1
|
Berggren E, Worth AP. Towards a future regulatory framework for chemicals in the European Union - Chemicals 2.0. Regul Toxicol Pharmacol 2023:105431. [PMID: 37315707 PMCID: PMC10390824 DOI: 10.1016/j.yrtph.2023.105431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/03/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
Abstract
The body of EU chemicals legislation has evolved since the 1960s, producing the largest knowledge base on chemicals worldwide. Like any evolving system, however, it has become increasingly diverse and complex, resulting in inefficiencies and potential inconsistencies. In the light of the EU Chemicals Strategy for Sustainability, it is therefore timely and reasonable to consider how aspects of the system could be simplified and streamlined, without losing the hard-earned benefits to human health and the environment. In this commentary, we propose a conceptual framework that could be the basis of Chemicals 2.0 - a future safety assessment and management approach that is based on the application of New Approach Methodologies (NAMs), mechanistic reasoning and cost-benefit considerations. Chemicals 2.0 is designed to be a more efficient and more effective approach for assessing chemicals, and to comply with the EU goal to completely replace animal testing, in line with Directive 2010/63/EU. We propose five design criteria for Chemicals 2.0 to define what the future system should achieve. The approach is centered on a classification matrix in which NAMs for toxicodynamics and toxicokinetics are used to classify chemicals according to their level of concern. An important principle is the need to ensure an equivalent, or higher, protection level.
Collapse
Affiliation(s)
| | - Andrew P Worth
- European Commission, Joint Research Centre (JRC), Ispra, Italy.
| |
Collapse
|
2
|
Westmoreland C, Bender HJ, Doe JE, Jacobs MN, Kass GE, Madia F, Mahony C, Manou I, Maxwell G, Prieto P, Roggeband R, Sobanski T, Schütte K, Worth AP, Zvonar Z, Cronin MT. Use of New Approach Methodologies (NAMs) in regulatory decisions for chemical safety: Report from an EPAA Deep Dive Workshop. Regul Toxicol Pharmacol 2022; 135:105261. [DOI: 10.1016/j.yrtph.2022.105261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/07/2022] [Indexed: 11/30/2022]
|
3
|
Cronin MTD, Bauer FJ, Bonnell M, Campos B, Ebbrell DJ, Firman JW, Gutsell S, Hodges G, Patlewicz G, Sapounidou M, Spînu N, Thomas PC, Worth AP. A scheme to evaluate structural alerts to predict toxicity - Assessing confidence by characterising uncertainties. Regul Toxicol Pharmacol 2022; 135:105249. [PMID: 36041585 PMCID: PMC9585125 DOI: 10.1016/j.yrtph.2022.105249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/12/2022] [Accepted: 08/17/2022] [Indexed: 11/26/2022]
Abstract
Structure-activity relationships (SARs) in toxicology have enabled the formation of structural rules which, when coded as structural alerts, are essential tools in in silico toxicology. Whilst other in silico methods have approaches for their evaluation, there is no formal process to assess the confidence that may be associated with a structural alert. This investigation proposes twelve criteria to assess the uncertainty associated with structural alerts, allowing for an assessment of confidence. The criteria are based around the stated purpose, description of the chemistry, toxicology and mechanism, performance and coverage, as well as corroborating and supporting evidence of the alert. Alerts can be given a confidence assessment and score, enabling the identification of areas where more information may be beneficial. The scheme to evaluate structural alerts was placed in the context of various use cases for industrial and regulatory applications. The analysis of alerts, and consideration of the evaluation scheme, identifies the different characteristics an alert may have, such as being highly specific or generic. These characteristics may determine when an alert can be used for specific uses such as identification of analogues for read-across or hazard identification. Structural alerts are useful tools for predictive toxicology. 12 criteria to evaluate structural alerts have been identified. A strategy to determine confidence of structural alerts is presented. Different use cases require different characteristics of structural alerts. A Scheme to Evaluate Structural Alerts to Predict Toxicity – Assessing Confidence By Characterising Uncertainties.
Collapse
Affiliation(s)
- Mark T D Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Franklin J Bauer
- KREATiS SAS, 23 rue du Creuzat, ZAC de St-Hubert, 38080, L'Isle d'Abeau, France
| | - Mark Bonnell
- Science and Risk Assessment Directorate, Environment & Climate Change Canada, 351 St. Joseph Blvd, Gatineau, Quebec, K1A 0H3, Canada
| | - Bruno Campos
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Bedfordshire, MK44 1LQ, UK
| | - David J Ebbrell
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - James W Firman
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Steve Gutsell
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Bedfordshire, MK44 1LQ, UK
| | - Geoff Hodges
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Bedfordshire, MK44 1LQ, UK
| | - Grace Patlewicz
- Center for Computational Toxicology and Exposure (CCTE), US Environmental Protection Agency, 109 TW Alexander Dr, RTP, NC, 27709, USA
| | - Maria Sapounidou
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Nicoleta Spînu
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Paul C Thomas
- KREATiS SAS, 23 rue du Creuzat, ZAC de St-Hubert, 38080, L'Isle d'Abeau, France
| | - Andrew P Worth
- European Commission, Joint Research Centre (JRC), Ispra, Italy.
| |
Collapse
|
4
|
Spînu N, Cronin MT, Lao J, Bal-Price A, Campia I, Enoch SJ, Madden JC, Mora Lagares L, Novič M, Pamies D, Scholz S, Villeneuve DL, Worth AP. Probabilistic modelling of developmental neurotoxicity based on a simplified adverse outcome pathway network. Computational Toxicology 2022; 21:100206. [PMID: 35211661 PMCID: PMC8857173 DOI: 10.1016/j.comtox.2021.100206] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/08/2021] [Accepted: 11/25/2021] [Indexed: 12/14/2022]
Abstract
A developmental neurotoxicity Adverse Outcome Pathway network was simplified. Common key events were chosen based on topology analysis and expert judgement. Quantification of causal relationships was informed by key event relationships. Various types of information were integrated for probability prediction. Bayesian hierarchical modelling was applied for hazard identification.
In a century where toxicology and chemical risk assessment are embracing alternative methods to animal testing, there is an opportunity to understand the causal factors of neurodevelopmental disorders such as learning and memory disabilities in children, as a foundation to predict adverse effects. New testing paradigms, along with the advances in probabilistic modelling, can help with the formulation of mechanistically-driven hypotheses on how exposure to environmental chemicals could potentially lead to developmental neurotoxicity (DNT). This investigation aimed to develop a Bayesian hierarchical model of a simplified AOP network for DNT. The model predicted the probability that a compound induces each of three selected common key events (CKEs) of the simplified AOP network and the adverse outcome (AO) of DNT, taking into account correlations and causal relations informed by the key event relationships (KERs). A dataset of 88 compounds representing pharmaceuticals, industrial chemicals and pesticides was compiled including physicochemical properties as well as in silico and in vitro information. The Bayesian model was able to predict DNT potential with an accuracy of 76%, classifying the compounds into low, medium or high probability classes. The modelling workflow achieved three further goals: it dealt with missing values; accommodated unbalanced and correlated data; and followed the structure of a directed acyclic graph (DAG) to simulate the simplified AOP network. Overall, the model demonstrated the utility of Bayesian hierarchical modelling for the development of quantitative AOP (qAOP) models and for informing the use of new approach methodologies (NAMs) in chemical risk assessment.
Collapse
Affiliation(s)
- Nicoleta Spînu
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Mark T.D. Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Junpeng Lao
- Department of Psychology, University of Fribourg, Fribourg CH-1700, Switzerland
| | - Anna Bal-Price
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Ivana Campia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Steven J. Enoch
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Judith C. Madden
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Liadys Mora Lagares
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Marjana Novič
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - David Pamies
- Department of Biomedical Science, University of Lausanne, Lausanne, Vaud, Switzerland
- Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland
| | - Stefan Scholz
- Helmholtz-Centre for Environmental Research − UFZ, Department of Bioanalytical Ecotoxicology, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Daniel L. Villeneuve
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, MN 55804, MN, USA
| | - Andrew P. Worth
- European Commission, Joint Research Centre (JRC), Ispra, Italy
- Corresponding author.
| |
Collapse
|
5
|
Spînu N, Cronin MT, Madden JC, Worth AP. A matter of trust: Learning lessons about causality will make qAOPs credible. Computational Toxicology 2022; 21:100205. [PMID: 35224319 PMCID: PMC8855346 DOI: 10.1016/j.comtox.2021.100205] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/01/2021] [Accepted: 11/25/2021] [Indexed: 12/03/2022]
Abstract
Quantitative AOPs are toxicodynamic models based on Adverse Outcome Pathways. Mathematical models, e.g. Bayesian networks, can inform the quantification of AOPs. Model credibility is enhanced by applying the principles of causality theory. A causal diagram is illustrated for an AOP for Parkinsonian motor deficits. Computational resources to help assess causality are listed.
Toxicology in the 21st Century has seen a shift from chemical risk assessment based on traditional animal tests, identifying apical endpoints and doses that are “safe”, to the prospect of Next Generation Risk Assessment based on non-animal methods. Increasingly, large and high throughput in vitro datasets are being generated and exploited to develop computational models. This is accompanied by an increased use of machine learning approaches in the model building process. A potential problem, however, is that such models, while robust and predictive, may still lack credibility from the perspective of the end-user. In this commentary, we argue that the science of causal inference and reasoning, as proposed by Judea Pearl, will facilitate the development, use and acceptance of quantitative AOP models. Our hope is that by importing established concepts of causality from outside the field of toxicology, we can be “constructively disruptive” to the current toxicological paradigm, using the “Causal Revolution” to bring about a “Toxicological Revolution” more rapidly.
Collapse
|
6
|
Abstract
In this chapter, we give a brief overview of the regulatory requirements for acute systemic toxicity information in the European Union, and we review structure-based computational models that are available and potentially useful in the assessment of acute systemic toxicity. Emphasis is placed on quantitative structure-activity relationship (QSAR) models implemented by means of a range of software tools. The most recently published literature models for acute systemic toxicity are also discussed, and perspectives for future developments in this field are offered.
Collapse
Affiliation(s)
- Ivanka Tsakovska
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Antonia Diukendjieva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Andrew P Worth
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| |
Collapse
|
7
|
Yang C, Cronin MTD, Arvidson KB, Bienfait B, Enoch SJ, Heldreth B, Hobocienski B, Muldoon-Jacobs K, Lan Y, Madden JC, Magdziarz T, Marusczyk J, Mostrag A, Nelms M, Neagu D, Przybylak K, Rathman JF, Park J, Richarz AN, Richard AM, Ribeiro JV, Sacher O, Schwab C, Vitcheva V, Volarath P, Worth AP. COSMOS next generation - A public knowledge base leveraging chemical and biological data to support the regulatory assessment of chemicals. Comput Toxicol 2021; 19:100175. [PMID: 34405124 PMCID: PMC8351204 DOI: 10.1016/j.comtox.2021.100175] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/19/2021] [Accepted: 05/27/2021] [Indexed: 11/19/2022]
Abstract
The COSMOS Database (DB) was originally established to provide reliable data for cosmetics-related chemicals within the COSMOS Project funded as part of the SEURAT-1 Research Initiative. The database has subsequently been maintained and developed further into COSMOS Next Generation (NG), a combination of database and in silico tools, essential components of a knowledge base. COSMOS DB provided a cosmetics inventory as well as other regulatory inventories, accompanied by assessment results and in vitro and in vivo toxicity data. In addition to data content curation, much effort was dedicated to data governance - data authorisation, characterisation of quality, documentation of meta information, and control of data use. Through this effort, COSMOS DB was able to merge and fuse data of various types from different sources. Building on the previous effort, the COSMOS Minimum Inclusion (MINIS) criteria for a toxicity database were further expanded to quantify the reliability of studies. COSMOS NG features multiple fingerprints for analysing structure similarity, and new tools to calculate molecular properties and screen chemicals with endpoint-related public profilers, such as DNA and protein binders, liver alerts and genotoxic alerts. The publicly available COSMOS NG enables users to compile information and execute analyses such as category formation and read-across. This paper provides a step-by-step guided workflow for a simple read-across case, starting from a target structure and culminating in an estimation of a NOAEL confidence interval. Given its strong technical foundation, inclusion of quality-reviewed data, and provision of tools designed to facilitate communication between users, COSMOS NG is a first step towards building a toxicological knowledge hub leveraging many public data systems for chemical safety evaluation. We continue to monitor the feedback from the user community at support@mn-am.com.
Collapse
Key Words
- AOP, Adverse Outcome Pathway
- Analogue selection
- CERES, Chemical Evaluation and Risk Estimation System
- CFSAN, Center for Food Safety and Applied Nutrition
- CMS-ID, COSMOS Identification Number
- COSMOS DB, COSMOS Database
- COSMOS MINIS, Minimum Inclusion Criteria of Studies in COSMOS DB
- COSMOS NG, COSMOS Next Generation
- CRADA, Cooperative Research and Development Agreement
- CosIng, Cosmetic Ingredient Database
- DART, Developmental & Reproductive Toxicity
- DB, Database
- DST, Dempster Shafer Theory
- Database
- ECHA, European Chemicals Agency
- EFSA, European Food Safety Authority
- Guided workflow
- HESS, Hazard Evaluation Support System
- HNEL, Highest No Effect Level
- HTS, High throughput screening
- ILSI, International Life Sciences Institute
- IUCLID, International Uniform Chemical Information Database
- Knowledge hub
- LEL, Lowest Effect Level
- LOAEL, Lowest Observed Adverse Effect Level
- LogP, Logarithm of the octanol:water partition coefficient
- NAM, New Approach Methodology
- NGRA, Next Generation Risk-Assessment
- NITE, National Institute of Technology and Evaluation (Japan)
- NOAEL, No Observed Adverse Effect Level
- NTP, National Toxicology Program
- OECD, Organisation for Economic Co-operation and Development
- OpenFoodTox, EFSA’s OpenFoodTox database
- PAFA, Priority-based Assessment of Food Additive database
- PK/TK, Pharmacokinetics/Toxicokinetics
- Public database
- QA, Quality Assurance
- QC, Quality Control
- REACH, Registration, Evaluation, Authorisation and Restriction of Chemicals
- SCC, Science Committee on Cosmetics (EU)
- SCCNFP, Scientific Committee of Cosmetic Products and Non-food Products intended for Consumers (EU)
- SCCP, Scientific Committee on Consumer Products (EU)
- SCCS, Scientific Committee on Consumer Safety (EU)
- Study reliability
- TTC, Threshold of Toxicological Concern
- ToxRefDB, Toxicity Reference Database
- Toxicity
- US EPA, United States Environmental Protection Agency
- US FDA, United States Food and Drug Administration
Collapse
Affiliation(s)
- C Yang
- MN-AM, Columbus, OH, USA
- MN-AM Nürnberg, Germany
| | - M T D Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
| | | | | | - S J Enoch
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
| | - B Heldreth
- Cosmetic Ingredient Review, Washington, DC, USA
| | | | | | - Y Lan
- University of Bradford, UK
| | - J C Madden
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
| | | | | | | | - M Nelms
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
| | | | - K Przybylak
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
| | - J F Rathman
- MN-AM, Columbus, OH, USA
- The Ohio State University, Columbus OH, USA
| | | | - A-N Richarz
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
| | | | | | | | | | - V Vitcheva
- MN-AM, Columbus, OH, USA
- MN-AM Nürnberg, Germany
| | | | - A P Worth
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| |
Collapse
|
8
|
Patterson EA, Whelan MP, Worth AP. The role of validation in establishing the scientific credibility of predictive toxicology approaches intended for regulatory application. ACTA ACUST UNITED AC 2021; 17:100144. [PMID: 33681540 PMCID: PMC7903516 DOI: 10.1016/j.comtox.2020.100144] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 09/15/2020] [Accepted: 11/04/2020] [Indexed: 12/14/2022]
Abstract
The role of validation in establishing the credibility of predictive methods is discussed. Various assessment frameworks for predictive methods have evolved independently, being developed by different communities. A set of seven credibility factors is proposed as a method-agnostic means of comparing the various assessment frameworks. It is hoped this will facilitate communication and cross-disciplinary collaboration between method developers and users.
New approaches in toxicology based on in vitro methods and computational modelling offer considerable potential to improve the efficiency and effectiveness of chemical hazard and risk assessment in a variety of regulatory contexts. However, this presents challenges both for developers and regulatory assessors because often these two communities do not share the same level of confidence in a new approach. To address this challenge, various assessment frameworks have been developed over the past 20 years with the aim of creating harmonised and systematic approaches for evaluating new methods. These frameworks typically focus on specific methodologies and technologies, which has proven useful for establishing the validity and credibility of individual methods. However, given the increasing need to compare methods and combine their use in integrated assessment strategies, the multiplicity of frameworks is arguably becoming a barrier to their acceptance. In this commentary, we explore the concepts of model validity and credibility, and we illustrate how a set of seven credibility factors provides a method-agnostic means of comparing different kinds of predictive toxicology approaches. It is hoped that this will facilitate communication and cross-disciplinarity among method developers and users, with the ultimate aim of increasing the acceptance and use of predictive approaches in toxicology.
Collapse
Affiliation(s)
| | | | - Andrew P Worth
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| |
Collapse
|
9
|
Dearden JC, Barratt MD, Benigni R, Bristol DW, Combes RD, Cronin MT, Judson PN, Payne MP, Richard AM, Tichy M, Worth AP, Yourick JJ. The Development and Validation of Expert Systems for Predicting Toxicity. Altern Lab Anim 2020. [DOI: 10.1177/026119299702500303] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- John C. Dearden
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Martin D. Barratt
- Environmental Safety Laboratory, Unilever Research, Colworth House, Sharnbrook, Bedford MK44 1LQ, UK
| | - Romualdo Benigni
- Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | | | - Robert D. Combes
- FRAME, Russell & Burch House, 96–98 North Sherwood Street, Nottingham NG1 4EE, UK
| | - Mark T.D. Cronin
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | | | - Martin P. Payne
- Health & Safety Laboratory, Broad Lane, Sheffield S3 7HQ, UK
| | - Ann M. Richard
- NHEERL, Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Milon Tichy
- Predictive Toxicology Laboratory, National Institute of Public Health, Srobarova 48, 100 42 Prague 10, Czech Republic
| | | | - Jeffrey J. Yourick
- Cosmetics Toxicology Branch, Food & Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA
| |
Collapse
|
10
|
Worth AP, Fentem JH, Balls M, Botham PA, Curren RD, Earl LK, Esdaile DJ, Liebsch M. An Evaluation of the Proposed OECD Testing Strategy for Skin Corrosion. Altern Lab Anim 2020. [DOI: 10.1177/026119299802600512] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The use of testing strategies which incorporate a range of alternative methods and which use animals only as a last resort is widely considered to provide a reliable way of predicting chemical toxicity while minimising animal testing. The widespread concern over the severity of the Draize rabbit test for assessing skin irritation and corrosion led to the proposal of a stepwise testing strategy at an OECD workshop in January 1996. Subsequently, the proposed testing strategy was adopted, with minor modifications, by the OECD Advisory Group on Harmonization of Classification and Labelling. This article reports an evaluation of the proposed OECD testing strategy as it relates to the classification of skin corrosives. By using a set of 60 chemicals, an assessment was made of the effect of applying three steps in the strategy, taken both individually and in sequence. The results indicate that chemicals can be classified as corrosive (C) or non-corrosive (NC) with sufficient reliability by the sequential application of three alternative methods, i.e., structure-activity relationships (where available), pH measurements, and a single in vitro method (either the rat skin transcutaneous electrical resistance (TER) assay or the EPISKIN™ assay). It is concluded that the proposed OECD strategy for skin corrosion can be simplified without compromising its predictivity. For example, it does not appear necessary to measure acid/alkali reserve (buffering capacity) in addition to pH for the classification of pure chemicals.
Collapse
Affiliation(s)
| | | | - Michael Balls
- ECVAM, JRC Environment Institute, 21020 Ispra (VA), Italy
| | - Philip A. Botham
- Central Toxicology Laboratory, ZENECA, Alderley Park, Macclesfield, Cheshire SK10 4TJ, UK
| | - Rodger D. Curren
- Institute for In Vitro Sciences, 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | - Lesley K. Earl
- SEAC Toxicology Unit, Unilever Research, Colworth House, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - David J. Esdaile
- Rhône-Poulenc Agro, 355 rue Dostoievski, 06903 Sophia Antipolis Cedex, France
| | | |
Collapse
|
11
|
Affiliation(s)
| | | | - J. Brian Houston
- School of Pharmacy and Pharmaceutical Sciences, The University of Manchester, Manchester M13 9PL, UK
| |
Collapse
|
12
|
Spinu N, Cronin MTD, Enoch SJ, Madden JC, Worth AP. Quantitative adverse outcome pathway (qAOP) models for toxicity prediction. Arch Toxicol 2020; 94:1497-1510. [PMID: 32424443 PMCID: PMC7261727 DOI: 10.1007/s00204-020-02774-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/04/2020] [Indexed: 01/06/2023]
Abstract
The quantitative adverse outcome pathway (qAOP) concept is gaining interest due to its potential regulatory applications in chemical risk assessment. Even though an increasing number of qAOP models are being proposed as computational predictive tools, there is no framework to guide their development and assessment. As such, the objectives of this review were to: (i) analyse the definitions of qAOPs published in the scientific literature, (ii) define a set of common features of existing qAOP models derived from the published definitions, and (iii) identify and assess the existing published qAOP models and associated software tools. As a result, five probabilistic qAOPs and ten mechanistic qAOPs were evaluated against the common features. The review offers an overview of how the qAOP concept has advanced and how it can aid toxicity assessment in the future. Further efforts are required to achieve validation, harmonisation and regulatory acceptance of qAOP models.
Collapse
Affiliation(s)
- Nicoleta Spinu
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Mark T D Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Steven J Enoch
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Judith C Madden
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Andrew P Worth
- European Commission, Joint Research Centre (JRC), Ispra, Italy.
| |
Collapse
|
13
|
Abstract
This commentary explores the contribution of computational toxicology to chemical safety assessment in the context of the broad policy challenges faced by the European Union. The state of the European Environment is considered from the perspective of chemical contributions to the burden of disease and ecosystem damage. This sets the scene for highlighting research and innovation opportunities to further develop computational approaches for assessing the human health and environmental effects of chemicals. Emphasis is placed on focus topics that are particularly relevant to the political priorities of the new European Commission. In particular, two of the six priorities are discussed - “The European Green Deal” and “A Europe fit for a Digital Age”. The former includes the zero pollution ambition for a toxic-free environment, including the need to develop safe and sustainable chemicals, while the latter includes the challenges and opportunities posed by Artificial Intelligence. This commentary is based on a presentation given at the 19th meeting of The Italian Society of Toxicology (SITOX), held in Bologna, Italy, in February 2020.
Collapse
Affiliation(s)
- Andrew P Worth
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| |
Collapse
|
14
|
Spinu N, Bal-Price A, Cronin MTD, Enoch SJ, Madden JC, Worth AP. Development and analysis of an adverse outcome pathway network for human neurotoxicity. Arch Toxicol 2019; 93:2759-2772. [DOI: 10.1007/s00204-019-02551-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 08/14/2019] [Indexed: 12/21/2022]
|
15
|
Clerbaux LA, Paini A, Lumen A, Osman-Ponchet H, Worth AP, Fardel O. Membrane transporter data to support kinetically-informed chemical risk assessment using non-animal methods: Scientific and regulatory perspectives. Environ Int 2019; 126:659-671. [PMID: 30856453 PMCID: PMC6441651 DOI: 10.1016/j.envint.2019.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/10/2019] [Accepted: 03/01/2019] [Indexed: 06/01/2023]
Abstract
Humans are continuously exposed to low levels of thousands of industrial chemicals, most of which are poorly characterised in terms of their potential toxicity. The new paradigm in chemical risk assessment (CRA) aims to rely on animal-free testing, with kinetics being a key determinant of toxicity when moving from traditional animal studies to integrated in vitro-in silico approaches. In a kinetically informed CRA, membrane transporters, which have been intensively studied during drug development, are an essential piece of information. However, how existing knowledge on transporters gained in the drug field can be applied to CRA is not yet fully understood. This review outlines the opportunities, challenges and existing tools for investigating chemical-transporter interactions in kinetically informed CRA without animal studies. Various environmental chemicals acting as substrates, inhibitors or modulators of transporter activity or expression have been shown to impact TK, just as drugs do. However, because pollutant concentrations are often lower in humans than drugs and because exposure levels and internal chemical doses are not usually known in contrast to drugs, new approaches are required to translate transporter data and reasoning from the drug sector to CRA. Here, the generation of in vitro chemical-transporter interaction data and the development of transporter databases and classification systems trained on chemical datasets (and not only drugs) are proposed. Furtheremore, improving the use of human biomonitoring data to evaluate the in vitro-in silico transporter-related predicted values and developing means to assess uncertainties could also lead to increase confidence of scientists and regulators in animal-free CRA. Finally, a systematic characterisation of the transportome (quantitative monitoring of transporter abundance, activity and maintenance over time) would reinforce confidence in the use of experimental transporter/barrier systems as well as in established cell-based toxicological assays currently used for CRA.
Collapse
Affiliation(s)
| | - Alicia Paini
- European Commission, Joint Research Centre, 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, Ispra, Italy
| | - Olivier Fardel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environment et travail), UMR_S 1085, F-35000 Rennes, France
| |
Collapse
|
16
|
Diukendjieva A, Tsakovska I, Alov P, Pencheva T, Pajeva I, Worth AP, Madden JC, Cronin MT. Advances in the prediction of gastrointestinal absorption: Quantitative Structure-Activity Relationship (QSAR) modelling of PAMPA permeability. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.comtox.2018.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
17
|
Cronin MT, Madden JC, Yang C, Worth AP. Unlocking the potential of in silico chemical safety assessment - A report on a cross-sector symposium on current opportunities and future challenges. Comput Toxicol 2019; 10:38-43. [PMID: 31218266 PMCID: PMC6559213 DOI: 10.1016/j.comtox.2018.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 12/17/2018] [Indexed: 12/21/2022]
Abstract
In silico chemical safety assessment can support the evaluation of hazard and risk following potential exposure to a substance. A symposium identified a number of opportunities and challenges to implement in silico methods, such as quantitative structure-activity relationships (QSARs) and read-across, to assess the potential harm of a substance in a variety of exposure scenarios, e.g. pharmaceuticals, personal care products, and industrial chemicals. To initiate the process of in silico safety assessment, clear and unambiguous problem formulation is required to provide the context for these methods. These approaches must be built on data of defined quality, while acknowledging the possibility of novel data resources tapping into on-going progress with data sharing. Models need to be developed that cover appropriate toxicity and kinetic endpoints, and that are documented appropriately with defined uncertainties. The application and implementation of in silico models in chemical safety requires a flexible technological framework that enables the integration of multiple strands of data and evidence. The findings of the symposium allowed for the identification of priorities to progress in silico chemical safety assessment towards the animal-free assessment of chemicals.
Collapse
Affiliation(s)
- Mark T.D. Cronin
- Liverpool John Moores University, School of Pharmacy and Biomolecular Sciences, Byrom Street, Liverpool L3 3AF, United Kingdom
| | - Judith C. Madden
- Liverpool John Moores University, School of Pharmacy and Biomolecular Sciences, Byrom Street, Liverpool L3 3AF, United Kingdom
| | - Chihae Yang
- Molecular Networks GmbH, Neumeyerstraße 28, 90411 Nürnberg, Germany
| | - Andrew P. Worth
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| |
Collapse
|
18
|
Affiliation(s)
- Andrew P. Worth
- ECVAM, Institute for Health & Consumer Protection, Joint Research Centre, European Commission, 21020 Ispra (VA), Italy
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Mark T.D. Cronin
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| |
Collapse
|
19
|
Abstract
The validation of a test method is the process by which the relevance and reliability of the method are assessed for a particular purpose. It is an essential stage in the evolution of the method from its development to its acceptance and application for regulatory purposes. The principles according to which alternative tests should be validated have been agreed upon at an international level, although the actual process by which the validation process is conducted varies between different validation authorities. This paper summarises the principles of alternative test development and validation and describes how the principles have been applied to the validation of in vitro tests by the European Centre for the Validation of Alternative Methods (ECVAM).
Collapse
Affiliation(s)
- Andrew P. Worth
- ECVAM, Institute for Health & Consumer Protection, European Commission Joint Research Centre, Ispra, Italy
| | - Michael Balls
- ECVAM, Institute for Health & Consumer Protection, European Commission Joint Research Centre, Ispra, Italy
| |
Collapse
|
20
|
Affiliation(s)
- Andrew P. Worth
- ECVAM, JRC Institute for Health & Consumer Protection, 21020 Ispra (VA), Italy
| | - Julia H. Fentem
- ECVAM, JRC Institute for Health & Consumer Protection, 21020 Ispra (VA), Italy
| |
Collapse
|
21
|
Abstract
This workshop addressed current issues with regard to establishing a framework for the validation of quantitative structure–activity relationships (QSARs) and other computational prediction models. QSARs and related models attempt to associate physicochemical and structural properties of compounds to their biological activity. As such, they may permit the prediction of biological activity from chemical structure alone. As yet, no formal validation criteria have been agreed internationally for QSARs and related techniques. However, some general and preliminary criteria were discussed and agreed upon at a European Chemical Industry Council/International Council of Chemical Associations (CEFIC/ICCA) workshop on the regulatory acceptance of QSARs, held in Setubal, Portugal, in March 2002. These criteria were presented at a Fourth World Congress workshop, along with a proposal for the practical validation of computer models, such as QSARs.
Collapse
Affiliation(s)
- Andrew P. Worth
- ECVAM, Institute for Health & Consumer Protection, European Commission Joint Research Centre, Ispra, Italy
| | - Mark T.D. Cronin
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool, UK
| |
Collapse
|
22
|
Bopp SK, Kienzler A, Richarz AN, van der Linden SC, Paini A, Parissis N, Worth AP. Regulatory assessment and risk management of chemical mixtures: challenges and ways forward. Crit Rev Toxicol 2019; 49:174-189. [DOI: 10.1080/10408444.2019.1579169] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
| | - Aude Kienzler
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | | | - Alicia Paini
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | - Andrew P. Worth
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| |
Collapse
|
23
|
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. Sci Total Environ 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
24
|
Worth AP, Louisse J, Macko P, Sala Benito JV, Paini A. Virtual Cell Based Assay simulations of intra-mitochondrial concentrations in hepatocytes and cardiomyocytes. Toxicol In Vitro 2017; 45:222-232. [PMID: 28911986 PMCID: PMC5745147 DOI: 10.1016/j.tiv.2017.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 09/04/2017] [Accepted: 09/08/2017] [Indexed: 01/16/2023]
Abstract
In order to replace the use of animals in toxicity testing, there is a need to predict human in vivo toxic doses from concentrations that cause adverse effects in in vitro test systems. The virtual cell based assay (VCBA) has been developed to simulate intracellular concentrations as a function of time, and can be used to interpret in vitro concentration-response curves. In this study we refine and extend the VCBA model by including additional target-organ cell models and by simulating the fate and effects of chemicals at the organelle level. In particular, we describe the extension of the original VCBA to simulate chemical fate in liver (HepaRG) cells and cardiomyocytes (ICell cardiomyocytes), and we explore the effects of chemicals at the mitochondrial level. This includes a comparison of: a) in vitro results on cell viability and mitochondrial membrane potential (mmp) from two cell models (HepaRG cells and ICell cardiomyocytes); and b) VCBA simulations, including the cell and mitochondrial compartment, simulating the mmp for both cell types. This proof of concept study illustrates how the relationship between intra cellular, intra mitochondrial concentration, mmp and cell toxicity can be obtained by using the VCBA.
Collapse
Affiliation(s)
- Andrew P Worth
- European Commission, Joint Research Centre, Directorate F - Health, Consumers and Reference Materials, Chemical Safety and Alternative Methods Unit, EURL ECVAM, Ispra, Italy
| | - Jochem Louisse
- European Commission, Joint Research Centre, Directorate F - Health, Consumers and Reference Materials, Chemical Safety and Alternative Methods Unit, EURL ECVAM, Ispra, Italy
| | - Peter Macko
- European Commission, Joint Research Centre, Directorate F - Health, Consumers and Reference Materials, Chemical Safety and Alternative Methods Unit, EURL ECVAM, Ispra, Italy
| | - J V Sala Benito
- European Commission, Joint Research Centre, Directorate F - Health, Consumers and Reference Materials, Chemical Safety and Alternative Methods Unit, EURL ECVAM, Ispra, Italy
| | - Alicia Paini
- European Commission, Joint Research Centre, Directorate F - Health, Consumers and Reference Materials, Chemical Safety and Alternative Methods Unit, EURL ECVAM, Ispra, Italy.
| |
Collapse
|
25
|
Al Sharif M, Tsakovska I, Pajeva I, Alov P, Fioravanzo E, Bassan A, Kovarich S, Yang C, Mostrag-Szlichtyng A, Vitcheva V, Worth AP, Richarz AN, Cronin MT. The application of molecular modelling in the safety assessment of chemicals: A case study on ligand-dependent PPARγ dysregulation. Toxicology 2017; 392:140-154. [DOI: 10.1016/j.tox.2016.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 01/17/2016] [Accepted: 01/24/2016] [Indexed: 12/18/2022]
|
26
|
Paini A, Sala Benito JV, Bessems J, Worth AP. From in vitro to in vivo: Integration of the virtual cell based assay with physiologically based kinetic modelling. Toxicol In Vitro 2017; 45:241-248. [PMID: 28663056 PMCID: PMC5742636 DOI: 10.1016/j.tiv.2017.06.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 02/26/2017] [Accepted: 06/16/2017] [Indexed: 01/01/2023]
Abstract
Physiologically based kinetic (PBK) models and the virtual cell based assay can be linked to form so called physiologically based dynamic (PBD) models. This study illustrates the development and application of a PBK model for prediction of estragole-induced DNA adduct formation and hepatotoxicity in humans. To address the hepatotoxicity, HepaRG cells were used as a surrogate for liver cells, with cell viability being used as the in vitro toxicological endpoint. Information on DNA adduct formation was taken from the literature. Since estragole induced cell damage is not directly caused by the parent compound, but by a reactive metabolite, information on the metabolic pathway was incorporated into the model. In addition, a user-friendly tool was developed by implementing the PBK/D model into a KNIME workflow. This workflow can be used to perform in vitro to in vivo extrapolation and forward as backward dosimetry in support of chemical risk assessment.
Collapse
Affiliation(s)
- Alicia Paini
- Chemical Safety and Alternative Methods Unit, EURL ECVAM, Directorate F - Health, Consumers and Reference Materials, Joint Research Centre, European Commission, Ispra, Italy.
| | - Jose Vicente Sala Benito
- Chemical Safety and Alternative Methods Unit, EURL ECVAM, Directorate F - Health, Consumers and Reference Materials, Joint Research Centre, European Commission, Ispra, Italy
| | - Jos Bessems
- Chemical Safety and Alternative Methods Unit, EURL ECVAM, Directorate F - Health, Consumers and Reference Materials, Joint Research Centre, European Commission, Ispra, Italy
| | - Andrew P Worth
- Chemical Safety and Alternative Methods Unit, EURL ECVAM, Directorate F - Health, Consumers and Reference Materials, Joint Research Centre, European Commission, Ispra, Italy
| |
Collapse
|
27
|
Sala Benito JV, Paini A, Richarz AN, Meinl T, Berthold MR, Cronin MTD, Worth AP. Automated workflows for modelling chemical fate, kinetics and toxicity. Toxicol In Vitro 2017; 45:249-257. [PMID: 28323105 PMCID: PMC5745146 DOI: 10.1016/j.tiv.2017.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 03/10/2017] [Accepted: 03/16/2017] [Indexed: 01/15/2023]
Abstract
Automation is universal in today's society, from operating equipment such as machinery, in factory processes, to self-parking automobile systems. While these examples show the efficiency and effectiveness of automated mechanical processes, automated procedures that support the chemical risk assessment process are still in their infancy. Future human safety assessments will rely increasingly on the use of automated models, such as physiologically based kinetic (PBK) and dynamic models and the virtual cell based assay (VCBA). These biologically-based models will be coupled with chemistry-based prediction models that also automate the generation of key input parameters such as physicochemical properties. The development of automated software tools is an important step in harmonising and expediting the chemical safety assessment process. In this study, we illustrate how the KNIME Analytics Platform can be used to provide a user-friendly graphical interface for these biokinetic models, such as PBK models and VCBA, which simulates the fate of chemicals in vivo within the body and in vitro test systems respectively. The VCBA is a mathematical model that simulates in vitro fate of chemicals and the corresponding cellular effect. The VCBA has been implemented in an open access web-based KNIME platform for ease of use. KNIME Analytics Platform can be used to provide a user-friendly graphical interface for biokinetic models.
Collapse
Affiliation(s)
- J V Sala Benito
- Chemical Safety and Alternative Methods Unit, EURL ECVAM, Directorate F - Health, Consumers and Reference Materials, Joint Research Centre, European Commission, Ispra, Italy
| | - Alicia Paini
- Chemical Safety and Alternative Methods Unit, EURL ECVAM, Directorate F - Health, Consumers and Reference Materials, Joint Research Centre, European Commission, Ispra, Italy.
| | - Andrea-Nicole Richarz
- Liverpool John Moores University, School of Pharmacy and Biomolecular Sciences, Byrom Street, Liverpool L3 3AF, UK
| | | | - Michael R Berthold
- Universität Konstanz, Fachbereich Informatik und Informationswissenschaft, Box 712, 78457 Konstanz, Germany
| | - Mark T D Cronin
- Liverpool John Moores University, School of Pharmacy and Biomolecular Sciences, Byrom Street, Liverpool L3 3AF, UK
| | - Andrew P Worth
- Chemical Safety and Alternative Methods Unit, EURL ECVAM, Directorate F - Health, Consumers and Reference Materials, Joint Research Centre, European Commission, Ispra, Italy
| |
Collapse
|
28
|
Patlewicz G, Casati S, Basketter DA, Asturiol D, Roberts DW, Lepoittevin JP, Worth AP, Aschberger K. Can currently available non-animal methods detect pre and pro-haptens relevant for skin sensitization? Regul Toxicol Pharmacol 2016; 82:147-155. [DOI: 10.1016/j.yrtph.2016.08.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 08/18/2016] [Indexed: 11/28/2022]
|
29
|
Abstract
A survey was carried out to explore opportunities for waiving mammalian acute systemic toxicity tests. We were interested in finding out whether data from a sub-acute toxicity test could be used to predict the outcome of an acute systemic toxicity test. The survey was directed at experts in the field of toxicity testing, and was carried out in the context of the upcoming 2018 final registration deadline for chemicals under the EU REACH Regulation. In addition to the survey, a retrospective data analysis of chemicals that had already been registered with the European Chemicals Agency, and for which both acute and sub-acute toxicity data were available, was carried out. This data analysis was focused on chemicals that were administered via the oral route. The answers to the questionnaire showed a willingness to adopt waiving opportunities. In addition, the responses showed that data from a sub-acute toxicity test or dose-range finding study might be useful for predicting chemicals that do not require classification for acute oral toxicity (LD50 > 2000mg/kg body weight). However, with the exception of substances that fall into the non-classified category, it is difficult to predict current acute oral toxicity categories.
Collapse
Affiliation(s)
- Rabea Graepel
- European Union Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM), European Commission, Joint Research Centre, Ispra, Italy
| | - David Asturiol
- European Union Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM), European Commission, Joint Research Centre, Ispra, Italy
| | - Pilar Prieto
- European Union Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM), European Commission, Joint Research Centre, Ispra, Italy
| | - Andrew P Worth
- European Union Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM), European Commission, Joint Research Centre, Ispra, Italy
| |
Collapse
|
30
|
Leontaridou M, Gabbert S, Van Ierland EC, Worth AP, Landsiedel R. Evaluation of Non-animal Methods for Assessing Skin Sensitisation Hazard: A Bayesian Value-of-Information Analysis. Altern Lab Anim 2016; 44:255-69. [DOI: 10.1177/026119291604400309] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This paper offers a Bayesian Value-of-Information (VOI) analysis for guiding the development of non-animal testing strategies, balancing information gains from testing with the expected social gains and costs from the adoption of regulatory decisions. Testing is assumed to have value, if, and only if, the information revealed from testing triggers a welfare-improving decision on the use (or non-use) of a substance. As an illustration, our VOI model is applied to a set of five individual non-animal prediction methods used for skin sensitisation hazard assessment, seven battery combinations of these methods, and 236 sequential 2-test and 3-test strategies. Their expected values are quantified and compared to the expected value of the local lymph node assay (LLNA) as the animal method. We find that battery and sequential combinations of non-animal prediction methods reveal a significantly higher expected value than the LLNA. This holds for the entire range of prior beliefs. Furthermore, our results illustrate that the testing strategy with the highest expected value does not necessarily have to follow the order of key events in the sensitisation adverse outcome pathway (AOP).
Collapse
Affiliation(s)
- Maria Leontaridou
- Wageningen University, Environmental Economics and Natural Resources Group, Wageningen, The Netherlands
- BASF SE, Experimental Toxicology and Ecology, Ludwigshafen, Germany
| | - Silke Gabbert
- Wageningen University, Environmental Economics and Natural Resources Group, Wageningen, The Netherlands
| | - Ekko C. Van Ierland
- Wageningen University, Environmental Economics and Natural Resources Group, Wageningen, The Netherlands
| | - Andrew P. Worth
- European Commission, Joint Research Centre, Directorate F — Health, Consumer and Reference Materials, EURL ECVAM, Ispra, Italy
| | | |
Collapse
|
31
|
Burton J, Worth AP, Tsakovska I, Diukendjieva A. In Silico Models for Acute Systemic Toxicity. Methods Mol Biol 2016; 1425:177-200. [PMID: 27311468 DOI: 10.1007/978-1-4939-3609-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In this chapter, we give an overview of the regulatory requirements for acute systemic toxicity information in the European Union, and we review the availability of structure-based computational models that are available and potentially useful in the assessment of acute systemic toxicity. The most recently published literature models for acute systemic toxicity are also discussed, and perspectives for future developments in this field are offered.
Collapse
Affiliation(s)
- Julien Burton
- Systems Toxicology Unit and EURL ECVAM, Institute for Health and Consumer Protection, Joint Research Centre, European Commission, Ispra, Varese, Italy
| | - Andrew P Worth
- Systems Toxicology Unit and EURL ECVAM, Institute for Health and Consumer Protection, Joint Research Centre, European Commission, Ispra, Varese, Italy.
| | - Ivanka Tsakovska
- Department of QSAR & Molecular Modeling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Antonia Diukendjieva
- Department of QSAR & Molecular Modeling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| |
Collapse
|
32
|
Abstract
In this chapter, we provide an overview of how (Quantitative) Structure Activity Relationships, (Q)SARs, are validated and applied for regulatory purposes. We outline how chemical categories are derived to facilitate endpoint specific read-across using tools such as the OECD QSAR Toolbox and discuss some of the current difficulties in addressing the residual uncertainties of read-across. Finally we put forward a perspective of how non-testing approaches may evolve in light of the advances in new and emerging technologies and how these fit within the Adverse Outcome Pathway (AOP) framework.
Collapse
Affiliation(s)
- Grace Patlewicz
- Dupont Haskell Global Centers for Health and Environmental Sciences, Newark, DE, 19711, USA.
- National Center for Computational Toxicology (NCCT), US Environmental Protection Agency (EPA), Research Triangle Park, NC, 27711, USA.
| | - Andrew P Worth
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Nicholas Ball
- Toxicology and Environmental Research and Consulting (TERC), Environment, Health and Safety (EH&S), The Dow Chemical Company, Horgen, Zurich, 8810, Switzerland
| |
Collapse
|
33
|
Norlen H, Worth AP, Gabbert S. A Tutorial for Analysing the Cost-effectiveness of Alternative Methods for Assessing Chemical Toxicity: The Case of Acute Oral Toxicity Prediction. Altern Lab Anim 2014; 42:115-27. [DOI: 10.1177/026119291404200204] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Compared with traditional animal methods for toxicity testing, in vitro and in silico methods are widely considered to permit a more cost-effective assessment of chemicals. However, how to assess the cost-effectiveness of alternative methods has remained unclear. This paper offers a user-oriented tutorial for applying cost-effectiveness analysis (CEA) to alternative (non-animal) methods. The purpose is to illustrate how CEA facilitates the identification of the alternative method, or the combination of methods, that offers the highest information gain per unit of cost. We illustrate how information gains and costs of single methods and method combinations can be assessed. By using acute oral toxicity as an example, we apply CEA to a set of four in silico methods (ToxSuite, TOPKAT, TEST, ADMET Predictor), one in vitro method (the 3T3 Neutral Red Uptake cytotoxicity assay), and various combinations of these methods. Our results underline that in silico tools are more cost-effective than the in vitro test. Battery combinations of alternative methods, however, do not necessarily outperform single methods, because additional information gains from the battery are easily outweighed by additional costs.
Collapse
Affiliation(s)
- Hedvig Norlen
- Systems Toxicology Unit and EURL ECVAM, Institute for Health and Consumer Protection, European Commission Joint Research Centre, Ispra, Varese, Italy
| | - Andrew P. Worth
- Systems Toxicology Unit and EURL ECVAM, Institute for Health and Consumer Protection, European Commission Joint Research Centre, Ispra, Varese, Italy
| | - Silke Gabbert
- Department of Social Sciences, Environmental Economics and Natural Resources Group, Wageningen University, Wageningen, The Netherlands
| |
Collapse
|
34
|
|
35
|
Hollnagel HM, Ambrosio M, Boobis AR, Cronin M, Felter SP, Keller D, Jacobs KM, Safford R, Vitcheva V, Worth AP, Yang C. TTC Task Force: Development of a cosmetics database to support application of TTC to cosmetic ingredients (EU Cosmos project). Toxicol Lett 2013. [DOI: 10.1016/j.toxlet.2013.06.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
36
|
Fioravanzo E, Bassan A, Pavan M, Mostrag-Szlichtyng A, Worth AP. Role of in silico genotoxicity tools in the regulatory assessment of pharmaceutical impurities. SAR QSAR Environ Res 2012; 23:257-277. [PMID: 22369620 DOI: 10.1080/1062936x.2012.657236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The toxicological assessment of genotoxic impurities is important in the regulatory framework for pharmaceuticals. In this context, the application of promising computational methods (e.g. Quantitative Structure-Activity Relationships (QSARs), Structure-Activity Relationships (SARs) and/or expert systems) for the evaluation of genotoxicity is needed, especially when very limited information on impurities is available. To gain an overview of how computational methods are used internationally in the regulatory assessment of pharmaceutical impurities, the current regulatory documents were reviewed. The software recommended in the guidelines (e.g. MCASE, MC4PC, Derek for Windows) or used practically by various regulatory agencies (e.g. US Food and Drug Administration, US and Danish Environmental Protection Agencies), as well as other existing programs were analysed. Both statistically based and knowledge-based (expert system) tools were analysed. The overall conclusions on the available in silico tools for genotoxicity and carcinogenicity prediction are quite optimistic, and the regulatory application of QSAR methods is constantly growing. For regulatory purposes, it is recommended that predictions of genotoxicity/carcinogenicity should be based on a battery of models, combining high-sensitivity models (low rate of false negatives) with high-specificity ones (low rate of false positives) and in vitro assays in an integrated manner.
Collapse
|
37
|
Raevsky OA, Grigor'ev VY, Liplavskaya EA, Worth AP. Prediction of Acute Rodent Toxicity on the Basis of Chemical Structure and Physicochemical Similarity. Mol Inform 2011; 30:267-75. [DOI: 10.1002/minf.201000145] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 03/04/2010] [Indexed: 11/09/2022]
Affiliation(s)
- O A Raevsky
- Institute of Physiologically Active Compounds of the Russian Academy of Sciences, 142432, Chernogolovka, Moscow region, Russia. ,
| | - V Y Grigor'ev
- Institute of Physiologically Active Compounds of the Russian Academy of Sciences, 142432, Chernogolovka, Moscow region, Russia
| | - E A Liplavskaya
- Institute of Physiologically Active Compounds of the Russian Academy of Sciences, 142432, Chernogolovka, Moscow region, Russia
| | - A P Worth
- Institute for Health and Consumer Protection, European Commission - Joint Research Centre, Via Enrico Fermi 2749, 21027 Ispra (Va), Italy
| |
Collapse
|
38
|
Affiliation(s)
- Enrico Burello
- Systems Toxicology Unit, Institute for Health and Consumer Protection, Joint Research Centre, European Commission, Ispra, Varese, Italy
| | - Andrew P. Worth
- Systems Toxicology Unit, Institute for Health and Consumer Protection, Joint Research Centre, European Commission, Ispra, Varese, Italy
| |
Collapse
|
39
|
Zaldívar JM, Marinov D, Dueri S, Castro-Jiménez J, Micheletti C, Worth AP. An integrated approach for bioaccumulation assessment in mussels: towards the development of Environmental Quality Standards for biota. Ecotoxicol Environ Saf 2011; 74:244-252. [PMID: 21040971 DOI: 10.1016/j.ecoenv.2010.10.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 08/30/2010] [Accepted: 10/16/2010] [Indexed: 05/30/2023]
Abstract
The possible use of chemical concentrations measured in mussels (Mytillus galloprovincialis) for compliance checking against Environmental Quality Standards (EQS) established for biota is analyzed with the help of an integrated model. The model consists of a 3D planktonic module that provides biomasses in the different compartments, i.e., phytoplankton, zooplankton and bacteria; a 3D fate module that provides the concentrations of contaminants in the water column and in the sediments; and a 3D bioaccumulation module that calculates internal concentrations in relevant biotic compartments. These modules feed a 0D growth and bioaccumulation module for mussels, based on the Dynamic Energy Budget (DEB) approach. The integrated model has been applied to study the bioaccumulation of persistent organic pollutants (POPs) in the Thau lagoon (France). The model correctly predicts the concentrations of polychlorinated biphenyls (PCBs) and polychlorinated dibenzodioxins and dibenzofurans (PCDD/Fs) in mussels as a function of the concentrations in the water column and in phytoplankton. It also sheds light on the origin of the complexity associated with the use of EQS for biota and their conversion to water column concentrations. The integrated model is potentially useful for regulatory purposes, for example in the context of the European Water Framework (WFD) and Marine Strategy Framework Directives (MSFD).
Collapse
Affiliation(s)
- J M Zaldívar
- European Commission, Joint Research Centre, Institute for Health and Consumer Protection, via E. Fermi 2749, 21027 Ispra (VA), Italy.
| | | | | | | | | | | |
Collapse
|
40
|
|
41
|
Poater A, Gallegos Saliner A, Solà M, Cavallo L, Worth AP. Computational methods to predict the reactivity of nanoparticles through structure-property relationships. Expert Opin Drug Deliv 2010; 7:295-305. [PMID: 20201736 DOI: 10.1517/17425240903508756] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IMPORTANCE OF THE FIELD Innovative biomedical techniques operational at the nanoscale level are being developed in therapeutics, including advanced drug delivery systems and targeted nanotherapy. Given the large number of nanoparticles that are being developed for possible biomedical use, the use of computational methods in the assessment of their properties is of key importance. AREAS COVERED IN THIS REVIEW Among the in silico methods, quantum mechanics is still used rarely in the study of nanostructured particles. This review provides an overview of some of the main quantum mechanics methods that are already used in the assessment of chemicals. Furthermore, classical tools used in the chemistry field are described, to show their potential also in the pharmacological field. WHAT THE READER WILL GAIN The current status of computational methods in terms of availability and applicability to nanoparticles, and recommendations for further research are highlighted. TAKE HOME MESSAGE The in silico modelling of nanoparticles can assist in targeting and filling gaps in knowledge on the effects of these particular particles. Computational models of the behaviour of nanoparticles in biological systems, including simulation models for predicting intermolecular interactions and harmful side effects, can be highly valuable in screening candidate particles for potential biomedical use in diagnostics, imaging and drug delivery.
Collapse
Affiliation(s)
- Albert Poater
- Institut Català de Recerca de l'Aigua (ICRA), Parc Científic i Tecnològic de la Universitat de Girona, Emili Grahit 101, Girona, Spain.
| | | | | | | | | |
Collapse
|
42
|
Mostrag-Szlichtyng A, Zaldívar Comenges JM, Worth AP. Computational toxicology at the European Commission's Joint Research Centre. Expert Opin Drug Metab Toxicol 2010; 6:785-92. [DOI: 10.1517/17425255.2010.489551] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
43
|
Raevsky OA, Grigor'ev VJ, Modina EA, Worth AP. Prediction of acute toxicity to mice by the Arithmetic Mean Toxicity (AMT) modelling approach. SAR QSAR Environ Res 2010; 21:265-275. [PMID: 20544551 DOI: 10.1080/10629361003771025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A modelling approach based on the structural and physicochemical similarity of chemicals to their nearest neighbours is proposed for toxicity estimation. This approach, called Arithmetic Mean Toxicity (AMT) modelling, is illustrated by means of an AMT model for predicting acute rodent toxicity. The AMT approach uses one or a few pairs of nearest structural neighbours. Each pair contains a chemical with a higher descriptor value and with a smaller descriptor value compared with the chemical of interest. Arithmetic mean toxicity values of those pairs are considered as toxicity of chemical of interest. The toxicity of the chemical of interest was not included in the development of the AMT model. The approach was applied to calculate the toxicity of chemicals to mice following intravenous injection. A toxicity data set containing 10,241 organic neutral compounds was formed from the SYMYX Toxicity database. The toxicity (log (1/LD(50)), mmol/kg), where LD(50) is the median lethal dose, of 10,227 chemicals was calculated with a standard deviation +/-0.52. A cascade AMT model was applied to estimate error values in calculations of toxicity of chemicals having different number structural neighbours and level of similarity. It was found that 7085 chemicals (about 69% of all chemicals in the data set) were calculated with a standard deviation in the interval (+/-0.33)-(+/-0.48), which is comparable to the experimental error of determination. For the remaining 3142 chemicals (about 31% of the data set), the standard deviation was +/-0.64. In the regulatory assessment of chemicals, the AMT approach could be used as a means of filling data gaps when experimental data are missing.
Collapse
Affiliation(s)
- O A Raevsky
- Department of Computer-Aided Molecular Design, Institute of Physiologically Active Compounds of Russian Academy of Sciences, Chernogolovka, Moscow Region, Russia.
| | | | | | | |
Collapse
|
44
|
Saliner AG, Poater A, Worth AP. Toward in silico approaches for investigating the activity of nanoparticles in therapeutic development. IDrugs 2008; 11:728-732. [PMID: 18828072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The distinctive characteristics of nanoparticles (NPs), resulting from properties that arise at the nanoscale, are stimulating the use of these particles in the biomedical sector for diagnostic and therapeutic purposes. However, these same characteristics of NPs also underlie widespread concerns regarding potential toxic effects. Given the large number of NPs that are being developed for possible biomedical use, there is a need to develop rapid screening methods based on in silico methods. This feature review provides an overview of some of the main in silico methods that are already used in the assessment of chemicals. The current status of these methods, in terms of availability and applicability to NPs, and recommendations for further research, are highlighted.
Collapse
Affiliation(s)
- Ana Gallegos Saliner
- Institut de Química Computacional, Departament de Química, Universitat de Girona, Campus de Montilivi, E-17071 Girona, Catalonia, Spain
| | | | | |
Collapse
|
45
|
Gallegos-Saliner A, Poater A, Jeliazkova N, Patlewicz G, Worth AP. Toxmatch--a chemical classification and activity prediction tool based on similarity measures. Regul Toxicol Pharmacol 2008; 52:77-84. [PMID: 18617309 DOI: 10.1016/j.yrtph.2008.05.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 05/13/2008] [Accepted: 05/20/2008] [Indexed: 11/18/2022]
Abstract
Chemical similarity forms the underlying basis for the development of (Quantitative) Structure-Activity Relationships ((Q)SARs), expert systems and chemical groupings. Recently a new software tool to facilitate chemical similarity calculations named Toxmatch was developed. Toxmatch encodes a number of similarity indices to help in the systematic development of chemical groupings, including endpoint specific groupings and read-across, and the comparison of model training and test sets. Two rule-based classification schemes were additionally implemented, namely: the Verhaar scheme for assigning mode of action for aquatic toxicants and the BfR rulebase for skin irritation and corrosion. In this study, a variety of different descriptor-based similarity indices were used to evaluate and compare the BfR training set with respect to its test set. The descriptors utilised in this comparison were the same as those used to derive the original BfR rules i.e. the descriptors selected were relevant for skin irritation/corrosion. The Euclidean distance index was found to be the most predictive of the indices in assessing the performance of the rules.
Collapse
Affiliation(s)
- Ana Gallegos-Saliner
- Institute for Health and Consumer Protection, Joint Research Centre-European Commission, 21027 Ispra (VA), Italy.
| | | | | | | | | |
Collapse
|
46
|
Hoffmann S, Saliner AG, Patlewicz G, Eskes C, Zuang V, Worth AP. A feasibility study developing an integrated testing strategy assessing skin irritation potential of chemicals. Toxicol Lett 2008; 180:9-20. [DOI: 10.1016/j.toxlet.2008.05.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Revised: 03/05/2008] [Accepted: 05/14/2008] [Indexed: 11/25/2022]
|
47
|
Patlewicz G, Jeliazkova N, Gallegos Saliner A, Worth AP. Toxmatch-a new software tool to aid in the development and evaluation of chemically similar groups. SAR QSAR Environ Res 2008; 19:397-412. [PMID: 18484504 DOI: 10.1080/10629360802083848] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Chemical similarity is a widely used concept in toxicology, and is based on the hypothesis that similar compounds should have similar biological activities. This forms the underlying basis for performing read-across, forming chemical groups and developing (Quantitative) Structure-Activity Relationships ((Q)SARs). Chemical similarity is often perceived as structural similarity but in fact there are a number of other approaches that can be used to assess similarity. A systematic similarity analysis usually comprises two main steps. Firstly the chemical structures to be compared need to be characterised in terms of relevant descriptors which encode their physicochemical, topological, geometrical and/or surface properties. A second step involves a quantitative comparison of those descriptors using similarity (or dissimilarity) indices. This work outlines the use of chemical similarity principles in the formation of endpoint specific chemical groupings. Examples are provided to illustrate the development and evaluation of chemical groupings using a new software application called Toxmatch that was recently commissioned by the European Chemicals Bureau (ECB), of the European Commission's Joint Research Centre. Insights from using this software are highlighted with specific focus on the prospective application of chemical groupings under the new chemicals legislation, REACH.
Collapse
Affiliation(s)
- G Patlewicz
- European Commission, Joint Research Centre, Institute for Health and Consumer Protection, European Chemicals Bureau (ECB), Ispra, Italy.
| | | | | | | |
Collapse
|
48
|
Abstract
To promote the availability of reliable computer-based estimation methods for use in the regulatory assessment of chemicals, the European Chemicals Bureau (ECB) within the European Commission's Joint Research Centre (JRC) has developed a range of user-friendly and freely available software tools. The article gives an overview of four of these tools, explaining their main functionalities and applicability: Toxtree, Toxmatch, DART and the JRC QSAR Model Database. Toxtree predicts different types of toxicological hazard and modes of action by applying decision tree approaches; it can be used for initial hazard assessments. Toxmatch is a tool for chemical similarity assessment; it can be used to compare model training and test sets, to facilitate the formation of chemical categories and to support the application of read-across between analogues. DART (Decision Analysis by Ranking Techniques) provides a variety of Multi-criteria Decision Making (ranking) methods, and can be used to support the ranking of chemicals according to their environmental and toxicological concern. Finally, the JRC QSAR Model Database is a web-based inventory of (Q)SAR models to help industry and government authorities to identify suitable (Q)SARs for chemicals undergoing regulatory review.
Collapse
Affiliation(s)
- M Pavan
- Institute for Health and Consumer Protection, Joint Research Centre, European Commission, Ispra (VA), Italy
| | | |
Collapse
|
49
|
Spycher S, Netzeva TI, Worth AP, Escher BI. Mode of action-based classification and prediction of activity of uncouplers for the screening of chemical inventories. SAR QSAR Environ Res 2008; 19:433-463. [PMID: 18853296 DOI: 10.1080/10629360802348803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A new approach for classification of uncouplers of oxidative and photophosphorylation, also suitable for screening of large chemical inventories, is introduced. Earlier fragment-based approaches for this mode of toxic action are limited to phenols but weak acids of extremely diverse chemical classes can act as uncouplers. The proposed approach overcomes the limitation to phenolic uncouplers by combining structural fragments with the global information of physico-chemical descriptors. In a top-down approach to reduce the number of candidate chemicals, firstly substructure definitions for the detection of weak acids were applied. Subsequently, conservative physico-chemical thresholds for the two most important properties for the uncoupling activity were defined: an acid dissociation constant (pK(a)) between 3 and 9, and a sufficiently low energy barrier for the internal permeability of anions (17 kcal/mol). The later was derived from a novel approach to calculate the distribution of compounds across membranes. The combination of structural and physico-chemical criteria allowed a good separation of active from inactive chemicals with high sensitivity (95%) and slightly lower (more than 75%) specificity. Applying this approach to several thousand high and low production volume chemicals retrieved a surprisingly small number of 10 compounds with a predicted excess toxicity above 10. Nevertheless, uncoupling can be an important mode of action as highlighted with several examples ranging from pesticide metabolites to persistent organic compounds.
Collapse
Affiliation(s)
- S Spycher
- Department of Environmental Toxicology, UTOX, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.
| | | | | | | |
Collapse
|
50
|
Patlewicz G, Jeliazkova N, Safford RJ, Worth AP, Aleksiev B. An evaluation of the implementation of the Cramer classification scheme in the Toxtree software. SAR QSAR Environ Res 2008; 19:495-524. [PMID: 18853299 DOI: 10.1080/10629360802083871] [Citation(s) in RCA: 225] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Risk assessment for most human health effects is based on the threshold of a toxicological effect, usually derived from animal experiments. The Threshold of Toxicological Concern (TTC) is a concept that refers to the establishment of a level of exposure for all chemicals below which there would be no appreciable risk to human health. When carefully applied, the TTC concept can provide a means of waiving testing based on knowledge of exposure limits. Two main approaches exist; the first of these is a General Threshold of Toxicological Concern; the second approach is a TTC in relation to structural information and/or toxicological data of chemicals. The structural scheme most routinely used is that of Cramer and co-workers from 1978. Recently this scheme was encoded into a software program called Toxtree, specifically commissioned by the European Chemicals Bureau (ECB). Here we evaluate two published datasets using Toxtree to demonstrate its concordance and highlight potential software modifications. The results were promising with an overall good concordance between the reported classifications and those generated by Toxtree. Further evaluation of these results highlighted a number of inconsistencies which were examined in turn and rationalised as far as possible. Improvements for Toxtree were proposed where appropriate. Notable of these is a necessity to update the lists of common food components and normal body constituents as these accounted for the majority of false classifications observed. Overall Toxtree was found to be a useful tool in facilitating the systematic evaluation of compounds through the Cramer scheme.
Collapse
Affiliation(s)
- G Patlewicz
- European Commission, DG Joint Research Centre, Institute for Health and Consumer Protection, Ispra, Italy.
| | | | | | | | | |
Collapse
|