Literature DB >> 30584954

Development, validation and integration of in silico models to identify androgen active chemicals.

Serena Manganelli1, Alessandra Roncaglioni1, Kamel Mansouri2, Richard S Judson3, Emilio Benfenati1, Alberto Manganaro1, Patricia Ruiz4.   

Abstract

Humans are exposed to large numbers of environmental chemicals, some of which potentially interfere with the endocrine system. The identification of potential endocrine disrupting chemicals (EDCs) has gained increasing priority in the assessment of environmental hazards. The U.S. Environmental Protection Agency (U.S. EPA) has developed the Endocrine Disruptor Screening Program (EDSP) which aims to prioritize and screen potential EDCs. The Toxicity Forecaster (ToxCast) program has generated data using in vitro high-throughput screening (HTS) assays measuring activity of chemicals at multiple points along the androgen receptor (AR) activity pathway. In the present study, using a large and diverse data set of 1667 chemicals provided by the U.S. EPA from the combined ToxCast AR assays in the framework of the Collaborative Modeling Project for Androgen Receptor Activity (CoMPARA). Two models were built using ADMET Predictor™; one is based on Artificial Neural Networks (ANNs) technology and the other uses a Support Vector Machine (SVM) algorithm; one model is a Decision Tree (DT) developed in R; and two models make use of differently combined sets of structural alerts (SAs) automatically extracted by SARpy. We used two strategies to integrate predictions from single models; one is based on a majority vote approach and the other on prediction convergence. These strategies led to enhanced statistical performance in most cases. Moreover, the majority vote approach improved prediction coverage when one or more single models were not able to provide any estimations. This study integrates multiple in silico approaches as a virtual screening tool for use in risk assessment of endocrine disrupting chemicals. Published by Elsevier Ltd.

Entities:  

Keywords:  Androgen receptor; Artificial neural networks; Decision tree; Endocrine disrupting chemicals; High-throughput screening; In silico; Support vector machine

Mesh:

Substances:

Year:  2018        PMID: 30584954      PMCID: PMC6778835          DOI: 10.1016/j.chemosphere.2018.12.131

Source DB:  PubMed          Journal:  Chemosphere        ISSN: 0045-6535            Impact factor:   7.086


  23 in total

1.  Update on EPA's ToxCast program: providing high throughput decision support tools for chemical risk management.

Authors:  Robert Kavlock; Kelly Chandler; Keith Houck; Sid Hunter; Richard Judson; Nicole Kleinstreuer; Thomas Knudsen; Matt Martin; Stephanie Padilla; David Reif; Ann Richard; Daniel Rotroff; Nisha Sipes; David Dix
Journal:  Chem Res Toxicol       Date:  2012-05-15       Impact factor: 3.739

2.  Classification and virtual screening of androgen receptor antagonists.

Authors:  Jiazhong Li; Paola Gramatica
Journal:  J Chem Inf Model       Date:  2010-05-24       Impact factor: 4.956

3.  Docking-based classification models for exploratory toxicology studies on high-quality estrogenic experimental data.

Authors:  Daniela Trisciuzzi; Domenico Alberga; Kamel Mansouri; Richard Judson; Saverio Cellamare; Marco Catto; Angelo Carotti; Emilio Benfenati; Ettore Novellino; Giuseppe Felice Mangiatordi; Orazio Nicolotti
Journal:  Future Med Chem       Date:  2015-10-06       Impact factor: 3.808

4.  Integrated Model of Chemical Perturbations of a Biological Pathway Using 18 In Vitro High-Throughput Screening Assays for the Estrogen Receptor.

Authors:  Richard S Judson; Felicia Maria Magpantay; Vijay Chickarmane; Cymra Haskell; Nessy Tania; Jean Taylor; Menghang Xia; Ruili Huang; Daniel M Rotroff; Dayne L Filer; Keith A Houck; Matthew T Martin; Nisha Sipes; Ann M Richard; Kamel Mansouri; R Woodrow Setzer; Thomas B Knudsen; Kevin M Crofton; Russell S Thomas
Journal:  Toxicol Sci       Date:  2015-08-13       Impact factor: 4.849

5.  The ToxCast program for prioritizing toxicity testing of environmental chemicals.

Authors:  David J Dix; Keith A Houck; Matthew T Martin; Ann M Richard; R Woodrow Setzer; Robert J Kavlock
Journal:  Toxicol Sci       Date:  2006-09-08       Impact factor: 4.849

6.  Automatic knowledge extraction from chemical structures: the case of mutagenicity prediction.

Authors:  T Ferrari; D Cattaneo; G Gini; N Golbamaki Bakhtyari; A Manganaro; E Benfenati
Journal:  SAR QSAR Environ Res       Date:  2013-05-28       Impact factor: 3.000

7.  Integration of in silico methods and computational systems biology to explore endocrine-disrupting chemical binding with nuclear hormone receptors.

Authors:  P Ruiz; A Sack; M Wampole; S Bobst; M Vracko
Journal:  Chemosphere       Date:  2017-03-09       Impact factor: 7.086

Review 8.  Endocrine-disrupting chemicals: associated disorders and mechanisms of action.

Authors:  Sam De Coster; Nicolas van Larebeke
Journal:  J Environ Public Health       Date:  2012-09-06

Review 9.  An updated review of environmental estrogen and androgen mimics and antagonists.

Authors:  C Sonnenschein; A M Soto
Journal:  J Steroid Biochem Mol Biol       Date:  1998-04       Impact factor: 4.292

10.  Comparison of different approaches to define the applicability domain of QSAR models.

Authors:  Faizan Sahigara; Kamel Mansouri; Davide Ballabio; Andrea Mauri; Viviana Consonni; Roberto Todeschini
Journal:  Molecules       Date:  2012-04-25       Impact factor: 4.411

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  7 in total

Review 1.  In Silico Models for Skin Sensitization and Irritation.

Authors:  Gianluca Selvestrel; Federica Robino; Matteo Zanotti Russo
Journal:  Methods Mol Biol       Date:  2022

2.  Comparison of Machine Learning Models for the Androgen Receptor.

Authors:  Kimberley M Zorn; Daniel H Foil; Thomas R Lane; Wendy Hillwalker; David J Feifarek; Frank Jones; William D Klaren; Ashley M Brinkman; Sean Ekins
Journal:  Environ Sci Technol       Date:  2020-10-21       Impact factor: 9.028

3.  High-throughput toxicogenomic screening of chemicals in the environment using metabolically competent hepatic cell cultures.

Authors:  Jill A Franzosa; Jessica A Bonzo; John Jack; Nancy C Baker; Parth Kothiya; Rafal P Witek; Patrick Hurban; Stephen Siferd; Susan Hester; Imran Shah; Stephen S Ferguson; Keith A Houck; John F Wambaugh
Journal:  NPJ Syst Biol Appl       Date:  2021-01-27

4.  Consensus versus Individual QSARs in Classification: Comparison on a Large-Scale Case Study.

Authors:  Cecile Valsecchi; Francesca Grisoni; Viviana Consonni; Davide Ballabio
Journal:  J Chem Inf Model       Date:  2020-03-02       Impact factor: 4.956

Review 5.  Review of in silico studies dedicated to the nuclear receptor family: Therapeutic prospects and toxicological concerns.

Authors:  Asma Sellami; Manon Réau; Matthieu Montes; Nathalie Lagarde
Journal:  Front Endocrinol (Lausanne)       Date:  2022-09-13       Impact factor: 6.055

6.  Novel machine learning models to predict endocrine disruption activity for high-throughput chemical screening.

Authors:  Sean P Collins; Tara S Barton-Maclaren
Journal:  Front Toxicol       Date:  2022-09-20

7.  Combined Naïve Bayesian, Chemical Fingerprints and Molecular Docking Classifiers to Model and Predict Androgen Receptor Binding Data for Environmentally- and Health-Sensitive Substances.

Authors:  Alfonso T García-Sosa; Uko Maran
Journal:  Int J Mol Sci       Date:  2021-06-22       Impact factor: 5.923

  7 in total

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