Structure Based Drug Design

Structure-Based Drug Design brings together scientists working on different aspects of the subject, demonstrating the necessary collaboration and interdisciplinary approach to this complex area. The focus is on X-ray crystallographic and computational approaches. The general aspects of these approaches are introduced in the first six articles. The remaining articles provide examples of the application of X-ray crystallography, molecular modelling, molecular dynamics, QSAR, database analysis, and homology modelling. The papers cover a wealth of interesting problems in the design of new and enhanced pharmaceuticals.

The last decade has seen the confluence of several enabling technologies that have allowed protein crystallographic methods to live up to their true potential. Taken together, the numerous recent advances have made it possible to tackle difficult biological targets with a high probability of success: intact bacterial ribosomes have been structurally elucidated, as well as eukaryotic trans-membrane proteins like the potassium channel and GPCRs. It is now possible for medicinal chemists to have access to structural information on their latest small molecule candidates bound to the therapeutic target within days of compound synthesis, allowing structure guided ligand optimization to occur in "real time". Structure-Based Drug Discovery presents an array of methods used to generate crystal structures of biological macromolecules, how to leverage the structural information to design novel ligands anew, and how to iteratively optimize hits and convert them to leads. Written in the successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Structure-Based Drug Discovery aims to provide scientists interested in adding SBDD to their arsenal of drug discovery methods with well-honed, up-to-date methodologies.

Introducing the most recent advances in crystallography, nuclear magnetic resonance, molecular modeling techniques, and computational combinatorial chemistry, this unique, interdisciplinary reference explains the application of three-dimensional structural information in the design of pharmaceutical drugs. Furnishing authoritative analyses by world-renowned experts, Structure-Based Drug Design discusses protein structure-based design in optimizing HIV protease inhibitors and details the biochemical, genetic, and clinical data on HIV-1 reverse transcriptase presents recent results on the high-resolution three-dimensional structure of the catalytic core domain of HIV-1 integrase as a foundation for divergent combination therapy focuses on structure-based design strategies for uncovering receptor antagonists to treat inflammatory diseases demonstrates a systematic approach to the design of inhibitory compounds in cancer treatment reviews current knowledge on the Interleukin-1 (IL-1) system and progress in the development of IL-1 modulators describes the influence of structure-based methods in designing capsid-binding inhibitors for relief of the common cold and much more!

This book provides a complete snapshot of various experimental approaches to structure-based and ligand-based drug design and is illustrated with more than 200 images.

Drug design is a complex, challenging and innovative research area. Structure-based molecular design has transformed the drug discovery approach in modern medicine. Traditionally, focus has been placed on computational, structural or synthetic methods only in isolation. This one-of-akind guide integrates all three skill sets for a complete picture of contemporary structure-based design. This practical approach provides the tools to develop a high-affinity ligand with drug-like properties for a given drug target for which a high-resolution structure exists. The authors use numerous examples of recently developed drugs to present "best practice" methods in structurebased drug design with both newcomers and practicing researchers in mind. By way of a carefully balanced mix of theoretical background and case studies from medicinal chemistry applications, readers will quickly and efficiently master the basic skills of successful drug design. This book is aimed at new and active medicinal chemists, biochemists, pharmacologists, natural product chemists and those working in drug discovery in the pharmaceutical industry. It is highly recommended as a desk reference to guide students in medicinal and chemical sciences as well as to aid researchers engaged in drug design today.

This book describes some of the most exciting developments for the discovery of new drugs, such as Fragment-based methods. It contains the latest developments in technologies that can be used to obtain the 3-D structures. This book includes experimental approaches using X-ray crystallography and NMR for Fragment-based screening as well as other biophysical methods for studying protein/ligand interactions.

This book is not going to be an exhaustive survey covering all aspects of rational drug design. Instead, it is going to provide critical know-how through real-world examples. Relevant case studies will be presented and analyzed to illustrate the following: how to optimize a lead compound whether one has high or low levels of structural information; how to derive hits from competitors’ active compounds or from natural ligands of the targets; how to springboard from competitors’ SAR knowledge in lead optimization; how to design a ligand to interfere with protein-protein interactions by correctly examining the PPI interface; how to circumvent IP blockage using data mining; how to construct and fully utilize a knowledge-based molecular descriptor system; how to build a reliable QSAR model by focusing on data quality and proper selection of molecular descriptors and statistical approaches. A Practical Guide to Rational Drug Design focuses on computational drug design, with only basic coverage of biology and chemistry issues, such as assay design, target validation and synthetic routes. Discusses various tactics applicable to daily drug design Readers can download the materials used in the book, including structures, scripts, raw data, protocols, and codes, making this book suitable resource for short courses or workshops Offers a unique viewpoint on drug discovery research due to the author’s cross-discipline education background Explores the author’s rich experiences in both pharmaceutical and academic settings

A guide to applying the power of modern simulation tools to better drug design Biomolecular Simulations in Structure-based Drug Discovery offers an up-to-date and comprehensive review of modern simulation tools and their applications in real-life drug discovery, for better and quicker results in structure-based drug design. The authors describe common tools used in the biomolecular simulation of drugs and their targets and offer an analysis of the accuracy of the predictions. They also show how to integrate modeling with other experimental data. Filled with numerous case studies from different therapeutic fields, the book helps professionals to quickly adopt these new methods for their current projects. Experts from the pharmaceutical industry and academic institutions present real-life examples for important target classes such as GPCRs, ion channels and amyloids as well as for common challenges in structure-based drug discovery. Biomolecular Simulations in Structure-based Drug Discovery is an important resource that: -Contains a review of the current generation of biomolecular simulation tools that have the robustness and speed that allows them to be used as routine tools by non-specialists -Includes information on the novel methods and strategies for the modeling of drug-target interactions within the framework of real-life drug discovery and development -Offers numerous illustrative case studies from a wide-range of therapeutic fields -Presents an application-oriented reference that is ideal for those working in the various fields Written for medicinal chemists, professionals in the pharmaceutical industry, and pharmaceutical chemists, Biomolecular Simulations in Structure-based Drug Discovery is a comprehensive resource to modern simulation tools that complement and have the potential to complement or replace laboratory assays for better results in drug design.