Improved 3D-QSAR analyzes for the predictive toxicology of polybrominated diphenyl ethers with CoMFA/CoMSIA and DFT

Ecotoxicology and Environmental Safety

Volumn 73, Issue 6, 2010, Pages 1470-1479

  Gu, Chenggang ^a,b   Ju, Xuehai ^c   Jiang, Xin ^b   Yu, Kai ^a   Yang, Shaogui ^a   Sun, Cheng ^a  

^a NANJING UNIVERSITY   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^c NANJING UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

CoMFA; CoMSIA; DFT; Polybrominated diphenyl ethers; Predictive toxicology; QSARs

Indexed keywords

AROMATIC HYDROCARBON RECEPTOR; POLYBROMINATED DIPHENYL ETHER;

DIOXIN; HYDROPHOBICITY; MOLECULAR ANALYSIS; PBDE; TOXICITY; TOXICOLOGY;

ANALYTIC METHOD; ARTICLE; BINDING AFFINITY; CHEMICAL INTERACTION; CHEMICAL STRUCTURE; COMPARATIVE MOLECULAR FIELD ANALYSIS; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; CONFORMATION; CONTROLLED STUDY; DENSITY FUNCTIONAL THEORY; GEOMETRY; HYDROPHOBICITY; MOLECULAR MODEL; PREDICTION; QUANTITATIVE STRUCTURE ACTIVITY RELATION; RECEPTOR BINDING; TOXICITY; TOXICOLOGY;

HALOGENATED DIPHENYL ETHERS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; TOXICOLOGY;

EID: 77956185867     PISSN: 01476513     EISSN: 10902414     Source Type: Journal    
DOI: 10.1016/j.ecoenv.2009.11.003     Document Type: Article

References (74)

1. Allchin C.R., Law R.J., Morris S. Polybrominated diphenylethers in sediments and biota and downstream of potential sources in the UK. Environ. Pollut. 1999, 105:197-207.
2. Ashek A., Lee C., Park H., Cho S.J. 3D QSAR studies of dioxins and dioxin-like compounds using CoMFA and CoMSIA. Chemosphere 2006, 65:521-529.
3. Becke A.D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 1993, 98:5648-5652.
4. Behnisch P.A., Hosoe K., Sakai S.I. Brominated dioxin-like compunds: in vitro assessment in comparison to classical dioxin-like compounds and other polyaromatic compounds. Environ. Int. 2003, 29:861-877.
5. Benjamins H., Dar F.H., Chandler W.D. Conformations of bridged diphenyls. VI. Substituent effects and internal rotation in triply ortho-substituted diphenyl ethers. Can. J. Chem. 1974, 52:3297-3302.
6. Bezares-Cruz J., Jafvert C.T., Hua I. Solar photodecomposition of decabromodiphenyl ether: products and quantum yield. Environ. Sci. Technol. 2004, 38:4149-4156.
7. Bohm M., Sturzebecher J., Klebe G. Three-dimensional quantitative structure-activity relationship analyses using comparative molecular field analysis and comparative molecular similarity indices analysis to elucidate selectivity differences of inhibitors binding to Trypsin, Thrombin, and Factor Xa. J. Med. Chem. 1999, 42:458-477.
8. Borghesi N., Corsolini S., Focardi S. Levels of polybrominated diphenyl ethers (PBDEs) and organochlorine pollutants in two species of Antarctic fish (Chionodraco hamatus and Trematomus bernacchii). Chemosphere 2008, 73:155-160.
9. Branchi I., Capone F., Alleva E., Costa L.G. Polybrominated diphenyl ethers: neurobehavioral effects following developmental exposure. Neurotoxicology 2003, 24:449-462.
10. Chen G., Konstantinov A.D., Chittim B.G., Joyce E.M., Bols N.C., Bunce N.J. Synthesis of polybrominated dipheryl ethers and their capacity to induce CYP1A by the Ah receptor mediated pathway. Environ. Sci. Technol. 2001, 35:3749-3756.
11. Cheney B.V. Structural factors affecting aryl hydrocarbon hydroxylase induction by dibenzo-p-dioxins and dibenzofrurans. Int. J. Quantum Chem. 1982, 21:445-463.
12. 2-guided region selection for comparative molecular field analysis: a simple method to achieve consistent results. J. Med. Chem. 1995, 38:1060-1066.
13. Clark M., Cramer R.D., Opdenbosch N.V. Validation of the general purpose tripos 5.2 force field. J. Comput. Chem. 1989, 10:982-1012.
14. 2 parameter for QSAR validation. J. Chem. Inf. Model. 2009, 49:1669-1678.
15. Covaci A., Gheorghe A., Voorspoels S., Maervoet J., Redeker E.S., Blust R., Schepens P. Polybrominated diphenyl ethers, polychlorinated biphenyls and organochlorine pesticides in sediment cores from the Western Scheldt river (Belgium): analytical aspects and depth profiles. Environ. Int. 2005, 31:367-375.
16. Covaci A., Voorspoels S., Roosens L., Jacobs W., Blust R., Neels H. Polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) in human liver and adipose tissue samples from Belgium. Chemosphere 2008, 73:170-175.
17. Cramer R.D., Bunce J.D., Patterson D.E. Crossvalidation, bootstrapping, and partial least squares compared with multiple regression in conventional QSAR studies. Quant. Struct. Act. Relat. 1988, 7:18-25.
18. Cramer R.D., Patterson D.E., Bunce J.D. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc. 1988, 110:5959-5967.
19. Darnerud P.O. Toxic effects of brominated flame retardants in man and in wildlife. Environ. Int. 2003, 29:841-853.
20. Darnerud P.O. Brominated flame retardants as possible endocrine disrupters. Int. J. Androl. 2008, 31:152-160.
21. De Wit C.A. An overview of brominated flame retardants in the environment. Chemosphere 2002, 42:583-624.
22. Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Montgomery J.A., Vreven T., Kudin K.N., Burant J.C., Millam J.M., Iyengar S.S., Tomasi J., Barone V., Mennucci B., Cossi M., Scalmani G., Rega N., Petersson G.A., Nakatsuji H., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Klene M., Li X., Knox J.E., Hratchian H.P., Cross J.B., Adamo C., Jaramillo J., Gomperts R., Stratmann R.E., Yazyev O., Austin A.J., Cammi R., Pomelli C., Ochterski J.W., Ayala P.Y., Morokuma K., Voth G.A., Salvador P., Dannenberg J.J., Zakrzewski V.G., Dapprich S., Daniels A.D., Strain M.C., Farkas O., Malick D.K., Rabuck A.D., Raghavachari K., Foresman J.B., Ortiz J.V., Cui Q., Baboul A.G., Clifford S., Cioslowski J., tefanov B.B., Liu G., Liashenko A., Piskorz P., Komaromi I., Martin R.L., Fox D.J., Keith T., Al-Laham M.A., Peng C.Y., Nanayakkara A., Challacombe M., Gill P.M.W., Johnson B., Chen W., Wong M.W., Gonzalez C., Pople J.A. Gaussian 03, Revision B.03 2003, Gaussian Inc., Pittsburgh PA.
23. Geladi P. Notes on the history and nature of partial least squares (PLS) modeling. J. Chemometrics 1988, 2:231-246.
24. 2!. J. Mol. Graph. Model. 2002, 20:269-276.
25. 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.
26. Gu C.G., Jiang X., Ju X.H., Yu G.F., Bian Y.R. QSARs for the toxicity of polychlorinated dibenzofurans through DFT-calculated descriptors of polarizabilities, hyperpolarizabilities and hyper-order electric moments. Chemosphere 2007, 67:1325-1334.
27. Haglund P.S., Zook D.R., Buser H.R., Hu J. Identification and quantidication of polybrominated diphenyl ethers and methoxy-polybrominated diphenyl ethers in Baltic biota. Environ. Sci. Technol. 1997, 31:3281-3287.
28. Hale R.C., Guardia M.J.L., Harvey E.P., Mainor T.M., Duff W.H., Gaylor M.O. Polybrominated diphenyl ether flame retardants in Virginia freshwater fishes (USA). Environ. Sci. Technol. 2001, 35:4585-4591.
29. Harju M., Andersson P.L., Haglund P., Tysklind M. Multivariate physicochemical characterization and quantitative structure-property relationship modeling of polybrominated diphenyl ethers. Chemosphere 2002, 47:375-384.
30. Hawkins D.M., Basak S.C., Mills D. Assessing model fit by cross-validation. J. Chem. Inf. Comput. Sci. 2003, 43:579-586.
31. Hirokawa S., Imasaka T., Imasaka T. Chlorine substitution pattern, molecular electronic properties, and the nature of the ligand-receptor interaction: quantitative property-activity relationships of polychlorinated dibenzofurans. Chem. Res. Toxicol. 2005, 18:232-238.
32. Hu K., Bunce N.J. Metabolism of polychlorinated dibenzo-p-dioxins and related dioxin-like compounds. J. Toxicol. Environ. Health, Part B 1999, 2:183-210.
33. Ikonomou M.G., Fischer M., He T., Addison R.F., Smith T. Congener patterns, spatial and temporal trends of polybrominated diphenyl ethers in biota samples from the Canadian west coast and the Northwest Territories. Organohalogen Compd. 2000, 47:77-80.
34. Ikonomou M.G., Rayne S., Addison R.F. Exponential increases of the brominated flame retardant polybrominated diphenyl ethers in the Canadian Arctic from 1981-2000. Environ. Sci. Technol. 2002, 36:1886-1892.
35. Keum Y.S., Li Q.X. Reductive debromination of polybrominated diphenyl ethers by zerovalent iron. Environ. Sci. Technol. 2005, 39:2280-2286.
36. Kim K.S., Tarakeshwar P., Lee J.Y. Molecular cluster of p-systems: theoretical studies of structures, spectra, and origin of interaction energies. Chem. Rev. 2000, 100:4145-4185.
37. Klasson-Wehler E., Hovander L., Bergman Å. New organohalogens in human plasma-identification and quantification. Organohalogen Compd. 1997, 33:420-425.
38. Klebe G., Abraham U., Mietzner T. Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J. Med. Chem. 1994, 37:4130-4146.
39. Lee C., Yang W., Parr R.G. Development of the Colle-Salvetti correlation energy formula into a functional of the electron density. Phys. Rev. B 1988, 37:785-789.
40. Luross J.M., Alaee M., Sergeant D.B., Whittle D.M., Solomon K.R. Spatial and temporal distribution of polybrominated diphenyl ethers in lake trout from the great lakes. Organohalogen Compd. 2000, 47:73-76.
41. McKinney J.D., Richard A., Waller C., Newman M.C., Gerberick F. The practice of structure activity relationships (SAR) in toxicology. Toxicol. Sci. 2000, 56:8-17.
42. Meerts I.A.T.M., Luijks E.A.C., Marsh G., Jakobsson E., Bergman Å., Brouwer A. Polybrominated diphenyl ethers (PBDEs) as Ah-receptor agonists and antagonists. Organohalogen Compd. 1998, 35:147-150.
43. Meerts I.A.T.M., Zanden J.J.v., Luijks E.A.C., Leeuwen-Bol I.v., Marsh G., Jakobsson E., Bergman Å., Brouwer A. Potent competitive interactions of some brominated flame retardants and related compounds with human transthyretin in vitro. Toxicol. Sci. 2000, 56:95-104.
44. Meironyté D., Bergman Å., Norén K. Analysis of polybrominated diphenyl ethers in human milk. Organohalogen Compd. 1998, 35:387-390.
45. Mhin B.J., Lee J.E., Choi W. Understanding the congener-specific toxicity in polychlorinated dibenzo-p-dioxins: chlorination pattern and molecular quadrupole moment. J. Am. Chem. Soc. 2002, 124:144-148.
46. Norén K., Meironyté D. Certain organochlorine and organobromine contaminants in Swedish human milk in perspective of past 20-30 years. Chemosphere 2000, 40:1111-1123.
47. 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.
48. Parr R.G., Yang W. Density Functional Theory of Atoms and Molecules 1989, Oxford University Press, Oxford.
49. Pasha F.A., Muddassar M., Lee C., Cho S.J. Mechanism based QSAR studies of N-phenylbenzamides as antimicrobial agents. Environ. Toxicol. Pharm. 2008, 26:128-135.
50. Peters A.K., Sanderson J.T., Bergman Å., van den Berg M. Antagonism of TCDD-induced ethoxyresorufin-O-deethylation activity by polybrominated diphenyl ethers (PBDEs) in primary cynomolgus monkey (Macaca fascicularis) hepatocytes. Toxicol. Lett. 2006, 164:123-132.
51. Peterson S.D., Schaal W., Karlén A. Improved CoMFA modeling by optimization of settings. J. Chem. Inf. Model. 2006, 46:355-364.
52. Polder A., Venter B., Skaare J.U., Bouwman H. Polybrominated diphenyl ethers and HBCD in bird eggs of South Africa. Chemosphere 2008, 73:148-154.
53. Poso A., Tuppurainen K., Ruuskanen J., Gynther J. Binding of some dioxins and dibenzofurans to the Ah receptor. A QSAR model based on comparative molecular field analysis (CoMFA). J. Mol. Struct. (Theochem.) 1993, 282:259-264.
54. Renner R. What fate for brominated fire retardants?. Environ. Sci. Technol. 2000, 34:223A-226A.
55. Safe S.H. Polychlorinated biphenyls (PCBs), dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs), and related compounds: environmental and mechanistic consideration which support the development of toxic equivalency factors (TEFs). Crit. Rev. Toxicol. 1990, 21:51-88.
56. Sellström U., Kierkegaard A., de Wit C.A., Jansson B. Polybrominated diphenyl ethers and hexabromocyclododecane in sediment and fish from a Swedish river. Environ. Toxicol. Chem. 1998, 17:1065-1072.
57. Seminario J.M., Politzer P. Modern Density Functional Theory: A Tool for Chemistry 1995, Elsevier, Amsterdam.
58. Sjödin A., Hagmar L., Klasson-Wehler E., Kronholm-Diab K., Jakobsson E., Bergman Å. Polybrominated diphenyl ethers (PBDEs) in blood from Swedish workers. Environ. Health Perspect. 1999, 107:643-648.
59. SYBYL 7.3, 2007. Tripos Inc., St. Louis, MO 63144, USA.
60. Uno B., Iwanoto T., Okumura N. Importance of substituent intramolecular charge-transfer effect on the molecular conformation of diphenyl ethers. J. Org. Chem. 1998, 63:9794-9800.
61. Vetter W., von der Recke R., Herzke D., Nygård T. Detailed analysis of polybrominated biphenyl congeners in bird eggs from Norway. Environ. Pollut. 2008, 156:1204-1210.
62. Wahl M., Lahni B., Guenther R., Kuch B., Yang L., Straehle U., Strack S., Weiss C. A technical mixture of 2,2',4,4'-tetrabromo diphenyl ether (BDE47) and brominated furans triggers aryl hydrocarbon receptor (AhR) mediated gene expression and toxicity. Chemosphere 2008, 73:209-215.
63. Wang Y., Liu H., Zhao C., Liu H., Cai Z., Jiang G. Quantitative structure-activity relationship models for prediction of the toxicity of polybrominated diphenyl ether congeners. Environ. Sci. Technol. 2005, 39:4961-4966.
64. Wang Y., Zhao C., Ma W., Liu H., Wang T., Jiang G. Quantitative structure-activity relationship for prediction of the toxicity of polybrominated diphenyl ether (PBDE) congeners. Chemosphere 2006, 64:515-524.
65. Watanabe I., Sakai S. Environmental release and behavior of brominated flame retardants. Environ. Int. 2003, 29:665-682.
66. Whitlock J.P. Mechanistic aspects of dioxin action. Chem. Res. Toxicol. 1993, 6:754-763.
67. WHO Environmental Health Criteria 162. Brominated diphenyl ethers. Geneva 1994, International Programme on Chemical Safety, Switzerland. W.H. Organization (Ed.).
68. Wold S. Cross-validation estimation of the number of components in factor and principal components analysis. Technometrics 1978, 24:397-405.
69. Wold S., Albano C., Dunn W.J., Edlund U., Esbenson K., Geladi P., Hellberg S., Lindburg W., Sjostrom M. Chemometrics: Mathematics and Statistics in Chemistry 1984, 17-95. Reidel, Dordrecht, the Netherlands. B. Kowalski (Ed.).
70. Xu H.Y., Zhou J.W., Yu Q.S., Wang Y.H., Zhang J.Y., Jin H.X. QSPR/QSAR model for prediction of the physicochemical properties and biological activity of polybrominated diphenyl ethers. Chemosphere 2007, 66:1998-2010.
71. Zeng X., Freeman P.K., Vasiľev Y.V., Voinov V.G., Simonich S.L., Barofsky D.F. Theoretical calculation of thermodynamic properties of polybrominated diphenyl ethers. J. Chem. Eng. Data 2005, 50:1548-1556.
72. Zhao Y.Y., Tao F.M., Zeng E.Y. Theoretical study on the chemical properties of polybrominated diphenyl ethers. Chemosphere 2008, 70:901-907.
73. Zheng G., Xiao M., Lu X. Quantitative structure-activity relationships study on the Ah receptor binging affinities of polybrominated diphenyl ethers using a support vector machine. QSAR Comb. Sci. 2007, 26:536-541.
74. Zhou T., Taylor M.M., DeVito M.J., Crofton K.M. Developmental exposure to brominated diphenyl ethers results in thyroid hormone disruption. Toxicol. Sci. 2002, 66:105-116.