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Author: Nizar Ali Al-Shar'i Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
There are 518 protein kinases encoded within the human genome [1] that control cellular signal transduction and play a major role in almost all cellular events. Aberrant kinase activity is linked to pathological conditions including cancer, inflammation, diabetes and many others, making them a tractable target for drug discovery research [2-5]. To date, most of the current medicinal chemistry efforts target the ATP binding site, which is highly conserved amongst the kinase family, and many compounds suffer from cross-activity leading to undesirable side effects and toxicity. The ability to target allosteric sites on the catalytic domain of kinases, which are less conserved compared to ATP binding sites, would therefore provide an avenue for greater selectivity. Here we propose a computational approach to identify allosteric sites in target kinases. We use a combination of molecular dynamics (MD) simulations to explore the critical structural and dynamic conformational changes of the enzymes and simple intrasequence differences (SID) analysis which identifies the major interfaces in the enzyme that may be involved in allosteric modulation. This computational approach provides not only a new method of identifying allosteric sites but also a better understanding of the mechanisms of allosteric modulation of target kinases and the structural basis for the design and development of more selective and specific small molecules inhibitors as therapeutic agents.
Author: Nizar Ali Al-Shar'i Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
There are 518 protein kinases encoded within the human genome [1] that control cellular signal transduction and play a major role in almost all cellular events. Aberrant kinase activity is linked to pathological conditions including cancer, inflammation, diabetes and many others, making them a tractable target for drug discovery research [2-5]. To date, most of the current medicinal chemistry efforts target the ATP binding site, which is highly conserved amongst the kinase family, and many compounds suffer from cross-activity leading to undesirable side effects and toxicity. The ability to target allosteric sites on the catalytic domain of kinases, which are less conserved compared to ATP binding sites, would therefore provide an avenue for greater selectivity. Here we propose a computational approach to identify allosteric sites in target kinases. We use a combination of molecular dynamics (MD) simulations to explore the critical structural and dynamic conformational changes of the enzymes and simple intrasequence differences (SID) analysis which identifies the major interfaces in the enzyme that may be involved in allosteric modulation. This computational approach provides not only a new method of identifying allosteric sites but also a better understanding of the mechanisms of allosteric modulation of target kinases and the structural basis for the design and development of more selective and specific small molecules inhibitors as therapeutic agents.
Author: Jian Zhang Publisher: Springer Nature ISBN: 9811387192 Category : Medical Languages : en Pages : 384
Book Description
The book focuses on protein allostery in drug discovery. Allosteric regulation, ʹthe second secret of lifeʹ, fine-tunes virtually most biological processes and controls physiological activities. Allostery can both cause human diseases and contribute to development of new therapeutics. Allosteric drugs exhibit unparalleled advantages compared to conventional orthosteric drugs, rendering the development of allosteric modulators as an appealing strategy to improve selectivity and pharmacodynamic properties in drug leads. The Series delineates the immense significance of protein allostery—as demonstrated by recent advances in the repertoires of the concept, its mechanistic mechanisms, and networks, characteristics of allosteric proteins, modulators, and sites, development of computational and experimental methods to predict allosteric sites, small-molecule allosteric modulators of protein kinases and G-protein coupled receptors, engineering allostery, and the underlying role of allostery in precise medicine. Comprehensive understanding of protein allostery is expected to guide the rational design of allosteric drugs for the treatment of human diseases. The book would be useful for scientists and students in the field of protein science and Pharmacology etc.
Author: Robert Laprairie Publisher: Academic Press ISBN: 0128197722 Category : Business & Economics Languages : en Pages : 214
Book Description
Allosteric Modulation of G Protein-Coupled Receptors reviews fundamental information on G protein-coupled receptors (GPCRs) and allosteric modulation, presenting original research in the area and collectively providing a comprehensive description of key issues in GPCR allosteric modulation. The book provides background on core concepts of molecular pharmacology while also introducing the most important advances and studies in the area. It also discusses key methodologies. This is an essential book for researchers and advanced students engaged in pharmacology, toxicology and pharmaceutical sciences training and research. Many of the GPCR-targeted drugs released in the past decade have specifically worked via allosteric mechanisms. Unlike direct orthosteric-acting compounds that occupy a similar receptor site to that of endogenous ligands, allosteric modulators alter GPCR-dependent signaling at a site apart from the endogenous ligand. Recent methodological and analytical advances have greatly improved our ability to understand the signaling mechanisms of GPCRs. We now know that allostery is a common regulatory mechanism for all GPCRs and not – as we once believed – unique to a few receptor subfamilies. Introduces background on core concepts of molecular pharmacology, including statistical analyses, non-linear regression, complex models and GPCR-dependent signal transduction as they relate to allosteric modulation Discusses critical advances and landmark studies, including discoveries in the area of GPCR allosteric modulation, which are reviewed for their importance in positive and negative regulation, protein-protein interactions, and small molecule drug discovery Includes key methodologies used to study allosteric modulation at the in silico, in vitro, and in vivo levels of drug discovery and characterization
Author: Jean-Paul Renaud Publisher: John Wiley & Sons ISBN: 1118900502 Category : Medical Languages : en Pages : 1367
Book Description
With the most comprehensive and up-to-date overview of structure-based drug discovery covering both experimental and computational approaches, Structural Biology in Drug Discovery: Methods, Techniques, and Practices describes principles, methods, applications, and emerging paradigms of structural biology as a tool for more efficient drug development. Coverage includes successful examples, academic and industry insights, novel concepts, and advances in a rapidly evolving field. The combined chapters, by authors writing from the frontlines of structural biology and drug discovery, give readers a valuable reference and resource that: Presents the benefits, limitations, and potentiality of major techniques in the field such as X-ray crystallography, NMR, neutron crystallography, cryo-EM, mass spectrometry and other biophysical techniques, and computational structural biology Includes detailed chapters on druggability, allostery, complementary use of thermodynamic and kinetic information, and powerful approaches such as structural chemogenomics and fragment-based drug design Emphasizes the need for the in-depth biophysical characterization of protein targets as well as of therapeutic proteins, and for a thorough quality assessment of experimental structures Illustrates advances in the field of established therapeutic targets like kinases, serine proteinases, GPCRs, and epigenetic proteins, and of more challenging ones like protein-protein interactions and intrinsically disordered proteins
Author: Richard A. Ward Publisher: Royal Society of Chemistry ISBN: 1849731748 Category : Medical Languages : en Pages : 333
Book Description
Kinase drug discovery remains an area of significant interest across academia and in the pharmaceutical industry. There are now around 13 FDA approved small molecule drugs which target kinases and many more compounds in various stages of clinical development. Although there have been a number of reviews/publications on kinase research, this book fills a gap in the literature by considering the current and future opportunities and challenges in targeting this important family of enzymes. The book is forward-looking and identifies a number of hot topics and key areas for kinase drug discovery over the coming years. It includes contributions from highly respected authors with a combined experience in the industry of well over 200 years, which has resulted in a book of great interest to the kinase field and across drug discovery more generally. Readers will gain a real insight into the huge challenges and opportunities which this target class has presented drug discovery scientists. The many chapters cover a wide breadth of topics, are well written and include high quality colour and black and white images. Topics covered include an outline of how medicinal chemistry has been able to specifically exploit this unique target class, along with reflections on the mechanisms of kinases inhibitors. Also covered is resistance to kinase inhibitors caused by amino acid mutations, case studies of kinase programs and reviews areas beyond protein kinases and beyond the human kinome. Also described are modern approaches to finding kinase leads and the book finishes with a reflection of how kinase drug discovery may progress over the coming years.
Author: Paul Shapiro Publisher: Springer Nature ISBN: 3030482839 Category : Medical Languages : en Pages : 224
Book Description
Protein kinases are fascinating enzymes that maintain the proper function of nearly every task performed by the cells of the human body. By extracting a phosphate from the energy molecule ATP and linking it to another protein, protein kinases alter the structure and ultimate function of other proteins. In this way, protein kinases help monitor the extracellular environment and integrate signaling cues that, for the most part, are beneficial for human health and survival. However, protein kinases are often dysregulated and responsible for the initiation and progression of many types of cancers, inflammatory disorders, and other diseases. Thus, decades of research have revealed much about how protein kinases are regulated and approaches to inhibit these enzymes to treat disease. However, nearly 30 years since the identification of the first clinically beneficial small molecule protein kinase inhibitor, there are only a few examples where these drugs provide sustained and durable patient responses. The goal of this book is to provide biomedical scientists, graduate, and professional degree students insight into different approaches using small molecules to block specific protein kinase functions that promote disease.
Author: Sanjeev Kumar Singh Publisher: Springer Nature ISBN: 9811589364 Category : Science Languages : en Pages : 334
Book Description
This book presents various computer-aided drug discovery methods for the design and development of ligand and structure-based drug molecules. A wide variety of computational approaches are now being used in various stages of drug discovery and development, as well as in clinical studies. Yet, despite the rapid advances in computer software and hardware, combined with the exponential growth in the available biological information, there are many challenges that still need to be addressed, as this book shows. In turn, it shares valuable insights into receptor-ligand interactions in connection with various biological functions and human diseases. The book discusses a wide range of phylogenetic methods and highlights the applications of Molecular Dynamics Simulation in the drug discovery process. It also explores the application of quantum mechanics in order to provide better accuracy when calculating protein-ligand binding interactions and predicting binding affinities. In closing, the book provides illustrative descriptions of major challenges associated with computer-aided drug discovery for the development of therapeutic drugs. Given its scope, it offers a valuable asset for life sciences researchers, medicinal chemists and bioinformaticians looking for the latest information on computer-aided methodologies for drug development, together with their applications in drug discovery.
Author: Alberto Podjarny Publisher: Royal Society of Chemistry ISBN: 1849732663 Category : Science Languages : en Pages : 373
Book Description
The binding of small ligands to biological molecules is central to most aspects of biological function. The past twenty years has seen the development of an increasing armoury of biophysical methods that not only detect such binding, but also provide varying degrees of information about the kinetics, thermodynamics and structural aspects of the process. These methods have received increasing attention with the growth in more rational approaches to drug discovery and design. This book reviews the latest advances in the application of biophysics to the study of ligand binding. It provides a complete overview of current techniques to identify ligands, characterise their binding sites and understand their binding mechanisms. Particular emphasis is given to the combined use of different techniques and their relative strengths and weaknesses. Consistency in the way each technique is described makes it easy for readers to select the most suitable protocol for their research. The introduction explains why some techniques are more suitable than others and emphasizes the possible synergies between them. The following chapters, all written by a specialist in the particular technique, focus on each method individually. The book finishes by describing how several complimentary techniques can be used together for maximum effectiveness. This book is suitable for biomolecular scientists at graduate or post-doctoral level in academia and industry. Biologists and chemists will also find it a useful introduction to the techniques available.
Author: Nizar Ali Al-Shar'i
Author: Nizar Ali Al-Shar'i
Author: Nizar Al-Shar'i (Ali)
Author: Jian Zhang
Author: Robert Laprairie
Author: Jean-Paul Renaud
Author: Richard A. Ward
Author: Paul Shapiro
Author: Sanjeev Kumar Singh
Author: Alberto Podjarny
Author: Bruce Alberts