A combination of 3D-QSAR, docking, local-binding energy (LBE) and GRID study of the species differences in the carcinogenicity of benzene derivatives chemicals

Journal of Molecular Graphics and Modelling

Volumn 27, Issue 2, 2008, Pages 147-160

  Fratev, Filip ^a   Benfenati, Emilio ^a  

^a MARIO NEGRI INSTITUTE FOR PHARMACOLOGICAL RESEARCH   (Italy)

Author keywords

3D QSAR; Carcinogenicity; Docking; GRID; LBE; P450

Indexed keywords

ARSENIC COMPOUNDS; ATOMS; BENZENE; BINDING SITES; BIOCHEMISTRY; CARBON NANOTUBES; CHLORINE COMPOUNDS; COMPLEXATION; DOCKING; FOOD PROCESSING; MAPS; METABOLISM; MOLECULAR GRAPHICS; NUCLEAR ENERGY; NUCLEAR PHYSICS; OPTICAL PROJECTORS; POTENTIAL ENERGY; THREE DIMENSIONAL;

3-D MODELING; 3D-QSAR; BENZENE DERIVATIVES; CARCINOGENIC POTENTIAL; CARCINOGENICITY; GRID; GRID METHODS; GRID STUDY; LBE; MECHANISM OF ACTIONS; METABOLIC PROCESSING; NEW APPROACHES; P450; PROTEIN RESIDUES; QUANTITATIVE ASSESSMENTS; REGRESSION MAPS;

BINDING ENERGY;

BENZENE DERIVATIVE; CARCINOGEN; CYTOCHROME P450; CYTOCHROME P450 2E1;

ARTICLE; BINDING SITE; CARCINOGENICITY; ENERGY; ENZYME METABOLISM; METHODOLOGY; MOUSE; NONHUMAN; OXIDATION; PRIORITY JOURNAL; PROTEIN INTERACTION; QUANTITATIVE STRUCTURE ACTIVITY RELATION; RAT;

ANIMALS; BENZENE DERIVATIVES; BINDING SITES; CARCINOGENS; COMPUTER SIMULATION; CYTOCHROME P-450 CYP2E1; MICE; MODELS, BIOLOGICAL; MODELS, CHEMICAL; NEOPLASMS, EXPERIMENTAL; PROTEIN TRANSPORT; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RATS; SPECIES SPECIFICITY; STRUCTURAL HOMOLOGY, PROTEIN;

RATTUS;

EID: 52049085030     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2008.04.004     Document Type: Article

References (62)

1. Gini G., Lorenzini M., Benfenati E., Grasso P., and Bruschi M. Predictive carcinogenicity: a model for aromatic compounds, with nitrogen-containing substituents, based on molecular descriptors using an artificial neural network. J. Chem. Inf. Comp. Sci. 39 (1999) 1076-1080
2. Enslein K., Gombar V.K., and Blake B.W. Use of SAR in computer-assisted prediction of carcinogenicity and mutagenicity of chemicals by the TOPKAT program. Mutat. Res. 305 (1994) 47-61
3. Todeschini R., Gramatica P., Provenzani R., and Marengo E. Weighted holistic invariant molecular descriptors. Part 2. Theory development and applications on modeling physicochemical properties of polyaromatic hydrocarbons. Chem. Intell. Lab. Syst. 27 (1995) 221-229
4. Benfenati E., and Gini G. Computational predictive programs (expert systems) in toxicology. Toxicology 119 (1997) 213-225
5. Ford G.P., and Scribner J.D. Prediction of nucleoside-carcinogen reactivity. Alkylation of adenine, cytosine, guanine, and thymine and their deoxynucleosides by alkanediazonium ions. Chem. Res. Toxicol. 3 (1990) 219-230
6. Lewis D.F., Ioannides C., and Parke D.V. A quantitative structure-activity relationship (QSAR) study of mutagenicity in several series of organic chemicals likely to be activated by cytochrome P450 enzymes. Teratogen. Carcin. Mut. 1 (2003) 187-193
7. Evans W.E., and Relling M.V. Pharmacogenomics: translating functional genomics into rational therapeutics. Science 286 (1999) 487-491
8. Lewis D.F., and Dickins M. Factors influencing rates and clearance in P450-mediated reactions: QSARs for substrates of the xenobiotic-metabolizing hepatic microsomal P450s. Toxicology 170 (2002) 45-53
9. Turesky R.J., Parisod V., Huynh-Ba T., Langouët S., and Guengerich F.P. Regioselective differences in C(8)- and N-oxidation of 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline by human and rat liver microsomes and cytochromes P450 1A2. Chem. Res. Toxicol. 14 (2001) 901-911
10. Sello G., Sala L., and Benfenati E. Predicting toxicity: a mechanism of action model of chemical mutagenicity. Mutat. Res. 479 (2001) 141-171
11. Guengerich F.P. Common and uncommon cytochrome P450 reactions related to metabolism and chemical toxicity. Chem. Res. Toxicol. 14 (2001) 611-650
12. Gibson G.G., and Skett P. Introduction to Drug Metabolism (2001), Nelson Thornes Ltd., Cheltenham
13. Stiborová M., Frei E., Wiessler M., and Schmeiser H.H. Human enzymes involved in the metabolic activation of carcinogenic aristolochic acids: evidence for reductive activation by cytochromes P450 1A1 and 1A2. Chem. Res. Toxicol. 14 (2001) 1128-1137
14. Lewis D.F., Bird M.G., and Parke D.V. Molecular modelling of CYP2E1 enzymes from rat, mouse and man: an explanation for species differences in butadiene metabolism and potential carcinogenicity, and rationalization of CYP2E substrate specificity. Toxicology 118 (1997) 93-113
15. Nakajima T., Wang R.S., Elovaara E., Park S.S., Gelboin H.V., and Vainio H. Cytochrome P450-related differences between rat and mouse in the metabolism of benzene, toluene and trichloroethylene in liver microsomes. Biochem. Pharmacol. 45 (1993) 1079-1085
16. Hathway D.E. Toxic action/toxicity. Biol. Rev. Camb. Philos. Soc. 75 (2000) 95-127
17. Gallagher E.P., Kunze K.L., Stapleton P.L., and Eaton D.L. The kinetics of aflatoxin B1 oxidation by human cDNA-expressed and human liver microsomal cytochromes P450 1A2 and 3A4. Toxicol. Appl. Pharm. 141 (1996) 595-606
18. Kelly J.D., Eaton D.L., Guengerich F.P., and Coulombe R.A. Aflatoxin B1 activation in human lung. Toxicol. Appl. Pharm. 144 (1997) 88-95
19. Langouët S., Coles B., Morel F., Becquemont L., Beaune P., Guengerich F.P., Ketterer B., and Guillouzo A. Inhibition of CYP1A2 and CYP3A4 by oltipraz results in reduction of aflatoxin B1 metabolism in human hepatocytes in primary culture. Cancer Res. 55 (1995) 5574-5579
20. Cavin C., Bezencon C., Guignard G., and Schilter B. Coffee diterpenes prevent benzo[a]pyrene genotoxicity in rat and human culture systems. Biochem. Biophys. Res. Commun. 306 (2003) 488-495
21. Bu S., Kim Y., Kim S., and Lee M. Effects of enzyme inducers and inhibitor on the pharmacokinetics of intravenous 2-(allylthio) pyrazine, a new chemoprotective agent, in rats. Biopharm. Drug Dispos. 21 (2000) 157-164
22. Jin L., and Baillie T.A. Metabolism of the chemoprotective agent diallyl sulfide to glutathione conjugates in rats. Chem. Res. Toxicol. 10 (1997) 318-327
23. Mahéo K., Morel F., Langouët S., Kramer H., Le Ferrec E., Ketterer B., and Guillouzo A. Inhibition of cytochromes P-450 and induction of glutathione S-transferases by sulforaphane in primary human and rat hepatocytes. Cancer Res. 57 (1997) 3649-3652
24. Gut I., Nedelcheva V., Soucek P., Stopka P., Vodicka P., Gelboin H.V., and Ingelman-Sundberg M. The role of CYP2E1 and 2B1 in metabolic activation of benzene derivatives. Arch. Toxicol. 71 (1996) 45-56
25. Klaassen C.D. Casarett & Doull's Toxicology: The Basic Science of Poisons (2001), McGraw-Hill, New York
26. McCarthy D.J., Waud W.R., Struck R.F., and Hill D.L. Disposition and metabolism of aniline in Fischer 344 rats and C57BL/6 X C3H F1 mice. Cancer Res. 45 (1985) 174-180
27. Lo Piparo E., Fratev F., Mazzatorta P., Smiesko M., and Benfenati E. Toxicity in allelopathy: in silico approach. In: Reigosa M.J., Pedrol N., and González L. (Eds). Allelopathy: A Physiological Process with Ecological Implications (2006), Springer, Berlin 105-123 (Chapter 5)
28. Gold L.S., Slone T.H., Manley N.B., Garfinkel G.B., Hudes E.S., Rohrbach L., and Ames B.N. The carcinogenic potency database: analyses of 4000 chronic animal cancer experiments published in the general literature and by the U.S. National Cancer Institute/National Toxicology Program. Environ. Health Perspect. 96 (1991) 11-15
29. Vracko M. A study of structure-carcinogenicity relationship for 86 compounds from NTP database using topological indices as descriptors. SAR QSAR Environ. Res. 11 (2000) 103-115
30. ®, Chemical Design Ltd., Roundway House, Cromwell Parek, Chipping Norton, Oxfordskire OX 75 SR, UK, July 1999.
31. ®, Hypercube Inc., 1115 NW 4th Street, Gainesville, FL 32601, USA.
32. Stewart J.P. Optimization of parameters for semiempirical methods. I. Method. J. Comput. Chem. 10 (1989) 209-220
33. Chen X., Christopher A., Jones J., Guo Q., Xu F., Cao R., Wong L.-L., and Rao Z. Crystal structure of the F87W/Y96F/V247L mutant of cytochrome P-450cam with 1,3,5-trichlorobenzene bound and further protein engineering for the oxidation of pentachlorobenzene and hexachlorobenzene. J. Biol. Chem. 277 (2002) 37519-37526
34. Raag R., Swanson B.A., Poulos T.L., and Ortiz de Montellano P.R. Formation, crystal structure, and rearrangement of a cytochrome P-450cam iron-phenyl complex. Biochemistry 29 (1990) 8119-8126
35. Lewis D.F., Lake B.G., Dickins M., Ueng Y.F., and Goldfarb P.S. Homology modelling of human CYP1A2 based on the CYP2C5 crystallographic template structure. Xenobiotica 33 (2003) 239-254
36. Don M.J., Lewis D.F., Wang S.Y., Tsai M.W., and Ueng Y.F. Effect of structural modification on the inhibitory selectivity of rutaecarpine derivatives on human CYP1A1, CYP1A2, and CYP1B1. Bioorg. Med. Chem. Lett. 13 (2003) 2535-2538
37. Lewis D.F., Bird M.G., Dickins M., Lake B.G., Eddershaw P.J., Tarbit M.H., and Goldfarb P.S. Molecular modelling of human CYP2E1 by homology with the CYP102 haemoprotein domain: investigation of the interactions of substrates and inhibitors within the putative active site of the human CYP2E1 isoform. Xenobiotica 30 (2000) 1-25
38. Lewis D.F., Lake B.G., Bird M.G., Loizou G.D., Dickins M., and Goldfarb P.S. Homology modelling of human CYP2E1 based on the CYP2C5 crystal structure: investigation of enzyme-substrate and enzyme-inhibitor interactions. Toxicol. In Vitro 17 (2003) 93-105
39. Lewis D.F. Homology modelling of human CYP2 family enzymes based on the CYP2C5 crystal structure. Xenobiotica 32 (2002) 305-323
40. Lewis D.F., and Lake B.G. Species differences in coumarin metabolism: a molecular modelling evaluation of CYP2A interactions. Xenobiotica 32 (2002) 547-561
41. Ferro D.R., and Hermans J. A different best rigid-body molecular fit routine. Acta Crystallogr. A 33 (1977) 345-347
42. Kim K.H. 3D QSAR in Drug Design Recent Advances (1998), Kluwer/E SCOM, London
43. Cavalli A., Greco G., Novelliono E., and Recanatini M. Linking CoMFA and protein homology models of enzyme-inhibitor interactions: an application to non-steroidal aromatase inhibitors. Bioorg. Med. Chem. 8 (2000) 2771-2780
44. Boeckmann B., Bairoch A., Apweiler R., Blatter M.-C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I., Pilbout S., and Schneider M. The SWISS-PROT protein knowledge base and its supplement TrEMBL in 2003. Nucl. Acids Res. 31 (2003) 365-370
45. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The protein data bank. Nucl. Acids Res. 28 (2000) 235-242
46. Ginalski K., Elofsson A., Fischer D., and Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 22 (2003) 1015-1018
47. Ginalski K., Pas J., Wyrwicz S.L., Grotthuss M., Bujnicki J.M., and Rychlewski L. ORFeus: detection of distant homology using sequence profiles and predicted secondary structure. Nucl. Acids Res. 31 (2003) 3804-3807
48. Marti-Renom M.A., Stuart A., Fiser A., Sánchez R., Melo F., and Sali A. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29 (2000) 291-325
49. Cornell W.D., Cieplak P., Bayey C.I., Gould I., Merz T.K.M., Ferguson D.M., Spellmeyr D., Fox T., Caldmell J.W., and Kollman P.A. Second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117 (1995) 5179-5197
50. Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., and Olson A.J. Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function. J. Comput. Chem. 19 (1998) 1639-1662
51. P.J. Goodford, GRID 21, Molecular Discovery Ltd., University of Oxford, England, SGI.
52. SIMCA, Umetrics AB, Box 7960, S-90719 Umea, Schweden.
53. Xuan G.-D., and Liu Z.-Q. Cytochrome P450 metabolic intermediate formation from p-chloro-o-toluidine as a possible new probe to characterize cytochrome P450 IIB. Chin. J. Pharmacol. Toxicol. 9 (1995) 3-7
54. Leslie C., Reidy G.F., Murray M., and Stacey N.H. Induction of xenobiotic biotransformation by the insecticide chlordimeform, a metabolite 4-chloro-o-toluidine and a structurally related chemical o-toluidine. Biochem. Pharmacol. 37 (1988) 2529-2535
55. Pandey R.N., Armstrong A.P., and Hollenberg P.F. Oxidative N-demethylation of N,N-dimethylaniline by purified isozymes of cytochrome P-450. Biochem. Pharmacol. 38 (1989) 2181-2185
56. Cheever K.L., Richards D.E., and Plotnick H.B. Metabolism of ortho-, meta-, and para-toluidine in the adult male rat. Toxicol. Appl. Pharm. 56 (1980) 361-369
57. Gan J., Skipper P.L., and Tannenbaum S.R. Oxidation of 2,6-dimethylaniline by recombinant human cytochrome P450s and human liver microsomes. Chem. Res. Toxicol. 14 (2001) 672-677
58. Przybojewska B. Assessment of aniline derivatives-induced DNA damage in the liver cells of B6C3F1 mice using the alkaline single cell gel electrophoresis ('comet') assay. Cancer Lett. 147 (1999) 1-4
59. Williams P.A., Cosme J., Ward A., Angove H.C., Matak Vinkovic D., and Jhoti H. Crystal structure of human cytochrome P450 2C9 with bound warfarin. Nature 424 (2003) 464
60. Prasad J.C. Docking to large ensembles of homology models reliably explains the substrate binding differences in cytochrome P450 1As of human and fish species. The 229th ACS National Meeting, Poster 173. San Diego, CA, 13-17 March (2005)
61. Fratev F., and Benfenati E. 3D-QSAR and molecular mechanics study for the differences in the azole activity against yeast like and filamentous fungi and their relation to P450DM inhibition. 1. 3-Substituted-4(3H)-quinazolinones. J. Chem. Inf. Model. 45 (2005) 634-644
62. Sippl W. Development of biologically active compounds by combining 3D QSAR and structure-based design methods. J. Comput. Aided Mol. Des. 16 (2002) 825-830