Theoretical and experimental design of atypical kinase inhibitors: Application to p38 MAP kinase

Journal of Medicinal Chemistry

Volumn 48, Issue 18, 2005, Pages 5728-5737

  McClure, Kim F ^a   Abramov, Yuriy A ^a   Laird, Ellen R ^a   Barberia, John T ^a   Cai, Weiling ^a   Carty, Thomas J ^a   Cortina, Santo R ^a   Danley, Dennis E ^a   Dipesa, Alan J ^a   Donahue, Kathleen M ^a   Dombroski, Mark A ^a   Elliott, Nancy C ^a   Gabel, Christopher A ^a   Han, Seungil ^a   Hynes, Thomas R ^a   LeMotte, Peter K ^a   Mansour, Mahmoud N ^a   Marr, Eric S ^a   Letavic, Michael A ^a   Pandit, Jayvardhan ^a   Ripin, David B ^a   Sweeney, Francis J ^a   Tan, Douglas ^a   Tao, Yong ^a   more..

^a PFIZER INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

1 METHYL 1H BENZOTRIAZOLE; 1,3 DIMETHYL 1,3 DIHYDROBENZOIMIDAZOL 2 ONE; 3 METHYL 1,2,4 TRIAZOLO[4,3 A]PYRIDINE; 3 METHYLBENZO[D]ISOXAZOLE; 6 [4 (4 FLUOROPHENYL)OXAZOL 5 YL] 3 ISOPROPYL 1,2,4 TRIAZOLO[4,3 A]PYRIDINE; BENZIMIDAZOLE DERIVATIVE; BENZOTRIAZOLE DERIVATIVE; CP 808844; ISOXAZOLE DERIVATIVE; MITOGEN ACTIVATED PROTEIN KINASE P38; MITOGEN ACTIVATED PROTEIN KINASE P38 INHIBITOR; PYRIDINE DERIVATIVE; TRIAZOLE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; CALCULATION; CRYSTAL STRUCTURE; DRUG BINDING; DRUG DESIGN; DRUG POTENCY; DRUG STRUCTURE; DRUG SYNTHESIS; HYDROGEN BOND; STRUCTURE ANALYSIS; THEORY; X RAY CRYSTALLOGRAPHY;

BENZIMIDAZOLES; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ELECTROSTATICS; HYDROGEN BONDING; HYDROPHOBICITY; MODELS, MOLECULAR; MOLECULAR MIMICRY; MOLECULAR STRUCTURE; P38 MITOGEN-ACTIVATED PROTEIN KINASES; PROTEIN BINDING; PYRIDINES; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; TRIAZOLES;

EID: 24944516351     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm050346q     Document Type: Article

References (47)

1. Langmuir, I. Isomorphism, Isosterism and Covalence. J. Am. Chem. Soc. 1919, 41, 1543-1559.
2. Freidman, H. L. Influence of Isosteric Replacement Upon Biological Activity; National Academy of Sciences - National Research Council Publication No. 206; U.S. Government Printing Office: Washington DC, 1951, pp 295-357.
3. Thornber, C. W. Isosterism and Molecular Modification in Drug Design. Chem. Soc. Rev. 1979, 8, 563-580.
4. Badger, A. M.; Griswold, D. E.; Kapadia, R.; Blake, S.; Swift, B. A.; Hoffman, S. J.; Stroup, G. B.; Webb, E.; Rieman, D. J.; Gowen, M.; Boehm, J. C.; Adams, J. L.; Lee, J. C. Disease-modifying activity of SB 242235, a selective inhibitor of p38 mitogen-activated protein kinase, in rat adjuvant-induced arthritis. Arthritis Rheum. 2000, 43, 175-183.
5. Jackson, J. R.; Bolognese, B.; Hillegass, L.; Kassis, S.; Adams, J.; Griswold, D. E.; Winkler, J. D. Pharmacological effects of SB 220025, a selective inhibitor of P38 mitogen-activated protein kinase, in angiogenesis and chronic inflammatory disease models. J. Pharmacol. Exp. Ther. 1998, 284, 687-692.
6. Wadsworth, S. A.; Cavender, D. E.; Beers, S. A.; Lalan, P.; Schafer, P. H.; Malloy, E. A.; Wu, W.; Fahmy, B.; Olini, G. C.; Davis, J. E.; Pellegrino-Gensey, J. L.; Wachter, M. P.; Siekierka, J. J. RWJ 67657, a Potent, Orally Active Inhibitor of p38 Mitogen-Activated Protein Kinase. J. Pharmacol. Exp. Ther. 1999, 291, 680-687.
7. Tong, L.; Pav, S.; White, D. M.; Rogers, S.; Crane, K. M.; Cywin, C. L.; Brown, M. L.; Pargellis, C. A highly specific inhibitor of human p38 MAP kinase binds in the ATP pocket. Nat. Struct. Biol. 1997, 4, 311-316.
8. Wilson, K. P.; McCaffrey, P. G.; Hsiao, K.; Pazhanisamy, S.; Galullo, V.; Bemis, G. W.; Fitzgibbon, M. J.; Caron, P. R.; Murcko, M. A.; Su, M. S. The structural basis for the specificity of pyridinylimidazole inhibitors of p38 MAP kinase. Chem. Biol. 1997, 4, 423-431.
9. 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.
10. Stelmach, J. E.; Liu, L.; Patel, S. B.; Pivnichny, J. V.; Scapin, G.; Singh, S.; Hop, C. E.; Wang, Z.; Strauss, J. R.; Cameron, P. M.; Nichols, E. A.; Keefe, S. J.; Neill, E. A.; Schmatz, D. M.; Schwartz, C. D.; Thompson, C. M.; Zaller, D. M.; Doherty, J. B. Design and synthesis of potent, orally bioavailable dihydroquinazolinone inhibitors of p38 MAP kinase. Bioorg. Med. Chem. Lett. 2003, 13, 277-280.
11. Wang, Z.; Harkins, P. C.; Ulevitch, R. J.; Han, J.; Cobb, M. H.; Goldsmith, E. J. The structure of mitogen-activated protein kinase p38 at 2.1-Å resolution. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 2327-2332.
12. Dombroski, M. A.; Letavic, M. A.; McClure, K. F.; Barberia, J. T.; Carty, T. J.; Cortina, S. R.; Csiki, C.; Dipesa, A. J.; Elliott, N. C.; Gabel, C. A.; Jordan, C. K.; Labasi, J. M.; Martin, W. H.; Peese, K. M.; Stock, I. A.; Svensson, L.; Sweeney, F. J.; Yu, C. H. Benzimidazolone p38 inhibitors. Bioorg. Med. Chem. Lett. 2004, 14, 919-923.
13. de Dios, A.; Shih, C.; de Uralde, B. L.; Sánchez, C.; del Prado, M.; Cabrejas, L. M. M.; Pleite, S.; Blanco-Urgoiti, J.; María José Lorite; Nevill, C. R., Jr.; Bonjouklian, R.; York, J.; Vieth, M.; Wang, Y.; Magnus, N.; Campbell, R. M.; Andersen, B. D.; McCann, D. J.; Giera, D. D.; Lee, P. A.; Schultz, R. M.; Li, L. C.; Johnson, L. M.; Wolos, J. A. Design of Potent and Selective 2-Aminobenzimidazole Based p38α MAP Kinase Inhibitors with Excellent in Vivo Efficacy. J. Med. Chem. 2005, 48, 2270-2273.
14. Nobeli, I.; Price, S. L.; Lommerse, J. P. M.; Taylor, R. Hydrogen bonding properties of oxygen and nitrogen acceptors in aromatic heterocycles. J. Comput. Chem. 1997, 18, 2060-2074.
15. Mao, L.; Wang, Y.; Liu, Y.; Hu, X. Molecular Determinants for ATP-binding in Proteins: A Data Mining and Quantum Chemical Analysis. J. Mol. Biol. 2004, 336, 787-807.
16. Davis, A. M.; Teague, S. J. Hydrogen Bonding, Hydrophobic Interactions, and Failure of the Rigid Receptor Hypothesis. Angew. Chem., Int. Ed. 1999, 38, 736-749.
17. Murray, J. S.; Ranganathan, S.; Politzer, P. Correlations between the Solvent Hydrogen Bond Acceptor Parameter β and the Calculated Molecular Electrostatic Potential. J. Org. Chem. 1991, 56, 3734-3737.
18. +. J. Am. Chem. Soc. 1975, 97, 955-965.
19. Henry, J. R.; Rupert, K. C.; Dodd, J. H.; Turchi, I. J.; Wadsworth, S. A.; Cavender, D. E.; Schafer, P. H.; Siekierka, J. J. Potent inhibitors of the MAP kinase p38. Bioorg. Med. Chem. Lett. 1998, 8, 3335-3340.
20. Henry, J. R.; Rupert, K. C.; Dodd, J. H.; Turchi, I. J.; Wadsworth, S. A.; Cavender, D. E.; Fahmy, B.; Olini, G. C.; Davis, J. E.; Pellegrino-Gensey, J. L.; Schafer, P. H.; Siekierka, J. J. 6-Amino-2-(4-fluorophenyl)-4-methoxy-3- (4-pyridyl)-1H-pyrrolo[2,3-b]-pyridine (RWJ 68354): A Potent and Selective p38 Kinase Inhibitor. J. Med. Chem. 1998, 41, 4196-4198.
21. Abramov, Y. A.; Volkov, A.; Coppens, P. Anisotropic atom-atom potentials from X-ray charge densities: application to intermolecular interactions and lattice energies in some biological and nonlinear optical materials. J. Mol. Struct. (THEOCHEM) 2000, 529, 27-35.
22. Stone, A. J. The Theory of Intermolecular Forces; Oxford University Press: Oxford, 1996.
23. Jin, P.; Murray, J. S.; Politzer, P. Local ionization energy and local polarizability Int. J. Quantum Chem. 2004, 96, 394-401.
24. Mancera, R. L.; Buckingham, A. D. Temperature Effects on the Hydrophobic Hydration of Ethane. J. Phys. Chem. 1995, 99, 14632-14640.
25. Raschke, T. M.; Tsai, J.; Levitt, M. Quantification of the hydrophobic interaction by simulations of the aggregation of small hydrophobic solutes in water. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 5965-5969.
26. Hansch, C.; Leo, A. Exploring QSAR; American Chemical Society: Washington, DC, 1995.
27. Tsuzuki, S.; Honda, K.; Uchimaru, T.; Mikami, M.; Tanabe, K. Origin of Attraction and Directionality of the π/π Interaction: Model Chemistry Calculations of Benzene Dimer Interaction. J. Am. Chem. Soc. 2002, 124, 104-112.
28. De Proft, F.; Geerlings, P. Conceptual and Computational DFT in the Study of Aromaticity. Chem. Rev. 2001, 101, 1451-1464.
29. Revesz, L.; Di Padova, F. E.; Buhl, T.; Feifel, R.; Gram, H.; Hiestand, P.; Manning, U.; Zimmerlin, A. G. SAR of 4-hydroxypiperidine and hydroxyalkyl substituted heterocycles as novel p38 map kinase inhibitors. Bioorg. Med. Chem. Lett. 2000, 10, 1261-1264.
30. Sisko, J.; Kassick, A. J.; Mellinger, M.; Filan, J. J.; Allen, A.; Olsen, M. A. An investigation of imidazole and oxazole syntheses using aryl-substituted TosMIC reagents. J. Org. Chem. 2000, 65, 1516-1524.
31. Adams, J. L.; Gallagher, T. F.; Boehm, J. C.; Thompson, S. M. 6288062; SmithKline Beecham Corporation: Philadelphia, 2001.
32. Einhorn, J.; Einhorn, C.; Ratajczak, F.; Pierre, J.-L. Efficient and Highly Selective Oxidation of Primary Alcohols to Aldehydes by N-Chlorosuccinimide Mediated by Oxoammonium Salts. J. Org. Chem. 1996, 61, 7452-7454.
33. Abarbri, M.; Dehmel, F.; Knochel, P. Bromine-magnesium-exchange as a general tool for the preparation of polyfunctional aryl and heteroarylmagnesium- reagents. Tetrahedron Lett. 1999, 40, 7449-7453.
34. Potts, K. T.; Surapaneni, C. R. 1,2,4-Triazoles. XXV. The Effect of Pyridine Substitution on the Isomerization of s-Triazolo[4,3-alpyridines into s-Triazolo[l,5-a]pyridines (1). J. Heterocycl. Chem. 1970, 7, 1019-1027.
35. El Khadem, H. S.; Kawai, J.; Swartz, D. L. Synthesis and Rearrangements of Imidazolo- and Triazolo-Diazines. Heterocycles 1989, 28, 239-248.
36. PDB accession code IZZL.
37. Fitzgerald, C. E.; Patel, S. B.; Becker, J. W.; Cameron, P. M.; Zaller, D.; Pikounis, V. B.; O'Keefe, S. J.; Scapin, G. Structural basis for p38α MAP kinase quinazolinone and pyridol-pyrimidine inhibitor specificity. 2003, 10, 764-769.
38. Deleted in proof.
39. Andrews, P. R.; Craik, D. J.; Martin, J. L. Functional Group Contributions to Drug-Receptor Interactions. J. Med. Chem. 1984, 27, 1648-1657.
40. Kunz, I. D.; Chen, K.; Sharp, K. A.; Kollman, P. A. The maximal affinity of ligands. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9997-10002.
41. Breneman, C. M.; Wiberg, K. B. Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis. J. Comput. Chem. 1990, 11, 361-373.
42. Cossi, M.; Scalmani, G.; Rega, N.; Barone, V. New developments in the polarizable continuum model for quantum mechanical and classical calculations on molecules in solution. J. Chem. Phys. 2002, 117, 43-54.
43. Cances, E.; Mennucci, B.; Tomasi, J. A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics. J. Chem. Phys. 1997, 107, 3032-3041.
44. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, Jr., J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision B.04; Gaussian, Inc.: Wallingford, CT, 2004.
45. Spartan '02, Wavefunction Inc: Irvine, CA.
46. ACDI Labs package, release 6.0, Advanced Chemistry Development Inc: Toronto, Ontario, Canada.
47. MOE, Molecular Operating Environment; Chemical Computing Group (Distributor): Montreal, Canada.