Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations

Journal of Medicinal Chemistry

Volumn 42, Issue 5, 1999, Pages 868-881

  Eriksson, Mats A L ^a,b   Pitera, Jed ^a   Kollman, Peter A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

4,5,6,7 TETRAHYDRO 5 METHYL 6 (3 METHYL 2 BUTENYL)IMIDAZO[4,5,1 JK][1,4]BENZODIAZEPINE 2(1H) THIONE; 9 CHLORO 4,5,6,7 TETRAHYDRO 5 METHYL 6 (3 METHYL 2 BUTENYL)IMIDAZO[4,5,1 JK][1,4]BENZODIAZEPINE 2(1H) THIONE; CHLORINE; RNA DIRECTED DNA POLYMERASE INHIBITOR; TIVIRAPINE;

ANTIVIRAL ACTIVITY; ARTICLE; BINDING AFFINITY; DRUG BINDING; DRUG CLASSIFICATION; DRUG STRUCTURE; DRUG SYNTHESIS; ENERGY METABOLISM; ENTHALPY; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS;

ALGORITHMS; BENZODIAZEPINES; HIV-1 REVERSE TRANSCRIPTASE; IMIDAZOLES; MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEIN BINDING; REVERSE TRANSCRIPTASE INHIBITORS; THERMODYNAMICS;

EID: 0033545623     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm980277y     Document Type: Article

References (55)

1. Esnouf, R.; Ren, J.; Ross, C.; Jones, Y.; Stammers, D.; Stuart, D. Mechanism of inhibition of HIV-1 reverse transcriptase by nonnucleoside inhibitors. Struct. Biol. 1995, 2, 303-308.
2. Larder, B. A. Inhibitors of HIV reverse transcriptase as antiviral agents and drug resistance, Cold Spring Harbor Lab. Press: Cold Spring Harbor, NY, 1993; pp 205-222.
3. Schinazi, R. F. Competitive inhibitors of human immunodeficiency virus reverse transcriptase. Perspect. Drug Discov. Des. 1993, 1, 151-180.
4. De Clercq, E. Antiviral therapy of human immunodeficiency virus infections. Clin. Microbiol. Rev. 1995, 8, 200-239.
5. DeClercq, E. HIV resistance to reverse transcriptase inhibitors. Biochem. Pharmacol. 1994, 47, 155-169.
6. Young, S. D. Nonnucleoside inhibitors of HIV-1 reverse transcriptase. Perspect. Drug Discov. Des. 1993, 1, 181-192.
7. De Clercq, E. Toward improved anti-HIV chemotherapy: therapeutic strategies for intervention with HIV infections. J. Med. Chem. 1995, 38, 2491-2517.
8. Arnold, E.; Das, K.; Ding, J.; Yadav, P. N. S.; Hsiou, Y.; Boyer, P. L.; Hughes, S. H. Targeting HIV reverse transcriptase for anti-AIDS drug design. Drug Des. Discov. 1996, 13, 29-47.
9. Ding, J.; Das, K.; Moereels, H.; Koymans, L.; Andries, K.; Janssen, P. A. J.; Hughes, S. H.; Arnold, E. Structure of HIV-1 RT/TIBO R 86183 complex reveals similarity in the binding of diverse nonnucleoside inhibitors. Struct. Biol. 1995, 2, 407-415.
10. Das, K.; Ding, J.; Hsiou, Y.; Clark, A. D. J.; Moereels, H.; Koymans, L.; Andries, K.; Pauwels, R.; Janssen, P, A. J.; Boyer, P. L.; Clark, P.; Smith, R. H. J.; Kroeger-Smith, M. B.; Michedja, C. J.; Hughes, S. H.; Arnold, E. Crystal structures of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT drug-resistant mutant. J. Mol. Biol. 1996, 264, 1085-1100.
11. Tantillo, C.; Ding, J.; Jacobo-Molina, A.; Nanni, R. G.; Boyer, P. L.; Hughes, S. H.; Pauwels, R.; Andries, K.; Janssen, P. A. J.; Arnold, E. Locations of anti-AIDS drug binding sites and resistance mutations in the three-dimensional structure of HIV-1 reverse transcriptase. J. Mol. Biol. 1994, 243, 369-387.
12. Beveridge, D. L.; DiCapua, F. M. Free energy via molecular simulation: Application of chemical and biochemical systems. Annu. Rev. Biophys. Biophys. Chem. 1983, 18, 431-492.
13. Kollman, P. Free energy calculations: Applications to chemical and biochemical phenomena. Chem. Rev. 1993, 93, 2395-2417.
14. Rao, B. G.; Kim, E. E.; Murcko, M. A. Calculation of solvation and binding free energy differences between VX-478 and its analogues by free energy perturbation and AMSOL methods. J. Comput.-Aided Mol. Des. 1996, 10, 23-30.
15. Pitera, J.; Kollman, P. Designing an optimum guest for a host using multimolecule free energy calculations: Predicting the best ligand for Rebek's "Tennis Ball". J. Am. Chem. Soc. 1998, 120, 7557-7567.
16. Gilson, M. K.; Honig, B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies and conformational analysis. Proteins: Struct. Funct., Genet. 1988, 4, 7-18.
17. Sharp, K. A.; Honig, B. Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Biophys. Chem. 1990, 19, 301-332.
18. Nozaki, Y.; Tanford, C. The solubility of amino acids and two glycine peptides in aqueous solution and dixonane solutions. Establishment of a hydrophobicity scale. J. Biol. Chem. 1971, 246, 2211-2217.
19. Hermann, R. B. Theory of hydrophobic binding. II. The correlation of hydrocarbon solubility in water with solvent cavity surface area. J. Phys. Chem. 1971, 76, 2754-2759.
20. Wendoloski, J. J.; Shen, J.; Oliva, M. T.; Weber, P. C. Biophysical tools for structure-based drug design. Pharmacol. Ther. 1993, 66, 169-183.
21. Jackson, R. M.; Sternberg, M. J. E. A continuum model for protein-protein interactions: Application to the docking problem. J. Mol. Biol. 1995, 250, 258-275.
22. Shen, J.; Quiocho, F. A. Calculation of binding energy differences receptor-ligand systems using the Poisson-Boltzmann method. J. Comput. Chem. 1995, 16, 445-448.
23. Shen, J.; Wendoloski, J. Binding of phosphorus-containing inhibitors to thermolysin studied by the Poisson-Boltzmann method. J. Comput. Chem. 1996, 17, 350-357.
24. Zhang, T.; Koshland, J. D. E. Computational method for relative binding energies of enzyme-substrate complexes. Protein Sci. 1996, 5, 348-356.
25. 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.
26. 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.
27. Åqvist, J.; Mowbray, S. L. Sugar recognition by a glucose/ galactose receptor. J. Biol. Chem. 1995, 270, 9978-9981.
28. Hansson, T.; Åqvist, J. Estimation of binding free energies for HIV-1 protease inhibitors by molecular dynamics simulations. Protein Eng. 1995, 8, 1137-1144.
29. Paulsen, M. D.; Ornstein, R. L. Binding free energy calculations for P450cam-substrate complexes. Protein Eng. 1996, 9, 567-571.
30. Åqvist, J. Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions. J. Comput. Chem. 1996, 17, 1587-1597.
31. Radmer, R. J.; Kollman, P. A. The application of three approximative free energy calculation methods to structure based ligand design: Trypsin and its complex inhibitors. J. Comput.-Aided Mol. Des. 1998, 12, 215-227.
32. Pauwels, R.; Andries, K.; Debyser, Z.; Kukla, M. J.; Schols, D.; Breslin, H. J.; Woestenborghs, R.; Desmyter, J.; Janssen, M. A. C.; de Clercq, E.; Janssen, P. A. J. New tetrahydroimidazo[4,5,1-jk][1,4]-benzodiazepin-2(1H)-one and -thione derivatives are potent inhibitors of human immunodeficiency virus type 1 replication and are synergistic with 2', 3'-dideoxynucleoside analogues. Antimicrob. Agents Chemother. 1994, 38, 2863-2870.
33. Miyamoto, S.; Kollman, P. A. Absolute and relative binding free energy calculations of the interaction of biotin and its analogues with streptavidin using molecular dynamics/free energy perturbation approaches. Proteins: Struct., Funct., Genet. 1993, 16, 226-245.
34. Fox, T.; Thomas, B. E.; McCarrick, M.; Kollman, P. A. Application of free energy perturbation calculations to the "tennis ball" dimer: Why is CF4 not encapsulated by this host? J. Phys. Chem. 1996, 100, 10779-10783.
35. Liaw, Y. C.; Gao, Y. G.; Robinson, H.; Wang, A. H. J. Molecular structure of a potent HIV-1 inhibitor belonging to TIBO family. J. Am. Chem. Soc. 1991, 113, 1857-1859.
36. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Gill, P. M. W.; Jonhson, B. G.; Robb, M. A.; Cheeseman, J. R.; Keith, T.; Petersson, G. A.; Montegomery, J. A.; Rahavachari, K.; Al-Laham, M. A.; Zakrzewski, V. G.; Ortiz, J. V.; Foresman, J. B.; Peng, C. Y.; Ayala, P. Y.; Chen, W.; Wong, M. W.; Andres, J. L.; Replogle, E. S.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Binkley, J. S.; Defrees, D. J.; Baker, J.; Stewart, J. P.; Head-Gordon, M.; Gonzalez, C.; Pople, J. A. Gaussian 94, Revision B.3; Gaussian Inc.: Pittsburgh, PA. 1995.
37. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges - the RESP model. J. Phys. Chem. 1993, 97, 10269-10280.
38. Pearlman, D. A.; Case, D. A.; Caldwell, J. C.; Ross, W. S.; Cheatham, T. E., III; Ferguson, D. M.; Seibel, G. L.; Singh, U. C.; Weiner, P.; Kollman, P. A. AMBER 4.1 (UCSF); University of California: San Francisco, 1994.
39. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
40. Jorgensen, W. L.; Chandraseklar, 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.
41. 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.
42. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Di Nola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984, 81, 3684-3690.
43. Ferrin, T. E.; Huang, C. C.; Jarvis, L. E.; Langridge, R. The Midas display system. J. Mol. Graph. 1988, 6, 13-27.
44. Metropolis, N. R.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. Equation of state calculations by fast computing machines. J. Chem. Phys. 1953, 21, 1087-1092.
45. Torrie, G. M.; Valleau, J. P. Nonphysical sampling distributions in Monte Carlo free energy estimation: Umbrella sampling. J. Comput. Phys. 1977, 23, 187-199.
46. Kumar, S.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. The weighted histogram analysis for free energy calculations on biomolecules. 1. The method. J. Comput. Chem. 1992, 13, 1011-1021.
47. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 1990, 112, 6127-6129.
48. Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. MacroModel - An integrated software system for modeling organic and bioorganic molecules using molecular mechanics. J. Comput. Chem. 1990, 11, 440-467.
49. Gilson, M. K.; Sharp, K. A.; Honig, B. Calculating the electrostatic potential of molecules in solution: method and error assessment. J. Comput. Chem. 1988, 9, 327-335.
50. Honig, B.; Nicholls, A. Classical electrostatics in biology and chemistry. Science 1995, 268, 1144-1149.
51. Connolly, M. L. Solvent-accessible surfaces of proteins and nucleic acids. Science 1983, 221, 709-713.
52. Zacharias, M.; Straatsma, T. P.; McCammon, J. A. Separation-shifted scaling, a new method for Lennard-Jones interactions in thermodynamic integration. J. Chem. Phys. 1994, 100, 9025-9031.
53. Beutler, T. C.; Mark, A. E.; van Schaik, R. C.; Gerber, P. R.; van Gunsteren, W. F. Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. Chem. Phys. Lett. 1994, 222, 529-539.
54. Simmerling, C.; Fox, T.; Kollman, P. Use of locally enhanced sampling in free energy calculations: Testing and application to the α→β anomerization of glucose. J. Am. Chem. Soc. 1998, 120, 5771-5782.
55. Hine, J.; Mookerjee, P. K. The intrinsic character of organic compounds. Correlations in terms of structural contributions. J. Org. Chem. 1975, 40, 292-298.