The computational differentiation of binding modes for CDK2 bound purine analogs

Medicinal Chemistry Research

Volumn 12, Issue 8, 2003, Pages 435-443

  Shen, Jian ^a   Borcherding, David ^a  

^a SANOFI   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE 2; PURINE DERIVATIVE;

ARTICLE; CALCULATION; CARBON NUCLEAR MAGNETIC RESONANCE; CHEMICAL BINDING; ELECTRICITY; HYDROGEN BOND; INFRARED SPECTROSCOPY; PROTEIN BINDING; PROTON NUCLEAR MAGNETIC RESONANCE; X RAY CRYSTALLOGRAPHY;

EID: 3042615324     PISSN: 10542523     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (23)

1. Reyes, V. M.; Sawaya, M. R.; Brown, K. A.; Kraut, J. Isomorphous crystal structures of Escherichia coli dihydrofolate reductase complexed with folate, 5-deazafolate, and 5,10-dideazatetrahydrofolate: mechanistic implications. Biochemistry 1995, 34, 2710-2723.
2. Backbro, K.; Lowgren, S.; Osterlund, K.; Atepo, J.; Unge, T.; Hulten, J.; Bonham, N. M.; Schaal, W.; Karlen, A.; Hallberg, A. Unexpected binding mode of a cyclic sulfamide HIV-1 protease inhibitor. J Med Chem 1997, 40, 898-902.
3. Schulze-Gahmen, U.; Brandsen, J.; Jones, H. D.; Morgan, D. O.; Meijer, L.; Vesely, J.; Kim, S. H. Multiple modes of ligand recognition: crystal structures of cyclin- dependent protein kinase 2 in complex with ATP and two inhibitors, olomoucine and isopentenyladenine. Proteins 1995, 22, 378-391.
4. Russo, A. A.; Jeffrey, P. D.; Pavletich, N. P. Structural basis of cyclin-dependent kinase activation by phosphorylation. Nat Struct Biol 1996, 3, 696-700.
5. Gray, N. S.; Wodicka, L.; Thunnissen, A. M.; Norman, T. C.; Kwon, S.; Espinoza, F. H.; Morgan, D. O.; Barnes, G.; LeClerc, S.; Meijer, L.; Kim, S. H.; Lockhart, D. J.; Schultz, P. G. Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors. Science 1998, 281, 533-538.
6. De Azevedo, W. F.; Leclerc, S.; Meijer, L.; Havlicek, L.; Strnad, M.; Kim, S. H. Inhibition of cyclin-dependent kinases by purine analogues: crystal structure of human cdk2 complexed with roscovitine. European Journal of Biochemistry 1997, 243, 518-526.
7. Legraverend, M.; Tunnah, P.; Noble, M.; Ducrot, P.; Ludwig, O.; Grierson, D. S.; Leost, M.; Meijer, L.; Endicott, J. Cyclin-dependent kinase inhibition by new C-2 alkynylated purine derivatives and molecular structure of a CDK2-inhibitor complex. In Journal of Medicinal Chemistry: United States, 2000; pp 1282-1292.
8. Arris, C. E.; Boyle, F. T.; Calvert, A. H.; Curtin, N. J.; Endicott, J. A.; Garman, E. F.; Gibson, A. E.; Golding, B. T.; Grant, S.; Griffin, R. J.; Jewsbury, P.; Johnson, L. N.; Lawrie, A. M.; Newell, D. R.; Noble, M. E.; Sausville, E. A.; Schultz, R.; Yu, W. Identification of novel purine and pyrimidine cyclin-dependent kinase inhibitors with distinct molecular interactions and tumor cell growth inhibition profiles. J Med Chem 2000, 43, 2797-2804.
9. Dreyer, M. K.; Borcherding, D. R.; Dumont, J. A.; Peet, N. P.; Tsay, J. T.; Wright, P. S.; Bitonti, A. J.; Shen, J.; Kim, S. H. Crystal structure of human cyclin-dependent kinase 2 in complex with the adenine-derived inhibitor H717. J Med Chem 2001, 44, 524-530.
10. Davies, T. G.; Bentley, J.; Arris, C. E.; Boyle, F. T.; Curtin, N. J.; Endicott, J. A.; Gibson, A. E.; Golding, B. T.; Griffin, R. J.; Hardcastle, I. R.; Jewsbury, P.; Johnson, L. N.; Mesguiche, V.; Newell, D. R.; Noble, M. E.; Tucker, J. A.; Wang, L.; Whitfield, H. J. Structure-based design of a potent purine-based cyclin-dependent kinase inhibitor. Nat Struct Biol 2002, 9, 745-749.
11. Shen, J.; Pearlstein, R. A.; Vaz, R. J.; Kominos, D.; Effland, R. C. The use of interaction energy and solvation entropy to rank order docked ligand-protein complexes for lead optimization: application to thermolysin inhibitors. In Medicinal Chemistry Research, 1999; pp 501-512.
12. Trosset, J. Y.; Scheraga, H. A. Reaching the global minimum in docking simulations: a Monte Carlo energy minimization approach using Bezier splines. Proc Natl Acad Sci USA 1998, 95, 8011-8015.
13. Luty, B. A.; Wasserman, Z. R.; Stouten, P. F. W.; Hodge, C. N.; Zacharias, M.; McCammon, J. A. A molecular mechanics/grid method for evaluation of ligand-receptor interactions. Journal of Computational Chemistry 1995, 16, 454-464.
14. Ortiz, A. R.; Pisabarro, M. T.; Gago, F.; Wade, R. C. Prediction of drug binding affinities by comparative binding energy analysis. J Med Chem 1995, 38, 2681-2691.
15. Wong, C. F.; McCammon, J. A. Dynamics and design of enzymes and inhibitors. J. Am. Chem. Soc. 1986, 108, 3830.
16. Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A. Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science 1987, 235, 574-576.
17. Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R.; Ferrin, T. E. A geometric approach to macromolecule-ligand interactions. J Mol Biol 1982, 161, 269-288.
18. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J Mol Biol 1996, 261, 470-489.
19. Bamborough, P.; Cohen, F. E. Modeling protein-ligand complexes. Curr Opin Struct Biol 1996, 6, 236-241.
20. Dixon, J. S. Evaluation of the CASP2 docking section. Proteins 1997, Suppl, 198-204.
21. Buzko, O. V.; Bishop, A. C.; Shokat, K. M. Modified AutoDock for accurate docking of protein kinase inhibitors. J Comput Aided Mol Des 2002, 16, 113-127.
22. 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.
23. Denessiouk, K. A.; Johnson, M. S. When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families. Proteins 2000, 38, 310-326.