: 49, the light chain CDR2 of SEQ ID NO: 24, SEQ ID NO: 30, SEQ ID NO: 36, SEQ ID NO: 47, or SEQ ID NO: 50, and the light chain CDR3 of SEQ ID NO: 25, SEQ ID NO: 31, SEQ ID NO: 37, SEQ ID NO: 48, or SEQ ID NO: 51. 
     
     
         23 . The method of  claim 14 , wherein the disorder-associated protein is beta amyloid, and wherein said antibody or antigen-binding fragment thereof comprises a VH and a VL, wherein the VH comprises a first complementarity determining region (VHCDR1) with the amino acid sequence SEQ ID NO: 20, a VHCDR2 with the amino acid sequence SEQ ID NO: 21, and a VHCDR3 with the amino acid sequence SEQ ID NO: 22, and wherein the VL comprises a VLCDR1 with the amino acid sequence SEQ ID NO: 23, a VLCDR2 with the amino acid sequence SEQ ID NO: 24, and a VLCDR3 with the amino acid sequence SEQ ID NO: 25.