Binding constants of neuraminidase inhibitors: An investigation of the linear interaction energy method

Journal of Medicinal Chemistry

Volumn 42, Issue 25, 1999, Pages 5142-5152

  Wall, Ian D ^a   Leach, Andrew R ^b   Salt, David W ^c   Ford, Martyn G ^c   Essex, Jonathan W ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^b GLAXOSMITHKLINE   (United Kingdom)

^c UNIVERSITY OF PORTSMOUTH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

SIALIDASE; SIALIDASE INHIBITOR;

ARTICLE; BINDING AFFINITY; CALCULATION; DRUG BINDING; DRUG STRUCTURE; ENZYME ACTIVE SITE; FACTORIAL ANALYSIS; PROTEIN CONFORMATION;

CRYSTALLOGRAPHY, X-RAY; ENZYME INHIBITORS; MODELS, MOLECULAR; NEURAMINIDASE; PROTEIN BINDING; THERMODYNAMICS;

EID: 0033576654     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm990105g     Document Type: Article

References (42)

1. Kollman, P. Free-energy calculations - applications to chemical and biochemical phenomena. Chem. Rev. 1993, 93, 2395-2417.
2. Reynolds, C. A.; King, P. M.; Richards, W. G. Free-energy calculations in molecular biophysics. Mol. Phys. 1992, 76, 251-275.
3. Beveridge, D. L.; DiCapua, F. M. Free-energy via molecular simulation - applications to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 1989, 18, 431-492.
4. Liu, H. Y.; Mark, A. E.; van Gunsteren, W. F. Estimating the relative free energy of different molecular states with respect to a single reference state. J. Phys. Chem. 1996, 100, 9485-9494.
5. Smith, P. E.; van Gunsteren, W. F. Predictions of free-energy differences from a single simulation of the initial-state. J. Chem. Phys. 1994, 100, 577-585.
6. Beutler, T. C.; van Gunsteren, W. F. Molecular-dynamics free-energy calculation in 4 dimensions. J. Chem. Phys. 1994, 101, 1417-1422.
7. 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.
8. Levy, R. M.; Belhadj, M.; Kitchen, D. B. Gaussian fluctuation formula for electrostatic free-energy changes in solution. J. Chem. Phys. 1991, 95, 3627-3633.
9. 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.
10. Åqvist, J.; Medina, C.; Samuelsson, J. E. New method for predicting binding-affinity in computer-aided drug design. Protein Eng. 1994, 7, 385-391.
11. Åqvist, J.; Hansson, T. On the validity of electrostatic linear response in polar solvents. J. Phys. Chem. 1996, 100, 9512-9521.
12. Hansson, T.; Åqvist, J. Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations. Protein Eng. 1995, 8, 1137-1144.
13. Hansson, T.; Marelius, J.; Åqvist, J. Ligand binding affinity prediction by linear interaction energy methods. J. Comput.-Aided Mol. Des. 1998, 12, 27-35.
14. Åqvist, J.; Mowbray, S. L. Sugar recognition by a glucose/ galactose receptor - evaluation of binding energetics from molecular-dynamics simulations. J. Biol. Chem. 1995, 270, 9978-9981.
15. Jones-Hertzog, D. K.; Jorgensen, W. L. Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response method. J. Med. Chem. 1997, 40, 1539-1549.
16. Paulsen, M. D.; Ornstein, R. L. Binding free energy calculations for P450cam-substrate complexes. Protein Eng. 1996, 9, 567-571.
17. Hulten, J.; Bonham, N. M.; Nillroth, U.; Hansson, T.; Zuccarello, G.; Bouzide, A.; Åqvist, J.; Classon, B.; Danielson, U. H.; Karlen, A.; Kvarnstrom, I.; Samuelsson, B.; Hallberg, A. Cyclic HIV-1 protease inhibitors derived from mannitol: synthesis, inhibitory potencies, and computational predictions of binding affinities. J. Med. Chem. 1997, 40, 885-897.
18. 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.
19. Wang, J.; Dixon, R.; Kollman, P. A. Ranking ligand binding affinities with avidin: a molecular dynamics-based interaction energy study. Proteins: Struct. Funct. Genet. 1999, 34, 69-81.
20. 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.
21. Henchman, R. H.; Essex, J. W. Free energies of hydration using restrained electrostatic potential derived (REPD) charges via free energy perturbations and linear response. J. Comput. Chem. 1999, 20, 499-510.
22. Carlson, H. A.; Jorgensen, W. L. An extended linear-response method for determining free-energies of hydration. J. Phys. Chem. 1995, 99, 10667-10673.
23. McDonald, N. A.; Carlson, H. A.; Jorgensen, W. L. Free energies of solvation in chloroform and water from a linear response approach. J. Phys. Org. Chem. 1997, 10, 563-576.
24. Taylor, N. R.; von Itzstein, M. A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase. J. Comput.-Aided Mol. Des. 1996, 10, 233-246.
25. Smith, P. W.; Sollis, S. L.; Howes, P. D.; Cherry, P. C.; Cobley, K. N.; Taylor, H.; Whittington, A. R.; Scicinski, J.; Bethell, R. C.; Taylor, N.; Skarzynski, T.; Cleasby, A.; Singh, O.; Wonacott, A.; Varghese, J.; Colman, P. Novel inhibitors of influenza sialidases related to GG167 - structure-activity, crystallographic and molecular dynamic studies with 4H-pyran-2-carboxylic acid 6-carboxamides. Bioog. Med. Chem. Lett. 1996, 6, 2931-2936.
26. 50 of an enzymatic reaction. Biochem. Pharmacol. 1973, 22, 3099-3108.
27. Bethell, R. Personal communication.
28. Unpublished stucture obtained from GlaxoWellcome.
29. von Itzstein, M.; Wu, W. Y.; Kok, G. B.; Pegg, M. S.; Dyason, J. C.; Jin, B.; Phan, T. V.; Smythe, M. L.; White, H. F.; Oliver, S. W.; Colman, P. M.; Varghese, J. N.; Ryan, D. M.; Woods, J. M.; Bethell, R. C.; Hotham, V. J.; Cameron, J. M.; Penn, C. R. Rational design of potent sialidase-based inhibitors of influenza-virus replication. Nature 1993, 363, 418-423.
30. Jorgensen, W. L. Theoretical studies of medium effects on conformational equilibria. J. Phys. Chem. 1983, 87, 5304-5314.
31. Jorgensen, W. L. MCPRO 1.4, Yale University, New Haven, CT, 1996.
32. Jorgensen, W. L.; Chandrasekhar, 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.
33. Essex, J. W.; Severance, D. L.; Tirado-Rives, J.; Jorgensen, W. L. Monte Carlo simulations for proteins: binding affinities for trypsin-benzamidine complexes via free-energy perturbations. J. Phys. Chem. B 1997, 101, 9663-9669.
34. Essex, J. W.; Jorgensen, W. L. An empirical boundary potential for water droplet simulations. J. Comput. Chem. 1995, 16, 951-972.
35. Richmond, T. J. Solvent accessible surface-area and excluded volume in proteins - analytical equations for overlapping spheres and implications for the hydrophobic effect. J. Mol. Biol. 1984, 178, 63-89.
36. Ponder, J. W. TINKER, Version 3.6; Washington University, St. Louis, MO, 1998.
37. Jorgensen, W. L.; Tirado-Rives, J. The OPLS potential functions for proteins - energy minimizations for crystals of cyclic-peptides and crambin. J. Am. Chem. Soc. 1988, 110, 1657-1666.
38. Livingstone, D. Data Analysis for Chemists; Oxford University Press: Oxford, 1995.
39. Stone, M.; Brooks, R. J. Continuum regression - cross-validated sequentially constructed prediction embracing ordinary least-squares, partial least-squares and principal components regression. J. R. Stat. Soc. Ser. B-Methodol. 1990, 52, 237-269.
40. Malpass, J.; Salt, D.; Ford, M.; Wynn, E.; Livingstone, D. Continuum regression: A new algorithm for the prediction of biological activity. In Methods and Principles in Medicinal Chemistry, 3, Advanced computer assisted techniques in drug discovery; VCH Publishers: Weinheim, 1995.
41. Malpass, J.; Salt, D.; Ford, M. Continuum regression: optimised prediction of biological activity. Pestic. Sci. 1996, 46, 282-284.
42. Ford, M.; Crichton, R.; Salt, D.; Livingstone, D. PARAGON Drug Design Software, V1.09.01; University of Portsmouth, UK, 1999.