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Tice RR, Bassan A, Amberg A, Anger LT, Beal MA, Bellion P, Benigni R, Birmingham J, Brigo A, Bringezu F, Ceriani L, Crooks I, Cross K, Elespuru R, Faulkner DM, Fortin MC, Fowler P, Frericks M, Gerets HHJ, Jahnke GD, Jones DR, Kruhlak NL, Lo Piparo E, Lopez-Belmonte J, Luniwal A, Luu A, Madia F, Manganelli S, Manickam B, Mestres J, Mihalchik-Burhans AL, Neilson L, Pandiri A, Pavan M, Rider CV, Rooney JP, Trejo-Martin A, Watanabe-Sailor KH, White AT, Woolley D, Myatt GJ. In Silico Approaches In Carcinogenicity Hazard Assessment: Current Status and Future Needs. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 20. [PMID: 35368437 DOI: 10.1016/j.comtox.2021.100191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Historically, identifying carcinogens has relied primarily on tumor studies in rodents, which require enormous resources in both money and time. In silico models have been developed for predicting rodent carcinogens but have not yet found general regulatory acceptance, in part due to the lack of a generally accepted protocol for performing such an assessment as well as limitations in predictive performance and scope. There remains a need for additional, improved in silico carcinogenicity models, especially ones that are more human-relevant, for use in research and regulatory decision-making. As part of an international effort to develop in silico toxicological protocols, a consortium of toxicologists, computational scientists, and regulatory scientists across several industries and governmental agencies evaluated the extent to which in silico models exist for each of the recently defined 10 key characteristics (KCs) of carcinogens. This position paper summarizes the current status of in silico tools for the assessment of each KC and identifies the data gaps that need to be addressed before a comprehensive in silico carcinogenicity protocol can be developed for regulatory use.
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Affiliation(s)
- Raymond R Tice
- RTice Consulting, Hillsborough, North Carolina, 27278, USA
| | | | - Alexander Amberg
- Sanofi Preclinical Safety, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Lennart T Anger
- Genentech, Inc., South San Francisco, California, 94080, USA
| | - Marc A Beal
- Healthy Environments and Consumer Safety Branch, Health Canada, Government of Canada, Ottawa, Ontario, Canada K1A 0K9
| | | | | | - Jeffrey Birmingham
- GlaxoSmithKline, David Jack Centre for R&D, Ware, Hertfordshire, SG12 0DP, United Kingdom
| | - Alessandro Brigo
- Roche Pharmaceutical Research & Early Development, Pharmaceutical Sciences, Roche Innovation, Center Basel, F. Hoffmann-La Roche Ltd, CH-4070, Basel, Switzerland
| | | | - Lidia Ceriani
- Humane Society International, 1000 Brussels, Belgium
| | - Ian Crooks
- British American Tobacco (Investments) Ltd, GR&D Centre, Southampton, SO15 8TL, United Kingdom
| | | | - Rosalie Elespuru
- Food and Drug Administration, Center for Devices and Radiological Health, Silver Spring, Maryland, 20993, USA
| | - David M Faulkner
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Marie C Fortin
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, New Jersey, 08855, USA
| | - Paul Fowler
- FSTox Consulting (Genetic Toxicology), Northamptonshire, United Kingdom
| | | | | | - Gloria D Jahnke
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA
| | | | - Naomi L Kruhlak
- Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, Maryland, 20993, USA
| | - Elena Lo Piparo
- Chemical Food Safety Group, Nestlé Research, CH-1000 Lausanne 26, Switzerland
| | - Juan Lopez-Belmonte
- Cuts Ice Ltd Chemical Food Safety Group, Nestlé Research, CH-1000 Lausanne 26, Switzerland
| | - Amarjit Luniwal
- North American Science Associates (NAMSA) Inc., Minneapolis, Minnesota, 55426, USA
| | - Alice Luu
- Healthy Environments and Consumer Safety Branch, Health Canada, Government of Canada, Ottawa, Ontario, Canada K1A 0K9
| | - Federica Madia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Serena Manganelli
- Chemical Food Safety Group, Nestlé Research, CH-1000 Lausanne 26, Switzerland
| | | | - Jordi Mestres
- IMIM Institut Hospital Del Mar d'Investigacions Mèdiques and Universitat Pompeu Fabra, Doctor Aiguader 88, Parc de Recerca Biomèdica, 08003 Barcelona, Spain; and Chemotargets SL, Baldiri Reixac 4, Parc Científic de Barcelona, 08028, Barcelona, Spain
| | | | - Louise Neilson
- Broughton Nicotine Services, Oak Tree House, Earby, Lancashire, BB18 6JZ United Kingdom
| | - Arun Pandiri
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA
| | | | - Cynthia V Rider
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA
| | - John P Rooney
- Integrated Laboratory Systems, LLC., Morrisville, North Carolina, 27560, USA
| | | | - Karen H Watanabe-Sailor
- School of Mathematical and Natural Sciences, Arizona State University, West Campus, Glendale, Arizona, 85306, USA
| | - Angela T White
- GlaxoSmithKline, David Jack Centre for R&D, Ware, Hertfordshire, SG12 0DP, United Kingdom
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Emara Y, Fantke P, Judson R, Chang X, Pradeep P, Lehmann A, Siegert MW, Finkbeiner M. Integrating endocrine-related health effects into comparative human toxicity characterization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 762:143874. [PMID: 33401053 DOI: 10.1016/j.scitotenv.2020.143874] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 06/12/2023]
Abstract
Endocrine-disrupting chemicals have the ability to interfere with and alter functions of the hormone system, leading to adverse effects on reproduction, growth and development. Despite growing concerns over their now ubiquitous presence in the environment, endocrine-related human health effects remain largely outside of comparative human toxicity characterization frameworks as applied for example in life cycle impact assessments. In this paper, we propose a new methodological framework to consistently integrate endocrine-related health effects into comparative human toxicity characterization. We present two quantitative and operational approaches for extrapolating towards a common point of departure from both in vivo and dosimetry-adjusted in vitro endocrine-related effect data and deriving effect factors as well as corresponding characterization factors for endocrine-active/endocrine-disrupting chemicals. Following the proposed approaches, we calculated effect factors for 323 chemicals, reflecting their endocrine potency, and related characterization factors for 157 chemicals, expressing their relative endocrine-related human toxicity potential. Developed effect and characterization factors are ready for use in the context of chemical prioritization and substitution as well as life cycle impact assessment and other comparative assessment frameworks. Endocrine-related effect factors were found comparable to existing effect factors for cancer and non-cancer effects, indicating that (1) the chemicals' endocrine potency is not necessarily higher or lower than other effect potencies and (2) using dosimetry-adjusted effect data to derive effect factors does not consistently overestimate the effect of potential endocrine disruptors. Calculated characterization factors span over 8-11 orders of magnitude for different substances and emission compartments and are dominated by the range in endocrine potencies.
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Affiliation(s)
- Yasmine Emara
- Department of Environmental Technology, Technical University Berlin, 10623 Berlin, Germany.
| | - Peter Fantke
- Quantitative Sustainability Assessment, Department of Technology, Management and Economics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | - Richard Judson
- Office of Research and Development, Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711.
| | - Xiaoqing Chang
- Integrated Laboratory Systems, LLC., Morrisville, NC 27560, United States.
| | - Prachi Pradeep
- Biomolecular and Computational Toxicology Division, Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711.
| | - Annekatrin Lehmann
- Department of Environmental Technology, Technical University Berlin, 10623 Berlin, Germany.
| | - Marc-William Siegert
- Department of Environmental Technology, Technical University Berlin, 10623 Berlin, Germany.
| | - Matthias Finkbeiner
- Department of Environmental Technology, Technical University Berlin, 10623 Berlin, Germany.
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Cotterill JV, Palazzolo L, Ridgway C, Price N, Rorije E, Moretto A, Peijnenburg A, Eberini I. Predicting estrogen receptor binding of chemicals using a suite of in silico methods - Complementary approaches of (Q)SAR, molecular docking and molecular dynamics. Toxicol Appl Pharmacol 2019; 378:114630. [PMID: 31220507 DOI: 10.1016/j.taap.2019.114630] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/17/2019] [Accepted: 06/17/2019] [Indexed: 11/18/2022]
Abstract
With the aim of obtaining reliable estimates of Estrogen Receptor (ER) binding for diverse classes of compounds, a weight of evidence approach using estimates from a suite of in silico models was assessed. The predictivity of a simple Majority Consensus of (Q)SAR models was assessed using a test set of compounds with experimental Relative Binding Affinity (RBA) data. Molecular docking was also carried out and the binding energies of these compounds to the ERα receptor were determined. For a few selected compounds, including a known full agonist and antagonist, the intrinsic activity was determined using low-mode molecular dynamics methods. Individual (Q)SAR model predictivity varied, as expected, with some models showing high sensitivity, others higher specificity. However, the Majority Consensus (Q)SAR prediction showed a high accuracy and reasonably balanced sensitivity and specificity. Molecular docking provided quantitative information on strength of binding to the ERα receptor. For the 50 highest binding affinity compounds with positive RBA experimental values, just 5 of them were predicted to be non-binders by the Majority QSAR Consensus. Furthermore, agonist-specific assay experimental values for these 5 compounds were negative, which indicates that they may be ER antagonists. We also showed different scenarios of combining (Q)SAR results with Molecular docking classification of ER binding based on cut-off values of binding energies, providing a rational combined strategy to maximize terms of toxicological interest.
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Affiliation(s)
- J V Cotterill
- Fera Science Limited, Sand Hutton, York YO41 1LZ, UK
| | - L Palazzolo
- Università degli Studi di Milano, Dipartimento di Scienze Farmacologiche e Biomolecolari, Via Balzaretti 9, 20133 Milano, Italy
| | - C Ridgway
- Fera Science Limited, Sand Hutton, York YO41 1LZ, UK
| | - N Price
- Fera Science Limited, Sand Hutton, York YO41 1LZ, UK
| | - E Rorije
- Centre for Safety of Substances and Products, National Institute for Public Health and Environment (RIVM), P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
| | - A Moretto
- Università degli Studi di Milano, Dipartimento di Scienze Biomediche e Cliniche, Ospedale L. Sacco, Padiglione 17, Via G.B. Grassi 74, 20157 Milano, Italy
| | - A Peijnenburg
- Wageningen University & Research, Wageningen, The Netherlands
| | - I Eberini
- Università degli Studi di Milano, Dipartimento di Scienze Farmacologiche e Biomolecolari & DSRC, Via Balzaretti 9, 20133 Milano, Italy.
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Gonzalez TL, Rae JM, Colacino JA, Richardson RJ. Homology models of mouse and rat estrogen receptor- α ligand-binding domain created by in silico mutagenesis of a human template: molecular docking with 17ß-estradiol, diethylstilbestrol, and paraben analogs. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 10:1-16. [PMID: 30740556 PMCID: PMC6363358 DOI: 10.1016/j.comtox.2018.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Crystal structures exist for human, but not rodent, estrogen receptor-α ligand-binding domain (ERα-LBD). Consequently, rodent studies involving binding of compounds to ERα-LBD are limited in their molecular-level interpretation and extrapolation to humans. Because the sequences of rodent and human ERα-LBDs are > 95% identical, we expected their 3D structures and ligand binding to be highly similar. To test this hypothesis, we used the human ERα-LBD structure (PDB 3UUD) as a template to produce rat and mouse homology models. Employing the rodent models and human structure, we generated docking poses of 23 Group A ligands (17ß-estradiol, diethylstilbestrol, and 21 paraben analogs) in AutoDock Vina for interspecies comparisons. Ligand RMSDs (Å) (median, 95% CI) were 0.49 (0.21-1.82) (human-mouse) and 1.19 (0.22-1.82) (human-rat), well below the 2.0-2.5 Å range for equivalent docking poses. Numbers of interspecies ligand-receptor residue contacts were highly similar, with Sorensen Sc (%) = 96.8 (90.0-100) (human-mouse) and 97.7 (89.5-100) (human-rat). Likewise, numbers of interspecies ligand-receptor residue contacts were highly correlated: Pearson r = 0.913 (human-mouse) and 0.925 (human-rat). Numbers of interspecies ligand-receptor atom contacts were even more tightly correlated: r = 0.979 (human-mouse) and 0.986 (human-rat). Pyramid plots of numbers of ligand-receptor atom contacts by residue exhibited high interspecies symmetry and had Spearman r s = 0.977 (human-mouse) and 0.966 (human-rat). Group B ligands included 15 ring-substituted parabens recently shown experimentally to exhibit decreased binding to human ERα and to exert increased antimicrobial activity. Ligand efficiencies calculated from docking ligands into human ERα-LBD were well correlated with those derived from published experimental data (Pearson partial r p = 0.894 and 0.918; Groups A and B, respectively). Overall, the results indicate that our constructed rodent ERα-LBDs interact with ligands in like manner to the human receptor, thus providing a high level of confidence in extrapolations of rodent to human ligand-receptor interactions.
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Affiliation(s)
- Thomas L. Gonzalez
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - James M. Rae
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Rudy J. Richardson
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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