Biomolecular Simulations in Structure-Based Drug Discovery

A timely and topical survey of modern simulation tools and their applications in real-life drug discovery, allowing for better and quicker results in structure-based drug design. The first part of this practical guide for industry professionals describes common tools used in the biomolecular simulation of drugs and their targets. A critical analysis of the accuracy of the predictions, the integration of modeling with other experimental data combined with numerous case studies from different therapeutic fields enable users to quickly adopt these new methods for their current projects. The second part then shows how these tools can be applied to drug discovery and development projects. Modeling experts from the pharmaceutical industry and from leading academic institutions present real-life examples for important target classes such as GPCRs, kinases and amyloids as well as for common challenges in structure-based drug discovery. With its inclusion of novel methods and strategies for the modeling of drug-target interactions in the framework of real-life drug discovery and development, this application-oriented reference is tailor-made for medicinal chemists and those working in the pharmaceutical industry.

Fragment-based drug discovery (FBDD) is a new paradigm in drug discovery that utilizes very small molecules – fragments of larger molecules. It is a faster, cheaper, smarter way to do drug discovery, as shown by the number of pharmaceutical companies that have embraced this approach and the biotechnology companies who use fragments as their sole source of drug discovery. Fragment-Based Drug Discovery: A Practical Approach is a guide to the techniques and practice of using fragments in drug screening. The emphasis is on practical guidance, with procedures, case studies, practical tips, and contributions from industry. Topics covered include: an introduction to fragment based drug discovery, why using fragments is a more efficient process than predominant models, and what it means to have a successful FBDD effort. setting up an FBDD project library building and production NMR in fragment screening and follow up application of protein-ligand NOE matching to the rapid evaluation of fragment binding poses target immobilized NMR screening: validation and extension to membrane proteins in situ fragment-based medicinal chemistry: screening by mass spectrometry computational approaches to fragment and substructure discovery and evaluation virtual fragment scanning: current trends, applications and web based tools fragment-based lead discovery using covalent capture methods case study from industry: the identification of high affinity beta-secretase inhibitors using fragment-based lead generation With contributions from industry experts who have successfully set up an industrial fragment-based research program, Fragment-Based Drug Discovery: A Practical Approach offers essential advice to anyone embarking on drug discovery using fragments and those looking for a new approach to screening for drugs.

From its origins as a niche technique more than 15 years ago, fragment-based approaches have become a major tool for drug and ligand discovery, often yielding results where other methods have failed. Written by the pioneers in the field, this book provides a comprehensive overview of current methods and applications of fragment-based discovery, as well as an outlook on where the field is headed. The first part discusses basic considerations of when to use fragment-based methods, how to select targets, and how to build libraries in the chemical fragment space. The second part describes established, novel and emerging methods for fragment screening, including empirical as well as computational approaches. Special cases of fragment-based screening, e. g. for complex target systems and for covalent inhibitors are also discussed. The third part presents several case studies from recent and on-going drug discovery projects for a variety of target classes, from kinases and phosphatases to targeting protein-protein interaction and epigenetic targets.

Born out of a project of the IUPAC's committee on Medicinal Chemistry and Drug Development, this reference addresses past and current strategies for successful drug analog development, extending the previously published volume by nine new analog classes and eight case studies. Like its precursor, this volume also contains a general section discussing universally applicable strategies for analog discovery and development. Spanning a wide range of therapeutic fields and chemical classes, the two volumes together constitute the first systematic approach to drug analog development. Of interest to virtually every researcher working in drug discovery and pharmaceutical chemistry.

Most drugs are analogue drugs. There are no general rules how a new drug can be discovered, nevertheless, there are some observations which help to find a new drug, and also an individual story of a drug discovery can initiate and help new discoveries. Volume III is a continuation of the successful book series with new examples of established and recently introduced drugs. The major part of the book is written by key inventors either as a case study or a study of an analogue class. With its wide range across a variety of therapeutic fields and chemical classes, this is of interest to virtually every researcher in drug discovery and pharmaceutical chemistry, and – together with the previous volumes – constitutes the first systematic approach to drug analogue development.

An essential outline of the main facets of polypharmacology in drug discovery research Extending drug discovery opportunities beyond the «one drug, one target» philosophy, a polypharmacological approach to the treatment of complex diseases is emerging as a hot topic in both industry and academic research. Polypharmacology in Drug Discovery presents an overview of the various facets of polypharmacology and how it can be applied as an innovative concept for developing medicines for treating bacterial infections, epilepsy, cancer, psychiatric disorders, and more. Filled with a collection of instructive case studies that reinforce the material and illuminate the subject, this practical guide: Covers the two-sided nature of polypharmacology—its contribution to adverse drug reactions and its benefit in certain therapeutic drug classes Addresses the important topic of polypharmacology in drug discovery, a subject that has not been thoroughly covered outside of scattered journal articles Overviews state-of-the-art approaches and developments to help readers understand concepts and issues related to polypharmacology Fosters interdisciplinary drug discovery research by embracing computational, synthetic, in vitro and in vivo pharmacological and clinical aspects of polypharmacology A clear road map for helping readers successfully navigate around the problems involved with promiscuous ligands and targets, Polypharmacology in Drug Discovery provides real examples, in-depth explanations and discussions, and detailed reviews and opinions to spark inspiration for new drug discovery projects.

The rational, structure-based approach has become standard in present-day drug design. As a consequence, the availability of high-resolution structures of target proteins is more often than not the basis for an entire drug development program. Protein structures suited for rational drug design are almost exclusively derived from crystallographic studies, and drug developers are relying heavily on the power of this method. Here, researchers from leading pharmaceutical companies present valuable first-hand information, much of it published for the first time. They discuss strategies to derive high-resolution structures for such important target protein classes as kinases or proteases, as well as selected examples of successful protein crystallographic studies. A special section on recent methodological developments, such as for high-throughput crystallography and microcrystallization, is also included. A valuable companion for crystallographers involved in protein structure determination as well as drug developers pursuing the structure-based approach for use in their daily work.

GENOME EDITING IN DRUG DISCOVERY A practical guide for researchers and professionals applying genome editing techniques to drug discovery In Genome Editing in Drug Discovery, a team of distinguished biologists delivers a comprehensive exploration of genome editing in the drug discovery process, with coverage of the technology’s history, current issues and techniques, and future perspectives and research directions. The book discusses techniques for disease modeling, target identification with CRISPR, safety studies, therapeutic editing, and intellectual property issues. The safety and efficacy of drugs and new target discovery, as well as next-generation therapeutics are also presented. Offering practical suggestions for practitioners and academicians involved in drug discovery, Genome Editing in Drug Discovery is a fulsome treatment of a technology that has become part of nearly every early step in the drug discovery pipeline. Selected contributions also include: A thorough introduction to the applications of CRISPRi and CRISPRa in drug discovery Comprehensive explorations of genome-editing applications in stem cell engineering and regenerative medicine Practical discussions of the safety aspects of genome editing with respect to immunogenicity and the specificity of CRISPR-Cas9 gene editing In-depth examinations of critical socio-economic and bioethical challenges in the CRISPR-Cas9 patent landscape Perfect for academic researchers and professionals in the biotech and pharmaceutical industries, Genome Editing in Drug Discovery will also earn a place in the libraries of medicinal chemists, biochemists, and molecular biologists.

Enables researchers to fully realize the potential to discover new pharmaceuticals among heterocyclic compounds Integrating heterocyclic chemistry and drug discovery, this innovative text enables readers to understand how and why these two fields go hand in hand in the effective practice of medicinal chemistry. Contributions from international leaders in the field review more than 100 years of findings, explaining their relevance to contemporary drug discovery practice. Moreover, these authors have provided plenty of practical guidance and tips based on their own academic and industrial laboratory experience, helping readers avoid common pitfalls. Heterocyclic Chemistry in Drug Discovery is ideal for readers who want to fully realize the almost limitless potential to discover new and effective pharmaceuticals among heterocyclic compounds, the largest and most varied family of organic compounds. The book features: Several case studies illustrating the role and application of 3, 4, 5, and 6+ heterocyclic ring systems in drug discovery Step-by-step descriptions of synthetic methods and practical techniques Examination of the physical properties for each heterocycle, including NMR data and quantum calculations Detailed explanations of the complexity and intricacies of reactivity and stability for each class of heterocycles Heterocyclic Chemistry in Drug Discovery is recommended as a textbook for organic and medicinal chemistry courses, particularly those emphasizing heterocyclic chemistry. The text also serves as a guide for medicinal and process chemists in the pharmaceutical industry, offering them new insights and new paths to explore for effective drug discovery.

Written for drug developers rather than computer scientists, this monograph adopts a systematic approach to mining scientifi c data sources, covering all key steps in rational drug discovery, from compound screening to lead compound selection and personalized medicine. Clearly divided into four sections, the first part discusses the different data sources available, both commercial and non-commercial, while the next section looks at the role and value of data mining in drug discovery. The third part compares the most common applications and strategies for polypharmacology, where data mining can substantially enhance the research effort. The final section of the book is devoted to systems biology approaches for compound testing. Throughout the book, industrial and academic drug discovery strategies are addressed, with contributors coming from both areas, enabling an informed decision on when and which data mining tools to use for one's own drug discovery project.