Computational Systems Pharmacology and Toxicology

Table of contents

Table of contents :
Content: Cover
Computational Systems Pharmacology and Toxicology
Preface
Contents
Chapter 1 —
Systems Biology Approaches in Pharmacology and Toxicology
1.1 Introduction
1.2 Systems Toxicology
1.3 Chemical Toxicities
1.3.1 Single-Target Toxicity Concepts
1.3.2 Toxicological Profiling for Potential Adverse Reactions
1.3.3 Toxicological Concepts for Safer Chemical Design
1.3.4 Biomarkers
1.4 Environmental Toxicology
1.4.1 Adverse Outcome Pathway
1.4.2 Expanding Exposure Concepts
1.4.3 Exposome
1.5 Systems and Network Pharmacology
1.5.1 Secondary Pharmacology and Off-Target Effects 1.5.2 Prediction of Potential Adverse Effects1.6 Conclusions
References
Chapter 2 —
Databases Facilitating Systems Biology Approaches in Toxicology
2.1 Introduction
2.2 Categorized Lists of Databases for Systems Toxicology
2.2.1 TOXNET Databases (Including Those with Direct Links from TOXNET)
2.2.2 US EPA Chemical Toxicity Databases
2.2.3 National Toxicology Program Databases
2.2.4 Additional Toxicity Databases
2.2.5 Chemical-Gene-Protein Databases
2.2.6 Pathway-Network Databases
2.2.7 Chemistry, Structural Alert, and QSAR Databases and Tools
2.2.8 Drug and Drug Target Databases 2.3 Websites with Extensive Links to Databases and Tools2.4 Conclusions
References
Chapter 3 —
Tools for Green Molecular Design to Reduce Toxicological Risk
3.1 Introduction
3.2 Physiochemical, Genotoxicity, and Blood-Brain Barrier Passage Properties of Chemicals
3.3 Tools for Green Molecular Design
3.3.1 Expert Systems
3.3.2 Decision Trees
3.3.3 QSAR Tools
3.3.4 Representative Tools
3.3.4.1 ACD Percepta (www.acdlabs.com)
3.3.4.2 ADMET Predictor (www.simulations-plus.com)
3.3.4.3 Medchem Designer
3.3.4.4 Derek and Meteor Nexus from Lhasa Limited (www.lhasalimited.org) 3.3.4.5 Qikprop (www.schrodinger.com/QikProp)3.3.4.6 OECD QSAR Toolbox
3.3.4.7 Toxtree (http://toxtree.sourceforge.net/)
3.3.4.8 Chemaxon Suite (Marvin Sketch and Metabolizer) (www.chemaxon.com/)
3.3.4.9 Chemicalize (www.chemicalize.com)
3.3.4.10 AIM (Analog Identification Methodology) (http://www.epa.gov/tsca-screening-tools/analog-identification-methodology-aim-t…
3.3.4.11 Chemspider (www.chemspider.com)
3.3.4.12 Mobyle@RPBS (http://mobyle.rpbs.univ-paris-diderot.fr)
3.4 Case Study
3.5 The Design of Ideal Tools for Chemists
3.6 Conclusions
References Chapter 4 —
Linking Environmental Exposure to Toxicity†4.1 Introduction
4.2 The AOP Framework: An Organizing Principle for Toxicological Data
4.2.1 AOP Knowledge Management
4.2.2 Phases of AOP Development
4.2.3 Data Resources for AOP Development
4.3 Environmental Exposure and Pharmacokinetic Considerations for Adverse Outcome Development
4.4 The AEP Framework: An Organizing Principle for Exposure Data
4.4.1 Data resources for AEP development
4.5 AEP-AOP Integration for Linking Toxicity to Exposure: Applications of the AOP and AEP Frameworks for Risk Assessments and Che…