Inhibitors for androgen antagonist refractory prostate cancer

• US 20070087352A9
• Filed: 11/06/2003
• Published: 04/19/2007
• Est. Priority Date: 11/06/2003
• Status: Abandoned Application

• Current Assignee: Karo Pharma AB, Regents of the University of California (University of California)
• Original Assignee: Regents of the University of California (University of California)
• Inventors: Fletterick, Robert, Hur, Eugene, Estebanez-Perpina, Eva, Pfaff, Samuel, Buehrer, Benjamin
• Application Number:
  US10/705,165
• Publication Number:
  US 20050202440A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: G01N 2500/04 Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)
• CPC Class Codes: G01N 33/743 Steroid hormones
• CPC Class Codes: G16B 15/00 ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
• CPC Class Codes: G16B 15/30 Drug targeting using structural data; Docking or binding prediction
• CPC Class Codes: G16C 20/50 Molecular design, e.g. of drugs
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

The present invention relates to methods and antagonist compounds for modulating androgen receptor activity. The invention includes a method for identifying molecules that bind to a coactivator binding site of a receptor in the androgen receptor family. Also included is a cocrystal of an androgen receptor ligand binding domain complexed with a ligand and a coactivator. The invention further includes a method for inhibiting androgen receptor activity in a mammal, thereby facilitating treatment of diseases such as prostate cancer.

Claims

1. A method of identifying a compound that modulates nuclear receptor activity, the method comprising:

modeling a test compound that fits spatially into an atomic structural model of the androgen receptor coactivator binding site or portion thereof, wherein said atomic structural model comprises atomic coordinates of an androgen receptor coactivator binding site and a molecule bound to the coactivator binding site; and

screening said test compound in an assay characterized by binding of the test compound to the coactivator binding site of a nuclear receptor, thereby identifying a test compound that modulates nuclear receptor activity.

2. The method of claim 1 wherein nuclear receptor activity is measured by binding of a coactivator to the coactivator binding site.

3. The method of claim 1 wherein nuclear receptor activity is measured by the suppression of transcriptional activity.

4. The method of claim 1 wherein nuclear receptor activity is measured by inhibition of coactivator binding.

5. The method of claim 1 wherein said screening is in vitro.

6. The method of claim 5 wherein said screening is high throughput screening.

7. The method of claim 1 wherein said atomic structural model of the human androgen receptor comprise coordinates of amino acid residues Leu 712, Val 713, Val716, Lys720, Phe725, Gln 733, Met734, Ile737, Gln738, Trp741, Glu 893, Met894, Glu 897, and Ile898.

8. The method of claim 1 wherein said test compound is a small organic molecule, a peptide, or a peptidomimetic.

9. The method of claim 1 wherein said test compound is an antagonist of coactivator binding.

10. The method of claim 1 wherein said nuclear receptor is selected from the group consisting of estrogen receptors, thyroid receptors, retinoid receptors, glucocorticoid receptors, progestin receptors, mineralocorticoid receptors, androgen receptors, peroxisome receptors and vitamin D receptors.

11. The method of claim 1 wherein the modeling comprises providing the atomic coordinates of the androgen receptor coactivator binding site to a computerized modeling system.

12. The method of claim 1 wherein said atomic structural coordinates are found in any one of Table 1 (A) and (B), and Table 2 (A)-(H), found respectively in the files identified as Table1_ARLBD_DHT_CDP.txt and Table2_ARLBD_DHT_CRP.txt, presented on CD-R herewith.

13. The method of claim 1 wherein said atomic structural coordinates further comprise a portion of the androgen receptor ligand binding domain.

14. The method of claim 12 wherein said atomic structural coordinates further comprise coordinates of a ligand bound to the ligand binding domain.

15. The method of claim 13 wherein said ligand is a hormone.

16. The method of claim 13 wherein said ligand is an agonist of androgen receptor activity.

17. The method of claim 1 wherein said molecule is a peptide.

18. The method of claim 17 wherein said peptide comprises a motif whose sequence is Z₁XXZ₂Z₃, wherein Z₁ and Z₃ are each independently F, L, W, or Y, and Z₂ is L, F, V, or Y, and X is any amino acid residue.

19. The method of claim 18 wherein the motif consists of residue sequences selected from the group consisting of:

FXXLF, WXXLF, FXXFF, FXXLY, FXXYF, WXXVW, and FXXLW, wherein X is any amino acid.

20. The method of claim 17 wherein said modeling further comprises overlapping an atomic model of the test compound with the coordinates of the peptide.

21. The method of claim 18 wherein said modeling comprises identifying a fragment of said test molecule that fits into a cleft in said coactivator binding site that is occupied by the Z₁+1 residue of said peptide.

22. The method of claim 18 wherein said modeling comprises identifying a fragment of said test molecule that fits into a cleft in said coactivator binding site that is occupied by the Z₃+5 residue of said peptide.

23. The method of claim 18 wherein said test compound interacts with at least one residue selected from the group consisting of:

Leu 712, Val 716, Met 734, Gln 738, Met 894, and Ile 898.

24. The method of claim 18 wherein said test compound interacts with at least one residue selected from the group consisting of:

Val 716, Lys 720, Phe 725, Val 730, Gln 733, Ile 737.

25. The method of claim 1 wherein said test molecule is selected from a library of molecules.

26. The method of claim 1 wherein said test molecule is constructed from at least two fragments that are overlapped with the molecule bound to the coactivator binding site.

27. A method of identifying a compound that modulates nuclear receptor activity, the method comprising:

screening a test compound in an assay characterized by binding of a test compound to the coactivator binding site of a nuclear receptor, wherein the test compound has been modeled by spatially fitting an atomic model of the test compound into an atomic structural model of a portion of the androgen receptor coactivator binding site, wherein said atomic structural model comprises atomic coordinates of amino acid residues of the androgen receptor coactivator binding site and a molecule bound to the coactivator binding site, thereby identifying a test compound that modulates nuclear receptor activity.

28. The method of claim 27 wherein said nuclear receptor is selected from the group consisting of estrogen receptors, thyroid receptors, retinoid receptors, glucocorticoid receptors, progestin receptors, mineralocorticoid receptors, androgen receptors, peroxisome receptors and vitamin D receptors.

29. The method of claim 27 wherein said screening is in vitro.

30. The method of claim 27 wherein said screening is high throughput screening.

31. The method of claim 27 wherein said atomic coordinates of the human androgen receptor comprise coordinates of amino acid residues Leu 712, Val 713, Val716, Lys720, Phe725, Gln 733, Met734, Ile737, Gln738, Trp741, Glu 893, Met894, Glu 897, and Ile898.

32. The method of claim 27 wherein said test compound is an antagonist of coactivator binding.

33. The method of claim 27 wherein said test compound is a small organic molecule, a peptide, or a peptidomimetic.

34. The method of claim 27, wherein said atomic structural model is defined by the set of structure coordinates depicted in any one of Table 1 (A) and (B), and Table 2 (A)-(H), found respectively in the files identified as Table1_ARLBD_DHT_CDP.txt and Table2_ARLBD_DHT_CRP.txt, presented on CD-R herewith, or a homologue thereof, said homologue having a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å

.

35. A method of identifying an antagonist of coactivator binding to a nuclear receptor, the method comprising:

modeling a test compound which fits spatially into an atomic structural model of the androgen receptor coactivator binding site wherein the atomic structural model comprises atomic coordinates of amino acid residues of human androgen receptor coactivator binding site and a molecule bound to the coactivator binding site; and

screening said test compound in an assay for nuclear receptor activity, thereby identifying a compound which decreases the activity of the nuclear receptor by binding the coactivator binding site of said nuclear receptor.

36. The method of claim 35 wherein said nuclear receptor is selected from the group consisting of estrogen receptors, thyroid receptors, retinoid receptors, glucocorticoid receptors, progestin receptors, mineralocorticoid receptors, androgen receptors, peroxisome receptors, and vitamin D receptors.

37. The method of claim 35 wherein said atomic coordinates include the amino acid residues of human androgen receptor Leti 712, Val 713, Val716, Lys 720, Phe725, Gln 733, Met734, Ile737, Gln738, Trp741, Glu 893, Met894, Glu 897, and Ile898.

38. The method of claim 35 wherein said test compound contacts at least one residue selected from the group consisting of:

Leu 712, Val 716, Met 734, Gln 738, Met 894, and Ile 898.

39. The method of claim 35 wherein said test compound contacts at least one residue selected from the group consisting of:

Val 716, Lys 720, Phe 725, Val 730, Gln 733, Ile 737.

40. The method of claim 35 wherein the modeling comprises providing the atomic coordinates of an androgen receptor coactivator binding site and a molecule bound to the coactivator binding site to a computerized modeling system.

41. The method of claim 35 wherein the atomic structural model is experimentally derived.

42. The method of claim 35 wherein the atomic structural model has a resolution of better than 2.00 Å

.

43. The method of claim 35, wherein said atomic structural model additionally comprises atomic coordinates of a ligand molecule bound to the ligand binding domain.

44. The method of claim 43, wherein said ligand is an androgen receptor agonist.

45. The method of claim 35 wherein the atomic structural model has coordinates presented in any one of Table 1 (A) and (B), and Table 2 (A)-(H), found respectively in the files identified as Table1_ARLBD_DHT_CDP.txt and Table2_ARLBD_DHT_CRP.txt, presented on CD-R herewith, or a homologue thereof, said homologue having a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å

.

46. A method of identifying a compound that modulates androgen receptor activity, said method comprising:

modeling a test compound that fits spatially into an atomic structural model of an androgen receptor coactivator binding site, wherein said atomic structural model comprises atomic coordinates of amino acid residues of the androgen receptor coactivator binding site, and a molecule bound to the coactivator binding site; and

screening said test compound in an assay characterized by binding of the test compound to the androgen receptor coactivator binding site, thereby identifying a compound that modulates coactivator binding to the androgen receptor.

47. The method of claim 46 wherein the modeling comprises providing the atomic coordinates of an androgen receptor coactivator binding site and a molecule bound to the coactivator binding site to a computerized modeling system.

48. The method of claim 46, wherein said atomic structural model additionally comprises atomic coordinates of a ligand molecule bound to the ligand binding domain.

49. The method of claim 48, wherein said ligand is an androgen receptor agonist.

50. The method of claim 46 wherein the atomic structural model is experimentally derived.

51. The method of claim 46 wherein the atomic structural model has a resolution of better than 2.00 Å

.

52. The method of claim 46 wherein the atomic structural model has coordinates presented in any one of Table 1 (A) and (B), and Table 2 (A)-(H), found respectively in the files identified as Table1_ARLBD_DHT_CDP.txt and Table2_ARLBD_DHT_CRP.txt, presented on CD-R herewith, or a homologue thereof, said homologue having a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å

.

53. The method of claim 46 wherein said atomic coordinates of the human androgen receptor comprise coordinates of amino acid residues Leu 712, Val 713, Val716, Lys720, Phe725, Gln 733, Met734, Ile737, Gln738, Trp741, Glu 893, Met894, Glu 897, and Ile898.

54. The method of claim 46 wherein said test molecule contacts at least one residue selected from the group consisting of:

Leu 712, Val 716, Met 734, Gln 738, Met 894, and Ile 898.

55. The method of claim 46 wherein said test molecule contacts at least one residue selected from the group consisting of:

Val 716, Lys 720, Phe 725, Val 730, Gln 733, Ile 737.

56. A method of identifying an antagonist of coactivator binding to an androgen receptor, said method comprising:

modeling a test compound that fits spatially into the androgen receptor coactivator binding site using an atomic structural model of the androgen receptor coactivator binding site, wherein said atomic structural model comprises coordinates of the androgen receptor coactivator binding site, and coordinates of a coactivator bound to said coactivator binding site, and

screening said test compound in an assay characterized by binding of a test compound to the nuclear receptor coactivator binding site, thereby identifying a compound that inhibits coactivator binding to the androgen receptor.

57. The method of claim 56 wherein the modeling comprises providing the atomic coordinates of an androgen receptor coactivator binding site and a molecule bound to the coactivator binding site to a computerized modeling system.

58. The method of claim 56 wherein the atomic structural model has coordinates presented in any one of Table 1 (A) and (B), and Table 2 (A)-(H), found respectively in the files identified as Table1_ARLBD_DHT_CDP.txt and Table2_ARLBD_DHT_CRP.txt, presented on CD-R herewith, or a homologue thereof, said homologue having a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å

.

59. The method of claim 56 wherein the atomic structural model is experimentally derived.

60. The method of claim 56 wherein the atomic structural model has a resolution of better than 2.00 Å

.

61. The method of claim 56 wherein said atomic structural model additionally comprises coordinates of a ligand bound to said ligand binding domain.

62. The method of claim 61 wherein said ligand is an androgen receptor agonist.

63. The method of claim 56 wherein said atomic coordinates of the human androgen receptor comprise coordinates of amino acid residues Leu 712, Val 713, Val716, Lys720,Phe725, Gln 733, Met734, Ile737, Gln738, Trp741, Glu 893, Met894, Glu 897, and Ile898.

64. The method of claim 56 wherein said test molecule contacts at least one residue selected from the group consisting of:

Leu 712, Val 716, Met 734, Gln 738, Met 894, and Ile 898.

65. The method of claim 56 wherein said test molecule contacts at least one residue selected from the group consisting of:

Val 716, Lys 720, Phe 725, Val 730, Gln 733, Ile 737.

66. A computational method of designing an inhibitor of androgen receptor coactivator binding, comprising:

fitting an atomic model of the compound into an atomic structural model of the coactivator binding site of the androgen receptor, wherein said compound consists of a first moiety that fits into a first cleft on the coactivator binding site and contacts at least one residue selected from the group consisting of Leu 712, Val 716, Met 734, Gln 738, Met 894, and Ile 898, and a second moiety that fits into a second cleft on the coactivator binding site, and contacts at least one residue selected from the group consisting of Val 716, Lys 720, Phe 725, Val 730, Gln 733, Ile 737, wherein said first moiety and said second moiety are joined by a linking group.

67. The method of claim 66 wherein said atomic structural model has coordinates in any one of Table 1 (A) and (B), and Table 2 (A)-(H), found respectively in the files identified as Table1_ARLBD_DHT_CDP.txt and Table2_ARLBD_DHT_CRP.txt, presented on CD-R herewith, or a homologue thereof, said homologue having a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å

.

68. The method of claim 66 wherein the compound additionally makes a hydrogen bonding interaction with at least one residue selected from the group consisting of:

Lys 720, Glu 897, and Gln 733.

69. The method of claim 66 wherein said contacts between said first moiety and said amino acid residue include a hydrogen bonding interaction, electrostatic interaction, van der Waals interaction, or a hydrophobic interaction.

70. The method of claim 66 wherein said contacts between said first moiety and said amino acid residue include a hydrogen bonding interaction, electrostatic interaction, van der Waals interaction or a hydrophobic interaction.

71. The method of claim 66 wherein said androgen receptor is selected from the group consisting of:

human, chimpanzee, rat, and mouse.

72. A method of modulating androgen receptor activity in a mammal by administering to a mammal in need thereof a sufficient amount of a compound that fits spatially and preferentially into a coactivator binding site of the androgen receptor, wherein said compound is designed by a computational method that involves fitting an atomic model of the compound into an atomic structural model of the coactivator binding site of the androgen receptor, and wherein said compound consists of a first moiety that fits into a first cleft on the coactivator binding site and contacts at least one residue selected from the group consisting of Leu 712, Val 716, Met 734, Gln 738, Met 894, and Ile 898, and a second moiety that fits into a second cleft on the coactivator binding site, and contacts at least one residue selected from the group consisting of Val 716, Lys 720, Phe 725, Val 730, Gln 733, Ile 737, wherein said first moiety and said second moiety are joined by a linking group.

73. The method of claim 72 wherein the compound additionally makes a hydrogen bonding interaction with at least one residue selected from the group consisting of:

Lys 720, Glu 897, and Gln 733.

74. The method of claim 72 wherein said compound inhibits an endogenous coregulator from binding to the coactivator binding site.

75. The method of claim 72 wherein the compound has been desired using an atomic structural model of the coactivator binding site of the androgen receptor ligand that has a set of structure coordinates depicted in any one of Table 1 (A) and (B), and Table 2 (A)-(H), found respectively in the files identified as Table1_ARLBD_DHT_CDP.txt and Table2_ARLBD_DHT_CRP.txt, presented on CD-R herewith, or a homologue thereof, said homologue having a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å

.

76. A method of inhibiting the binding of a coactivator to an androgen receptor, said method comprising:

contacting a molecule with a coactivator binding site on the androgen receptor, wherein the molecule fits spatially into the coactivator binding site, and wherein the molecule binds more strongly to the receptor than does the coactivator.

77. The method of claim 76, wherein the molecule consists of a first moiety that fits into a first cleft on the coactivator binding site and contacts at least one residue selected from the group consisting of Leu 712, Val 716, Met 734, Gln 738, Met 894, and Ile 898, and a second moiety that fits into a second cleft on the coactivator binding site, and contacts at least one residue selected from the group consisting of Val 716, Lys 720, Phe 725, Val 730, Gln 733, Ile 737, and Met 734, wherein said first moiety and said second moiety are joined by a linking group.

78. The method of claim 77 wherein the molecule additionally makes a hydrogen bonding interaction with at least one residue selected from the group consisting of:

Lys 720, Glu 897, and Gln 733.

79. The method of claim 76, wherein the molecule is a peptide that comprises a motif whose sequence is Z₁XXZ₂Z₃, wherein Z₁ and Z₃ are each independently F, L, W, or Y, and Z₂ is L, F, V, or Y, and X is any amino acid residue.

80. The method of claim 76, wherein the motif consists of residue sequences selected from the group consisting of:

FXXLF, WXXLF, FXXFF, FXXLY, FXXYF, WXXVW, and FXXLW, wherein X is any amino acid.

81. The method of claim 76 wherein the molecule has been designed using an atomic structural model of the coactivator binding site of the androgen receptor ligand that has a set of structure coordinates depicted in any one of Table 1 (A) and (B), and Table 2 (A)-(H), found respectively in the files identified as Table1_ARLBD_DHT_CDP.txt and Table2_ARLBD_DHT_CRP.txt, presented on CD-R herewith, or a homologue thereof, said homologue having a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å

.

82. A method of modulating the activity of an androgen receptor, said method comprising:

contacting a molecule with a coactivator binding site on the androgen receptor, wherein the molecule fits spatially into the coactivator binding site, and wherein the molecule has been designed by modeling at least one test compound into an atomic structural model of the coactivator binding site of the androgen receptor, wherein said atomic structural model comprises atomic coordinates of amino acid residues of the androgen receptor coactivator binding site and a second molecule bound to the coactivator binding site.

83. The method of claim 82 wherein said compound inhibits an endogenous coregulator from binding to the coactivator binding site.

84. The method of claim 82 wherein the atomic structural model of the coactivator binding site of the androgen receptor ligand has a set of structure coordinates depicted in any one of Table 1 (A) and (B), and Table 2 (A)-(H), found respectively in the files identified as Table1_ARLBD_DHT_CDP.txt and Table2_ARLBD_DHT_CRP.txt, presented on CD-R herewith, or a homologue thereof, said homologue having a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å

.

85. A method of modulating androgen receptor activity in a mammal by administering to a mammal in need thereof a sufficient amount of a compound that fits spatially and preferentially into a coactivator binding site of the androgen receptor, wherein said compound is designed by fitting an atomic model of the compound into an atomic structural model of the coactivator binding site of the androgen receptor, wherein said atomic structural model comprises atomic coordinates of amino acid residues of the androgen receptor coactivator binding site and a second molecule bound to the coactivator binding site.

86. The method of claim 85 wherein said compound inhibits an endogenous coregulator from binding to the coactivator binding site.

87. The method of claim 85 wherein the atomic structural model of the coactivator binding site of the androgen receptor ligand nas a set of structure coordinates depicted in any one of Table 1 (A) and (B), and Table 2 (A)-(H), found respectively in the files identified as Table1_ARLBD_DHT_CDP.txt and Table2_ARLBD_DHT_CRP.txt, presented on CD-R herewith, or a homologue thereof, said homologue having a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å

.

88. A machine-readable data storage medium encoded with machine readable data which, when using a machine programmed with instructions for using said data, is capable of causing a graphical three-dimensional representation of a molecular complex to be displayed, comprising:

at least a portion of an androgen receptor ligand binding domain, including an androgen receptor coactivator binding site;

a molecule bound to the androgen receptor coactivator binding site; and

a ligand bound to the ligand binding domain.

89. The machine-readable data storage medium of claim 88 wherein the androgen receptor ligand binding domain is a homologue having a root mean square deviation of not more than 1.5 Å

from the backbone atoms of said amino acids in the ligand binding domain of AR in any one of Table 1 (A) and (B), and Table 2 (A)-(H), found respectively in the files identified as Table1_ARLBD_DHT_CDP.txt and Table2_ARLBD_DHT_CRP.txt, presented on CD-R herewith.

90. The machine-readable data storage medium of claim 88 wherein said machine readable data comprises a set of structure coordinates depicted in any one of Table 1 (A) and (B), and Table 2 (A)-(H), found respectively in the files identified as Table1_ARLBD_DHT_CDP.txt and Table2_ARLBD_DHT_CRP.txt, presented on CD-R herewith.

91. The machine-readable data storage medium of claim 88, wherein said androgen receptor is human.

92. The machine-readable data storage medium of claim 88, wherein said molecule is a peptide.

93. The machine-readable data storage medium of claim 88, wherein said peptide comprises a Nuclear Receptor Box amino acid sequence or derivative thereof.

94. Use of a machine-readable data storage medium, comprising machine readable data, in conjunction with a machine programmed with instructions for using said data, for identifying a molecule that modulates coactivator binding to an androgen receptor, wherein the computer displays a graphical three-dimensional representation of a complex of the molecule bound to a coactivator binding site of the androgen receptor, and wherein the data comprises structure coordinates in any one of Table 1 (A) and (B), and Table 2 (A)-(H), found respectively in the files identified as Table1_ARLBD_DHT_CDP.txt and Table2_ARLBD_DHT_CRP.txt, presented on CD-R herewith.

95. The use of claim 94, wherein the androgen receptor ligand binding domain is a homologue having a root mean square deviation of not more than 1.5 Å

from the backbone atoms of the amino acids of the androgen receptor ligand binding domain defined by a set of structure coordinates depicted in any one of Table 1 (A) and (B), and Table 2 (A)-(H), found respectively in the files identified as Table1_ARLBD_DHT_CDP.txt and Table2_ARLBD_DHT_CRP.txt, presented on CD-R herewith.

96. A cocrystal comprising:

a portion of an androgen receptor ligand binding domain;

a ligand bound to the ligand binding domain of the receptor; and

a coactivator bound to a coactivator binding site of the receptor.

97. The cocrystal of claim 96 wherein said cocrystal diffracts with at least 1.9 Å

resolution.

98. The cocrystal of claim 96 wherein said androgen receptor is human.

99. The cocrystal of claim 96 wherein said androgen receptor is a homolog of the human androgen receptor.

100. The cocrystal of claim 96 wherein said ligand is a naturally occurring hormone.

101. The cocrystal of claim 96 wherein said coactivator is a peptide.

102. The cocrystal of claim 101 wherein said peptide comprises a NR-box amino acid sequence.

103. The cocrystal of claim 101 wherein said peptide comprises a motif whose sequence is Z₁XXZ₂Z₃, wherein Z₁ and Z₃ are each independently F, L, W, or Y, and Z₂ is L, F, V, or Y, and X is any amino acid residue.

104. The cocrystal of claim 103 wherein said peptide is a coactivator-derived peptide.

105. The cocrystal of claim 103 wherein said peptide consists of 15 amino acid residues.

106. The cocrystal of claim 103 wherein said motif consists of residue sequences selected from the group consisting of:

FXXLF, WXXLF, FXXFF, FXXLY, WXXVW, FXXYF, and FXXLW.

107. The cocrystal of claim 96 having the structure defined by the structural coordinates as shown in any one of Table 1 (A) and (B), and Table 2 (A)-(H), found respectively in the files identified as Table1_ARLBD_DHT_CDP.txt and Table2_ARLBD_DHT_CRP.txt, presented on CD-R herewith, or a homologue thereof, said homologue having a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å

.

108. A cocrystal consisting of:

an androgen receptor ligand binding domain;

a ligand bound to the ligand binding domain of the receptor;

a coactivator bound to a coactivator binding site of the receptor; and

crystallographically bound water.

109. An isolated and purified protein complex comprising:

a portion of an androgen receptor ligand binding domain;

a ligand bound to the ligand binding domain of the receptor; and

a coactivator bound to a coactivator binding site of the receptor.

110. An isolated and purified homolog of the protein complex of claim 109.

111. The isolated and purified protein complex of claim 109, wherein said coactivator is a peptide that comprises a motif whose sequence is Z₁XXZ₂Z₃, wherein Z₁ and Z₃ are each independently F, L, W, or Y, and Z₂ is L, F, V, or Y, and X is any amino acid residue.

112. An isolated and purified protein complex consisting of:

an androgen receptor ligand binding domain;

a ligand bound to the ligand binding domain of the receptor;

a coactivator bound to a coactivator binding site of the receptor; and

at least one molecule of solvent bound thereto.

113. An isolated and purified polypeptide consisting of a portion of the human androgen receptor starting at amino acid residue 669 and ending at amino acid residue 918, as set forth in SEQ ID NO:

29, bound to a ligand, and bound to a coactivator.

114. An isolated and purified homolog of the polypeptide of claim 113.

115. The isolated and purified polypeptide of claim 113, wherein said coactivator is a peptide that comprises a motif whose sequence is Z₁XXZ₂Z₃, wherein Z₁ and Z₃ are each independently F, L, W, or Y, and Z₂ is L, F, V, or Y, and X is any amino acid residue.

116. A compound of formula:

117. A method of treating prostate cancer by administering a pharmaceutical composition comprising a compound of formula: