Library design: Reactant and product-based approaches

Comprehensive Medicinal Chemistry II

Volumn 4, Issue , 2006, Pages 337-377

  Pickett, S D ^a  

^a GLAXOSMITHKLINE   (United Kingdom)

Author keywords

[No Author keywords available]

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EID: 58149123334     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (313)

1. Merrifield, R. B. J. Am. Chem. Soc. 1963, 85, 2149-2154.
2. Geysen, H. M.; Meloen, R. H.; Barreling, S. J. Proc. Natl. Acad. Sci. USA 1984, 81, 3998-4002.
3. Houghten, R. A. Proc. Natl. Acad. Sci. USA 1985, 82, 5131-5135.
4. Lam, K. S.; Salmon, S. E.; Hersh, E. M.; Hruby, V. J.; Kazmierski, W M.; Knap, R. J. Nature 1991,, 82-84.
5. Bunin, B. A.; Ellman, J. A. J. Am. Chem. Soc 1992, 114, 10997-10998.
6. Simon, R. J.; Kaina, R. S.; Zuckermann, R. N.; Huebner, V. D.; Jewell, D. A.; Banville, S.; Ng, S.; Wang, L.; Rosenberg, S.; Marlowe, C. K. et al. Proc. Natl. Acad. Sci. USA 1992, 89, 9367-9371.
7. DeWitt, S. H.; Kiely, J. S.; Stankovic, C. J.; Schroeder, M. C.; Cody, D. M. R.; Pavia, M. R. Proc. Natl. Acad. Sci. USA 1993, 90, 6909-6913.
8. Ugi, I.; Steinbruckner, C. Chem. Ber. 1961, 94, 734.
9. Dolle, R. E. Mol. Divers. 1997, 3, 199-233.
10. Dolle, R. E. Mol. Divers. 1998, 4, 233-256.
11. Dolle, R. E.; Nelson, K. H., Jr. J. Comb. Chem. 1999, 1, 235-282.
12. Dolle, R. E. J. Comb. Chem. 2000, 2, 383-433.
13. Dolle, R. E. J. Comb. Chem. 2001, 3, 477-517.
14. Dolle, R. E. J. Comb. Chem. 2002, 4, 369-418.
15. Dolle, R. E. J. Comb. Chem. 2003, 5, 693-753.
16. Dolle, R. E. J. Comb. Chem. 2004, 6, 623-679.
17. Wolcke, J.; Ullmann, D. Drug Disc. Today 2001, 6, 637-646.
18. Willoughby, C. A.; Hutchins, S. M.; Rosauer, K. G.; Dhar, M. J.; Chapman, K. T; Chicchi, G. G.; Sadowski, S.; Weinberg, D. H.; Patel, S.; Malkowitz, L. et al. Bioorg. Med. Chem. Lett. 2002, 12, 93-96.
19. Lee, A.; Breitenbucher, J. G. Curr. Opin. Drug. Disc. Dev. 2003, 6, 494-508.
20. Lipinski, C. A.; Lombardo, F; Dominy, B. W; Feeney, P. J. Adv. Drug Deliv. Rev. 1997, 23, 3-25.
21. Agrafiotis, D. K.; Myslik, J. C.; Salemme, F R. Mol. Divers. 1999, 4, 1-22.
22. Blaney, J. M.; Martin, E. J. Curr. Opin. Chem. Biol. 1997, 1, 54-59.
23. Bures, M. G.; Martin, Y C. Curr. Opin. Chem. Biol. 1998, 2, 376-380.
24. Green, D. V S.; Pickett, S. D. Mini-Rev. Med. Chem. 2004, 4, 1067-1076.
25. Laird, E. R.; Blake, J. F Curr. Opin. Drug. Disc. Dev. 2004, 7, 354-359.
26. Lewis, R. A.; Pickett, S. D.; Clark, D. E. Computer-Aided Molecular Diversity Analysis and Combinatorial Library Design. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; John Wiley: New York, 2000; Vol. 16, pp 1-51.
27. Mason, J. S.; Pickett, S. D. Combinatorial Library Design, Molecular Similarity and Diversity Applications. In Burger's Medicinal Chemistry and Drug Discovery; Abraham, D. J., Ed.; John Wiley: New York, 2003; Vol. 1.
28. Matter, H.; Baringhaus, K.-H.; Naumann, T.; Klabunde, T; Pirard, B. Comb. Chem. HTS 2001, 4, 453-475.
29. Young, S. S.; Ge, N. Curr. Opin. Drug. Disc. Dev. 2004, 7, 318-324.
30. Chanda, S. K.; Caldwell, J. S. Drug Disc. Today 2003, 8, 168-174.
31. Drews, J. Science 2000, 287, 1960-1964.
32. Drews, J. Drug Disc. Today 2003, 8, 411-420.
33. Handen, J. S. Drug Disc. Today 2002, 7, 83-85.
34. Sams-Dodd, F Drug Disc. Today 2005, 10, 139-147.
35. Muller, K. J. Mol. Struct. (Theochem.) 1997, 398-399, 467-471.
36. Salemme, F R.; Spurlino, J.; Bone, R. Structure 1997, 5, 319-324.
37. Valler, M. J.; Green, D. V S. Drug Disc. Today 2000, 5, 286-293.
38. Schneider, G. Curr. Med. Chem. 2002, 9, 2095-2101.
39. Ghose, A. K.; Viswanadhan, V N.; Wendoloski, J. J. Recept. Signal Transduct. Res. 2001, 21, 357-375.
40. Harper, G.; Bradshaw, J.; Gittins, J. C.; Green, D. V S.; Leach, A. R. J. Chem. Inf. Comput. Sci. 2001, 41, 1295-1300.
41. Shen, J. J. Chem. Inf. Comput. Sci. 2003, 43, 1668-1672.
42. Diller, D. J.; Hobbs, D. W. J. Med. Chem. 2004, 47, 6373-6383.
43. Engels, M. F; Wouters, L.; Verbeeck, R.; Vanhoof, G. J. Biomol. Screen. 2002, 7, 341-351.
44. Harper, G.; Bravi, G. S.; Pickett, S. D.; Hussain, J.; Green, D. V S. J. Chem. Inf. Comput. Sci. 2004, 44, 2145-2156.
45. Kubinyi, H. Curr. Opin. Drug Disc. Dev. 1998, 1, 16-27.
46. McKenna, J. M.; Halley, F; Souness, J.; McLay, I. M.; Pickett, S. D.; Page, K.; Ahmed, I. J. Med. Chem. 2002, 45, 2173-2184.
47. Cowell, S. M.; Gu, X.; Vagner, J.; Hruby, V J. Methods Enzymol. 2003, 369, 288-297.
48. Senderowitz, H.; Rosenfeld, R. J. Recept. Signal Transduct. Res. 2001, 21, 489-506.
49. Wise, A.; Jupe, S. C.; Rees, S. Annu. Rev. Pharmacol. Toxicol. 2004, 44, 43-66.
50. Civelli, O. Trends Pharmacol. Sci. 2005, 26, 15-19.
51. Nilakantan, R.; Nunn, D. S. Drug Disc. Today 2003, 8, 668-672.
52. Harper, G.; Pickett, S. D.; Green, D. V S. Comb. Chem. HTS 2004, 7, 63-70.
53. Frye, S. V Chem. Biol. 1999, 6, R3-R7.
54. Jacoby, E.; Schuffenhauer, A.; Acklin, P. The Contribution of Molecular Informatics to Chemogenomics: Knowledge-Based Discovery of Biological Targets and Chemical Lead Compounds. In Chemogenomics in Drug Discovery: A Medicinal Chemistry Perspective; Kubinyi, H., Muller, G., Eds.; Methods and Principles in Medicinal Chemistry; Mannhold, R., Kubinyi, H., Folkers, G., Eds.; Wiley-VCH: Weinheim, Germany, 2004; Vol. 22, pp 139-166.
55. Schnur, D.; Beno, B. R.; Good, A. C.; Tebben, A. Approaches to Target Class Combinatorial Library Design. In Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery; Bajorath, J., Ed.; Methods in Molecular Biology; Humana Press: Totowa, NJ, 2004; Vol. 275, pp 379-398.
56. Lowrie, J. F; DeLisle, R. K.; Hobbs, D. W; Diller, D. J. Comb. Chem. HTS 2004, 7, 495-510.
57. Crossley, R. Curr. Top. Med. Chem. 2004, 4, 581-589.
58. Prien, O. ChemBioChem 2005, 6, 500-505.
59. Klabunde, T; Hessler, G. ChemBioChem 2002, 3, 929-944.
60. Manning, G.; Whyte, D. B.; Martinez, R.; Hunter, T; Sundarsanam, S. Science 2002, 298, 1912-1934.
61. Beavers, M. P.; Chen, X. J. Mol Graph. Model 2002, 20, 463-468.
62. Clark, D. E.; Pickett, S. D. Drug Disc. Today 2000, 5, 49-58.
63. Davis, A. M.; Riley, R. J. Curr. Opin. Chem. Biol. 2004, 8, 378-386.
64. Lepre, C. A. Strategies for NMR Screening and Library Design. In BioNMR in Drug Research; Zerbe, O., Ed.; Methods and Principles in Medicinal Chemistry; Mannhold, R., Kubinyi, H., Folkers, G., Eds.; Wiley-VCH: Weinheim, Germany, 2003; Vol. 16, pp. 391-415.
65. Hartshorn, M. J.; Murray, C. W; Cleasby, A.; Frederickson, M.; Tickle, I. J.; Jhoti, H. J. Med. Chem. 2005, 48, 403-413.
66. Parlow, J. J.; Case, B. L.; Dice, T. A.; Fenton, R. L.; Hayes, M. J.; Jones, D. E.; Neumann, W L.; Wood, R. S.; Lachance, R. M.; Girard, T J. et al. J. Med. Chem. 2003, 46, 4050-4062.
67. Han, Q.; Dominguez, C.; Stouten, P F W; Park, J. M.; Duffy, D. E.; Galemmo, R. A.; Rossi, K. A.; Alexander, R. S.; Smallwood, A. M.; Wong, P. C. et al. J. Med. Chem. 2000, 43, 4389-4415.
68. Pickett, S. D.; Luttmann, C.; Guerin, V; Laoui, A.; James, E. J. Chem. Inf Comput. Sci. 1998, 38, 144-150.
69. Available Chemicals Directory. MDL Information Systems, Inc.: San Leandro, CA.
70. Leach, A. R.; Green, D. V S.; Hann, M. M.; Judd, D. B.; Good, A. C. J. Chem. Inf. Comput. Sci. 2000, 40, 1262-1269.
71. Hann, M. M.; Hudson, B. D.; Lewell, X. Q.; Lifely, R.; Miller, L.; Ramsden, N. J. Chem. Inf Comput. Sci 1999, 39, 897-902.
72. Leach, A. R.; Bradshaw, J.; Green, D. V S.; Hann, M. M.; Delany, J. J. J. Chem. Inf. Comput. Sci. 1999, 39, 1161-1172.
73. James, C. A.; Weininger, D.; Delaney, J. Daylight Theory Manual, Daylight Chemical Information Systems. http://www.daylight.com/dayhtml/doc/theory/theory.toc.html, 2005 (accessed April 2006).
74. Downs, G. M.; Barnard, J. M. J. Chem. Inf Comput. Sci. 1997, 37, 59-61.
75. Taylor, R. J. Chem. Inf. Comput. Sci. 1995, 35, 59-67.
76. Gillet, V J.; Khatib, W; Willett, P; Fleming, P. J.; Green, D. V S. J. Chem. Inf. Comput. Sci 2002, 42, 375-385.
77. Martin, E. J.; Blaney, J. M.; Siani, M. A.; Spellmeyer, D. C.; Wong, A. K.; Moos, W H. J. Med. Chem. 1995, 38, 1431-1436.
78. Jackson, J. E. A User's Guide to Principal Components; John Wiley: New York, 1991.
79. Leo, A. J. Chem. Rev. 1993, 93, 1281-1306.
80. CLOGP. Daylight Chemical Information Systems Inc., 120 Vantis-Suite 550, Aliso Viejo, CA 92656.
81. Hall, L. H.; Kier, L. B. The Molecular Connectivity Chi Indexes and Kappa Shape Indexes in Structure-Property Modelling. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH: NewYork, 1991; Vol. 2, pp 367-421
82. Hall, L. H.; Kier, L. B. J. Mol Graph. Model 2001, 20, 4-18.
83. Randić, M. J. Mol. Graph. Model 2001, 20, 19-35.
84. Hall Associates Consulting. MOLCONN-Z. eduSoft L.C. 2 Davis Street, Quincy, MA.
85. Agrafiotis, D. K. J. Chem. Inf. Comput. Sci. 1997, 37, 576-580.
86. Zuckermann, R. N.; Martin, E. J.; Spellmeyer, D. C.; Stauber, G. B.; Shoemaker, K. R.; Kerr, J. M.; Figliozzi, G. M.; Siani, M. A.; Simon, R. J.; Banville, S. C. J. Med. Chem. 1994, 37, 2678-2685.
87. Martin, E. J.; Wong, A. K. J. Chem. Inf. Comput. Sci. 2000, 40, 215-220.
88. Martin, E. J.; Critchlow, R. E. J. Comb. Chem. 1999, 1, 32-45.
89. Miller, A.; Nguyen, N.-K. Appl. Stat. 1994, 43, 669-678.
90. Pickett, S. D.; Mason, J. S.; McLay, I. M. J. Chem. Inf. Comput. Sci. 1996, 36, 1214-1223.
91. Mason, J. S.; Morize, I.; Menard, P. R.; Cheney, D. L.; Hulme, C.; Labaudiniere, R. F J. Med. Chem. 1999, 42, 3251-3264.
92. McGregor, M. J.; Muskal, S. M. J. Chem. Inf. Comput. Sci. 1999, 39, 569-574.
93. Pickett, S. D. The Biophore Concept. In Protein-Ligand Interactions: From Molecular Recognition to Drug Design; Bohm, H. J., Schneider, G., Eds.; Methods and Principles in Medicinal Chemistry; Mannhold, R., Kubinyi, H., Folkers, G., Eds.; John Wiley: New York, 2003; Vol. 19, pp 73-105.
94. Beno, B. R.; Mason, J. S. Drug Disc. Today 2001, 6, 251-258.
95. Eksterowicz, J. E.; Evensen, E.; Lemmen, C.; Brady, G. P.; Lanctot, J. K.; Bradley, E. K.; Saiah, E.; Robinson, L. A.; Grootenhuis, P. D. J. et al. J. Mol. Graphics Model 2002, 20, 469-477.
96. McGregor, M. J.; Muskal, S. M. J. Chem. Inf. Comput. Sci. 2000, 40, 117-125.
97. Martin, E. J.; Hoeffel, T J. J. Mol. Graph. Model. 2000, 18, 383-403.
98. Good, A. C.; Lewis, R. A. J. Med. Chem. 1997, 40, 3926-3936.
99. Cramer, R. D.; Clark, R. D.; Patterson, D. E.; Ferguson, A. M. J. Med. Chem. 1996, 39, 3060-3069.
100. Cramer, R. D.; Patterson, D. E.; Clark, R. D.; Soltanshahi, F; Lawless, M. S. J. Chem. Inf. Comput. Sci. 1998, 6, 1010-1023.
101. Cramer, R. D.; Poss, M. A.; Hermsmeier, M. A.; Caulfield, T J.; Kowala, M. C.; Valentine, M. T J. Med. Chem. 1999, 42, 3919-3933.
102. Andrews, K. M.; Cramer, R. D. J. Med. Chem. 2000, 43, 1723-1740.
103. Jilek, R. J.; Cramer, R. D. J. Chem. Inf. Comput. Sci. 2004, 44, 1221-1227.
104. Cramer, R. D.; Jilek, R. J.; Guessregen, S.; Clark, S. J.; Wendt, B.; Clark, R. D. J. Med. Chem. 2004, 47, 6777-6791.
105. Pearlman, R. S. Chem. Design Autom. News 1987, 2, 1.
106. Rusinko, A., III; Skell, J. M.; Balducci, R.; McGarity, C. M.; Pearlman, R. S. CONCORD. Program available from Tripos, Inc., St. Louis, MO.
107. ChemSpace is a licensed Trademark of Tripos, Inc., St. Louis, MO.
108. Leach, A. R. J. Mol. Graph. Model. 1997, 15, 158-160.
109. Fontaine, F; Pastor, M.; Zamora, I.; Sanz, F J. Med. Chem. 2005, 48, 2687-2694.
110. Pastor, M.; Cruciani, G.; McLay, I. M.; Pickett, S. D.; Clementi, S. J. Med. Chem. 2000, 43, 3233-3243.
111. Cramer, R. D.; Patterson, D. E.; Bunce, J. D. J. Am. Chem. Soc. 1988, 110, 5959-5967.
112. Goodford, P. J. J. Med. Chem. 1985, 28, 849-857.
113. Cruciani, G.; Fontaine, F; Pastor, M. ALMOND. Molecular Discovery Ltd, Perugia, Italy.
114. Clark, D. E. Evolutionary Algorithms in Molecular Design; Methods and Principles in Medicinal Chemistry; Mannhold, R., Kubinyi, H., Timmerman, H., Eds.; Wiley-VCH: Weinheim, Germany, 2000; Vol. 8.
115. Goldberg, D. E. Genetic Algorithms in Search, Optimization, and Machine Learning; Addison-Wesley: Reading, MA, 1989.
116. Kirkpatrick, S. Science 1983, 220, 671-690.
117. Van Laarhoven, P. J. M.; Aarts, E. H. L. Simulated Annealing: Theory and Applications; Reidel: Dordrecht, Netherlands, 1987.
118. Allen, M. P; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: New York, 1987.
119. Leach, A. R. A Survey of Methods for Searching the Conformational Space of Small and Medium-Sized Molecules. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH: New York, 1991; Vol. 2, pp 1-55.
120. Sheridan, R. P.; Kearsley, S. K. J. Chem. Inf. Comput. Sci. 1995, 35, 310-320.
121. Sheridan, R. P.; SanFeliciano, S. G.; Kearsley, S. K. J. Mol. Graph. Model. 2000, 18, 320-324.
122. Miller, M. D.; Sheridan, R. P; Kearsley, S. K. J. Med. Chem. 1999, 42, 1505-1514.
123. Miller, M. D.; Kearsley, S. K.; Underwood, D. J.; Sheridan, R. P. J. Comput. Aided Mol. Design 1994, 8, 153-174.
124. Lewis, R. A.; Good, A. C.; Pickett, S. D. Quantification of Molecular Similarity and Its Application to Combinatorial Chemistry. In Computer-Assisted Lead Finding and Optimization: Current Tools for Medicinal Chemistry; van de Waterbeemd, H., Testa, B., Folkers, G., Eds.; Wiley-VCH: New York, 1997, pp 135-156.
125. Janda, K. D. Proc. Natl. Acad. Sci. USA 1994, 91, 10779-10785.
126. Choong, I. C. Annu. Rep. Med. Chem. 1996, 31, 309-318.
127. Loo, J. A. Annu. Rep. Med. Chem. 1996, 31, 319-325.
128. Brown, R. D.; Martin, Y. C. J. Med. Chem. 1997, 40, 2304-2313.
129. Gillet, V J.; Willett, P.; Bradshaw, J.; Green, D. V S. J. Chem. Inf. Comput. Sci. 1999, 39, 169-177.
130. World Drug Index. Thomson Scientific: London, 2006.
131. Holliday, J. D.; Ranade, S. S.; Willett, P. Quant. Struct.-Act. Relat. 1995, 14, 501-506.
132. Snarey, M.; Terrett, N. K.; Willett, P.; Wilton, D. J. J. Mol. Graphics Model. 1997, 15, 372-385.
133. Beasley, D.; Bull, D. R.; Martin, R. R. Evol. Comput. 1993, 1, 101-125.
134. Agrafiotis, D. K. J. Comput. Aided Mol. Des. 2002, 16, 335-356.
135. Agrafiotis, D. K. Protein Sci. 1997, 6, 287-293.
136. Agrafiotis, D. K.; Lobanov, V S. J. Chem. Inf. Comput. Sci. 2000, 40, 1356-1362.
137. Rassokhin, D. N.; Lobanov, V. S.; Agrafiotis, D. K. J. Comput. Chem. 2000, 22, 373-386.
138. Agrafiotis, D. K.; Lobanov, V S. J. Chem. Inf. Comput. Sci. 1999, 39, 51-58.
139. Rassokhin, D. N.; Agrafiotis, D. K. J. Mol. Graph. Model. 2000, 18, 370-384.
140. Brown, R. D.; Hassan, M.; Waldman, M. J. Mol. Graph. Model. 2000, 18, 427-437.
141. Mason, J. S.; Beno, B. R. J. Mol. Graph. Model. 2000, 18, 438-451.
142. Chen, G.; Zheng, S.; Luo, X.; Shen, J.; Zhu, W; Liu, H.; Gui, C.; Zhang, J.; Zheng, M.; Puah, C. M. et al. J. Comb. Chem. 2005, 7, 398-406.
143. Zheng, W; Cho, S. J.; Waller, C. L.; Tropsha, A. J. Chem. Inf. Comput. Sci. 1999, 39, 738-746.
144. Jamois, E. A.; Lin, C. T.; Waldman, M. J. Mol. Graph. Model. 2003, 22, 141-149.
145. Agrafiotis, D. K.; Lobanov, V S. J. Chem. Inf. Comput. Sci. 2000, 40, 1030-1038.
146. Bravi, G.; Green, D. V S.; Hann, M. M.; Leach, A. R. J. Chem. Inf. Comput. Sci. 2000, 40, 1441-1448.
147. Zheng, W; Cho, S. J.; Tropsha, A. J. Chem. Inf. Comput. Sci. 1998, 38, 251-258.
148. Young, S. S.; Wang, M.; Gu, F. J. Chem. Inf. Comput. Sci. 2003, 43, 1916-1921.
149. Lam, R. L.; Welch, W J.; Young, S. S. Technometrics 2002, 44, 99-109.
150. Le Bailly de Tilleghen, C.; Beck, B.; Boulanger, B.; Govaerts, G. J. Chem. Inf. Model. 2005, 45, 758-767.
151. Zheng, W; Hung, S. T.; Saunders, J. T; Seibel, G. L. Proc. Pacific Symp. BioComput. 2000, 5, 588-599.
152. Teig, S. L. J. Biomol. Screen. 1998, 3, 85-88.
153. Shannon, C. E. Bell System Tech. J. 1948, 27, 379-423.
154. Shannon, C. E. Bell System Tech. J. 1948, 27, 623-656.
155. Miller, J. L.; Bradley, E. K.; Teig, S. L. J. Chem. Inf. Comput. Sci. 2003, 43, 47-54.
156. Everett, J.; Gardner, M.; Pullen, F; Smith, G. F; Snarey, M.; Terrett, N. Drug Disc. Today 2001, 6, 779-785.
157. Lipkin, M. J.; Rose, V S.; Wood, J. SAR QSAR Environ. Res. 2002, 13, 425-432.
158. Wood, J.; Rose, V. S. Method of designing chemical substances 99/26901. PCT Int. Appl. (1999), WO1999026901.
159. Cochran, W G.; Cox, G. M. Experimental Designs; John Wiley: New York, 1957.
160. Clark, R. D.; Kar, J.; Akella, L.; Soltanshahi, F J. Chem. Inf. Comput. Sci. 2003, 43, 829-836.
161. Clark, R. D. J. Chem. Inf. Comput. Sci. 1997, 37, 1181-1188.
162. Pickett, S. D.; Clark, D. E.; McLay, I. M. J. Chem. Inf. Comput. Sci. 2000, 40, 263-272.
163. Brown, R. D.; Martin, Y C. SAR QSAR Environ. Res. 1998, 8, 23-39.
164. Brown, R. D.; Martin, Y C. J. Chem. Inf. Comput. Sci. 1997, 37, 1-9.
165. Patterson, D. E.; Cramer, R. D.; Ferguson, A. M.; Clark, R. D.; Weinberger, L. E. J. Med. Chem. 1996, 39, 3049-3059.
166. Good, A. C.; Cho, S. J.; Mason, J. S. J. Comput. Aided Mol. Des. 2004, 18, 523-527.
167. Gillet, V. J.; Willett, P.; Bradshaw, J. J. Chem. Inf. Comput. Sci. 1997, 37, 731-740.
168. Gillet, V. J.; Nicolotti, O. Perspect. Drug Disc. Des. 2000, 20, 265-287.
169. Jamois, E. A.; Hassan, M.; Waldman, M. J. Chem. Inf. Comput. Sci. 2000, 40, 63-70.
170. Linusson, A.; Gottfries, J.; Lindgren, F; Wold, S. J. Med. Chem. 2000, 43, 1320-1328.
171. Mitchell, T. J. Technometrics 1974, 2, 203-210.
172. MODDE. Umetri AB, Box 7960, S-907 19 Umea, Sweden.
173. Marengo, E.; Todeschini, R. Chemom. Intell. Lab. Syst. 1992, 16, 37-44.
174. Dunbar, J. B. J. Perspect. Drug Disc. Des. 1997, 7/8, 51-63.
175. Eriksson, L.; Johansson, E.; Muller, M.; Wold, S. Quant. Struct.-Act. Relat. 1997, 16, 383-390.
176. Bezdek, J. C. Pattern Recognition with Fuzzy Objective Function Algorithms; Plenum Press: NewYork, 1981.
177. Linusson, A.; Wold, S.; Norden, B. Chemom. Intell. Lab. Syst. 1998, 44, 213-227.
178. Gillet, V. J.; Willett, P.; Fleming, P. J.; Green, D. V S. J. Mol. Graph. Model. 2002, 20, 491-498.
179. Fonseca, C. M.; Fleming, P. J. Evol. Comput. 1995, 3, 1116.
180. Wright, T; Gillet, V J.; Green, D. V S.; Pickett, S. D. J. Chem. Inf. Comput. Sci. 2003, 43, 381-390.
181. Waldman, M.; Li, H.; Hassan, M. J. Mol Graph. Model 2000, 18, 412-426.
182. The Structural Genomics Consortium is a not-for-profit company that aims to determine the three dimensional structures of proteins of medical relevance, and place them in the public domain without restriction. http://www.sgc.utoronto.ca/(accessed April 2006).
183. Taylor, R. D.; Jewsbury, P. J.; Essex, J. W J. Comput. Aided Mol. Design 2002, 16, 151-166.
184. Beavers, M. P.; Chen, X. J. Mol Graph. Model 2002, 20, 463-468.
185. Kick, E. K.; Roe, D. C.; Skillman, A. G.; Liu, G.; Ewing, T J. A.; Sun, Y; Kuntz, I. D.; Ellman, J. A. Chem. Biol. 1997, 4, 297-307.
186. Kick, E. K.; Ellman, J. A. J. Med. Chem. 1995, 38, 1427-1430.
187. Lewis, R. A.; Roe, D. C.; Huang, C.; Ferrin, T E.; Langridge, R.; Kuntz, I. D. J. Mol. Graph. Model. 1992, 10, 66-79.
188. Roe, D. C.; Kuntz, I. D. J. Comput. Aided Mol Des. 1995, 9, 269-282.
189. 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, 6796-6800.
190. Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R.; Ferrin, TE. J. Mol. Biol. 1982, 161, 269-288.
191. Shoichet, B. K.; Bodian, D. L.; Kuntz, I. D. J. Comput. Chem. 1992, 13, 380-397.
192. Meng, E. C.; Shoichet, B. K.; Kuntz, I. D. J. Comput. Chem. 1992, 13, 505-524.
193. Ewing, T J. A.; Kuntz, I. D. J. Comput. Chem. 1997, 18, 1175-1189.
194. Sun, Y; Ewing, T J. A.; Skillman, A. G.; Kuntz, I. D. J. Comput. Aided Mol. Des. 1998, 12, 597-604.
195. Murray, C. W; Clark, D. E.; Auton, T R.; Firth, M. A.; Li, J.; Sykes, R. A.; Waszkowycz, B.; Westhead, D. R.; Young, S. C. J. Comput. Aided Mol. Des. 1997, 11, 193-207.
196. Liebeschuetz, J. W; Jones, S. D.; Morgan, P J.; Murray, C. W; Rimmer, A. D.; Roscoe, J. M. E.; Waszkowycz, B.; Welsh, P. M.; Wylie, W; Young, S. C. et al. J. Med. Chem. 2002, 45, 1221-1232.
197. Liebeschuetz, J. W pers. comm. 2005.
198. Rarey, M.; Kramer, B.; Lengauer, T; Klebe, G. J. Mol Biol 1996, 261, 470-489.
199. Rarey, M.; Kramer, B.; Lengauer, T J. Comput. Aided Mol. Des. 1997, 11, 369-384.
200. Kramer, B.; Rarey, M.; Lengauer, T Proteins: Struct., Fund., Genet. 1999, 37, 228-241.
201. Rarey, M.; Lengauer, T. Persped. Drug Disc. Des. 2000, 20, 63-81.
202. Boobbyer, D. N.; Goodford, P. J.; McWhinnie, P. M.; Wade, R. C. J. Med. Chem. 1989, 32, 1083-1094.
203. Wade, R. C.; Clark, K. J.; Goodford, P. J. J. Med. Chem. 1993, 36, 140-147.
204. Mason, J. S.; Cheney, D. L. Proc. Pacific Symp. BioComput. 1999, 4, 456-467.
205. Mason, J. S.; Cheney, D. L. Proc. Pacific Symp. BioComput. 2000, 5, 576-587.
206. Murray, C. M.; Cato, S. J. J. Chem. Inf. Comput. Sci. 1999, 39, 46-50.
207. Gillet, V; Johnson, A. P; Mata, P.; Sike, S.; Williams, P J. Comput. Aided Mol. Des. 1993, 7, 127-153.
208. Gillet, V J.; Newell, W; Mata, P.; Myatt, G.; Sike, S.; Zsoldos, Z.; Johnson, A. P. J. Chem. Inf. Comput. Sci. 1994, 34, 207-217.
209. Gillet, V. J.; Myatt, G.; Zsoldos, Z.; Johnson, A. P. Perspect. Drug Disc. Des. 1995, 3, 34-50.
210. Mata, P; Gillet, V J.; Johnson, A. P.; Lampreia, J.; Myatt, G. J.; Sike, S.; Stebbings, A. L. J. Chem. Inf. Comput. Sci. 1995, 35, 479-493.
211. Johnson, A. P, Boda, K., Marchland, J.-F, and Ting, A. De novo design of synthetically accessible ligands. Book of Abstracts, 219th National Meeting of the American Chemical Society, San Francisco, CA, Mar 26-30, 2000.
212. MDL Information Systems, Inc., San Leandro, CA.
213. Cahart, R. E.; Smith, D. H.; Venkataraghavan, R. J. Chem. Inf. Comput. Sci. 1985, 25, 64-73.
214. Nilakantan, R.; Bauman, N.; Dixon, J. S.; Venkataraghavan, R. J. Chem. Inf. Comput. Sci. 1987, 27, 82-85.
215. Kearsley, S. K.; Sallamack, S.; Fluder, E. M.; Andose, J. D.; Mosley, R. T.; Sheridan, R. P. J. Chem. Inf. Comput. Sci. 1996, 36, 118-127.
216. Sheridan, R. P.; Miller, M. D.; Underwood, D. J.; Kearsley, S. K. J. Chem. Inf. Comput. Sci. 1996, 36, 128-136.
217. Willett, P; Barnard, J. M.; Downs, G. M. J. Chem. Inf. Comput. Sci. 1998, 38, 983-996.
218. Schneider, G.; Neidhart, W; Giller, T; Schmid, G. Angew. Chem. Int. Ed. Engl. 1999, 38, 2894-2896.
219. Schneider, G.; Clement-Chomienne, O.; Hilfiger, L.; Schneider, P; Kirsch, S.; Bohm, H. J.; Neidhart, W Angew. Chem. Int. Ed. Engl. 2000, 39, 4130-4133.
220. Barker, E. J.; Gardiner, E. J.; Gillet, V J.; Kitts, P; Morris, J. J. Chem. Inf. Comput. Sci. 2003, 43, 346-356.
221. Gillet, V J.; Willett, P.; Bradshaw, J. J. Chem. Inf. Comput. Sci. 2003, 43, 338-345.
222. Randić, M. J. Am. Chem. Soc. 1975, 97, 6609-6615.
223. Kier, L. B.; Hall, L. H.; Murray, W J.; Randić, M. J. Pharm. Sci. 1975, 64, 1971-1974.
224. Hall, L. H.; Kier, L. B.; Murray, W. J. J. Pharm. Sci. 1975, 64, 1974-1977.
225. Agrafiotis, D. K. J. Chem. Inf. Comput. Sci. 1997, 37, 841-851.
226. Hassan, M.; Bielawski, J. P.; Hempel, J. C.; Waldman, M. Mol. Divers. 1996, 2, 64-74.
227. Pearlman, R. S.; Smith, K. M. Perspect. Drug Disc. Des. 1998, 9, 339-353.
228. Pearlman, R. S.; Smith, K. M. Drugs Future 1998, 23, 885-895.
229. Burden, F R. Quant. Struct.-Act. Relat. 1997, 16, 309-314.
230. Gao, H. J. Chem. Inf. Comput Sci. 2001, 41, 402-407.
231. Stanton, D. T J. Chem. Inf. Comput. Sci. 1999, 39, 11-20.
232. Schnur, D. J. Chem. Inf. Comput. Sci. 1999, 39, 36-45.
233. Pirard, B.; Pickett, S. D. J. Chem. Inf. Comput Sci. 2000, 40, 1431-1440.
234. Schnur, D.; Venkatarangan, P. In Combinatorial Library Design and Evaluation; Ghose, A. K., Viswanadhan, V N., Eds.; Marcel Dekker: New York, 2001, pp 473-501.
235. Pearlman, R. S.; Smith, K. M. DiverseSolutions. Distributed by Tripos Inc., St. Louis, MO.
236. Good, A. C.; Ewing, T J. A.; Gschwend, D. A.; Kuntz, I. D. J. Comput. Aided Mol. Des. 1995, 9, 1-12.
237. Abrahamian, E.; Fox, P. C.; Nrum, L.; Christensen, I. T.; Thogersen, H.; Clark, R. D. J. Chem. Inf. Comput. Sci. 2003, 43, 458-468.
238. Good, A. C.; Mason, J. S.; Pickett, S. D. Pharmacophore Pattern Application in Virtual Screening, Library Design and QSAR. In Virtual Screening for Bioactive Molecules; Bohm, H. J., Schneider, G., Eds.; Wiley-VCH: New York, 2000, pp 131-159.
239. Cruciani, G.; Meniconi, M.; Carosati, E.; Zamora, I.; Mannhold, R. VOLSURF: A Tool for Drug ADME-Properties Prediction. In Drug Bioavailability: Estimation of Solubility, Permeability and Absorption; van de Waterbeemd, H., Lennernas, H., Artursson, P, Eds.; Methods and Principles in Medicinal Chemistry; Mannhold, R., Kubinyi, H., Folkers, G., Eds.; Wiley-VCH: Weinheim, Germany, 2003; Vol. 18, pp 391-415.
240. Cruciani, G.; Pastor, M.; Guba, W. Eur. J. Pharm. Sci. 2000, 11, S29-S39.
241. Zamora, I.; Oprea, T; Cruciani, G.; Pastor, M.; Ungell, A. L. J. Med. Chem. 2003, 46, 25-33.
242. Grant, J. A.; Pickup, B. T J. Phys. Chem. 1995, 99, 3505-3510.
243. Rush, T S.; Grant, A. J.; Mosyak, L.; Nicholls, A. J. Med. Chem. 2005, 48, 1489-1495.
244. Hahn, M. J. Chem. Inf. Comput. Sci. 1997, 37, 80-86.
245. Haigh, J. A.; Pickup, B. T; Grant, J. A.; Nicholls, A. J. Chem. Inf. Model. 2005, 45, 673-684.
246. Briem, H.; Kuntz, I. D. J. Med. Chem. 1996, 39, 3401-3408.
247. Matter, H. J. Med. Chem. 1997, 40, 1219-1229.
248. Computational Tools for the Analysis of Molecular Diversity; Willett, P, Ed.; Perspectives in Drug Discovery and Design 1997, 7/8.
249. Agrafiotis, D. K.; Lobanov, V S. J. Chem. Inf. Comput. Sci. 1999, 39, 51-58.
250. Barnard, J. M.; Downs, G. M. J. Chem. Inf. Comput. Sci. 1992, 32, 644-649.
251. Downs, G. M.; Barnard, J. M. Rev. Comput. Chem. 2002, 18, 1-40.
252. Mason, J. S.; Pickett, S. D. Perspect Drug Disc. Des. 1997, 7/8, 85-114.
253. Lewis, R. A.; Mason, J. S.; McLay, I. M. J. Chem. Inf. Comput. Sci. 1997, 37, 599-614.
254. Pearlman, R. S.; Smith, K. M. J. Chem. Inf. Comput. Sci. 1999, 39, 28-35.
255. Walters, W P.; Murcko, M. A. Adv. Drug Deliv. Rev. 2002, 54, 255-271.
256. Vieth, M.; Siegel, M. G.; Higgs, R. E.; Watson, I. A.; Robertson, D. H.; Savin, K. A.; Durst, G. L.; Hipskind, P. A. J. Med. Chem. 2004, 47, 224-232.
257. Vieth, M.; Lajiness, M. S.; Erickson, J. Curr. Opin. Drug Disc. Dev. 2004, 7, 470-477.
258. Leeson, P. D.; Davis, A. M. J. Med. Chem. 2004, 47, 6338-6348.
259. Ajay, A.; Walters, W P.; Murcko, M. A. J. Med. Chem. 1998, 41, 3314-3324.
260. Sadowski, J.; Kubinyi, H. J. Med. Chem. 1998, 41, 3325-3329.
261. Wagener, M.; van Geerestein, V. J. J. Chem. Inf. Comput. Sci. 2000, 40, 280-292.
262. Byvatov, E.; Fechner, U.; Sadowski, J.; Schneider, G. J. Chem. Inf. Comput. Sci. 2003, 43, 1882-1889.
263. Hann, M. M.; Leach, A. R.; Harper, G. J. Chem. Inf. Comput. Sci. 2001, 41, 856-864.
264. Proudfoot, J. R. Bioorg. Med. Chem. Lett. 2002, 12, 1647-1650.
265. Rishton, G. M. Drug Disc. Today 2003, 8, 86-96.
266. Oprea, T I.; Davis, A. M.; Teague, S. J.; Leeson, P. D. J. Chem. Inf. Comput. Sci. 2001, 41, 1308-1315.
267. Teague, S. J.; Davis, A. M.; Leeson, P. D.; Oprea, T. I. Angew. Chem. Int. Ed. Engl. 1999, 38, 3742-3748.
268. Wenlock, M. C.; Austin, R. P.; Barton, P; Davis, A. M.; Leeson, P. D. J. Med. Chem. 2003, 46, 1250-1256.
269. Abraham, M. H.; Ibrahim, A.; Zissimos, A. M.; Zhao, Y H.; Comer, J.; Reynolds, D. P. Drug Disc. Today 2002, 7, 1056-1063.
270. van de Waterbeemd, H.; Jones, B. C. Prog. Med. Chem. 2003, 41, 1-59.
271. de Groot, M. J.; Ekins, S. Adv. Drug Deliv. Rev. 2002, 54, 367-383.
272. Lewis, D. F V J. Chem. Technol. Biotechnol 2001, 76, 237-244.
273. Stouch, T. R.; Kenyon, J. R.; Johnson, S. R.; Chen, X.-Q.; Doweyko, A.; Li, Y J. Comput. Aided Mol. Design 2003, 17, 83-92.
274. Bruneau, P. J. Chem. Inf. Comput. Sci. 2001, 41, 1605-1616.
275. van de Waterbeemd, H.; Gifford, E. Nat. Rev. Drug Disc. 2003, 2, 192-204.
276. Davis, A. M.; Riley, R. J. Curr. Opin. Chem. Biol. 2004, 8, 378-386.
277. Nilakantan, R.; Immermann, F; Haraki, K. Comb. Chem. HTS 2002, 5, 105-110.
278. Nilakantan, R.; Bauman, N.; Haraki, K. S. J. Comput. Aided Mol. Des. 1997, 11, 447-452.
279. Nilakantan, R.; Bauman, N.; Haraki, K. S.; Venkataraghavan, R. J. Chem. Inf. Comput. Sci. 1990, 30, 65-68.
280. Martin, Y C.; Kofron, J. L.; Traphagen, L. M. J. Med. Chem. 2002, 45, 4350-4358.
281. Bailey, W J.; Vanti, W B.; George, S. R.; Blevins, R.; Swaminathan, S.; Bonini, J. A.; Smith, K. E.; Weinshank, R. L.; O'Dowd, R. F Expert Opin. Therapeut. Patents 2001, 11, 1861-1887.
282. G-Protein-Coupled Receptors in Drug Discovery; Saunders, J., ed.; Bioorg. Med. Chem. Lett. 2005, 15.
283. Jimonet, P.; Jager, R. Curr. Opin. Drug. Disc. Dev. 2004, 7, 334-341.
284. Astles, P C.; Brown, T J.; Handscombe, C. M.; Harper, M. F; Harris, N. V; Lewis, R. A.; Lockey, P. M.; McCarthy, C.; McLay, I. M.; Porter, B.Eur. J. Med. Chem. 1997, 32, 409-423.
285. Astles, P C.; Brealey, C.; Brown, T. J.; Facchini, V; Handscombe, C. M.; Harris, N. V; McCarthy, C.; McLay, I. M.; Porter, B.; Roach, A. G. et al. J. Med. Chem. 1998, 41, 2732-2744.
286. Astles, P C.; Brown, T J.; Halley, F; Handscombe, C. M.; Harris, N. V; Majid, T. N.; McCarthy, C.; McLay, I. M.; Morley, A.; Porter, B. et al. J. Med. Chem. 2000, 43, 900-910.
287. Marriott, D. P.; Dougall, I. G.; Meghani, P; Liu, Y J.; Flower, D. R. J. Med. Chem. 1999, 42, 3210-3216.
288. Beeley, N. R. A.; Sage, C. TARGETS 2003, 2, 19-25.
289. Palczewski, K.; Kumasaka, T; Hori, T.; Behnke, C. A.; Motoshima, H.; Fox, B. A.; Le Trong, I.; Teller, D. C.; Okada, T; Stenkamp, R. E. et al. Science 2000, 289, 739-745.
290. Bosch, L.; Iarriccio, L.; Garriga, P. Curr. Pharm. Des. 2005, 11, 2243-2256.
291. Teller, D. C.; Okada, T; Behnke, C. A.; Palczewski, K.; Stenkamp, R. E. Biochemistry (Mose). 2001, 40, 7761-7772.
292. Evers, A.; Hessler, G.; Matter, H.; Klabunde, T. J. Med. Chem. 2005, 48, 5448-5465.
293. Evers, A.; Klabunde, T. J. Med. Chem. 2005, 48, 1088-1097.
294. Evans, B. E.; Rittle, K. E.; Bock, M. G.; DiPardo, R. M.; Freidinger, R. M.; Whitter, W L.; Lundell, G. F; Veber, D. F; Anderson, S.; Chang, S. L. et al. J. Med. Chem. 1988, 31, 2235-2246.
295. Patchett, A. A.; Nargund, R. P. Annu. Rep. Med. Chem. 2000, 35, 289-298.
296. Guo, T; Hobbs, D. W Assay Drug Dev. Technol. 2003, 1, 579-592.
297. MDL Drug Data Report. MDL Information Systems, Inc., San Leandro, CA.
298. Lavrador, K.; Murphy, B.; Saunders, J.; Struthers, S.; Wang, X.; Williams, J. J. Med. Chem. 2004, 47, 6864-6874.
299. Jacoby, E.; Fauchére, J.-L.; Raimbaud, E.; Ollivier, S.; Michel, A.; Spedding, M. Quant. Struct.-Act. Relat. 1999, 18, 561-572.
300. Jacoby, E. Quant. Struct.-Act. Relat. 2001, 20, 115-123.
301. Williams, D. H.; Mitchell, T. Curr. Opin. Pharmacol. 2002, 2, 567-573.
302. The Kinome map at www.kinase.com/human/kinome (accessed May 2006).
303. Stahura, F L.; Xue, L.; Godden, J. W; Bajorath, J. J. Mol. Graph. Model. 1999, 17, 1-9.
304. Todorov, N. P.; Buenemann, C. L.; Alberts, I. L. J. Chem. Inf. Model. 2005, 45, 314-320.
305. Dean, P. M.; Lloyd, D. G.; Todorov, N. P. Curr. Opin. Drug Disc. Dev. 2004, 7, 347-353.
306. Todorov, N. P.; Dean, P. M. J. Comput. Aided Mol. Design 1997, 11, 175-192.
307. Stahl, M.; Todorov, N. P.; James, T; Mauser, H.; Boehm, H. J.; Dean, P. M. J. Comput. Aided Mol. Design 2002, 16, 459-478.
308. Stahl, M.; Rarey, M. J. Med. Chem. 2001, 44, 1035-1042.
309. Birault, V; Harris, C. J.; Le, J.; Lipkin, M.; Nerella, R.; Stevens, A. Curr. Med. Chem. 2006, 13, 1735-1748.
310. Weber, L.; Wallbaum, S.; Broger, C.; Gubernator, K. Angew. Chem., Int. Ed. Engl. 1995, 34, 2280-2282.
311. Singh, J.; Ator, M. A.; Jaeger, E. P; Allen, M. P; Whipple, D. A.; Soloweij, J. E.; Chowdhary, S.; Treasurywala, A. M. J. Am. Chem. Soc. 1996,118, 1669-1676.
312. Yokobayashi, Y; Ikebukuro, I.; McNiven, K. I. J. Chem. Soc. Perkin Trans. 1996, 1, 2435-2439.
313. Brauer, S.; Almstetter, M.; Antuch, W; Behnke, D.; Taube, R.; Furer, P.; Hess, S. J. Comb. Chem. 2005, 7, 218-226.