Computational Systems Toxicology

This detailed volume explores key state-of-the-art computational applications that are crucial in Systems Toxicology. The recent technological developments in experimental biology and multi-omics measurements that enable Systems Biology and Systems Toxicology can only be fully leveraged by the application of a broad range of computational approaches ranging from data management to mathematical modeling. Taking this into account, chapters in this book cover data management and processing, data analysis, biological network building and analysis, as well as the application of computational methods to toxicological assessment. Written for the Methods in Pharmacology and Toxicology series, Computational Systems Toxicology includes the kind of key practical advice that will aid readers in furthering our knowledge of toxic substances and reactions to them.

The network approaches of systems pharmacology and toxicology serve as early predictors of the most relevant screening approach to pursue both in drug discovery and development and ecotoxicological assessments. Computational approaches have the potential to improve toxicological experimental design, enable more rapid drug efficacy and safety testing and also reduce the number of animals used in experimentation. Rapid advances in availability of computing technology hold tremendous promise for advancing applied and basic science and increasing the efficiency of risk assessment. This book provides an understanding of the basic principles of computational toxicology and the current methods of predictive toxicology using chemical structures, toxicity-related databases, in silico chemical-protein docking, and biological pathway tools. The book begins with an introduction to systems pharmacology and toxicology and computational tools followed by a section exploring modelling adverse outcomes and events. The second part of the book covers the discovery of protein targets and the characterisation of toxicant-protein interactions. Final chapters include case studies and additionally discuss interactions between phytochemicals and Western therapeutics. This book will be useful for scientists involved in environmental research and risk assessment. It will be a valuable resource for postgraduate students and researchers wishing to learn about key methods used in studying biological targets both from a toxicity and pharmacological activity standpoint.

This book provides a comprehensive review of both traditional and cutting-edge methodologies that are currently used in computational toxicology and specifically features its application in regulatory decision making. The authors from various government agencies such as FDA, NCATS and NIEHS industry, and academic institutes share their real-world experience and discuss most current practices in computational toxicology and potential applications in regulatory science. Among the topics covered are molecular modeling and molecular dynamics simulations, machine learning methods for toxicity analysis, network-based approaches for the assessment of drug toxicity and toxicogenomic analyses. Offering a valuable reference guide to computational toxicology and potential applications in regulatory science, this book will appeal to chemists, toxicologists, drug discovery and development researchers as well as to regulatory scientists, government reviewers and graduate students interested in this field.

Systems Biology in Toxicology and Environmental Health uses a systems biological perspective to detail the most recent findings that link environmental exposures to human disease, providing an overview of molecular pathways that are essential for cellular survival after exposure to environmental toxicants, recent findings on gene-environment interactions influencing environmental agent-induced diseases, and the development of computational methods to predict susceptibility to environmental agents. Introductory chapters on molecular and cellular biology, toxicology and computational biology are included as well as an assessment of systems-based tools used to evaluate environmental health risks. Further topics include research on environmental toxicants relevant to human health and disease, various high-throughput technologies and computational methods, along with descriptions of the biological pathways associated with disease and the developmental origins of disease as they relate to environmental contaminants. Systems Biology in Toxicology and Environmental Health is an essential reference for undergraduate students, graduate students, and researchers looking for an introduction in the use of systems biology approaches to assess environmental exposures and their impacts on human health. Provides the first reference of its kind, demonstrating the application of systems biology in environmental health and toxicology Includes introductions to the diverse fields of molecular and cellular biology, toxicology, and computational biology Presents a foundation that helps users understand the connections between the environment and health effects, and the biological mechanisms that link them

Computational Toxicology: Methods and Applications for Risk Assessment is an essential reference on the translation of computational toxicology data into information that can be used for more informed risk assessment decision-making. This book is authored by leading international investigators who have real-world experience in relating computational toxicology methods to risk assessment. Key topics of interest include QSAR modeling, chemical mixtures, applications to metabolomic and metabonomic data sets, toxicogenomic analyses, applications to REACH informational strategies and much more. The examples provided in this book are based on cutting-edge technologies and set out to stimulate the further development of this promising field to offer rapid, better and more cost-effective answers to major public health concerns. Authored by leading international researchers engaged in cutting-edge applications of computational methods for translating complex toxicological data sets into useful risk assessment information Incorporates real-world examples of how computational toxicological methods have been applied to advance the science of risk assessment Provides the framework necessary for new technologies and fosters common vocabularies and principles upon which the effects of new chemical entities should be compared

A comprehensive analysis of state-of-the-art molecular modeling approaches and strategies applied to risk assessment for pharmaceutical and environmental chemicals This unique volume describes how the interaction of molecules with toxicologically relevant targets can be predicted using computer-based tools utilizing X-ray crystal structures or homology, receptor, pharmacophore, and quantitative structure activity relationship (QSAR) models of human proteins. It covers the in vitro models used, newer technologies, and regulatory aspects. The book offers a complete systems perspective to risk assessment prediction, discussing experimental and computational approaches in detail, with: * An introduction to toxicology methods and an explanation of computational methods * In-depth reviews of QSAR methods applied to enzymes, transporters, nuclear receptors, and ion channels * Sections on applying computers to toxicology assessment in the pharmaceutical industry and in the environmental arena * Chapters written by leading international experts * Figures that illustrate computational models and references for further information This is a key resource for toxicologists and scientists in the pharmaceutical industry and environmental sciences as well as researchers involved in ADMET, drug discovery, and technology and software development.

A key resource for toxicologists across a broad spectrum of fields, this book offers a comprehensive analysis of molecular modelling approaches and strategies applied to risk assessment for pharmaceutical and environmental chemicals. Provides a perspective of what is currently achievable with computational toxicology and a view to future developments Helps readers overcome questions of data sources, curation, treatment, and how to model / interpret critical endpoints that support 21st century hazard assessment Assembles cutting-edge concepts and leading authors into a unique and powerful single-source reference Includes in-depth looks at QSAR models, physicochemical drug properties, structure-based drug targeting, chemical mixture assessments, and environmental modeling Features coverage about consumer product safety assessment and chemical defense along with chapters on open source toxicology and big data

This book is intended to be an introduction to various applications of computational toxicology and to show how these approaches are currently being used effectively for risk assessment purposes in the near term. It is important to note that the field of computational toxicology is rapidly evolving and that subsequent editions of this book will take up new methods that are currently under development, such as high-throughput screening, and others that are still in a conceptual stage. There are many advantages for including computational toxicology approaches in the risk assessment process. Among these are reducing costs, minimizing use of animals in toxicology testing, improving speed in providing answers regarding chemicals in emergency situations such as the Gulf Oil spill, and dealing with the common problem of decision making for chemical mixtures. In addition, computational methods may be used for extrapolating or translating data from both in vitro and in vivo experimental animal test systems for human risk assessments of chemicals and drugs. In addition, computational methods may be used for focusing laboratory studies into productive areas by data mining the published literature and developing testable hypotheses by application of systems biology approaches to identify chemical interactions with functional molecular pathways to generate a more comprehensive picture of likely primary and secondary modes of chemical or drug activity. In summary, there is much that computational toxicology is now contributing to helping make better societal risk assessment decisions about chemicals and drugs. The future for these approaches is optimistic and limited only by human ingenuity and availability of resources.