Download or read book Inhibitor Synthesis and Biophysical Characterization of Protein Ligand Solvent Interactions An Analysis of the Thermodynamics and Kinetics of Ligand Binding to Thermolysin written by Jonathan Cramer and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Inhibitor Synthesis and Biophysical Charaterization of Protein ligand solvent Interactions written by Jonathan Cramer and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Biophysical Approaches Determining Ligand Binding to Biomolecular Targets written by Alberto Podjarny and published by Royal Society of Chemistry. This book was released on 2011-04-01 with total page 373 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Protein Ligand Interactions written by Holger Gohlke and published by John Wiley & Sons. This book was released on 2012-04-06 with total page 359 pages. Available in PDF, EPUB and Kindle. Book excerpt: Innovative and forward-looking, this volume focuses on recent achievements in this rapidly progressing field and looks at future potential for development. The first part provides a basic understanding of the factors governing protein-ligand interactions, followed by a comparison of key experimental methods (calorimetry, surface plasmon resonance, NMR) used in generating interaction data. The second half of the book is devoted to insilico methods of modeling and predicting molecular recognition and binding, ranging from first principles-based to approximate ones. Here, as elsewhere in the book, emphasis is placed on novel approaches and recent improvements to established methods. The final part looks at unresolved challenges, and the strategies to address them. With the content relevant for all drug classes and therapeutic fields, this is an inspiring and often-consulted guide to the complexity of protein-ligand interaction modeling and analysis for both novices and experts.
Download or read book Thermodynamics and Kinetics of Drug Binding written by György Keserü and published by John Wiley & Sons. This book was released on 2015-03-09 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: This practical reference for medicinal and pharmaceutical chemists combines the theoretical background with modern methods as well as applications from recent lead finding and optimization projects. Divided into two parts on the thermodynamics and kinetics of drug-receptor interaction, the text provides the conceptual and methodological basis for characterizing binding mechanisms for drugs and other bioactive molecules. It covers all currently used methods, from experimental approaches, such as ITC or SPR, right up to the latest computational methods. Case studies of real-life lead or drug development projects are also included so readers can apply the methods learned to their own projects. Finally, the benefits of a thorough binding mode analysis for any drug development project are summarized in an outlook chapter written by the editors.
Download or read book Reversible Ligand Binding written by Andrea Bellelli and published by John Wiley & Sons. This book was released on 2018-01-09 with total page 309 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents the physical background of ligand binding and instructs on how experiments should be designed and analyzed Reversible Ligand Binding: Theory and Experiment discusses the physical background of protein-ligand interactions—providing a comprehensive view of the various biochemical considerations that govern reversible, as well as irreversible, ligand binding. Special consideration is devoted to enzymology, a field usually treated separately from ligand binding, but actually governed by identical thermodynamic relationships. Attention is given to the design of the experiment, which aids in showing clear evidence of biochemical features that may otherwise escape notice. Classical experiments are reviewed in order to further highlight the importance of the design of the experiment. Overall, the book supplies students with the understanding that is necessary for interpreting ligand binding experiments, formulating plausible reaction schemes, and analyzing the data according to the chosen model(s). Topics covered include: theory of ligand binding to monomeric proteins; practical considerations and commonly encountered problems; oligomeric proteins with multiple binding sites; ligand binding kinetics; hemoglobin and its ligands; single-substrate enzymes and their inhibitors; two-substrate enzymes and their inhibitors; and rapid kinetic methods for studying enzyme reactions. Bridges theory of ligand binding and allostery with experiments Applies historical and physical insight to provide a clear understanding of ligand binding Written by a renowned author with long-standing research and teaching expertise in the area of ligand binding and allostery Based on FEBS Advanced Course lectures on the topic Reversible Ligand Binding: Theory and Experiment is an ideal text reference for students and scientists involved in biophysical chemistry, physical biochemistry, biophysics, molecular biology, protein engineering, drug design, pharmacology, physiology, biotechnology, and bioengineering.
Download or read book Protein Ligand Interactions written by Tina Daviter and published by Humana. This book was released on 2021-04-19 with total page 496 pages. Available in PDF, EPUB and Kindle. Book excerpt: This third edition provides new and updated chapters detailing a complete introduction to common and emerging procedures for characterizing the interactions of individual proteins with their natural ligands, drugs or other binding partners. Chapters detail natural substrates, potential drug leads, quantitative understanding of the mechanism of interaction, and different techniques. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Protein Ligand Interactions: Methods and Applications, Third Edition serves as an ideal guide for researchers new to the field of biophysical characterization of protein interactions.
Download or read book Protein Ligand Binding Thermodynamics written by Justin M. Miller and published by American Chemical Society. This book was released on 2023-06-01 with total page 217 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ligand binding by macromolecules represents a core event of broad relevance to a range of systems, including catalytic systems alongside noncatalytic systems such as nucleic acid binding by transcription factors or extracellular ligand binding by proteins involved in signaling pathways. The scope of this primer is constrained to introduce only foundational models without significant discussion of more advanced topics such as allosteric or linkage effects. Linkage occurs when the binding of a ligand is influenced by the binding of another molecule of the same ligand (homotropic linkage), the binding of a different ligand (heterotropic linkage), physical variables such as temperature or pressure (physical linkage), or changes in macromolecular assembly state (polysteric linkage). Taking this into account, the foundational themes presented in this primer can be used to describe any macromolecule–ligand interaction either by direct use of the models and techniques described here or by applying them to develop more advanced models to explain additional complexities such as those allosteric or linkage effects just mentioned. The target audience of this primer is the senior undergraduate or junior graduate student who lacks a foundation in ligand-binding thermodynamics. As such, we have focused primarily on foundational thermodynamic treatments and presented only general discussions of relevant experimental designs. Readers of this primer will learn how to build a working understanding of common factors that promote energetic favorability for ligand binding; develop a functional toolbox to understand ligand binding from the perspective of collecting, plotting, and interpreting ligand-binding data; enhance proficiency in deriving thermodynamic mechanisms for ligand binding; and become comfortable in interpreting binding data reported in the literature and independently expanding knowledge beyond the scope introduced in this primer.
Download or read book Protein Ligand Interactions written by Hans-Joachim Böhm and published by John Wiley & Sons. This book was released on 2006-03-06 with total page 262 pages. Available in PDF, EPUB and Kindle. Book excerpt: The lock-and-key principle formulated by Emil Fischer as early as the end of the 19th century has still not lost any of its significance for the life sciences. The basic aspects of ligand-protein interaction may be summarized under the term 'molecular recognition' and concern the specificity as well as stability of ligand binding. Molecular recognition is thus a central topic in the development of active substances, since stability and specificity determine whether a substance can be used as a drug. Nowadays, computer-aided prediction and intelligent molecular design make a large contribution to the constant search for, e. g., improved enzyme inhibitors, and new concepts such as that of pharmacophores are being developed. An up-to-date presentation of an eternally young topic, this book is an indispensable information source for chemists, biochemists and pharmacologists dealing with the binding of ligands to proteins.
Download or read book Mechanisms thermodynamics and kinetics of ligand binding revealed from molecular simulations and machine learning written by Yinglong Miao and published by Frontiers Media SA. This book was released on 2023-02-24 with total page 179 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Quantitative Characterization of Ligand Binding written by Donald J. Winzor and published by Wiley-Liss. This book was released on 1995-10-30 with total page 184 pages. Available in PDF, EPUB and Kindle. Book excerpt: This study of ligand binding presents both the methodological and interpretative aspects of the process. Designed to direct researchers towards the appropriate protocols, the work focuses on the experimental measurement of interactions with appropriate attention to the assumptions and approximations inherent in data analysis.
Download or read book Thermodynamic Analysis of Protein ligand Interactions of Linear Tripeptide HCV NS3 Protease Inhibitors and Progress Toward the Total Synthesis of arboridinine written by Rachel Marie Wypych and published by . This book was released on 2017 with total page 526 pages. Available in PDF, EPUB and Kindle. Book excerpt: Interactions between proteins and small molecules dictate an overwhelmingly large number of biological processes, yet our knowledge of the effects of ligand structural changes on the thermodynamics of these interactions is fundamentally lacking. In an effort to expand our understanding of protein-ligand thermodynamics, the binding profiles of a series of linear tripeptide HCV NS3 protease inhibitors were analyzed by ITC. Substituents on the P2 proline residue were examined individually, and important trends were elucidated. The addition of a phenyl group to the 2-position of the heteroaryl subunit of the P2 residue resulted in more favorable binding entropy, which is possibly due to the desolvation of nonpolar surface area. Quinolines without a 2-phenyl substituent were found to bind in an alternate conformation with thermodynamic profiles that were dominated by favorable binding enthalpies rather than entropies. This could possibly be due to a favorable hydrogen bonding interaction between the quinoline nitrogen and Asp81 of the catalytic triad. A series of analogs were prepared to examine the effect of incrementally increasing steric bulk at the P3 side chain of HCV NS3 inhibitors in order to preorganize the ligand into the extended conformation. As steric bulk was increased, the binding affinities improved in turn, notably due to increasingly favorable binding enthalpies along with small gains in entropy. This could possibly attributed to a combination of factors including the entropic benefit derived from preorganization and an enthalpy-driven hydrophobic effect. Several concise synthetic routes were designed toward the total synthesis of the pentacyclic indole alkaloid (±)-arboridinine. A novel Diels-Alder cycloaddition of an indole-3-glyoxamide with a diene to form a key tricyclic intermediate was attempted, but no reaction was observed under a variety of conditions. A second-generation attempt featured attempts at a challenging cascade reaction involving a conjugate addition of an indole-3-glyoxamide into an enone and subsequent attack of an enolate into the intermediate 3,3-disubstituted indolenine. The conjugate addition was successful, providing the first example of indole-3-glyoxamides as substrates for conjugate additions into enones. The resulting indolenine was found to be unreactive under acidic conditions and underwent a retro-Michael reaction to return the indole-3-glyoxamide under basic conditions.
Download or read book Protein ligand Interactions Structure and Spectroscopy written by Stephen E. Harding and published by Oxford University Press, USA. This book was released on 2001 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text on protein-ligand interactions offers a selection of the most useful and easily applied methods and acts as a guide to the principal techniques used.
Download or read book Advances in Bioanalytical Methods for Probing Ligand Target Interactions written by Quezia B. Cass and published by Frontiers Media SA. This book was released on 2020-07-02 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Inhibitors of Protein Protein Interactions written by Ali Tavassoli and published by Royal Society of Chemistry. This book was released on 2020-11-25 with total page 357 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein–protein interactions (PPI) are at the heart of the majority of cellular processes, and are frequently dysregulated or usurped in disease. Given this central role, the inhibition of PPIs has been of significant interest as a means of treating a wide variety of diseases. However, there are inherent challenges in developing molecules capable of disrupting the relatively featureless and large interfacial areas involved. Despite this, there have been a number of successes in this field in recent years using both traditional drug discovery approaches and innovative, interdisciplinary strategies using novel chemical scaffolds. This book comprehensively covers the various aspects of PPI inhibition, encompassing small molecules, peptidomimetics, cyclic peptides, stapled peptides and macrocycles. Illustrated throughout with successful case studies, this book provides a holistic, cutting-edge view of the subject area and is ideal for chemical biologists and medicinal chemists interested in developing PPI inhibitors.
Download or read book Ligands written by Paula Gawryszewska and published by Nova Science Publishers. This book was released on 2014 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: To meet the search for new therapeutic compounds this book summarises the research on biologically active organic molecules (chapters 1, 2 and 3), metal complexes with biological activity (chapter 4), and shows the possibilities for co-ordination chemistry in the planning of metal complexes with interesting properties for application (chapters 5, 6, 7, 8, and 9). It should be remembered that in the design of a new potentially active metallodrug, beyond the nature of the metal, the choice of appropriate ligands which affect the thermodynamic and kinetic stability, as well as the solubility and lipophilicity of the complexes is of paramount importance. The information contained in the book concerns: 1) the interactions involving the members of the Nuclear Receptor superfamily and their ligands; 2) the role of chemokine ligands and their receptors in normal and disease processes, and the emerging therapeutic approaches of using chemokine antagonists for appropriately targeted therapy; 3) the inhibition of alkaline phosphatases by calix[4]arenes functionalysed at the macrocyclic upper rim by one or two methylenebisphosphonic acid fragments; 4) the main biological applications, enzyme modelling and antiproliferative and antimicrobial activity of such scorpionate-type complexes, which are classified by ligand and also by transition metal; 5) the silver(I) discrete and polymeric coordination compounds bearing 1,3,5-triaza-7-phosphaadamantane or its derivatives towards engineering functional silver-organic frameworks (MOFs); 6) arylhydrazones of methylene active nitriles and their use as starting materials for the generation of new organic and coordination compounds; 7) amidophosphate ligands as promising sensitisers of lanthanide ions emission; 8) N-acetylsalicylhydrazidate as a versatile ligand for the synthesis of higher nuclearity metal complexes, which are illustrated herein along with their applications; 9) the chemistry and some applications of formazans which can be used for the simultaneous selective determination of several metal cations. All chapters were compiled by renowned scientists, providing both beginners in the field and advanced researchers with comprehensive information on the subject.
Download or read book Insights Into Protein Ligand Molecular Recognition Thermodynamic Kinetic and Structural Characterization of Inhibitor Binding to Aldose Reductase and Carbonic Anhydrase II written by Chris Rechlin and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
