A combined ligand-based and target-based drug design approach for G-protein coupled receptors: Application to salvinorin A, a selective kappa opioid receptor agonist

Journal of Computer-Aided Molecular Design

Volumn 20, Issue 7-8, 2006, Pages 471-493

  Singh, Nidhi ^a   Chevé, Gwénaël ^a   Ferguson, David M ^d   McCurdy, Christopher R ^b,c  

^a UNIVERSITY OF MISSISSIPPI   (United States)

^b UNIVERSITY OF MISSISSIPPI   (United States)

^c UNIVERSITY OF MISSISSIPPI   (United States)

^d UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Comparative modeling; Docking; G protein coupled receptor (GPCR); Homology; Kappa opioid receptor; Modeler; Molecular dynamics; New molecular entities (NMEs); Pharmacophore; Salvinorin A

Indexed keywords

HYDROGEN BONDS; LEAD COMPOUNDS; MOLECULAR DYNAMICS; PHARMACODYNAMICS; PROTEINS;

COMPARATIVE MODELING; DOCKING; G PROTEIN COUPLED RECEPTORS; G-PROTEIN COUPLED RECEPTOR; HOMOLOGY; KAPPA OPIOID RECEPTOR; MODELER; MOLECULAR ENTITIES; NEW MOLECULAR ENTITY; PHARMACOPHORES; SALVINORIN A;

LIGANDS;

3,4 DICHLORO N METHYL N [2 (1 PYRROLIDINYL)CYCLOHEXYL]BENZENEACETAMIDE METHANESULFONATE; FENTANYL; G PROTEIN COUPLED RECEPTOR; HYDROGEN; KAPPA OPIATE RECEPTOR; KAPPA OPIATE RECEPTOR AGONIST; MORPHINE; RHODOPSIN; SALVINORIN A;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; COMPUTER PROGRAM; CONTROLLED STUDY; CORRELATION ANALYSIS; DRUG DEPENDENCE; DRUG DESIGN; DRUG IDENTIFICATION; DRUG RESEARCH; DRUG SCREENING; DRUG STRUCTURE; DRUG TARGETING; FINANCIAL MANAGEMENT; GENE MUTATION; HYDROGEN BOND; HYDROPHOBICITY; HYPOTHESIS; MODEL; NUCLEOTIDE SEQUENCE; PHARMACOPHORE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; RELIABILITY; SCORING SYSTEM; SEQUENCE ALIGNMENT; STRUCTURE ACTIVITY RELATION; TIME; VALIDATION STUDY;

EID: 34249277652     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-006-9067-x     Document Type: Article

References (121)

1. Bleicher KH, Bohm HJ, Muller K, Alanine AI (2004) Curr Opin Chem Biol 8:287
2. Oprea TI, Matter H (2004) Curr Opin Chem Biol 8:349
3. Bajorath J (2001) J Chem Inf Comput Sci 41:233
4. Good AC, Krystek SR, Mason JS (2000) Drug Discov Today 5:61
5. Patel Y, Gillet VJ, Bravi G, Leach AR (2002) J Comput Aided Mol Des 16:653
6. Schneider G, Böhm HJ (2002) Drug Discov Today 7:64
7. Abagyan R, Totrov M (2001) Curr Opin Chem Biol 5:375
8. Bissantz C, Folkers G, Rognan D (2000) J Med Chem 43:4759
9. Taylor RD, Jewsbury PJ, Essex JW (2002) J Comput Aided Mol Des 16:151
10. Brooijmans N, Kuntz ID (2003) Annu Rev Biophys Biomol Struct 32:335
11. Lyne PD (2002) Drug Discov Today 7:047
12. Halperin I, Ma B, Wolfson H, Nussinov R (2002) Proteins 47:409
13. Guner O (ed) (2000) Pharmacophore perception, development and use in drug design. International University Line, La Jolla, CA
14. Marrone TJ, Briggs JM, McCammon JA (1997) Ann Rev Pharmacol Toxicol 37:71
15. Dixon JS (1997) Proteins Suppl 1:198
16. Tame JRH (1999) J Comput Aided Mol Des 13:99
17. Gohlke H, Klebe G (2001) Curr Opin Struct Biol 11:231
18. Schwalbe H, Wess G (2002) Chembiochem 3:915
19. Flower DR (1999) Biochim Biophys Acta 1422:207
20. Wise A, Gearing K, Rees S (2002) Drug Discov Today 7:235
21. Drews J (2000) Science 287:1960
22. Takeda S, Kadowaki S, Haga T, Takaesu H, Mitaku S (2002) FEBS Lett 520:97
23. Collins FS (2004) Nature 431:931
24. Marriott DP, Dougall IG, Meghani P, Liu YJ, Flower DR (1999) J Med Chem 42:3210
25. Flohr S, Kurz M, Kostenis E, Brokovich A, Fournier A, Klabunde T (2002) J Med Chem 45:799
26. Pebay-Peyroula E, Rummel G, Rosenbusch JP, Landau EM (1997) Science 277:1676
27. Belrhali H, Nollert P, Royant A, Menzel C, Rosenbusch JP, Landau EM, Pebay-Peyroula E (1999) Struct Fold Des 7:909
28. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M (2000) Science 289:739
29. Teller DC, Okada T, Behnke CA, Palczewski K, Stenkamp RE (2001) Biochemistry 40:7761
30. Ballesteros J, Palczewski K (2001) Curr Opin Drug Discov Dev 4:561
31. Okada T, Sugihara M, Bondar AN, Elstner M, Entel P, Buss V (2004) J Mol Biol 342:571
32. Beeley NRA, Sage C (2003) Targets 2:19
33. Evers A, Klabunde T (2005) J Med Chem 48:1088
34. Varady J, Wu X, Fang X, Min J, Hu Z, Levant B, Wang S (2003) J Med Chem 46:4377
35. Bissantz C, Bernard P, Hibert M, Rognan D (2003) Proteins 50:5
36. Evers A, Hessler G, Matter H, Klabunde T (2005) J Med Chem 48:5448
37. Evers A, Klebe G (2004) J Med Chem 47:5381
38. Kieffer BL (1995) Cell Mol Neurobiol 15:615
39. Ulloa-Aguirre A, Stanislaus D, Janovick JA, Conn PM (1999) Arch Med Res 30:420
40. Gether U (2000) Endocr Rev 21:90
41. Chen Y, Mestek A, Liu J, Yu L (1993) Biochem J 295:625
42. Evans CJ, Keith DE Jr, Morrison H, Magendzo K, Edwards RH (1992) Science 258:1952
43. Kieffer BL, Befort K, Gaveriaux-Ruff C, Hirth CG (1992) Proc Natl Acad Sci USA 89:12048
44. Yasuda K, Raynor K, Kong H, Breder CD, Takeda J, Reisine T, Bell GI (1993) Proc Natl Acad Sci USA 90:6736
45. Meng F, Xie GX, Thompson RC, Mansour A, Goldstein A, Watson SJ, Akil H (1993) Proc Natl Acad Sci USA 90:9954
46. Chen Y, Mestek A, Liu J, Hurley JA, Yu L (1993) Mol Pharmacol 44:8
47. Fukuda K, Kato S, Mori K, Nishi M, Takeshima H (1993) FEBS Lett 327:311
48. Knapp RJ, Malatynska E, Fang L, Li X, Babin E, Nguyen M, Santoro G, Varga EV, Hruby VJ, Roeske WR et al (1994) Life Sci 54:PL463
49. Wang JB, Johnson PS, Persico AM, Hawkins AL, Griffin CA, Uhl GR (1994) FEBS Lett 338:17
50. Mansson E, Bare L, Yang D (1994) Biochem Biophys Res Commun 202:1431
51. Mollereau C, Parmentier M, Mailleux P, Butour JL Moisand C, Chalon P, Caput D, Vassart G, Meunier JC (1994) FEBS Lett 341:33
52. Meunier JC (1997) Eur J Pharmacol 340:1
53. Pogozheva ID, Przydzial MJ, Mosberg HI (2005) AAPS J 7:E434
54. Metcalf MD, Coop A (2005) AAPS J 7:E704
55. Rees DC (1992) Prog Med Chem 29:109
56. Roth BL, Baner K, Westkaemper R, Siebert D, Rice KC, Steinberg S, Ernsberger P, Rothman RB (2002) Proc Natl Acad Sci USA 99:11934
57. Chavkin C, Sud S, Jin W, Stewart J, Zjawiony JK, Siebert DJ, Toth BA, Hufeisen SJ, Roth BL (2004) J Pharmacol Exp Ther 308:1197
58. Siebert DJ (1994) J Ethnopharmacol 43:53
59. Wang Y,Tang K, Inan S, Siebert D, Holzgrabe U, Lee DY, Huang P, Li JG, Cowan A, Liu-Chen LY (2005) J Pharmacol Exp Ther 312:220
60. Yan F, Roth BL (2004) Life Sci 75:2615
61. Ortega A, Blount JF, Manchand PS (1982) J Chem Soc Perkins Trans 1:505
62. Wasson RG (1962) Bot Mus Leafl Harv Univ 20:77
63. Valdes LJ, Butler WM, Hatfield GM, Paul AG, Koreeda M (1984) J Org Chem 49:4716
64. Valdes LJ III, Diaz JL, Paul AG (1983) J Ethnopharmacol 7:287
65. Rees DC, Hunter JC (1990) Comprehensive medicinal chemistry. Pergammon, New York, p 805
66. Beguin C, Richards MR, Wang Y, Chen Y, Liu-Chen LY, Ma Z, Lee DY, Carlezon WA Jr, Cohen BM (2005) Bioorg Med Chem Lett 15:2761
67. Mowry M, Mosher M, Briner W (2003) J Psychoactive Drugs 35:379
68. Valdes LJ III (1994) J Psychoactive Drugs 26:277
69. McCurdy CR, Sufka KJ, Smith GH, Warnick JE, Nieto MJ (2006) Pharmacol Biochem Behav 83:109
70. Evers A, Gohlke H, Klebe GJ (2003) Mol Biol 334:327
71. Catalyst, version 48, Accelrys: Burlington, MA
72. Thompson JD, Higgins DG, Gibson TJ (1994) Nucleic Acid Res 22:4673
73. InsightII, Molecular Modeling Program Package, Accelrys: 9685 Sranton Road, San Diego, CA 92121-3752, USA
74. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) J Appl Cryst 26:283
75. GOLD version 21, Cambridge Crystallographic Data Centre: Cambridge, UK
76. Sybyl version 72, Tripos Inc, St Louis, MO, USA
77. Munro TA, Rizzacasa MA, Roth BL, Toth BA, Yan F (2005) J Med Chem 48:345
78. Harding WW, Tidgewell K, Byrd N, Cobb H, Dersch CM, Butelman ER, Rothman RB, Prisinzano TE (2005) J Med Chem 48:4765
79. Lee DY, He M, Kondaveti L, Liu-Chen LY, Ma Z, Wang Y, Chen Y, Li JG, Beguin C, Carlezon WA Jr, Cohen B (2005) Bioorg Med Chem Lett 15:4169
80. Lee DY, Karnati VV, He M, Liu-Chen LY, Kondaveti L, Ma Z, Wang Y, Chen Y, Beguin C, Carlezon WA Jr, Cohen B (2005) Bioorg Med Chem Lett 15:3744
81. Li H, Sutter J, Hoffman R (1999) In: Guner OF (ed) Pharmacophore: perception, development and use in drug design. International University Line, La Jolla CA, p 173
82. Gund P (1977) In: Hahn FE (ed) Progress in molecular and subcellular biology, vol 5. Springer-Verlag, New York, p 117
83. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) J Comp Chem 4:187
84. Smellie A, Teig SL, Towbin P (1999) J Comput Chem 16:171
85. English philosopher and Franciscan Monk, William of Ockham, 1285
86. Sutter J, Guner OF, Hoffman R, Li H, Waldman M (1999) In: Guner OF (ed) Pharmacophore: Perception, development and use in drug design. International University Line, La Jolla CA, p 501
87. Fischer R (1966) The design of experiments, 8th edn, Chapter II. Hafner Publishing Co, New York
88. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneide M (2003) Nucleic Acids Res 31:365
89. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucleic Acids Res 28:235
90. Henikoff S, Henikoff JG (1992) Proc Natl Acad Sci USA 89:10915
91. Sali A, Blundell TL (1993) J Mol Biol 234:779
92. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F et al (2000) Annu Rev Biophys Biomol Struct 29:291
93. Yan F, Mosier PD, Westkaemper RB, Stewart J, Zjawiony JK, Vortherms TA, Sheffler DJ, Roth BL (2005) Biochemistry 44:8643
94. Andersen HC (1980) J Chem Phys 72:2384
95. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) J Mol Biol 267:727
96. Ballesteros JA, Weinstein H (1995) Methods Neurosci 25:366
97. Costanzi S, Lambertucci C, Vittori S, Volpini R, Cristalli G (2003) J Mol Graph Model 21:253
98. Hulme EC, Lu ZL, Ward SDC, Allman K, Curtis CA (1999) Eur J Pharmacol 375:247
99. Ghanouni P, Steenhuis JJ, Farrens DL, Kobilka BK (2001) Proc Natl Acad Sci USA 98:5997
100. Farrens DL, Altenbach C, Yang K, Hubbell WL, Khorana HG (1996) Science 274:768
101. Kim JM, Altenbach C, Kono M, Oprian DD, Hubbell WL, Khorana HG (2004) Proc Natl Acad Sci USA 101:12508
102. Hubbell WL, Altenbach C, Hubbell CM, Khorana HG (2003) Adv Protein Chem 63:243
103. Hanson SM, Francis DJ, Vishnivetskiy SA, Kolobova EA, Hubbell WL, Klug CS, Gurevich VV (2006) Proc Natl Acad Sci USA 103:4900
104. Patel AB, Crocker E, Reeves PJ, Getmanova EV, Eilers M, Khorana HG, Smith SO (2005) J Mol Biol 347:803
105. Han SJ, Hamdan FF, Kim SK, Jacobson KA, Bloodworth LM, Li B, Wess J (2005) J Biol Chem 280:34849
106. Becker OM, Marantz Y, Shacham S, Inbal B, Heifetz A, Kalid O, Bar-Haim S, Warshaviak D, Fichman M, Noiman S (2004) Proc Natl Acad Sci USA 101:11304
107. Hiramoto T, Nonaka Y, Inoue K, Yamamoto T, Omatsu-Kanbe M, Matsuura H, Gohda K, Fujita N (2004) J Pharmacol Sci 95:81
108. (a) Subramanian G, Paterlini MG, Larson D, Portoghese PS, Ferguson DM (1998) J Med Chem 41:4777; (b) Pogozheva ID, Lomize AL, Mosberg HI (1998) Biophys J 75:612; (c) Cappelli A, Anzini M, Vomero S, Menziani MC, De Benedetti PG, Sbacchi M, Clarke GD, Mennuni L (1996) J Med Chem 39:860; (d) Metzger TG, Paterlini MG, Portoghese PS, Ferguson DM (1996) Neurochem Res 21:1287; (e) Strahs D, Weinstein H (1997) Protein Eng 10:1019
109. Lee KW, Briggs JM (2004) Proteins 54:693
110. Archer E, Maigret B, Escrieut C, Pradayrol L, Fourmy D (2003) Trends Pharmacol Sci 24:36
111. Oliveira L, Hulsen T, Lutje Hulsik D, Paiva AC, Vriend G (2004) FEBS Lett 564:269
112. Waldhoer M, Bartlett SE, Whistler JL (2004) Annu Rev Biochem 73:953
113. (a) Karnik SS, Khorana HG (1990) J Biol Chem 265:17520; (b) Kurtenbach E, Curtis CA, Pedder EK, Aitken A, Harris AC, Hulme EC (1990) J Biol Chem 265:13702; (c) Dohlman HG, Caron MG, DeBlasi A, Frielle T, Lefkowitz RJ (1990) Biochemistry 29:2335
114. Kane BE, Nieto MJ, McCurdy CR, Ferguson DM (2006) FEBS J 273:1966
115. (a) Thirstrup K, Elling CE, Hjorth SA, Schwartz TW (1996) J Biol Chem 271:7875; (b) Hjorth SA, Thirstrup K, Schwartz TW (1996) Mol Pharmacol 50:977 (c) Xue JC, Chen C, Zhu J, Kunapuli S, DeRiel JK, Yu L, Liu-Chen LY (1994) J Biol Chem, 269:30195
116. Ballesteros J, Kitanovic S, Guarnieri F, Davies P, Fromme BJ, Konvicka K, Chi L, Millar RP, Davidson JS, Weinstein H, Sealfon SC (1998) J Biol Chem 273:10445
117. Scheer A, Fanelli F, Costa T, De Benedetti PG, Cotecchia S (1996) EMBO J 15:3566
118. Fritze O, Filipek S, Kuksa V, Palczewski K, Hofmann KP, Ernst OP (2003) Proc Natl Acad Sci USA 100:290
119. Zhou W, Flanagan C, Ballesteros JA, Konvicka K, Davidson JS, Weinstein H, Millar RP, Sealfon SC (1994) Mol Pharmacol 45:165
120. Sealfon SC, Chi L, Ebersole BJ, Rodic V, Zhang D, Ballesteros JA, Weinstein H (1995) J Biol Chem 270:16683
121. Folkers G (1998) In: Codding PW (ed) Structure-based drug design experimental and computational approaches. Kluwer Academic Publishers, Norwell, MA USA, p 271