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PREFACE PART ONE: Principles BIOISOSTERISM IN MEDICINAL CHEMISTRY Introduction Isosterism Bioisosterism Bioisosterism in Lead Optimization Conclusions CLASSICAL BIOISOSTERES Introduction Historical Background Classical Bioisosteres Nonclassical Bioisosteres Summary CONSEQUENCES OF BIOISOSTERIC REPLACEMENT Introduction Bioisosteric Groupings to Improve Permeability Bioisosteric Groupings to Lower Intrinsic Clearance Bioisosteric Groupings to Improve Target Potency Conclusions and Future Perspectives PART TWO: Data BIOSTER: A DATABASE OF BIOISOSTERES AND BIOANALOGUES Introduction Historical Overview and the Development of BIOSTER Description of BIOSTER Database Examples Applications Summary Appendix MINING THE CAMBRIDGE STRUCTURAL DATABASE FOR BIOISOSTERES Introduction The Cambridge Structural Database The Cambridge Structural Database System The Relevance of the CSD to Drug Discovery Assessing Bioisosteres: Conformational Aspects Assessing Bioisosteres: Nonbonded Interactions Finding Bioisosteres in the CSD: Scaffold Hopping and Fragment Linking A Case Study: Bioisosterism of 1H–Tetrazole and Carboxylic Acid Groups Conclusions MINING FOR CONTEXT–SENSITIVE BIOISOSTERIC REPLACEMENTS IN LARGE CHEMICAL DATABASES Introduction Definitions Background Materials and Methods Results and Discussion Conclusions PART THREE: Methods PHYSICOCHEMICAL PROPERTIES Introduction Methods to Identify Bioisosteric Analogues Descriptors to Characterize Properties of Substituents and Spacers Classical Methods for Navigation in the Substituent Space Tools to Identify Bioisosteric Groups Based on Similarity in Their Properties Conclusions MOLECULAR TOPOLOGY Introduction Controlled Fuzziness Graph Theory Data Mining Topological Pharmacophores Reduced Graphs Summary MOLECULAR SHAPE Methods Applications Future Prospects PROTEIN STRUCTURE Introduction Database of Ligand – Protein Complexes Generation of Ideas for Bioisosteres Context–Specific Bioisostere Generation Using Structure to Understand Common Bioisosteric Replacements Conclusions PART FOUR: Applications THE DRUG GURU PROJECT Introduction Implementation of Drug Guru Bioisosteres Application of Drug Guru Quantitative Assessment of Drug Guru Transformations Related Work Summary: The Abbott Experience with the Drug Guru Project BIOISOSTERES OF AN NPY–Y5 ANTAGONIST Introduction Background Potential Bioisostere Approaches Template Molecule Preparation Database Molecule Preparation Alignment and Scoring Results and Monomer Selection Synthesis and Screening Discussion SAR and Developability Optimization Summary and Conclusion PERSPECTIVES FROM MEDICINAL CHEMISTRY Introduction Pragmatic Bioisostere Replacement in Medicinal Chemistry: A Software Maker.s Viewpoint The Role of Quantum Chemistry in Bioisostere Prediction Learn from ''Naturally Drug–Like'' Compounds Bioisosterism at the University of Sheffield