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Morger A, Mathea M, Achenbach JH, Wolf A, Buesen R, Schleifer KJ, Landsiedel R, Volkamer A. KnowTox: pipeline and case study for confident prediction of potential toxic effects of compounds in early phases of development. J Cheminform 2020; 12:24. [PMID: 33431007 PMCID: PMC7157991 DOI: 10.1186/s13321-020-00422-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/09/2020] [Indexed: 02/07/2023] Open
Abstract
Risk assessment of newly synthesised chemicals is a prerequisite for regulatory approval. In this context, in silico methods have great potential to reduce time, cost, and ultimately animal testing as they make use of the ever-growing amount of available toxicity data. Here, KnowTox is presented, a novel pipeline that combines three different in silico toxicology approaches to allow for confident prediction of potentially toxic effects of query compounds, i.e. machine learning models for 88 endpoints, alerts for 919 toxic substructures, and computational support for read-across. It is mainly based on the ToxCast dataset, containing after preprocessing a sparse matrix of 7912 compounds tested against 985 endpoints. When applying machine learning models, applicability and reliability of predictions for new chemicals are of utmost importance. Therefore, first, the conformal prediction technique was deployed, comprising an additional calibration step and per definition creating internally valid predictors at a given significance level. Second, to further improve validity and information efficiency, two adaptations are suggested, exemplified at the androgen receptor antagonism endpoint. An absolute increase in validity of 23% on the in-house dataset of 534 compounds could be achieved by introducing KNNRegressor normalisation. This increase in validity comes at the cost of efficiency, which could again be improved by 20% for the initial ToxCast model by balancing the dataset during model training. Finally, the value of the developed pipeline for risk assessment is discussed using two in-house triazole molecules. Compared to a single toxicity prediction method, complementing the outputs of different approaches can have a higher impact on guiding toxicity testing and de-selecting most likely harmful development-candidate compounds early in the development process.
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Affiliation(s)
- Andrea Morger
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité Universitätsmedizin Berlin, Charitéplatz 1, Berlin, Germany
| | | | | | | | | | | | | | - Andrea Volkamer
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité Universitätsmedizin Berlin, Charitéplatz 1, Berlin, Germany.
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Burgdorf T, Piersma AH, Landsiedel R, Clewell R, Kleinstreuer N, Oelgeschläger M, Desprez B, Kienhuis A, Bos P, de Vries R, de Wit L, Seidle T, Scheel J, Schönfelder G, van Benthem J, Vinggaard AM, Eskes C, Ezendam J. Workshop on the validation and regulatory acceptance of innovative 3R approaches in regulatory toxicology - Evolution versus revolution. Toxicol In Vitro 2019; 59:1-11. [PMID: 30946968 DOI: 10.1016/j.tiv.2019.03.039] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/28/2019] [Accepted: 03/28/2019] [Indexed: 12/21/2022]
Abstract
At a joint workshop organized by RIVM and BfR, international experts from governmental institutes, regulatory agencies, industry, academia and animal welfare organizations discussed and provided recommendations for the development, validation and implementation of innovative 3R approaches in regulatory toxicology. In particular, an evolutionary improvement of our current approach of test method validation in the context of defined approaches or integrated testing strategies was discussed together with a revolutionary approach based on a comprehensive description of the physiological responses of the human body to chemical exposure and the subsequent definition of relevant and predictive in vitro, in chemico or in silico methods. A more comprehensive evaluation of biological relevance, scientific validity and regulatory purpose of new test methods and assessment strategies together with case studies that provide practical experience with new approaches were discussed as essential steps to build up the necessary confidence to facilitate regulatory acceptance.
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Affiliation(s)
- T Burgdorf
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Berlin, Germany
| | - A H Piersma
- National Institute for Public Health and the Environment (RIVM), Center for Health Protection, Bilthoven, Netherlands; Institute for Risk Assessment Sciences, Utrecht University, Netherlands
| | | | - R Clewell
- 21(st) Century Tox Consulting, Chapel Hill, NC 27515, USA
| | | | - M Oelgeschläger
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Berlin, Germany.
| | | | - A Kienhuis
- National Institute for Public Health and the Environment (RIVM), Center for Health Protection, Bilthoven, Netherlands
| | - P Bos
- National Institute for Public Health and the Environment (RIVM), Centre for Nutrition, Prevention and Health Services, Bilthoven, Netherlands
| | - R de Vries
- Evidence-based Toxicology Collaboration, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA & SYRCLE, Department for Health Evidence, Radboud Institute for Health Sciences, Radboudumc, Nijmegen, the Netherlands
| | - L de Wit
- National Institute for Public Health and the Environment (RIVM), Centre for Nutrition, Prevention and Health Services, Bilthoven, Netherlands
| | - T Seidle
- Humane Society International, Toronto, Canada
| | - J Scheel
- Evonik Performance Materials GmbH, Darmstadt, Germany
| | - G Schönfelder
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Berlin, Germany; Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
| | - J van Benthem
- National Institute for Public Health and the Environment (RIVM), Center for Health Protection, Bilthoven, Netherlands
| | - A M Vinggaard
- National Food Institute, Technical University of Denmark, Kemitorvet building 202, DK-2800 Kgs.Lyngby, Denmark
| | - C Eskes
- Swiss 3R Competence Centre (3RCC), Switzerland
| | - J Ezendam
- National Institute for Public Health and the Environment (RIVM), Center for Health Protection, Bilthoven, Netherlands
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Piersma A, Burgdorf T, Louekari K, Desprez B, Taalman R, Landsiedel R, Barroso J, Rogiers V, Eskes C, Oelgeschläger M, Whelan M, Braeuning A, Vinggaard A, Kienhuis A, van Benthem J, Ezendam J. Workshop on acceleration of the validation and regulatory acceptance of alternative methods and implementation of testing strategies. Toxicol In Vitro 2018; 50:62-74. [DOI: 10.1016/j.tiv.2018.02.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/28/2018] [Accepted: 02/28/2018] [Indexed: 01/01/2023]
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