Using quantitative structure-activity relationships (QSAR) to predict toxic endpoints for polycyclic aromatic hydrocarbons (PAH)

Journal of Toxicology and Environmental Health - Part A: Current Issues

Volumn 71, Issue 16, 2008, Pages 1073-1084

  Bruce, Erica D ^a,d   Autenrieth, Robin L ^a   Burghardt, Robert C ^b   Donnelly, K C ^c   McDonald, Thomas J ^c  

^a TEXAS A AND M UNIVERSITY   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

^c TEXAS A AND M HEALTH SCIENCE CENTER   (United States)

^d BAYLOR UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ETHOXYRESORUFIN DEETHYLASE; POLYCYCLIC AROMATIC HYDROCARBON; CARCINOGEN; CYTOCHROME P450 1A1;

AMES TEST; ARTICLE; BIOASSAY; CARCINOGENESIS; MATHEMATICAL MODEL; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; RISK ASSESSMENT; BIOLOGICAL MODEL; CELL JUNCTION; DRUG EFFECT; HUMAN; METABOLISM; METHODOLOGY; MICROSOME; SALMONELLA;

ANIMALIA;

CARCINOGENS; CYTOCHROME P-450 CYP1A1; ENDPOINT DETERMINATION; GAP JUNCTIONS; HUMANS; MICROSOMES; MODELS, BIOLOGICAL; POLYCYCLIC HYDROCARBONS, AROMATIC; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RISK ASSESSMENT; SALMONELLA;

EID: 46749135177     PISSN: 15287394     EISSN: 10872620     Source Type: Journal    
DOI: 10.1080/15287390802114337     Document Type: Article

References (77)

1. Abraham, M. H., Autenrieth, R., and Dimitriou-Christidis, P. 2005. The estimation of physicochemical properties of methyl and other alkyl naphthalenes. J. Environ. Monit. 7:445-449.
2. 2, Release 4.10.
3. Ames, B. N., McCann, J., and Yamasaki, E. 1975a. Methods for detecting carcinogens and mutagens with the Salmonella/mammalian-microsome mutagenicity test. Mutat. Res. 31:347-364.
4. Ames, B. N., McCann, J., and Yamasaki, E. 1975b. Proceedings: Carcinogens are mutagens: A simple test system. Mutat. Res. 33:27-28.
5. Analogues, Committee on Pyrene and Selected, and Hazards, Board on Toxicology and Environmental Health. 1983. Polycyclic aromatic hydrocarbons - Evaluation of sources and effects, ed. The National Academies. Washington, DC: National Academies Press.
6. Ashurst, S. W., Cohen, G. M., Nesnow, S., DiGiovanni, J., and Slaga, T. J. 1983. Formation of benzo(a)pyrene/DNA adducts and their relationship to tumor initiation in mouse epidermis. Cancer Res. 43:1024-1029.
7. Agency for Toxic Substances and Disease Registry. 1990. Toxicological profile for polycyclic aromatic hydrocarbons. Washington, DC: U.S. Department of Health and Human Services, ATSDR/TP-Draft.
8. Barhoumi, R., Bowen, J. A., Stein, L. S., Echols, J., and Burghardt, R. C. 1993. Concurrent analysis of intracellular glutathione content and gap junctional intercellular communication. Cytometry 14:747-756.
9. Bersohn, M. 1983. A fast algorithm for calculation of the distance matrix. J. Comput. Chem. 4:110-113.
10. Billiard, S. M., Bols, N. C., and Hodson, P. V. 2004. In vitro and in vivo comparisons of fish-specific CYP1A induction relative potency factors for selected polycyclic aromatic hydrocarbons. Ecotoxicol. Environ. Safety 59:292-299.
11. Bonchev, D. 1983. Information theoretic indices for characterization of chemical structures. In Chemometrics series, ed. D. D. Bawden, pp. 4656-468. New York: Research Studies Press.
12. Bonchev, D., Mekenyan, O., and Trinajstic, N. 1981. Isomer discrimination by topological information approach. J. Comput. Chem. 2:127-148.
13. Bosveld, A. T., de Bie, P. A., van den Brink, N. W., Jongepier, H., and Klomp, A. V. 2002. In vitro EROD induction equivalency factors for the 10 PAHs generally monitored in risk assessment studies in The Netherlands. Chemosphere 49:75-83.
14. Braga, R. S., Barone, P. M. V. B., and Galvao, D. S. 2000. Identifying carcinogenic activity of methylated and non-methylated polycyclic aromatic hydrocarbons (PAHs) through electronic and topological indices. Braz. J. Phys. 30:560-568.
15. Bruce, E. D. 2007. Modeling toxic endpoints for improving human health risk assessment. Department of Civil Engineering-Environmental and Water Resources Divison, Texas A&M University, College Station.
16. Brunstrom, B., Broman, D., and Naf, C. 1991. Toxicity and EROD-inducing potency of 24 polycyclic aromatic hydrocarbons (PAHs) in chick embryos. Arch. Toxicol. 65:485-489.
17. Centers for Disease Control and Prevention. 2005. Third national report on human exposure to environmental chemicals. http://www.cdc.gov/ exposurereport [accessed February 10 2007].
18. Clement Associates, Inc. 1988. Comparative potency approach for estimating the caner risks associated with exposure to mixtures of polycyclic aromatic hydrocarbons (Interim final report). Fairfax, VA: Prepared for the U.S. EPA under contract 68-02-4403.
19. Couch, D. B. 1996. Carcinogenesis: Basic principles. In Toxicology and risk assessment: Principles, methods and application, eds. A. M. Fan and L. W. Chang, pp. 9-24. New York: Marcel Dekker.
20. Debnath, A. K. 2001. Quantitative structure-activity relationship (QSAR) paradigm - Hansch era to new millennium. Mini Rev. Med. Chem 1:187-195.
21. Dimitrov, S., Dimitrova, G., Pavlov, T., Dimitrova, N., Patlewicz, G., Niemela, J., and Mekenyan, O. 2005. A stepwise approach for defining the applicability domain of SAR and QSAR models. J. Chem. Inform. Model. 45:839-849.
22. Donato, M. T., Gomez-Lechon, M. J., and Castell, J. V. 1993. A microassay for measuring cytochrome P450IA1 and P450IIB1 activities in intact human and rat hepatocytes cultured on 96-well plates. Anal. Biochem. 213:29-33.
23. El-Alawi, Y. S., Huang, X. D., Dixon, D. G., and Greenberg, B. M. 2002. Quantitative structure-activity relationship for the photoinduced toxicity of polycyclic aromatic hydrocarbons to the luminescent bacteria Vibrio fischeri. Environ. Toxicol. Chem. 21:2225-2232.
24. Falahatpisheh, M., Kerzee, J., Metz, R., Donnelly, K., and Ramos, K. 2004. Inducible cytochrome P450 activities in renal glomerular mesangial cells: Biochemical basis for antagonistic interactions among nephrocarcinogenic polycyclic aromatic hydrocarbons. J. Carcinogen. 3:12.
25. Friedman, J. H. 1991. Multivariate adaptive regression splines (with discussion). Appl. Stat. 19:1-141.
26. Geacintov, N. E. 1986. Is intercalation a critical factor in the covalent binding of mutagenic and tumorigenic polycyclic aromatic diol epoxides to DNA? Carcinogenesis 7:759-766.
27. Gombar, V.A. 1998. Quantitative structure-activity relationships in toxicology: From fundamentals to applications. In Advances in molecular toxicology, eds. C. Reiss, Simone Parvez, Gilles Labbe, and Hasan Parvez, pp. 125-139. St. Louis, MO: Elsevier.
28. Govers, H., Ruepert, C., and Aiking, H. 1984. Quantitative structure-activity relationships for polycyclic aromatic hydrocarbons - Correlation between molecular connectivity, physicochemical properties, bioconcentration and toxicity in Daphnia pulex. Chemosphere 13:227-236.
29. Guerin, M. R. 1978. Energy sources of polycyclic aromatic hydrocarbons In Polycyclic hydrocarbons and cancer, eds. H. V. Gelboin and P. O. P. Tso, pp. 219-253. New York: Academic Press.
30. Hansch, C., and Leo, A. J. 1995. Exploring QSAR: Fundamentals and applications in chemistry and biology, ed. S. Heller, pp. 125-139. ACS Professional Reference Book. Washington, DC: American Chemical Society.
31. Harvey, R. G. 1991. Polycyclic aromatic hydrocarbons: Chemistry and carcinogenicity. Cambridge: Cambridge University Press.
32. Harvey, R. G. 1997. Polycyclic aromatic hydrocarbons. New York: Wiley-VCH.
33. Hill, T. L. 1960. Introduction to statistical thermodynamics. Reading, MA: Addison-Wesley.
34. Hong, H., Tong, W., Fang, H., Shi, L., Xie, Q., Wu, J., Perkins, R., Walker, J. D., Branham, W., and Sheehan, D. M. 2002. Prediction of estrogen receptor binding for 58,000 chemicals using an integrated system of a tree-based model with structural alerts. Environ. Health Perspect. 110:29-36.
35. IARC. 1983. Certain polycyclic aromatic hydrocarbons and heterocyclic compounds. IARC Monographs on the Evaluation of Carcinogenic Risk of the Chemical to Man, Vol. 3. Lyon, France: IARC.
36. Jaworska, J., Nikolova-Jeliazkova, N., and Aldenberg, T. 2005. QSAR applicabilty domain estimation by projection of the training set descriptor space: A review. Altern. Lab. Anim. 33:445-459.
37. Katritzky, A. R., and Gordeeva, E. V. 1993. Traditional topological indices vs. electronic, geometrical, and combined molecular descriptors in QSAR/QSPR research. J. Chem. Inform. Comput. Sci. 33:835-857.
38. Kennedy, S. W., and Jones, S. P. 1994. Simultaneuos measurement of cytochrome P4501A catalytic acitivity and total protein concnetration with a fluorescence plate reader. Anal. Biochem. 222:217-223.
39. Kier, L. B. 1990. An electrotopological-state index for atoms in molecules. Pharm. Res. 7:801-807.
40. Kier, L. B., and Hall, L. H. 1991. An index of electrotopological state of atoms in molecules. J. Math. Chem 7:229.
41. Koenemann, H. 1981. Quantitative structure-activity relationships in fish toxicity studies 1. Relationship for 50 industrial pollutants. Toxicology 19:209-211.
42. Lewis, D. F. V., and Parke, D. V. 1995. The genotoxicity of benzanthracenes - A quantitative structure-activity study. Mutat. Res. Fundam. Mol. Mech. Mutagen. 328:207-214.
43. Maple, J. R., Hwang, M. J., Stockfish, T. P., Dinur, U., Waldman, M., Ewig, C. S., and Hagler, A. T. 1994. Derivation of class II force fields. 1. Methodology and quantumforce field for the alkyl functional group and alkane molecules. J. Comput. Chem. 15:162-182.
44. McCann, J., and Ames, B. N. 1976. Detection of carcinogens as mutagens in the Salmonella/microsome test: Assay of 300 chemicals: Discussion. Proc. Natl. Acad. Sci. USA 73 :950-954.
45. McCann, J., Choi, E., Yamasaki, E., and Ames, B. N. 1975. Detection of carcinogens as mutagens in the Salmonella/microsome test: Assay of 300 chemicals. Proc. Natl. Acad. Sci. USA 72:5135-5139.
46. McKinney, J. D., and Waller, C. L. 1998. Molecular determinants of hormone mimicry: halogenated aromatic hydrocarbon environmental agents. J. Toxicol. Environ. Health. B. Crit. Rev. 1:27-58.
47. Muller, W.R. 1987. An algorithm for construction of the molecular distance matrix. J. Comput. Chem. 8:170-173.
48. Netzeva, T. I., Worth, A., Aldenberg, T., Benigni, R., Cronin, M. T., Gramatica, P., Jaworska, J. S., Kahn, S., Klopman, G., Marchant, C. A., Myatt, G., Nikolova-Jeliazkova, N., Patlewicz, G. Y., Perkins, R., Roberts, D., Schultz, T., Stanton, D. W., van de Sandt, J. J., Tong, W., Veith, G., and Yang, C. 2005. Current status of methods for defining the applicability domain of (quantitative) structure-activity relationships. The report and recommendations of ECVAM Workshop 52. Altern. La.b Anim. 33:155-173.
49. Nisbet, I. C., and LaGoy, P. K. 1992. Toxic equivalency factors (TEFs) for polycyclic aromatic hydrocarbons (PAHs). Regul.. Toxicol. Pharmacol. 16:290-300.
50. Parkinson, A. 1996. Biotransformation of xenobiotics. In Casarett and Doull's toxicology: The basic science of poisons, eds. C. D. Klaassen, M. O. Amdur, and J. Doull, pp. 133-224. New York: McGraw-Hill.
51. Petrulis, J. R., Chen, G., Benn, S., LaMarre, J., and Bunce, N. J. 2001. Application of the ethoxyresorufin-O-deethylase (EROD) assay to mixtures of halogenated aromatic compounds. Environ. Toxicol. 16:177-184.
52. Pitot, H. C., and Dragan, Y. P. 1996. Chemical carcinogenesis. In Casarett and Doull's toxicology: The basic science of poisons, eds. C. D. Klaassen, M. O. Amdur, and J. Doull, pp. 241-320. New York: McGraw-Hill.
53. Purcell, W. P., Bass, G. E., and Clayton, J. M. 1973. Strategy of drug design: A guide to biological activity. New York: John Wiley and Sons.
54. Radenac, G., Coteur, G., Danis, B., Dubois, P., and Warnau, M. 2004. Measurement of EROD activity: Caution on spectral properties of standards used. Mar. Biotechnol. 6:307-311.
55. Rogers, D., and Hopfinger, A. J. 1994. Application of genetic function approximation to quantitative structure-activity relationships and quantitative structure-property relationships. J. Chem. Inform. Comput. Sci. 34:854-866.
56. Rohrbaugh, R. H., and Jurs, P. C. 1987. Descriptions of molecular shape applied in studies of structure/activity and structure/property relationships. Anal. Chim. Acta 199:99-109.
57. Roy, D. R., Sarkar, U., Chattaraj, P. K., Mitra, A., Padmanabhan, J., Parthasarathi, R., Subramanian, V., Van Damme, S., and Bultinck, P. 2006. Analyzing toxicity through electrophilicity. Mol. Divers. 10:119-131.
58. Rummel, A. M., Trosko, J. E., Wilson, M. R., and Upham, B. L. 1999. Polycyclic aromatic hydrocarbons with bay-like regions inhibited gap junctional intercellular communication and stimulated MAPK activity. Toxicol. Sci. 49:232-240.
59. Safe, S. 2001. Molecular biology of the Ah receptor and its role in carcinogenesis. Toxicol. Lett. 120:1-7.
60. Singer, B., and Grunberger, D. 1983. Molecular biology of mutagens and carcinogens. New York: Plenum Press.
61. Stanton, D. T., Dimitrov, S., Grancharov, V., and Mekenyan, O. G. 2002. Charged partial surface area (CPSA) descriptors QSAR applications. SAR QSAR Environ. Res. 13:341-351.
62. Stanton, D. T., and Jurs, P. C. 1990. Development and use of charge partial surface area structural descriptors in computer-assisted quantitative structure-property relationship studies. Anal. Chem. 62:2323-2329.
63. Szklarz, G. D., and Paulsen, M. D. 2002. Molecular modeling of cytochrome P450 1A1: Enzyme-substrate interactions and substrate binding affinities. J. Biomol. Struct. Dyn. 20:155-162.
64. Trosko, J. E., Chang, C. C., Upham, B., and Wilson, M. 1998. Epigenetic toxicology as toxicant-induced changes in intracellular signalling leading to altered gap junctional intercellular communication. Toxicol. Lett. 102-103:71-78.
65. Trosko, J. E., and Ruch, R. J. 1998. Cell-cell communication in carcinogenesis. Front. Biosci. 3:d208-d236.
66. Upham, B. L., Weis, L. M., and Trosko, J. E. 1998. Modulated gap junctional intercellular communication as a biomarker of PAH epigenetic toxicity: Structure-function relationship. Environ. Health Perspect. 106(Suppl. 4):975-981.
67. Upham, B., Weis, L. M., Rummel, A. M., Masten, S. J., and Trosko, J. E. 1996. The effects of anthracene and methylated anthracenes on gap junction intercelluar communication in rat liver epithelial cells. Fundam. Appl. Toxicol. 34:260-264.
68. U.S. Environmental Protection Agency. 1993. Provisional guidance for quantitative risk assessment of polycyclic aromatic hydrocarbons. Washington, DC: Office of Research and Development.
69. U.S. Environmental Protection Agency. 2000. Supplementary guidance for conducting health risk assessment of chemical mixtures. Washington, DC: Office of Research and Development.
70. Votano, J. R., Parham, M., Hall, L. H., and Kier, L. B. 2004. New predictors for several ADME/Tox properties: Aqueous solubility, human oral absorption, and Ames genotoxicity using topological descriptors. Mol. Divers. 8:379-391.
71. Vyas, K. P., Levin, W., Yagi, H., Thakker, D. R., Ryan, D. E., Thomas, P. E., Conney, A. H., and Jerina, D. M. 1982a. Stereoselective metabolism of the (+)- and (-)-enantiomers of trans-1,2-dihydroxy-1,2-dihydrochrysene to bay-region 1,2-diol-3,4-epoxide diastereomers by rat liver enzymes. Mol. Pharmacol. 22:182-189.
72. Vyas, K. P., Thakker, D. R., Levin, W., Yagi, H., Conney, A. H., and Jerina, D. M. 1982b. Stereoselective metabolism of the optical isomers of trans-1,2-dihydroxy-1,2-dihydrophenanthrene to bay-region diol epoxides by rat liver microsomes. Chem. Biol. Interact. 38:203-213.
73. Warshawsky, D., and Landolph, J. R., eds. 2006. Molecular carcinogenesis and the molecular biology of human cancer. Boca Raton, FL: CRC Press.
74. Whyte, J. J., Jung, R. E., Schmitt, C. J., and Tillitt, D. E. 2000. Ethoxyresorufin-O-deethylase (EROD) activity in fish as a biomarker of chemical exposure. Crit. Rev. Toxicol. 30:347-570.
75. Winkler, D. A., and Burden, F. R. 2004. Modelling blood-brain barrier partitioning using Bayesian neural nets. J. Mol. Graph. Model. 22:499-505.
76. Young, J. F., Tsai, C.-A., Chen, J. J., Latendresse, J. R., and Kodell, R. L. 2006. Database composition can affect the structure-activity relationship prediction. J .Toxicol. Environ. Health A 69:1527-1540.
77. Zeiger, E. 1998. Identification of rodent carcinogens and noncarcinogens using genetic toxicity tests: Premises, promises, and performance. Regul. Toxicol. Pharmacol. 28:85-95.