Cross-docking of inhibitors into CDK2 structures. 1

Journal of Chemical Information and Modeling

Volumn 48, Issue 3, 2008, Pages 659-668

  Duca, José S ^a   Madison, Vincent S ^a   Voigt, Johannes H ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOCKING; ENZYME INHIBITION; LIGANDS;

BINDING AFFINITY; COMPUTATIONAL CHEMISTRY;

PROTEINS;

CYCLIN DEPENDENT KINASE 2; PROTEIN KINASE INHIBITOR;

ARTICLE; CHEMISTRY; CONFORMATION; DRUG ANTAGONISM;

CYCLIN-DEPENDENT KINASE 2; MOLECULAR CONFORMATION; PROTEIN KINASE INHIBITORS;

EID: 42149184268     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci7004274     Document Type: Article

References (30)

1. Leach, A. R.; Shoichet, B. K.; Peishoff, C. E. Prediction of Protein-Ligand Interactions. Docking and Scoring: Successes and Gaps. J. Med. Chem. 2006, 49, 5851-5855, and references therein.
2. Perola, E.; Walters, W. P.; Charifson, P. S. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins: Struct., Funct., Bioinf. 2004, 56, 235-249.
3. Perola, E.; Walters, W. P.; Charifson, P. Comments on the Article On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors. J. Chem. Inf. Model. 2007, 47, 251-253.
4. Cavasotto, C. N.; Abagyan, R. A. Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases. J. Mol. Biol. 2004, 337, 209-225.
5. Fedorov, O.; Sundström, M.; Marsden, B.; Knapp, S. Insights for the development of specific kinase inhibitors by targeted structural genomics. Drug Discovery Today 2007, 12, 365-372.
6. (a) Pavletich, N. P. Mechanisms of cyclin-dependent kinase regulation: structures of cdks, their cyclin activators, and cip and INK4 inhibitors. J. Mol. Biol. 1999, 287, 821-828.
7. (b) Russo, A. A.; Tong, L.; Lee, J. O.; Jeffrey, P. D.; Pavletich, N. P. Structural basis for inhibition of the cyclin-dependent kinase Cdk6 by the tumour suppressor p16 INK4a. Nature 1998, 395, 237-243.
8. (a) Park, H.; Yeom, M. S.; Lee, S. Loop Flexibility and Solvent Dynamics as Determinants for the Selective Inhibition of Cyclin-Dependent Kinase 4: Comparative Molecular Dynamics Simulation Studies of CDK 2 and CDK 4. Chem. Bio. Chem. 2004, 5, 1662-1672.
9. (b) Kriz, Z.; Otyepka, M.; Bártová, I.; Koca, J. Analysis of CDK2 Active-Site Hydration: A Method to Design New Inhibitors. Proteins: Struct., Funct., Bioinf. 2004, 55, 258-274.
10. (c) Villacanas, O.; Perez, J. J.; Rubio-Martinez, J. Structural analysis of the inhibition of Cdk4 and Cdk6 by p16 (INK4a) through molecular dynamics simulations. J. Biomol. Struct. Dyn. 2002, 20, 347-358.
11. Dwyer, M. P.; Paruch, K.; Alvarez, C.; Doll, R. J.; Keertikar, K. et al. Versatile templates for the development of novel kinase inhibitors: Discovery of novel CDK inhibitors. Bioorg. Med. Chem. Lett. 2007, 17, 6216-6219.
12. Fischmann, T. O.; Hruza, A.; Duca, J. S.; Ramanathan, L.; Mayhood, T. et al. Structure-guided discovery of cyclin-dependent kinase inhibitors. Biopolymers (Pept. Sci.) 2008, 89, 372-379.
13. Schrödinger, LLC, New York, NY, 2007.
14. Pipeline Pilot v. 6.0.3.0; Accelrys, Inc.: San Diego, CA.
15. Jones, G.; Willett, P.; Glen, R. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J. Mol. Biol. 1995, 245, 43-53.
16. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727-748.
17. Ihlenfeldt, W. D.; Takahashi, Y.; Abe, H.; Sasaki, S. Computation and management of chemical properties in CACTVS: An extensible networked approach toward modularity and compatibility. J. Chem. Inf. Comput. Sci. 1994, 34, 109-116.
18. Hawkins, P. C. D.; Skillman, A. G.; Nicholls, A. Comparison of shape-matching and docking as virtual screening tools. J. Med. Chem. 2007, 50, 74-82.
19. Warren, G. L.; Andrews, C. W.; Capelli, A. M.; Clarke, B.; LaLonde, J. et al. A critical assessment of docking programs and scoring functions. J. Med. Chem. 2006, 49, 5912-5931.
20. Shoichet, B. Virtual screening of chemical libraries. Nature 2004, 432, 862-865.
21. All histograms are centered, which means e.g. a bin labeled with 10% contains items from 5% to 15% and a 1 Å RMSD or average RMSD bin with a bin size of 0.5 Å contains items ranging from 0.75 to 1.25
22. Cummings, M. D.; DesJarlais, R. L.; Gibbs, A. C.; Mohan, V.; Jaeger, E. P. Comparison of automated docking programs as virtual screening tools. J. Med. Chem. 2005, 48, 962-976.
23. Chen, H.; Lyne, P. D.; Giordanetto, F.; Lovell, T.; Li, J. On evaluating molecular-docking methods for pose prediction and enrichment factors, J. Chem. Inf. Model. 2006, 46, 401-415.
24. Lovell, T.; Chen, H.; Lyne, P. D.; Giordanetto, F.; Li, J. On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors. J. Chem. Inf. Model. 2006, 46, 401-415.
25. (a) Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J. 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.
26. (b) Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R. 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.
27. Tirado-Rives, J.; Jorgensen, W. L. Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding. J. Med. Chem. 2006, 49, 5880-5884.
28. CCDC. Gold v2.2; Cambridge Crystallography Data Centre, 12 Union Road, Cambridge, England.
29. Chang, C. A.; Chen, W.; Gilson, M. K. Ligand configurational entropy and protein binding. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 1534.
30. Voigt, J. H.; Elkin, C.; Madison, V. S.; Duca, J. S. Cross docking of inhibitors into CDK2 structures. 2. J. Chem. Inf. Model. 2008, 48, 669-678.