In Silico methods to predict toxicity have become increasingly important recently, particularly in light of European legislation such as REACH and the Cosmetics Regulation. They are also being used extensively worldwide e.g. in the USA, Canada, Japan and Australia. In assessing the risk that a chemical may pose to human health or to the environment, focus is now being directed towards exploitation of in silico methods to replace in vivo or in vitro techniques. A prediction of potential toxicity requires several stages: 1) Collation and organisation of data available for the compound, or if this is not available, information for related compounds. 2) An assessment of the quality of the data. 3) Generation of additional information about the compound using computational techniques at various levels of complexity - calculation of physico-chemical properties, 2-D, 3-D / MO descriptors and specific receptor modelling / interaction. 4) Use of an appropriate strategy to predict toxicity - ie a statistically valid method which makes best use of all available information (mechanism of action, activity for related compounds, extrapolation across species and endpoints, likely exposure scenario amounts over time etc). 5) Consideration then needs to be given to how this information is used in the real world ie use of expert systems / tools as relevant to assessors (if sufficiently different to previous) - weight of evidence approaches. 6) Finally evidence should be presented from case studies within this area. No other publication brings together information on all of these areas in one book and this publication is unique in that it provides a logical progression through every one of these key stages and defines the use of computational approaches to predict the environmental toxicity and human health effects of organic chemicals. The volume is aimed at the developers and users of in silico toxicology and provides an analysis of all aspects required for in silico prediction of toxicology, including data collation, quality assessment and computational approaches. The contributions from recognised leaders in each of these areas include evidence of the use and applicability of approaches using real world case studies concerning both environmental and human health effects. The book provides a very useful single source reference for people working in this area including academics, professionals, under- and post-graduate students as well as Governmental Regulatory Scientists involved in chemical risk assessment and REACH.
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Mark Cronin is Professor of Predictive Toxicology at the Liverpool John Moores University. He has a BSc in Applied Biology and a PhD in Environmental QSAR and has co-edited 1 book and over 150 papers. He was the co-organiser of the 11th International Workshop on the Human Health and Environmental Sciences, Liverpool, May 2004 as well as a number of one day meetings at the Society of Chemical Industry, London. Judith Madden is a Senior Lecturer in Pharmaceutical and Chemical Sciences at the Liverpool John Moores University. She has a BSc in Chemistry and Pharmacology and a PhD in QSAR and Drug Design and over 25 publications to her name. She was the co-organiser of the 11th International Workshop on the Human Health and Environmental Sciences, Liverpool, May 2004 and the SETAC-UK Annual Meeting, Liverpool, September 2006.
In silico methods to predict toxicity are becoming increasingly important, particularly in light of European legislation such as REACH and the Cosmetics Regulation. They are also being used extensively worldwide e.g. in the USA, Canada, Japan and Australia. The objective of In Silico Toxicology: Principles and Applications is to enable the reader to develop new, and use existing, in silico methods to predict the toxicity and fate of chemicals. It develops the theme in a logical sequence leading the user through the retrieval, and assessment of quality, of toxicological data and information; the calculation of descriptors and properties; the basis of statistical techniques for quantitative structure-activity relationships (QSARs); the interpretation and validation of models for regulatory use; the mechanistic basis to modelling; as well as chemical grouping approaches and application of the models for risk assessment. The book also addresses other aspects of in silico toxicology including how to predict both external and internal exposure and the role of in silico approaches in integrated testing strategies. The contributions from recognised leaders in each of these areas include evidence of the use and applicability of approaches using real world case studies concerning both environmental and human health effects. The book is relevant to toxicologists and modellers using in silico toxicological approaches to perform risk assessment for regulatory purposes and product development.
In silico methods to predict toxicity are becoming increasingly important, particularly in light of European legislation such as REACH and the Cosmetics Regulation. They are also being used extensively worldwide e.g. in the USA, Canada, Japan and Australia. The objective of In Silico Toxicology: Principles and Applications is to enable the reader to develop new, and use existing, in silico methods to predict the toxicity and fate of chemicals. It develops the theme in a logical sequence leading the user through the retrieval, and assessment of quality, of toxicological data and information; the calculation of descriptors and properties; the basis of statistical techniques for quantitative structure-activity relationships (QSARs); the interpretation and validation of models for regulatory use; the mechanistic basis to modelling; as well as chemical grouping approaches and application of the models for risk assessment. The book also addresses other aspects of in silico toxicology including how to predict both external and internal exposure and the role of in silico approaches in integrated testing strategies. The contributions from recognised leaders in each of these areas include evidence of the use and applicability of approaches using real world case studies concerning both environmental and human health effects. The book is relevant to toxicologists and modellers using in silico toxicological approaches to perform risk assessment for regulatory purposes and product development.
Chapter 1 In Silico Toxicology — An Introduction M. T. D. Cronin and J. C. Madden, 1,
Chapter 2 Introduction to QSAR and Other In Silico Methods to Predict Toxicity J. C. Madden, 11,
Chapter 3 Finding the Data to Develop and Evaluate (Q)SARs and Populate Categories for Toxicity Prediction M. T. D. Cronin, 31,
Chapter 4 Data Quality Assessment for In Silico Methods: A Survey of Approaches and Needs M. Nendza, T. Aldenberg, E. Benfenati, R. Benigni, M.T.D. Cronin, S. Escher, A. Fernandez, S. Gabbert, F. Giralt, M. Hewitt, M. Hrovat, S. Jeram, D. Kroese, J. C. Madden, I. Mangelsdorf, R. Rallo, A. Roncaglioni, E. Rorije, H. Segner, B. Simon-Hettich and T. Vermeire, 59,
Chapter 5 Calculation of Physico-Chemical and Environmental Fate Properties T. H. Webb and L. A. Morlacci, 118,
Chapter 6 Molecular Descriptors from Two-Dimensional Chemical Structure U. Maran, S. Sild, I. Tulp, K. Takkis and M. Moosus, 148,
Chapter 7 The Use of Frontier Molecular Orbital Calculations in Predictive Reactive Toxicology S. J. Enoch, 193,
Chapter 8 Three-Dimensional Molecular Modelling of Receptor-Based Mechanisms in Toxicology J. C. Madden and M. T. D. Cronin, 210,
Chapter 9 Statistical Methods for Continuous Measured Endpoints in In Silico Toxicology P. H. Rowe, 228,
Chapter 10 Statistical Methods for Categorised Endpoints in In Silico Toxicology P. H. Rowe, 252,
Chapter 11 Characterisation, Evaluation and Possible Validation of In Silico Models for Toxicity: Determining if a Prediction is Valid M. T. D. Cronin, 275,
Chapter 12 Developing the Applicability Domain of In Silico Models: Relevance, Importance and Methods M. Hewitt and C. M. Ellison, 301,
Chapter 13 Mechanisms of Toxic Action in In Silico Toxicology D. W. Roberts, 334,
Chapter 14 Adverse Outcome Pathways: A Way of Linking Chemical Structure to In Vivo Toxicological Hazards T. W. Schultz, 346,
Chapter 15 An Introduction to Read-Across for the Prediction of the E.ects of Chemicals S. Dimitrov and O. Mekenyan, 372,
Chapter 16 Tools for Category Formation and Read-Across: Overview of the OECD (Q)SAR Application Toolbox R. Diderich, 385,
Chapter 17 Open Source Tools for Read-Across and Category Formation N. Jeliazkova, J. Jaworska and A. P. Worth, 408,
Chapter 18 Biological Read-Across: Mechanistically-Based Species–Species and Endpoint–Endpoint Extrapolations M. T. D. Cronin, 446,
Chapter 19 Expert Systems for Toxicity Prediction J. C. Dearden, 478,
Chapter 20 Exposure Modelling for Risk Assessment J. Marquart, 508,
Chapter 21 Toxicokinetic Considerations in Predicting Toxicity J. C. Madden, 531,
Chapter 22 Multiple Test In Silico Weight-of-Evidence for Toxicological Endpoints T. Aldenberg and J. S. Jaworska, 558,
Chapter 23 Integrated Testing Strategies and the Prediction of Toxic Hazard M. Balls, 584,
Chapter 24 Using In Silico Toxicity Predictions: Case Studies for Skin Sensitisation M. T. D. Cronin and J. C. Madden, 606,
Appendix 1, 624,
Appendix 2, 645,
Subject Index, 659,
In Silico Toxicology — An Introduction
M. T. D. CRONIN AND J. C. MADDEN
School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
1.1 Introduction
Chemistry is a vital part of everyday life. In order for our interactions with chemicals to be safe, we must understand their properties. Traditional methods to determine the safety of chemicals are centred around toxicological assessment and testing, often using animals. There is, however, great interest and a need to develop alternatives to the traditional testing regime. Given the breadth and complexity of toxicological endpoints it is likely that, to ensure the safety of all chemicals, a variety of techniques will be required. This will require a paradigm shift in thinking, both in terms of acceptance of alternatives and the recognition that these alternatives will seldom be 'one for one' replacements.
In silico toxicology is viewed as one of the alternatives to animal testing. It is a broad term that is taken, in this book, to indicate a variety of computational techniques which relate the structure of a chemical to its toxicity or fate. The purpose of in silico toxicology is to provide techniques to retrieve relevant data and/or make predictions regarding the fate and effects of chemicals. In this sense the term 'in silico' is used in the same manner as in vitro and in vivo, with 'silico' relating to the computational nature of the work. There are, obviously, many advantages to in silico techniques, including their cost-effectiveness, speed compared with traditional testing, and reduction in animal use.
The science of in silico toxicology encompasses many techniques. These include:
• Use of existing data. If suitable data exist for a compound, there should be no requirement to initiate a new test or make a new prediction (unless prediction is for the purposes of model validation). If data are lacking for the chemical of interest, then other data can be used to develop (and subsequently evaluate) a new predictive model. Data sources include the ever increasing number of available databases as well as the open scientific literature. In addition, those working in industry may be able to utilise their own in-house data. More details on the retrieval and use of existing data are given in Chapter 3.
• Structure–activity relationships (SARs) are qualitative and can be used to demonstrate that a fragment of a molecule or a sub-structural feature is associated with a particular event. SARs become particularly powerful if they are formalised into structural alerts. A structural alert can be used to associate a particular toxicity endpoint with a specific molecular fragment such that, if the fragment is present in a new molecule, that molecule may elicit the same toxicity. The use of SARs and structural fragments is discussed in more detail in Chapters 8, 13, 16 and 19.
• There is a strong theme in this book towards forming groups of similar molecules. These groupings are also termed chemical categories. There are a number of approaches to 'categorise' a molecule including mechanistic profilers (structural alerts) and chemical similarity. Once a robust group of structures has been formed, it can be populated with toxicity data for those members of the group where experimental measurements are available. This allows for a read-across approach to be used to predict the toxicity of those members of the group for which no data are available. Various strategies for category formation and read across are discussed in Chapters 13–17.
• Quantitative structure–activity relationships (QSARs) provide a statistical relationship between the effects (toxicity and fate) of a chemical and its physico-chemical properties and structural characteristics. Linear regression analysis is often used but a variety of other multivariate statistical techniques are also used. The generation and use of QSARs are discussed in many chapters in this book.
• Expert systems (in the sense of in silico toxicology used in this book) are formalised and computerised...
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