Computational toxicology: Application in environmental chemicals

Methods in Molecular Biology

Volumn 929, Issue , 2012, Pages 9-19

  Tan, Yu Mei ^a   Conolly, Rory ^b   Chang, Daniel T ^a   Tornero Velez, Rogelio ^a   Goldsmith, Michael R ^a   Peterson, Shane D ^a   Dary, Curtis C ^a  

^a U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^b U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

Author keywords

Biologically based dose response model; Clonal growth model; Computational toxicology; Dosimetry; Fate and transport; Physiologically based pharmacokinetic model; Signaling pathway; Source to effect continuum; Virtual tissue

Indexed keywords

ENVIRONMENTAL CHEMICAL;

ADVECTION; ARTICLE; BEHAVIOR; COMPUTATIONAL FLUID DYNAMICS; COMPUTATIONAL TOXICOLOGY; DIFFUSION; DISPERSION; DOSIMETRY; HUMAN; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; RESPIRATORY SYSTEM; TOXICOLOGY;

EID: 84934443569     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-50-2_2     Document Type: Article

References (49)

1. ASTM (1998) 1998 Annual book of ASTM standards: standard guide for remediation of ground water by natural attenuation at petroleum release sites (Designation: E 1943-98), vol 11.04. American Society for Testing and Materials, West Conshohocken, pp 875-917
2. Williams PRD, Hubbell WBJ, Weber E et al (2010) An overview of exposure assessment models used by the U.S. Environmental Protection Agency. In: Hanrahan G (ed) Modeling of pollutants in complex environmental systems, vol 2. ILM Publications, St Albans
3. US EPA (1992) Guidelines for exposure assessment. EPA/600/Z-92/001. US Environmental Protection Agency, Washington, DC
4. Zartarian VG, Xue J, Ozkaynak H, Dang W, Glen G, Smith L, Stallings C (2006) A probabilistic arsenic exposure assessment for children who contact CCA-treated playsets and decks, Part 1: model methodology, variability results, and model evaluation. Risk Anal 26 (2):515-531
5. Glen G, Smith L, Isaacs K, Mccurdy T, Langstaff J (2008) A new method of longitudinal diary assembly for human exposure modeling. J Expo Sci Environ Epidemiol 18(3):299-311
6. Tran NL, Barraj L, Smith K, Javier A, Burke T (2004) Combining food frequency and survey data to quantify long-term dietary exposure: a methyl mercury case study. Risk Anal 24 (1):19-30
7. Song C, Qu Z, Blumm N, Barabasi AL (2010) Limits of predictability in human mobility. Science 327(5968):1018-1021
8. US EPA (1997) Exposure factors handbook. US Environmental Protection Agency, Washington, DC. http://www.epa.gov/NCEA/pdfs/efh/front.pdf
9. Watanabe PG, Gehring PJ (1976) Dosedependent fate of vinyl chloride and its possible relationship to oncogenicity in rats. Environ Health Perspect 17:145-152
10. Reddy MB, Yang RSH, Clewell HJ, Andersen ME (2005) Physiologically based pharmacokinetic modeling: science and applications. Wiley, Hoboken
11. Emmen HH, Hoogendijk EM, Klopping- Ketelaars WA, Muijser H, Duisterrnaat E, Ravensberg JC, Alexander DJ, Borkhataria D, Rusch GM, Schmit B (2000) Human safety and pharmacokinetics of the CFC alternative propellants HFC 134a (1,1,1,2- tetrafluoroethane) and HFC 227 (1,1,1,2,3,3,3-heptafluoropropane) following whole-body exposure. Regul Toxicol Pharmacol 32(1):22-35
12. Ernstgard L, Andersen M, Dekant W, Sjogren B, Johanson G (2010) Experimental exposure to 1,1,1,3,3-pentafluoropropane (HFC- 245fa): uptake and disposition in humans. Toxicol Sci 113(2):326-336
13. Sexton K, Kleffman DE, Cailahan MA (1995) An introduction to the National Human Exposure Assessment Survey (NHEXAS) and related phase I field studies. J Expo Anal Environ Epidemiol 5(3):229-232
14. Shin BS, Hwang SW, Bulitta JB, Lee JB, Yang SD, Park JS, Kwon MC, do Kim J, Yoon HS, Yoo SD (2010) Assessment of bisphenol A exposure in Korean pregnant women by physiologically based pharmacokinetic modeling. J Toxicol Environ Health A 73 (21-22):1586-1598
15. Wilson NK, Chuang JC, Morgan MK, Lordo RA, Sheldon LS (2007) An observational study of the potential exposures of preschool to pentachlorophenol, bisphenol-A, and nonylphenol at home and daycare. Environ Res 103(1):9-20
16. Andersen ME (2003) Toxicokinetic modeling and its applications in chemical risk assessment. Toxicol Lett 138(1-2):9-27
17. Rapaport DC (2004) The art of molecular dynamics simulation, 2nd edn. Cambridge University, New York
18. Obach RS (1999) Prediction of human clearance of twenty-nine drugs from hepatic microsomal intrinsic clearance data: an examination of in vitro half-life approach and nonspecific binding to microsomes. Drug Metab Dispos 27(11):1350-1359
19. Obach RS, Baxter JG, Liston TE, Silber BM, Jones BC, MacIntyre F, Rance DJ, Wastall P (1997) The prediction of human pharmacokinetic parameters from preclinical and in vitro metabolism data. J Pharmacol Exp Ther 283 (1):46-58
20. Tornero-Velez R, Mirfazaelina A, Kim KB, Anand SS, Kim HJ, Haines WT, Bruckner JV, Fisher JW (2010) Evaluation of deltamethrin kinetics and dosimetry in the maturing rats using a PBPK model. Toxicol Appl Pharmacol 244(2):208-217
21. Bohm G (1996) New approaches in molecular structure prediction. Biophys Chem 59 (1-2):1-32
22. Fielden MR, Matthews JB, Fertuck KC et al (2002) In silico approaches to mechanistic and predictive toxicology: an introduction to bioinformatics for toxicologists. Crit Rev Toxicol 32(2):67-112
23. Marrone TJ, Briggs JM, McCammon JA (1997) Structure-based drug design: computational advances. Annu Rev Pharmacol Toxicol 37:71-90
24. Leo A, Handsch C, Elkins D (1971) Partition coefficients and their uses. Chem Rev 71 (6):525-616
25. Valko K (2002) Measurements and predictions of physicochemical properties. In: Darvas F, Dorman G (eds) High-throughput ADMETox estimation. Eaton Publishing, Westborough
26. Topliss JG (ed) (1983) Quantitative structureactivity relationships of drugs. Academic, New York
27. Cronin MTD, Dearden JC, Duffy JC, Edwards R, Manga N, Worth AP, Worgan ADP (2002) The importance of hydrophobicity and electrophilicity descriptors in mechanistically-based QSARs for toxicological endpoints. SAR QSAR Environ Res 13:167-176
28. Pratt WB, Taylor P (eds). (1990) Principles of drug action. Churchill-Livingstone, Inc, New York
29. Rabinowitz J.R., Little S, Laws SC, Goldsmith R (2009) Molecular modeling for screening environmental chemicals for estrogenicity: use of the toxicant-target approach. Chem Res Toxicol 22(9):1594-1602
30. Allen MP, Tildesley DJ (2002) Computer simulations of liquids. Oxford University, New York
31. Car R, Parrinello M (1985) Unified approach for molecular dynamics and density-functional theory. Phys Rev Lett 55(22):2471-2474
32. Colombo MC, Guidoni L, Laio A, Magistrato A, Maurer P, Piana S, Rohrig U, Spiegel K, Sulpizi M, VandeVondele J, Zumstein M, Rothlisberger U (2002) Hybrid QM/MM Carr-Parrinello simulations of catalytic and enzymatic reactions. CHIMIA 56(1-2):13-19
33. Geva E, Shi Q, Voth GA (2001) Quantummechanical reaction rate constants from centroid molecular dynamics simulations. J Chem Phys 115:9209-9222
34. Prezhdo OV, Rossky PJ (1997) Evaluation of quantum transition rates from quantum classical molecular dynamics simulation. J Chem Phys 107:5863
35. Truhlar DG, Garrett BC (1980) Variational transition-state theory. Acc Chem Res 13:440-448
36. Tuckerman M, Laasonen K, Sprik M, Parrinello M (1995) Ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water. J Chem Phys 103:150-161
37. Wang H, Sun X, Miller WH (1998) Semiclassical approximations for trhe calculation of thermal rate constants for chemical reactions in complex molecular systems. J Phys Chem 108 (23):9726-9736
38. Kimbell JS, Gross EA, Joyner DR, Godo MN, Morgan KT (1993) Application of computational fluid dynamics to regional dosimetry of inhaled chemicals in the upper respiratory tract of the rat. Toxicol Appl Pharmacol 121:253-263
39. Overton JH, Kimbell JS, Miller FJ (2001) Dosimetry modeling of inhaled formaldehyde: the human respiratory tract. Toxicol Sci 64:122-134
40. Roux PP, Blenis J (2004) ERK and p38 MAPK-activated protein kinases: a family of protein kinases with diverse biological functions. Microbiol Mol Biol Rev 68:320-344
41. Bhalla US, Prahlad RT, Iyengar R (2002) MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 297:1018-1023
42. Hoffman A, Levchenko A, Scott ML, Baltimore D (2005) The IkB-NF-kB signaling module: temporal control and selective gene activation. Science 298:1241-1245
43. National Research Council (NRC) Committee on Toxicity and Assessment of Environmental Agents (2007) Toxicity testing in the twentyfirst century: a vision and a strategy. National Academies, Washington, DC. ISBN 0-309-10989-2
44. Crump KS, Hoel DG, Langley CH, Peto R (1976) Fundamental carcinogenic processes and their implications for low dose risk assessment. Cancer Res 36:2937-2979
45. Moolgavkar SH, Dewanji A, Venzon DJ (1988) A stochastic two-stage model for cancer risk assessment. The hazard function and probability of tumor. Risk Anal 8:383-392
46. Conolly RB, Kimbell JS, Janszen D, Schlosser PM, Kalisak D, Preston J, Miller FJ (2004) Human respiratory tract cancer risks of inhaled formaldehyde: dose-response predictions derived from biologically-motivated computational modeling of a combined rodent and human dataset. Toxicol Sci 82:279-296
47. Adra S, Sun T, MacNeil S, Holcombe M, Smallwood R (2010) Development of a threedimensional multiscale computational model of the human epidermis. PLoS One 5(1): e8511. doi:10.1371/journal.pone.0008511
48. Shah I, Wambaugh J (2010) Virtual tissues in toxicology. J Toxicol Environ Health 13 (2-4):314-328
49. Wambaugh J, Shah I (2010) Simulating microdosimetry in a virtual hepatic lobule. PLoS Comput Biol 6(4):e1000756. doi:10.1371/journal.pcbi. 1000756