Protein-Ligand Interactions

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.

Treating protein-protein interactions as a novel and highly promising class of drug targets, this volume introduces the underlying strategies step by step, from the biology of PPIs to biophysical and computational methods for their investigation. The main part of the book describes examples of protein targets for which small molecule modulators have been developed, covering such diverse fields as cancer, autoimmune disorders and infectious diseases. Tailor-made for the practicing medicinal chemist, this ready reference includes a wide selection of case studies taken straight from the development pipeline of major pharmaceutical companies to illustrate the power and potential of this approach. From the contents: * Prediction of intra- and inter-species protein-protein interactions facilitating systems biology studies * Modulators of protein-protein interactions: The importance of Three-Dimensionality * Interactive technologies for leveraging the known chemistry of anchor residues * SH3 Domains as Drug Targets * P53 MDM2 Antagonists: Towards Non Genotoxic Anticancer Treatments * Inhibition of LFA-1/ICAM interaction for treatment of autoimmune diseases * The PIF-binding pocket of AGC kinases * Peptidic inhibitors of protein-protein interactions for cell adhesion receptors * The REPLACE Strategy for generating Non-ATP competitive Inhibitors of Cell-Cycle Protein Kinases and more

The authoritative guide to analyzing protein interactions by mass spectrometry Mass spectrometry (MS) is playing an increasingly important role in the study of protein interactions. Mass Spectrometry of Protein Interactionspresents timely and definitive discussions of the diverse range of approaches for studying protein interactions by mass spectrometry with an extensive set of references to the primary literature. Each chapter is written by authors or teams of authors who are international authorities in their fields. This leading reference text: * Discusses the direct detection of protein interactions through electrospray ionization (ESI-MS); ion mobility analysis; and matrix-assisted laser desorption/ionization (MALDI-MS) * Covers the indirect analysis of protein interactions through hydrogen-deuterium exchange (HX-MS); limited proteolysis; cross-linking; and radial probe (RP-MS) * Guides researchers in the use of mass spectrometry in structural biology, biochemistry, and protein science to map and define the huge number and diversity of protein interactions * Reviews the latest discoveries and applications and addresses new and ongoing challenges This is a comprehensive reference for researchers in academia and industry engaged in studies of protein interactions and an excellent text for graduate and postgraduate students.

The growing flood of new experimental data generated by genome sequencing has provided an impetus for the development of automated methods for predicting the functions of proteins that have been deduced by sequence analysis and lack experimental characterization. Prediction of Protein Structures, Functions and Interactions presents a comprehensive overview of methods for prediction of protein structure or function, with the emphasis on their availability and possibilities for their combined use. Methods of modeling of individual proteins, prediction of their interactions, and docking of complexes are put in the context of predicting gene ontology (biological process, molecular function, and cellular component) and discussed in the light of their contribution to the emerging field of systems biology. Topics covered include: first steps of protein sequence analysis and structure prediction automated prediction of protein function from sequence template-based prediction of three-dimensional protein structures: fold-recognition and comparative modelling template-free prediction of three-dimensional protein structures quality assessment of protein models prediction of molecular interactions: from small ligands to large protein complexes macromolecular docking integrating prediction of structure, function, and interactions Prediction of Protein Structures, Functions and Interactions focuses on the methods that have performed well in CASPs, and which are constantly developed and maintained, and are freely available to academic researchers either as web servers or programs for local installation. It is an essential guide to the newest, best methods for prediction of protein structure and functions, for researchers and advanced students working in structural bioinformatics, protein chemistry, structural biology and drug discovery.

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.

Most drugs bind to a clearly defined macromolecular target that is complementary in terms of structure and chemistry. This observation is the basic paradigm of structure-based ligand design. Although this method first emerged in the 1980s, it has already become a powerful tool for pharmaceutical research. Much has been learned, however, since the first attempts to discover drugs on the basis of available biochemical and structural data. Nowadays, structure-based ligand design is an established method for creating drugs with new structural features, for modifying binding activities and pharmacokinetic properties, and for elucidating binding modes and structure-activity relationships. This volume presents the underlying principles of the approach and highlights real-life applications such as the discovery of HIV-protease inhibitors. It shows that structure-based ligand design has many advantages over other more traditional approaches to designing new drugs, providing it is employed properly and with a thorough knowledge of the pitfalls to avoid. The straightforward presentation and extensive list of references to the original literature as well as numerous color figures illustrating structural relationships make this volume an indispensable tool for every scientist working in the area of drug discovery.

The design of ancillary ligands used to modify the structural and reactivity properties of metal complexes has evolved into a rapidly expanding sub-discipline in inorganic and organometallic chemistry. Ancillary ligand design has figured directly in the discovery of new bonding motifs and stoichiometric reactivity, as well as in the development of new catalytic protocols that have had widespread positive impact on chemical synthesis on benchtop and industrial scales. Ligand Design in Metal Chemistry presents a collection of cutting-edge contributions from leaders in the field of ligand design, encompassing a broad spectrum of ancillary ligand classes and reactivity applications. Topics covered include: Key concepts in ligand design Redox non-innocent ligands Ligands for selective alkene metathesis Ligands in cross-coupling Ligand design in polymerization Ligand design in modern lanthanide chemistry Cooperative metal-ligand reactivity P,N Ligands for enantioselective hydrogenation Spiro-cyclic ligands in asymmetric catalysis This book will be a valuable reference for academic researchers and industry practitioners working in the field of ligand design, as well as those who work in the many areas in which the impact of ancillary ligand design has proven significant, for example synthetic organic chemistry, catalysis, medicinal chemistry, polymer science and materials chemistry.

A modern, comprehensive text and reference describing intermolecular forces, this book begins with coverage of the concepts and methods for simpler systems, then moves on to more advanced subjects for complex systems – emphasizing concepts and methods used in calculations with realistic models and compared with empirical data. Contains applications to many physical systems and worked examples Proceeds from introductory material to advanced modern treatments Has relevance for new materials, biological phenomena, and energy and fuels production

Increasing the potency of therapeutic compounds, while limiting side-effects, is a common goal in medicinal chemistry. Ligands that effectively bind metal ions and also include specific features to enhance targeting, reporting, and overall efficacy are driving innovation in areas of disease diagnosis and therapy. Ligand Design in Medicinal Inorganic Chemistry presents the state-of-the-art in ligand design for medicinal inorganic chemistry applications. Each individual chapter describes and explores the application of compounds that either target a disease site, or are activated by a disease-specific biological process. Ligand design is discussed in the following areas: Platinum, Ruthenium, and Gold-containing anticancer agents Emissive metal-based optical probes Metal-based antimalarial agents Metal overload disorders Modulation of metal-protein interactions in neurodegenerative diseases Photoactivatable metal complexes and their use in biology and medicine Radiodiagnostic agents and Magnetic Resonance Imaging (MRI) agents Carbohydrate-containing ligands and Schiff-base ligands in Medicinal Inorganic Chemistry Metalloprotein inhibitors Ligand Design in Medicinal Inorganic Chemistry provides graduate students, industrial chemists and academic researchers with a launching pad for new research in medicinal chemistry.

Understanding the play between heredity and environment, and relating it to disease causation, is the task of ecogenetics. Gene-Environment Interactions: Fundamentals of Ecogenetics presents the first comprehensive survey of this discipline, reflecting its relationship with toxicology, epidemiology, pharmacology, public health, and other medical and biological fields. Divided into four sections, the text elucidates key basic and advanced topics: * Section 1 covers fundamentals, including the history of the discipline, a discussion of the molecular laboratory tools currently available to assess genotypes, using such measurements in molecular epidemiology studies, and the statistical issues involved in their analysis. * Section 2 focuses on a number of key genetic polymorphisms relevant for ecogenetics, including enzymes of phase I and phase II metabolism, enzymes involved in DNA repair, as well as receptors and ion channels. This highlights characteristics of selected, widely studied genotypic/phenotypic differences, and allows discussion of how given genetic variations can influence responses to exogenous chemicals. * Section 3 examines gene-environment interactions through a disease-based approach, addressing how genetic polymorphisms can influence susceptibility to various diseases. Chapters cover important disease conditions such as various types of cancer, neurodegenerative diseases, cardiovascular disease, chronic pulmonary diseases, infectious diseases, diabetes, and obesity. * The final section discusses the ethical, legal, and social issues that arise when investigating and evaluating genetic polymorphisms in human populations, as well as the impact of ecogenetics on risk assessment, regulatory policies, and medicine and public health. Packed with clear examples illustrating concepts, as well as numerous tables and figures, Gene-Environment Interactions: Fundamentals of Ecogenetics is a unique resource for a wide range of physicians, students, and other specialists.