Evaluating the molecular mechanics Poisson-Boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP Kinase

Journal of Medicinal Chemistry

Volumn 48, Issue 24, 2005, Pages 7796-7807

  Pearlman, David A ^a  

^a NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; MITOGEN ACTIVATED PROTEIN KINASE P38;

ARTICLE; BINDING AFFINITY; CALCULATION; ENERGY; MOLECULAR MECHANICS; SIMULATION; THERMODYNAMICS;

EID: 28144441347     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm050306m     Document Type: Article

References (58)

1. Postma, J. P. M.; Berendsen, H. J. C.; Haak, J. R. Thermodynamics of cavity formation in water. Faraday Symp. Chem. Soc. 1982, 17, 55-67.
2. Tembe, B. L.; McCammon, J. A. Ligand-receptor interactions. Comput. Chem. 1984, 8, 281-283.
3. Jorgensen, W. L.; Ravimohan, C. Monte Carlo simulation of differences in free energies of hydration. J. Chem. Phys. 1985, 83, 3050-3054.
4. Zwanzig, R. W. High-temperature equation of state by a perturbation method. I. Nonpolar gases. J. Chem. Phys. 1954, 22, 1420-1426.
5. Straatsma, T. P.; Berendsen, H. J. C.; Postma, J. P. M. Free energy of hydrophobic hydration: A molecular dynamics study of noble gases in water. J. Chem. Phys. 1986, 85, 6720-6727.
6. Lybrand, T.; McCammon, J. A.; Wipff, G. Theoretical calculation of relative binding affinity in host-guest systems. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 833-835.
7. Hwang, J. K.; Warshel, A. Semiquantitative calculations of catalytic free energies in genetically modified enzymes. Biochemistry 1987, 26, 2669-2673.
8. Mitchell, M. J.; McCammon, J. A. Free energy difference calculations by thermodynamic integration. Difficulties in obtaining a precise value. J. Comput. Chem. 1991, 12, 271-275.
9. Pearlman, D. A.; Kollman, P. A. The overlooked bond-stretching contribution in free energy perturbation calculations. J. Chem. Phys. 1991, 94, 4532-4545.
10. Pearlman, D. A. Determining the contributions of constraints in free energy calculations: development, characterization, and recommendations. J. Chem. Phys. 1993, 98, 8946-8957.
11. Straatsma, T. P.; McCammon, J. A. Multiconfiguration thermodynamic integration. J. Chem. Phys. 1991, 95, 1175-1188.
12. Pearlman, D. A. Free energy derivatives: a new method for probing the convergence problem in free energy calculations. J. Comput. Chem. 1994, 15, 105-123.
13. Mazor, M.; Pettitt, B. M. Convergence of the chemical potential in aqueous simulations. Mol. Simul. 1991, 6, 1-4.
14. Helms, V.; Wade, R. C. Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy. J. Comput. Chem. 1997, 18, 449-462.
15. Hodel, A.; Simonson, T.; Fox, R. O.; Brunger, A. T. Conformational substates and uncertainty in macromolecular free energy calculations. J. Phys. Chem. 1993, 97, 3409-3417.
16. Gordon, E. M.; Barrett, R. W.; Dower, W. J.; Fodor, S. P.; Gallop, M. A. Applications of combinatorial technologies to drug discovery. 2. Combinatorial organic synthesis, library screening strategies, and future directions. J. Med. Chem. 1994, 37, 1385-1401.
17. Frank, R. Simultaneous and combinatorial chemical synthesis techniques for the generation and screening of molecular diversity. J. Biotechnol. 1995, 41, 259-272.
18. Walters, W. P.; Stahl, M. T.; Murcko, M. A. Virtual screening. An overview. Drug Discovery Today 1998, 3, 160-178.
19. Aqvist, J.; Medina, C.; Samuelsson, J. E. A new method for predicting binding affinity in computer-aided drug design. Protein Eng. 1994, 7, 385-391.
20. Wang, W.; Wang, J.; Kollman, P. A. What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations? Proteins 1999, 34, 395-402.
21. Carlson, H. A.; Jorgensen, W. L. An extended linear response method for determining free energies of hydration. J. Phys. Chem. 1995, 99, 10667-10673.
22. Radmer, R. J.; Kollman, P. A. The application of three approximate free energy calculations methods to structure based ligand design: trypsin and its complex with inhibitors. J. Comput.-Aided Mol. Des. 1998, 12, 215-227.
23. Pearlman, D. A. Free energy grids: a practical qualitative application of free energy perturbation to ligand design using the OWFEG method. J. Med. Chem. 1999, 42, 4313-4324.
24. Srinivasan, J.; Miller, J.; Kollman, P. A.; Case, D. A. Continuum solvent studies of the stability of RNA hairpin loops and helices. J. Biomol. Struct. Dyn. 1998, 16, 671-682.
25. Vorobjev, Y. N.; Almagro, J. C.; Hermans, J. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model. Proteins 1998, 32, 399-413.
26. Jayaram, B.; Sprous, D.; Yong, M. A.; Beveridge, D. L. Free energy analysis of the conformational preferences of A and B forms of DNA in solution. J. Am. Chem. Soc. 1998, 120, 10629-10633.
27. Sims, P. A.; Wong, C. F.; McCammon, J. A. A computational model of binding thermodynamics: the design of cyclin-dependent kinase 2 inhibitors. J. Med. Chem. 2003, 46, 3314-3325.
28. Honig, B.; Sharp, K. A.; Yang, A.-S. Macroscopic models of aqueous solutions. Biological and chemical applications. J. Phys. Chem. 1993, 97, 1101-1109.
29. Pearlman, D. A.; Rao, B. G. Free energy calculations: methods and applications. Encycl. Comput. Chem. 1998, 1036-1061.
30. Wang, J.; Morin, P.; Wang, W.; Kollman, P. A. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J. Am. Chem. Soc. 2001, 123, 5221-5230.
31. Gohlke, H.; Kiel, C.; Case, D. A. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J. Mol. Biol. 2003, 330, 891-913.
32. Huo, S.; Wang, J.; Cieplak, P.; Kollman, P. A.; Kuntz, I. D. Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design. J. Med. Chem. 2002, 45, 1412-1419.
33. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 2000, 33, 889-897.
34. Kuhn, B.; Kollman, P. A. Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. J. Med. Chem. 2000, 43, 3786-3791.
35. Gouda, H.; Kuntz, I. D.; Case, D. A.; Kollman, P. A. Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods. Biopolymers 2003, 68, 16-34.
36. Chong, L. T.; Duan, Y.; Wang, L.; Massova, I.; Kollman, P. A. Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 14330-14335.
37. Pearlman, D. A.; Charifson, P. S. Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system. J. Med. Chem. 2001, 44, 3417-3423.
38. Charifson, P. S.; Corkery, J. J.; Murcko, M. A.; Walters, W. P. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J. Med. Chem. 1999, 42, 5100-5109.
39. Murray, C. W.; Auton, T. R.; Eldridge, M. D. Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model. J. Comput.-Aided Mol. Des. 1998, 12, 503-519.
40. Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. 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. 1997, 11, 425-445.
41. Gehlhaar, D. K.; Verkhivker, G. M.; Rejto, P. A.; Sherman, C. J.; Fogel, D. B.; et al. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. Chem. Biol. 1995, 2, 317-324.
42. Meng, E. C.; Shoichet, B. K.; Kuntz, I. D. Automated docking with grid-based energy evaluation. J. Comput. Chem. 1992, 13, 505-524.
43. Ewing, T. J. A.; Kuntz, I. D. Critical evaluation of search algorithms for automated molecular docking and database screening. J. Comput. Chem. 1997, 18, 1175-1189.
44. Wilson, K. P.; McCaffrey, P. G.; Hsiao, K.; Pazhanisamy, S.; Galullo, V.; et al. The structural basis for the specificity of pyridinylimidazole inhibitors of p38 MAP kinase. Chem. Biol. 1997, 4, 423-431.
45. Pearlman, D. A.; Charifson, P. S. Improved scoring of ligand-protein interactions using OWFEG free energy grids. J. Med. Chem. 2001, 44, 502-511.
46. Pearlman, D. A.; Walters, W. P. Manuscript in preparation.
47. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; 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.
48. Pearlman, D. A.; Case, D. A.; Caldwell, J. C.; Ross, W. S.; Cheatham, T. E., III; et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Comm. 1995, 91, 1-41.
49. Warwicker, J.; Watson, H. C. Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. J. Mol. Biol. 1982, 157, 671-679.
50. Sharp, K. A.; Honig, B. Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Biophys. Chem. 1990, 19, 301-332.
51. Honig, B.; Nicholls, A. Classical electrostatics in biology and chemistry. Science 1995, 268, 1144-1149.
52. Sitkoff, D.; Sharp, K. A.; Honig, B. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 1994, 98, 1978-1988.
53. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B. G.; Chen, W.; Wong, M. W.; Andres, J. L.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98, revision A.3; Gaussian, Inc.: Pittsburgh, PA, 1998.
54. Sanner, M. F.; Olson, A. J.; Spehner, J. C. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 1996, 38, 305-320.
55. Brooks, B. R.; Janezic, D.; Karplus, M. Harmonic analysis of large systems. J. Comput. Chem. 1995, 16, 1522-1553.
56. MacKerell, J. A. D. D.; Bashford, D.; Bellot, M.; Dunbrack, R. L.; Evanseck, J. D.; et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102, 3586-3616.
57. 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.
58. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating water. J. Chem. Phys. 1983, 79, 926-935.