1
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Dorne JLCM, Cortiñas‐Abrahantes J, Spyropoulos F, Darney K, Lautz L, Louisse J, Kass GEN, Carnesecchi E, Liem AKD, Tarazona JV, Billat P, Beaudoin R, Zeman F, Bodin C, Smith A, Nathanail A, Di Nicola MR, Kleiner J, Terron A, Parra‐Morte JM, Verloo D, Robinson T. TKPlate 1.0: An Open-access platform for toxicokinetic and toxicodynamic modelling of chemicals to implement new approach methodologies in chemical risk assessment. EFSA J 2023; 21:e211101. [PMID: 38027439 PMCID: PMC10644227 DOI: 10.2903/j.efsa.2023.e211101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
This publication is linked to the following EFSA Supporting Publications articles: http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2023.EN-8441/full, http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2023.EN-8440/full, http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2023.EN-8437/full.
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Petrović S, Arsić B, Zlatanović I, Milićević J, Glišić S, Mitić M, Đurović-Pejčev R, Stojanović G. In Silico Investigation of Selected Pesticides and Their Determination in Agricultural Products Using QuEChERS Methodology and HPLC-DAD. Int J Mol Sci 2023; 24:ijms24098003. [PMID: 37175728 PMCID: PMC10179243 DOI: 10.3390/ijms24098003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/11/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
In this study, we considered some pesticides as active substances within formulations for the protection of plant-based food in the Republic of Serbia in silico, because these pesticides have not often been investigated in this way previously, and in an analytical way, because there are not very many available fast, cheap, and easy methods for their determination in real agricultural samples. Seven pesticides were detected in selected agricultural products (tomatoes, cucumbers, peppers, and grapes) using the QuEChERS methodology and HPLC-DAD. Standard curves for the investigated pesticides (chlorantraniliprole, methomyl, metalaxyl, thiacloprid, acetamiprid, emamectin benzoate, and cymoxanil) show good linearity, with R2 values from 0.9785 to 0.9996. The HPLC-DAD method is fast, and these pesticides can be determined in real spiked samples in less than 15 min. We further characterized the pesticides we found in food based on physicochemical properties and molecular descriptors to predict the absorption, distribution, metabolism, elimination, and toxicity (ADMET) of the compounds. We summarized the data supporting their effects on humans using various computational tools to determine their potential adverse effects. The results of our prediction study show that all of the selected pesticides considered in this study have good oral bioavailability, and those with high toxicity, therefore, could be harmful to human health. Chlorantraniliprole was shown in a molecular docking study as a good starting point for a new Alzheimer's disease drug candidate.
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Grants
- 451-03-68/2022-14/200124 (S. Petrović, B. Arsić, I. Zlatanović, M. Mitić, G. Stojanović), 451-03-68/2022-14/200017 (J. Milićević, S. Glišić), 451-03-68/2022-14/200214 (R. Đurović-Pejčev) Ministry of Education, Science and Technological Development of the Republic of Serbia
- 451-03-47/2023-01/200124 (S. Petrović, B. Arsić, I. Zlatanović, M. Mitić, G. Stojanović), 451-03-47/2023-01/200017 (J. Milićević, S. Glišić), 451-03-47/2023-01/200214 (R. Đurović-Pejčev) Ministry of Science, Technological Development and Innovations of the Republic of Serbia
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Affiliation(s)
- Stefan Petrović
- Department of Chemistry, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18106 Niš, Serbia
| | - Biljana Arsić
- Department of Chemistry, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18106 Niš, Serbia
| | - Ivana Zlatanović
- Department of Chemistry, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18106 Niš, Serbia
| | - Jelena Milićević
- Laboratory for Bioinformatics and Computational Chemistry, Vinča Institute of Nuclear Sciences, The University of Belgrade, Mike Petrovića Alasa 12-14, Vinča, 11351 Belgrade, Serbia
| | - Sanja Glišić
- Laboratory for Bioinformatics and Computational Chemistry, Vinča Institute of Nuclear Sciences, The University of Belgrade, Mike Petrovića Alasa 12-14, Vinča, 11351 Belgrade, Serbia
| | - Milan Mitić
- Department of Chemistry, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18106 Niš, Serbia
| | - Rada Đurović-Pejčev
- Institute of Pesticides and Environmental Protection, Banatska 31b, 11080 Belgrade, Serbia
| | - Gordana Stojanović
- Department of Chemistry, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18106 Niš, Serbia
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3
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Algharably EA, Di Consiglio E, Testai E, Pistollato F, Mielke H, Gundert-Remy U. In Vitro- In Vivo Extrapolation by Physiologically Based Kinetic Modeling: Experience With Three Case Studies and Lessons Learned. FRONTIERS IN TOXICOLOGY 2022; 4:885843. [PMID: 35924078 PMCID: PMC9340473 DOI: 10.3389/ftox.2022.885843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/09/2022] [Indexed: 11/27/2022] Open
Abstract
Physiologically based kinetic (PBK) modeling has been increasingly used since the beginning of the 21st century to support dose selection to be used in preclinical and clinical safety studies in the pharmaceutical sector. For chemical safety assessment, the use of PBK has also found interest, however, to a smaller extent, although an internationally agreed document was published already in 2010 (IPCS/WHO), but at that time, PBK modeling was based mostly on in vivo data as the example in the IPCS/WHO document indicates. Recently, the OECD has published a guidance document which set standards on how to characterize, validate, and report PBK models for regulatory purposes. In the past few years, we gained experience on using in vitro data for performing quantitative in vitro–in vivo extrapolation (QIVIVE), in which biokinetic data play a crucial role to obtain a realistic estimation of human exposure. In addition, pharmaco-/toxicodynamic aspects have been introduced into the approach. Here, three examples with different drugs/chemicals are described, in which different approaches have been applied. The lessons we learned from the exercise are as follows: 1) in vitro conditions should be considered and compared to the in vivo situation, particularly for protein binding; 2) in vitro inhibition of metabolizing enzymes by the formed metabolites should be taken into consideration; and 3) it is important to extrapolate from the in vitro measured intracellular concentration and not from the nominal concentration to the tissue/organ concentration to come up with an appropriate QIVIVE for the relevant adverse effects.
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Affiliation(s)
- Engi Abdelhady Algharably
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Clinical Pharmacology and Toxicology, Berlin, Germany
| | - Emma Di Consiglio
- Mechanisms, Biomarkers and Models Unit, Environment and Health Department, Istituto Superiore di Sanità, Rome, Italy
| | - Emanuela Testai
- Mechanisms, Biomarkers and Models Unit, Environment and Health Department, Istituto Superiore di Sanità, Rome, Italy
| | | | - Hans Mielke
- Federal Institute for Risk Assessment, Berlin, Germany
| | - Ursula Gundert-Remy
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Clinical Pharmacology and Toxicology, Berlin, Germany.,Federal Institute for Risk Assessment, Berlin, Germany
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4
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Crofton KM, Bassan A, Behl M, Chushak YG, Fritsche E, Gearhart JM, Marty MS, Mumtaz M, Pavan M, Ruiz P, Sachana M, Selvam R, Shafer TJ, Stavitskaya L, Szabo DT, Szabo ST, Tice RR, Wilson D, Woolley D, Myatt GJ. Current status and future directions for a neurotoxicity hazard assessment framework that integrates in silico approaches. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 22:100223. [PMID: 35844258 PMCID: PMC9281386 DOI: 10.1016/j.comtox.2022.100223] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Neurotoxicology is the study of adverse effects on the structure or function of the developing or mature adult nervous system following exposure to chemical, biological, or physical agents. The development of more informative alternative methods to assess developmental (DNT) and adult (NT) neurotoxicity induced by xenobiotics is critically needed. The use of such alternative methods including in silico approaches that predict DNT or NT from chemical structure (e.g., statistical-based and expert rule-based systems) is ideally based on a comprehensive understanding of the relevant biological mechanisms. This paper discusses known mechanisms alongside the current state of the art in DNT/NT testing. In silico approaches available today that support the assessment of neurotoxicity based on knowledge of chemical structure are reviewed, and a conceptual framework for the integration of in silico methods with experimental information is presented. Establishing this framework is essential for the development of protocols, namely standardized approaches, to ensure that assessments of NT and DNT based on chemical structures are generated in a transparent, consistent, and defendable manner.
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Affiliation(s)
| | - Arianna Bassan
- Innovatune srl, Via Giulio Zanon 130/D, 35129 Padova,
Italy
| | - Mamta Behl
- Division of the National Toxicology Program, National
Institutes of Environmental Health Sciences, Durham, NC 27709, USA
| | - Yaroslav G. Chushak
- Henry M Jackson Foundation for the Advancement of Military
Medicine, Wright-Patterson AFB, OH 45433, USA
| | - Ellen Fritsche
- IUF – Leibniz Research Institute for Environmental
Medicine & Medical Faculty Heinrich-Heine-University, Düsseldorf,
Germany
| | - Jeffery M. Gearhart
- Henry M Jackson Foundation for the Advancement of Military
Medicine, Wright-Patterson AFB, OH 45433, USA
| | | | - Moiz Mumtaz
- Agency for Toxic Substances and Disease Registry, US
Department of Health and Human Services, Atlanta, GA, USA
| | - Manuela Pavan
- Innovatune srl, Via Giulio Zanon 130/D, 35129 Padova,
Italy
| | - Patricia Ruiz
- Agency for Toxic Substances and Disease Registry, US
Department of Health and Human Services, Atlanta, GA, USA
| | - Magdalini Sachana
- Environment Health and Safety Division, Environment
Directorate, Organisation for Economic Co-Operation and Development (OECD), 75775
Paris Cedex 16, France
| | - Rajamani Selvam
- Office of Clinical Pharmacology, Office of Translational
Sciences, Center for Drug Evaluation and Research (CDER), U.S. Food and Drug
Administration (FDA), Silver Spring, MD 20993, USA
| | - Timothy J. Shafer
- Biomolecular and Computational Toxicology Division, Center
for Computational Toxicology and Exposure, US EPA, Research Triangle Park, NC,
USA
| | - Lidiya Stavitskaya
- Office of Clinical Pharmacology, Office of Translational
Sciences, Center for Drug Evaluation and Research (CDER), U.S. Food and Drug
Administration (FDA), Silver Spring, MD 20993, USA
| | | | | | | | - Dan Wilson
- The Dow Chemical Company, Midland, MI 48667, USA
| | | | - Glenn J. Myatt
- Instem, Columbus, OH 43215, USA
- Corresponding author.
(G.J. Myatt)
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5
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Astuto MC, Di Nicola MR, Tarazona JV, Rortais A, Devos Y, Liem AKD, Kass GEN, Bastaki M, Schoonjans R, Maggiore A, Charles S, Ratier A, Lopes C, Gestin O, Robinson T, Williams A, Kramer N, Carnesecchi E, Dorne JLCM. In Silico Methods for Environmental Risk Assessment: Principles, Tiered Approaches, Applications, and Future Perspectives. Methods Mol Biol 2022; 2425:589-636. [PMID: 35188648 DOI: 10.1007/978-1-0716-1960-5_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This chapter aims to introduce the reader to the basic principles of environmental risk assessment of chemicals and highlights the usefulness of tiered approaches within weight of evidence approaches in relation to problem formulation i.e., data availability, time and resource availability. In silico models are then introduced and include quantitative structure-activity relationship (QSAR) models, which support filling data gaps when no chemical property or ecotoxicological data are available. In addition, biologically-based models can be applied in more data rich situations and these include generic or species-specific models such as toxicokinetic-toxicodynamic models, dynamic energy budget models, physiologically based models, and models for ecosystem hazard assessment i.e. species sensitivity distributions and ultimately for landscape assessment i.e. landscape-based modeling approaches. Throughout this chapter, particular attention is given to provide practical examples supporting the application of such in silico models in real-world settings. Future perspectives are discussed to address environmental risk assessment in a more holistic manner particularly for relevant complex questions, such as the risk assessment of multiple stressors and the development of harmonized approaches to ultimately quantify the relative contribution and impact of single chemicals, multiple chemicals and multiple stressors on living organisms.
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Affiliation(s)
| | | | | | - A Rortais
- European Food Safety Authority, Parma, Italy
| | - Yann Devos
- European Food Safety Authority, Parma, Italy
| | | | | | | | | | | | | | | | | | | | | | - Antony Williams
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, NC, USA
| | - Nynke Kramer
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Edoardo Carnesecchi
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
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6
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Hernandez‐Jerez AF, Adriaanse P, Aldrich A, Berny P, Coja T, Duquesne S, Focks A, Marinovich M, Millet M, Pelkonen O, Pieper S, Tiktak A, Topping CJ, Widenfalk A, Wilks M, Wolterink G, Gundert‐Remy U, Louisse J, Rudaz S, Testai E, Lostia A, Dorne J, Parra Morte JM. Scientific Opinion of the Scientific Panel on Plant Protection Products and their Residues (PPR Panel) on testing and interpretation of comparative in vitro metabolism studies. EFSA J 2021; 19:e06970. [PMID: 34987623 PMCID: PMC8696562 DOI: 10.2903/j.efsa.2021.6970] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
EFSA asked the Panel on Plant Protection Products and their residues to deliver a Scientific Opinion on testing and interpretation of comparative in vitro metabolism studies for both new active substances and existing ones. The main aim of comparative in vitro metabolism studies of pesticide active substances is to evaluate whether all significant metabolites formed in the human in vitro test system, as a surrogate of the in vivo situation, are also present at comparable level in animal species tested in toxicological studies and, therefore, if their potential toxicity has been appropriately covered by animal studies. The studies may also help to decide which animal model, with regard to a particular compound, is the most relevant for humans. In the experimental strategy, primary hepatocytes in suspension or culture are recommended since hepatocytes are considered the most representative in vitro system for prediction of in vivo metabolites. The experimental design of 3 × 3 × 3 (concentrations, time points, technical replicates, on pooled hepatocytes) will maximise the chance to identify unique (UHM) and disproportionate (DHM) human metabolites. When DHM and UHM are being assessed, test item-related radioactivity recovery and metabolite profile are the most important parameters. Subsequently, structural characterisation of the assigned metabolites is performed with appropriate analytical techniques. In toxicological assessment of metabolites, the uncertainty factor approach is the first alternative to testing option, followed by new approach methodologies (QSAR, read-across, in vitro methods), and only if these fail, in vivo animal toxicity studies may be performed. Knowledge of in vitro metabolites in human and animal hepatocytes would enable toxicological evaluation of all metabolites of concern, and, furthermore, add useful pieces of information for detection and evaluation of metabolites in different matrices (crops, livestock, environment), improve biomonitoring efforts via better toxicokinetic understanding, and ultimately, develop regulatory schemes employing physiologically based or physiology-mimicking in silico and/or in vitro test systems to anticipate the exposure of humans to potentially hazardous substances in plant protection products.
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7
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Bassan A, Alves VM, Amberg A, Anger LT, Auerbach S, Beilke L, Bender A, Cronin MT, Cross KP, Hsieh JH, Greene N, Kemper R, Kim MT, Mumtaz M, Noeske T, Pavan M, Pletz J, Russo DP, Sabnis Y, Schaefer M, Szabo DT, Valentin JP, Wichard J, Williams D, Woolley D, Zwickl C, Myatt GJ. In silico approaches in organ toxicity hazard assessment: current status and future needs in predicting liver toxicity. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 20:100187. [PMID: 35340402 PMCID: PMC8955833 DOI: 10.1016/j.comtox.2021.100187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Hepatotoxicity is one of the most frequently observed adverse effects resulting from exposure to a xenobiotic. For example, in pharmaceutical research and development it is one of the major reasons for drug withdrawals, clinical failures, and discontinuation of drug candidates. The development of faster and cheaper methods to assess hepatotoxicity that are both more sustainable and more informative is critically needed. The biological mechanisms and processes underpinning hepatotoxicity are summarized and experimental approaches to support the prediction of hepatotoxicity are described, including toxicokinetic considerations. The paper describes the increasingly important role of in silico approaches and highlights challenges to the adoption of these methods including the lack of a commonly agreed upon protocol for performing such an assessment and the need for in silico solutions that take dose into consideration. A proposed framework for the integration of in silico and experimental information is provided along with a case study describing how computational methods have been used to successfully respond to a regulatory question concerning non-genotoxic impurities in chemically synthesized pharmaceuticals.
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Affiliation(s)
- Arianna Bassan
- Innovatune srl, Via Giulio Zanon 130/D, 35129 Padova, Italy
| | - Vinicius M. Alves
- The National Institute of Environmental Health Sciences, Division of the National Toxicology, Program, Research Triangle Park, NC 27709, USA
| | - Alexander Amberg
- Sanofi, R&D Preclinical Safety Frankfurt, Industriepark Hoechst, D-65926 Frankfurt am Main, Germany
| | | | - Scott Auerbach
- The National Institute of Environmental Health Sciences, Division of the National Toxicology, Program, Research Triangle Park, NC 27709, USA
| | - Lisa Beilke
- Toxicology Solutions Inc., San Diego, CA, USA
| | - Andreas Bender
- AI and Data Analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW
| | - Mark T.D. Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | | | - Jui-Hua Hsieh
- The National Institute of Environmental Health Sciences, Division of the National Toxicology, Program, Research Triangle Park, NC 27709, USA
| | - Nigel Greene
- Data Science and AI, DSM, IMED Biotech Unit, AstraZeneca, Boston, USA
| | - Raymond Kemper
- Nuvalent, One Broadway, 14th floor, Cambridge, MA, 02142, USA
| | - Marlene T. Kim
- US Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, MD, 20993, USA
| | - Moiz Mumtaz
- Office of the Associate Director for Science (OADS), Agency for Toxic Substances and Disease, Registry, US Department of Health and Human Services, Atlanta, GA, USA
| | - Tobias Noeske
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Manuela Pavan
- Innovatune srl, Via Giulio Zanon 130/D, 35129 Padova, Italy
| | - Julia Pletz
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Daniel P. Russo
- Department of Chemistry, Rutgers University, Camden, NJ 08102, USA
- The Rutgers Center for Computational and Integrative Biology, Camden, NJ 08102, USA
| | - Yogesh Sabnis
- UCB Biopharma SRL, Chemin du Foriest – B-1420 Braine-l’Alleud, Belgium
| | - Markus Schaefer
- Sanofi, R&D Preclinical Safety Frankfurt, Industriepark Hoechst, D-65926 Frankfurt am Main, Germany
| | | | | | - Joerg Wichard
- Bayer AG, Genetic Toxicology, Müllerstr. 178, 13353 Berlin, Germany
| | - Dominic Williams
- Functional & Mechanistic Safety, Clinical Pharmacology & Safety Sciences, AstraZeneca, Darwin Building 310, Cambridge Science Park, Milton Rd, Cambridge CB4 0FZ, UK
| | - David Woolley
- ForthTox Limited, PO Box 13550, Linlithgow, EH49 7YU, UK
| | - Craig Zwickl
- Transendix LLC, 1407 Moores Manor, Indianapolis, IN 46229, USA
| | - Glenn J. Myatt
- Instem, 1393 Dublin Road, Columbus, OH 43215. USA
- Corresponding author. (G.J. Myatt)
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8
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Transcriptomics analysis of hepatotoxicity induced by the pesticides imazalil, thiacloprid and clothianidin alone or in binary mixtures in a 28-day study in female Wistar rats. Arch Toxicol 2021; 95:1039-1053. [PMID: 33426623 PMCID: PMC7904562 DOI: 10.1007/s00204-020-02969-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/23/2020] [Indexed: 01/01/2023]
Abstract
Co-occurrence of pesticide residues in food commodities raises a potential safety issue as their mixture effects on human health are largely unknown. In a previous study, we reported the toxicological effects (pathology and histopathology) of imazalil (IMZ), thiacloprid (THI), and clothianidin (CTD) alone and in binary mixtures in a 28-day oral gavage study in female Wistar rats. Five dose levels (up to 350 mg/kg body weight/day) ranging from a typical toxicological reference value to a clear effect dose were applied. In the present study, we undertook a transcriptomics analysis of rat livers by means of total RNA sequencing (RNA-Seq). Bioinformatic data analysis involving Ingenuity Pathway Analysis (IPA) was used to gain mechanistic information on hepatotoxicity-related pathways affected after treatment with the pesticides, alone and in mixtures. Our data show that 2986 genes were differentially regulated by CTD while IMZ and THI had effects on 194 and 225 genes, respectively. All three individual compounds shared a common subset of genes whose network is associated with xenobiotic metabolism and nuclear receptor activation. Similar networks were retrieved for the mixtures. Alterations in the expression of individual genes were in line with the assumption of dose addition. Our results bring new insight into the hepatotoxicity mechanisms of IMZ, THI, and CTD and their mixtures.
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9
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Dorne JLCM, Richardson J, Livaniou A, Carnesecchi E, Ceriani L, Baldin R, Kovarich S, Pavan M, Saouter E, Biganzoli F, Pasinato L, Zare Jeddi M, Robinson TP, Kass GEN, Liem AKD, Toropov AA, Toropova AP, Yang C, Tarkhov A, Georgiadis N, Di Nicola MR, Mostrag A, Verhagen H, Roncaglioni A, Benfenati E, Bassan A. EFSA's OpenFoodTox: An open source toxicological database on chemicals in food and feed and its future developments. ENVIRONMENT INTERNATIONAL 2021; 146:106293. [PMID: 33395940 DOI: 10.1016/j.envint.2020.106293] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 05/12/2023]
Abstract
Since its creation in 2002, the European Food Safety Authority (EFSA) has produced risk assessments for over 5000 substances in >2000 Scientific Opinions, Statements and Conclusions through the work of its Scientific Panels, Units and Scientific Committee. OpenFoodTox is an open source toxicological database, available both for download and data visualisation which provides data for all substances evaluated by EFSA including substance characterisation, links to EFSA's outputs, applicable legislations regulations, and a summary of hazard identification and hazard characterisation data for human health, animal health and ecological assessments. The database has been structured using OECD harmonised templates for reporting chemical test summaries (OHTs) to facilitate data sharing with stakeholders with an interest in chemical risk assessment, such as sister agencies, international scientific advisory bodies, and others. This manuscript provides a description of OpenFoodTox including data model, content and tools to download and search the database. Examples of applications of OpenFoodTox in chemical risk assessment are discussed including new quantitative structure-activity relationship (QSAR) models, integration into tools (OECD QSAR Toolbox and AMBIT-2.0), assessment of environmental footprints and testing of threshold of toxicological concern (TTC) values for food related compounds. Finally, future developments for OpenFoodTox 2.0 include the integration of new properties, such as physico-chemical properties, exposure data, toxicokinetic information; and the future integration within in silico modelling platforms such as QSAR models and physiologically-based kinetic models. Such structured in vivo, in vitro and in silico hazard data provide different lines of evidence which can be assembled, weighed and integrated using harmonised Weight of Evidence approaches to support the use of New Approach Methodologies (NAMs) in chemical risk assessment and the reduction of animal testing.
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Affiliation(s)
- J L C M Dorne
- European Food Safety Authority, Via Carlo Magno, 1A, 43126 Parma, Italy.
| | - J Richardson
- European Food Safety Authority, Via Carlo Magno, 1A, 43126 Parma, Italy
| | - A Livaniou
- European Food Safety Authority, Via Carlo Magno, 1A, 43126 Parma, Italy
| | - E Carnesecchi
- Istituto di Ricerche Farmacologico Mario Negri, Via La Masa 19, 20156 Milano, Italy; Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80177, 3508 TD Utrecht, the Netherlands
| | - L Ceriani
- S-IN Soluzioni Informatiche, Via Ferrari 14, 36100 Vicenza, Italy
| | - R Baldin
- S-IN Soluzioni Informatiche, Via Ferrari 14, 36100 Vicenza, Italy
| | - S Kovarich
- S-IN Soluzioni Informatiche, Via Ferrari 14, 36100 Vicenza, Italy
| | - M Pavan
- S-IN Soluzioni Informatiche, Via Ferrari 14, 36100 Vicenza, Italy
| | - E Saouter
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - F Biganzoli
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - L Pasinato
- European Food Safety Authority, Via Carlo Magno, 1A, 43126 Parma, Italy
| | - M Zare Jeddi
- European Food Safety Authority, Via Carlo Magno, 1A, 43126 Parma, Italy; Istituto di Ricerche Farmacologico Mario Negri, Via La Masa 19, 20156 Milano, Italy
| | - T P Robinson
- European Food Safety Authority, Via Carlo Magno, 1A, 43126 Parma, Italy
| | - G E N Kass
- European Food Safety Authority, Via Carlo Magno, 1A, 43126 Parma, Italy
| | - A K D Liem
- European Food Safety Authority, Via Carlo Magno, 1A, 43126 Parma, Italy
| | - A A Toropov
- Istituto di Ricerche Farmacologico Mario Negri, Via La Masa 19, 20156 Milano, Italy
| | - A P Toropova
- Istituto di Ricerche Farmacologico Mario Negri, Via La Masa 19, 20156 Milano, Italy
| | - C Yang
- MN-AM, 90411 Nürnberg, Germany
| | | | | | | | | | - H Verhagen
- European Food Safety Authority, Via Carlo Magno, 1A, 43126 Parma, Italy; University of Ulster, Coleraine, Northern Ireland, UK
| | - A Roncaglioni
- Istituto di Ricerche Farmacologico Mario Negri, Via La Masa 19, 20156 Milano, Italy
| | - E Benfenati
- Istituto di Ricerche Farmacologico Mario Negri, Via La Masa 19, 20156 Milano, Italy
| | - A Bassan
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80177, 3508 TD Utrecht, the Netherlands
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10
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Arantes MR, Peijnenburg A, Hendriksen PJM, Stoopen G, Almeida TS, Souza TM, Farias DF, Carvalho AFU, Rocha TM, Leal LKAM, Vasconcelos IM, Oliveira JTA. In vitro toxicological characterisation of the antifungal compound soybean toxin (SBTX). Toxicol In Vitro 2020; 65:104824. [PMID: 32165152 DOI: 10.1016/j.tiv.2020.104824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/13/2020] [Accepted: 03/08/2020] [Indexed: 12/18/2022]
Abstract
Soybean toxin (SBTX) is a protein isolated from soybean seeds and composed of two polypeptide subunits (17 and 27 kDa). SBTX has in vitro activity against phytopathogenic fungi such as Cercospora sojina, Aspergillus niger, and Penicillium herguei, and yeasts like Candida albicans, C. parapsilosis, Kluyveromyces marxiannus, and Pichia membranifaciens. The present study aimed to analyze in vitro whether SBTX causes any side effects on non-target bacterial and mammalian cells that could impede its potential use as a novel antifungal agent. SBTX at 100 μg/mL and 200 μg/mL did not hinder the growth of the bacteria Salmonella enterica (subspecies enterica serovar choleraesuis), Bacillus subtilis (subspecies spizizenii) and Staphylococcus aureus. Moreover, SBTX at concentrations up to 500 μg/mL did not significantly affect the viability of erythrocytes, neutrophils, and human intestinal Caco-2 cells. To study whether SBTX could induce relevant alterations in gene expression, in vitro DNA microarray experiments were conducted in which differentiated Caco-2 cells were exposed for 24 h to 100 μg/mL or 200 μg/mL SBTX. SBTX up-regulated genes involved in cell cycle and immune response pathways, but down-regulated genes that play a role in cholesterol biosynthesis and platelet degranulation pathways. Thus, although SBTX did not affect bacteria, nor induced cytotoxity in mammalian cells, it affected some biological pathways in the human Caco-2 cell line that warrants further investigation.
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Affiliation(s)
- Mariana Reis Arantes
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60020-181 Fortaleza, CE, Brazil
| | - Ad Peijnenburg
- WFSR, Wageningen University and Research Centre, P.O. Box 230, 6700 AE Wageningen, the Netherlands.
| | - Peter J M Hendriksen
- WFSR, Wageningen University and Research Centre, P.O. Box 230, 6700 AE Wageningen, the Netherlands.
| | - Geert Stoopen
- WFSR, Wageningen University and Research Centre, P.O. Box 230, 6700 AE Wageningen, the Netherlands.
| | - Thiago Silva Almeida
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60020-181 Fortaleza, CE, Brazil
| | - Terezinha Maria Souza
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht 6229, ER, the Netherlands.
| | - Davi Felipe Farias
- Department of Molecular Biology, Federal University of Paraíba, 58051-900 Joao Pessoa, PB, Brazil.
| | | | | | | | - Ilka Maria Vasconcelos
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60020-181 Fortaleza, CE, Brazil.
| | - Jose Tadeu Abreu Oliveira
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60020-181 Fortaleza, CE, Brazil.
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11
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Villaverde JJ, Sevilla-Morán B, López-Goti C, Alonso-Prados JL, Sandín-España P. QSAR/QSPR models based on quantum chemistry for risk assessment of pesticides according to current European legislation. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:49-72. [PMID: 31766890 DOI: 10.1080/1062936x.2019.1692368] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 11/10/2019] [Indexed: 06/10/2023]
Abstract
In Europe, agencies and official organizations involved in the pesticide control such as the EFSA, ECHA, JRC and ECETOC or even the OECD are pointing out that the software tools based on quantitative structure relationship models, i.e. QSAR and QSPR, have a huge potential to improve the pesticide risk assessment process. In this sense, these non-animal test methods can promote the competitiveness of agriculture in this region: the consumer safety is increased with them due to the possibility of perform an overall better risk assessment of the degradation products and metabolites from pesticides. However, the use of theses computational-based (in silico) tools must be much more systematised and harmonised, improving their validation and including case studies to test them. To open databases, incorporating critical data in an orderly manner for building the models, becomes also necessary. Moreover, quantum chemistry through the Density Functional Theory should be promoted as tool for calculation of quantum descriptors, especially for the study of similar compounds with the same carbon skeleton but differing substitution patterns, e.g. isomers.
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Affiliation(s)
| | | | - C López-Goti
- Unit of Plant Protection Products, INIA, Madrid, Spain
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12
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Battilani P, Palumbo R, Giorni P, Dall’Asta C, Dellafiora L, Gkrillas A, Toscano P, Crisci A, Brera C, De Santis B, Rosanna Cammarano R, Della Seta M, Campbell K, Elliot C, Venancio A, Lima N, Gonçalves A, Terciolo C, Oswald IP. Mycotoxin mixtures in food and feed: holistic, innovative, flexible risk assessment modelling approach:. ACTA ACUST UNITED AC 2020. [DOI: 10.2903/sp.efsa.2020.en-1757] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Viant MR, Ebbels TMD, Beger RD, Ekman DR, Epps DJT, Kamp H, Leonards PEG, Loizou GD, MacRae JI, van Ravenzwaay B, Rocca-Serra P, Salek RM, Walk T, Weber RJM. Use cases, best practice and reporting standards for metabolomics in regulatory toxicology. Nat Commun 2019; 10:3041. [PMID: 31292445 PMCID: PMC6620295 DOI: 10.1038/s41467-019-10900-y] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/07/2019] [Indexed: 12/23/2022] Open
Abstract
Metabolomics is a widely used technology in academic research, yet its application to regulatory science has been limited. The most commonly cited barrier to its translation is lack of performance and reporting standards. The MEtabolomics standaRds Initiative in Toxicology (MERIT) project brings together international experts from multiple sectors to address this need. Here, we identify the most relevant applications for metabolomics in regulatory toxicology and develop best practice guidelines, performance and reporting standards for acquiring and analysing untargeted metabolomics and targeted metabolite data. We recommend that these guidelines are evaluated and implemented for several regulatory use cases.
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Affiliation(s)
- Mark R Viant
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | | | | | | | - David J T Epps
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | | | | | | | | | | | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, OX1 3QG, UK
| | - Reza M Salek
- International Agency for Research on Cancer, Lyon, France
| | - Tilmann Walk
- BASF Metabolome Solutions, 10589, Berlin, Germany
| | - Ralf J M Weber
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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14
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Agapito-Tenfen SZ, Okoli AS, Bernstein MJ, Wikmark OG, Myhr AI. Revisiting Risk Governance of GM Plants: The Need to Consider New and Emerging Gene-Editing Techniques. FRONTIERS IN PLANT SCIENCE 2018; 9:1874. [PMID: 30622546 PMCID: PMC6308909 DOI: 10.3389/fpls.2018.01874] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/04/2018] [Indexed: 05/14/2023]
Abstract
New and emerging gene-editing techniques make it possible to target specific genes in species with greater speed and specificity than previously possible. Of major relevance for plant breeding, regulators and scientists are discussing how to regulate products developed using these gene-editing techniques. Such discussions include whether to adopt or adapt the current framework for GMO risk governance in evaluating the impacts of gene-edited plants, and derived products, on the environment, human and animal health and society. Product classification or definition is one of several aspects of the current framework being criticized. Further, knowledge gaps related to risk assessments of gene-edited organisms-for example of target and off-target effects of intervention in plant genomes-are also of concern. Resolving these and related aspects of the current framework will involve addressing many subjective, value-laden positions, for example how to specify protection goals through ecosystem service approaches. A process informed by responsible research and innovation practices, involving a broader community of people, organizations, experts, and interest groups, could help scientists, regulators, and other stakeholders address these complex, value-laden concerns related to gene-editing of plants with and for society.
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Affiliation(s)
| | - Arinze S. Okoli
- GenØk - Centre for Biosafety, SIVA Innovation Centre, Tromsø, Norway
| | | | - Odd-Gunnar Wikmark
- GenØk - Centre for Biosafety, SIVA Innovation Centre, Tromsø, Norway
- Unit for Environmental Science and Management, North West University, Potchefstroom, South Africa
| | - Anne I. Myhr
- GenØk - Centre for Biosafety, SIVA Innovation Centre, Tromsø, Norway
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15
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Clerbaux LA, Coecke S, Lumen A, Kliment T, Worth AP, Paini A. Capturing the applicability of in vitro-in silico membrane transporter data in chemical risk assessment and biomedical research. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:97-108. [PMID: 30015123 PMCID: PMC6162338 DOI: 10.1016/j.scitotenv.2018.07.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 06/01/2023]
Abstract
Costs, scientific and ethical concerns related to animal tests for regulatory decision-making have stimulated the development of alternative methods. When applying alternative approaches, kinetics have been identified as a key element to consider. Membrane transporters affect the kinetic processes of absorption, distribution, metabolism and excretion (ADME) of various compounds, such as drugs or environmental chemicals. Therefore, pharmaceutical scientists have intensively studied transporters impacting drug efficacy and safety. Besides pharmacokinetics, transporters are considered as major determinant of toxicokinetics, potentially representing an essential piece of information in chemical risk assessment. To capture the applicability of transporter data for kinetic-based risk assessment in non-pharmaceutical sectors, the EU Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM) created a survey with a view of identifying the improvements needed when using in vitro and in silico methods. Seventy-three participants, from different sectors and with various kinds of expertise, completed the survey. The results revealed that transporters are investigated mainly during drug development, but also for risk assessment purposes of food and feed contaminants, industrial chemicals, cosmetics, nanomaterials and in the context of environmental toxicology, by applying both in vitro and in silico tools. However, to rely only on alternative methods for chemical risk assessment, it is critical that the data generated by in vitro and in silico methods are scientific integer, reproducible and of high quality so that they are trusted by decision makers and used by industry. In line, the respondents identified various challenges related to the interpretation and use of transporter data from non-animal methods. Overall, it was determined that a combined mechanistically-anchored in vitro-in silico approach, validated against available human data, would gain confidence in using transporter data within an animal-free risk assessment paradigm. Finally, respondents involved primarily in fundamental research expressed lower confidence in non-animal studies to unravel complex transporter mechanisms.
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Affiliation(s)
- Laure-Alix Clerbaux
- European Commission, Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, Italy.
| | - Sandra Coecke
- European Commission, Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, Italy
| | - Annie Lumen
- National Center for Toxicological Research, US Food and Drug Administration (FDA), Jefferson, AR, USA
| | | | - Andrew P Worth
- European Commission, Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, Italy
| | - Alicia Paini
- European Commission, Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, Italy
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16
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Aguilera J, Aguilera‐Gomez M, Barrucci F, Cocconcelli PS, Davies H, Denslow N, Lou Dorne J, Grohmann L, Herman L, Hogstrand C, Kass GEN, Kille P, Kleter G, Nogué F, Plant NJ, Ramon M, Schoonjans R, Waigmann E, Wright MC. EFSA Scientific Colloquium 24 – 'omics in risk assessment: state of the art and next steps. ACTA ACUST UNITED AC 2018. [DOI: 10.2903/sp.efsa.2018.en-1512] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | - Lutz Grohmann
- Federal Office of Consumer Protection and Food Safety
| | | | | | | | | | | | - Fabien Nogué
- French National Institute for Agricultural Research INRA
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17
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Quignot N, Wiecek W, Amzal B, Dorne JL. The Yin–Yang of CYP3A4: a Bayesian meta-analysis to quantify inhibition and induction of CYP3A4 metabolism in humans and refine uncertainty factors for mixture risk assessment. Arch Toxicol 2018; 93:107-119. [DOI: 10.1007/s00204-018-2325-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/02/2018] [Indexed: 12/19/2022]
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18
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Venko K, Drgan V, Novič M. Classification models for identifying substances exhibiting acute contact toxicity in honeybees (Apis mellifera) $. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:743-754. [PMID: 30220217 DOI: 10.1080/1062936x.2018.1513953] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Indexed: 06/08/2023]
Abstract
Nowadays, environmental and biological endpoints can be predicted with in silico approaches if sufficient experimental data of good quality are available. Since the experimental evaluation of acute contact toxicity towards honeybees (Apis mellifera) is a complex and expensive assay, the computational models that follow OECD principles for this endpoint prediction represent important alternatives for safety prioritisation of chemicals, especially pesticides. We developed and validated counter-propagation artificial neural network (CPANN) models for in silico evaluation of toxicity of pesticides towards honeybees by using new in-house software. The data set included 254 pesticides with their toxicological experimental values (acute contact toxicity after 48 h of exposure - LD50 [μg/bee]). The 2D structures of compounds were mathematically represented with 56 Dragon molecular descriptors (MDs). The two-category models were developed to separate compounds as toxic or non-toxic for two different thresholds: (i) toxic when LD50 < 1 μg/bee and (ii) toxic when LD50 < 100 μg/bee. The models give reliable predictions in an external validation set and cover a large structural space. They were applied to a structurally diverse data set of 395 experimentally untested pesticides; 19% of them were predicted as highly toxic towards bees.
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Affiliation(s)
- K Venko
- a Laboratory for Cheminformatics, Theory Department , National Institute of Chemistry , Ljubljana , Slovenia
| | - V Drgan
- a Laboratory for Cheminformatics, Theory Department , National Institute of Chemistry , Ljubljana , Slovenia
| | - M Novič
- a Laboratory for Cheminformatics, Theory Department , National Institute of Chemistry , Ljubljana , Slovenia
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19
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Mavroudis PD, Hermes HE, Teutonico D, Preuss TG, Schneckener S. Development and validation of a physiology-based model for the prediction of pharmacokinetics/toxicokinetics in rabbits. PLoS One 2018; 13:e0194294. [PMID: 29561908 PMCID: PMC5862475 DOI: 10.1371/journal.pone.0194294] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/28/2018] [Indexed: 01/08/2023] Open
Abstract
The environmental fates of pharmaceuticals and the effects of crop protection products on non-target species are subjects that are undergoing intense review. Since measuring the concentrations and effects of xenobiotics on all affected species under all conceivable scenarios is not feasible, standard laboratory animals such as rabbits are tested, and the observed adverse effects are translated to focal species for environmental risk assessments. In that respect, mathematical modelling is becoming increasingly important for evaluating the consequences of pesticides in untested scenarios. In particular, physiologically based pharmacokinetic/toxicokinetic (PBPK/TK) modelling is a well-established methodology used to predict tissue concentrations based on the absorption, distribution, metabolism and excretion of drugs and toxicants. In the present work, a rabbit PBPK/TK model is developed and evaluated with data available from the literature. The model predictions include scenarios of both intravenous (i.v.) and oral (p.o.) administration of small and large compounds. The presented rabbit PBPK/TK model predicts the pharmacokinetics (Cmax, AUC) of the tested compounds with an average 1.7-fold error. This result indicates a good predictive capacity of the model, which enables its use for risk assessment modelling and simulations.
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Affiliation(s)
| | - Helen E. Hermes
- Bayer AG, Engineering & Technology- Systems Pharmacology, Leverkusen, Germany
| | - Donato Teutonico
- Bayer AG, Engineering & Technology- Systems Pharmacology, Leverkusen, Germany
| | | | - Sebastian Schneckener
- Bayer AG, Engineering & Technology- Systems Pharmacology, Leverkusen, Germany
- * E-mail:
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20
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Patel M, Chilton ML, Sartini A, Gibson L, Barber C, Covey-Crump L, Przybylak KR, Cronin MTD, Madden JC. Assessment and Reproducibility of Quantitative Structure–Activity Relationship Models by the Nonexpert. J Chem Inf Model 2018; 58:673-682. [DOI: 10.1021/acs.jcim.7b00523] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Mukesh Patel
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds LS11 5PS, England
| | - Martyn L. Chilton
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds LS11 5PS, England
| | - Andrea Sartini
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds LS11 5PS, England
| | - Laura Gibson
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds LS11 5PS, England
| | - Chris Barber
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds LS11 5PS, England
| | - Liz Covey-Crump
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds LS11 5PS, England
| | - Katarzyna R. Przybylak
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, England
| | - Mark T. D. Cronin
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, England
| | - Judith C. Madden
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, England
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21
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Dellafiora L, Dall'Asta C, Galaverna G. Toxicodynamics of Mycotoxins in the Framework of Food Risk Assessment-An In Silico Perspective. Toxins (Basel) 2018; 10:E52. [PMID: 29360783 PMCID: PMC5848153 DOI: 10.3390/toxins10020052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 01/16/2018] [Accepted: 01/20/2018] [Indexed: 12/11/2022] Open
Abstract
Mycotoxins severely threaten the health of humans and animals. For this reason, many countries have enforced regulations and recommendations to reduce the dietary exposure. However, even though regulatory actions must be based on solid scientific knowledge, many aspects of their toxicological activity are still poorly understood. In particular, deepening knowledge on the primal molecular events triggering the toxic stimulus may be relevant to better understand the mechanisms of action of mycotoxins. The present work presents the use of in silico approaches in studying the mycotoxins toxicodynamics, and discusses how they may contribute in widening the background of knowledge. A particular emphasis has been posed on the methods accounting the molecular initiating events of toxic action. In more details, the key concepts and challenges of mycotoxins toxicology have been introduced. Then, topical case studies have been presented and some possible practical implementations of studying mycotoxins toxicodynamics have been discussed.
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Affiliation(s)
- Luca Dellafiora
- Department of Food and Drug, University of Parma, 43124 Parma, Italy.
| | - Chiara Dall'Asta
- Department of Food and Drug, University of Parma, 43124 Parma, Italy.
| | - Gianni Galaverna
- Department of Food and Drug, University of Parma, 43124 Parma, Italy.
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22
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Parallel in vivo and in vitro transcriptomics analysis reveals calcium and zinc signalling in the brain as sensitive targets of HBCD neurotoxicity. Arch Toxicol 2017; 92:1189-1203. [PMID: 29177809 PMCID: PMC5866835 DOI: 10.1007/s00204-017-2119-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 09/18/2017] [Indexed: 11/04/2022]
Abstract
Hexabromocyclododecane (HBCD) is a brominated flame retardant (BFR) that accumulates in humans and affects the nervous system. To elucidate the mechanisms of HBCD neurotoxicity, we used transcriptomic profiling in brains of female mice exposed through their diet to HBCD (199 mg/kg body weight per day) for 28 days and compared with those of neuronal N2A and NSC-19 cell lines exposed to 1 or 2 µM HBCD. Similar pathways and functions were affected both in vivo and in vitro, including Ca2+ and Zn2+ signalling, glutamatergic neuron activity, apoptosis, and oxidative stress. Release of cytosolic free Zn2+ by HBCD was confirmed in N2A cells. This Zn2+ release was partially quenched by the antioxidant N-acetyl cysteine indicating that, in accordance with transcriptomic analysis, free radical formation is involved in HBCD toxicity. To investigate the effects of HBCD in excitable cells, we isolated mouse hippocampal neurons and monitored Ca2+ signalling triggered by extracellular glutamate or zinc, which are co-released pre-synaptically to trigger postsynaptic signalling. In control cells application of zinc or glutamate triggered a rapid rise of intracellular [Ca2+]. Treatment of the cultures with 1 µM of HBCD was sufficient to reduce the glutamate-dependent Ca2+ signal by 50%. The effect of HBCD on zinc-dependent Ca2+ signalling was even more pronounced, resulting in the reduction of the Ca2+ signal with 86% inhibition at 1 µM HBCD. Our results show that low concentrations of HBCD affect neural signalling in mouse brain acting through dysregulation of Ca2+ and Zn2+ homeostasis.
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23
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Vuorinen A, Bellion P, Beilstein P. Applicability of in silico genotoxicity models on food and feed ingredients. Regul Toxicol Pharmacol 2017; 90:277-288. [DOI: 10.1016/j.yrtph.2017.09.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 01/12/2023]
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24
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Genotoxicity assessment of piperitenone oxide: An in vitro and in silico evaluation. Food Chem Toxicol 2017; 106:506-513. [PMID: 28606765 DOI: 10.1016/j.fct.2017.06.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/20/2017] [Accepted: 06/09/2017] [Indexed: 01/24/2023]
Abstract
Piperitenone oxide, a natural flavouring agent also known as rotundifolone, has been studied for the genotoxicity assessment by an integrated in vitro and in silico experimental approach, including the bacterial reverse mutation assay, the micronucleus test, the comet assay and the computational prediction by Toxtree and VEGA tools. Under our experimental conditions, the monoterpene showed to induce both point mutations (i.e. frameshift, base-substitution and/or oxidative damage) and DNA damage (i.e. clastogenic or aneuploidic damage, or single-strand breaks). Computational prediction for piperitenone oxide agreed with the toxicological data, and highlighted the presence of the epoxide function and the α,β-unsaturated carbonyl as possible structural alerts for DNA damage. However, improving the toxicological libraries for natural occurring compounds is required in order to favour the applicability of in silico models to the toxicological predictions. Further in vivo evaluations are strictly needed in order to evaluate the role of the bioavailability of the substance and the metabolic fate on its genotoxicity profile. To the best of our knowledge, these data represent the first evaluation of the genotoxicity for this flavour compound and suggest the need of further studies to assess the safety of piperitenone oxide as a flavouring agent.
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25
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Dorne JL, Richardson J, Kass G, Georgiadis N, Monguidi M, Pasinato L, Cappe S, Verhagen H, Robinson T. Editorial: OpenFoodTox: EFSA's open source toxicological database on chemical hazards in food and feed. EFSA J 2017; 15:e15011. [PMID: 32625280 PMCID: PMC7009813 DOI: 10.2903/j.efsa.2017.e15011] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
- Jean Lou Dorne
- Senior Scientific Officer EFSA Scientific Committee and Emerging Risks Unit
| | | | - Georges Kass
- Senior Scientific Officer EFSA Scientific Committee and Emerging Risks Unit
| | | | | | | | | | - Hans Verhagen
- Director of Department of Risk Assessment and Scientific Assistance
| | - Tobin Robinson
- Head of the Scientific Committee and Emerging Risks Unit
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26
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Overview of existing methodologies for the estimation of non‐dietary exposure to chemicals from the use of consumer products and via the environment. EFSA J 2016. [DOI: 10.2903/j.efsa.2016.4525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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27
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Dorne JLCM, Bottex B, Merten C, Germini A, Georgiadis N, Aiassa E, Martino L, Rhomberg L, Clewell HJ, Greiner M, Suter GW, Whelan M, Hart ADM, Knight D, Agarwal P, Younes M, Alexander J, Hardy AR. Weighing evidence and assessing uncertainties. EFSA J 2016. [DOI: 10.2903/j.efsa.2016.s0511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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28
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Hanlon P, Brorby GP, Krishan M. A Risk-Based Strategy for Evaluating Mitigation Options for Process-Formed Compounds in Food: Workshop Proceedings. Int J Toxicol 2016; 35:358-70. [PMID: 27102178 PMCID: PMC4871173 DOI: 10.1177/1091581816640262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Processing (eg, cooking, grinding, drying) has changed the composition of food throughout the course of human history; however, awareness of process-formed compounds, and the potential need to mitigate exposure to those compounds, is a relatively recent phenomenon. In May 2015, the North American Branch of the International Life Sciences Institute (ILSI North America) Technical Committee on Food and Chemical Safety held a workshop on the risk-based process for mitigation of process-formed compounds. This workshop aimed to gain alignment from academia, government, and industry on a risk-based process for proactively assessing the need for and benefit of mitigation of process-formed compounds, including criteria to objectively assess the impact of mitigation as well as research needed to support this process. Workshop participants provided real-time feedback on a draft framework in the form of a decision tree developed by the ILSI North America Technical Committee on Food and Chemical Safety to a panel of experts, and they discussed the importance of communicating the value of such a process to the larger scientific community and, ultimately, the public. The outcome of the workshop was a decision tree that can be used by the scientific community and could form the basis of a global approach to assessing the risks associated with mitigation of process-formed compounds.
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Affiliation(s)
| | | | - Mansi Krishan
- North American Branch of the International Life Sciences Institute, Washington, DC, USA
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Jónsdóttir SÓ, Reffstrup TK, Petersen A, Nielsen E. Physicologically Based Toxicokinetic Models of Tebuconazole and Application in Human Risk Assessment. Chem Res Toxicol 2016; 29:715-34. [DOI: 10.1021/acs.chemrestox.5b00341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Svava Ósk Jónsdóttir
- National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, DK-2860 Søborg, Denmark
| | - Trine Klein Reffstrup
- National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, DK-2860 Søborg, Denmark
| | - Annette Petersen
- National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, DK-2860 Søborg, Denmark
| | - Elsa Nielsen
- National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, DK-2860 Søborg, Denmark
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Brinke A, Buchinger S. Toxicogenomics in Environmental Science. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 157:159-186. [DOI: 10.1007/10_2016_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Marx-Stoelting P, Braeuning A, Buhrke T, Lampen A, Niemann L, Oelgeschlaeger M, Rieke S, Schmidt F, Heise T, Pfeil R, Solecki R. Application of omics data in regulatory toxicology: report of an international BfR expert workshop. Arch Toxicol 2015; 89:2177-84. [PMID: 26486796 DOI: 10.1007/s00204-015-1602-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 09/15/2015] [Indexed: 02/07/2023]
Abstract
Advances in omics techniques and molecular toxicology are necessary to provide new perspectives for regulatory toxicology. By the application of modern molecular techniques, more mechanistic information should be gained to support standard toxicity studies and to contribute to a reduction and refinement of animal experiments required for certain regulatory purposes. The relevance and applicability of data obtained by omics methods to regulatory purposes such as grouping of chemicals, mode of action analysis or classification and labelling needs further improvement, defined validation and cautious expert judgment. Based on the results of an international expert workshop organized 2014 by the Federal Institute for Risk Assessment in Berlin, this paper is aimed to provide a critical overview of the regulatory relevance and reliability of omics methods, basic requirements on data quality and validation, as well as regulatory criteria to decide which effects observed by omics methods should be considered adverse or non-adverse. As a way forward, it was concluded that the inclusion of omics data can facilitate a more flexible approach for regulatory risk assessment and may help to reduce or refine animal testing.
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Affiliation(s)
- P Marx-Stoelting
- Federal Institute for Risk Assessment, Max-Dohrn-Str 8-10, 10589, Berlin, Germany.
| | - A Braeuning
- Federal Institute for Risk Assessment, Max-Dohrn-Str 8-10, 10589, Berlin, Germany
| | - T Buhrke
- Federal Institute for Risk Assessment, Max-Dohrn-Str 8-10, 10589, Berlin, Germany
| | - A Lampen
- Federal Institute for Risk Assessment, Max-Dohrn-Str 8-10, 10589, Berlin, Germany
| | - L Niemann
- Federal Institute for Risk Assessment, Max-Dohrn-Str 8-10, 10589, Berlin, Germany
| | - M Oelgeschlaeger
- Federal Institute for Risk Assessment, Max-Dohrn-Str 8-10, 10589, Berlin, Germany
| | - S Rieke
- Federal Institute for Risk Assessment, Max-Dohrn-Str 8-10, 10589, Berlin, Germany
| | - F Schmidt
- Federal Institute for Risk Assessment, Max-Dohrn-Str 8-10, 10589, Berlin, Germany
| | - T Heise
- Federal Institute for Risk Assessment, Max-Dohrn-Str 8-10, 10589, Berlin, Germany
| | - R Pfeil
- Federal Institute for Risk Assessment, Max-Dohrn-Str 8-10, 10589, Berlin, Germany
| | - R Solecki
- Federal Institute for Risk Assessment, Max-Dohrn-Str 8-10, 10589, Berlin, Germany
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Harrison P, Holmes P, Bevan R, Kamps K, Levy L, Greim H. Regulatory risk assessment approaches for synthetic mineral fibres. Regul Toxicol Pharmacol 2015; 73:425-41. [DOI: 10.1016/j.yrtph.2015.07.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 07/30/2015] [Accepted: 07/31/2015] [Indexed: 11/28/2022]
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