Connecting traditional QSAR and molecular simulations of papain hydrolysis - Importance of charge transfer

Bioorganic and Medicinal Chemistry

Volumn 13, Issue 9, 2005, Pages 3093-3105

  Lepp, Zsolt ^a   Chuman, Hiroshi ^a  

^a UNIVERSITY OF TOKUSHIMA   (Japan)

Author keywords

Charge transfer; Field inductive effect; Hydrophobic effect; Linear regression; LocalSCF; Molecular dynamics; N Benzoylglycine esters; Papain; Principal components analysis; QSAR; Semi empirical quantum mechanics

Indexed keywords

ESTER DERIVATIVE; PAPAIN;

AB INITIO CALCULATION; ARTICLE; CORRELATION ANALYSIS; ELECTROCHEMISTRY; ELECTRON TRANSPORT; HYDROLYSIS; LIGAND BINDING; MOLECULAR MECHANICS; MOLECULAR MODEL; PHYSICAL CHEMISTRY; QUANTITATIVE STRUCTURE ACTIVITY RELATION; QUANTUM MECHANICS; RECEPTOR BINDING; SIMULATION; STRUCTURE ANALYSIS;

EID: 16244391486     PISSN: 09680896     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bmc.2005.02.057     Document Type: Article

References (33)

1. C. Hansch, and A. Leo Exploring QSAR 1995 American Chemical Society Washington
2. R.D. Taylor, P.J. Jewsbury, and J.W. Essex A review of protein-small molecule docking methods J. Comput.-Aided Mol. Des. 16 2002 151 166
3. P. Ferrara, H. Gohlke, D.J. Price, G. Klebe, and C.L. Brooks III Assessing scoring functions for protein-ligand interactions J. Med. Chem. 47 2004 3032 3034
4. P.A. Kollman Free energy calculations: application to chemical and biochemical phenomena Chem. Rev. 93 1993 2395 2417
5. K.M. Masukawa, P.A. Kollman, and I.D. Kuntz Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations J. Med. Chem. 46 2003 5628 5637
6. Y. Tominaga, and W.L. Jorgensen Genaral model for estimation of the inhibition of protein kinases using Monte Carlo simulations J. Med. Chem. 47 2004 2534 2549
7. R.N. Smith, C. Hansch, K.H. Kim, B. Omiya, G. Fukumura, C.D. Selassie, P.Y.C. Jow, J.M. Blaney, and R. Langridge Arch. Biochem. Biophys. 215 1982 319
8. C.M. Compadre, C. Hansch, T.E. Klein, and R. Langridge The structure-activity relationship of the papain hydrolysis of N-benzoylglycine esters Biochim. Biophys. Acta 1038 1990 158 163
9. C. Hansch, and T.E. Klein Molecular graphics and QSAR in the study of enzyme-ligand interactions. On the definition of bioreceptors Acc. Chem. Res. 19 1986 392 400
10. D.S. Selassie, and T.E. Klein Building Bridges: QSAR and Molecular Graphics. 3D QSAR in Drug Design 1993 Escom Science Publishers B.V. Leiden
11. C.G. Swain, and E.C. Lupton Jr. Field and resonance components of substituent effects J. Am. Chem. Soc. 90 1968 4328
12. C. Hansch, and A. Leo Substituent constant for correlation analysis in chemistry and biology 1979 Wiley-Interscience New York
13. Janowski, R.; Kozak, M.; Jankowska, E.; Grzonka, Z.; Jaskolski, M. Two polymorphic forms of papain in covalent complex With ZLFG-DAM, to be published
14. L. Morgenstern, M. Recanatini, T.E. Klein, W. Steinmetz, C.Z. Yang, R. Langridge, and C. Hansch Chymotrypsin hydrolysis of X-phenyl hippurates. A quantitative structure-activity relationship and molecular graphics analysis J. Biol. Chem. 262 1987 10767 10772
15. SYBYL® 6.9.2 Tripos Inc., 1699 South Hanley Road, St. Louis, MI 63144, USA
16. Spartan'04 Wavefunction, Inc. Irvine, CA
17. T. Halgren Maximally diagonal force constants in dependent angle-bending coordinates. II. Implications for the design of empirical force fields J. Am. Chem. Soc. 112 1990 4710 4723
18. R.D. Clark, A. Strizhev, J.M. Leonard, J.F. Blake, and J.B. Matthew Consensus scoring for ligand/protein interactions J. Mol. Graph. Model. 20 2002 281
19. M. Clark, R.D. Cramer III, and N. Van Opdenbosch J. Comput. Chem. 10 1989 982 1012
20. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E., III; Wang, J.; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Tsui, V.; Gohlke, H.; Radmer, R.J.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G.L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. AMBER 7, University of California, San Francisco, 2002
21. J. Wang, P. Cieplak, and P.A. Kollman How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21 2000 1049 1074
22. J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollamn, and D.A. Case Development and testing of a general Amber force field J. Comput. Chem. 25 2004 1157 1174
23. Gaussian 98. Gaussian, Inc., Pittsburgh PA, 1998
24. C.I. Bayly, P. Cieplak, W.D. Cornell, and P.A. Kollman A well-behaved electrostatic potential based method using charge restraints for determining atom-centered charges: the RESP model J. Phys. Chem. 97 1993 10269
25. N.A. Anikin, V.M. Anisimov, V.L. Bugaenko, V.V. Bobrikov, and A.M. Andreyev LocalSCF method for semiempirical quantum-chemical calculation of ultralarge biomolecules J. Chem. Phys. 3 2004 1266 1270
26. LocalSCF2003. Fujitsu Limited, Tokyo, Japan, 2003
27. M.J.S. Dewar, M.J.S. Zoebisch, E.F. Healy, and J.J.P. Stewart Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model J. Am. Chem. Soc. 107 1985 3902 3909
28. XLSTAT-Pro 7.5 Addinsoft, Brooklyn, NY, USA
29. J.C. Gower Some distance properties of latent root and vector methods used in multivariate analysis Biometrika 53 1966 325 338
30. W.R. Dillon, and M. Goldstein Multivariate analysis. Methods and applications 1984 John Wiley & Sons New York 23-52
31. MVSP 3.12. Kovach Computing Services, Wales, UK
32. C. Walsh Enzymatic Reaction Mechanisms 1979 Freeman San Francisco p 98
33. R.N. Smith, C. Hansch, K.H. Kim, B. Omiya, G. Fukumura, C.D. Selassie, P.Y. Jow, J.M. Blaney, and R. Langridge The use of crystallography, graphics, and quantitative structure-activity relationships in the analysis of the papain hydrolysis of X-phenyl hippurates Arch. Biochem. Biophys. 215 1981 319 328