Molecular docking, molecular dynamics simulation, and structure-based 3D-QSAR studies on the aryl hydrocarbon receptor agonistic activity of hydroxylated polychlorinated biphenyls

Environmental Toxicology and Pharmacology

Volumn 36, Issue 2, 2013, Pages 626-635

  Cao, Fu ^a   Li, Xiaolin ^a   Ye, Li ^b   Xie, Yuwei ^a   Wang, Xiaoxiang ^a   Shi, Wei ^a   Qian, Xiangping ^b,c   Zhu, Yongliang ^b   Yu, Hongxia ^a  

^a NANJING UNIVERSITY   (China)

^b Suzhou NeuPharma Co Ltd   (China)

^c SOOCHOW UNIVERSITY   (China)

Author keywords

3D QSAR; Ah receptor; HO PCBs; Molecular docking; Molecular dynamics

Indexed keywords

AROMATIC HYDROCARBON RECEPTOR; POLYCHLORINATED BIPHENYL DERIVATIVE;

ARTICLE; CHEMICAL ANALYSIS; CHEMICAL STRUCTURE; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; COMPARATIVE STUDY; ENZYME ACTIVITY; MOLECULAR DOCKING; MOLECULAR DYNAMICS; NONHUMAN; POLLUTION; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN FUNCTION; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STATISTICAL ANALYSIS; THREE DIMENSIONAL QUANTITATIVE STRUCTURE ACTIVITY RELATION;

3D-QSAR; AH RECEPTOR; HO-PCBS; MOLECULAR DOCKING; MOLECULAR DYNAMICS;

ANIMALS; BINDING SITES; COMPUTER GRAPHICS; HUMANS; HYDROXYLATION; LIGANDS; MOLECULAR DOCKING SIMULATION; MOLECULAR STRUCTURE; POLYCHLORINATED BIPHENYLS; PROTEIN BINDING; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RECEPTORS, ARYL HYDROCARBON;

EID: 84880347382     PISSN: 13826689     EISSN: 18727077     Source Type: Journal    
DOI: 10.1016/j.etap.2013.06.004     Document Type: Article

References (35)

1. Case D.A., Cheatham T.E., Darden T., Gohlke H., Luo R., Merz K.M., Onufriev A., Simmerling C., Wang B., Woods R.J. The Amber biomolecular simulation programs. J. Comput. Chem. 2005, 26:1668-1688.
2. Clark M., Cramer R.D., Vanopdenbosch N. Validation of the general-purpose Tripos 5.2 force field. J. Comput. Chem. 1989, 10:982-1012.
3. Diao J., Li Y., Shi S., Sun Y., Sun Y. QSAR models for predicting toxicity of polychlorinated dibenzo-p-dioxins and dibenzofurans using quantum chemical descriptors. Bull. Environ. Contam. Toxicol. 2010, 85:109-115.
4. Duan Y., Wu C., Chowdhury S., Lee M.C., Xiong G.M., Zhang W., Yang R., Cieplak P., Luo R., Lee T., Caldwell J., Wang J.M., Kollman P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 2003, 24:1999-2012.
5. Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., Pedersen L.G. A smooth particle mesh ewald method. J. Chem. Phys. 1995, 103:8577-8593.
6. Gharaghani S., Khayamian T., Keshavarz F. Docking, molecular dynamics simulation studies, and structure-based QSAR model on cytochrome P450 2A6 inhibitors. Struct. Chem. 2012, 23:341-350.
7. Glynn A., Larsdotter M., Aune M., Darnerud P.O., Bjerselius R., Bergman A. Changes in serum concentrations of polychlorinated biphenyls (PCBs), hydroxylated PCB metabolites and pentachlorophenol during pregnancy. Chemosphere 2011, 83:144-151.
8. Gu C.G., Jiang X., Ju X.H., Yang X.L., Yu G.F. DFT study on the structure-toxicity relationship of dioxin compounds using PLS analysis. SAR QSAR Environ. Res. 2007, 18:603-619.
9. Gutleb A.C., Cenijn P., van Velzen M., Lie E., Ropstad E., Skaare J.U., Malmberg T., Bergman A., Gabrielsen G.W., Legler J. In vitro assay shows that PCB metabolites completely saturate thyroid hormone transport capacity in blood of wild polar bears (Ursus maritimus). Environ. Sci. Technol. 2010, 44:3149-3154.
10. Hankinson O. Role of coactivators in transcriptional activation by the aryl hydrocarbon receptor. Arch. Biochem. Biophys. 2005, 433:379-386.
11. Hevener K.E., Ball D.M., Buolamwini J.K., Lee R.E. Quantitative structure-activity relationship studies on nitrofuranyl anti-tubercular agents. Bioorg. Med. Chem. 2008, 16:8042-8053.
12. Jain A.N. Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. J. Comput. Aided Mol. Des. 2007, 21:281-306.
13. 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.
14. Kamata R., Shiraishi F., Nakajima D., Takigami H., Shiraishi H. Mono-hydroxylated polychlorinated biphenyls are potent aryl hydrocarbon receptor ligands in recombinant yeast cells. Toxicol. In Vitro 2009, 23:736-743.
15. Key J., Scheuermann T.H., Anderson P.C., Daggett V., Gardner K.H. Principles of ligand binding within a completely buried cavity in HIF2 alpha PAS-B. J. Am. Chem. Soc. 2009, 131:17647-17654.
16. Kothandana G., Gadhe C.G., Madhavan T., Choi C.H., Cho S.J. Docking and 3D-QSAR (quantitative structure activity relationship) studies of flavones, the potent inhibitors of p-glycoprotein targeting the nucleotide binding domain. Eur. J. Med. Chem. 2011, 46:4078-4088.
17. Laskowski R.A., Rullmann J.A.C., MacArthur M.W., Kaptein R., Thornton J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 1996, 8:477-486.
18. Li F., Li X.H., Liu X.L., Zhang L.B., You L.P., Zhao J.M., Wu H.F. Docking and 3D-QSAR studies on the Ah receptor binding affinities of polychlorinated biphenyls (PCBs), dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs). Environ. Toxicol. Pharmacol. 2011, 32:478-485.
19. Li X.L., Ye L., Wang X.X., Wang X.Z., Liu H.L., Qian X.P., Zhu Y.L., Yu H.X. Molecular docking, molecular dynamics simulation, and structure-based 3D-QSAR studies on estrogenic activity of hydroxylated polychlorinated biphenyls. Sci. Total Environ. 2012, 441:230-238.
20. Morse D.C., Wehler E.K., Vandepas M., Debie A., Vanbladeren P.J., Brouwer A. Metabolism and biochemical effects of 3,3',4,4'-tetrachlorobiphenyl in pregnant and fetal rats. Chem. Biol. Interact. 1995, 95:41-56.
21. Mortensen A.S., Braathen M., Sandvik M., Arukwe A. Effects of hydroxy-polychlorinated biphenyl (OH-PCB) congeners on the xenobiotic biotransformation gene expression patterns in primary culture of Atlantic salmon (Salmo salar) hepatocytes. Ecotoxicol. Environ. Saf. 2007, 68:351-360.
22. Motto I., Bordogna A., Soshilov A.A., Denison M.S., Bonati L. New aryl hydrocarbon receptor homology model targeted to improve docking reliability. J. Chem. Inf. Model. 2011, 51:2868-2881.
23. Munoz C., Adasme F., Alzate-Morales J.H., Vergara-Jaque A., Kniess T., Caballero J. Study of differences in the VEGFR2 inhibitory activities between semaxanib and SU5205 using 3D-QSAR, docking, and molecular dynamics simulations. J. Mol. Graphics Modell. 2012, 32:39-48.
24. Nomiyama K., Yonehara T., Yonemura S., Yamamoto M., Koriyama C., Akiba S., Shinohara R., Koga M. Determination and characterization of hydroxylated polychlorinated biphenyls (OH-PCBs) in serum and adipose tissue of Japanese women diagnosed with breast cancer. Environ. Sci. Technol. 2010, 44:2890-2896.
25. Okey A.B., Riddick D.S., Harper P.A. The Ah receptor: mediator of the toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and related compounds. Toxicol. Lett. 1994, 70:1-22.
26. Safe S. Polychlorinated biphenyls (PCBs) and polybrominated biphenyls (PBBs): biochemistry, toxicology, and mechanism of action. Crit. Rev. Toxicol. 1984, 13:319-395.
27. Safe S. Polychlorinated biphenyls (PCBs), dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs), and related compounds: environmental and mechanistic considerations which support the development of toxic equivalency factors (TEFs). Crit. Rev. Toxicol. 1990, 21:51-88.
28. Safe S., Bandiera S., Sawyer T., Zmudzka B., Mason G., Romkes M., Denomme M.A., Sparling J., Okey A.B., Fujita T. Effects of structure on binding to the 2,3,7,8-TCDD receptor protein and AHH induction-halogenated biphenyls. Environ. Health Perspect. 1985, 61:21-33.
29. Scheuermann T.H., Tomchick D.R., Machius M., Guo Y., Bruick R.K., Gardner K.H. Artificial ligand binding within the HIF2 alpha PAS-B domain of the HIF2 transcription factor. Proc. Natl. Acad. Sci. USA 2009, 106:450-455.
30. Takeuchi S., Shiraishi F., Kitamura S., Kuroki H., Jin K., Kojima H. Characterization of steroid hormone receptor activities in 100 hydroxylated polychlorinated biphenyls, including congeners identified in humans. Toxicology 2011, 289:112-121.
31. Wang J.M., Wolf R.M., Caldwell J.W., Kollman P.A., Case D.A. Development and testing of a general amber force field. J. Comput. Chem. 2004, 25:1157-1174.
32. Wang Y.W., Liu H.X., Zhao C.Y., Cai Z.W., Jiang G.B. Quantitative structure-activity relationship models for prediction of the toxicity of polybrominated diphenyl ether congeners. Environ. Sci. Technol. 2005, 39:4961-4966.
33. Wold S., Ruhe A., Wold H., Dunn W.J. The collinearity problem in linear regression: the partial least squares (PLS) approach to generalized inverses. SIAM J. Sci. Stat. Comput. 1984, 5:735-743.
34. Yang W.H., Liu X., Liu H.L., Wu Y., Giesy J.P., Yu H.X. Molecular docking and comparative molecular similarity indices analysis of estrogenicity of polybrominated diphenyl ethers and their analogues. Environ. Toxicol. Chem. 2010, 29:660-668.
35. Zhang W.S., Sargis R.M., Volden P.A., Carmean C.M., Sun X.J., Brady M.J. PCB 126 and other dioxin-like PCBs specifically suppress hepatic PEPCK expression via the aryl hydrocarbon receptor. PLoS ONE 2012, 7.