Computational Methods for GPCR Drug Discovery

Computational Methods for GPCR Drug Discovery
Author: Alexander Heifetz
Publisher: Humana Press
Total Pages: 436
Release: 2017-11-30
Genre: Medical
ISBN: 9781493974641

This volume looks at modern computational strategies and techniques used in GPCR drug discovery including structure and ligand-based approaches and cheminformatics. The chapters in this book describe how these approaches can be applied to address key drug discovery issues, such as receptor structure modelling, function and dynamics, prediction of protein-water-ligand interactions and binding kinetics, free energy of binding, interconversion between agonists and antagonists, deorphanization of GPCRs, and the discovery of biased and allosteric modulators. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary software and tools, step-by-step, readily reproducible modelling protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and unique,Computational Methods for GPCR Drug Discovery is a valuable resource for structural and molecular biologists, computational and medicinal chemists, pharmacologists, and drug designers.

The Fragment Molecular Orbital Method

The Fragment Molecular Orbital Method
Author: Dmitri Fedorov
Publisher: CRC Press
Total Pages: 304
Release: 2009-05-14
Genre: Science
ISBN: 1420078496

Answering the need to facilitate quantum-chemical calculations of systems with thousands of atoms, Kazuo Kitaura and his coworkers developed the Fragment Molecular Orbital (FMO) method in 1999. Today, the FMO method can be applied to the study of whole proteins and protein-ligand interactions, and is extremely effective in calculating the propertie

GPCR Signalling Complexes – Synthesis, Assembly, Trafficking and Specificity

GPCR Signalling Complexes – Synthesis, Assembly, Trafficking and Specificity
Author: Denis J. Dupré
Publisher: Springer Science & Business Media
Total Pages: 298
Release: 2012-11-19
Genre: Medical
ISBN: 9400747659

Main Question: G protein coupled receptors are involved in highly efficient and specific activation of signalling pathways. How do GPCR signalling complexes get assembled to generate such specificity? In order to answer this question, we need to understand how receptors and their signalling partners are synthesized, folded and quality-controlled in order to generate functional proteins. Then, we need to understand how each partner of the signalling complex is selected to join a complex, and what makes this assembly possible. GPCRs are known to be able to function as oligomers, what drives the assembly into oligomers and what will be the effects of such organization on specificity and efficacy of signal transduction. Once the receptor complexes are assembled, they need to reach different locations in the cell; what drives and controls the trafficking of GPCR signalling complexes. Finally, defects in synthesis, maturation or trafficking can alter functionality of GPCRs signalling complexes; how can we manipulate the system to make it function normally again? Pharmacological chaperones may just be part of the answer to this question.

The G-Protein Linked Receptor Facts Book

The G-Protein Linked Receptor Facts Book
Author: Steve P. Watson
Publisher: Academic Press
Total Pages: 452
Release: 1994-02-28
Genre: Medical
ISBN:

Catalogues major facts about receptors, G-proteins and effector molecules. Each entry has a common format, using a minimum amount of text, and contains information on the sequence, gene structure, distribution, agonists/antagonists and physiochemical properties of these proteins.

Structural Biology in Drug Discovery

Structural Biology in Drug Discovery
Author: Jean-Paul Renaud
Publisher: John Wiley & Sons
Total Pages: 1437
Release: 2020-01-09
Genre: Medical
ISBN: 1118900502

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

Regulation of G Protein Coupled Receptor Function and Expression

Regulation of G Protein Coupled Receptor Function and Expression
Author: Jeffrey L. Benovic
Publisher: Wiley-Liss
Total Pages: 0
Release: 1999-11-12
Genre: Medical
ISBN: 9780471252771

Recent advances in molecular and cell biology enabling the cloning, expression, and mutagenesis of signal transduction proteins has prompted an explosion of knowledge in the field of receptor regulation, facilitating the discovery of new classes of regulatory proteins, and providing a basis and means for manipulating receptor function through multiple intracellular targets. This volume covers methods used to examine how the function(s) of receptors are regulated. Understanding how to regulate the function and expression of these receptors is critical in determining how to modify receptors and to translocating receptors away from the cell surface and its recycling. Individual chapters focus on specific techniques used to characterize receptors (epitope tagging, measurement and analysis of receptor phosphorylation, analysis of the kinetics of receptor desensitization, and assessment of receptor/G protein coupling); the role of regulatory proteins (receptor kinases and phosphatases, arrestins) in modulating receptor function; and the methods used to measure receptor trafficking (ligand binding, immunofluoresence) and expression (transcriptional and translational regulation). * Covers a broad range of important concepts and methodologies which are current in the study of G protein-coupled receptors (GPCRs) * G-protein coupled receptors make up over 40% of the current pharmacological targets * Provides detailed protocols for executing various strategies and offers informed judgments as to what approaches are and aren't useful * Volume Editor, Jeffrey Benovic, is a dominant world leader in the study of receptor regulation of GPCR kinases and is highly respected in the field

Computational Approaches to Nuclear Receptors

Computational Approaches to Nuclear Receptors
Author: Pietro Cozzini
Publisher: Royal Society of Chemistry
Total Pages: 191
Release: 2012-11-30
Genre: Medical
ISBN: 1849735352

Nuclear receptors (NR) are ligand-induced activated transcription factors that are involved in numerous biological processes. Since the 1990's when the first structures were determined by means of X ray diffraction, the number of NR structures has increased considerably. Moreover several 'omics' projects (genomics, pharmcogenomics and proteomics) have opened up great opportunities for the discovery of new targets, the characterization of abnormal protein patterns, the selection of "tailored" drugs and the evaluation of drug efficacy even with a lack of structural data. Furthermore, structure-based drug design, computational methods for in silico screening and nanobiotechnology- based tools are simplifying this time-consuming and money-intensive research of lead compounds and, possibly, new drugs. Biological interactions such as those that occur between a protein and ligand are concerted events where flexible molecules interact. Thus understanding flexibility of large molecules or biological complexes is of primary importance to help define the right model to approximate the reality for drug discovery, virtual screening, food safety analysis, etc. NRs are known as flexible targets, with many structural similarities, in particular for their Ligand Binding Domain: these similarities could be assumed to share behavioural qualities that belong to this class of compounds. Thus to supply a possible, complete and exhaustive answer to questions about the behaviour of NRs, their interactions with new potential drugs, endocrine disruptors such as animal and human food toxins, food additives or industry residuals, it is mandatory to approach the problem from a different point of view: a molecular modelling approach, steered synthesis, and in vitro and in vivo tests, etc. The aim of this book is to provide a state of the art review on investigations into Nuclear Receptors.

Principles of Endocrinology and Hormone Action

Principles of Endocrinology and Hormone Action
Author: Antonino Belfiore
Publisher: Springer
Total Pages: 0
Release: 2018-02-08
Genre: Medical
ISBN: 9783319446745

This volume provides comprehensive coverage of the current knowledge of the physiology of the endocrine system and hormone synthesis and release, transport, and action at the molecular and cellular levels. It presents essential as well as in-depth information of value to both medical students and specialists in Endocrinology, Gynecology, Pediatrics, and Internal Medicine. Although it is well established that the endocrine system regulates essential functions involved in growth, reproduction, and homeostasis, it is increasingly being recognized that this complex regulatory system comprises not only hormones secreted by the classic endocrine glands but also hormones and regulatory factors produced by many organs, and involves extensive crosstalk with the neural and immune system. At the same time, our knowledge of the molecular basis of hormone action has greatly improved. Understanding this complexity of endocrine physiology is crucial to prevent endocrine disorders, to improve the sensitivity of our diagnostic tools, and to provide the rationale for pharmacological, immunological, or genetic interventions. It is such understanding that this book is designed to foster.

G Protein-Coupled Receptors - Modeling and Simulation

G Protein-Coupled Receptors - Modeling and Simulation
Author: Marta Filizola
Publisher: Springer
Total Pages: 0
Release: 2016-08-23
Genre: Science
ISBN: 9789402402582

G protein-coupled receptors (GPCRs) are heptahelical transmembrane receptors that convert extra-cellular stimuli into intra-cellular signaling, and ultimately into biological responses. Since GPCRs are natural targets for approximately 40% of all modern medicines, it is not surprising that they have been the subject of intense research. Notwithstanding the amount of data generated over the years, discovering ligands of these receptors with optimal therapeutic properties is not straightforward and has certainly been hampered for years by the lack of high-resolution structural information about these receptors. Luckily, there has been a steady increase of high-resolution crystal structures of these receptors since 2007, and this information, integrated with dynamic inferences from computational and experimental methods, holds great potential for the discovery of new, improved drugs. This book, which provides, for the first time, state-of-the-art views on modeling and simulation of GPCRs, is divided into 4 parts. In the first part, the impact of currently available GPCR crystal structures on structural modeling is discussed extensively as are critical insights from simulations in the second part of the book. The third part reports recent progress in rational ligand discovery and mathematical modeling, whereas the fourth part provides an overview of bioinformatics tools and resources that are available for GPCRs.