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Sotriffer, Christoph (Herausgeber)

Virtual Screening Principles, Challenges, and Practical Guidelines (Gebundene Ausgabe)

Reihe: Methods and Principles in Medicinal Chemistry 48

Wiley VCH Verlag GmbH, Wiley-VCH, Januar 2011

519 S. - Sprache: Englisch - 52 schwarz-weiße und 49 farbige Abbildungen, 26 schwarz-weiße Tabellen - 250x182x30 mm

ISBN: 3527326367 EAN: 9783527326365

Drug discovery is all about finding small molecules that interact in a desired way with larger molecules, namely proteins and other macromolecules in the human body. If the three-dimensional structures of both the small and large molecule are known, their interaction can be tested by computer simulation with a reasonable degree of accuracy. Alternatively, if active ligands are already available, molecular similarity searches can be used to find new molecules. This virtual screening can even be applied to compounds that have yet to be synthesized, as opposed to "real" screening that requires cost- and labor-intensive laboratory testing with previously synthesized drug compounds. Unique in its focus on the end user, this is a real "how to" book that does not presuppose prior experience in virtual screening or a background in computational chemistry. It is both a desktop reference and practical guide to virtual screening applications in drug discovery, offering a comprehensive and up-to-date overview. Clearly divided into four major sections, the first provides a detailed description of the methods required for and applied in virtual screening, while the second discusses the most important challenges in order to improve the impact and success of this technique. The third and fourth, practical parts contain practical guidelines and several case studies covering the most important scenarios for new drug discovery, accompanied by general guidelines for the entire workflow of virtual screening studies. Throughout the text, medicinal chemists from academia, as well as from large and small pharmaceutical companies report on their experience and pass on priceless practical advice on how to make best use of these powerful methods.

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Preface PART I: Principles VIRTUAL SCREENING OF CHEMICAL SPACE: FROM GENERIC COMPOUND COLLECTIONS TO TAILORED SCREENING LIBRARIES Introduction Concepts of Chemical Space Concepts of Druglikeness and Leadlikeness Diversity-Based Libraries Focused Libraries Virtual Combinatorial Libraries and Fragment Spaces Databases of Chemical and Biological Information Conclusions and Outlook Glossary PREPARING AND FILTERING COMPOUND DATABASES FOR VIRTUAL AND EXPERIMENTAL SCREENING Introduction Ligand Databases Considering Physicochemical Properties Undesirables Property-Based Filtering for Selected Targets Summary LIGAND-BASED VIRTUAL SCREENING Introduction Descriptors Search Databases and Queries Virtual Screening Techniques Conclusions THE BASIS FOR TARGET-BASED VIRTUAL SCREENING: PROTEIN STRUCTURES Introduction Selecting a Protein Structure for Virtual Screening Setting Up a Protein Model for vHTS Summary Glossary of Crystallographic Terms PHARMACOPHORE MODELS FOR VIRTUAL SCREENING Introduction Compilation of Compounds Pharmacophore Model Generation Validation of Pharmacophore Models Pharmacophore-Based Screening Postprocessing of Pharmacophore-Based Screening Hits Pharmacophore-Based Parallel Screening Application Examples for Synthetic Compound Screening Application Examples for Natural Product Screening Conclusions DOCKING METHODS FOR VIRTUAL SCREENING: PRINCIPLES AND RECENT ADVANCES Principles of Molecular Docking Docking-Based Virtual Screening Flowchart Recent Advances in Docking-Based VS Methods Future Trends in Docking PART II: Challenges THE CHALLENGE OF AFFINITY PREDICTION: SCORING FUNCTIONS FOR STRUCTURE-BASED VIRTUAL SCREENING Introduction Physicochemical Basis of Protein-Ligand Recognition Classes of Scoring Functions Interesting New Approaches to Scoring Functions Comparative Assessment of Scoring Functions Tailoring Scoring Strategies in Virtual Screening Caveats for Development of Scoring Functions Conclusion PROTEIN FLEXIBILITY IN STRUCTURE-BASED VIRTUAL SCREENING: FROM MODELS TO ALGORITHMS How Flexible Are Proteins? - A Historical Perspective Flexible Protein Handling in Protein-Ligand Docking Flexible Protein Handling in Docking-Based Virtual Screening Summary HANDLING PROTEIN FLEXIBILITY IN DOCKING AND HIGH-THROUGHPUT DOCKING: FROM ALGORITHMS TO APPLICATIONS Introduction: Docking and High-Throughput Docking in Drug Discovery The Challenge of Accounting for Protein Flexibility in Docking Accounting for Protein Flexibility in Docking-Based Drug Discovery and Design Conclusions CONSIDERATION OF WATER AND SOLVATION EFFECTS IN VIRTUAL SCREENING Introduction Experimental Approaches for Analyzing Water Molecules Computational Approaches for Analyzing Water Molecules Water-Sensitive Virtual Screening: Approaches and Applications Conclusions and Recommendations PART III: Applications and Pracitcal Guidelines APPLIED VIRTUAL SCREENING: STRATEGIES, RECOMMENDATIONS, AND CAVEATS Introduction What Is Virtual Screening? Spectrum of Virtual Screening Approaches Molecular Similarity as a Foundation and Caveat of Virtual Screening Goals of Virtual Screening Applicability Domain Reference and Database Compounds Biological Activity versus Compound Potency Methodological Complexity and Compound Class Dependence Search Strategies and Compound Selection Virtual and High-Throughput Screening Practical Applications: An Overview LFA-1 Antagonist Selectivity Searching Concluding Remarks APPLICATIONS AND SUCCESS STORIES IN VIRTUAL SCREENING Introduction Practical Considerations Successful Applications of Virtual Screening Conclusions PART IV: Scenarios and Case Studies: Routes to Success SCENARIOS AND CASE STUDIES: EXAMPLES FOR LIGAND-BASED VIRTUAL SCREENING Introduction 1D Ligand-Based Virtual Screening 2D Ligand-Based Virtual Screening 3D Ligand-Based Virtual Screening Summary VIRTUAL SCREENING ON HOMOLOGY MODELS Introduction Homology Models versus Crystal Structures: Comparative Evaluation of Screening Performance Challenges of Homology Model-Based Virtual Screening Case Studies TARGET-BASED VIRTUAL SCREENING ON SMALL-MOLECULE PROTEIN BINDING SITES Introduction Structure-Based VS for Histone Arginine Methyltransferase PRMT1 Inhibitors Identification of Nanomolar Histamine H3 Receptor Antagonists by Structure- and Pharmacophore-Based VS Summary TARGET-BASED VIRTUAL SCREENING TO ADDRESS PROTEIN-PROTEIN INTERFACES Introduction Some Recent PPIM Success Stories Protein-Protein Interfaces PPIM's Chemical Space and ADME/Tox Properties Drug Discovery, Chemical Biology, and In Silico Screening Methods: Overview and Suggestions for PPIM Search Case Studies Conclusions and Future Directions FRAGMENT-BASED APPROACHES IN VIRTUAL SCREENING Introduction In Silico Fragment-Based Approaches Our Approach to High-Throughput Fragment-Based Docking Lessons Learned from Our Fragment-Based Docking Challenges of Fragment-Based Approaches APPENDIX Software Overview Virtual Screening Application Studies

Über den Autor

Christoph Sotriffer is Professor for Pharmaceutical Chemistry at the University ofWürzburg, Germany. He graduated as a chemist from the University of Innsbruck, Austria, where he obtained his PhD in 1999. After conducting postdoctoral research at the University of California, San Diego, USA, and the University of Marburg, Germany, he moved to the University ofWürzburg in 2006, where he has built a research group for computational medicinal chemistry. Besides structure-based drug design and virtual screening, his prime scientific interest is the computational analysis and prediction of protein-ligand interactions. His work was awarded by the Austrian Chemical Society GÖCH in 2005 and the German Chemical and Pharmaceutical Societies GDCh and DPhG in 2007.


"Virtual Screening is a comprehensive and up-to-date overview, this is both a desktop reference and practical guide for virtual screening applications in drug discovery". (Laboratory Journal, 18 January 2011)

ISBN 3-527-32636-7

ISBN 978-3-527-32636-5

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