. 2019 Oct:107:104403.

doi: 10.1016/j.yrtph.2019.104403. Epub 2019 Jun 11.

Genetic toxicology in silico protocol

Catrin Hasselgren¹, Ernst Ahlberg², Yumi Akahori³, Alexander Amberg⁴, Lennart T Anger⁴, Franck Atienzar⁵, Scott Auerbach⁶, Lisa Beilke⁷, Phillip Bellion⁸, Romualdo Benigni⁹, Joel Bercu¹⁰, Ewan D Booth¹¹, Dave Bower¹², Alessandro Brigo¹³, Zoryana Cammerer¹⁴, Mark T D Cronin¹⁵, Ian Crooks¹⁶, Kevin P Cross¹², Laura Custer¹⁷, Krista Dobo¹⁸, Tatyana Doktorova¹⁹, David Faulkner²⁰, Kevin A Ford²¹, Marie C Fortin²², Markus Frericks²³, Samantha E Gad-McDonald²⁴, Nichola Gellatly²⁵, Helga Gerets²⁶, Véronique Gervais²⁷, Susanne Glowienke²⁸, Jacky Van Gompel²⁹, James S Harvey³⁰, Jedd Hillegass¹⁷, Masamitsu Honma³¹, Jui-Hua Hsieh³², Chia-Wen Hsu³³, Tara S Barton-Maclaren³⁴, Candice Johnson¹², Robert Jolly³⁵, David Jones³⁶, Ray Kemper³⁷, Michelle O Kenyon¹⁸, Naomi L Kruhlak³³, Sunil A Kulkarni³⁴, Klaus Kümmerer³⁸, Penny Leavitt¹⁷, Scott Masten⁶, Scott Miller¹², Chandrika Moudgal³⁹, Wolfgang Muster¹³, Alexandre Paulino⁴⁰, Elena Lo Piparo⁴¹, Mark Powley⁴², Donald P Quigley¹², M Vijayaray Reddy⁴², Andrea-Nicole Richarz⁴³, Benoit Schilter⁴¹, Ronald D Snyder⁴⁴, Lidiya Stavitskaya³³, Reinhard Stidl⁴⁵, David T Szabo⁴⁶, Andrew Teasdale⁴⁷, Raymond R Tice⁴⁸, Alejandra Trejo-Martin¹⁰, Anna Vuorinen⁸, Brian A Wall⁴⁹, Pete Watts⁵⁰, Angela T White³⁰, Joerg Wichard⁵¹, Kristine L Witt⁶, Adam Woolley⁵², David Woolley⁵², Craig Zwickl⁵³, Glenn J Myatt¹²

Affiliations

¹ Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA. Electronic address: hasselgren.catrin@gene.com.
² Predictive Compound ADME & Safety, Drug Safety & Metabolism, AstraZeneca IMED Biotech Unit, Mölndal, Sweden.
³ Chemicals Evaluation and Research Institute, 1-4-25 Kouraku, Bunkyo-ku, Tokyo, 112-0004, Japan.
⁴ Sanofi, R&D Preclinical Safety Frankfurt, Industriepark Hoechst, D-65926, Frankfurt am Main, Germany.
⁵ UCB BioPharma SPRL, Chemin du Foriest, B-1420 Braine-l'Alleud, Belgium.
⁶ The National Institute of Environmental Health Sciences, Division of the National Toxicology Program, Research Triangle Park, NC, 27709, USA.
⁷ Toxicology Solutions Inc., San Diego, CA, USA.
⁸ DSM Nutritional Products, Kaiseraugst, Switzerland.
⁹ Alpha-PreTox, via G.Pascoli 1, 00184, Roma, Italy.
¹⁰ Gilead Sciences, 333 Lakeside Drive, Foster City, CA, USA.
¹¹ Syngenta, Product Safety Department, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK.
¹² Leadscope, Inc, 1393 Dublin Rd, Columbus, OH, 43215, USA.
¹³ Roche Pharmaceutical Research & Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland.
¹⁴ Janssen Research & Development, 1400 McKean Road, Spring House, PA, 19477, USA.
¹⁵ School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK.
¹⁶ British American Tobacco, Research and Development, Regents Park Road, Southampton, Hampshire, SO15 8TL, UK.
¹⁷ Bristol-Myers Squibb, Drug Safety Evaluation, 1 Squibb Dr, New Brunswick, NJ, 08903, USA.
¹⁸ Pfizer Global Research & Development, 558 Eastern Point Road, Groton, CT, 06340, USA.
¹⁹ Douglas Connect GmbH, Technology Park Basel, Hochbergerstrasse 60C, CH-4057, Basel / Basel-Stadt, Switzerland.
²⁰ Lawrence Berkeley National Laboratory, One Cyclotron Road, MS 70A-1161A, Berkeley, CA, 947020, USA.
²¹ Global Blood Therapeutics, 171 Oyster Point Boulevard, South San Francisco, CA, 94080, USA.
²² Jazz Pharmaceuticals, Inc., 200 Princeton South Corporate Center, Suite 180, Ewing, NJ, 08628, USA; Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, 170 Frelinghuysen Rd, Piscataway, NJ, 08855, USA.
²³ BASF SE, 67056, Ludwigshafen, Germany.
²⁴ Gad Consulting Services, 4008 Barrett Drive, Suite 201, Raleigh, NC, 27609, USA.
²⁵ National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs), Gibbs Building, 215 Euston Road, London, NW1 2BE, UK.
²⁶ UCB BioPharma SPRL, Chemin du Foriest, B-1420, Braine-l'Alleud, Belgium.
²⁷ Servier Group, 905 route de Saran, 45520, Gidy, France.
²⁸ Novartis Pharma AG, Pre-Clinical Safety, Werk Klybeck, CH, 4057, Basel, Switzerland.
²⁹ Janssen Pharmaceutical Companies of Johnson & Johnson, 2340, Beerse, Belgium.
³⁰ GlaxoSmithKline Pre-Clinical Development, Park Road, Ware, Hertfordshire, SG12 0DP, UK.
³¹ Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kanagawa, 210-9501, Japan.
³² Kelly Government Solutions, Research Triangle Park, NC, 27709, USA.
³³ FDA Center for Drug Evaluation and Research, Silver Spring, MD, USA.
³⁴ Existing Substances Risk Assessment Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada.
³⁵ Toxicology Division, Eli Lilly and Company, Indianapolis, IN, USA.
³⁶ Medicines and Healthcare Products Regulatory Agency, 10 South Colonnade, Canary Wharf, London, E14 4PU, UK.
³⁷ Vertex Pharmaceuticals Inc., Predictive and Investigative Safety Assessment, 50 Northern Ave, Boston, MA, USA.
³⁸ Institute for Sustainable and Environmental Chemistry, Leuphana University Lüneburg, Scharnhorststraße 1/C13.311b, 21335, Lüneburg, Germany.
³⁹ Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
⁴⁰ Oro Agri Setúbal, Portugal.
⁴¹ Nestlé Research Vers-chez-les-Blanc, Lausanne, Switzerland.
⁴² Merck Research Laboratories, West Point, PA, 19486, USA.
⁴³ European Commission, Joint Research Centre (JRC), Ispra, Italy.
⁴⁴ RDS Consulting Services, 2936 Wooded Vista Ct, Mason, OH, 45040, USA.
⁴⁵ Safetree Consulting e.U, Vienna, Austria.
⁴⁶ PPG Industries, Pittsburgh, PA, 15146, USA.
⁴⁷ AstraZeneca, Macclesfield, Cheshire, UK.
⁴⁸ RTice Consulting, Hillsborough, NC, USA.
⁴⁹ Colgate-Palmolive Company, Piscataway, NJ, 08854, USA.
⁵⁰ Bibra, Cantium House, Railway Approach, Wallington, Surrey, SM6 0DZ, UK.
⁵¹ Bayer AG, Pharmaceuticals Division, Investigational Toxicology, Muellerstr. 178, D-13353, Berlin, Germany.
⁵² ForthTox Limited, PO Box 13550, Linlithgow, EH49 7YU, UK.
⁵³ Transendix LLC, 1407 Moores Manor, Indianapolis, IN, 46229, USA.

PMID: 31195068
PMCID: PMC7485926
DOI: 10.1016/j.yrtph.2019.104403

Genetic toxicology in silico protocol

Catrin Hasselgren et al. Regul Toxicol Pharmacol. 2019 Oct.

. 2019 Oct:107:104403.

doi: 10.1016/j.yrtph.2019.104403. Epub 2019 Jun 11.

Authors

Affiliations

¹ Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA. Electronic address: hasselgren.catrin@gene.com.
² Predictive Compound ADME & Safety, Drug Safety & Metabolism, AstraZeneca IMED Biotech Unit, Mölndal, Sweden.
³ Chemicals Evaluation and Research Institute, 1-4-25 Kouraku, Bunkyo-ku, Tokyo, 112-0004, Japan.
⁴ Sanofi, R&D Preclinical Safety Frankfurt, Industriepark Hoechst, D-65926, Frankfurt am Main, Germany.
⁵ UCB BioPharma SPRL, Chemin du Foriest, B-1420 Braine-l'Alleud, Belgium.
⁶ The National Institute of Environmental Health Sciences, Division of the National Toxicology Program, Research Triangle Park, NC, 27709, USA.
⁷ Toxicology Solutions Inc., San Diego, CA, USA.
⁸ DSM Nutritional Products, Kaiseraugst, Switzerland.
⁹ Alpha-PreTox, via G.Pascoli 1, 00184, Roma, Italy.
¹⁰ Gilead Sciences, 333 Lakeside Drive, Foster City, CA, USA.
¹¹ Syngenta, Product Safety Department, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK.
¹² Leadscope, Inc, 1393 Dublin Rd, Columbus, OH, 43215, USA.
¹³ Roche Pharmaceutical Research & Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland.
¹⁴ Janssen Research & Development, 1400 McKean Road, Spring House, PA, 19477, USA.
¹⁵ School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK.
¹⁶ British American Tobacco, Research and Development, Regents Park Road, Southampton, Hampshire, SO15 8TL, UK.
¹⁷ Bristol-Myers Squibb, Drug Safety Evaluation, 1 Squibb Dr, New Brunswick, NJ, 08903, USA.
¹⁸ Pfizer Global Research & Development, 558 Eastern Point Road, Groton, CT, 06340, USA.
¹⁹ Douglas Connect GmbH, Technology Park Basel, Hochbergerstrasse 60C, CH-4057, Basel / Basel-Stadt, Switzerland.
²⁰ Lawrence Berkeley National Laboratory, One Cyclotron Road, MS 70A-1161A, Berkeley, CA, 947020, USA.
²¹ Global Blood Therapeutics, 171 Oyster Point Boulevard, South San Francisco, CA, 94080, USA.
²² Jazz Pharmaceuticals, Inc., 200 Princeton South Corporate Center, Suite 180, Ewing, NJ, 08628, USA; Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, 170 Frelinghuysen Rd, Piscataway, NJ, 08855, USA.
²³ BASF SE, 67056, Ludwigshafen, Germany.
²⁴ Gad Consulting Services, 4008 Barrett Drive, Suite 201, Raleigh, NC, 27609, USA.
²⁵ National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs), Gibbs Building, 215 Euston Road, London, NW1 2BE, UK.
²⁶ UCB BioPharma SPRL, Chemin du Foriest, B-1420, Braine-l'Alleud, Belgium.
²⁷ Servier Group, 905 route de Saran, 45520, Gidy, France.
²⁸ Novartis Pharma AG, Pre-Clinical Safety, Werk Klybeck, CH, 4057, Basel, Switzerland.
²⁹ Janssen Pharmaceutical Companies of Johnson & Johnson, 2340, Beerse, Belgium.
³⁰ GlaxoSmithKline Pre-Clinical Development, Park Road, Ware, Hertfordshire, SG12 0DP, UK.
³¹ Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kanagawa, 210-9501, Japan.
³² Kelly Government Solutions, Research Triangle Park, NC, 27709, USA.
³³ FDA Center for Drug Evaluation and Research, Silver Spring, MD, USA.
³⁴ Existing Substances Risk Assessment Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada.
³⁵ Toxicology Division, Eli Lilly and Company, Indianapolis, IN, USA.
³⁶ Medicines and Healthcare Products Regulatory Agency, 10 South Colonnade, Canary Wharf, London, E14 4PU, UK.
³⁷ Vertex Pharmaceuticals Inc., Predictive and Investigative Safety Assessment, 50 Northern Ave, Boston, MA, USA.
³⁸ Institute for Sustainable and Environmental Chemistry, Leuphana University Lüneburg, Scharnhorststraße 1/C13.311b, 21335, Lüneburg, Germany.
³⁹ Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
⁴⁰ Oro Agri Setúbal, Portugal.
⁴¹ Nestlé Research Vers-chez-les-Blanc, Lausanne, Switzerland.
⁴² Merck Research Laboratories, West Point, PA, 19486, USA.
⁴³ European Commission, Joint Research Centre (JRC), Ispra, Italy.
⁴⁴ RDS Consulting Services, 2936 Wooded Vista Ct, Mason, OH, 45040, USA.
⁴⁵ Safetree Consulting e.U, Vienna, Austria.
⁴⁶ PPG Industries, Pittsburgh, PA, 15146, USA.
⁴⁷ AstraZeneca, Macclesfield, Cheshire, UK.
⁴⁸ RTice Consulting, Hillsborough, NC, USA.
⁴⁹ Colgate-Palmolive Company, Piscataway, NJ, 08854, USA.
⁵⁰ Bibra, Cantium House, Railway Approach, Wallington, Surrey, SM6 0DZ, UK.
⁵¹ Bayer AG, Pharmaceuticals Division, Investigational Toxicology, Muellerstr. 178, D-13353, Berlin, Germany.
⁵² ForthTox Limited, PO Box 13550, Linlithgow, EH49 7YU, UK.
⁵³ Transendix LLC, 1407 Moores Manor, Indianapolis, IN, 46229, USA.

PMID: 31195068
PMCID: PMC7485926
DOI: 10.1016/j.yrtph.2019.104403

Abstract

In silico toxicology (IST) approaches to rapidly assess chemical hazard, and usage of such methods is increasing in all applications but especially for regulatory submissions, such as for assessing chemicals under REACH as well as the ICH M7 guideline for drug impurities. There are a number of obstacles to performing an IST assessment, including uncertainty in how such an assessment and associated expert review should be performed or what is fit for purpose, as well as a lack of confidence that the results will be accepted by colleagues, collaborators and regulatory authorities. To address this, a project to develop a series of IST protocols for different hazard endpoints has been initiated and this paper describes the genetic toxicity in silico (GIST) protocol. The protocol outlines a hazard assessment framework including key effects/mechanisms and their relationships to endpoints such as gene mutation and clastogenicity. IST models and data are reviewed that support the assessment of these effects/mechanisms along with defined approaches for combining the information and evaluating the confidence in the assessment. This protocol has been developed through a consortium of toxicologists, computational scientists, and regulatory scientists across several industries to support the implementation and acceptance of in silico approaches.

Keywords: (Q)SAR; Computational toxicology protocols; Expert alerts; Expert review; Genetic toxicology; In silico; In silico toxicology.

PubMed Disclaimer

Conflict of interest statement

Declaration of interests

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

**Figure 1**
Basic decision scheme for genetic toxicity.

**Figure 2**
Common genetic toxicology mechanism/effects and corresponding studies

**Figure 3**
Effect assessment of the reverse bacterial mutation assay.

**Figure 4**
Combining information to assess the “gene mutation” endpoint. *The assignment of the “Confidence” is discussed in the following sections.

**Figure 5**
Current *in silico* components most relevant to genotoxicity.

**Figure 6**
Assessment of an acid chloride compound

**Figure 7**
The conflicting *in silico* and experimental results of API X feeding into the overall bacterial gene mutation assessment.

**Figure 8**
Bacterial gene mutation assessment of 3-Methyl-5-isothiazolamine

**Figure 9**
Gene mutation assessment of an aromatic amide compound

**Figure 10**
The initial *in silico* genetic toxicology assessment for the plant protection product active ingredient metabolite. Note the change in assessment outcome for *in vitro* CA before and after expert review. *NA refers to “Not available” since these results were not possible to generate.

**Figure 11**
Influence of including the experimental results in genetic toxicology assessment for the plant protection AI metabolite. Differences compared to Figure 10 are indicated in red text. *NA refers to “Not available” since these results were not possible to generate.

**Figure 12**
*In silico* assessment of a plant protection product metabolite.

See this image and copyright information in PMC

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Genetic toxicology in silico protocol

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Genetic toxicology in silico protocol

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