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 recombinant polynucleotide encoding a binding molecule, or subunit thereof, wherein the binding molecule, or a binding molecule comprising the subunit, can selectively recognize a neoepitope of a disorder-associated protein, wherein the disorder-associated protein does not substantially recognize the protein in its non-disorder-associated form. 
     
     
         2 . The polynucleotide of  claim 1 , wherein the binding molecule is an antibody or antigen-binding fragment thereof. 
     
     
         3 . The polynucleotide of  claim 2 , wherein the antibody a human antibody. 
     
     
         4 . The polynucleotide 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. 
     
     
         5 . The polynucleotide 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. 
     
     
         6 . The polynucleotide of  claim 5 , 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: 1e; 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. 
     
     
         7 - 8 . (canceled) 
     
     
         9 . The polynucleotide of  claim 5  encoding at least the variable region of an immunoglobulin chain of the antibody or antigen-binding fragment thereof. 
     
     
         10 . A vector comprising the polynucleotide of  claim 1 . 
     
     
         11 . A host cell comprising the polynucleotide of  claim 1 . 
     
     
         12 . A method for preparing a disorder-associated protein specific binding molecule, an antibody or antigen-binding fragment or immunoglobulin chain(s) thereof, the method comprising
 (a) culturing the host cell of  claim 11 ; and   (b) isolating the binding molecule, antibody or antigen-binding fragment or immunoglobulin chain(s) thereof from the culture.   
     
     
         13 . A composition comprising the polynucleotide of  claim 1 . 
     
     
         14 . The composition of  claim 13 , further comprising an additional agent useful for treating Alzheimer's disease, selected from the group consisting of small organic molecules, anti-Abeta antibodies, or any combination thereof. 
     
     
         15 - 17 . (canceled) 
     
     
         18 . A kit for the diagnosis of a disorder which is characterized by abnormal accumulation and/or deposition of a disorder-associated protein in the brain comprising the polynucleotide of  claim 1 . 
     
     
         19 . (canceled) 
     
     
         20 . A recombinant polynucleotide encoding an isolated antibody or antigen-binding fragment thereof, or a subunit of 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 . A recombinant polynucleotide encoding an isolated antibody or antigen-binding fragment thereof, or a subunit of an isolated antibody or antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof competitively inhibits 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. 
     
     
         22 . A recombinant polynucleotide encoding an isolated antibody or antigen-binding fragment thereof, or a subunit of an antibody or antigen-binding fragment thereof, wherein the antibody, or an antibody comprising the subunit, 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 polynucleotide of  claim 2 , 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. 
     
     
         24 . The polynucleotide of  claim 6 , which comprises the nucleic acid sequence of a VH selected from the group consisting of: SEQ ID NO: 3; SEQ ID NO: 5; SEQ ID NO: 9; SEQ ID NO: 13; SEQ ID NO: 38; SEQ ID NO: 52; SEQ ID NO: 53; and SEQ ID NO: 56, and/or a VL selected from the group consisting of: SEQ ID NO: 7; SEQ ID NO: 11; SEQ ID NO: 15; SEQ ID NO: 40; SEQ ID NO: 54; and SEQ ID NO: 55.