On scaffolds and hopping in medicinal chemistry

Mini-Reviews in Medicinal Chemistry

Volumn 6, Issue 11, 2006, Pages 1217-1229

  Brown, Nathan ^a   Jacoby, Edgar ^a  

^a NOVARTIS PHARMA AG   (Switzerland)

Author keywords

Chemoinformatics; Isofunctional; Lead hopping; Markush; Scaffold; Scaffold hopping

Indexed keywords

DYE; PYRAZOLONE; THROMBIN INHIBITOR; VALSARTAN;

ANALYTIC METHOD; CHEMICAL STRUCTURE; COMBINATORIAL CHEMISTRY; COMPUTER ANALYSIS; COMPUTER MODEL; COMPUTER PROGRAM; DRUG DESIGN; DRUG POTENCY; DRUG RESEARCH; DRUG STRUCTURE; HIGH THROUGHPUT SCREENING; HYDROGEN BOND; LIPOPHILICITY; PATENT; PHARMACOPHORE; REVIEW; SCIENTIFIC LITERATURE; STRUCTURE ANALYSIS;

CHEMISTRY, PHARMACEUTICAL; COMPUTER SIMULATION; DRUG DESIGN; LIGANDS; MODELS, MOLECULAR; TIME FACTORS;

EID: 33750701141     PISSN: 13895575     EISSN: None     Source Type: Journal    
DOI: 10.2174/138955706778742768     Document Type: Review

References (68)

1. Schuffenhauer, A.; Popov, M.; Schopfer, U.; Acklin, P.; Stanek, J.; Jacoby, E. Comb. Chem. High Throughput Screen. 2004, 7, 771.
2. Schneider, G.; Neidhazt, W.; Giller, T.; Schmid, G. Angew. Chem., Int. Ed. 1999, 38, 2894.
3. Stanton, D. T.; Morris, T. W.; Roychoudhury, S.; Parker, C. N. J. Chem. Inf. Comput. Sci. 1999, 39, 21.
4. Bohl, M.; Dunbar, J.; Gifford, E. M.; Heritage, T.; Wild, D. J.; Willett, P.; Wilton, D. J. Quant. Struct. Act. Relat. 2002, 21, 590.
5. Böhm, H.-J.; Flohr, A.; Stahl, MScaffold hopping. Drug Discov. Today Technologies 2004, 1, 217.
6. Markush, E. A. Pyrazolone Dye and Process of Making the Same. U.S. Patent No. 1,506,316, Granted: 26th August, 1924.
7. Reich, H. J.; Cram, D. J. J. Am. Chem. Soc. 1969, 91, 3527.
8. Bemis, G. W.; Murcko, M. A. J. Med. Chem. 1996, 39, 2887.
9. Roberts, G.; Myatt, G. J.; Johnson, W. P.; Cross, K. P.; Blower, Jr., P. E. J. Chem. Inf. Comput. Sci. 2000, 40, 1302.
10. Nicolau, C. A.; Tamura, S. Y.; Kelley, B. P.; Bassett, S. L; Nutt, R. F. J. Chem. Inf. Comput. Sci. 2002, 42, 1069.
11. Cases, M.; Garciá-Serna, R.; Hettne, K.; Weeber, M.; van der Lei, J.; Boyer, S.; Mestres, J. Curr. Top. Med. Chem. 2005, 5, 763.
12. Koch, M. A.; Schuffenhauer, A.; Scheck, M.; Wetzel, S.; Casaulta, M.; Odermatt, A.; Ertl, P.; Waldmann, H. Proc. Natl. Acad Sci. USA 2005, 102, 17272.
13. Lloyd, D. G.; Buenemann, C. L.; Todorov, N. P.; Manallack, D. T.; Dean, P. M. J. Med. Chem. 2004, 47, 493.
14. Schneider, G.; Fechner, U. Nat. Rev. Drug Discov. 2005, 4, 649.
15. Schneider, G.; Böhm, H.-J. Drug Discov. Today 2002, 7, 64.
16. Halperin, I.; Ma, B,; Wolfson, H.; Nussinov, R. PROTEINS: Structure, Function, and Genetics 2002, 47, 409.
17. Ferrara, P.; Curioni, A.; Vangrevelinghe, E.; Meyer, T.; Mordasini, T.; Andreonin, W.; Acklin, P.; Jacoby, E. J. Chem. Inf. Mod. 2006, 46, 254.
18. Good, A. C.; 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. Mod. 2003, 22, 31.
19. Stiefl, N.; Watson, I. A.; Baumann, K.; Zaliani, A. J. Chem. Inf. Mod. 2006, 46, 208.
20. Xu, Y.-J.; Johnson, M. J. Chem. Inf. Comput. Sci. 2002, 42, 912.
21. Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. J. Chem. Inf. Mod. 2006, 46, 462.
22. Godden, J. W.; Stahura, F. L.; Bajorath, J. J. Chem. Inf. Mod. 2005, 45, 1812.
23. Renner, S.; Schneider, G. Chem. Med. Chem. 2006, 1, 181.
24. Broto, P.; Moreau, G.; Vandyke, C. Eur. J. Med. Chem. 1984, 19, 66.
25. Fechner, U.; Franke, L.; Renner, S.; Schneider, P.; Schneider, G. J. Comput. Aided Mol. Des. 2003, 17, 687.
26. CORINA is available from Molecular Networks, GmbH at http://www.mol-net.de.
27. Bush, B. L.; Sheridan, R. P. J. Chem. Inf. Comput. Sci. 1993, 33, 756.
28. The Molecular Operating Environment (MOE) is available from Chemical Computing Group, at http://www.chemcomp.com/.
29. Renner, S.; Ludwig, V.; Boden, O.; Scheffer, U.; Göbel, M.; Schneider, G. Chembiochem, 2005, 6, 1119.
30. Renner, S.; Schneider, G. J. Med. Chem. 2004, 47, 4653.
31. Schuffenhauer, A.; Floersheim, P.; Acklin, P.; Jacoby, E. J. Chem. Inf. Comput. Sci. 2003, 43, 391.
32. Gillet V. J.; Downs, G. M.; Ling, A.; Lynch, A F.; Venkataram, P.; Wood, J. V.; Dethlefsen, W. J. Chem. Inf. Comput. Sci. 1987, 27, 126.
33. Gillet V. J.; Downs, G. M.; Holliday, J. D.; Lynch, M. F.; Dethlefsen, W. J. Chem. Inf. Comput. Sci. 1991, 31, 260.
34. Takahashi, Y.; Sukekawa, M.; Sasaki, S. J. Chem. Inf. Comput. Sci. 1992, 32, 639.
35. Fisanick, W.; Lipkus, A. H.; Rusinko, A., III. J. Chem. Inf. Comput. Sci. 1994, 34, 130.
36. Gillet, V. J.; Willett, P.; Bradshaw, J. J. Chem. Inf. Comput. Sci. 2003, 43, 338.
37. Barker, E. J.; Gardiner, E. J.; Gillet, V. J.; Kitts, P.; Morris, J. J. Chem. Inf. Comput. Sci. 2003, 43, 346.
38. Rarey, M.; Dixon, J. S. J. Comput. Aided Mol. Des. 1998, 12, 471.
39. Rarey, M.; Stahl, M. J. Comput. Aided Mol. Des. 2001, 15, 497.
40. Lengauer, T.; Lemmen, C.; Rarey, M.; Zimmermann, M. Drug Discov. Today 2004, 9, 27.
41. Barker, E. J.; Cosgrove, D. A.; Gardiner, E. J.; Gillet, V. J.; Kitts, P.; Willett, P. J. Chem. Inf. Mod. 2006, 46, 503.
42. Bron, C.; Kerbosch, J. Commun. ACM 1973, 16, 575.
43. 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.
44. Cramer, R. D.; Patterson, D. E.; Clark, R. D.; Soltanshahi, F.; Lawless, M. S. J. Chem. Inf. Comput. Sci. 1998, 38, 1010.
45. Cramer, R. D.; Poss, M. A.; Hermsmeier, M. A.; Caulfield, T. J.; Kowala, M. C.; Valentine, M. T. J. Med. Chem. 1999, 42, 3919.
46. Andrews, K. M.; Cramer, R. D. J. Med. Chem. 2000, 43, 1723.
47. Cramer, R. D.; Jilek, R. J.; Andrews, K. M. J. Mol. Graph. Model. 2002, 20, 447.
48. Cramer, R. D.; Jilek, R. J.; Guessregen, S.; Clark, S. J.; Wendt, B.; Clark, R. D. J. Med. Chem. 2004, 47, 6777.
49. Concord is available from Tripos, Inc. at http://www.tripos.com.
50. Wild, D. J.; Willett, P. J. Chem. Inf. Comput. Sci. 1996, 36, 159.
51. Thorner, D. A.; Wild, D. J.; Willett, P.; Wright, P. M. J. Chem. Inf. Comput. Sci. 1996, 36, 900.
52. Good, A. C.; Richards, W. G. J. Chem. Inf. Comput. Sci. 1993, 33, 112.
53. Schuffenhauer, A.; Gillet, V. J.; Willett, P. J. Chem. Inf. Comput. Sci. 2000, 40, 295.
54. The FieldScreen, FieldTemplater, FieldAlign, and XedeX software are available from Cresset BioMolecular Discovery Ltd. at http://www.cresset-bmd.com/.
55. Kalindjian, S. B.; Buck, I. M.; Davies, J. M. R.; Dunstone, D. J.; Hudson, M. L.; Low, C. M. R.; McDonald, I. M.; Pether, M. J.; Steel, K. I. M.; Tozer, M. J.; Vinter, J. G. J. Med. Chem. 1996, 39, 1806.
56. Cheeseright, T.; Mackey, M.; Rose, S.; Vinter, A. J. Chem. Inf. Mod. 2006, 46, 665.
57. Low, C. M. R.; Buck, I. M. Cooke, T.; Cushnir, J. R.; Kalindjian, S. B.; Kotecha, A.; Pether, M. J.; Shankley, N. P.; Vinter, J. G.; Wright, L. J. Med. Chem. 2005, 48, 6790.
58. ROCS and EON are both available from OpenEye Scientific Software, Inc. at http://www.eyesopen.com.
59. Rush, T. S., III.; Grant, J. A.; Mosyak, L.; Nicholls, A. J. Med. Chem. 2005, 48, 1489.
60. Nicholls, A.; MacCuish, N. E.; MacCuish, J. D. J. Comput. Aided Mol. Des. 2004, 18, 451.
61. Jenkins, J. L.; Glick, M.; Davies, J. W. J. Med. Chem. 2004, 47, 6144.
62. Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. J. Chem. Inf. Comput. Sci. 2004, 44, 170.
63. Bender, A.; Mussa, H. Y.; Gill, G. S.; Glen, R. C. J. Med. Chem 2004, 47, 6569.
64. Goodford, P. J. J. Med. Chem. 1985, 28, 849.
65. Hemmer, M. C.; Steinhauer, V.; Gasteiger, J. Vib. Spectrosc. 1999, 19, 151.
66. Brown, N.; McKay, B.; Gasteiger, J. QSAR Comb. Sci. 2005, 24, 480.
67. Hirons, L.; Holliday, J. D.; Jelfs, S. P.; Willet, P.; Gedeck, P. QSAR Comb. Sci. 2005, 24, 611.
68. Willett, P. J. Med. Chem. 2005, 48, 4183.