Dynamics and binding modes of free cdk2 and its two complexes with inhibitors studied by computer simulations

Journal of Biomolecular Structure and Dynamics

Volumn 20, Issue 2, 2002, Pages 141-154

  Otyepka, Michal ^a   Kříž, Zdeněk ^b   Koča, Jaroslav ^b  

^a PALACKÝ UNIVERSITY   (Czech Republic)

^b MASARYK UNIVERSITY   (Czech Republic)

Author keywords

Cyclin dependent kinase; Drug design; Inhibitors; Molecular dynamics; Roscovitine

Indexed keywords

6 N (3,3 DIMETHYLALLYL)ADENOSINE; ADENINE; CYCLIN DEPENDENT KINASE; DRUG DERIVATIVE; LIGAND; N(6) (DELTA(2) ISOPENTENYL)ADENINE; N(6)-(DELTA(2)-ISOPENTENYL)ADENINE; PURINE DERIVATIVE; ROSCOVITINE; 6 N (3,3 DIMETHYLALLYL)ADENINE; ADENOSINE TRIPHOSPHATE; BUTYROLACTONE; CYCLIN DEPENDENT KINASE 2; CYCLIN DEPENDENT KINASE INHIBITOR; FLAVOPIRIDOL; INDIRUBIN; PAULLONE; STAUROSPORINE; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; DRUG ANTAGONISM; DRUG DESIGN; ELECTRICITY; HYDROGEN BOND; KINETICS; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY; CANCER THERAPY; CELL CYCLE; COMPLEX FORMATION; ENZYME ACTIVE SITE; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL;

ADENINE; BINDING SITES; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; CYCLIN-DEPENDENT KINASES; DRUG DESIGN; ELECTROSTATICS; HYDROGEN BONDING; ISOPENTENYLADENOSINE; KINETICS; LIGANDS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; PURINES;

EID: 1842866544     PISSN: 07391102     EISSN: None     Source Type: Journal    
DOI: 10.1080/07391102.2002.10506830     Document Type: Article

References (47)

1. D. O. Morgan, Annu. Rev. Cell Dev. Biol. 13, 261-291 (1997).
2. D. O. Morgan and H. L. De Bondt, Curr. Opin. Cell Biol. 6, 239-246 (1994).
3. L. N. Johnson and R. J. Lewis, Chem. Rev. 101, 2209-2242 (2001).
4. W. F. de Azevedo, S. Leclerc, L. Meijer, L. Havlíček, M. Strnad and S.-H. Kim, European Journal of Biochemistry 243, 518-526 (1997).
5. U. Pindur, Y.-S. Kim and F. Mehrabani, Curr. Med. Chem. 6, 29-69 (1999).
6. M. D. Losiewicz, B. A. Carlson, G. Kaur, E. A. Sausville and P. Worland, Biochem. Biophys. Res. Commun. 201, 589-595 (1994).
7. M. Kitagava, T. Okabe, H. Ogino, H. Matsumo, I. Suzuki-Takahashi, T. Kobudo, H. Higashi, S. Saitoh, Y. Taya, H. Yasuda, Y. Ohba, S. Nishimura, N. Tanaka and A. Okuyama, Oncogene 8, 2433-2441 (1993).
8. J. Vesely̌, L. Havlíček, M. Strnad, J. J. Blow, A. Donella-Deana, L. Pinna, D. S. Letham, J.-Y. Kato, L. Detivaud, S. Leclerc and L. Meijer, Eur J. Biochem. 224, 771-786 (1994).
9. C. E. Arris, T. F. Boyle, A. H. Calvert, N. J. Curtin, J. A. Endicott, E. F. Garman, A. E. Gibson, B. T. Golding, S. Grant, R. J. Griffin, P. Jewsbury, L. N. Johnson, A. M. Lawrie, D. R. Newell, M. E. M. Noble, E. A. Sausville and Y. W. Schultz R., J. Med. Chem. 43, 2797-2804 (2000).
10. M. Legraverend, P. Tunnah, M. Noble, P. Ducrot, O. Ludwig, D. S. Grierson, M. Leost, L. Meijer and J. Endicott, J. Med. Chem. 43, 1282-1292 (2000).
11. R. Hoessel, S. Leclerc, J. A. Endicott, M. Noble, A. Lawrie, P. Tunnah, M. Leost, E. Damiens, M. Domonique, D. Marko, E. Niederberger, W. Tang, G. Eisenbrand and L. Meijer, Nature Cell Biol. 1, 60-67 (1999).
12. D. W. Zaharevitz, R. Gussio, M. Leost, A. M. Sanderowitz, T. Lahusen, C. Kunick, L. Meijer and E. A. Sausville, Cancer Res. 59, 2566-2569 (1999).
13. L. L. Kent, N. E. Hull-Campbell, T. Lau, J. C. Wu, S. A. Thompson and M. Nori, Biochem. Biophys. Res. Commun. 260, 768-774 (1999).
14. N. Gray, L. Détivaud, C. Doering and L. Meijer, Curr. Med. Chem. 6, 859-875 (1999).
15. C. M. Crews and R. Mohan, Curr. Opin. Chem. Biol. 4, 47-53 (2000).
16. T. M. Sielecki, J. F. Boylan, P. A. Benfield and G. L. Trainor, J. Med. Chem. 43, 1-18 (2000).
17. J. Rosenblatt, Y. Gu and D. O. Morgan, Proc. Natl. Acad. Sci. 89, 2824-2828 (1992).
18. H. L. de Bondt, J. Rosenblatt, J. Jancarik, H. D. Jones, D. O. Morgan and S. H. Kim, Nature 363, 595-602 (1993).
19. M. E. M. Noble and J. A. Endicott, Pharmacol. Theor. 82, 269-278 (1999).
20. D. O. Morgan, Curr. Opin. Cell Biol. 8, 767-772 (1996).
21. P. D. Jeffrey, A. A. Russo, K. Polyak, E. Gibbs, J. Hurwitz, J. Massague and N. P. Pavletich, Nature 376, 313-320 (1995).
22. A. A. Russo, P. D. Jeffrey and N. P. Pavletich, Nature Struct. Biol. 3, 696-700 (1996).
23. T. G. Davies, P. Tunnah, L. Meijer, D. Marko, G. Eisenbrand, J. A. Endicott and M. E. M. Noble, Structure 9, 389-397 (2001).
24. A. Cavalli, C. Dezi, G. Folkers, L. Scapozza and M. Recanatini, Proteins: Struct., Funct., Genet. 45, 478-485 (2001).
25. D. A. Case, D. A. Pearlman, J. W. Caldwell, T. E. Cheatham III., W. S. Ross, C. L. Simmerling, T. A. Darden, K. M. Merz, R. V. Stanton, A. L. Cheng, J. J. Vincent, M. Crosley, D. M. Ferguson, R, J. Radmer, G. L. Seibel, U. C. Singh, P. K. Weiner and P. A. Kollman, AMBER 5. 1997: University of California, San Francisco.
26. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, J. K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell and P. A. Kollman, J. Am. Chem. Soc. 117, 5179-5197 (1995).
27. M. J. Frisch, G. W. Trucks, H. B. Schlegel, P. M. W. Gill, B. G. Johnson, M. A. Robb, J. R. Cheeseman, T. Keith, G. A. Petersson, J. A. Montgomery, K. Raghavachari, M. A. A1 Al-Laham, V. G. Zakrzewski, J. V. Ortiz, J. B. Foresman, C. Y. Peng, P. Y. Ayala, W. Chen, M. W. Wong, J. L. Andres, E. S. Replogle, R. Gomperts, R. L. Martin, D. J. Fox, J. S. Binkley, D. J. Defrees, J. Baker, J. J. Stewart, M. Head-Gordon, C. Gonzales, and J. A. Pople, Gaussian 94. 1995, Gaussian, Inc.: Pittsburgh, PA.
28. G. Vriend, J. Mol. Graph. 8, 52-56 (1990).
29. U. Essmann, L. Perera, M. L. Berkowitz, T. A. Darden, H. Lee and L. G. Pedersen, J. Chem. Phys. 103, 8577-8593 (1995).
30. H. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola and J. R. Haak, J. Comp. Phys. 81, 3684-3690 (1984).
31. J. P. Ryckaert, G. Ciccotti and H. C. Berendsen, J. Comput. Phys. 23, 327-341 (1977).
32. H. Resat and M. Mezei, Biophys. J. 71, 1179-1190 (1996).
33. R. C. Wade, A. R. Ortiz, and F. Gago, Comparative Binding Energy Analysis, in 3D QSAR in Drug Design, Kluwer Academic Publishers. 19-34 (1998).
34. J. Srivivasan, T. E. Cheatham III., P. Cieplak, P. A. Kollman and D. A. Case, J. Am. Chem. Soc. 120, 9401-9409 (1998).
35. P. A. Kollman, I. Massova, C. Reyes, B. Kuhn, H. Shuanghong, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D. A. Case and T. E. Cheatham III., Acc. Chem. Res. 33, 889-897 (2000).
36. J. Wang, P. Morin, W. Wang and P. A. Kollman, J. Am. Chem. Soc. 123, 5221-5230 (2001).
37. M. K. Gilson, K. A. Sharp and B. H. Honig, J. Comput. Chem. 9, 327-335 (1987).
38. B. Jayaram, D. Sprous and D. L. Beveridge, J. Phys. Chem. B 102, 9571-9576 (1998).
39. M. F. Sanner, A. J. Olson and J. Spehner, Biopolymers 38, 305-320 (1996).
40. D. A. Case, D. A. Pearlman, J. W. Caldwell, T. E. Cheatham III., W. S. Ross, C. L. Simmerling, T. A. Darden, K. M. Merz, R. V. Stanton, A. L. Cheng, J. J. Vincent, M. Crowley, V. Tsui, R. J. Radmer, Y. Duan, J. Pitera, I. Massova, G. L. Seibel, U. C. Singh, P. K. Weiner and P. A. Kollman, AMBER 6. 1999, University of California: San Francisco.
41. D. van der Spoel, A. R. van Buuren, E. Apol, P. J. Maulenhoff, P. D. Tieleman, A. L. T. M. Sijbers, B. Hess, K. A. Feenstra, E. Lindhal, R. V. Drunen and H. J. C. Berendsen, Gromacs User Manual Version 2.0. 1999: Groningen.
42. W. Kabsch and C. Sander, Biopolymers 22, 2577-2637 (1983).
43. S. J. Hubbard and J. M. Thornton, NACCESS. 1993: London.
44. A. B. M. Linssen, Moledular Dynamics Simulation of Haloalkane Dehalogenase: A Statistical Analysis of Protein Motions. (Ph. D. Theses), Groningen. (1998).
45. M. Otyepka, V. Kryštof, L. Havlíček, V. Siglerová, M. Strnad, and J. Koča, J. Med. Chem. 43, 2506-2513 (2000).
46. U. Schulze-Gahmen, J. Brandsen, H. D. Jones, D. Morgan, L. Meijer, J. Veselý, and S.-H. Kim, Proteins 22, 378-391 (1995).
47. M. K. Dreyer, J. Med. Chem. 44, 524-530 (2001).