Cluster hydration model for binding energy calculations of protein-ligand complexes

Journal of Physical Chemistry B

Volumn 113, Issue 3, 2009, Pages 809-817

  Murata, Katsumi ^a   Fedorov, Dmitri G ^b   Nakanishi, Isao ^a,c   Kitaura, Kazuo ^a,b  

^a KYOTO UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c KINKI UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; BINDING SITES; CARBON NANOTUBES; COMPLEXATION; CONCRETES; HYDRATION; LIGANDS; NUCLEAR ENERGY; POTENTIAL ENERGY;

BINDING AFFINITIES; CORRELATION COEFFICIENTS; DE SOLVATIONS; DESOLVATION ENERGIES; ELECTROSTATIC INTERACTION ENERGIES; ENERGY CALCULATIONS; EXPLICIT SOLVENTS; FK506-BINDING PROTEINS; GOOD CORRELATIONS; LIGAND INTERACTIONS; NEW MODELS; NON-POLAR; PROTEIN-LIGAND COMPLEXES;

BINDING ENERGY;

EID: 61949343293     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp805007f     Document Type: Article

References (36)

1. Beveridge, D. L.; Dicapua, F. M. Free-energy via molecular simulation: Applications to chemical and biomolecular systems. Annu. Rev. Biophys. Bio. 1989, 18, 431-492.
2. Straatsma, T. P.; McCammon, J. A. Computational alchemy. Annu. Rev. Phys. Chem. 1992, 43, 407-435.
3. Tomioka, N.; Itai, A.; Iitaka, Y. J. A method for fast energy estimation and visualization of protein-ligand interaction. J. Comput.-Aided Mol. Des. 1987, 1, 197-210.
4. Bohm, H. J. 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. 1994, 8, 243-256.
5. Wallqvist, A.; Jernigan, R. L.; Covell, D. G. A preference-based free-energy parameterization of enzyme-inhibitor binding: Applications to HIV-1-protease inhibitor design. Protein Sci. 1995, 4, 1881-1903.
6. Verkhivker, G.; Appelt, K.; Freer, S. T.; Villafranca, J. E. Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity. Protein Eng. 1995, 8, 677-691.
7. Åqvist, J.; Medina, C.; Samuelsson, J.-E. A New Method for Predicting Binding Affinity in Computer-Aided Drug Design. Protein Eng. 1994, 7, 385-391.
8. Hanson, T.; Åqvist, J. Estimation of Binding Free Energies for HIV Proteinase Inhibitors by Molecular Dynamics Simulations. Protein Eng. 1995, 8, 1137-1144.
9. Åqvist, J.; Hanson, T. On the Validity of Electrostatic Linear Response in Polar Solvents. J. Phys. Chem. 1996, 100, 9512-9521.
10. Ersmark, K.; Nervall, M.; Hamelink, E.; Janka, L. K.; Clemente, J. C.; Dunn, B. M.; Blackman, M. J.; Samuelsson, B.; Åqvist, J.; Hallberg, A. Synthesis of Malarial Plasmepsin Inhibitors and Prediction of Binding Modes by Molecular Dynamics Simulations. J. Med. Chem. 2005, 48, 6090-6106.
11. Bortolato, A.; Moro, S. In silico binding free energy predictability by using the linear interaction energy (LIE) Method: bromobenzimidazole CK2 Inhibitors as a case study. J. Chem. Inf. Model 2007, 47, 572-582.
12. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., III. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 2000, 33, 889-897.
13. Van Duyne, G. D.; Standaert, R. F.; Schreiber, S. L.; Clardy, J. Atomic structure of the rapamycin human immunophilin FKBP12 complex. J. Am. Chem. Soc. 1991, 113, 7374-7375.
14. Van Duyne, G. D.; Standaert, R. F.; Karplus, P. A.; Schreiber, S. L.; Clardy, J. Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex. Science 1991, 252, 839.
15. Holt, D. A.; Luengo, J. I.; Yamashita, D. S.; Oh, H. J.; Konialian, A. L.; Yen, H. K.; Rozamus, L. W.; Brandt, M.; Bossard, M. J.; Levy, M. A.; Eggleston, D. S.; Liang, J.; Schultz, L. W.; Stout, T. J.; Clardy, J. Design, synthesis, and kinetic evaluation of high-affinity FKBP ligands and the X-ray crystal structures of their complexes with FKBP12. J. Am. Chem. Soc. 1993, 115, 9925-9938.
16. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, i. W.; Ayala, P. Y.; Morokuma, K., Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03; Gaussian, Inc.: Wallingford, CT, 2004.
17. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Wang, B.; Pearlman, D. A.; Crowley, M.; Brozell, S.; Tsui, V.; Gohlke, H.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Schafmeister, C.; Caldwell, J. W.; Ross, W. D.; Kollman, P. A. AMBER 8; University of California: San Francisco, 2004.
18. Jorgensen, W. L.; Chandrasekhar, J.; Madurs, J.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926-935.
19. Wang, J.; Cieplak, P.; Kollman, P. A. How does well a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules. J. Comput. Chem. 2000, 21, 1049-1074.
20. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general amber force field. J. Comput. Chem. 2004, 25, 1157-1174.
21. 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.
22. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the cartesian eqations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys. 1977, 23, 327-341.
23. Connelly, P. R.; Thomson, J. A. Heat capacity changes and hydrophobic interactions in the binding of FK506 and rapamycin to the FK506 binding protein. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 4781-4785.
24. Swanson, J. M.; Henchman, R. H.; McCammon, J. A. Revisiting free energy calculations: a theoretical connection to MM/PB/SA and direct calculation of the association free energy. Biophys. J. 2004, 86, 67-74.
25. Xu, Y.; Wang, R. A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method. Proteins: Struct., Funct., Bioinf. 2006, 64, 1058-1068.
26. Lee, M. S.; Olson, M. A. Calculation of absolute protein-ligand binding affinity using path and endpoint approaches. Biophys. J. 2006, 90, 864-877.
27. Phillips, G.; Guilford, W. J.; Buckman, B. O.; Davey, D. D.; Eagen, K. A.; Koovakkat, S.; Liang, A.; McCarrick, M.; Mohan, R.; Ng, H. P.; Pinkerton, M.; Subramanyam, B.; Ho, E.; Trinh, L.; Whitlow, M.; Wu, S.; Xu, W.; Morrissey, M. M. Design, synthesis, and activity of a novel series of factor Xa inhibitors: Optimization of arylamidine groups. J. Med. Chem. 2002, 45, 2484-2493.
28. Linus, S. L.; Sookhee, H.; Richard, G. B.; Nancy, N. T.; Laurie, A. C; George, A. D.; Tung, M. F.; hun-Pyn, S.; Jing, C. X.; Mark, T. G.; William, K. H. Conformational analysis and receptor docking of N-[(15,25)-3-(4-Chlorophenyl) -2-(3-cyanophenyl)-l-methylpropyl]-2-methyl-2-{[5-(trifluoromefhyl)pyridin-2-yl] oxy)propanamide (Taranabant, MK-0364), a novel, acyclic cannabinoid-1 receptor inverse agonist. J. Med. Chem. 2008, 57, 2108-2114.
29. Michael, R. D.; Willy, B. T.; Akhilesh, B. B.; Scott Perrin Jr.; Jyotsna, T.; Alison, R.; Challa, V. K. Contributions of Hydroxy ethyl Groups to the DNA Binding Affinities of Anthracene Probes. J. Phys. Chem. B 2006, 110, 20693-20701.
30. Ajay, A.; Murcko, M. A. Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes. J. Med. Chem. 1995, 38, 2484-2493.
31. Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R.; Halgren, T. A.; Sanschagrin, P. C; Mainz, D. T. Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem. 2006, 49, 6177-96.
32. Watson, K. A.; Mitchell, E. P.; Johnson, L. N.; Son, J. C.; Bichard, C. J. F.; Orchard, M. G.; Fleet, G. W. J.; Oikonomakos, N. G.; Leonidas, D. D.; Kontou, M.; Papageorgiouil, A. Design of inhibitors of glycogen phosphorylase: A study of α-and β-C-glucosides and l-thio-β-D-glucose compounds. Biochemistry 1994, 33, 5745-5758.
33. Nakanishi, I.; Fedorov, D. G.; Kitaura, K. Molecular recognition mechanism of FK506 binding protein: an all-electron fragment molecular orbital study. Proteins: Struct., Funct., Bioinf. 2007, 68, 145-158.
34. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. In Intermolecular Forces; Pullman, B., Ed.; Reidel: Dordrecht, The Netherlands, 1981; p 331.
35. Yu, H.; van Gunsteren, W. F. Charge-on-spring polarizable water models revisited: from water clusters to liquid water to ice. J. Chem. Phys. 2004, 121, 9549-9564.
36. Stllinger, H. F.; Rahman, A. Improved simulation of liquid water by molecular dynamics. J. Phys. 1974, 60, 1545-1557.