Structure-based discovery of GPCR ligands from crystal structures and homology models

Topics in Medicinal Chemistry

Volumn 30, Issue , 2019, Pages 65-99

  Ranganathan, Anirudh ^b   Rodríguez, David ^b   Carlsson, Jens ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

Agonist; Antagonist; Comparative modeling; Drug discovery; Fragment based lead discovery; G protein coupled receptor; Homology modeling; Molecular docking; Structure based drug design; Virtual screening

Indexed keywords

ADENOSINE RECEPTOR; ADRENERGIC RECEPTOR; CHEMOKINE RECEPTOR; DOPAMINE RECEPTOR; G PROTEIN COUPLED RECEPTOR; HISTAMINE RECEPTOR; LIGAND; MUSCARINIC RECEPTOR; OPIATE RECEPTOR; SEROTONIN RECEPTOR;

COMPUTER MODEL; CRYSTAL STRUCTURE; DRUG DESIGN; DRUG RESEARCH; DRUG TARGETING; HIGH ACCURACY MODELING; HOMOLOGY MODEL; HUMAN; INTERMEDIATE ACCURACY MODELING; LOW ACCURACY MODELING; MOLECULAR DOCKING; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION;

EID: 85070565180     PISSN: 18622461     EISSN: 1862247X     Source Type: Book Series    
DOI: 10.1007/7355_2016_25     Document Type: Chapter

References (143)

1. Alexander SP, Benson HE, Faccenda E, Pawson AJ, Sharman JL, Spedding M, Peters JA, Harmar AJ, CGTP Collaborators (2013) Br J Pharmacol 170:1459
2. Lagerstrom MC, Schioth HB (2008) Nat Rev Drug Discov 7:339
3. Rosenbaum DM, Rasmussen SG, Kobilka BK (2009) Nature 459:356
4. Liu W, Chun E, Thompson AA, Chubukov P, Xu F, Katritch V, Han GW, Roth CB, Heitman LH, IJzerman AP, Cherezov V, Stevens RC (2012) Science 337:232
5. Overington JP, Al-Lazikani B, Hopkins AL (2006) Nat Rev Drug Discov 5:993
6. Macarron R, Banks MN, Bojanic D, Burns DJ, Cirovic DA, Garyantes T, Green DV, Hertzberg RP, Janzen WP, Paslay JW, Schopfer U, Sittampalam GS (2011) Nat Rev Drug Discov 10:188
7. Eckert H, Bajorath J (2007) Drug Discov Today 12:225
8. Shoichet BK (2004) Nature 432:862
9. Kitchen DB, Decornez H, Furr JR, Bajorath J (2004) Nat Rev Drug Discov 3:935
10. Katritch V, Cherezov V, Stevens RC (2013) Annu Rev Pharmacol Toxicol 53:531
11. Cooke RM, Brown AJ, Marshall FH, Mason JS (2015) Drug Discov Today 20:1355
12. Rodriguez D, Ranganathan A, Carlsson J (2015) Curr Top Med Chem 15:2484
13. Deupi X, Kobilka BK (2010) Physiology (Bethesda) 25:293
14. Piscitelli CL, Kean J, de Graaf C, Deupi X (2015) Mol Pharmacol 88:536
15. Rasmussen SGF, Choi H-J, Rosenbaum DM, Kobilka TS, Thian FS, Edwards PC, Burghammer M, Ratnala VRP, Sanishvili R, Fischetti RF, Schertler GFX, Weis WI, Kobilka BK (2007) Nature 450:383
16. Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SGF, Thian FS, Kobilka TS, Choi H-J, Kuhn P, Weis WI, Kobilka BK, Stevens RC (2007) Science 318:1258
17. Lebon G, Warne T, Tate CG (2012) Curr Opin Struct Biol 22:482
18. Rasmussen SG, DeVree BT, Zou Y, Kruse AC, Chung KY, Kobilka TS, Thian FS, Chae PS, Pardon E, Calinski D, Mathiesen JM, Shah ST, Lyons JA, Caffrey M, Gellman SH, Steyaert J, Skiniotis G, Weis WI, Sunahara RK, Kobilka BK (2011) Nature 477:549
19. Kooistra AJ, de Graaf C, Timmerman H (2014) Neurochem Res 39:1850
20. Vaidehi N, Floriano WB, Trabanino R, Hall SE, Freddolino P, Choi EJ, Zamanakos G, Goddard WA (2002) Proc Natl Acad Sci U S A 99:12622
21. Michino M, Chen J, Stevens RC, Brooks 3rd CL (2010) Proteins 78:2189
22. Shacham S, Topf M, Avisar N, Glaser F, Marantz Y, Bar-Haim S, Noiman S, Naor Z, Becker OM (2001) Med Res Rev 21:472
23. Cavasotto CN, Palomba D (2015) Chem Commun 51:13576
24. Martí-Renom MA, Stuart AC, Fiser A, Sánchez R, Melo F, Sali A (2000) Annu Rev Biophys Biomol Struct 29:291
25. Sali A, Blundell TL (1993) J Mol Biol 234:779
26. Goldfeld DA, Zhu K, Beuming T, Friesner RA (2011) Proc Natl Acad Sci U S A 108:8275
27. Kmiecik S, Jamroz M, Kolinski M (2014) Biophys J 106:2408
28. de Graaf C, Foata N, Engkvist O, Rognan D (2008) Proteins 71:599
29. Chen KY, Sun J, Salvo JS, Baker D, Barth P (2014) PLoS Comput Biol 10:e1003636
30. Ray A, Lindahl E, Wallner B (2010) Bioinformatics 26:3067
31. Shen MY, Sali A (2006) Protein Sci 15:2507
32. Katritch V, Rueda M, Abagyan R (2012) Methods Mol Biol 857:189
33. Rodríguez D, Bello X, Gutiérrez-de-Terán H (2012) Mol Inf 31:334
34. Worth CL, Kreuchwig A, Kleinau G, Krause G (2011) BMC Bioinformatics 12:185
35. Sandal M, Duy TP, Cona M, Zung H, Carloni P, Musiani F, Giorgetti A (2013) PLoS One 8: e74092
36. Latek D, Pasznik P, Carlomagno T, Filipek S (2013) PLoS One 8:e56742
37. Isberg V, Vroling B, van der Kant R, Li K, Vriend G, Gloriam D (2014) Nucleic Acids Res 42:D422
38. Costanzi S, Tikhonova IG, Harden TK, Jacobson KA (2009) J Comput Aided Mol Des 23:747
39. Kooistra AJ, Roumen L, Leurs R, de Esch IJ, de Graaf C (2013) Methods Enzymol 522:279
40. Rodríguez D, Gutiérrez-de-Teran H (2013) Curr Pharm Des 19:2216
41. Engel S, Skoumbourdis AP, Childress J, Neumann S, Deschamps JR, Thomas CJ, Colson AO, Costanzi S, Gershengorn MC (2008) J Am Chem Soc 130:5115
42. Kellenberger E, Springael JY, Parmentier M, Hachet-Haas M, Galzi JL, Rognan D (2007) J Med Chem 50:1294
43. 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 U S A 101:11304
44. Evers A, Klabunde T (2005) J Med Chem 48:1088
45. Michino M, Abola E, GPCR Dock 2008 Participants, Brooks CL, Dixon JS, Moult J, Stevens RC (2009) Nat Rev Drug Discov 8:455
46. Kufareva I, Rueda M, Katritch V, GPCR Dock 2010 Participants, Stevens RC, Abagyan R (2011) Structure 19:1108
47. Kufareva I, Katritch V, Participants of GPCR Dock 2013, Stevens RC, Abagyan R (2014) Structure 22:1120
48. Carlsson J, Yoo L, Gao Z-G, Irwin JJ, Shoichet BK, Jacobson KA (2010) J Med Chem 53:3748
49. Lenselink EB, Beuming T, Sherman W, van Vlijmen HW, IJzerman AP (2014) J Chem Inf Model 54:1737
50. de Beer SB, Vermeulen NP, Oostenbrink C (2010) Curr Top Med Chem 10:55
51. Lorber DM, Shoichet BK (2005) Curr Top Med Chem 5:739
52. Neves MA, Totrov M, Abagyan R (2012) J Comput Aided Mol Des 26:675
53. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) J Comput Chem 30:2785
54. Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL (2004) J Med Chem 47:1750
55. Korb O, Stutzle T, Exner TE (2009) J Chem Inf Model 49:84
56. Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD (2003) Proteins 52:609
57. Leach AR, Shoichet BK, Peishoff CE (2006) J Med Chem 49:5851
58. Sousa SF, Fernandes PA, Ramos MJ (2006) Proteins 65:15
59. Mysinger MM, Carchia M, Irwin JJ, Shoichet BK (2012) J Med Chem 55:6582
60. Phatak SS, Gatica EA, Cavasotto CN (2010) J Chem Inf Model 50:2119
61. Evers A, Klebe G (2004) Angew Chem Int Ed Engl 43:248
62. de Graaf C, Rognan D (2009) Curr Pharm Des 15:4026
63. Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG (2012) J Chem Inf Model 52:1757
64. eMolecules. http://www.emolecules.com
65. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (2001) Adv Drug Deliv Rev 46:3
66. Baell JB, Holloway GA (2010) J Med Chem 53:2719
67. Sabio M, Jones K, Topiol S (2008) Bioorg Med Chem Lett 18:5391
68. Kolb P, Rosenbaum DM, Irwin JJ, Fung JJ, Kobilka BK, Shoichet BK (2009) Proc Natl Acad Sci U S A 106:6843
69. Weiss DR, Ahn S, Sassano MF, Kleist A, Zhu X, Strachan R, Roth BL, Lefkowitz RJ, Shoichet BK (2013) ACS Chem Biol 8:1018
70. Katritch V, Jaakola VP, Lane JR, Lin J, Ijzerman AP, Yeager M, Kufareva I, Stevens RC, Abagyan R (2010) J Med Chem 53:1799
71. Chen D, Ranganathan A, IJzerman AP, Siegal G, Carlsson J (2013) J Chem Inf Model 53:2701
72. Rodríguez D, Gao ZG, Moss SM, Jacobson KA, Carlsson J (2015) J Chem Inf Model 55:550
73. Kolb P, Phan K, Gao ZG, Marko AC, Sali A, Jacobson KA (2012) PLoS One 7:e49910
74. Langmead CJ, Andrews SP, Congreve M, Errey JC, Hurrell E, Marshall FH, Mason JS, Richardson CM, Robertson N, Zhukov A, Weir M (2011) J Med Chem 55:1904
75. Ranganathan A, Stoddart LA, Hill SJ, Carlsson J (2015) J Med Chem 58:9578
76. Carlsson J, Coleman RG, Setola V, Irwin JJ, Fan H, Schlessinger A, Sali A, Roth BL, Shoichet BK (2011) Nat Chem Biol 7:769
77. Vass M, Schmidt E, Horti F, Keseru GM (2014) Eur J Med Chem 77:38
78. Lane JR, Chubukov P, Liu W, Canals M, Cherezov V, Abagyan R, Stevens RC, Katritch V (2013) Mol Pharmacol 84:794
79. Mysinger MM, Weiss DR, Ziarek JJ, Gravel S, Doak AK, Karpiak J, Heveker N, Shoichet BK, Volkman BF (2012) Proc Natl Acad Sci U S A 109:5517
80. Schmidt D, Bernat V, Brox R, Tschammer N, Kolb P (2015) ACS Chem Biol 10:715
81. de Graaf C, Kooistra AJ, Vischer HF, Katritch V, Kuijer M, Shiroishi M, Iwata S, Shimamura T, Stevens RC, de Esch IJ, Leurs R (2011) J Med Chem 54:8195
82. Sirci F, Istyastono EP, Vischer HF, Kooistra AJ, Nijmeijer S, Kuijer M, Wijtmans M, Mannhold R, Leurs R, de Esch IJP, de Graaf C (2012) J Chem Inf Model 52:3308
83. Istyastono EP, Kooistra AJ, Vischer HF, Kuijer M, Roumen L, Nijmeijer S, Smits RA, de Esch IJP, Leurs R, de Graaf C (2015) MedChemComm 6:1003
84. Negri A, Rives ML, Caspers MJ, Prisinzano TE, Javitch JA, Filizola M (2013) J Chem Inf Model 53:512
85. Kruse AC, Weiss DR, Rossi M, Hu J, Hu K, Eitel K, Gmeiner P, Wess J, Kobilka BK, Shoichet BK (2013) Mol Pharmacol 84:528
86. Rodríguez D, Brea J, Loza MI, Carlsson J (2014) Structure 22:1140
87. Lam V, Rodriguez D, Zhang T, Koh E, Carlsson J, Salahpour A (2015) MedChemComm 6:2216
88. Rosenbaum DM, Cherezov V, Hanson MA, Rasmussen SGF, Thian FS, Kobilka TS, Choi H-J, Yao X-J, Weis WI, Stevens RC, Kobilka BK (2007) Science 318:1266
89. Taylor MR (2007) Pharmacogenomics J 7:29
90. Wacker D, Fenalti G, Brown MA, Katritch V, Abagyan R, Cherezov V, Stevens RC (2010) J Am Chem Soc 132:11443
91. Rasmussen SG, Choi HJ, Fung JJ, Pardon E, Casarosa P, Chae PS, Devree BT, Rosenbaum DM, Thian FS, Kobilka TS, Schnapp A, Konetzki I, Sunahara RK, Gellman SH, Pautsch A, Steyaert J, Weis WI, Kobilka BK (2011) Nature 469:175
92. Rosenbaum DM, Zhang C, Lyons JA, Holl R, Aragao D, Arlow DH, Rasmussen SG, Choi HJ, Devree BT, Sunahara RK, Chae PS, Gellman SH, Dror RO, Shaw DE, Weis WI, Caffrey M, Gmeiner P, Kobilka BK (2011) Nature 469:236
93. Mysinger MM, Shoichet BK (2010) J Chem Inf Model 50:1561
94. Ballesteros JA, Weinstein H (1995) Methods Neurosci 25:366
95. Muller CE, Jacobson KA (2011) Biochim Biophys Acta 1808:1290
96. Fredholm BB, IJzerman AP, Jacobson KA, Linden J, Muller CE (2011) Pharmacol Rev 63:1
97. Jaakola V-P, Griffith MT, Hanson MA, Cherezov V, Chien EYT, Lane JR, IJzerman AP, Stevens RC (2008) Science 322:1211
98. Xu F, Wu H, Katritch V, Han GW, Jacobson KA, Gao ZG, Cherezov V, Stevens RC (2011) Science 332:322
99. Lebon G, Warne T, Edwards PC, Bennett K, Langmead CJ, Leslie AG, Tate CG (2011) Nature 474:521
100. Tosh DK, Phan K, Gao ZG, Gakh AA, Xu F, Deflorian F, Abagyan R, Stevens RC, Jacobson KA, Katritch V (2012) J Med Chem 55:4297
101. Beaulieu JM, Espinoza S, Gainetdinov RR (2015) Br J Pharmacol 172:1
102. Chien EYT, Liu W, Zhao Q, Katritch V, Han GW, Hanson MA, Shi L, Newman AH, Javitch JA, Cherezov V, Stevens RC (2010) Science 330:1091
103. Scholten DJ, Canals M, Maussang D, Roumen L, Smit MJ, Wijtmans M, de Graaf C, Vischer HF, Leurs R (2012) Br J Pharmacol 165:1617
104. Wu B, Chien EY, Mol CD, Fenalti G, Liu W, Katritch V, Abagyan R, Brooun A, Wells P, Bi FC, Hamel DJ, Kuhn P, Handel TM, Cherezov V, Stevens RC (2010) Science 330:1066
105. Panula P, Chazot PL, Cowart M, Gutzmer R, Leurs R, Liu WL, Stark H, Thurmond RL, Haas HL (2015) Pharmacol Rev 67:601
106. Shimamura T, Shiroishi M, Weyand S, Tsujimoto H, Winter G, Katritch V, Abagyan R, Cherezov V, Liu W, Han GW, Kobayashi T, Stevens RC, Iwata S (2011) Nature 475:65
107. Dhawan BN, Cesselin F, Raghubir R, Reisine T, Bradley PB, Portoghese PS, Hamon M (1996) Pharmacol Rev 48:567
108. Vanderah TW (2010) Clin J Pain 26:5
109. Granier S, Manglik A, Kruse AC, Kobilka TS, Thian FS, Weis WI, Kobilka BK (2012) Nature 485:400
110. Manglik A, Kruse AC, Kobilka TS, Thian FS, Mathiesen JM, Sunahara RK, Pardo L, Weis WI, Kobilka BK, Granier S (2012) Nature 485:321
111. Wu H, Wacker D, Mileni M, Katritch V, Han GW, Vardy E, Liu W, Thompson AA, Huang XP, Carroll FI, Mascarella SW, Westkaemper RB, Mosier PD, Roth BL, Cherezov V, Stevens RC (2012) Nature 485:327
112. Kruse AC, Kobilka BK, Gautam D, Sexton PM, Christopoulos A, Wess J (2014) Nat Rev Drug Discov 13:549
113. Kruse AC, Hu J, Pan AC, Arlow DH, Rosenbaum DM, Rosemond E, Green HF, Liu T, Chae PS, Dror RO, Shaw DE, Weis WI, Wess J, Kobilka BK (2012) Nature 482:552
114. Haga K, Kruse AC, Asada H, Yurugi-Kobayashi T, Shiroishi M, Zhang C, Weis WI, Okada T, Kobilka BK, Haga T, Kobayashi T (2012) Nature 482:547
115. Wess J, Eglen RM, Gautam D (2007) Nat Rev Drug Discov 6:721
116. Berger M, Gray JA, Roth BL (2009) Annu Rev Med 60:355
117. McCorvy JD, Roth BL (2015) Pharmacol Ther 150:129
118. Saxena PR, Peer T-H (2001) J Headache Pain 2:8
119. Wacker D, Wang C, Katritch V, Han GW, Huang XP, Vardy E, McCorvy JD, Jiang Y, Chu M, Siu FY, Liu W, Xu HE, Cherezov V, Roth BL, Stevens RC (2013) Science 340:615
120. Wang C, Jiang Y, Ma J, Wu H, Wacker D, Katritch V, Han GW, Liu W, Huang XP, Vardy E, McCorvy JD, Gao X, Zhou XE, Melcher K, Zhang C, Bai F, Yang H, Yang L, Jiang H, Roth BL, Cherezov V, Stevens RC, Xu HE (2013) Science 340:610
121. Langmead CJ, Christopoulos A (2014) Curr Opin Cell Biol 27:94
122. Kruse AC, Ring AM, Manglik A, Hu J, Hu K, Eitel K, Hubner H, Pardon E, Valant C, Sexton PM, Christopoulos A, Felder CC, Gmeiner P, Steyaert J, Weis WI, Garcia KC, Wess J, Kobilka BK (2013) Nature 504:101
123. Dore AS, Okrasa K, Patel JC, Serrano-Vega M, Bennett K, Cooke RM, Errey JC, Jazayeri A, Khan S, Tehan B, Weir M, Wiggin GR, Marshall FH (2014) Nature 511:557
124. Wu H, Wang C, Gregory KJ, Han GW, Cho HP, Xia Y, Niswender CM, Katritch V, Meiler J, Cherezov V, Conn PJ, Stevens RC (2014) Science 344:58
125. Kooistra AJ, Leurs R, de Esch IJ, de Graaf C (2015) J Chem Inf Model 55:1045
126. Hert J, Irwin JJ, Laggner C, Keiser MJ, Shoichet BK (2009) Nat Chem Biol 5:479
127. Moult J (2005) Curr Opin Struct Biol 15:285
128. Lensink MF, Méndez R, Wodak SJ (2007) Proteins 69:704
129. Damm-Ganamet KL, Smith RD, Dunbar Jr JB, Stuckey JA, Carlson HA (2013) J Chem Inf Model 53:1853
130. Geballe MT, Skillman AG, Nicholls A, Guthrie JP, Taylor PJ (2010) J Comput Aided Mol Des 24:259
131. Okada T, Sugihara M, Bondar AN, Elstner M, Entel P, Buss V (2004) J Mol Biol 342:571
132. Murakami M, Kouyama T (2008) Nature 453:363
133. Warne T, Serrano-Vega MJ, Baker JG, Moukhametzianov R, Edwards PC, Henderson R, Leslie AGW, Tate CG, Schertler GFX (2008) Nature 454:486
134. Katritch V, Rueda M, Lam PC, Yeager M, Abagyan R (2010) Proteins 78:197
135. Dore AS, Robertson N, Errey JC, Ng I, Hollenstein K, Tehan B, Hurrell E, Bennett K, Congreve M, Magnani F, Tate CG, Weir M, Marshall FH (2011) Structure 19:1283
136. Roumen L, Sanders MPA, Vroling B, De Esch IJP, De Vlieg J, Leurs R, Klomp JPG, Nabuurs SB, De Graaf C (2011) Pharmaceuticals 4:1196
137. Wang C, Wu H, Evron T, Vardy E, Han GW, Huang XP, Hufeisen SJ, Mangano TJ, Urban DJ, Katritch V, Cherezov V, Caron MG, Roth BL, Stevens RC (2014) Nat Commun 5:4355
138. Wang C, Wu H, Katritch V, Han GW, Huang XP, Liu W, Siu FY, Roth BL, Cherezov V, Stevens RC (2013) Nature 497:338
139. Rodríguez D, Ranganathan A, Carlsson J (2014) J Chem Inf Model 54:2004
140. Leo D, Mus L, Espinoza S, Hoener MC, Sotnikova TD, Gainetdinov RR (2014) Neuropharmacology 81:283
141. Anighoro A, Bajorath J, Rastelli G (2014) J Med Chem 57:7874
142. Vass M, Agai-Csongor E, Horti F, Keseru GM (2014) ACS Med Chem Lett 5:1010
143. Zhukov A, Andrews SP, Errey JC, Robertson N, Tehan B, Mason JS, Marshall FH, Weir M, Congreve M (2011) J Med Chem 54:4312