Computation of the physio-chemical properties and data mining of large molecular collections

Journal of Computational Chemistry

Volumn 23, Issue 1, 2002, Pages 172-183

  Cheng, Ailan ^a   Diller, David J ^a   Dixon, Steven L ^a   Egan, William J ^a   Lauri, George ^a   Merz, Kenneth M ^a  

^a PHARMACOPEIA INC   (United States)

Author keywords

Data mining; Large molecular collections; Physico chemical properties

Indexed keywords

AMINO ACID; STATINE;

ALGORITHM; ARTICLE; BINDING SITE; BIOLOGY; BLOOD BRAIN BARRIER; CHEMICAL STRUCTURE; CHEMISTRY; COMBINATORIAL CHEMISTRY; CONFORMATION; DRUG DESIGN; DRUG INDUSTRY; METHODOLOGY; PHARMACOKINETICS; PHYSIOLOGY;

ALGORITHMS; AMINO ACIDS; BINDING SITES; BLOOD-BRAIN BARRIER; COMBINATORIAL CHEMISTRY TECHNIQUES; COMPUTATIONAL BIOLOGY; DRUG DESIGN; DRUG INDUSTRY; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; PHARMACOKINETICS;

EID: 0037079584     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.1164     Document Type: Article

References (82)

1. 1 TRIPOS, Inc., 1699 S. Hanley Road, St. Louis, MO 63144.
2. 2 Livingstone, D. J. J Chem Inf Comput Sci 2000, 40, 195.
3. 3 Grover, M. M. ; Singh, B. B. ; Bakshi, M. M. ; Singh, S. S. Pharm Sci Technol Today 2000, 3, 50.
4. 4 Grover, M. M. ; Singh, B. B. ; Bakshi, M. M. ; Singh, S. S. Pharm Sci Technol Today 2000, 3, 28.
5. 5 Brown, R. D. ; Martin, Y. C. J Chem Inf Comput Sci 1996, 36, 572.
6. 6 Downs, G. M. ; Willett, P. Rev Comput Chem 1996, 7, 1.
7. 7 Willett, P. ; Barnard, J. M. ; Downs, G. M. J Chem Inf Comput Sci 1998, 38, 983.
8. 8 Guner, O. F. Pharmacophore Perception, Development and Use in Drug Design ; International University Line: La Jolla, CA, 1999 ; p. 537.
9. 9 Bohm, H.‐J. J Comput‐Aided Mol Design 1992, 6, 593.
10. 10 Frenkel, D. ; Clark, D. E. ; Li, J. ; Murray, C. W. ; Robson, B. ; Waszkowycz, B. ; Westhead, D. R. J Comput‐Aided Mol Design 1995, 9, 213.
11. 11 Moon, J. B. ; Howe, W. J. Proteins Struct Funct Genet 1991, 11, 314.
12. 12 Diller, D. J. ; Verlinde, C. L. M. J Comput Chem 1999, 20, 1740.
13. 13 Goodsell, D. S. ; Olson, A. J. Proteins Struct Funct Genet 1990, 8, 195.
14. 14 Jones, G. ; Willett, P. ; Glen, R. C. ; Leach, A. R. ; Taylor, R. J Mol Biol 1997, 267, 727.
15. 15 Kramer, B. ; Rarey, M. ; Lengauer, T. Proteins Struct Funct Genet 1999, 37, 228.
16. 16 Kuntz, I. D. ; Blaney, J. M. ; Oatley, S. J. ; Langridge, R. ; Ferrin, T. E. J Mol Biol 1982, 161, 269.
17. 17 Kuntz, I. D. Science 1992, 257, 1078.
18. 18 Rutenber, E. ; Fauman, E. B. ; Keenan, R. J. ; Fong, S. ; Furth, P. S. ; de Montellano, P. R. ; Oritz Meng, E. ; Kuntz, I. D. ; DeCamp, D. L. J Biol Chem 1993, 268, 15343.
19. 19 Nicklaus, M. C. ; Neamati, N. ; Hong, H. ; Mazumder, A. ; Sunder, S. ; Chen, J. ; Milne, G. W. A. ; Pommier, Y. J Med Chem 1997, 40, 920.
20. 20 Ohlmeyer, M. H. J. ; Swanson, R. N. ; Dillard, L. ; Reader, J. C. ; Asouline, G. ; Kobayashi, R. ; Wigler, M. ; Still, W. C. Proc Natl Acad Sci USA 1993, 90, 10922.
21. 21 DiMasi, J. A. Clin Pharmacol Ther 1995, 58, 1.
22. 22 Arlington, S. Pharm Exec 2000, 74.
23. 23 Caldwell, J. ; Gardner, I. ; Swales, N. Toxicol Pathol 1995, 23, 102.
24. 24 Rodrigues, A. D. Pharm Res 1997, 14, 1504.
25. 25 Smith, D. A. ; de Waterbeemd, H. Curr Opin Chem Biol 1999, 3, 373.
26. 26 Tarbit, M. H. ; Berman, J. Curr Opin Chem Biol 1998, 2, 411.
27. 27 Caldwell, G. W. Curr Opin Drug Disc Dev 2000, 30.
28. 28 Sinko, P. J. Curr Opin Drug Disc Dev 1999, 2, 42.
29. 29 Walters, W. P. ; Stahl, M. T. ; Murcko, M. A. Drug Disc Today 1998, 3, 160.
30. 30 Walters, W. P. ; Ajay ; Murcko, M. A. Curr Opin Chem Biol 1999, 3, 384.
31. 31 Lipper, R. A. Modern Drug Disc 1999, 2, 55.
32. 32 Bohacek, R. S. M. ; Guida, W. C. C. Med Res Rev 1996, 16, 3.
33. 33 Diller, D. J. ; Merz, K. M., Jr. Proteins, to appear.
34. 34 Smellie, A. ; Kahn, S. D. ; Teig, S. L. J Chem Inf Comput Sci 1995, 35, 295.
35. 35 Smellie, A. ; Kahn, S. D. ; Teig, S. L. J Chem Inf Comput Sci 1995, 35, 285.
36. 36 Smellie, A. ; Teig, S. L. ; Towbin, P. J Comput Chem 1995, 16, 171.
37. 37 Catalyst v4.5.; Molecular Simulations, Inc.: San Diego, CA.
38. 38 Carroll, C. D. ; Johnson, T. O. ; Tao, S. ; Lauri, G. ; Orlowski, M. ; Gluzman, I. Y. ; Goldberg, D. E. ; Dolle, R. E. Bioorg Med Chem Lett 1998, 8, 3203.
39. 39 Carroll, C. D. ; Patel, H. ; Johnson, T. O. ; Guo, T. ; Orlowski, M. ; He, Z.‐M. ; Cavallaro, C. L. ; Guo, J. ; Oksman, A. ; Gluzman, I. Y. ; Connelly, J. ; Chelsky, D. ; Goldberg, D. E. ; Dolle, R. E. Bioorg Med Chem Lett 1998, 8, 2315.
40. 40 Bernstein, N. K. ; Cherney, M. M. ; Loetscher, H. ; Ridley, R. G. ; James, M. N. G. Nat Struct Biol 1999, 6, 32.
41. 41 Baldwin, E. T. ; Bhat, T. N. ; Gulnik, S. ; Hosur, M. V. ; Sowder, R. C. ; Cachau, R. E. ; Collins, J. ; Silva, A. M. ; Erickson, J. W. Proc Natl Acad Sci USA 1993, 90, 6796.
42. 42 Leung, D. ; Abbenante, G. ; Fairlie, D. P. J Med Chem 2000, 43, 305.
43. 43 Van Drie, J. H. ; Weininger, D. ; Martin, Y. C. J Comput‐Aided Mol Design 1989, 3, 225.
44. 44 Guner, O. F. ; Henry, D. R. ; Pearlman, R. S. J Chem Inf Comput Sci 1992, 32, 101.
45. 45 Clark, D. E. ; Jones, G. ; Willett, P. ; Kenny, P. W. ; Glen, R. C. J Chem Inf Comput Sci 1994, 34, 197.
46. 46 Greene, J. ; Kahn, S. ; Savoj, H. ; Sprague, P. ; Teig, S. J Chem Inf Comput Sci 1994, 34, 1297.
47. 47 Carbo, R. ; Leyda, L. ; Arnau, M. Int J Quantum Chem 1980, 17, 1185.
48. 48 Meyer, A. Y. ; Richards, W. G. J Comput‐Aided Mol Design 1991, 5, 427.
49. 49 Klebe, G. ; Abraham, U. ; Mietzner, T. J Med Chem 1994, 37, 4130.
50. 50 Cramer, R. D. ; Clark, R. D. ; Patterson, D. E. ; Ferguson, A. M. J Med Chem 1996, 39, 3060.
51. 51 Jain, A. N. J Comput‐Aided Mol Design 2000, 14, 199.
52. 52 Matter, H. J Med Chem 1997, 40, 1219.
53. 53 Shah, A. V. ; Walters, W. P. ; Murcko, M. A. J Med Chem 1998, 41, 3314.
54. 54 Hunt, P. A. J Comput‐Aided Mol Design 1999, 13, 453.
55. 55 Dixon, S. L. ; Villar, H. O. J Comput‐Aided Mol Design 1999, 13, 533.
56. 56 Rarey, M. ; Dixon, J. S. J Comput‐Aided Mol Design 1998, 12, 471.
57. 57 Moreau, G. ; Broto, P. Nouv J Chim 1980, 4, 757.
58. 58 Wagener, M. ; Sadowski, J. ; Gasteiger, J. J Am Chem Soc 1995, 117, 7769.
59. 59 Daylight Chemical Information Systems, Inc., 27401 Los Altos, Suite 370, Mission Veijo, CA 92691.
60. 60 Weininger, D. J Chem Inf Comput Sci 1988, 28, 31.
61. 61 Needleman, S. B. ; Wunsch, C. D. J Mol Biol 1970, 48, 443.
62. 62 Borg, I. ; Groenen, P. Modern Multidimensional Scaling ; Springer‐Verlag: New York, 1997.
63. 63 Dixon, S. L. ; Merz, K. M., Jr. J Med Chem, to be submitted.
64. 64 Unless otherwise noted, 3D models were generated using the default energy minimizer from the Catalyst Program.
65. 65 Cerius2 4.0 ; Molecular Simulations, Inc., 9685 Scranton Road, San Diego, CA 92121.
66. 66 Structures and activity data were obtained directly from the Gasteiger website publication: Dataset of 31 Steroids Binding to the Corticosteroid Binding Globulin (CBG) Receptor ; http://www2.ccc.uni‐erlangen.de/services/steroids/. 1D representations were generated for heavy atoms only using the provided 3D coordinates with no further modeling.
67. 67 Coats, E. A. The CoMFA Steroids as a Benchmark Dataset for the Development of 3D QSAR Methods ; Kubinyi, H. ; Folkers, G. ; Martin, Y., Eds.; Kluwer/ESCOM: 1998 ; p. 199, vol. 3.
68. 68 ISIS/Base CMC‐3D 1999.1 ; MDL Information Systems, Inc., 14600 Catalina Street, San Leandro, CA 94577.
69. 69 Egan, W. J. ; Merz, K. M., Jr. ; Baldwin, J. J. J Med Chem 2000, 43, 3867.
70. 70 Ghose, A. K. ; Viswanadhan, V. N. ; Wendoloski, J. J. J Phys Chem A 1998, 102, 3762.
71. 71 Clark, D. E. J Pharm Sci 1999, 88, 807.
72. 72 Egan, W. J. ; Morgan, S. L. Anal Chem 1998, 70, 2372.
73. 73 Lipinski, C. A. ; Lombardo, F. ; Dominy, B. W. ; Feeney, P. J. Adv Drug Deliv Rev 1997, 23, 3.
74. 74 Pardridge, W. M. J Neurochem 1998, 70, 1781.
75. 75 Abraham, M. H. ; Chadha, H. S. ; Mitchell, R. C. J Pharm Sci 1994, 83, 1257.
76. 76 Norinder, U. ; Sjoberg, P. ; Osterberg, T. J Pharm Sci 1998, 87, 952.
77. 77 Luco, J. M. J Chem Inf Comput Sci 1999, 39, 396.
78. 78 Clark, D. E. J Pharm Sci 1999, 88, 815.
79. 79 Rousseeuw, P. J. ; Leroy, A. M. Robust Regression and Outlier Detection ; John Wiley & Sons: New York, 1987.
80. 80 Hall, L. H. ; Kier, L. B. J Chem Inf Comput Sci 1995, 35, 1039.
81. 81 Ertl, P. ; Rohde, B. ; Selzer, P. J Med Chem 2000, 43, 3714.
82. 82 Labute, P. J Mol Graphics Modell 2000, 18, 464.