An in silico approach for the discovery of CDK5/p25 interaction inhibitors

Biotechnology Journal

Volumn 6, Issue 7, 2011, Pages 871-881

  Zhang, Bing ^a,b   Corbel, Caroline ^c   Guéritte, Françoise ^d   Couturier, Cyril ^e   Bach, Stéphane ^c   Tan, Vincent B C ^a  

^a NORTH CHINA ELECTRIC POWER UNIVERSITY   (China)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c Protein Phosphorylation and Human Disease Group   (France)

^d INSTITUT DE CHIMIE DES SUBSTANCES NATURELLES   (France)

^e UNIV LILLE   (France)

Author keywords

CDK5; Molecular dynamics; Protein protein interaction inhibitor; Virtual screening; Virtural alanine scanning

Indexed keywords

AMINO ACIDS; BINDING SITES; ENZYME INHIBITION; MOLECULES;

ATP BINDING POCKETS; CDK5; CYCLIN-DEPENDENT KINASE; INHIBITION MECHANISMS; MOLECULAR DYNAMICS SIMULATIONS; PROTEIN-PROTEIN INTERACTIONS; SELECTIVE INHIBITORS; VIRTUAL SCREENING;

MOLECULAR DYNAMICS;

3ALPHA AMINO 5ALPHA ANDROSTANE; ALANINE; ANDROSTANE DERIVATIVE; CYCLIN DEPENDENT KINASE 5; CYCLIN DEPENDENT KINASE INHIBITOR; HYDROCORTISONE; NSC 280997; NSC 88915; PROTEIN P25; ROSCOVITINE; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; BIOASSAY; COMPUTER MODEL; DRUG PROTEIN BINDING; DRUG SCREENING; ENZYME INHIBITION; ENZYME SUBSTRATE COMPLEX; IC 50; INHIBITION KINETICS; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; STRUCTURE ACTIVITY RELATION;

EID: 79960022984     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.201100139     Document Type: Article

References (48)

1. Harper, J. W., Adams, P. D., Cyclin-dependent kinases. Chem. Rev. 2001, 101, 2511-2526.
2. Hunter, T., Pines, J., Cyclins and cancer. II: Cyclin D and CDK inhibitors come of age. Cell 1994, 79, 573-582.
3. Norbury, C., Nurse, P., Animal cell cycles and their control. Annu. Rev. Biochem. 1992, 61, 441-470.
4. De Azevedo, W. F. Jr., Mueller-Dieckmann, H. J., Schulze-Gahmen, U., Worland, P. J. et al., Structural basis for specificity and potency of a flavonoid inhibitor of human CDK2, a cell cycle kinase. Proc. Natl. Acad. Sci. USA 1996, 93, 2735-2740.
5. De Azevedo, W. F., Leclerc, S., Meijer, L., Havlicek, L. et al., Inhibition of cyclin-dependent kinases by purine analogues: crystal structure of human cdk2 complexed with roscovitine. Eur. J. Biochem. 1997, 243, 518-526.
6. Garrett, M. D., Fattaey, A., CDK inhibition and cancer therapy. Curr. Opin. Genet. Dev. 1999, 9, 104-111.
7. Webster, K. R., The therapeutic potential of targeting the cell cycle. Expert. Opin. Investig. Drugs 1998, 7, 865-887.
8. Tarricone, C., Dhavan, R., Peng, J., Areces, L. B. et al., Structure and regulation of the CDK5-p25(nck5a) complex. Mol. Cell. 2001, 8, 657-669.
9. Smith, D. S., Greer, P. L., Tsai, L. H., Cdk5 on the brain. Cell Growth Differ. 2001, 12, 277-283.
10. Dhavan, R., Tsai, L. H., A decade of CDK5. Nat. Rev. Mol. Cell Biol. 2001, 2, 749-759.
11. Bibb, J. A., Snyder, G. L., Nishi, A., Yan, Z. et al., Phosphorylation of DARPP-32 by Cdk5 modulates dopamine signalling in neurons. Nature 1999, 402, 669-671.
12. Nguyen, M. D., Julien, J. P., Cyclin-dependent kinase 5 in amyotrophic lateral sclerosis. Neurosignals 2003, 12, 215-220.
13. Lau, L. F., Ahlijanian, M. K., Role of cdk5 in the pathogenesis of Alzheimer's disease. Neurosignals 2003, 12, 209-214.
14. Smith, P. D., Crocker, S. J., Jackson-Lewis, V., Jordan-Sciutto, K. L. et al., Cyclin-dependent kinase 5 is a mediator of dopaminergic neuron loss in a mouse model of Parkinson's disease. Proc. Natl. Acad. Sci. USA 2003, 100, 13650-13655.
15. Bu, B., Li, J., Davies, P., Vincent, I., Deregulation of cdk5, hyperphosphorylation, and cytoskeletal pathology in the Niemann-Pick type C murine model. J. Neurosci. 2002, 22, 6515-6525.
16. Wang, J., Liu, S., Fu, Y., Wang, J. H., Lu, Y., Cdk5 activation induces hippocampal CA1 cell death by directly phosphorylating NMDA receptors. Nat. Neurosci. 2003, 6, 1039-1047.
17. Mapelli, M., Massimiliano, L., Crovace, C., Seeliger, M. A. et al., Mechanism of CDK5/p25 binding by CDK inhibitors. J. Med. Chem. 2005, 48, 671-679.
18. Jeffrey, P. D., Russo, A. A., Polyak, K., Gibbs, E. et al., Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex. Nature 1995, 376, 313-320.
19. Leclerc, S., Garnier, M., Hoessel, R., Marko, D. et al., Indirubins inhibit glycogen synthase kinase-3 beta and CDK5/p25, two protein kinases involved in abnormal tau phosphorylation in Alzheimer's disease. A property common to most cyclin-dependent kinase inhibitors? J. Biol. Chem. 2001, 276, 251-260.
20. Sausville, E. A., Complexities in the development of cyclin-dependent kinase inhibitor drugs. Trends Mol. Med. 2002, 8, S32-37.
21. Noble, M. E., Endicott, J. A., Johnson, L. N., Protein kinase inhibitors: Insights into drug design from structure. Science 2004, 303, 1800-1805.
22. Noble, M., Barrett, P., Endicott, J., Johnson, L. et al., Exploiting structural principles to design cyclin-dependent kinase inhibitors. Biochim. Biophys. Acta 2005, 1754, 58-64.
23. Blazer, L. L., Neubig, R. R., Small molecule protein-protein interaction inhibitors as CNS therapeutic agents: current progress and future hurdles. Neuropsychopharmacology 2009, 34, 126-141.
24. Fry, D. C., Vassilev, L. T., Targeting protein-protein interactions for cancer therapy. J. Mol. Med. 2005, 83, 955-963.
25. Arkin, M. R., Wells, J. A., Small-molecule inhibitors of protein-protein interactions: Progressing towards the dream. Nat. Rev. Drug Discov. 2004, 3, 301-317.
26. Zhang, B., Su, Z. C., Tay, T. E., Tan, V. B., Mechanism of CDK5 activation revealed by steered molecular dynamics simulations and energy calculations. J. Mol. Model. 2010, 16, 1159-1168.
27. Morris, M. C., Gondeau, C., Tainer, J. A., Divita, G., Kinetic mechanism of activation of the Cdk2/cyclin A complex. Key role of the C-lobe of the Cdk. J. Biol. Chem. 2002, 277, 23847-23853.
28. Endicott, J. A., Nurse, P., Johnson, L. N., Mutational analysis supports a structural model for the cell cycle protein kinase p34. Protein Eng. 1994, 7, 243-253.
29. Clackson, T., Wells, J. A., A hot spot of binding energy in a hormone-recepotr interface. Science 1995, 27, 383-386.
30. DeLano, W. L., Unraveling hot spots in binding interfaces: Progress and challenges. Curr Opin. Struct. Biol. 2002, 12, 14-20.
31. Ma, B., Wolfson, H. J., Nussinov, R., Protein functional epitopes: Hot spots, dynamics and combinatorial libraries. Curr. Opin. Struct. Biol. 2001, 11, 364-369.
32. Massova, I., Kollman, P. A., Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies. J. Am. Chem. Soc. 1999, 121, 8133-8143.
33. Corbel, C., Wang, Q., Bousserouel, H., Hamdi, A. et al., First BRET-based screening assay performed in budding yeast leads to the discovery of CDK5/p25 interaction inhibitors. Biotechnol. J., in press.
34. Bacart, J., Corbel, C., Jockers, R., Bach, S., Couturier, C., The BRET technology and its application to screening assays. Biotechnol. J. 2008, 3, 311-324.
35. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., Klein, M. L., Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926-935.
36. Case, D. A., Darden, T. A., Cheatham, I., T. E., Simmerling, C. L. et al., AMBER 9. University of California, San Francisco 2006.
37. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R. et al., A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
38. Darden, T., York, D., Pedersen, L., Particle mesh Ewald: An N.log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089-10092.
39. Ryckaert, J. P., Ciccotti, G., Berendsen, H. J. C., Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys. 1977, 23, 327-341.
40. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., Haak, J. R., Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984, 81, 3684-3690.
41. Massova, I., Kollman, P. A., Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding. Perspect. Drug Discov. Design 2000, 18, 113-135.
42. Connolly, M. L., Analytical molecular surface calculation. J. Appl. Cryst. 1983, 16, 548-558.
43. Sitkoff, D., Sharp, K. A., Honig, B., Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 1994, 98, 1978-1988.
44. Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A. et al., Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 2004, 47, 1739-1749.
45. Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L. et al., Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem. 2006, 49, 6177-6196.
46. Lipinski, C. A., Lombardo, F., Dominy, B. W., Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 1997, 23, 3-25.
47. Zhang, B., Tan, V. B., Lim, K. M., Tay, T. E., Molecular dynamics simulations on the inhibition of cyclin-dependent kinases 2 and 5 in the presence of activators. J. Comput. Aided Mol. Des. 2006, 20, 395-404.
48. Zhang, B., Tan, V. B., Lim, K. M., Tay, T. E., Significance of water molecules in the inhibition of cylin-dependent kinase 2 and 5 complexes. J. Chem. Inf. Model. 2007, 47, 1877-1885.