Claims
- 1. A crystalline form comprising a substantially pure LXR ligand binding domain polypeptide and a ligand.
- 2. The crystalline form of claim 1, wherein the LXR ligand binding domain polypeptide comprises the amino acid sequence of SEQ ID NO: 8.
- 3. The crystalline form of claim 1, wherein the ligand is N-(2,2,2-trifluoroethyl)-N-[4-(2,2,2-trifluoro-1-hydroxy-1-trifluoromethyl-ethyl)-phenyl]-benzenesulfonamide.
- 4. The crystalline form of claim 1, wherein the ligand is 24(S), 25-epoxycholesterol.
- 5. The crystalline form of claim 1, wherein the crystalline form has lattice constants of a=60.25 Å, b=82.45 Å, c=123.18 Å, α=90°, β=90°, γ=90°.
- 6 The crystalline form of claim 1, wherein the crystalline form is an orthorhombic crystalline form.
- 7. The crystalline form of claim 1, wherein the crystalline form has a space group of P212121.
- 8. The crystalline form of claim 1, wherein the crystalline form contains two LXR ligand binding domain polypeptides in the asymmetric unit.
- 9. The crystalline form of claim 1, wherein the crystalline form is further characterized by the coordinates corresponding to Table 2.
- 10. The crystalline form of claim 1, wherein the crystalline form is such that the three-dimensional structure of the crystalline form can be determined to a resolution of about 2.8 Å or better.
- 11. The crystalline form of claim 1, wherein the crystalline form contains one or more atoms having a atomic weight of 40 grams/mol or greater.
- 12. A crystalline form comprising a substantially pure LXR ligand binding domain polypeptide, a coactivator polypeptide and a ligand.
- 13. The crystalline form of claim 12, wherein the LXR ligand binding domain polypeptide comprises the amino acid sequence shown of SEQ ID NO: 8.
- 14. The crystalline form of claim 12, wherein the ligand is 24(S), 25-epoxycholesterol, and the coactivator polypeptide is a SRC1 fragment.
- 15. The crystalline form of claim 12, wherein the SRC1 fragment comprises the amino acid sequence of SEQ ID NO: 9.
- 16. The crystalline form of claim 12, wherein the crystalline form has lattice constants selected from the group consisting of a=71.17 Å, b=120.01 Å, c=147.56 Å, α=90, β=90°, γ=90°.
- 17. The crystalline form of claim 12, wherein the crystalline form is an orthorhombic crystalline form.
- 18. The crystalline form of claim 12, wherein the crystalline form has a space group of C2221.
- 19. The crystalline form of claim 12, wherein the crystalline form contains two LXR ligand binding domain polypeptides and two coactivator polypeptides in the asymmetric unit.
- 20. The crystalline form of claim 12, wherein the crystalline form is further characterized by the coordinates corresponding to Table 3.
- 21. The crystalline form of claim 12, wherein the crystalline form is such that the three-dimensional structure of the crystalline form can be determined to a resolution of about 2.8 Å or better.
- 22. The crystalline form of claim 12, wherein the crystalline form comprises one or more atoms having a atomic weight of 40 grams/mol or greater.
- 23. A method for determining the three-dimensional structure of a crystallized LXR ligand binding domain polypeptide in complex with one or more of a ligand and a coactivator polypeptide to a resolution of about 2.8 Å or better, the method comprising:
(a) crystallizing a LXR ligand binding domain polypeptide in complex with one or more of a ligand and a coactivator fragment to form a crystallized complex; and (b) analyzing the crystallized complex to determine the three-dimensional structure of the LXR ligand binding domain polypeptide in complex with one or more of a ligand and a coactivator polypeptide, whereby the three-dimensional structure of a crystallized LXR ligand binding domain polypeptide in complex with one or more of a ligand and a coactivator polypeptide is determined to a resolution of about 2.8 Å or better.
- 24. The method of claim 23, wherein the analyzing is by X-ray diffraction.
- 25. The method of claim 23, wherein the crystallization is accomplished by the hanging drop vapor diffusion method, and wherein the LXR ligand binding domain polypeptide and the ligand are mixed with an equal volume of reservoir.
- 26. The method of claim 25, wherein the reservoir comprises 10-12% PEG3350-8000 and 0.2 M salt.
- 27. The method of claim 23, wherein the salt is selected from the group consisting of NaF, KF, NaCl, KCl, Na formate, Na acetate, K acetate, ammonium sulfate and lithium sulfate.
- 28. The method of claim 23, wherein the LXR ligand binding domain polypeptide comprises the amino acid sequence of SEQ ID NO: 8.
- 29. The method of claim 23, wherein the ligand is selected from the group consisting of 24(S), 25-epoxycholesterol and N-(2,2,2-trifluoroethyl)-N-[4-(2,2,2-trifluoro-1-hydroxy-1-trifluoromethyl-ethyl)-phenyl]-benzenesulfonamide.
- 30. The method of claim 23, wherein the coactivator polypeptide is a SRC1 polypeptide.
- 31. The method of claim 30, wherein the SRC1 polypeptide comprises the sequence of SEQ ID NO: 9.
- 32. A method of generating a crystalline form comprising a LXR ligand binding domain polypeptide in complex with one or more of a ligand and a coactivator polypeptide, the method comprising:
(a) incubating a solution comprising a LXR ligand binding domain and one or more of a ligand and a coactivator polypeptide with an equal volume of reservoir; and (b) crystallizing the LXR ligand binding domain polypeptide and one or more of a ligand and a coactivator polypeptide using the hanging drop method, whereby a crystalline form of a LXR ligand binding domain polypeptide in complex with one or more of a ligand and a coactivator polypeptide is generated.
- 33. The method of claim 32, wherein the LXR ligand binding domain comprises the amino acid sequence of SEQ ID NO: 8.
- 34. The method of claim 32, wherein the ligand is selected from the group consisting of 24(S), 25-epoxycholesterol and N-(2,2,2-trifluoroethyl)-N-[4-(2,2,2-trifluoro-1-hydroxy-1-trifluoromethyl-ethyl)-phenyl]-benzenesulfonamide.
- 35. The method of claim 32, wherein the coactivator polypeptide comprises a SRC1 polypeptide.
- 36. The method of claim 35, wherein the SRC1 polypeptide comprises the sequence of SEQ ID NO: 9.
- 37. A crystalline form of a LXR ligand binding domain polypeptide in complex with one or more of a ligand and a coactivator polypeptide produced by the method of claim 32.
- 38. A method of designing a modulator of a NR polypeptide, the method comprising:
(a) designing a potential modulator of a NR polypeptide that will make interactions with amino acids in a ligand binding site of the NR polypeptide, based upon a crystalline structure comprising a LXR ligand binding domain polypeptide in complex with a one or more of a ligand and a coactivator polypeptide; (b) synthesizing the modulator; and (c) determining whether the potential modulator modulates the activity of the NR polypeptide, whereby a modulator of a NR polypeptide is designed.
- 39. The method of claim 38, wherein the ligand is selected from the group consisting of 24(S), 25-epoxycholesterol and N-(2,2,2-trifluoroethyl)-N-[4-(2,2,2-trifluoro-1-hydroxy-1-trifluoromethyl-ethyl)-phenyl]-benzenesulfonamide.
- 40. The method of claim 38, wherein the coactivator polypeptide comprises a SRC1 polypeptide.
- 41. The method of claim 38, wherein the SRC1 polypeptide comprises the sequence of SEQ ID NO: 9.
- 42. The method of claim 38, wherein the NR comprises a LXR.
- 43. The method of claim 42, wherein the LXR comprises a LXRβ.
- 44. The method of claim 43, wherein the LXRβ comprises the amino acid sequence of SEQ ID NO: 4.
- 45. The method of claim 38, wherein the ligand is selected from the group consisting of N-(2,2,2-trifluoroethyl)-N-[4-(2,2,2-trifluoro-1-hydroxy-1-trifluoromethyl-ethyl)-phenyl]-benzenesulfonamide and 24(S), 25-epoxycholesterol.
- 46. A method of designing a modulator that selectively modulates the activity of a NR polypeptide compared to other polypeptides, the method comprising:
(a) obtaining a crystalline form comprising a LXRβ ligand binding domain polypeptide in complex with one or more of a ligand and a coativator polypeptide; (b) evaluating the three-dimensional structure of the crystallized LXRβ ligand binding domain polypeptide in complex with one or more of a ligand and a coactivator polypeptide; and (c) synthesizing a potential modulator based on the three-dimensional structure of the crystallized LXRβ ligand binding domain polypeptide in complex with one or more of a ligand and a coactivator polypeptide, whereby a modulator that selectively modulates the activity of a NR polypeptide compared to other polypeptides is designed.
- 47. The method of claim 46, wherein the method further comprises contacting a NR ligand binding domain polypeptide with the potential modulator and one or more of a ligand and a coactivator polypeptide; and assaying the NR ligand binding domain polypeptide for binding of the potential modulator, for a change in activity of the NR ligand binding domain polypeptide, or both.
- 48. The method of claim 46, wherein the LXRβ ligand binding domain polypeptide comprises the amino acid sequence of SEQ ID NO: 8.
- 49. The method of claim 46, wherein the NR comprises a LXR.
- 50. The method of claim 49, wherein the LXR comprises LXRβ.
- 51. The method of claim 46, wherein the crystalline form is an orthorhombic form.
- 52. The method of claim 46, wherein the crystalline form is further characterized by the atomic structural coordinates of one of Table 2 and Table 3.
- 53. The method of claim 46, wherein the crystalline form is such that the three-dimensional structure of the crystallized LXRβ ligand binding domain polypeptide in complex with one or more of a ligand and a coactivator polypeptide can be determined to a resolution of about 2.8 Å or better.
- 54. The method of claim 46, wherein the coactivator polypeptide comprises a SRC1 peptide.
- 55. Then method of claim 54, wherein the SRC1 peptide comprises the sequence of SEQ ID NO: 9.
- 56. The method of claim 46, wherein the ligand is selected from the group consisting of N-(2,2,2-trifluoroethyl)-N-[4-(2,2,2-trifluoro-1-hydroxy-1-trifluoromethyl-ethyl)-phenyl]-benzenesulfonamide and 24(S), 25-epoxycholesterol.
- 57. A method of screening a plurality of compounds for a modulator of a NR ligand binding domain polypeptide, the method comprising:
(a) providing a library of test samples; (b) contacting a crystalline form comprising a LXR ligand binding domain polypeptide in complex with one or more of a ligand and a coactivator polypeptide with each test sample; (c) detecting an interaction between a test sample and the crystalline LXR ligand binding domain polypeptide in complex with one or more of a ligand and a coactivator polypeptide; (d) identifying a test sample that interacts with the crystalline LXR ligand binding domain polypeptide in complex with one or more of a ligand and a coactivator polypeptide; and (e) isolating a test sample that interacts with the crystalline LXR ligand binding domain polypeptide in complex with one or more of a ligand and a coregulator polypeptide, whereby a plurality of compounds is screened for a modulator of a NR ligand binding domain polypeptide.
- 58. The method of claim 57, wherein the crystalline form is further characterized by an atomic structural coordinate set selected from the group consisting of Table 2 and Table 3.
- 59. The method of claim 57, wherein the LXR ligand binding domain polypeptide comprises a LXRβ ligand binding domain polypeptide.
- 60. The method of claim 59, wherein the LXRβ ligand binding domain polypeptide comprises the amino acid sequence of SEQ ID NO: 8.
- 61. The method of claim 57, wherein the test samples are bound to a substrate.
- 62. The method of claim 57, wherein the test samples are synthesized directly on a substrate.
- 63. The method of claim 57, wherein the coregulator polypeptide comprises a SRC1 polypeptide.
- 64. The method of claim 63, wherein the SRC1 polypeptide comprises the sequence of SEQ ID NO: 9.
- 65. The method of claim 57, wherein the ligand is selected from the group consisting of N-(2,2,2-trifluoroethyl)-N-[4-(2,2,2-trifluoro-1-hydroxy-1-trifluoromethyl-ethyl)-phenyl]-benzenesulfonamide and 24(S), 25-epoxycholesterol.
- 66. A method for identifying a NR modulator, the method comprising:
(a) providing atomic structural coordinates describing a LXR ligand binding domain in complex with one or more of a ligand and a coactivator polypeptide to a computerized modeling system; and (b) modeling ligands that fit spatially into the binding pocket of the LXR ligand binding domain to thereby identify a NR modulator.
- 67. The method of claim 66, wherein the method further comprises identifying in an assay for NR-mediated activity a modeled ligand that increases or decreases the activity of the NR.
- 68. The method of claim 66, wherein the atomic structural coordinates are selected from the group consisting of the coordinates of Table 2 and the coordinates of Table 3.
- 69. The method of claim 66, wherein the LXR comprises LXRβ.
- 70. The method of claim 66, wherein the LXRβ ligand binding domain comprises the amino acid sequence of SEQ ID NO: 8.
- 71. The method of claim 66, wherein the coactivator polypeptide comprises a SRC1 polypeptide.
- 72. The method of claim 71, wherein the SRC1 polypeptide comprises the sequence of SEQ ID NO: 9.
- 73. The method of claim 66, wherein the ligand is selected from the group consisting of N-(2,2,2-trifluoroethyl)-N-[4-(2,2,2-trifluoro-1-hydroxy-1-trifluoromethyl-ethyl)-phenyl]-benzenesulfonamide and 24(S), 25-epoxycholesterol.
- 74. A method of identifying a LXR modulator that selectively modulates the activity of a LXRβ polypeptide compared to other polypeptides, the method comprising:
(a) providing atomic structural coordinates describing a LXRβ ligand binding domain in complex with one or more of a ligand and a coactivator polypeptide to a computerized modeling system; and (b) modeling a ligand that fits into the binding pocket of a LXRβ ligand binding domain and that interacts with residues of a LXRβ that are conserved among LXR subtypes to thereby identify a LXRβ modulator that selectively modulates the activity of a LXRβ polypeptide compared to other polypeptides.
- 75. The method of claim 74, wherein the method further comprises identifying in a biological assay for LXRβ activity a modeled ligand that selectively binds to said LXRβ and increases or decreases the activity of said LXRβ.
- 76. The method of claim 74, wherein the atomic structural coordinates are selected from the group consisting of the coordinates of Table 2 and the coordinates of Table 3.
- 77. The method of claim 74, wherein the LXRβ ligand binding domain comprises the amino acid sequence shown in SEQ ID NO: 8.
- 78. The method of claim 74, wherein the coactivator polypeptide comprises a SRC1 polypeptide.
- 79. The method of claim 78, wherein the SRC1 polypeptide comprises the sequence of SEQ ID NO: 9.
- 80. The method of claim 74, wherein the ligand is selected from the group consisting of N-(2,2,2-trifluoroethyl)-N-[4-(2,2,2-trifluoro-1-hydroxy-1-trifluoromethyl-ethyl)-phenyl]-benzenesulfonamide and 24(S), 25-epoxycholesterol.
- 81. A method of designing a modulator of a NR polypeptide, the method comprising:
(a) selecting a candidate NR ligand; (b) determining which amino acid or amino acids of a NR polypeptide interact with the ligand using a three-dimensional model of a crystallized protein, the model comprising a LXRβ ligand binding domain in complex with one or more of a ligand and a coactivator polypeptide; (c) identifying in a biological assay for NR activity a degree to which the ligand modulates the activity of the NR polypeptide; (d) selecting a chemical modification of the ligand wherein the interaction between the amino acids of the NR polypeptide and the ligand is predicted to be modulated by the chemical modification; (e) synthesizing a ligand having the chemical modified to form a modified ligand; (f) contacting the modified ligand with the NR polypeptide; (g) identifying in a biological assay for NR activity a degree to which the modified ligand modulates the biological activity of the NR polypeptide; and (h) comparing the biological activity of the NR polypeptide in the presence of modified ligand with the biological activity of the NR polypeptide in the presence of the unmodified ligand, whereby a modulator of a NR polypeptide is designed.
- 82. The method of claim 81, wherein the NR polypeptide is a LXR polypeptide.
- 83. The method of claim 81, wherein the LXR is selected from the group consisting of a LXRα polypeptide and a LXRβ polypeptide.
- 84. The method of claim 83, wherein the LXRβ polypeptide has the amino acid sequence shown in SEQ ID NO: 4.
- 85. The method of claim 81, wherein the LXRA polypeptide comprises the amino acid sequence of SEQ ID NO: 2.
- 86. The method of claim 81, wherein the three-dimensional model of a crystallized protein is further characterized by atomic structural coordinates selected from the group consisting of the coordinates of Table 2 and the coordinates of Table 3.
- 87. The method of claim 81, wherein the coactivator polypeptide is a SRC1 polypeptide.
- 88. The method of claim 87, wherein the SRC1 polypeptide comprises the sequence of SEQ ID NO: 9.
- 89. The method of claim 81, wherein the ligand is selected from the group consisting of N-(2,2,2-trifluoroethyl)-N-[4-(2,2,2-trifluoro-1-hydroxy-1-trifluoromethyl-ethyl)-phenyl]-benzenesulfonamide and 24(S), 25-epoxycholesterol.
- 90. The method of claim 81, wherein the method further comprises repeating steps (a) through (f), if the biological activity of the NR polypeptide in the presence of the modified ligand varies from the biological activity of the NR polypeptide in the presence of the unmodified ligand.
- 91. A method of identifying a LXR modulator that selectively modulates the biological activity of one LXR subtype compared to LXRβ, the method comprising:
(a) providing an atomic structure coordinate set describing a LXRβ ligand binding domain structure in complex with one or more of a ligand and a coactivator polypeptide and at least one other atomic structure coordinate set describing a LXR ligand binding domain, each ligand binding domain comprising a ligand binding site; (b) comparing the LXR atomic structure coordinate sets to identify at least one difference between the sets; (c) designing a candidate ligand predicted to interact with the difference of step (b); (d) synthesizing the candidate ligand; and (e) testing the synthesized candidate ligand for an ability to selectively modulate a LXR subtype as compared to LXRβ, whereby a LXR modulator that selectively modulates the biological activity of one LXR subtype compared to LXRβ is identified.
- 92. The method of claim 91, wherein the LXR subtype whose biological activity is to be modulated comprises LXRA.
- 93. The method of claim 92, wherein the LXRα comprises the amino acid sequence of SEQ ID NO: 2.
- 94. The method of claim 91, wherein the atomic structure coordinate set describing a LXRβ ligand binding domain structure is selected from the group consisting of the coordinates of Table 2 and the coordinates of Table 3.
- 95. The method of claim 91, wherein the coactivator polypeptide comprises a SRC1 polypeptide.
- 96. The method of claim 95, wherein the SRC1 polypeptide comprises the sequence of SEQ ID NO: 9.
- 97. The method of claim 91, wherein the atomic structure coordinate set further describes an associated ligand.
- 98. The method of claim 97, wherein the ligand is selected from the group consisting of N-(2,2,2-trifluoroethyl)-N-[4-(2,2,2-trifluoro-1-hydroxy-1-trifluoromethyl-ethyl)-phenyl]-benzenesulfonamide and 24(S), 25-epoxycholesterol.
- 99. A method of modeling a three-dimensional structure of a target NR in complex with one or more of a ligand and a coactivator polypeptide from a template comprising the X-ray structure of a LXRβ LBD in complex with one or more of a ligand and a coactivator polypeptide, the method comprising:
(a) selecting an X-ray structure of a target NR LBD as a starting model for the target NR LBD; (b) manipulating the starting model for the target NR as a rigid body to superimpose its backbone atoms onto corresponding backbone atoms of a three-dimensional template structure comprising a LXRβ in complex with one or more of a ligand and a coactivator polypeptide to form a manipulated model; (c) making a copy of the coactivator peptide from the template structure to form a model of a coactivator polypeptide bound to a template LXRβ; (d) merging the model of the coactivator polypeptide into the manipulated model to form a modified model; (e) removing one or more amino acids from the modified model; and (f) optimizing side-chain conformations, whereby a three-dimensional structure of a target NR in complex with one or more of a ligand and a coactivator polypeptide is modeled from a template comprising the X-ray structure of an NR in complex with one or more of a ligand and a coactivator polypeptide.
- 100. The method of claim 99, wherein the X-ray structure of a target NR LBD is a structure built by homology modeling
- 101. The method of claim 99, wherein the LXRβ ligand binding domain comprises the sequence of SEQ ID NO: 8.
- 102. The method of claim 99, wherein the coactivator polypeptide is a SRC1 polypeptide.
- 103. The method of claim 102, wherein the SRC1 polypeptide comprises the sequence of SEQ ID NO: 9.
- 104. The method of claim 99, wherein the three-dimensional template structure is a structure characterized by the coordinates selected from the group consisting of the coordinates of Table 2, the coordinates of Table 3 and the coordinates of Table 4.
- 105. The method of claim 99, wherein the optimizing comprises varying distance constraints.
RELATED APPLICATIONS
[0001] This application claims priority to U.S. application No. 60/376,019 filed Apr. 26, 2002.
Provisional Applications (1)
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Number |
Date |
Country |
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60376019 |
Apr 2002 |
US |