EP1883418A2

Sclerostin and the inhibition of wnt signaling and bone formation

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35 claims: 13 independent, 22 dependent

  1. 1
    Claims of equivalent WO 2006102070 A2 CLAIMS 1. ■ A method for promoting bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that prevents the binding of sclerostin to a receptor or- co-receptor involved in bone formation or bone remodeling. ' ' 2. A method for promoting bone formation or bone remodeling comprising administering at least one- non-native compound, at least one fragment of a non-native compound, or any combination thereof, that prevents the binding of sclerostin to the LRP5 or LRP6 receptor. 3. A method for promoting bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that prevents the binding of sclerostin to a homologue of the LRP5 or LRP6 receptor. ' 4. A method for promoting bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that prevents the binding of sclerostin to at least one domain of the LRP5 or LRP6 receptor. 5. A method for promoting bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound,, or any combination thereof, that prevents the binding of sclerostin to the first or second domain of the LRP5 or LRP6 receptor. 6. The method of claims 1 to 5 wherein said compound or said fragment of a compound comprises IIIC3 or IIC8. . 7. The method of claims 1 to 5 wherein said compound or said fragment of a compound comprises IIIC3, IIC8, or any derivative or analog thereof. 8. The method of claims 6 or 7 wherein said two or more compounds, or said fragments of. compounds are directly linked together with cross-linking, or indirectly linked together with a linker arm. 9. The method of claim 8 wherein said compounds, said fragments of a compound, or any combination thereof, dock in a first location and a second location on the same binding site, receptor or protein. 10. The method of claim 8 wherein said compounds, said fragments of a compound, or any combination thereof, dock in a first location and a second location on different binding sites, receptors or proteins. 11. The method of claims 1 to 5 wherein said compounds, or said fragments of a compound, are linked together with a linker arm or cross-linking. 17 12. The method of claims 1 to 11 wherein said compound or said fragment of a compound comprises a small molecule, protein, peptide, polypeptide, cyclic molecule, heterocyclic organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glycolipid, lipoprotein, chemical, or a fragment of a compound that comprises a heterocyclic organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glycolipid, lipoprotein, or chemical. 13. The method of claims 1 to 5 wherein said administering step comprises administration by inhalation, oral,, intravenous, intraperitoneal, intramuscular, parenteral, transdermal, intravaginal, intranasal, mucosal, sublingual, topical, rectal, or subcutaneous administration, or any combination thereof. 14. The method of claims 1 to 12 wherein said compound or said fragment of a compound comprises at least one agonist, antagonist, partial agonist, or any combination thereof. 15. The method of claims 1 to 14 wherein said compound is identified using a method comprising:a. screening for a compound that fits into the cavity on the receptor using the UNITY™ program;b. docking said compound into the cavity using the Flexx M program;and c. obtaining the compound with the highest binding affinity using the Cscore™ program. 16. A method for the treatment of a bone fracture, bone disease, bone injury, or bone abnormality in a mammalian subject comprising administering at least one non-native compound, at least one fragment of a non-native compound or any combination thereof, that prevents the binding of sclerostin to a receptor or co-receptor involved in bone formation or bone remodeling. 17. A method for the treatment of a bone fracture, bone disease, bone injury, or bone abnormality in a mammalian subject comprising administering at least one non-native compound, at least one fragment of a non-native compound or any combination thereof, that prevents the binding of sclerostin to the LRP5 or LRP6 receptor. 18. A method for the treatment of a bone fracture, bone disease, bone injury, or bone abnormality in a mammalian subject comprising administering at least one non-native compound, at least one fragment of a non-native compound or any combination thereof, that prevents the binding of sclerostin to a homolbgue of the LRP5 or LRP6 receptor. 19. The method of claims 16 to 18 wherein said compound comprises IIIC3 or IIC8. 20. The method of claims 16 to 18 wherein said compound or said fragment of a compound comprises IIIC3 or IIC8 21. The method of claims 19 or 20 wherein said two or more compounds or said fragments of compounds are directly linked together with cross-linking, or indirectly linked together with a linker arm. 18 22. The method of claim 21 wherein said compounds, said fragments of a compound, or any combination thereof, dock in a first location and a second location on the same binding site, receptor or protein. 23. The method of claim 21 wherein said compounds, said fragments of a compound, or any combination thereof, dock in a first location and a second location on different binding sites, receptors or proteins. 24. The method of claims 16 to 18 wherein said compounds, or said fragments of a compound, are linked together with a linker arm or cross-linking. 25. The method of claims 16 to 24 wherein said compound or said fragment of a compound comprises a small molecule, protein, peptide, polypeptide, cyclic molecule, heterocyclic organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glycolipid, lipoprotein, chemical, or a fragment of a compound that comprises a heterocyclic organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glycolipid, lipoprotein, or chemical. 26. The method of claims 16 to 18 wherein said administering step comprises administration by inhalation, oral, intravenous, intraperitoneal, intramuscular, parenteral, transdermal, intravaginal, intranasal, mucosal, sublingual, topical, rectal, or subcutaneous administration, or any combination thereof. 27. The method of claims 16 to 25 wherein said compound or said fragment of a compound comprises at least one agonist, antagonist, partial agonist, or any combination thereof. 28. The method of claims 16 to 27 wherein said compound is identified using a method comprising: a. screening for a compound that fits into the cavity on the receptor using the UNITY™ program;b. docking said compound into the cavity using the Flexx™ program;and c. obtaining the compound with the highest binding affinity using the Cscore™ program. 29. A therapeutic composition for the treatment of a bone fracture, bone disease, bone injury or bone abnormality in a mammalian subject comprising at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that prevents the binding of sclerostin to a receptor or co-receptor in bone formation or bone remodeling. 30. A therapeutic composition for the treatment of a bone fracture, bone disease, bone injury or bone abnormality in a mammalian subject comprising at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that prevents the binding of sclerostin to the LRP5 or LRP6 receptor. 31. A therapeutic composition for the treatment of a bone fracture, bone disease, bone injury 19 or bone abnormality in a mammalian subject comprising at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, . that prevents the binding of sclerostin to a homologue of the LRP5 or LRP6 receptor, 32. The composition of claims 29 to 30 wherein said compound or said fragment of a compound comprises IJIC3 or IIC8 . , , 33. The composition of claims 29 to 31 wherein said compound or said fragment of a compound comprises IIIC3 or IIC8, or any derivative or analog thereof. 34. The composition of claim 32 or 33 wherein said two or more compounds or fragments of compounds are directly linked together with cross-linking, or indirectly linked together with a linker arm. 35. The method of claim 34 wherein said compounds, said fragments of a compound, or any combination thereof, dock in a first location and a second location on the same binding site, receptor or protein. 36. The composition of claim 34 wherein said compounds, said fragments of a compound, or any combination thereof, dock in .a first location and a second location on different binding sites receptors or proteins. 37. The composition of claims 29 to 31 wherein said compounds, or said fragments of a compound, are linked together with a linker arm or cross-linking. 38. The composition of claims 29 to 37 wherein said compound or said fragment of a compound comprises a small molecule, protein, peptide, polypeptide, cyclic molecule, heterocyclic organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glycolipid, lipoprotein, chemical, or a fragment of a compound that comprises a heterocyclic organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glycolipid, lipoprotein, or chemical. 39. The composition of claims 29 to 31 wherein said administering step comprises administration by inhalation, oral, intravenous, intraperitoneal, intramuscular, parenteral, transdermal, intravaginal, intranasal, mucosal, sublingual, topical, rectal, or subcutaneous administration, or any combination thereof. 40. The composition of claims 29 to 38 wherein said compound or said fragment of a compound comprises at least one agonist, antagonist, partial agonist, or any combination thereof. 41. The composition of claims 29 to 40 wherein said non-native compound is identified using a method comprising: a. screening for a compound that fits into the cavity on the receptor using the UNITY™ program;b. docking said compound into the cavity using the Flexx™ program;and c. obtaining the compound with the highest binding affinity using the Cscore™ 20 program. 42. The composition of claims 29 to 41 wherein said composition further comprises a pharmaceutically acceptable carrier. 43. The composition of claims 29 to 41 wherein said composition is formulated as a tablet, pill, dragee, liquid, gel, capsule, syrup, slurry or suspension. 44. A method for the regulation of bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound or any combination thereof, that disrupts the interaction of sclerostin with a receptor or co-receptor involved in bone formation or bone remodeling. 45. A method for the regulation of bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with the LRP5 or LRP6 receptor. 46. A method for the regulation of bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with a homologue of the LRP5 or LRP6 receptor. 47. A method for the regulation of bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with at least one domain of the LRP5 or LRP6 receptor. 48. A method for the regulation of bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with the first or second domain of the LRP5 or LRP6 receptor. 49. The method of claims 44 to 48 wherein said compound or said fragment of a compound comprises IIIC3 or IIC8. 50. The method of claims 44 to 48 wherein said compound or said fragment of a compound comprises IIIC3, or IIC8, or any derivative or analog thereof. 51. The method of claims 49 or 50 wherein said two or more compounds or said fragments of compounds are directly linked together with cross-linking, or indirectly linked together with a linker arm. 52. The method of claim 51 wherein said compounds, said fragments of a compound, or any combination thereof, dock in a first location and a second location on the same binding site, receptor or protein. 53. The method of claim 51 wherein said compounds, said fragments of a compound, or any 11 combination thereof, dock in a first location and a second location on different binding sites, receptors or proteins. 54. The method of claims 44 to 48 wherein said compounds, or said fragments of a compound, are linked together with a linker arm or cross-linking. 55. The method of claims 44 to 54 wherein said compound or said fragment of a compound comprises a small molecule, protein, peptide, polypeptide, cyclic molecule, heterocyclic organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glycolipid, lipoprotein, chemical, or a fragment of a compound that comprises a heterocyclic organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glycolipid, lipoprotein, or chemical. 56. ' The method of claims 44 to 48 wherein said administering step comprises administration by inhalation, oral, intravenous, intraperitoneal, intramuscular, parenteral, transdermal, intravaginal, intranasal, mucosal, sublingual, topical, rectal, or subcutaneous administration, or any combination thereof. 57. The method of claims 44 to 55 wherein said compound or said fragment of a compound comprises at least one agonist, antagonist, partial agonist, or any combination thereof. 58. The method of claims 44 to 57 wherein said non-native compound is identified using a method comprising: a. screening for a compound that fits into the cavity on the receptor using the UNITY™ program;b. docking said compound into the cavity using the Flexx™ program;and c. obtaining the compound with the highest binding affinity using the Cscore™ program. 59. A method for the treatment of a bone fracture, bone disease, bone injury, or bone abnormality in a mammalian subject comprising administering at least one non-native compound, at least one fragment of a non-native compound or any combination thereof, that disrupts the interaction of sclerostin with a receptor or co-receptor involved in bone formation or bone remodeling. 60. A method for the treatment of a bone fracture, bone disease, bone injury, or bone abnormality in a mammalian subject comprising administering at least one non-native compound, at least one fragment of a non-native compound or any combination thereof, that disrupts the interaction of sclerostin with the LRP5 or LRP6 receptor. 61. A method for the treatment of a bone fracture, bone disease, bone injury, or bone abnormality in a mammalian subject comprising administering at least one non-native compound, at least one fraction of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with a homologue of the LRP5 or LRP6 receptor. 62. A method for the treatment of a bone fracture, bone disease, bone injury, or bone abnormality in a mammalian subject comprising administering at least one non-native 9? compound, at least one fragment of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with at least one domain of the LRP5 or LRP6 receptor. 63. A method for the treatment of a bone fracture, bone disease, bone injury, or bone abnormality in a mammalian subject comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with the first or second domain of the LRP5 or LRP 6 receptor. 64. The method of claims 59 to 63 wherein said compound or said fragment of a compound comprises IIIC3 or HC 8. 65. The method of claims 59 to 63 wherein said compound or said fragment of a compound comprises IIIC3, IIC8 or any derivative or analog thereof. 66. The method of claim 64 or 65 wherein said two or more compounds or said fragments of compounds are directly linked together with cross-linking, or indirectly linked together with a linker arm. 67. The method of claim 66 wherein said compounds, said fragments of a compound, or any. combination thereof, dock in a first location and a second location on the same binding site, receptor or protein. 68. The method of claim 66 wherein said compounds, said fragments of a compound, or any combination thereof, dock in a first location and a second location on different binding sites, receptors or proteins. 69. The method of claims 59 to 63 wherein said compounds, or said fragments of a compound, are linked together with a linker arm or cross-linking. 70. The method of claims 59 to 69 wherein said compound or said fragment of. a compound comprises a small molecule, protein, peptide, polypeptide, cyclic molecule, heterocyclic organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar* glycoprotein, glycolipid, lipoprotein, chemical, or a fragment of a compound that comprises a heterocyclic organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glycolipid, lipoprotein, or chemical. 71. The method of claims 59 to 63 wherein said administering step comprises administration by inhalation, oral, intravenous, intraperitoneal, intramuscular, parenteral, transdermal, intravaginal, intranasal, mucosal, sublingual, topical, rectal, or subcutaneous administration, or any combination thereof. 72. The method of claims 59 to 69 wherein said compound or said fragment of a compound ■ comprises at least one agonist, antagonist, partial agonist, or any combination thereof. 73. The method of claims 59 to 72 wherein said non-native compound is identified using a 23 method comprising: a. screening for a compound that fits into the cavity on the receptor using the ' . UNITY™ program;b. docking said compound into the cavity using the Flexx™ program;and c. obtaining the compound with the highest binding affinity using the Cscore™ program. ■ 74. A therapeutic composition for the treatment of a bone fracture, bone disease, bone injury or bone abnormality in a mammalian subject comprising at least one non-native compound, at least one fragment of a compound, or any combination thereof, that disrupts the interaction of sclerostin with a receptor or co-receptor involved in bone formation or bone remodeling. 75. A therapeutic composition for the treatment of a bone fracture, bone disease, bone injury or bone abnormality in a mammalian subject comprising at least one non-native compound, at least one fragment of a compound, or any combination thereof, that disrupts the interaction of sclerostin with the LRP5 or LRP6 receptor. 76. A therapeutic composition for the treatment of a bone fracture, bone disease, bone injury or bone abnormality in a mammalian subject comprising at least one non-native compound, at least one fragment of a compound, or any combination thereof, that disrupts the interaction of sclerostin with a homologue of the LRP5 or LRP6 receptor. 77. A therapeutic composition for the treatment of a bone-fracture, bone disease, bone injury or bone abnormality in a mammalian subject comprising at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with at least one domain of the LRP5 or LRP6 receptor. 78. A therapeutic composition for the treatment of a bone fracture, bone disease, bone injury or bone abnormality in a mammalian subject comprising at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with the first or second domain of the LRP5 or LRP6 receptor. . 79. The composition of claims 74 to 78 wherein said compound comprises IIΪC3 or IIC8. 80. The composition of claims 74 to 78 wherein said compound comprises IIIC3, IIC8 or any derivative or analog thereof. 81. The composition of claim 79 or 80 wherein said two or more compounds or said fragments of compounds are directly linked together with cross-linking, or indirectly linked together with a linker arm. 82. The method of claim 81 wherein said compounds, said fragments of a compound, or any combination thereof, dock in a first location and a second location on the same binding 24 site, receptor or protein. ■ 83. ' . The method of claim 81 wherein said compounds, said fragments of a compound, or any combination thereof, dock in a first location and a second location on different binding sites, receptors or proteins. 84. The method of claims 74 to 78 wherein said compounds, or said fragments of a compound, are linked together with a linker arm or cross-linking. 85. The composition of claims 74 to 84 wherein said compound or said fragment of a compound comprises a small molecule, protein, peptide, polypeptide, cyclic molecule, heterocyclic organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glycolipid, lipoprotein, chemical, or a fragment of a compound that comprises a heterocyclic organic molecule, nucleic acid, lipid, . charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glycolipid, lipoprotein, or chemical. 86. The . composition of claims 74 to 78 wherein said administering step comprises administration by inhalation, oral, intravenous, intraperitoneal, intramuscular, parenteral, transdermal, intravaginal, intranasal, mucosal, sublingual, topical, rectal, or subcutaneous administration, or .any combination thereof. 87. The composition of claims 74 to 86 wherein said non-native compound is identified using a method comprising: a. screening for a compound that fits into the cavity on the receptor using the UNITY™ program;b. docking said compound into the cavity using the Flexx™ program;and c. obtaining the compound with the highest binding affinity using the Cscore™ program. 88. The composition of claims 74 to 87 further comprising a pharmaceutically acceptable carrier. 89. The composition of claims 74 to 87 wherein said composition is formulated as a tablet, pill, dragee, liquid, gel, capsule, syrup, slurry or suspension. 90. A method for preventing or blocking bone formation in a mammalian subject by administering sclerostin. 91. A method for the treatment of abnormal bone growth in a mammalian subject comprising administering an antibody for sclerostin, or any other non-native compound or fragment of a compound which decreases or eliminates sclerostin. 92. The method of claim 91 wherein said compound or said fragment of a compound comprises a small molecule, protein, peptide, polypeptide, cyclic molecule, heterocyclic organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glycolipid, lipoprotein or chemical. 25 93. The method of claim 91 or 92 wherein said administering step comprises administration by inhalation, oral, intravenous, intraperitoneal, intramuscular, parenteral, transdermal, intravaginal, intranasal, mucosal;- sublingual, topical, rectal, or subcutaneous administration, or any combination thereof. 94. The method of claims 90 to 92 wherein said sclerostin comprises a related protein, an unrelated protein with analogous functions, or any homologue or derivative of sclerostin. 95. A therapeutic composition for preventing . or blocking bone formation in a mammalian subject comprising sclerostin. 96. A therapeutic composition for preventing or blocking bone formation in a mammalian subject comprising a sclerostin antibody or any other non-native compound or fragment of a compound which decreases or eliminates sclerostin. 97. The method or composition of claims 91 to 96 wherein said non-native compound is identified using a method comprising: a. screening for a compound that fits into the cavity on the receptor using the UNITY™ program;. b. docking said compound into the cavity using the Flexx™ program;and c. obtaining the compound with the highest binding affinity using the Cscore™ program. 98. A method for identifying a drug candidate or compound which promotes or inhibits a protein-protein interaction comprising: a. determining the virtual structure of a receptor protein;b. identifying a particular binding cavity on said receptor protein;c. identifying a specific site within said binding cavity;and d. screening for a compound that fits into said specific site. 99. The method of claim 98 further comprising the step of identifying the compound with the highest binding affinity using the Cscore program. 100. The method of claim 98 wherein said step of identifying a particular binding cavity comprises conducting experiments based on the biological functions of the compounds. ' 101. The method of claim 100 wherein said experiments comprise mutational analyses. 102. The method of claim 98 wherein said receptor protein is non-soluble or membrane bound. 103. A method for identifying a- drug candidate or compound which promotes or inhibits a protein-protein interaction comprising: a. determining the virtual structure of a receptor protein;b. identifying a particular binding cavity on said receptor protein;c. identifying a specific site within said binding cavity;d. screening for a compound that fits into said specific site using the UNITY™ program;26 e. docking said compound into the cavity using the Flexx™ program;and " f. obtaining the compound with the highest binding affinity using the Cscore™ program. . . . . • ' 104. The method of claim 103 wherein said step of identifying a particular binding cavity comprises conducting experiments based on the biological functions of the compounds., 105. The method of claim 104 wherein said experiments comprise mutational analyses. , ■ 106. The method of claim 103 wherein said receptor protein is non-soluble or membrane- bound. • ' " 107. A method for identifying a drug candidate compound which binds to a receptor protein involved in bone formation or bone remodeling comprising: a. determining the virtual or computational structure of a non-soluble receptor protein comprising the use of amino acid sequencing, X-ray crystallography, NMR, analogs or derivatives of said receptor protein, or any combination thereof;b. identifying a particular binding cavity on said receptor protein through the use of experiments based on biological function comprising mutational analysis, chemical modification of amino acids, co-crystallography, NMR, or any combination thereof;c. identifying a specific binding site within said binding cavity based on mutations or chemical modifications;d. screening for a compound that fits into said specific site using the UNITY™ program.;and e.. identifying the compound with the highest binding affinity or the lowest energy using the Cscore™ program to find the compound with the best fit. 108. A method for identifying a drug candidate compound which binds to a receptor protein involved in bone formation or bone remodeling. comprising: a. determining the virtual or computational structure of a signal peptide comprising the use of amino acid sequencing, X-ray crystallography, NMR, analogs or derivatives of said signal peptide, or any combination thereof;b. identifying a particular binding cavity on said receptor protein through the use of experiments based on biological function comprising mutational analysis, chemical modification, co-crystallography, NMR or any combination thereof;c. identifying a specific binding site within said binding cavity based on the results obtained from said experiments;d. screening for a compound that fits into said binding cavity or said specific site in said binding cavity using the UNITY™ program;e. docking said compound into said binding cavity or said specific site in said binding cavity using the Flexx™ program;and f. identifying the compound with the highest binding affinity or the lowest energy using the Cscore™ program. 109. A method for identifying a drug candidate or compound which binds to a protein involved in a signal transduction system comprising: 27 a. providing or determining the virtual or computational structure of said protein comprising the use of amino acid sequencing, X-ray crystallography, NMR 5 analogs or derivatives of said receptor protein, or any combination thereof;b. identifying a particular binding cavity, site or domain on said protein using various experiments comprising mutational analysis, chemical modification of amino acids, co-crystallography, NMR, or any combination thereof;c. identifying a specific binding site within said binding cavity, site or domain based on the results of said experiments;and d. screening a library of drug candidate compounds to identify the drug candidate or compound having the best fit with said specific binding site or said binding cavity, site or domain. 110. A method for identifying a drug candidate or compound which binds to a nonsoluble or membrane-bound protein involved in a signal transduction system comprising: a. providing or determining the virtual or computational structure of said protein comprising the use of amino acid sequencing, X-ray crystallography, NMR, analogs or derivatives of said receptor protein, or any combination thereof;b. identifying a particular binding cavity, site or domain or said protein using various experiments comprising mutational analysis, chemical modification of amino acids, co-crystallography, NMR, or any combination thereof;c. identifying a specific binding site within said binding cavity, site or domain based on the results of said experiments;and d. screening a library of drug candidate compounds to identify the drug candidate or compound having the best fit with said specific binding site or said binding cavity, site or domain. 111. A method for identifying a drug candidate or compound which binds to a protein involved in a Wnt signaling pathway comprising: a. providing or determining the virtual or computational structure of said protein comprising the use of amino acid sequencing, X-ray crystallography, NMR, analogs or derivatives of said receptor protein, or any combination thereof;• b. identifying a particular binding cavity, site or domain or said protein using various experiments comprising mutational analysis, chemical modification of amino acids, co-crystallography, NMR, or any combination thereof;c. identifying a specific binding site within said binding cavity, site or domain based on the results of said experiments;and d. screening a library of drug candidate compounds to identify the drug candidate or compound having the best fit with said specific binding site or said binding cavity, site or domain. ' ■ 112. A method for identifying a drug candidate or compound which binds to a protein involved in a signal transduction system for promoting or inhibiting bone growth comprising: a. providing or determining the virtual or computational structure of said protein comprising the use of amino acid sequencing, X-ray crystallography, NMR, analogs or derivatives of said receptor protein, or any combination thereof;b. identifying a particular binding cavity, site or domain or said protein using 28 various experiments comprising mutational analysis, chemical modification' of amino acids, co-crystallography, NMR, or any combination thereof;c. identifying a specific binding site within said binding cavity, site or domain based on the results of said experiments;and d. screening a library of drug candidate compounds to identify the drug candidate or compound having the best fit with said specific binding site or said bindin,g cavity, site or domain. 113. A method for the regulation of bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native . compound, or any combination thereof, that decreases or eliminates the affinity of sclerostin to a receptor or co-receptor involved in bone formation or bone remodeling. 29 CLAIMS 1. A method for promoting bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that prevents the binding of sclerostin to a receptor or co-receptor involved in bone formation or bone remodeling.
  2. 2
    A method for promoting bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that prevents the binding of sclerostin to the LRP5 or LRP6 receptor.
  3. 3
    A method for promoting bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that prevents the binding of sclerostin to a homologue of the LRP5 or LRP6 receptor.
  4. 4
    A method for promoting bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that prevents the binding of sclerostin to at least one domain of the LRP5 or LRP6 receptor.
  5. 5
    A method for promoting bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that prevents the binding of sclerostin to the first or second domain of the LRP5 or LRP6 receptor.
  6. 8
    8, or any derivative or analog thereof. 17 ■ I p— r\ r*\ 8. The method of claims 6 or 7 wherein said two or more compounds, or said fragments of compounds are directly linked together with cross-linking, or indirectly linked together with a linker arm.
  7. 16
    A method for the treatment of a bone fracture, bone disease, bone injury, or bone abnormality in a mammalian subject comprising administering at least one non-native compound, at least one fragment of a non-native compound or any combination thereof, that prevents the binding of sclerostin to a receptor or co-receptor involved in bone formation or bone remodeling.
  8. 17
    A method for the treatment of a bone fracture, bone disease, bone injury, or bone abnormality in a mammalian subject comprising administering at least one non-native compound, at least one fragment of a non-native compound or any combination thereof, that prevents the binding of sclerostin to the LRP5 or LRP6 receptor.
  9. 18
    A method for the treatment of a bone fracture, bone disease, bone injury, or bone abnormality in a mammalian subject comprising administering at least one non-native compound, at least one fragment of a non-native compound or any combination thereof, that prevents the binding of sclerostin to a homologue of the LRP5 or LRP6 receptor.
  10. 22
    22 41. The composition of claims 29 to 40 wherein said non-native compound is identified using a method comprising:a. screening for a compound that fits into the cavity on the receptor using the UNITY™ program;b. docking said compound into the cavity using the Flexx™ program;and c. obtaining the compound with the highest binding affinity using the Cscore™ program. 42. The composition of claims 29 to 41 wherein said composition further comprises a pharmaceutically acceptable carrier. 43. The composition of claims 29 to 41 wherein said composition is formulated as a tablet, pill, dragee, liquid, gel, capsule, syrup, slurry or suspension. 44. A method for the regulation of bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound or any combination thereof, that disrupts the interaction of sclerostin with a receptor or co-receptor involved in bone formation or bone remodeling. 45. A method for the regulation of bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with the LRP5 or LRP6 receptor. 46. A method for the regulation of bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with a homologue of the LRP5 or LRP6 receptor. 47. A method for the regulation of bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native
  11. 23
    23 compound, or any combination thereof, that disrupts the interaction of sclerostin with at least one domain of the LRP5 or LRP6 receptor. 48. A method for the regulation of bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with the first or second domain of the LRP5 or LRP6 receptor. 49. The method of claims 44 to 48 wherein said compound or said fragment of a compound comprises IIIC3 or IIC8. 50. The method of claims 44 to 48 wherein said compound or said fragment of a compound comprises IIIC3, or IIC8, or any derivative or analog thereof. 51. The method of claims 49 or 50 wherein said two or more compounds or said fragments of compounds are directly linked together with cross-linking, or indirectly linked together with a linker arm. 52. The method of claim 51 wherein said compounds, said fragments of a compound, or any combination thereof, dock in a first location and a second location on the same binding site, receptor or protein. 53. The method of claim 51 wherein said compounds, said fragments of a compound, or any combination thereof, dock in a first location and a second location on different binding sites, receptors or proteins. 54. The method of claims 44 to 48 wherein said compounds, or said fragments of a compound, are linked together with a linker arm or cross-linking. 55. The method of claims 44 to 54 wherein said compound or said fragment of a compound comprises a small molecule, protein, peptide, polypeptide, cyclic molecule, heterocyclic
  12. 24
    24 organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glycolipid, lipoprotein, chemical, or a fragment of a compound that comprises a heterocyclic organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glycolipid, lipoprotein, or chemical. 56. The method of claims 44 to 48 wherein said administering step comprises administration by inhalation, oral, intravenous, intraperitoneal, intramuscular, parenteral, transdermal, intravaginal, intranasal, mucosal, sublingual, topical, rectal, or subcutaneous administration, or any combination thereof. 57. The method of claims 44 to 55 wherein said compound or said fragment of a compound comprises at least one agonist, antagonist, partial agonist, or any combination thereof. 58. The method of claims 44 to 57 wherein said non-native compound is identified using a method comprising:a. screening for a compound that fits into the cavity on the receptor using the UNITY™ program;b. docking said compound into the cavity using the Flexx program;and c. obtaining the compound with the highest binding affinity using the Cscore™ program. 59. A method for the treatment of a bone fracture, bone disease, bone injury, or bone abnormality in a mammalian subject comprising administering at least one non-native compound, at least one fragment of a non-native compound or any combination thereof, that disrupts the interaction of sclerostin with a receptor or co-receptor involved in bone formation or bone remodeling. 60. A method for the treatment of a bone fracture, bone disease, bone injury, or bone abnormality in a mammalian subject comprising administering at least one non-native compound, at least one fragment of a non-native compound or any combination thereof, that disrupts the interaction of sclerostin with the LRP5 or LRP6 receptor.
  13. 25
    25 61. A method for the treatment of a bone fracture, bone disease, bone injury, or bone abnormality in a mammalian subject comprising administering at least one non-native compound, at least one fraction of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with a homologue of the LRP5 or LRP6 receptor. 62. A method for the treatment of a bone fracture, bone disease, bone injury, or bone abnormality in a mammalian subject comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with at least one domain of the LRP5 or LRP6 receptor. 63. A method for the treatment of a bone fracture, bone disease, bone injury, or bone abnormality in a mammalian subject comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with the first or second domain of the LRP5 or LRP6 receptor. 64. The method of claims 59 to 63 wherein said compound or said fragment of a compound comprises IIIC3 or IIC8. 65. The method of claims 59 to 63 wherein said compound or said fragment of a compound comprises IIIC3, IIC8 or any derivative or analog thereof. 66. The method of claim 64 or 65 wherein said two or more compounds or said fragments of compounds are directly linked together with cross-linking, or indirectly linked together with a linker arm. 67. The method of claim 66 wherein said compounds, said fragments of a compound, or any combination thereof, dock in a first location and a second location on the same binding site, receptor or protein.
  14. 27
    27 74. A therapeutic composition for the treatment of a bone fracture, bone disease, bone injury or bone abnormality in a mammalian subject comprising at least one non-native compound, at least one fragment of a compound, or any combination thereof, that disrupts the interaction of sclerostin with a receptor or co-receptor involved in bone formation or bone remodeling. 75. A therapeutic composition for the treatment of a bone fracture, bone disease, bone injury or bone abnormality in a mammalian subject comprising at least one non-native compound, at least one fragment of a compound, or any combination thereof, that disrupts the interaction of sclerostin with the LRP5 or LRP6 receptor. 76. A therapeutic composition for the treatment of a bone fracture, bone disease, bone injury or bone abnormality in a mammalian subject comprising at least one non-native compound, at least one fragment of a compound, or any combination thereof, that disrupts the interaction of sclerostin with a homologue of the LRP5 or LRP6 receptor. 77. A therapeutic composition for the treatment of a bone fracture, bone disease, bone injury or bone abnormality in a mammalian subject comprising at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with at least one domain of the LRP5 or LRP6 receptor. 78. A therapeutic composition for the treatment of a bone fracture, bone disease, bone injury or bone abnormality in a mammalian subject comprising at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that disrupts the interaction of sclerostin with the first or second domain of the LRP5 or LRP6 receptor. 79. The composition of claims 74 to 78 wherein said compound comprises IIIC3 or IIC8.
  15. 28
    28 80. The composition of claims 74 to 78 wherein said compound comprises IIIC3, IIC8 or any derivative or analog thereof. 81. The composition of claim 79 or 80 wherein said two or more compounds or said fragments of compounds are directly linked together with cross-linking, or indirectly linked together with a linker arm. 82. The method of claim 81 wherein said compounds, said fragments of a compound, or any combination thereof, dock in a first location and a second location on the same binding site, receptor or protein. 83. The method of claim 81 wherein said compounds, said fragments of a compound, or any combination thereof, dock in a first location and a second location on different binding sites, receptors or proteins. 84. The method of claims 74 to 78 wherein said compounds, or said fragments of a compound, are linked together with a linker arm or cross-linking. 85. The composition of claims 74 to 84 wherein said compound or said fragment of a compound comprises a small molecule, protein, peptide, polypeptide, cyclic molecule, heterocyclic organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glycolipid, lipoprotein, chemical, or a fragment of a compound that comprises a heterocyclic organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glycolipid, lipoprotein, or chemical. 86. The composition of claims 74 to 78 wherein said administering step comprises administration by inhalation, oral, intravenous, intraperitoneal, intramuscular, parenteral, transdermal, intravaginal, intranasal, mucosal, sublingual, topical, rectal, or subcutaneous administration, or any combination thereof. 87. The composition of claims 74 to 86 wherein said non-native compound is identified using a method comprising:
  16. 29
    29 a. screening for a compound that fits into the cavity on the receptor using the UNITY™ program;b. docking said compound into the cavity using the Flexx™ program;and c. obtaining the compound with the highest binding affinity using the Cscore™ program. 88. The composition of claims 74 to 87 further comprising a pharmaceutically acceptable carrier. 89. The composition of claims 74 to 87 wherein said composition is formulated as a tablet, pill, dragee, liquid, gel, capsule, syrup, slurry or suspension. 90. A method for preventing or blocking bone formation in a mammalian subject by administering sclerostin. 91. A method for the treatment of abnormal bone growth in a mammalian subject comprising administering an antibody for sclerostin, or any other non-native compound or fragment of a compound which decreases or eliminates sclerostin. 92. The method of claim 91 wherein said compound or said fragment of a compound comprises a small molecule, protein, peptide, polypeptide, cyclic molecule, heterocyclic organic molecule, nucleic acid, lipid, charged lipid, polar lipid, non-polar lipid, sugar, glycoprotein, glyco lipid, lipoprotein or chemical. 93. The method of claim 91 or 92 wherein said administering step comprises administration by inhalation, oral, intravenous, intraperitoneal, intramuscular, parenteral, transdermal, intravaginal, intranasal, mucosal, sublingual, topical, rectal, or subcutaneous administration, or any combination thereof. 94. The method of claims 90 to 92 wherein said sclerostin comprises a related protein, an unrelated protein with analogous functions, or any homologue or derivative of sclerostin.
  17. 30
    30 95. A therapeutic composition for preventing or blocking bone formation in a mammalian subject comprising sclerostin. 96. A therapeutic composition for preventing or blocking bone formation in a mammalian subject comprising a sclerostin antibody or any other non-native compound or fragment of a compound which decreases or eliminates sclerostin. 97. The method or composition of claims 91 to 96 wherein said non-native compound is identified using a method comprising:a. screening for a compound that fits into the cavity on the receptor using the UNITY™ program;b. docking said compound into the cavity using the Flexx™ program;and c. obtaining the compound with the highest binding affinity using the Cscore™ program. 98. A method for identifying a drug candidate or compound which promotes or inhibits a protein-protein interaction comprising: a. determining the virtual structure of a receptor protein;b. identifying a particular binding cavity on said receptor protein;c. identifying a specific site within said binding cavity;and d. screening for a compound that fits into said specific site. 99. The method of claim 98 further comprising the step of identifying the compound with the highest binding affinity using the Cscore™ program. 100. The method of claim 98 wherein said step of identifying a particular binding cavity comprises conducting experiments based on the biological functions of the compounds. 101. The method of claim 100 wherein said experiments comprise mutational analyses.
  18. 32
    32 c. identifying a specific binding site within said binding cavity based on mutations or chemical modifications; d. screening for a compound that fits into said specific site using the UNITY™ program.; and e. identifying the compound with the highest binding affinity or the lowest energy using the Cscore™ program to find the compound with the best fitst n, 108. A method for identifying a drug candidate compound which binds to a receptor protein involved in bone formation or bone remodeling comprising:a. determining the virtual or computational structure of a signal peptide comprising the use of amino acid sequencing, X-ray crystallography, NMR, analogs or derivatives of said signal peptide, or any combination thereof;b. identifying a particular binding cavity on said receptor protein through the use of experiments based on biological function comprising mutational analysis, chemical modification, co-crystallography, NMR or any combination thereof;c. identifying a specific binding site within said binding cavity basedton the results obtained from said experiments;, d. screening for a compound that fits into said binding cavity or said specific site in said binding cavity using the UNITY™ program;e. docking said compound into said binding cavity or said specific site in said binding cavity using the Flexx™ program;and f. identifying the compound with the highest binding affinity or the lowest energy using the Cscore™ program. 109. A method for identifying a drug candidate or compound which binds to a protein involved in a signal transduction system comprising: a. providing or determining the virtual or computational structure of said protein comprising the use of amino acid sequencing, X-ray crystallography, NMR, analogs or derivatives of said receptor protein, or any combination thereof;
  19. 33
    33 b. identifying a particular binding cavity, site or domain on said protein using various experiments comprising mutational analysis, chemical modification of amino acids, co-crystallography, NMR, or any combination thereof; c. identifying a specific binding site within said binding cavity, site or domain based on the results of said experiments; and d. screening a library of drug candidate compounds to identify the drug candidate or compound having the best fit with said specific binding site or said binding cavity, site or domain. 110. A method for identifying a drug candidate or compound which binds to a nonsoluble or membrane-bound protein involved in a signal transduction system comprising:a. providing or determining the virtual or computational structure of said protein comprising the use of amino acid sequencing, X-ray crystallography, NMR, analogs or derivatives of said receptor protein, or any combination thereof;b. identifying a particular binding cavity, site or domain or said protein using various experiments comprising mutational analysis, chemical modification of amino acids, co-crystallography, NMR, or any combination thereof;c. identifying a specific binding site within said binding cavity, site or domain based on the results of said experiments;and d. screening a library of drug candidate compounds to identify the drug candidate or compound having the best fit with said specific binding site or said binding cavity, site or domain. 111. A method for identifying a drug candidate or compound which binds to a protein involved in a Wnt signaling pathway comprising: a. providing or determining the virtual or computational structure of said protein comprising the use of amino acid sequencing, X-ray crystallography, NMR, analogs or derivatives of said receptor protein, or any combination thereof;
  20. 34
    34 b. identifying a particular binding cavity, site or domain or said protein using various experiments comprising mutational analysis, chemical modification of amino acids, co-crystallography, NMR, or any combination thereof; c. identifying a specific binding site within said binding cavity, site or domain based on the results of said experiments; and d. screening a library of drug candidate compounds to identify the drug candidate or compound having the best fit with said specific binding site or said binding cavity, site or domain. 112. A method for identifying a drug candidate or compound which binds to a protein involved in a signal transduction system for promoting or inhibiting bone growth comprising:a. providing or determining the virtual or computational structure of said protein comprising the use of amino acid sequencing, X-ray crystallography, NMR, analogs or derivatives of said receptor protein, or any combination thereof;b. identifying a particular binding cavity, site or domain or said protein using various experiments comprising mutational analysis, chemical modification of amino acids, co-crystallography, NMR, or any combination thereof;c. identifying a specific binding site within said binding cavity, site or domain based on the results of said experiments;and d. screening a library of drug candidate compounds to identify the drug candidate or compound having the best fit with said specific binding site or said binding cavity, site or domain. 113. A method for the regulation of bone formation or bone remodeling comprising administering at least one non-native compound, at least one fragment of a non-native compound, or any combination thereof, that decreases or eliminates the affinity of sclerostin to a receptor or co-receptor involved in bone formation or bone remodeling.
  21. 35
    35
Independent claims21