FlexE ensemble docking approach to virtual screening for CDK2 inhibitors

Molecular Simulation

Volumn 33, Issue 8, 2007, Pages 667-676

  Kim, J ^a   Park, J G ^a   Chong, Y ^a  

^a Konkuk University   (South Korea)

Author keywords

CDK2; Docking; FlexE; Virtual screening

Indexed keywords

ADENOSINETRIPHOSPHATE; AMINO ACIDS; BINDING ENERGY; CONFORMATIONS; ENZYME INHIBITION; MOLECULAR STRUCTURE;

CDK2; FLEXE; TORSION ANGLES; VIRTUAL SCREENING;

LIGANDS;

EID: 34548119525     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020701297401     Document Type: Article

References (35)

1. M. Huse, J. Kuriyan. The conformational plasticity of protein kinases. Cell, 109, 275 (2002).
2. S.Y. Wu, I. McNae, G. Kontopidis, S.J. McClue, C Mclnnes, K.J. Stewart, S. Wang, D.I. Zheleva, H. Marriage, D.P. Lane, P. Taylor, P.M. Fischer, M.D. Walkinshaw. Discovery of a novel family of CDK inhibitors with the program LIDAEUS: structural basis for ligand-induced disordering of the activation loop. Structure, 11, 399 (2003).
3. H. Claußen, C Buning, M. Rarey, T. Lengauer. FLEXE: efficient molecular docking considering protein structure variations. J. Mol. BIol., 308, 377 (2001).
4. A. Steffen, J. Günther, H. Briem. Evaluation of the applicability of the FlexE ensemble docking approach to virtual screening for CDK2 inhibitors, paper presented at the Darmstädter Molecular Modelling Workshop, Erlangen, Germany, 19th April (2004).
5. T. Polgár, G.M. Keseru. Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and β-secretase. J. Chem. Inf. Model., 46, 1795 (2006).
6. T. Polgár, A. Baki, G.I. Szendrei, G.M. Keserü. Comparative virtual and experimental high-throughput screening for glycogen synthase kinase-3β inhibitors. J. Med. Chem., 48, 7946 (2005).
7. M.P. Thomas, C. McInnes, P.M. Fischer. Protein structures in virtual screening: a case study with CDK2. J. Med. Chem., 49, 92 (2006).
8. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne. The Protein Data Bank. Nucleic Acids Res., 28, 235 (2000).
9. A.M. Lawrie, M.E. Noble, P. Tunnah, N.R. Brown, L.N. Johnson, J.A. Endicott. Protein kinase inhibition by staurosporine revealed in details of the molecular interaction with CDK2. Nat. Struct. Biol., 4, 796 (1997).
10. N.R. Brown, M.E. Noble, A.M. Lawrie, M.C. Morris, P. Tunnah, G. Divita, L.N. Johnson, J.A. Endicott. Effects of phosphorylation of threonine 160 on cyclin-dependent kinase 2 structure and activity. J. Biol. Chem., 274, 8746 (1999).
11. L. Shewchuk, A. Hassell, B. Wisely, W. Rocque, W. Holmes, J. Veal, L.F. Kuyper. Binding mode of the 4-anilinoquinazoline class of protein kinase inhibitor: X-ray crystallographic studies of 4-anilinoquinazolines bound to cyclin-dependent kinase 2 and p38 kinase. J. Med. Chem., 43, 133 (2000).
12. L. Meijer, A.M. Thunnissen, A.W. White, M. Garnier, M. Nikolic, L.H. Tsai, J. Walter, K.E. Cleverley, P.C. Salinas, Y.Z. Wu, J. Biernat, E.M. Mandelkow, S.H. Kim, G.R. Pettit. Inhibition of cyclin-dependent kinases, GSK-3β and CK1 by hymenialdisine, a marine sponge constituent. Chem. Biol., 7, 51 (2000).
13. CE. Arris, FT. 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. Noble, E.A. Sausville, R. Schultz, W. Yu. Identification of novel purine and pyrimidine cyclin-dependent kinase inhibitors with distinct molecular interactions and tumor cell growth inhibition profiles. J. Med. Chem., 43, 2797 (2000).
14. P.D. Jeffrey, A.A. Russo, K. Polyak, E. Gibbs, J. Hurwitz, J. Massague, N.R Pavletich. Mechanism, of CDK activation revealed by the structure of a cyclinA-CDK2 complex. Nature, 376, 313 (1995).
15. S.T. Davis, B.G. Benson, H.N. Bramson, D.E. Chapman, S.H. Dickerson, K.M. Dold, DJ. Eberwein, M. Edelstein, S.V. Frye, R.T. Gampe Jr., R.J. Griffin, P.A. Hams, A.M. Hassell, W.D. Holmes, R.N. Hunter, V.B. Knick, K. Lackey, B. Lovejoy, M.J. Luzzio, D. Murray, P. Parker, W.J. Rocque, L. Shewchuk, J.M. Veal, D.H. Walker, L.F. Kuyper. Prevention of chemotherapy-induced alopecia in rats by CDK inhibitors. Science, 291, 134 (2001).
16. M.K. Dreyer, D.R. Borcherding, J.A. Dumont, N.P. Peet, J.T. Tsay, P.S. Wright, A.J. Bitonti, J. Shen, S.H. Kim. Crystal structure of human cyclin-dependent kinase 2 in complex with the adeninederived inhibitor H717. J. Med. Chem., 44, 524 (2001).
17. A.E. Gibson, CE. Arris, J. Bentley, F.T. Boyle, N.J. Davies, T.G. Curtin, J.A. Endicott, B.T. Golding, S. Grant, R.J. Griffin, P. Jewsbury, L.N. Johnson, V. Mesguiche, D.R. Newell, M.E. Noble, J.A. Tucker, H.J. Whitfield. Probing the ATP ribose-binding domain of cyclin-dependent kinases 1 and 2 with 06-substituted guanine derivatives. J. Med., Chem., 45, 3381 (2002).
18. J.F. Beattie, G.A. Breault, R.P.A. Elision, S. Green, P.J. Jewsbury, C.J. Midgley, R.T. Naven, CA. Minshull, R.A. Pauptit, J.A. Tucker, J.E. Pease. Cyclin-dependent kinase 4 inhibitors as a treatment for cancer. Part 1 : identification and optimisation of substituted 4,6-bis anilino pyrimidines. Bioorg. Med. Chem. Lett., 13, 2955 (2003).
19. C.W. Carter Jr., J. Kraut, S.T. Freer, N.H. Xuong, R.A, Alden, R.G. Bartsch. Two angstrom, crystal structure of oxidized chromatium high potential iron protein. J. Biol. Chem., 249, 4212 (1974).
20. U. Schulze-Gahmen, H.L. De Bondt, S.H. Kim. High-resolution crystal structures of human cyclin-dependent kinase 2 with and without ATP: Bound waters and natural, ligand as guides for inhibitor design. J. Med. Chem., 39, 4540 (1996).
21. U. Schulze-Gahmen, J. Brandsen, H.D. Jones, D.O. Morgan, L. Meijer, J. Vesely, S.H. Kim. Multiple modes of ligand recognition: crystal structures of cyclin-dependent protein kinase 2 in complex with ATP and two inhibitors, olomoucine and isopentenyladenine. Proteins, 22, 378 (1995).
22. P. Furet, T. Meyer, A. Strauss, S. Raccuglia, J.M. Rondeau. Structure-based design and protein X-ray analysis of a protein kinase inhibitor. Bioorg. Med. Chem. Lett., 12, 221 (2002).
23. M. Anderson, J. Beattie, G. Breault, J. Breed, K. Byth, J. Culshaw, R. Ellston, S. Green, C Minshull, R. Norman, R. Pauptit, J. Stanway, A. Thomas, P. Jewsbury. Imidazo[1,2-a]pyridines: a potent and selective class of cyclin-dependent kinase inhibitors identified through structure-based hybridization. Bioorg. Med. Chem. Lett., 13, 3021 (2003).
24. H.N. Bramson, J. Corona, S.T. Davis, S.H. Dickerson, M. Edelstein, S.V. Frye, R.T. Gampe Jr., P.A. Harris, A. Hassell, W.D. Holmes, R.N. Hunter, K.E. Lackey, B. Lovejoy, M.J. Luzzio, V. Montana, W.J. Rocque, D. Rusnak, L. Shewchuk, J.M. Veal, D.H. Walker, L.F. Kuyper. Oxindole-based inhibitors of cyclin-dependent kinase 2 (CDK2): design, synthesis, enzymatic activities, and X-ray crystallographic analysis. J. Med. Chem., 44, 4339 (2001).
25. (a) C Meng, B.K. Shoichet, I.D. Kuntz. Automated docking with grid-based energy evaluation. J. Comp. Chem., 13, 505 (1992)
26. (b) S.J. Weiner, RA. Kollman, D.T. Nguyen, D.A. Case. An all atom force field for simulations of proteins and nucleic acids. J. Comp. Chem. 7, 230 (1986).
27. (c) R.M.A. Knegtel, D.M. Bayada, R.A. Engh, W. v.d. Saal, V.J.v. Geerestein, P.D.J. Grootenhuis. Comparison of two implementations of the incremental construction algorithm, in flexible docking of thrombin inhibitors. J. Comput. Aided. Mol. Des. 13, 167 (1999).
28. M.D. Eldridge, C.W. Murray, T.R. Auton, G.V. Paolinine, R.P. Mee. Empirical scoring functions: I. The development of a fast empirical, scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput. Aided Mol. Des., 11, 425 (1997).
29. (a) M. Rarey, B. Kramer, T. Lengauer, G Klebe. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol., 261, 470 (1996)
30. (b) M. Rarey, B. Kramer, T. Lengauer. Docking of hydrophobic ligands with interaction-based matching algorithms. Bioinformatics, 15, 243 (1999).
31. (c) H.-J. Böhm. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional, structure. J. Comput. Aided Mol Des. 8, 243 (1994).
32. (a) I. Muegge, Y.C. Martin. A general, and fast scoring function for protein-ligand interactions: a simplified potential approach. J. Med. Chem., 42, 791 (1999)
33. (b) F.C. Bernstein, T.F. Koetzle, G.J.B. Williams, E.F. Meyer Jr., M.D. Brice, J.R. Rodgers, O. Kennard, T. Shimanouchi, M. Tasumi. The Protein Data Bank. A computer based archival file for macromolecular structures. Eur. J. Biochem. 80, 319 (1977).
34. (a) G. Jones, P. Willett, R.C. Glen. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J. Mol. Biol., 245, 43 (1995)
35. (b) G. Jones, P. Willett, R.C. Glen, A.R. Leach, R. Taylor. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267, 727 (1997).