Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease

Proteins: Structure, Function and Genetics

Volumn 39, Issue 4, 2000, Pages 393-407

  Sham, Yuk Yin ^a,b   Chu, Zhen Tao ^a   Tao, Holly ^a,c   Warshel, Arieh ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c DoubleTwist Inc   (United States)

Author keywords

Binding entropy; Drug design; Ligand binding; Linear Response Approximation

Indexed keywords

ANTIRETROVIRUS AGENT; ANTIVIRUS AGENT; PROTEINASE INHIBITOR;

ARTICLE; DRUG DESIGN; ENERGY; ENTROPY; HUMAN IMMUNODEFICIENCY VIRUS; HYDROPHOBICITY; LIGAND BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEINASE INHIBITION; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

HUMAN IMMUNODEFICIENCY VIRUS;

EID: 0342321950     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(20000601)39:4<393::AID-PROT120>3.0.CO;2-H     Document Type: Article

References (36)

1. Warshel A, Sussman F, Hwang J-K. Evaluation of catalytic free energies in genetically modified proteins. J Mol Biol 1988;201:139-159.
2. Kollman P. Free energy calculations: applications to chemical and biochemical phenomena. Chem Rev 1993;93:2395-2417.
3. Merz KM, Jr, Rossi KA, Smith GM, Baldwin JJ. Application of the free energy perturbation method to human carbonic anhydrase II inhibitors. J Med Chem 1995;38:2061-2069.
4. Lee FS, Chu ZT, Bolger MB, Warshel A. Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603. Prot Eng 1992;5:215-228.
5. Åqvist J, Medina C, Samuelsson J-E. A new method for predicting binding affinity in computer-aided drug design. Prot Eng 1994;7: 385-391.
6. Åqvist J, Hansson T. Estimation of binding free energy for HIV proteinase inhibitors by molecular dynamics simulations. Prot Eng 1995;8:1137-1144.
7. Bohm HJ, Klebe G. What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs. Ang Chemie 1996;35:2589-2614.
8. Madura JD, Nakajima Y, Hamilton RM, Wierzbicki A, Warshel A. Calculations of the electrostatic free energy contributions to the binding free energy of sulfonamides to carbonic anhydrase. Struc Chem 1996;7:131-137.
9. Muegge I, Tao H, Warshel A, A fast estimate of electrostatic group contributions to the free energy of protein inhibitor binding. Prot Eng 1998;10:1363-1372.
10. Froloff N, Windemuth A, Honig B, On the calculation of binding free energies using continuum methods: application to MHC class-I protein-peptide interactions. Protein Sci 1997;6:1293-1301.
11. Warshel A, Dynamics of reactions in polar solvents: semiclassical trajectory studies of electron-transfer and proton-transfer reactions. J Phys Chem 1982;86:2218-2224.
12. Hwang J-K, Warshel A. Microscopic examination of free energy relationships for electron transfer in polar solvents. J Am Chem Soc 1987;109:715-720.
13. Warshel A, Hwang J-K. Simulation of the dynamics of electron transfer reactions in polar solvents: semiclassical trajectories and dispersed polaron approaches. J Chem Phys 1986;84:4938-4957.
14. King G, Warshel, A. Investigation of the free energy functions for electron transfer reactions. J Chem Phys 1990;93:8682-8692.
15. Kuharski RA, Bader JS, Chandler D, Sprik M, Klein M L, Impey RW. Molecular models for aqueous ferrous-ferric electron transfer. J Chem Phys 1988;89:3248.
16. Levy RM, Belhadj M, Kitchen DB. Gaussian fluctuation formuale for electrostatic free-energy changes in Soluton. J Chem Phys 1991;95:3627-3633.
17. Marcus RA. Chemical and electrochemical electron transfer theory. Annu Rev Phys Chem 1964;15:155.
18. Hermans J, Wang L. Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding: application to a complex of benzene and mutant T4 lysozyme. J Am Chem Soc 1997;119:2707-2714.
19. Warshel A. Computer modeling of chemical reactions in enzymes and solutions. New York: John Wiley & Sons; 1991.
20. Warshel A, Russell ST. calculations of electrostatic interactions in biological systems and in solutions. Q Rev Biophys 1984;17:283-421.
21. Marelius, J, Graffernorgberg, M, Hansson, T, Hallberg, A, and Åqvist J. Computation of affinity and selectivity-binding of 2,4-Diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases. J Comp-Aided Mol Des 1998;12:119-131.
22. Tao H, Chu ZT, Warshel A. Quantitative studies of ligand-receptor interactions: a rapid evaluation of binding free energies of endothiapepsin to its inhibitors. In: Pacific symposium on biocomputing. Singapore: World Scientific Press; 1996.
23. Langen R, Brayer GD, Berghuis AM, McLendon G, Sherman F, Warshel A. Effect of the Asn52→Ile mutation on the redox potential of yeast cytochrome c. J Mol Biol 1992;224:589-600.
24. Muegge I, Schweins T, Langen R, Warshel A. Electrostatic control of GTP and GDP Binding in the oncoprotein p21 ras. Structure 1996;4:475-489.
25. King G, Lee FS, Warshel A, Microscopic simulations of macroscopic dielectric constants of solvated proteins. J Chem Phys 1991;95:4366-4377.
26. Sham YY Chu, ZT, Warshel A. Consistent calculations of pka's of ionizable residues in proteins: semi-microscopic and macroscopic approaches. J Phys Chem B 1997;101:4458-4472.
27. Lee FS, Chu ZT, Warshel, A. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs. J Comp Chem 1993;14:161-185.
28. Lam PYS, Jadhav PK, Eyermann C, et al. Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. Science 1994;263:380-384.
29. Wlodawer A, Miller M, Jaskólski M, et al. Conserved folding of in retroviral proteases: crystal structure of synthetic HIV-1 protease. Science 1989;1989:616-621.
30. Lapatto R, Blundell T, Hemmings A, et al. X-ray analysis of HIV-1 proteinase at 2.7 Å resolution confirms structural homology among retroviral enzymes. Nature 1989;342:299-302.
31. Hultén J, Bonham NM, Nillroth U, et al. Cyclic HIV-1 protease inhibitors derived from Mannitol: synthesis, inhibitory potencies and computational predictions of binding affinities. J Med Chem 1997;40:885-897.
32. King G, Warshel A. A surface constrained all-atom solvent model for effective simulations of polar solutions. J Chem Phys 1989;91: 3647-3661.
33. Sham YY, Warshel A. The surface constrained all atom model provides size independent results in calculations of hydration free energies. J Chem Phys 1998;109:7940-7944.
34. Lee FS, Warshel A. A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations. J Chem Phys 1992;97:3100-3107.
35. Muegge I, Qi PX, Wand AJ, Chu ZT, Warshel A. The reorganization energy of cytochrome c revisited. J Phys Chem B 1997;101:825-836.
36. Wang J, Dixon R, Kollman PA. Ranking ligand binding affinities with Avidin: a molecular dynamic-based interaction energy study. Proteins: Struct Func Genet 1999;34:69-81.