Molecular modeling for screening environmental chemicals for estrogenicity: Use of the toxicant-target approach

Chemical Research in Toxicology

Volumn 22, Issue 9, 2009, Pages 1594-1602

  Rabinowitz, James R ^a   Little, Stephen B ^a   Laws, Susan C ^a   Goldsmith, Michael Rock ^a  

^a U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESTROGEN RECEPTOR;

ARTICLE; BINDING AFFINITY; BIOLOGY; CHEMICAL INTERACTION; CONTROLLED STUDY; ENDOCRINE FUNCTION; GEOMETRY; HUMAN; MALE; MOLECULAR MODEL; NONHUMAN; PHARMACOPHORE; RAT; RISK ASSESSMENT; SCREENING;

ALGORITHMS; ANIMALS; BINDING, COMPETITIVE; COMPUTER SIMULATION; DATABASES, FACTUAL; ENVIRONMENTAL POLLUTANTS; FEMALE; MODELS, CHEMICAL; RATS; RECEPTORS, ESTROGEN; STRUCTURE-ACTIVITY RELATIONSHIP;

RATTUS;

EID: 70349337874     PISSN: 0893228X     EISSN: 15205010     Source Type: Journal    
DOI: 10.1021/tx900135x     Document Type: Article

References (54)

1. Judson, R., Richard, A., Dix, D., Houck, K., Martin, M., Kavlock, R., Dellarco, V., Henry, T., Holderman, T., Sayre, P., Tan, S., Carpenter, T., and Smith, E. (2009) The toxicity data landscape for environmental chemicals. Environ. Health Perspect. 117 (5), 685-695.
2. Richard, A. M. (2006) Future of toxicology - predictive toxicology: An expanded view of "chemical toxicity". Chem. Res. Toxicol. 19 (10), 1257-1262.
3. National Research Council (NRC). (2007) Toxicity Testing in the 21st Century: A Vision and a Strategy. National Academy Press, Washington, DC. http://www.nas.edu.
4. Dix, D. J., Houck, K. A., Martin, M. T., Richard, A. M., Setzer, R. W., and Kavlock, R. J. (2007) The ToxCast program for prioritizing toxicity testing of environmental chemicals. Toxicol. Sci. 95, 9-12.
5. Rabinowitz, J. R., Goldsmith, M.-R., Little, S. B., and Pasquinelli, M. A. (2008) Computational molecular modeling for evaluating the toxicity of environmental chemicals: Prioritizing bioassay requirements. Environ. Health Perspect. 116, 573-577.
6. Kuntz, I. D. (1992) Structure-based strategies for drug design and discovery. Science 257 (5073), 1078-1082.
7. Halperin, I., Ma, B., Wolfson, H., and Nussinov, R. (2002) Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 47 (4), 409-443. (Pubitemid 34614722)
8. Sousa, S. F., Fernandes, P. A., and Ramos, M. J. (2006) Protein-ligand docking: current status and future challenges. Proteins: Struct., Funct., Bioinf. 65, 15-26. (Pubitemid 44320611)
9. Abagyan, R., and Totrov, M. (2001) High-throughput docking for lead generation. Curr. Opin. Chem. Biol. 5 (4), 375-382.
10. Bissantz, C., Folkers, G., and Rognan, D. (2000) Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/ scoring combinations. J. Med. Chem. 43, 4759-4767. (Pubitemid 32002687)
11. Cozzini, P., and Dottorini, T. (2004) Is it possible docking and scoring new ligands with few experimental data? Preliminary results on estrogen receptor as a case study. Eur. J. Med. Chem. 31, 601-609. (Pubitemid 38962495)
12. Amadasi, A., Mozzarelli, A., Meda, C., Maggi, A., and Cozzini, P. (2009) Identification of xenoestrogens in food additives by an integrated in silico and in vitro approach. Chem. Res. Toxicol. 22 (1), 52-63.
13. Ekins, S. (2004) Predicting undesirable drug interactions with promiscuous proteins in silico. Drug Discovery Today 9 (6), 276-285.
14. Laws, S. C., Yavanhxay, S., Cooper, R. L., and Eldridge, J. C. (2006) Nature of the binding interaction for 50 structurally diverse chemicals with rat estrogen receptors. Toxicol. Sci. 94, 46-56. (Pubitemid 44542329)
15. Richard, A. M., and Williams, C. R. (2002) Distributed structure-searchable toxicity (DSSTox) public database network: A proposal. Mutat. Res. 499, 27-52.
16. Laws, S., Kariya, J., Wolf, M., and Richard A. M. (2009) DSSTox EPA Estrogen Receptor Ki Binding Study (Laws et al.) Database - (KIERBL): SDF file and documentation, Launch version: KIERBL-v1a- 278-17Feb2009, www.epa.gov/ncct/dsstox/sdf-kierbl.html.
17. http://epa.gov/endo/pubs/edspoverview/finalrpt.htm (accessed Mar 24, 2009).
18. NIH NTP/ICCVAM Report (2002) Current Status of Test Methods for Detecting Endocrine Disruptors: In Vitro Estrogen Receptor Binding Assays, NIEHS, RTP, NC. http://iccvam.niehs.nih.gov/docs/endo-docs/final1002/erbndbrd/ERBd034504.pdf
19. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, G. H., Shindyalov, I. N., and Bourne, P. E. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235-242.
20. Wärnmark, A., Treuter, E., Gustafsson, J. A., Hubbard, R. E., Brzozowski, A. M., and Pike, A. C. (2002) PDB ID: 1GWR: Interaction of transcriptional intermediary factor 2 nuclear receptor box peptides with the coactivator binding site of estrogen receptor alpha. J. Biol. Chem. 277 (24), 21862-21868. (Pubitemid 34959959)
21. Shiau, A. K., Barstad, D., Loria, P. M., Cheng, L., Kushner, P. J., Agard, D. A., and Greene, G.L.,. (1998) PDB ID: 3ERT: The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell 95 (7), 927-937. (Pubitemid 29019045)
22. MOE, Chemical Computing Group, Inc., Montreal, Quebec, Canada, 2008.
23. Levitt, M. (1992) Accurate modelling of protein conformation by automatic segment matching. J. Mol. Biol. 226, 507-533.
24. Fechteler, T., Schomburg, U., and Dengler, D. (1995) Prediction of protein three-dimensional structures in insertion and deletion regions: A procedure for searching data bases of representative protein fragments using geometric criteria. J. Mol. Biol. 253, 114-131.
25. Cornell, W.D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, Jr, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117, 5179-5197.
26. Pike, A. C., Brzozowski, A. M., Walton, J., Hubbard, R. E., Thorsell, A. G., Li, Y. L., Gustafsson, J. A., and Carlquist, M. (2001) PDB ID: 1HJ1: Structural insights into the mode of action of a pure antiestrogen. Structure 9 (2), 145-153. (Pubitemid 32215278)
27. Pike, A. C. W., Brzozowski, A. M., Hubbard, R. E., Walton, J., Bonn, T., Thorsell, A.-G., Engstrom, O., Ljunggren, J., Gustaffson, J.-A., and Carlquist, M. PDB ID: 2J7X: Structure of agonist-bound estrogen receptor beta LBD in complex with Lxxll motif from Ncoa5, unpublished work.
28. Halgren, T. (1996) Merck molecular force field. I. Basis, form, scope, parameterization and performance of MMFF94;. J. Comput. Chem. 17, 490-519.
29. http://www.simbiosys.ca/ehits/index.html (accessed Feb 22, 2009).
30. Zsoldos, Z., Reid, D., Simon, A., Sadjad, B. S., and Johnson, A. P. (2006) eHiTS: An innovative approach to the docking and scoring function problems. Curr. Protein Pept. Sci. 7, 421-435. (Pubitemid 44524491)
31. http://www.eyesopen.com/products/applications/FRED.html (accessed Feb 22, 2009).
32. McGann, M. R., Almond, H. R., Nicholls, A., Grant, J. A., and Brown, F. K. (2003) Gaussian docking functions. Biopolymers 68, 76-90.
33. Schultz-Gasch, T., and Stahl, M. (2003) Binding characteristics in structure-based virtual screening:evaluation of current docking tools. J Mol Model 9, 47-57.
34. Kellenberger, E., Rodrigo, J., Muller, P., and Rognan, D. (2004) Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins: Struct., Funct., Bioinf. 57, 225-242. (Pubitemid 39223729)
35. Shughrue, P. J., Lane, M. V., Scrimo, P. J., and Merchenthaler, I. (1998) Comparative distribution of estrogen receptor-α (ER-α) and β (ER-β) mRNA in the rat pituitary, gonad, and reproductive tract. Steroids. 63 (10), 498-504.
36. Anstead, G. M., Carlson, K. E., and Katzenellenbogen, J. A. (1997) The estradiol pharmacophore: Ligand structure-estrogen receptor binding affinity relationships and a model for the receptor binding site. Steroids 62 (3), 268-303.
37. Stahl, M., and Rarey, M. (2001) Detailed analysis of scoring functions for virtual screening. J. Med. Chem. 44 (7), 1035-1042. (Pubitemid 32852130)
38. Jain, A. N. (2006) Scoring functions for protein-ligand docking. Curr. Protein Pept. Sci. 7 (5), 407-420.
39. Muthasa, D., Sabnis, Y. A., Lundborga, M., and Karlén, A. (2008) Is it possible to increase hit rates in structure-based virtual screening by pharmacophore filtering? An investigation of the advantages and pitfalls of post-filtering. J. Mol. Graphics Modell. 26 (8), 1237-1251.
40. Peach, M. L., and Nicklaus, M. C. (2009) Combining docking with pharmacophore filtering for improved virtual screening. J. Cheminf. 1 (6), 1-13.
41. Kuiper, G. G. J. M., Carlsson, B., Grandien, K., Enmark, E., Hagblad, J., Nilsson, S., and Gustafsson, J.-A. (1997) Comparison of ligand binding specificity and transcript tissue distribution of estrogen receptors α and β. Endocrinology 138 (3), 863-879. (Pubitemid 27089735)
42. Carlson, H. A. (2002) Protein flexibility and drug design: how to hit a moving target. Curr. Opin. Chem. Biol. 6 (4), 447-452.
43. Sherman, W., Day, T., Jacobson, M. P., Friesner, R. A., and Farid, R. (2006) Novel procedure for modeling ligand/receptor induced fit effects. J. Med. Chem. 49, 534-553. (Pubitemid 43157487)
44. Mukherjee, S., Nagar, S., Mullick, S., Mukherjee, A., and Saha, A. (2008) Pharmacophore mapping of arylbenzothiophene derivatives for MCF cell inhibition using classical and 3D space modeling approaches. J. Mol. Graphics Modell. 26 (6), 884-992. (Pubitemid 350213446)
45. Yang, J.-M., and Shen, T.-W. (2005) A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators. Proteins: Struct., Funct., Bioinf. 59, 205-220. (Pubitemid 40471560)
46. Ekins, S., and Erickson, J. A. (2002) A pharmacophore for human pregnane X receptor ligands. Drug Metab. Dispos. 30 (1), 96-99. (Pubitemid 34016946)
47. Podolyan, Y., and Karypis, G. (2009) Common pharmacophore identification using frequent clique detection algorithm. J. Chem. Inf. Model. 49 (1), 13-21.
48. Gaido, K. W., Leonard, L. S., Maness, S. C., Hall, J. M., McDonnell, D. P., Saville, B., and Safe, S. (1999) Differential Interaction of the methoxychlor metabolite 2,2-bis-(p-Hydroxyphenyl)-1,1,1-trichloroethane with estrogen receptors α and β. Endocrinology 140 (12), 5746-5753. (Pubitemid 30648838)
49. Blair, R. M., Fang, H., Branham, W. S., Hass, B. S., Dial, S. L., Moland, C. L., Tong, W., Shi, L., Perkins, R., and Sheehan, D. M. (2000) The estrogen receptor relative binding affinities of 188 natural and xenochemicals: Structural diversity of ligands. Toxicol. Sci. 54, 138-153. (Pubitemid 30152465)
50. Laws, S. C., Carey, S. A., Ferrell, J. M., Bodman, G. J., and Cooper, R. L. (2000) Estrogenic activity of octylphenol, nonylphenol, bisphenol A and methoxychlor in rats. Toxicol. Sci. 54, 154-167.
51. Fang, H., Tong, W., Welsh, W. J., and Sheehan, D. M. (2003) QSAR models in receptor-mediated effects: The nuclear receptor superfamily. J. Mol. Struct: THEOCHEM 622, 113-125.
52. Liu, T., Lin, Y., Wen, X., Jorrisen, R. N., and Gilson, M. K. (2007) BindingDB: A Web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res. 35, D198-D201. (Pubitemid 46056198)
53. Ertl, P., Rohde, B., and Selzer, P. (2000) Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties J. Med. Chem. 43, 3714-3717 (as implemented in 22). (Pubitemid 30764293)
54. Wildman, S. A., and Crippen, G. M. (1999) Prediction of physiochemical parameters by atomic contributions J. Chem. Inf. Comput. Sci. 39 (5), 868-873 (as implemented in 22).