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General Content: Research Articles

Docking-Based Classification Models for Exploratory Toxicology Studies on High-Quality Estrogenic Experimental Data

, , , , , , , , , & show all
Pages 1921-1936 | Published online: 06 Oct 2015

References

  • Merlot C . Computational toxicology – a tool for early safety evaluation. Drug Discov. Today15 (1–2), 16–22 (2010).
  • Kavlock R , DixD. Computational toxicology as implemented by the U.S. EPA: providing high throughput decision support tools for screening and assessing chemical exposure, hazard and risk. J. Toxicol. Environ. Health Part B13 (2–4), 197–217 (2010).
  • Nicolotti O , BenfenatiE, CarottiAet al. REACH and in silico methods: an attractive opportunity for medicinal chemists. Drug Discov. Today19 (11), 1757–1768 (2014).
  • Judson R , RichardA, DixDJet al. The toxicity data landscape for environmental chemicals. Environ. Health Perspect.117 (5), 685–695 (2009).
  • Judson R , RichardA, DixDet al. ACToR – aggregated computational toxicology resource. Toxicol. Appl. Pharmacol.233 (1), 7–13 (2008).
  • European Commission . Regulation (EC) No 1907/2006 of the European Parliament and of the Council of 18 December 2006 concerning the Registration, Evaluation, Authorization and Restriction of Chemicals (REACH), establishing a European Chemicals Agency, amending Directive 1999/45/EC and repealing Council Regulation (EEC) No 793/93 and Commission Regulation (EC) No 1488/94 as well as Council Directive 76/769/EEC and Commission Directives 91/155/EEC, 93/67/EEC, 93/105/EC and 2000/21/EC. J. Eur. Union Lett.396, 1–849 (2006).
  • Van Heerden S . Recent developments in global regulatory framework in the chemical industry. Popul. Plast. Packag.57, 46–50 (2012).
  • Diamanti-Kandarakis E , BourguignonJP, GiudiceLCet al. Endocrine-disrupting chemicals: an Endocrine Society scientific statement. Endocr. Rev.30 (4), 293–342 (2009).
  • Shi LM , FangH, TongWet al. QSAR models using a large diverse set of estrogens. J. Chem. Inf. Comput. Sci.41 (1), 186–195 (2000).
  • Devillers J , Marchand-GenesteN, CarpyA, PorcherJM. SAR and QSAR modeling of endocrine disruptors. SAR QSAR Environ. Res.17 (4), 393–412 (2006).
  • Jacobs MN . In silico tools to aid risk assessment of endocrine disrupting chemicals. Toxicology205 (1–2), 43–53 (2004).
  • Organization for Economic Cooperation and Development. www.qsartoolbox.org
  • Nicolotti O , GiangrecoI, MisciosciaTF, CarottiA. Improving quantitative structure–activity relationships through multiobjective optimization. J. Chem. Inf. Model.49 (10), 2290–2302 (2009).
  • Nicolotti O , MisciosciaTF, CarottiA, LeonettiF, CarottiA. An integrated approach to ligand- and structure-based drug design: development and application to a series of serine protease inhibitors. J. Chem. Inf. Model.48 (6), 1211–1226 (2008).
  • Kitchen DB , DecornezH, FurrJR, BajorathJ. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat. Rev. Drug Discov.3 (11), 935–949 (2004).
  • Shoichet BK . Virtual screening of chemical libraries. Nature432 (7019), 862–865 (2004).
  • Kolšek K , MavriJ, Sollner DolencM, GobecS, TurkS. Endocrine disruptome – an open source prediction tool for assessing endocrine disruption potential through nuclear receptor binding. J. Chem. Inf. Model.54 (4), 1254–1267 (2014).
  • Mueller SO , KorachKS. Estrogen receptors and endocrine diseases: lessons from estrogen receptor knockout mice. Curr. Opin. Pharmacol.1 (6), 613–619 (2001).
  • Shanle EK , XuW. Endocrine disrupting chemicals targeting estrogen receptor signaling: identification and mechanisms of action. Chem. Res. Toxicol.24 (1), 6–19 (2011).
  • Colborn T . Environmental estrogens: Health implications for humans and wildlife. Environ. Health Perspect.103 (Suppl. 7), 135–136 (1995).
  • Muegge I , OloffS. Advances in virtual screening. Drug Discov. Today Technol.3 (4), 405–411 (2006).
  • Ma XH , ZhuF, LiuXet al. Virtual screening methods as tools for drug lead discovery from large chemical libraries. Curr. Med. Chem.19 (32), 5562–5571 (2012).
  • Gissi A , GadaletaD, FlorisMet al. An alternative QSAR-based approach for predicting the bioconcentration factor for regulatory purposes. ALTEX31 (1), 23–36 (2014).
  • Fourches D , MuratovE, TropshaA. Trust, but verify: on the importance of chemical structure curation in cheminformatics and QSAR modeling research. J. Chem. Inf. Model.50 (7), 1189–1204 (2010).
  • Small-Molecule Drug Discovery Suite 2014–4: GLIDE, version 6.5, Schrödinger, LLC, New York, NY, 2014.
  • Jones G , WillettP, GlenRC, LeachAR, TaylorR. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol.267 (3), 727–748 (1997).
  • Hornberg JJ , LaursenM, BrendenNet al. Exploratory toxicology as an integrated part of drug discovery. Part I: why and how. Drug Discov. Today19 (8), 1131–1136 (2014).
  • Zhang L , SedykhA, TripathiAet al. Identification of putative estrogen receptor-mediated endocrine disrupting chemicals using QSAR- and structure-based virtual screening approaches. Toxicol. Appl. Pharmacol.272 (1), 67–76 (2013).
  • Heldring N , PikeA, AnderssonSet al. Estrogen receptors: how do they signal and what are their targets. Physiol. Rev.87 (3), 905–931 (2007).
  • Shiau AK , BarstadD, RadekJTet al. Structural characterization of a subtype-selective ligand reveals a novel mode of estrogen receptor antagonism. Nat. Struct. Mol. Biol.9 (5), 359–364 (2002).
  • Tanenbaum DM , WangY, WilliamsSP, SiglerPB. Crystallographic comparison of the estrogen and progesterone receptor's ligand binding domains. Proc. Natl Acad. Sci. USA95 (11), 5998–6003 (1998).
  • Fang J , Akwabi-AmeyawA, BrittonJEet al. Synthesis of 3-alkyl naphthalenes as novel estrogen receptor ligands. Bioorg. Med. Chem. Lett.18 (18), 5075–5077 (2008).
  • Kim S , WuJY, BirzinETet al. Estrogen receptor ligands. II. Discovery of benzoxathiins as potent, selective estrogen receptor α modulators. J. Med. Chem.47 (9), 2171–2175 (2004).
  • Möcklinghoff S , RoseR, CarrazM, VisserA, OttmannC, BrunsveldL. Synthesis and crystal structure of a phosphorylated estrogen receptor ligand binding domain. Chem. Biol. Chem.11 (16), 2251–2254 (2010).
  • Mewshaw RE , BowenSM, HarrisHA, XuZB, ManasES, CohnST. ERbeta ligands. Part 5: synthesis and structure–activity relationships of a series of 4′-hydroxyphenyl-aryl-carbaldehyde oxime derivatives. Bioorg. Med. Chem. Lett.17 (4), 902–906 (2007).
  • Pike AC , BrzozowskiAM, HubbardREet al. Structure of the ligand-binding domain of oestrogen receptor beta in the presence of a partial agonist and a full antagonist. EMBO J.18 (17), 4608–4618 (1999).
  • Schrödinger Release 2014–4: LigPrep, version 3.2, Schrödinger, LLC, New York, NY, 2014.
  • Schrödinger Release 2014–4: Schrödinger Suite 2014–4 Protein Preparation Wizard; Epik version 3.0, Schrödinger, LLC, New York, NY, 2014; Impact version 6.5, Schrödinger, LLC, New York, NY, 2014; Prime version 3.8, Schrödinger, LLC, New York, NY, 2014..
  • Banks JL , BeardHS, CaoYet al. Integrated modeling program, applied chemical theory (IMPACT). J. Comput. Chem.26 (16), 1752–1780 (2005).
  • Schapira M , AbagyanR, TotrovM. Nuclear hormone receptor targeted virtual screening. J. Med. Chem.46 (14), 3045–3059 (2003).
  • Klebe G . Virtual ligand screening: strategies, perspectives and limitations. Drug Discov. Today11 (13–14), 580–594 (2006).
  • Huang N , ShoichetBK, IrwinJJ. Benchmarking sets for molecular docking. J. Med. Chem.49 (23), 6789–6801 (2006).
  • Nam K , MarshallP, WolfRM, CornellW. Simulation of the different biological activities of diethylstilbestrol (DES) on estrogen receptor alpha and estrogen-related receptor gamma. Biopolymers68 (1), 130–138 (2003).
  • Walker VR , JeffersonWN, CouseJF, KorachKS. Estrogen receptor-α mediates diethylstilbestrol-induced feminization of the seminal vesicle in male mice. Environ. Health Perspect.120 (4), 560–565 (2012).
  • Sikoski P , RegisterTC, LeesCJet al. Effects of two novel selective estrogen receptor modulators, raloxifene, tamoxifen, and ethinyl estradiol on the uterus, vagina and breast in ovariectomized cynomolgus monkeys (macaca fascicularis). Am. J. Obstet. Gynecol.196 (1), 75.e1–75.e7 (2007).
  • Shiau AK , BarstadD, LoriaPMet al. The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell95 (7), 927–937 (1998).
  • Yin L , HuQ. Drug discovery for breast cancer and co-instantaneous cardiovascular disease: what is the future?Future Med. Chem.5 (4), 359–362 (2013).
  • Barkhem T , CarlssonB, NilssonY, EnmarkE, GustafssonJ, NilssonS. Differential response of estrogen receptor alpha and estrogen receptor beta to partial estrogen agonists/antagonists. Mol. Pharmacol.54 (1), 105–112 (1998).
  • Dinwiddie MT , TerryPD, ChenJ. Recent evidence regarding triclosan and cancer risk. Int. J. Environ. Res. Public Health.11 (2), 2209–2217 (2014).
  • Geens T , AertsD, BerthotCet al. A review of dietary and non-dietary exposure to bisphenol-A. Food Chem. Toxicol.50 (10), 3725–3740 (2012).
  • Rastogi SC , SchoutenA, de KruijfN, WeijlandJW. Contents of methyl-, ethyl-, propyl-, butyl- and benzylparaben in cosmetic products. Contact Dermatitis.32 (1), 28–30 (1995).
  • Bowers JL , TyulmenkovVV, JerniganSC, KlingeCM. Resveratrol acts as a mixed agonist/antagonist for estrogen receptors α and β. Endocrinology141 (10), 3657–3667 (2000).
  • Fuller HR , HumphreyEL, MorrisGE. Naturally occurring plant polyphenols as potential therapies for inherited neuromuscular diseases. Future Med. Chem.5 (17), 2091–2101 (2013).
  • Huang H , DuG, ZhangWet al. The in vitro estrogenic activities of triclosan and triclocarban. J. Appl. Toxicol.34 (9), 1060–1067 (2014).
  • Okubo T , YokoyamaY, KanoK, KanoI. ER-dependent estrogenic activity of parabens assessed by proliferation of human breast cancer MCF-7 cells and expression of ERα and PR. Food Chem. Toxicol.39 (12), 1225–1232 (2001).

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