Structure-based virtual screening

Frontiers in Drug Design and Discovery

Volumn 3, Issue 1, 2007, Pages 477-502

  Polgár, Tímea ^a   Keseru, György M ^a  

^a GEDEON RICHTER LTD   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77954061005     PISSN: 15740889     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (128)

1. Wu, G.; Doberstein, S.K. Drug Discov. Today, 2006, 11, 718-724.
2. Keseru, G.M.; Makara, G.M. Drug Discov. Today, 2006, 11, 741-748.
3. Lahana, R. Drug Discov. Today, 1999, 4, 447-448.
4. Ramesha, C.S. Drug Discov. Today, 2000, 5, 43-44.
5. Shoichet, B. Drug Discov. Today, 2006, 11, 607-615.
6. Shoichet, B. Nature, 2004, 432, 862-865.
7. Polgár, T.; Keseru, M.G. In Encyclopaedia of Pharmaceutical Technology; Swarbrick, J.; Boylan, J.C.; Ed.; Taylor & Francis, LLC, 2005.
8. Seifert, M.H.J.; Wolf, K.; Vitt, D. Biosilico, 2003, 1, 143-149.
9. Congreve, M.; Murray, C.W.; Blundell, T.L. Drug Discov. Today, 2005, 10, 895-907.
10. DesJarlais, R.L.; Seibel, G.L.; Kuntz, I.D.; Furth, P.S.; Alvarez, J.C.; de Montellano, P.R.O.; De-Camp, D.L.; Babe, L.M.; Craik, C.S. Proc. Natl. Acad. Sci. U. S. A., 1990, 87, 6644-6648.
11. Lyne, P.D. Drug Discov. Today, 2002, 7, 1047-1055.
12. Kitchen, D.B.; Decornez, H.; Furr, J.R.; Bajorath, J. Nature, 2004, 3, 935-949.
13. Barril, X.; Hubbard, R.E.; Morley, S.D. Mini Rev. Med. Chem., 2004, 4, 779-791.
14. Muegge, I.; Enyedi, I.J. Curr. Med. Chem., 2004, 11, 693-707.
15. Scapin, G. Drug Discov. Today, 2002, 7, 601-611.
16. Kubinyi, H. Curr. Opin. Drug Discov. Dev., 1998, 1, 16-27.
17. Kubinyi, H. In Success Stories of Computer AIDED Design, In: Computer Applications in Pharmaceutical Research and Development; Ekins, S. Ed.; Wiley Series in Drug Discovery and Development (Wang, B. Ed.), Wiley-Interscience, 2006; pp. 377-424.
18. Good, A. Curr. Opin. Drug Discov. Dev., 2001, 4, 301-307.
19. Good, A.; Cheney, D.L. J. Mol. Graph. Model., 2003, 22, 23-30.
20. Good, A.; Cheney, D.L.; Sitkoff, D.F.; Tokarski, J.S.; Stouch, T.R.; Bassolino, D.A.; Krystek, S.R.; Li, Y.; Mason, J.S.; Perkins, T.D.J. J. Mol. Graph. Model., 2003, 22, 31-40.
21. Bursulaya, B.D.; Totrov, M.; Abagyan, R.; Brooks III C.L. J. Comput. Aided Mol. Des., 2003, 17, 755-763.
22. Wyss, P.C.; Gerber, P.; Hartman, P.G.; Hubschwerlen, C.; Locher, H.; Marty, H.-P.; Stahl, M. J. Med. Chem., 2003, 46, 2304-2312.
23. Kick, E.K.; Roe, D.C.; Skillman, A.G.; Liu, G.; Ewing, T.J.A.; Sun, Y.; Kuntz, I.D.; Jonathan, J.A.; Ellman, A. Chem. Biol., 1997, 4, 297-307.
24. Doman, T.N.; McGovern, S.L.; Witherbee, B.J.; Kasten, T.P.; Kurumbail, R.; Stallings, W.C.; Connolly, D.T.; Shoichet, B.K. J. Med. Chem., 2002, 45, 2213-2221.
25. Jenkins, J.L.; Kao, R.Y.; Shapiro, R. Proteins, 2003, 50, 81-93.
26. Paiva, A.M.; Vanderwall, D.E.; Blanchard, J.S.; Kozarich, J.W.; Williamson, J.M.; Kelly, T.M. Biochim. Biophys. Acta, 2001, 1545, 67-77.
27. Polgár, T.; Baki, A.; Szendrei-Ignácz, G.; Keseru, G.M. J. Med. Chem., 2005, 48, 7946-7959.
28. WDI, ACD, Daylight Chemical Information Systems, Inc., http://www.daylight.com.
29. MDDR, ACD, MDL Information Systems, Inc., http://www.mdli.com.
30. Teague, S.J.; Davis, A.M.; Leeson, P.D.; Oprea, T.I. Angew. Chem. Int. Ed., 1999, 38, 3743-3748.
31. Oprea, T.I.; Bologa, C.; Olah, M. In Virtual Screening in Drug Discovery: Compound Selection for Virtual Screening, Alvarez, J.; Shoichet, B.; Ed., Taylor & Francis, LLC, 2005, pp. 89-104.
32. Verdonk, M.L.; Berdini, V.; Hartshorn, M.J.; Mooij, W.T.M.; Murray, C.W.; Taylor, R.D.; Watson, P. J. Chem. Inf. Comput. Sci., 2004, 3, 4289-4296.
33. Pan, Y.; Huang, N.; Cho, S.; MacKerell, Jr., A.D. J. Chem. Inf. Comput. Sci., 2003, 43, 267-272.
34. Beavers, M.P.; Chen, X. J. Mol. Graph. Model., 2000, 20, 463-468.
35. Fitzgerald, S.H.; Sabat, M.; Geysen, H.M. J. Chem. Inf. Model., 2006, 46, 1588-1597.
36. Roche, O.; Schneider, P.; Zuegge, J.; Guba, W.; Kansy, M.; Alanine, A.; Bleicher, K.; Danel, F.; Gutknecht, E.-M.; Rogers-Evans, M.; Neidhart, W.; Stalder, H.; Dillon, M.; Sjogren, E.; Fotouhi, N.; Gillespie, P.; Goodnow, R.; Harris, W.; Jones, P.; Taniguchi, M.; Tsujii, S.; von der Saal, W.; Zimmermann, G.; Schneider, G. J. Med. Chem., 2002, 45, 137-142.
37. Knox, A.J.S.; Meegan, M.J.; Carta, G.; Lloyd, D.G. J. Chem. Inf. Model., 2005, 45, 1908-1919.
38. Irwin, J.J.; Shoichet, B.K. J. Chem. Inf. Model., 2005, 45, 177-182.
39. Fishman, M.C.; Porter, J.A. Nature, 2005, 437, 491-493.
40. Hajduk, P.J.; Huth, J.R.; Fesik, S.W. J. Med. Chem., 2005, 48, 2518-2525.
41. Merlitz, H.; Burghardt, B.; Wenzel, W. Chem. Phys. Lett., 2004, 390, 500-505.
42. Thomas, M.P.; McInnes, C.; Fischer, P.M. J. Med. Chem., 2006, 49, 92-104.
43. McGovern, S.L.; Shoichet, B.K. J. Med. Chem., 2003, 46, 2895-2907.
44. Klebe, G. Drug Discov. Today, 2006, 11, 580-594.
45. Evers, A.; Gohlke, H.; Klebe, G. J. Mol. Biol., 2003, 334, 327-345.
46. Kratochwil, N.A.; Malherbe, P.; Lindemann, L.; Ebeling, M.; Hoener, M.C.; Muhlemann, A.; Porter, R.H.P.; Stahl, M.; Gerber, P.R. J. Chem. Inf. Model., 2005, 45, 1324-1336.
47. Evers, A.; Klebe, G. J. Med. Chem., 2004, 47, 5381-5392.
48. Evers, A.; Klabunde, T. J. Med. Chem., 2005, 48, 1088-1097.
49. Bissantz, C.; Logean, A.; Rognan, D. J. Chem. Inf. Comput. Sci., 2004, 44, 1162-1176.
50. Gohlke, H.; Hendlich, M.; Klebe, G. Persp. Drug Discov. Des., 2000, 20, 115-144.
51. Hindle, S.A.; Rarey, M.; Buning, C.; Lengauer, T. J. Comput. Aided Mol. Des., 2002, 16, 129-149.
52. Hendlich, M.; Rippmann, F.; Barnickel, G. J. Mol. Graph. Model., 1997, 15, 359-363.
53. Brady, G.P.; Stouten, P.F. J. Comput. Aided Mol. Des., 2000, 14, 383-401.
54. Schmitt, S.; Hendlich, M.; Klebe, G. Homology, 2001, 40, 3141-3144.
55. Brown, W. M.; Vander Jagt, D. L. J. Chem. Inf. Comput. Sci., 2004, 44, 1412-1422.
56. DOCK, http://dock.compbio.ucsf.edu/.
57. Weiser, J.; Shenkin, P.S.; Still, W.C. J. Comput. Chem., 1999, 20, 217-230.
58. AutoDock, http://www.scripps.edu/mb/olson/doc/autodock/.
59. GOLD, http://www.ccdc.cam.ac.uk/products/life_sciences/gold/.
60. FlexX, http://www.biosolveit.de/FlexX/.
61. Glide, http://www.schrodinger.com/.
62. Slide, http://www.bch.msu.edu/~kuhn/projects/slide/home.html.
63. eHiTS, http://www.simbiosys.ca/.
64. Surflex, http://www.biopharmics.com/.
65. MOE, http://www.chemcomp.com/software.htm.
66. ICM, http://www.molsoft.com/docking.html.
67. LigandFit, http://www.accelrys.com/.
68. Carlson, H.A.; McCammon, J.A. Mol. Pharmacol., 2000, 57, 213-218.
69. Claussen, H.; Buning, C.; Rarey, M.; Lengauer, T. J. Mol. Biol., 2001, 308, 377-395.
70. Cavasotto, C.N.; Abagyan, R.A. J. Mol. Biol., 2004, 337, 209-225.
71. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. J. Mol. Biol., 1996, 261, 470-489.
72. Kramer, B.; Rarey, M.; Lengauer, T. Proteins, 1999, 37, 228-241.
73. Zsoldos, Z.; Reid, D.; Simon, A.; Sadjad, S.B.; Johnson, A.P. J. Mol. Graph. Model., 2006,. [Epub ahead of print].
74. Clark, R.D.; Strizhev, A.; Leonard, J.M.; Blake, J.F.; Matthew, J.B. J. Mol. Graph. Model., 2002, 20, 281-295.
75. Charifson, P.S.; Corkery, J.J.; Murcko, M.A.; Walters, W.P. J. Med. Chem., 1999, 42, 5100-5109.
76. Wang, R.; Wang, S. J. Chem. Inf. Comput. Sci., 2001, 41, 1422-1426.
77. Gohlke, H.; Klebe, G. J. Med. Chem., 2002, 45, 4153-4170.
78. Antes, I.; Merkwirth, C.; Lengauer, T.; Antes, I.; Merkwirth, C.; Lengauer, T. J. Chem. Inf. Model., 2005, 45, 1291-1302.
79. Betzi, S.; Suhre, K.; Chetrit, B.; Guerlesquin, F.; Morelli, X. J. Chem. Inf. Model., 2006, 46, 1704-1712.
80. Schulz-Gash, T.; Stah, M. Drug Discov. Today, 2004, 1, 231-239.
81. Gohlke, H.; Klebe, G. Angew. Chem. Int. Ed., 2002, 41, 2644-2676.
82. Tame, J.R.H. J. Comput. Aided Mol. Des., 1999, 13, 99-108.
83. Meng, C.; Shoichet, B.K.; Kuntz, I.D. J. Comput. Chem., 1992, 13, 505-524.
84. Weiner, S.J.; Kollman, P.A.; Nguyen, D.T.; Case, D.A. J. Comput. Chem., 1986, 7, 230-252.
85. Böhm, H.J. J. Comput. Aided Mol. Des., 1994, 8, 243-256.
86. Rognan, D.; Lauemoller, S.L.; Holm, A.; Buus, S.; Tschinke, V. J. Med. Chem., 1999, 42, 4650-4658.
87. Wang, R.; Liu, L.; Lai, L.; Tang, Y. J. Mol. Model., 1998, 4, 379-394.
88. Welch, W.; Ruppert, J.; Jain, A.N. Chem. Biol., 1996, 3, 449-462.
89. Eldrige, D.; Murray, C.W.; Auton, T.R.; Paolini, G.V.; Mee, R.P. J. Comput. Aided Mol. Des., 1997, 11, 425-445.
90. Gohlke, H.; Hendlich, M.; Klebe, G. J. Mol. Biol., 2000, 295, 337-356.
91. Velec, H.F.G.; Gohlke, H.; Klebe, G. J. Med. Chem., 2005, 48, 6296-6303.
92. Muegge, I. J. Med. Chem., 2005, 49, 5895-5902.
93. Muegge, I.; Rarey, M. Rev. Comp. Chem., 2001, 17.
94. Taylor, R.D.; Jewsbury, P.J.; Essex, J.W. J. Comput. Aided Mol. Des., 2002, 16, 151-166.
95. Knegel, R.M.A.; Bayada, D.M.; Engh, R.A.; von der Saal, W.; van Geerestein, V.J.; Grootenhuis, P.D.J. J. Comput. Aided Mol. Des., 1999, 13, 167-183.
96. Kontoyianni, M.; McClellan, L. M.; Sokol, G. S. J. Med. Chem., 2004, 47, 558-565.
97. Cole, J.C.; Murray, C.W.; Nissink, J.W.M.; Taylor, R.D.; Taylor, R. Proteins, 2005, 60, 325-332.
98. Kroemer, R.T.; Vulpetti, A.; McDonald, J.J.; Rohrer, D.C.; Trosset, J.-Y.; Giordanetto, F.; Cotesta, S.; McMartin, C.; Kihlen, M.; Stouten, P.F.W. J. Chem. Inf. Comput. Sci., 2004, 44, 871-881.
99. Pang, Y.-P.; Perola, E.; Xu, K. J. Comput. Chem., 2001, 22, 1750-1771.
100. Halgren, T.A.; Murphy, R.B.; Friesner, R.A.; Beard, H.S.; Frye, L.L.; Pollard, W.T.; Banks, J.L. J. Med. Chem., 2004, 47, 1750-1759.
101. Krovat, E. M.; Langer, T. J. Chem. Inf. Comput. Sci., 2004, 44, 1123-1129.
102. Perola, E.; Walters, W.P.; Charifson, P.S. In Virtual Screening in Drug Discovery, Alvarez, J.; Shoichet, B.; Ed.; Taylor & Francis, LLC, 2005; pp. 47-87.
103. Stahl, M.; Rarey, M. J. Med. Chem., 2001, 44, 1035-1042.
104. Wang, R.; Lu, Y.; Wang, S. J. Med. Chem., 2003, 46, 2287-2303.
105. Wang, R.; Lu, Y.; Fang, X.; Wang, S. J. Chem. Inf. Comput. Sci., 2004, 44, 2114-2125.
106. Ferrara, P.; Gohlke, H.; Price, D.J.; Klebe, G.; Brooks III., C.L. J. Med. Chem., 2004, 47, 3032-3047.
107. Gasch-Schulz, T.; Stahl, M. J. Mol. Model., 2003, 9, 47-57.
108. Stahl, M.; Böhm, H.-J. J. Mol. Graph. Model., 1998, 16, 121-132.
109. Mpamhanga, C.P.; Chen, B.; McLay, I.M.; Willett, P. J. Chem. Inf. Model., 2006, 46, 686-698.
110. Burris, T.P. In Nuclear Receptors and Genetic Disease, Burris, T.P.; McCabe, E.R.B.; Ed., Academic, San Diego, 2001; pp. 1-57.
111. Kuiper, G.; Enmark, E.; Pelto Huikko, M.; Nilsson, S.; Gustafsson, J.A. Proc. Natl. Acad. Sci. U. S. A., 1996, 93, 5925-5930.
112. Pike, A.C.; Brzozowski, A.M.; Walton, J.; Hubbard, R.E.; Thorsell, A.G.; Li, Y.L.; Gustafsson, J.A.; Carlquist, M. Structure, 2001, 9, 145-153.
113. Henke, B.R.; Consler, T.G.; Go, N.; Hale, R.L.; Hohman, D.R.; Jones, S.A.; Lu, A.T.; Moore, L.B.; Moore, J.T.; Orband-Miller, L.A.; Robinett, R.G.; Shearin, J.; Spearing, P.K.; Stewart, E.L.; Turnbull, P.S.; Weaver, S.L.; Williams, S.P.; Wisely, G.B.; Lambert, M.H. J. Med. Chem., 2002, 45, 5492-5505.
114. Pike, A.C.W.; Brzozowski, A.M.; Hubbard, R.E.; Bonn, T.; Thorsell, A.G.; Engstrom, O.; Ljunggren, J.; Gustaffson, J.-A.; Carlquist, M. EMBO J., 1999, 18, 4608-4618.
115. Malamas, M.S.; Manas, E.S.; McDevitt, R.E.; Gunawan, I.; Xu, Z.B.; Collini, M.D.; Miller, C.P.; Dinh, T.; Henderson, R.A.; Keith, Jr., J.C.; Harris, H.A. J. Med. Chem., 2004, 47, 5021-5040.
116. Manas, E.S.; Unwalla, R.J.; Xu, Z.B.; Malamas, M.S.; Miller, C.P.; Harris, H.A.; Hsiao, C.; Akopian, T.; Hum, W.T.; Malakian, K.; Wolfrom, S.; Bapat, A.; Bhat, R.A.; Stahl, M.L.; Somers, W.S.; Alvarez, J.C. J. Am. Chem. Soc., 2004, 126, 15106-15548.
117. Manas, E.S.; Xu, Z.B.; Unwalla, R.J.; Somers, W.S. Structure, 2004, 12, 2197-2207.
118. Mewshaw, R.E.; Edsall, Jr., R.J.; Yang, C.; Manas, E.S.; Xu, Z.B.; Henderson, R.A.; Keith, Jr., J.C.; Harris, H.A. J. Med. Chem., 2005, 48, 3953-3979.
119. Shiau, A.K.; Barstad, D.; Radek, J.T.; Meyers, M.J.; Nettles, K.W.; Katzenellenbogen, B.S.; Katzenellenbogen, J.A.; Agard, D.A.; Greene, G.L. Nat. Struct. Biol., 2002, 9, 359-364.
120. Wang, Y.; Chirgadze, N.Y.; Briggs, S.L.; Khan, S.; Jensen, E.V.; Burris, T.P. Proc. Natl. Acad. Sci. U. S. A., 2006, 103, 9908-9911.
121. McDevitt, R.E.; Malamas, M.S.; Manas, E.S.; Unwalla, R.J.; Xu, Z.B.; Miller, C.P.; Harris, H.A. Bioorg. Med. Chem. Lett., 2005, 15, 3137-3142.
122. Tripos, Inc., ©2006, http://www.tripos.com.
123. Prous Integrity Drugs & Biologics, ©1995-2006 Prous Science. http://www.prous.com.
124. Viraag, I.; Polgaar, T.; Keseru, G.M. J. Mol. Struct. (THEOCHEM), 2005, 725, 239-242.
125. Bertrand, J. A.; Thieffine, S.; Vulpetti, A.; Cristiani, C.; Valsasina, B.; Knapp, S.; Kalisz, H. M.; Flocco, M. J. Mol. Biol., 2003, 333, 393-407.
126. Meijer, L.; Skaltsounis, A.-L.; Magiatis, P.; Polychronopoulous, P.; Knockaert, M.; Leost, M.; Ryan, X. P.; Vonica, C. A.; Brivanlou, A.; Dajani, R.; Crovace, C.; Tarricone, C.; Musacchio, A.; Roe, S. M.; Pearl, L. H.; Greengard, P. Chem. Biol., 2003, 10, 1255-1266.
127. Bhat, R.; Xue, Y.; Berg, S.; Hellberg, S.; Ormo, M.; Nilsson, Y.; Radesater, A. C.; Jerning, E.; Markgren, P. O.; Borgegard, T.; Nylof, M.; Gimenez-Cassina, A.; Hernandez, F.; Lucas, J. J.; Diaz-Nido, J.; Avila, J. J. Biol. Chem., 2003, 278, 45937-45945.
128. Baki, A.; Molnár, L.; Szendrei-Ignácz, G.; Keseru, G.M. Assay Drug Dev. Technol., 2006, in press.