Literature DB >> 29678766

In silico toxicology protocols.

Glenn J Myatt1, Ernst Ahlberg2, Yumi Akahori3, David Allen4, Alexander Amberg5, Lennart T Anger5, Aynur Aptula6, Scott Auerbach7, Lisa Beilke8, Phillip Bellion9, Romualdo Benigni10, Joel Bercu11, Ewan D Booth12, Dave Bower13, Alessandro Brigo14, Natalie Burden15, Zoryana Cammerer16, Mark T D Cronin17, Kevin P Cross13, Laura Custer18, Magdalena Dettwiler19, Krista Dobo20, Kevin A Ford21, Marie C Fortin22, Samantha E Gad-McDonald23, Nichola Gellatly15, Véronique Gervais24, Kyle P Glover25, Susanne Glowienke26, Jacky Van Gompel27, Steve Gutsell6, Barry Hardy28, James S Harvey29, Jedd Hillegass18, Masamitsu Honma30, Jui-Hua Hsieh31, Chia-Wen Hsu32, Kathy Hughes33, Candice Johnson13, Robert Jolly34, David Jones35, Ray Kemper36, Michelle O Kenyon20, Marlene T Kim32, Naomi L Kruhlak32, Sunil A Kulkarni33, Klaus Kümmerer37, Penny Leavitt18, Bernhard Majer38, Scott Masten7, Scott Miller13, Janet Moser39, Moiz Mumtaz40, Wolfgang Muster14, Louise Neilson41, Tudor I Oprea42, Grace Patlewicz43, Alexandre Paulino44, Elena Lo Piparo45, Mark Powley32, Donald P Quigley13, M Vijayaraj Reddy46, Andrea-Nicole Richarz47, Patricia Ruiz40, Benoit Schilter45, Rositsa Serafimova48, Wendy Simpson6, Lidiya Stavitskaya32, Reinhard Stidl38, Diana Suarez-Rodriguez6, David T Szabo49, Andrew Teasdale50, Alejandra Trejo-Martin11, Jean-Pierre Valentin51, Anna Vuorinen9, Brian A Wall52, Pete Watts53, Angela T White29, Joerg Wichard54, Kristine L Witt7, Adam Woolley55, David Woolley55, Craig Zwickl56, Catrin Hasselgren13.   

Abstract

The present publication surveys several applications of in silico (i.e., computational) toxicology approaches across different industries and institutions. It highlights the need to develop standardized protocols when conducting toxicity-related predictions. This contribution articulates the information needed for protocols to support in silico predictions for major toxicological endpoints of concern (e.g., genetic toxicity, carcinogenicity, acute toxicity, reproductive toxicity, developmental toxicity) across several industries and regulatory bodies. Such novel in silico toxicology (IST) protocols, when fully developed and implemented, will ensure in silico toxicological assessments are performed and evaluated in a consistent, reproducible, and well-documented manner across industries and regulatory bodies to support wider uptake and acceptance of the approaches. The development of IST protocols is an initiative developed through a collaboration among an international consortium to reflect the state-of-the-art in in silico toxicology for hazard identification and characterization. A general outline for describing the development of such protocols is included and it is based on in silico predictions and/or available experimental data for a defined series of relevant toxicological effects or mechanisms. The publication presents a novel approach for determining the reliability of in silico predictions alongside experimental data. In addition, we discuss how to determine the level of confidence in the assessment based on the relevance and reliability of the information.
Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Computational toxicology; Expert alert; Expert review; In silico; In silico toxicology; Predictive toxicology; QSAR

Mesh:

Year:  2018        PMID: 29678766      PMCID: PMC6026539          DOI: 10.1016/j.yrtph.2018.04.014

Source DB:  PubMed          Journal:  Regul Toxicol Pharmacol        ISSN: 0273-2300            Impact factor:   3.271


  41 in total

1.  In silico methods combined with expert knowledge rule out mutagenic potential of pharmaceutical impurities: an industry survey.

Authors:  Krista L Dobo; Nigel Greene; Charlotta Fred; Susanne Glowienke; James S Harvey; Catrin Hasselgren; Robert Jolly; Michelle O Kenyon; Jennifer B Munzner; Wolfgang Muster; Robin Neft; M Vijayaraj Reddy; Angela T White; Sandy Weiner
Journal:  Regul Toxicol Pharmacol       Date:  2012-01-31       Impact factor: 3.271

2.  Establishing best practise in the application of expert review of mutagenicity under ICH M7.

Authors:  Chris Barber; Alexander Amberg; Laura Custer; Krista L Dobo; Susanne Glowienke; Jacky Van Gompel; Steve Gutsell; Jim Harvey; Masamitsu Honma; Michelle O Kenyon; Naomi Kruhlak; Wolfgang Muster; Lidiya Stavitskaya; Andrew Teasdale; Jonathan Vessey; Joerg Wichard
Journal:  Regul Toxicol Pharmacol       Date:  2015-08-04       Impact factor: 3.271

3.  Computational Chemistry in the Pharmaceutical Industry: From Childhood to Adolescence.

Authors:  Alexander Hillisch; Nikolaus Heinrich; Hanno Wild
Journal:  ChemMedChem       Date:  2015-09-11       Impact factor: 3.466

4.  Current status of methods for defining the applicability domain of (quantitative) structure-activity relationships. The report and recommendations of ECVAM Workshop 52.

Authors:  Tatiana I Netzeva; Andrew Worth; Tom Aldenberg; Romualdo Benigni; Mark T D Cronin; Paolo Gramatica; Joanna S Jaworska; Scott Kahn; Gilles Klopman; Carol A Marchant; Glenn Myatt; Nina Nikolova-Jeliazkova; Grace Y Patlewicz; Roger Perkins; David Roberts; Terry Schultz; David W Stanton; Johannes J M van de Sandt; Weida Tong; Gilman Veith; Chihae Yang
Journal:  Altern Lab Anim       Date:  2005-04       Impact factor: 1.303

5.  QSAR modeling: where have you been? Where are you going to?

Authors:  Artem Cherkasov; Eugene N Muratov; Denis Fourches; Alexandre Varnek; Igor I Baskin; Mark Cronin; John Dearden; Paola Gramatica; Yvonne C Martin; Roberto Todeschini; Viviana Consonni; Victor E Kuz'min; Richard Cramer; Romualdo Benigni; Chihae Yang; James Rathman; Lothar Terfloth; Johann Gasteiger; Ann Richard; Alexander Tropsha
Journal:  J Med Chem       Date:  2014-01-06       Impact factor: 7.446

6.  Establishing the level of safety concern for chemicals in food without the need for toxicity testing.

Authors:  Benoît Schilter; Romualdo Benigni; Alan Boobis; Alessandro Chiodini; Andrew Cockburn; Mark T D Cronin; Elena Lo Piparo; Sandeep Modi; Anette Thiel; Andrew Worth
Journal:  Regul Toxicol Pharmacol       Date:  2013-09-05       Impact factor: 3.271

7.  A strategy for structuring and reporting a read-across prediction of toxicity.

Authors:  T W Schultz; P Amcoff; E Berggren; F Gautier; M Klaric; D J Knight; C Mahony; M Schwarz; A White; M T D Cronin
Journal:  Regul Toxicol Pharmacol       Date:  2015-05-21       Impact factor: 3.271

8.  A framework to facilitate consistent characterization of read across uncertainty.

Authors:  Karen Blackburn; Sharon B Stuard
Journal:  Regul Toxicol Pharmacol       Date:  2014-01-20       Impact factor: 3.271

Review 9.  Use of mechanistic and pharmacokinetic data for risk assessment at the National Institute of Environmental Health Sciences (NIEHS).

Authors:  B A Schwetz
Journal:  Toxicol Lett       Date:  1995-09       Impact factor: 4.372

Review 10.  In silico toxicology: computational methods for the prediction of chemical toxicity.

Authors:  Arwa B Raies; Vladimir B Bajic
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2016-01-06
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  28 in total

Review 1.  QSAR without borders.

Authors:  Eugene N Muratov; Jürgen Bajorath; Robert P Sheridan; Igor V Tetko; Dmitry Filimonov; Vladimir Poroikov; Tudor I Oprea; Igor I Baskin; Alexandre Varnek; Adrian Roitberg; Olexandr Isayev; Stefano Curtarolo; Denis Fourches; Yoram Cohen; Alan Aspuru-Guzik; David A Winkler; Dimitris Agrafiotis; Artem Cherkasov; Alexander Tropsha
Journal:  Chem Soc Rev       Date:  2020-05-01       Impact factor: 54.564

2.  Skin sensitization in silico protocol.

Authors:  Candice Johnson; Ernst Ahlberg; Lennart T Anger; Lisa Beilke; Romualdo Benigni; Joel Bercu; Sol Bobst; David Bower; Alessandro Brigo; Sarah Campbell; Mark T D Cronin; Ian Crooks; Kevin P Cross; Tatyana Doktorova; Thomas Exner; David Faulkner; Ian M Fearon; Markus Fehr; Shayne C Gad; Véronique Gervais; Amanda Giddings; Susanne Glowienke; Barry Hardy; Catrin Hasselgren; Jedd Hillegass; Robert Jolly; Eckart Krupp; Liat Lomnitski; Jason Magby; Jordi Mestres; Lawrence Milchak; Scott Miller; Wolfgang Muster; Louise Neilson; Rahul Parakhia; Alexis Parenty; Patricia Parris; Alexandre Paulino; Ana Theresa Paulino; David W Roberts; Harald Schlecker; Reinhard Stidl; Diana Suarez-Rodrigez; David T Szabo; Raymond R Tice; Daniel Urbisch; Anna Vuorinen; Brian Wall; Thibaud Weiler; Angela T White; Jessica Whritenour; Joerg Wichard; David Woolley; Craig Zwickl; Glenn J Myatt
Journal:  Regul Toxicol Pharmacol       Date:  2020-07-01       Impact factor: 3.271

3.  Exploring current read-across applications and needs among selected U.S. Federal Agencies.

Authors:  Grace Patlewicz; Lucina E Lizarraga; Diego Rua; David G Allen; Amber B Daniel; Suzanne C Fitzpatrick; Natàlia Garcia-Reyero; John Gordon; Pertti Hakkinen; Angela S Howard; Agnes Karmaus; Joanna Matheson; Moiz Mumtaz; Andrea-Nicole Richarz; Patricia Ruiz; Louis Scarano; Takashi Yamada; Nicole Kleinstreuer
Journal:  Regul Toxicol Pharmacol       Date:  2019-05-10       Impact factor: 3.271

4.  Genetic toxicology in silico protocol.

Authors:  Catrin Hasselgren; Ernst Ahlberg; Yumi Akahori; Alexander Amberg; Lennart T Anger; Franck Atienzar; Scott Auerbach; Lisa Beilke; Phillip Bellion; Romualdo Benigni; Joel Bercu; Ewan D Booth; Dave Bower; Alessandro Brigo; Zoryana Cammerer; Mark T D Cronin; Ian Crooks; Kevin P Cross; Laura Custer; Krista Dobo; Tatyana Doktorova; David Faulkner; Kevin A Ford; Marie C Fortin; Markus Frericks; Samantha E Gad-McDonald; Nichola Gellatly; Helga Gerets; Véronique Gervais; Susanne Glowienke; Jacky Van Gompel; James S Harvey; Jedd Hillegass; Masamitsu Honma; Jui-Hua Hsieh; Chia-Wen Hsu; Tara S Barton-Maclaren; Candice Johnson; Robert Jolly; David Jones; Ray Kemper; Michelle O Kenyon; Naomi L Kruhlak; Sunil A Kulkarni; Klaus Kümmerer; Penny Leavitt; Scott Masten; Scott Miller; Chandrika Moudgal; Wolfgang Muster; Alexandre Paulino; Elena Lo Piparo; Mark Powley; Donald P Quigley; M Vijayaray Reddy; Andrea-Nicole Richarz; Benoit Schilter; Ronald D Snyder; Lidiya Stavitskaya; Reinhard Stidl; David T Szabo; Andrew Teasdale; Raymond R Tice; Alejandra Trejo-Martin; Anna Vuorinen; Brian A Wall; Pete Watts; Angela T White; Joerg Wichard; Kristine L Witt; Adam Woolley; David Woolley; Craig Zwickl; Glenn J Myatt
Journal:  Regul Toxicol Pharmacol       Date:  2019-06-11       Impact factor: 3.271

5.  Implementation of in silico toxicology protocols within a visual and interactive hazard assessment platform.

Authors:  Glenn J Myatt; Arianna Bassan; Dave Bower; Candice Johnson; Scott Miller; Manuela Pavan; Kevin P Cross
Journal:  Comput Toxicol       Date:  2021-10-28

6.  Implementation of In Silico Toxicology Protocols in Leadscope.

Authors:  Kevin Cross; Candice Johnson; Glenn J Myatt
Journal:  Methods Mol Biol       Date:  2022

7.  In silico approaches in organ toxicity hazard assessment: current status and future needs in predicting liver toxicity.

Authors:  Arianna Bassan; Vinicius M Alves; Alexander Amberg; Lennart T Anger; Scott Auerbach; Lisa Beilke; Andreas Bender; Mark T D Cronin; Kevin P Cross; Jui-Hua Hsieh; Nigel Greene; Raymond Kemper; Marlene T Kim; Moiz Mumtaz; Tobias Noeske; Manuela Pavan; Julia Pletz; Daniel P Russo; Yogesh Sabnis; Markus Schaefer; David T Szabo; Jean-Pierre Valentin; Joerg Wichard; Dominic Williams; David Woolley; Craig Zwickl; Glenn J Myatt
Journal:  Comput Toxicol       Date:  2021-09-09

8.  Transitioning to composite bacterial mutagenicity models in ICH M7 (Q)SAR analyses.

Authors:  Curran Landry; Marlene T Kim; Naomi L Kruhlak; Kevin P Cross; Roustem Saiakhov; Suman Chakravarti; Lidiya Stavitskaya
Journal:  Regul Toxicol Pharmacol       Date:  2019-10-03       Impact factor: 3.271

9.  Leveraging complementary computational models for prioritizing chemicals of developmental and reproductive toxicity concern: an example of food contact materials.

Authors:  Chun-Wei Tung; Hsien-Jen Cheng; Chia-Chi Wang; Shan-Shan Wang; Pinpin Lin
Journal:  Arch Toxicol       Date:  2020-01-02       Impact factor: 5.153

10.  A cross-industry collaboration to assess if acute oral toxicity (Q)SAR models are fit-for-purpose for GHS classification and labelling.

Authors:  Joel Bercu; Melisa J Masuda-Herrera; Alejandra Trejo-Martin; Catrin Hasselgren; Jean Lord; Jessica Graham; Matthew Schmitz; Lawrence Milchak; Colin Owens; Surya Hari Lal; Richard Marchese Robinson; Sarah Whalley; Phillip Bellion; Anna Vuorinen; Kamila Gromek; William A Hawkins; Iris van de Gevel; Kathleen Vriens; Raymond Kemper; Russell Naven; Pierre Ferrer; Glenn J Myatt
Journal:  Regul Toxicol Pharmacol       Date:  2020-12-17       Impact factor: 3.271

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