A self-organizing algorithm for molecular alignment and pharmacophore development

Journal of Computational Chemistry

Volumn 29, Issue 6, 2008, Pages 965-982

  Agrafiotis, Dimitris K ^a   Bandyopadhyay, Deepak ^a  

^a JOHNSON AND JOHNSON PHARMACEUTICAL RESEARCH AND DEVELOPMENT   (United States)

Author keywords

Conformational analysis; Distance geometry; Molecular alignment; Pharmacophore development; Pharmacophore modeling; Self organizing; SPE; Stochastic proximity embedding

Indexed keywords

PHARMACOPHORE DEVELOPMENT; PHARMACOPHORE MODELING; STOCHASTIC PROXIMITY EMBEDDING;

ATOMS; CONFORMATIONS; GENETIC ALGORITHMS; LIGANDS;

MOLECULAR ORIENTATION;

DRUG; LIGAND;

ALGORITHM; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DRUG DESIGN; PHARMACOLOGY; STATISTICS; STRUCTURE ACTIVITY RELATION;

ALGORITHMS; BINDING SITES; DRUG DESIGN; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PHARMACEUTICAL PREPARATIONS; PHARMACOLOGY; STOCHASTIC PROCESSES; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 41549117981     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20854     Document Type: Article

References (84)

1. Schneider, G.; Neidhart, W.; Giller, T.; Schmid, G. Angew Chem Int Ed Engl 1999, 38, 2894.
2. Bradley, E. K.; Beroza, P.; Penzotti, J. E.; Grootenhuis, P. D.; Spellmeyer, D. C.; Miller, J. L. J Med Chem 2000, 43, 2770.
3. Aronov, A. M.; Goldman, B. B. Bioorg Med Chem 2004, 12, 2307.
4. Gillet, V. J.; Newell, W.; Mata, P.; Myatt, G.; Sike, S.; Zsoldos, Z.; Johnson, A. P. J Chem Inf Comput Sci 1994, 34, 207.
5. Hindle, S. A.; Rarey, M.; Buning, C.; Lengauer, T. J Comput Aided Mol Des 2002, 16, 129.
6. Joseph-McCarthy, D.; Thomas, B. E., IV; Belmarsh, M.; Moustakas, D.; Alvarez, J. C. Proteins 2003, 51, 172.
7. Daeyaert, F.; de Jonge, M.; Heeres, J.; Koymans, L.; Lewi, P.; Vinkers, M. H.; Janssen, P. A. J. Proteins 2004, 54, 526.
8. Goto, J.; Kataoka, R.; Hirayama, N. J Med Chem 2004, 47, 6804.
9. Moitessier, N.; Henry, C.; Maigret, B.; Chapleur, Y. J Med Chem 2004, 47, 4178.
10. Wang, J.; Kang, X.; Kuntz, I. D.; Kollman, P. A. J Med Chem 2005, 48, 2432.
11. Steindl, T. M.; Crump, C. E.; Hayden, F. G.; Langer, T. J. Med Chem 2005, 48, 6250.
12. Yamashita, F.; Hashida, M. Drug Metab Pharmacokinet 2004, 19, 327.
13. Güner, O. F., Ed. Pharmacophore Perception, Development, and Use in Drag Design; International University Line (IUL Biotechnology Series): La Jolla, CA, 2000.
14. Wolber, G.; Langer, T. J Chem Inf Model 2005, 45, 160.
15. Wolber, G.; Dornhofer, A. A.; Langer, T. J Comput Aided Mol Des 2007, 20, 773.
16. Lemmen, C.; Lengauer, T. J Comput Aided Mol Des 2000, 14, 215.
17. Mason, J. S.; Good, A. C.; Martin, E. J. Curr Pharm Des 2001, 7, 567.
18. Langer, T.; Krovat, E. M. Curr Opin Drug Discov Devel 2003, 6, 370.
19. Dror, O.; Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J. Curr Med Chem 2004, 11,71.
20. Hou, T.; Xu, X. Curr Pharm Des 2004, 10, 1011.
21. Lengauer, T.; Lemmen, C.; Rarey, M.; Zimmermann, M. Drug Discov Today 2004, 9, 27.
22. Balakin, K. V.; Kozintsev, A. V.; Kiselyov, A. S.; Savchuk, N. P. Curr Drug Discov Technol 2006, 3, 49.
23. Kurogi, Y.; Güner, O. F. Curr Med Chem 2001, 8, 1035.
24. Guner, O. F.; Clement, O.; Kurogi, Y. Curr Med Chem 2004, 11, 2991.
25. Clement, O. O.; Mehl, A. T. In Pharmacophore Perception, Development, and Use in Drag Design; Güner, O. F., Ed.; International University Line (IUL Biotechnology Series): 2000; pp. 69-83.
26. Li, H.; Sutter, J.; Hoffmann, R. In Pharmacophore Perception, Development, and Use in Drug Design; Güner, O. F., Ed.; International University Line (IUL Biotechnology Series): 2000; pp. 171-189.
27. Laggner, C.; Schieferer, C.; Fiechtner, B.; Poles, G.; Hoffmann, R. D.; Glossmann, H.; Langer, T.; Moebius, F. F. J Med Chem 2005, 48, 4754.
28. Olsen, L.; Jost, S.; Adolph, H.-W.; Pettersson, I.; Hemmingsen, L.; Jorgensen, F. S. Bioorg Med Chem 2006, 14, 2627.
29. Schuster, D.; Maurer, E. M.; Laggner, C.; Nashev, L. G.; Wilckens, T.; Langer, T.; Odermatt, A. J Med Chem 2006, 49, 3454.
30. Bernard, D.; Coop, A.; MacKerell, A. D. J. J Am Chem Soc 2003, 125, 3101.
31. Vedani, A.; Zbinden, P.; Snyder, J. P. J Recept Res 1993, 13, 163.
32. Seifert, M. H. J. J Chem Inf Model 2005, 45, 449.
33. Schuller, A.; Fechner, U.; Renner, S.; Franke, L.; Weber, L.; Schneider, G. Comb Chem High Throughput Screen 2006, 9, 359.
34. Renner, S.; Ludwig, V.; Boden, O.; Scheffer, U.; Gobel, M.; Schneider, G. Chembiochem 2005, 6, 1119.
35. Renner, S.; Schneider, G. J Med Chem 2004, 47, 4653.
36. Fechner, U.; Franke, L.; Renner, S.; Schneider, P.; Schneider, G. J Comput Aided Mol Des 2003, 17, 687.
37. Perola, E.; Charifson, P. S. J Med Chem 2004, 47, 2499.
38. Patel, Y.; Gillet, V. J.; Bravi, G.; Leach, A. R. J Comput Aided Mol Des 2002, 16, 653.
39. Kristam, R.; Gillet, V. J.; Lewis, R. A.; Thomer, D. J Chem Inf Model 2005, 45, 461.
40. Jones, G.; Willett, P.; Glen, R. C. J Comput Aided Mol Des 1995, 9, 532.
41. Richmond, N. J.; Abrams, C. A.; Wolohan, P. R. N.; Abrahamian, E.; Willett, P.; Clark, R. D. J Comput Aided Mol Des 2006, 20, 567.
42. Shepphird, J.; Clark, R. J Comput Aided Mol Des 2006, 20, 763.
43. Cottrell, S. J.; Gillet, V. J.; Taylor R.; Wilton, D. J. J Comput Aided Mol Des 2004, 18, 665.
44. Sheridan, R. P.; Nilakantan, R.; Dixon, J. S.; Venkataraghavan, R. J Med Chem 1986, 29, 899.
45. Agrafiotis, D. K.; Xu, H. Proc Natl Acad Sci USA 2002, 99, 15869.
46. Xu, H.; Izrailev, S.; Agrafiotis, D. K. J Chem Inf Comput Sci 2003, 43, 1186.
47. Agrafiotis, D. K. J Comput Chem 2003, 24, 1215.
48. Nathan Reed, post in discussion forum titled "Average Normal Vector" on devmaster.net,http://www.devmaster.net/forums/showthread. php?t=6741, accessed May 3, 2007.
49. Wang, S.; Milne, G. W.; Yan, X.; Posey, I. J.; Nicklaus, M. C.; Graham, L.; Rice, W. G. J Med Chem 1996, 39, 2047.
50. Martin, J.; Andrews, P. J Comput Aided Mol Des 1987, 1, 53.
51. Froimowitz, M. NIDA Res Monogr 1993, 134, 178.
52. Filizola, M.; Villar, H. O.; Loew, G. H. J Comput Aided Mol Des 2001, 15, 297.
53. Kaczor, A.; Matosiuk, D. Curr Med Chem 2002, 9, 1567.
54. Grundt, P.; Williams, I. A.; Lewis, J. W.; Husbands, S. M. J Med Chem 2004, 47, 5069.
55. Orsini, M. J.; Nesmelova, I.; Young, H. C.; Hargittai, B.; Beavers, M. P.; Liu, J.; Connolly, P. J.; Middleton, S. A.; Mayo, K. H. J Biol Chem 2005, 280, 8134.
56. Messer, W. S., Jr.Opioid systems. Available at: http://www.neurosci. pharm.utoledo.edu/MBC3320/opioids.htm, accessed May 3, 2007.
57. Portoghese, P. S.; Nagase, H.; Takemori, A. E. J Med Chem 1988, 31, 1344.
58. Lomize, A. L.; Pogozheva, I. D.; Mosberg, H. I. Biopolymers 1996, 38, 221.
59. Huang, P.; Kim, S.; Loew, G. J Comput Aided Mol Des 1997, 11, 21.
60. Liao, S.; Alfaro-Lopez, J.; Shenderovich, M. D.; Hosohata, K.; Lin, J.; Li, X.; Stropova, D.; Davis, P.; Jernigan, K. A.; Porreca, F.; Yamamura, H. I.; Hruby, V. J. J Med Chem 1998, 41, 4767.
61. Liu, D. X.; Tang, Y.; Jiang, H. L.; Chen, K. X.; Ji, R. Y. Zhongguo Yao Li Xue Bao 1998, 19, 445.
62. Shenderovich, M. D.; Liao, S.; Qian, X.; Hruby, V. J. Biopolymers 2000, 53, 565.
63. Munro, T. A.; Rizzacasa, M. A.; Roth, B. L.; Toth, B. A.; Yan, F. J Med Chem 2005, 48, 345.
64. Wu, Y. C.; Hsieh, J. Y.; Lin, H. C.; Hwang, C. C. J Mol Model 2006, 13, 171.
65. Pearce, H. L.; Safa, A. R.; Bach, N. J.; Winter, M. A.; Cirtain, M. C.; Beck, W. T. Proc Natl Acad Sci USA 1989, 86, 5128.
66. Pearce, H. L.; Winter, M. A.; Beck, W. T. Adv Enzyme Regul 1990, 30, 357.
67. Lovekamp, T.; Cooper, P. S.; Hardison, J.; Bryant, S. D.; Guerrini, R.; Balboni, G.; Salvadori, S.; Lazarus, L. H. Brain Res 2001, 902, 131.
68. Varma, S.; Hou, Z.Available at: http://www.accelrys.com/reference/ cases/studies/pharmacophore-patterns.html, accessed May 3, 2007.
69. Garrigues, A.; Loiseau, N.; Delaforge, M.; Ferte, J.; Garrigos, M.; Andre, F.; Orlowski, S. Mol Pharmacol 62, 1288.
70. Pajeva, I. K.; Globisch, C.; Wiese, M. J Med Chem 2004, 47, 2523.
71. Xue, Y.; Yap, C. W.; Sun, L. Z.; Cao, Z. W.; Wang, J. F.; Chen, Y. Z. J Chem Inf Comput Sci 2004, 44, 1497.
72. Cianchetta, G. R.; Singleton, W.; Zhang, M.; Wildgoose, M.; Giesing, D.; Fravolini, A.; Cruciani, G.; Vaz, R. J. J Med Chem 2005, 48, 2927.
73. Kubinyi, H. In Handbook of Cheminformatics; J.Gasteiger, Ed.; Wiley-VCH: Weinheim, 2003.
74. Pandit, D.; So, S.-S.; Sun, H. J Chem Inf Model 2006, 46, 1236.
75. Meagher, K. L.; Lerner, M. G.; Carlson, H. A. J Med Chem 2006, 49, 3478.
76. Nicklaus, M. C.; Neamati, N.; Hong, H.; Mazumder, A.; Sunder, S.; Chen, J.; Milne, G. W.; Pommier, Y. J Med Chem 1997, 40, 920.
77. Mustata, G. I.; Brigo, A.; Briggs, J. M. Bioorg Med Chem Lett 2004, 14, 1447.
78. Brigo, A.; Mustata, G. I.; Briggs, J. M.; Moro, S. Med Chem 2005, 1, 263.
79. Barreca, M. L.; Ferro, S.; Rao, A.; De Luca, L.; Zappala, M.; Monforte, A.-M.; Debyser, Z.; Witvrouw, M.; Chimirri, A. J Med Chem 2005, 48, 7084.
80. Deng, J.; Lee, K. W.; Sanchez, T.; Cui, M.; Neamati, N.; Briggs, J. M. J Med Chem 2005, 48, 1496.
81. Penzotti, J. E.; Lamb, M. L.; Evensen, E.; Grootenhuis, P. D. J. J Med Chem 2002, 45, 1737.
82. Wang, S.; Sakamuri, S.; Enyedy, I. J.; Kozikowski, A. P.; Deschaux, O.; Bandyopadhyay, B. C.; Telia, S. R.; Zaman, W. A.; Johnson, K. M. J Med Chem 2000, 43, 351.
83. Zhu, F.; Agrafiotis, D. K. J Comput Chem 2007, 28, 1234.
84. Agrafiotis, D. K.; Gibbs, A.; Zhu, F.; Izrailev, S.; Martin, E. J Chem Inf Model 2007, 47, 1067.