Classification of Kinase Inhibitors Using BCUT Descriptors

Journal of Chemical Information and Computer Sciences

Volumn 40, Issue 6, 2000, Pages 1431-1440

  Pirard, Bernard ^a,c   Pickett, Stephen D ^b,c  

^a SANOFI AVENTIS DEUTSCHLAND GMBH   (Germany)

^b ROCHE PRODUCTS LTD   (United Kingdom)

^c Aventis Pharma Ltd   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME INHIBITOR; EPIDERMAL GROWTH FACTOR RECEPTOR; PROTEIN KINASE INHIBITOR;

ARTICLE; CHEMISTRY; CLASSIFICATION; DRUG ANTAGONISM;

ENZYME INHIBITORS; PROTEIN KINASE INHIBITORS; RECEPTOR, EPIDERMAL GROWTH FACTOR;

EID: 0034322113     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci000386x     Document Type: Article

References (69)

1. Agrafiotis, D. K.; Myslik, J. C.; Salemme, F. R. Advances in Diversity Profiling and Combinatorial Series Design. Mol. Diversity 1999, 4, 1-22.
2. Mason, J. S.; Hermsmeier, M. A. Diversity Assessment. Curr. Opin. Chem. Biol. 1999, 3, 342-349.
3. Bures, M. G.; Martin, Y. C. Computational Methods in Molecular Diversity and Combinatorial Chemistry. Curr. Opin. Chem. Biol. 1998, 2, 376-380.
4. 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.; Wiley-VCH: New York, in press; Vol. 16.
5. Willett, P. Computational Tools for the Analysis of Molecular Diversity. In Perspectives in Drug Discovery and Design; Willett, P., Ed.; KLUWER/ESCOM: Dordrecht, 1997; Vols. 7/8, p 1.
6. Matter, H.; Pötter, T. Comparing 3D Pharmacophore Triplets and 2D Fingerprints for Selecting Diverse Compounds Subsets. J. Chem. Inf. Comput. Sci. 1999, 39, 1211-1225.
7. Patterson, D. E.; Cramer, R. D.; Ferguson, A. M.; Clark, R. D.; Weinberger, L. E. Neighborhood Behavior: A Useful Concept for Validation of Molecular Diversity Descriptors. J. Med. Chem. 1996, 39, 3049-3059.
8. Cramer, R. D.; Poss, M. A.; Hermsmeier, A. M.; Caulfield, T. J.; Kowala, M. C.; Valentine, M. T. Prospective Identification of Biologically Active Structures by Topomer Shape Similarity Searching. J. Med. Chem. 1999, 42, 3919-3933.
9. Schneider, G.; Neidhart, W.; Giller, T.; Schmid, G. "Scaffold Hopping" by Topological Pharmacophore Search: A Contribution to Virtual Screening. Angew. Chem., Int. Ed. 1999, 38, 2894-2896.
10. Schuffenhauer, A.; Gillet, V. J.; Willett, P. Similarity Searching in Files of Three-Dimensional Chemical Structures: Analysis of the BIOSTER Database Using Two-Dimensional Fingerprints and Molecular Field Descriptors. J. Chem. Inf. Comput. Sci. 2000, 40, 295-307.
11. Mason, J. S.; Morize, I.; Menard, P. R.; Cheney, D. L.; Hulme, C.; Labaudiniere, R. F. New 4-Point Pharmacophore Method for Molecular Similarity and Diversity Applications: Overview of the Method and Applications, Including a Novel Approach to the Design of Combinatorial Libraries Containing Privileged Substructures. J. Med. Chem. 1999, 42, 3251-3264.
12. Pickett, S. D.; McLay, I. M.; Clark, D. E. Enhancing the Hit-to-Lead Properties of Lead Optimization Libraries. J. Chem. Inf. Comput. Sci. 2000, 40, 263-272.
13. Livingstone, D. J. The Characterization of Chemical Structures Using Molecular Properties. A Survey. J. Chem. Inf. Comput. Sci. 2000, 40, 195-209.
14. Brown, R. D.; Martin, Y. C. Use of Structure-Activity Data to Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection. J. Chem. Inf. Comput. Sci. 1996, 36, 572-584.
15. Brown, R. D. Descriptors for Diversity Analysis. In Perspectives in Drug Discovery and Design: Willett, P., Ed.; KLUWER/ESCOM: Dordrecht, 1997; Vols. 7/8, p 31.
16. Pearlman, R. S.; Smith, K. M. Novel Software Tools for Chemical Diversity. In Perspective in Drug Discovery and Design; Kubinyi, H., Folkers, G., Martin, Y. C., Eds; KLUWER/ESCOM: Dordrecht, 1998; Vols. 9/10/11, p 339.
17. Burden, F. R. Molecular Identification Number for Substructure Searches. J. Chem. Inf. Comput. Sci. 1989, 29, 225-227.
18. DiverseSolutions, v4.0.5; University of Texas, Austin; distributed by Tripos. Inc.: 1669 S. Hanley Rd., Suite 303, St. Louis, MO 63144.
19. Pearlman, R. S.; Smith, K. M. Metric Validation and Receptor Relevant Subspace Concept. J. Chem. Inf. Comput. Sci. 1999, 39, 28-35.
20. Schnur, D. Design and Diversity Analysis of Large Combinatorial Libraries Using Cell-based Methods. J. Chem. Inf. Comput. Sci. 1999, 39, 36-45.
21. Menard, P. R.; Mason, J. S.; Morize, I.; Bauerschmidt, S. Chemistry Space Metrics in Diversity Analysis, Library Design and Compound Selection. J. Chem. Inf. Comput. Sci. 1998, 38, 1204-1213.
22. McGregor, M. J.; Muskal, S. M. Pharmacophore Fingerprinting. 2. Application to Primary Library Design. J. Chem. Inf. Comput. Sci. 2000, 40, 117-125.
23. McGregor, M. J.; Muskal, S. M. Pharmacophore Fingerprinting. 1. Application to QSAR and Focused Library Design. J. Chem. Inf. Comput. Sci. 1999, 39, 569-574.
24. Cohen, P. The Development and Therapeutic Potential of Protein Kinase Inhibitors. Curr. Opin. Chem. Biol. 1999, 3, 459-465.
25. McMahon, G.; Sun, L.; Liang, C.; Tang, C. Protein Kinase Inhibitors: Structural Determinants for Target Specificity. Curr. Opin. Drug Discovery Dev. 1998, 1, 131-146.
26. Toledo, L. M.; Lydon, N. B.; Elbaum, D. The Structure-Based Design of ATP Site-Directed Protein Kinase Inhibitors. Curr. Med. Chem. 1999, 6, 775-805.
27. Garcia-Echeverria, C.; Traxler, P.; Evans, D. B. ATP Site-Directed Competitive and Irreversible Inhibitors of Protein Kinases. Med. Res. Rev. 2000, 20, 28-57.
28. Adams, J. L.; Lee, D. Recent Progress towards the Identification of Selective Inhibitors of Serine/Threonine Protein Kinases. Curr. Opin. Drug Discovery Dev. 1999, 2, 96-109.
29. de Laszlo, S. E.; Visco, D.; Agarwal, L.; Chang, L.; Chin, J.; Croft, G.; Forsyth, A.; Fletcher, D.; Frantz, B.; Hacker, C.; Hanlon, W.; Harper, C.; Kostura, M.; Li, B.; Luell, S.; MacCoss, M.; Mantlo, N.; O'Neill, E. A.; Orevillo, C.; Pang, M.; Parsons, J.; Rolando, A.; Sahly, Y.; Sidler, K.; Widmer, W. R.; O'Keefe, S. J. Pyrroles and Other Heterocycles as Inhibitors of P38 Kinase. Bioorg. Med. Chem. Lett. 1998, 8, 2689-2694.
30. Gallagher, T. F.; Seibel, G. L.; Kassis, S.; Laydon, J. T.; Blumenthal, M. J.; Lee, J. C.; Lee, D.; Boehm, J. C.; Fier-Thompson, S. M.; Abt, J. W.; Soreson, M. E.; Smietana, J. M.; Hall, R. F.; Garigipati, R. S.; Bender, P. E.; Erhard, K. F.; Krog, A. J.; Hofmann, G. A.; Sheldrake, P. L.; McDonnell, P. C.; Kumar, S.; Young, P. R.; Adams, J. L. Regulation of Stress-Induced Cytokine Production by Pyridinylimidazoles; Inhibition of CSBP Kinase. Bioorg. Med. Chem. 1997, 5, 49-64.
31. Chang, Y.-T.; Gray, N. S.; Rosania, G. R.; Sutherlin, D. P.; Kwon, S.; Norman, T. C.; Sarohia, R.; Leost, M.; Meijer, L.; Schultz, P. G. Synthesis and Application of Functionally Diverse 2,6,9-Trisubstituted Purine Libraries as CDK Inhibitors. Chem. Biol. 1999, 6, 361-375.
32. Schultz, C.; Link, A.; Leost, M.; Zaharevitz, D. W.; Gussio, R.; Sausville, E. A.; Meijer, L.; Kunick, C. Paullones, a Series of Cyclin-Dependent Kinase Inhibitors: Synthesis, Evaluation of CDK1/Cyclin B Inhibiton, and in Vitro Antitumor Activity. J. Med. Chem. 1999, 42, 2909-2919.
33. Traxler, P.; Green, J.; Mett, H.; Séquin, U.; Furet, P. Use of a Pharmacophore Model for the Design of EGFR Tyrosine Kinase Inhibitors: Isoflavones and 3-Phenyl-4(1H)-quinolones. J. Med. Chem. 1999, 42, 1018-1026.
34. Trumpp-Kallmeyer, S.; Rubin, J. R.; Humblet, C.; Hamby, J. M.; Showalter, H. D. H. Development of a Binding Model to Protein Tyrosine Kinases for Substituted Pyrido[2,3-d]pyrimidine Inhibitors. J. Med. Chem. 1998, 41, 1752-1763.
35. Rewcastle, G. W.; Murray, D. K.; Elliott, W. L.; Fry, D. W.; Howard, C. T.; Nelson, J. M.; Roberts, B. J.; Vincent, P. W.; Showalter, H. D. H.; Winters, R. T.; Denny, W. A. Tyrosine Kinase Inhibitors. 14. Structure-Activity Relationships for Methyl-amino-Substituted Derivatives of 4-[(3-Bromophenyl)amino]-6-(methylamino)-pyrido[3,4-d]-pyrimidine (PD 158780), a Potent and Specific Inhibitor of the Tyrosine Kinase Activity of Receptors for the EGF Family of Growth Factors. J. Med. Chem. 1998, 41, 742-751.
36. Thompson, A. M.; Murray, D. K.; Elliott; W. L.; Fry, D. W.; Nelson, J. A.; Showalter, H. H. D.; Roberts, B. J.; Vincent, P. W.; Denny, W. A. Tyrosine Kinase Inhibitors. 13. Structure-Activity Relationships for Soluble 7-Substituted 4-[(3-Bromophenyl)amino]pyrido[4,3-d]-pyrimidines Designed as Inhibitors of the Tyrosine Kinase Activity of the Epidermal Growth Factor Receptor. J. Med. Chem. 1997, 40, 3915-3925.
37. Traxler, P.; Bold, G.; Frei, J.; Lang, M.; Lydon, N.; Mett, H.; Buchdunger, E.; Meyer, T.; Mueller, M.; Furet, P. Use of a Pharmacophore Model for the Design of EGF-R Tyrosine Kinase Inhibitors: 4-(Phenylamino)pyrazolo[3,4-d]pyrimidines. J. Med. Chem. 1997, 40, 3601-3616.
38. Rewcastle, G. W.; Bridges, A. J.; Fry, D. W.; Rubin, J. R.; Denny, W. A. Tyrosine Kinase Inhibitors. 12. Synthesis and Structure-Activity Relationships for 6-Substituted 4-(Phenylamino)pyrimido[5,4-d]pyrimidines Designed as Inhibitors of the Epidermal Growth Factor Receptor. J. Med. Chem. 1997, 40, 1820-1826.
39. Gibson, K. H.; Grundy, W.; Godfrey, A. A.; Woodburn, J. R.; Ashton, S. E.; Curry, B. J.; Scarlett, L.; Barker, A. J.; Brown, D. S. Epidermal Growth Factor Receptor Tyrosine Kinase: Structure-Activity Relationships and Antitumor Activity of Novel Quinazolines. Bioorg. Med. Chem. Lett. 1997, 7, 2723-2728.
40. lck and EGF-R Tyrosine Kinase Activity. Bioorg. Med. Chem. Lett. 1997, 7, 417-420.
41. Myers, M. R.; Setzer, N. N.; Spada, A. P.; Persons, P. E.; Ly, C. Q.; Maguire, M. P.; Zulli, A. L.; Cheney, D. L.; Zilberstein, A.; Johnson, S. E.; Franks, C. F.; Mitchell, K. J. The Synthesis and SAR of New 4-(N-Alkyl-N-Phenyl)Amino-6,7-Dimethoxyquinazolines and 4-(N-Alkyl-N-Phenyl)amino-Pyrazolo[3,4-d]Pyrimidines, Inhibitors of CSF-1R Tyrosine Kinase Activity. Bioorg. Med. Chem. Lett. 1997, 4, 421-424.
42. Traxler, P. M.; Furet, P.; Mett, H.; Buchdunger, E.; Meyer, T.; Lydon, N. 4-(Phenylamino)pyrrolopyrimidines: Potent and Selective, ATP Site Directed Inhibitors of EGF-Receptor Protein Tyrosine Kinase. J. Med. Chem. 1996, 39, 2285-2292.
43. Rewcastle, G. W.; Palmer, B. D.; Thompson, A. M., Bridges, A. J.; Cody, D. R.; Zhou, H.; Fry, D. W.; McMichael, A.; Denny, W. A. Tyrosine Kinase Inhibitors. 10. Isomeric 4-[(3-Bromophenyl)amino]-pyrido[d]-pyrimidines Are Potent ATP Binding Site Inhibitors of the Tyrosine Kinase Function of the Epidermal Growth Factor Receptor. J. Med. Chem. 1996, 39, 1823-1835.
44. Thompson, A. M.; Bridges, A. J.; Fry, D. W.; Kraker, A. J.; Denny, W. A. Tyrosine Kinase Inhibitors. 7. 7-Amino-4-(phenylamino)-and 7-amino-4-[(phenylmethyl)amino]pyrido[4,3-d]pyrimidines: A New Class of Inhibitors of the Tyrosine Kinase Activity of the Epidermal Growth Factor Receptor. J. Med. Chem. 1995, 38, 3780-3788.
45. Rewcastle, G. W.; Denny, W. A.; Bridges, A. J.; Zhou, H.; Cody, D. R.; McMichael, A.; Fry, D. W. Tyrosine Kinase Inhibitors. 5. Synthesis and Structure-Activity Relationship for 4-[(Phenylmethyl)amino]- and 4-(Phenylamino)quinazolines as Potent Adenosine 5′-Triphosphate Binding Site Inhibitors of the Tyrosine Kinase Domain of the Epidermal Growth Factor Receptor. J. Med. Chem. 1995, 38, 3482-3487.
46. Showalter, H. D. H.; Bridges, A. J.; Zhou, H.; Sercel, A. D.; McMichael, A.; Fry, D. W. Tyrosine Kinase Inhibitors. 16. 6,5,6-Tricyclic Benzothieno[3,2-d]pyrimidines and Pyrimido[5,4-b]- and -[4,5-b]indoles as Potent Inhibitors of the Epidermal Growth Factor Receptor Tyrosine Kinase. J. Med. Chem. 1999, 42, 5464-5474.
47. Smaill, J. B.; Palmer, B. D.; Rewcastle, G. W.; Denny, W. A.; McNamara, D. J.; Dobrusin, E. M.; Bridges, A. J.; Zhou, H.; Showalter, H. H. D.; Winters, T. R.; Leopold, W. R.; Fry, D. W.; Nelson, J. M.; Slintak, V.; Elliot, W. L.; Roberts, B. J.; Vincent, P. W.; Patmore, S. J. Tyrosine Kinase Inhibitors. 15. 4-(Phenylamino)quinazoline and 4-(Phenylamino)pyrido[d]pyrimidine Acrylamides as Irreversible Inhibitors of the ATP Binding Site of the Epidermal Growth Factor Receptor. J. Med. Chem. 1999, 42, 1803-1815.
48. Weiniger, D. SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules. J. Chem. Inf. Comput. Sci. 1988, 28, 31-36.
49. Franke, R.; Gruska, A. Principle Component and Factor Analysis. In Chemometric Methods in Molecular Design, Methods and Principle in Medicinal Chemistry; van de Waterbeemd, H., Ed.; VCH Publishers: Weinheim, 1995; Vol. 2, p 113.
50. Dunbar, J. B. Jr. Cluster-based selection. In Perspectives in Drug Discovery and Design; Willett, P., Ed.; KLUWER/ESCOM: Dordrecht, 1997; Vols. 7/8, p 51.
51. SIMCA 7.0; Umetri AB: Umeå, Sweden, 1998.
52. 2 4.0; Molecular Simulation Inc.: San Diego, CA, 1999.
53. Multivariate Data Analysis with Emphasis on QSAR; Course organized by Umetri AB: Umeå, Sweden, June 26-28, 1996.
54. Daylight Chemical Information Systems Inc., version 4.51; Santa Fe, NM, 1997.
55. Lewis, R. A. Personal communication, September 1997.
56. Pickett, S. D.; Mason, J. S.; McLay, I. M. Diversity Profiling Using 3D Pharmacophores: Pharmacophores-Derived Queries (PDQ). J. Chem. Inf. Comput. Sci. 1996, 36, 1214-1223.
57. Pickett, S. D.; Luttmann, C.; Guerin, V.; Laoui, A.; James, E. DIVSEL and COMPLIB - Strategies for the Design and Comparison of Combinational Libraries Using Pharmacophoric Descriptors. J. Chem. Inf. Comput. Sci. 1998, 38, 144-150.
58. Pearlman, R. S. Rapid Generation of High Quality Approximate 3D Molecular Structures. Chem. Des. Auto. News. 1987, 2, 1-7.
59. Balducci, R.; McGarity, C. M.; Rusinko, A. III; Skell, J.; Smith, K.; Pearlman, R. S. CONCORD, v4.0.2; University of Texas, Austin; Distributed by Tripos, Inc.: 1669 S. Hanley Rd., Suite 303, St. Louis, MO 63144.
60. ChemDiverse; Oxford Molecular Group plc, The Medawar Centre, Oxford Science Park, Oxford, OX4 4GA U.K.
61. Wang, Z.; Canagarajah, B. J.; Boehm, J. C.; Kassisa, S.; Cobb, M. H.; Young, P. R.; Abdel-Meguid, S.; Adams, J. L.; Goldsmith, E. J. Structural Basis of Inhibitor Selectivity in Map Kinases. Structure 1998, 6, 1117-1128.
62. Wilson, K. P.; McCaffrey, P. G.; Hsiao, K.; Pazharisamy, S.; Galullo, V.; Bemis, G. W.; Fitzgibbon, M. J.; Caron, P. R.; Murcko, M. A.; Su, M. S. S. The Structural Basis for the Specificity of Pyridinylimidazole Inhibitors of P38 MAP Kinase. Chem. Biol. 1997, 4, 423-431.
63. Tong, L.; Pav, S.; White, D. M.; Rogers, S.; Crane, K. M.; Cywin, C. L.; Brown, M. L.; Pargelis, C. A. A Highly Specific Inhibitor of Human P38 MAP Kinase Binds to the ATP Pocket. Nat. Struct. Biol. 1997, 4, 311-316.
64. Lisnock, J. M.; Tebben, A.; Frantz, B.; O'Neill, E. A.; Croft, G.; O'Keefe, S. J.; Li, B.; Hacker, C.; de Laszlo, S.; Smith, A.; Libby, B.; Liverton, N.; Hermes, J.; LoGrasso, P. Molecular Basis for P38 Protein Kinase Inhibitor Specificity. Biochemistry 1998, 37, 16573-16581.
65. Boehm, J. C.; Adams, J. L. New Inhibitors of P38 Kinase. Exp. Opin. Ther. Patents 2000, 10, 25-37.
66. Shewchuck, L.; Hassell, A.; Wisely, B.; Rocque, W.; Holmes, W.; Veal, J.; Kuyper, L. F. Binding Mode of the 4-Anilinoquinazoline Class of Protein Kinase Inhibitor: X-ray Crystallographic Studies of the 4-Anilinoquinazolines Bound to Cyclin-Dependent Kinase 2 and P38 Kinase. J. Med. Chem. 2000, 43, 133-138.
67. Lamers, M. B. A. C.; Antson, A. A.; Hubbard, R. E.; Scott, R. K.; Williams, D. H. Structure of the Tyrosine Kinase Domain of C-terminal Src Kinase (CSK) in Complex with Staurosporine. J. Mol. Biol. 1999, 285, 713-725.
68. Mohammadi, M.; Froum, S.; Hamby, J. M.; Schroeder, M. C.; Panek, R. L.; Lu, G. H.; Eliseenkova, A. V.; Green, D.; Schlessinger. J.; Hubbard, S. R. Crystal Structure of an Angiogenesis Inhibitor Bound to the FGF Receptor Tyrosine Kinase Inhibitor. EMBO J. 1998, 17, 5896-5904.
69. Mohammadi, M.; McMahon, G.; Sun, L.; Tang, C.; Hirth, P.; Yeh, B. K.; Hubbard, S. R.; Schlessinger, J. Structures of the Tyrosine Kinase Domain of Fibroblast Growth Factor Receptor in Complex with Inhibitors. Science 1997, 276, 955-960.