Single domain tdf-related compounds and analogs thereof

Abstract

The present invention relates generally to tissue differentiation factor (TDF) analogs. More specifically, the invention relates to structure-based methods and compositions useful in designing, identifying, and producing molecules which act as functional modulators of TDF-like receptors. The invention further relates to methods of detecting, preventing, and treating TDF-associated disorders.

1 . A compound comprising an amino acid sequence selected from the group consisting of, SEQ ID NOs:1-208, polynucleotides encoding SEQ ID NOs:1-208, and variants, analogs, homologs, or fragments thereof. 
     
     
         2 . The compound of  claim 1 , wherein the compound modulates signal transduction across a membrane of a cell that expresses a tissue differentiation factor receptor. 
     
     
         3 . An isolated nucleic acid encoding the compound of  claim 1 . 
     
     
         4 . A vector comprising the nucleic acid of  claim 3 , and optionally comprising a promoter operable linked to the nucleic acid molecule. 
     
     
         5 . (canceled) 
     
     
         6 . A cell comprising the vector of  claim 5 . 
     
     
         7 . A pharmaceutical composition comprising a compound of  claim 1 , and a pharmaceutically acceptable carrier. 
     
     
         8 . An antibody or fragment thereof that binds immunospecifically to a compound of  claim 1 , optionally, wherein the antibody is a monoclonal antibody, or optionally wherein the antibody is a humanized antibody. 
     
     
         9 - 10 . (canceled) 
     
     
         11 . A pharmaceutical composition comprising an antibody of  claim 8 , and a pharmaceutically acceptable carrier. 
     
     
         12 . A pharmaceutical composition comprising the nucleic acid molecule of  claim 5  and a pharmaceutically-acceptable carrier. 
     
     
         13 . A method for preparing a compound, the method comprising:
 (a) culturing a cell containing a nucleic acid according to  claim 5  under conditions that provide for expression of the compound; and   (b) recovering the expressed compound.   
     
     
         14 . A method for determining the presence or amount of the compound of  claim 1  in a sample, the method comprising:
 (a) providing the sample; 
 (b) contacting the sample with an antibody that binds immunospecifically to the compound; and 
 (c) determining the presence or amount of antibody bound to the compound, thereby determining the presence or amount of compound in the sample. 
 
     
     
         15 . A method for determining the presence or amount of the nucleic acid molecule of  claim 3  in a sample, the method comprising:
 (a) providing the sample; 
 (b) contacting the sample with a probe that binds to the nucleic acid molecule; and 
 (c) determining the presence or amount of the probe bound to the nucleic acid molecule, thereby determining the presence or amount of the nucleic acid molecule in the sample. 
 
     
     
         16 . A method of identifying a compound that binds to a compound of  claim 1 , the method comprising:
 (a) contacting the compound with the compound of  claim 1 ; and   (b) determining whether the compound binds to the compound of  claim 1 .   
     
     
         17 . A method of treating or preventing a tissue differentiation factor associated disorder, the method comprising administering to a subject in which such treatment or prevention is desired the compound of  claim 1  in an amount sufficient to treat or prevent the tissue differentiation factor-associated disorder in the subject, optionally, wherein the subject is human. 
     
     
         18 . The method of  claim 17 , wherein the tissue differentiation factor associated disorder is selected from the group consisting of a tissue degenerative disease and tissue regeneration, optionally,
 wherein the tissue degenerative disease is selected from the group consisting of renal disease, traumatic brain injury, stroke, atherosclerosis, arthritis, emphysema, osteoporosis, cardiomyopathy, cirrhosis, degenerative nerve disease, Holt-Oram disease, eye disease, diabetic nephropathy, degenerative bone disease, periodontal disease, diabetes, cardiovascular disease, inflammatory disease, immune disease, skeletal disease, reproductive disease, haematopoietic disease, and cancer, or optionally   wherein the tissue regeneration is selected from the group consisting of muscle, dendritic tissue, nerve, kidney, brain, bone, skin, lung, ovary, testes, heart, spleen, cartilage, peridontal, dentin, liver, vascular, connective, lymphatic, haematopoietic, and renal tissue.   
     
     
         19 - 21 . (canceled) 
     
     
         22 . A method of treating or preventing a tissue differentiation factor associated disorder, the method comprising administering to a subject in which such treatment or prevention is desired the nucleic acid of  claim 5  in an amount sufficient to treat or prevent the tissue differentiation factor-associated disorder in the subject, optionally, wherein the subject is a human. 
     
     
         23 . (canceled) 
     
     
         24 . A kit comprising in one or more containers, the pharmaceutical composition of  claim 7  and instructions for using the contents therein. 
     
     
         25 . A kit comprising in one or more containers, the pharmaceutical composition of  claim 11  and instructions for using the contents therein. 
     
     
         26 . A kit comprising in one or more containers, the pharmaceutical composition of  claim 12  and instructions for using the contents therein. 
     
     
         27 . A method for determining the presence of or predisposition to a disease associated with altered levels of tissue differentiation factor receptor in a first mammalian subject, the method comprising:
 a) providing a test sample from the first mammalian subject;   (b) contacting the test sample from the first mammalian subject with a compound of  claim 1 ;   (c) detecting the level of compound/tissue differentiation factor receptor complex;   (d) quantifying the level of expression of the tissue differentiation factor receptor in the sample from the first mammalian subject; and   (e) comparing the amount of the tissue differentiation factor receptor in the sample of step (a) to the amount of the tissue differentiation factor receptor present in a control sample from a second mammalian subject known not to have. or not to be predisposed to. the disease, wherein an alteration in the expression level of the tissue differentiation factor receptor in the first subject as compared to the control sample indicates the presence of or predisposition to the disease.   
     
     
         28 . A method of treating a pathological state in a mammal, the method comprising administering to the mammal a compound in an amount that is sufficient to alleviate the pathological state, wherein the compound is a compound having an amino acid sequence at least 90% identical to a compound comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-208. 
     
     
         29 . A method of treating a pathological state in a mammal, the method comprising administering to the mammal the antibody of  claim 8  in an amount sufficient to alleviate the pathological state. 
     
     
         30 . A method of treating a tissue differentiation factor-associated disorder in a mammal. the method comprising administering to the mammal at least one compound which modulates the expression or activity of a compound selected from 20 the group consisting of SEQ ID NOs: 1-208, or a fragment, variant, or homolog thereof, optionally,
 wherein the tissue differentiation factor associated disorder is selected from the group consisting of renal disease, traumatic brain injury, stroke, atherosclerosis, arthritis, emphysema, osteoporosis, cardiomyopathy, cirrhosis, degenerative nerve disease, Holt-Oram disease, eye disease, diabetic nephropathy, degenerative bone disease, periodontal disease, diabetes, cardiovascular disease, inflammatory disease, immune disease, skeletal disease, reproductive disease, haematopoietic disease, and cancer.   
     
     
         31 . (canceled) 
     
     
         32 . A compound for use in treating a tissue differentiation factor-associated disorder, wherein the compound is selected from the group consisting of SEQ ID NOs: 1-208. 
     
     
         33 . The use of a compound for the manufacture of a medicament for treatment of a tissue differentiation factor-associated disorder, wherein the compound is selected from the group consisting of SEQ ID NOs: 1-208. 
     
     
         34 . A method of identifying a compound which binds to a tissue differentiation factor-related peptide (TDFRP) compound of  claim 1 , the method comprising the steps of:
 a) providing a candidate compound;   b) contacting the candidate compound with the TDFRP compound of  claim 1  under conditions which a complex is formed between the candidate compound and the TOFRP compound;   c) incubating the complex under conditLons where co-crystals of the complex form;   d) determining the structural atomic coordinates of the complex by x-ray diffraction; and   e) modeling the structure of the complex to determine the binding of the candidate compound to the TDFRP compound.   
     
     
         35 . A crystalline preparation of a compound and a test compound prepared by the method of  claim 34 . 
     
     
         36 . A method of identifying a compound which binds to a tissue differentiation factor-related peptides (TDFRP) compound of  claim 1 , the method comprising the steps of:
 a) providing a candidate compound;   b) contacting the candidate compound with the TDFRP compound of  claim 1  under conditions which a complex is formed between the candidate compound and the TDFRP compound;   c) determining the binding or structure of the complex by methods of nuclear magnetic resonance spectroscopy or mass; and optionally   e) modeling the structure of the complex.   
     
     
         37 . A transgenic non-human mammal, having genomically-integrated in non-human mammal cells, comprising a nucleic acid compound having a first segment which is a regulatory region and a second segment which is a polynucleotide sequence encoding a compound selected from the group consisting of SEQ ID NO: 1-208,
 (a) wherein the first segment is operably linked to the second segment;   (b) wherein the transgenic non-human mammal is a transgenic mouse; and/or   (c) wherein the first segment is a regulatable expression element or elements which are subject to cell or tissue-specific regulation.   
     
     
         38 - 39 . (canceled) 
     
     
         40 . Tissue or cells derived or cultured from the non-human transgenic mammal of  claim 37 .