Download or read book Applied Biophysics for Drug Discovery written by Donald Huddler and published by John Wiley & Sons. This book was released on 2017-10-02 with total page 148 pages. Available in PDF, EPUB and Kindle. Book excerpt: Applied Biophysics for Drug Discovery is a guide to new techniques and approaches to identifying and characterizing small molecules in early drug discovery. Biophysical methods are reasserting their utility in drug discovery and through a combination of the rise of fragment-based drug discovery and an increased focus on more nuanced characterisation of small molecule binding, these methods are playing an increasing role in discovery campaigns. This text emphasizes practical considerations for selecting and deploying core biophysical method, including but not limited to ITC, SPR, and both ligand-detected and protein-detected NMR. Topics covered include: • Design considerations in biophysical-based lead screening • Thermodynamic characterization of protein-compound interactions • Characterizing targets and screening reagents with HDX-MS • Microscale thermophoresis methods (MST) • Screening with Weak Affinity Chromatography • Methods to assess compound residence time • 1D-NMR methods for hit identification • Protein-based NMR methods for SAR development • Industry case studies integrating multiple biophysical methods This text is ideal for academic investigators and industry scientists planning hit characterization campaigns or designing and optimizing screening strategies.
Download or read book Applied Biophysics for Drug Discovery written by Donald Huddler and published by John Wiley & Sons. This book was released on 2017-07-14 with total page 313 pages. Available in PDF, EPUB and Kindle. Book excerpt: Applied Biophysics for Drug Discovery is a guide to new techniques and approaches to identifying and characterizing small molecules in early drug discovery. Biophysical methods are reasserting their utility in drug discovery and through a combination of the rise of fragment-based drug discovery and an increased focus on more nuanced characterisation of small molecule binding, these methods are playing an increasing role in discovery campaigns. This text emphasizes practical considerations for selecting and deploying core biophysical method, including but not limited to ITC, SPR, and both ligand-detected and protein-detected NMR. Topics covered include: • Design considerations in biophysical-based lead screening • Thermodynamic characterization of protein-compound interactions • Characterizing targets and screening reagents with HDX-MS • Microscale thermophoresis methods (MST) • Screening with Weak Affinity Chromatography • Methods to assess compound residence time • 1D-NMR methods for hit identification • Protein-based NMR methods for SAR development • Industry case studies integrating multiple biophysical methods This text is ideal for academic investigators and industry scientists planning hit characterization campaigns or designing and optimizing screening strategies.
Download or read book Biophysical Techniques in Drug Discovery written by Angeles Canales and published by Royal Society of Chemistry. This book was released on 2017-11-20 with total page 336 pages. Available in PDF, EPUB and Kindle. Book excerpt: With perspectives from academia and industry across a spectrum of techniques, this is a go-to volume for biophysicists, analytical chemists and medicinal chemists looking for a broad overview of techniques of contemporary interest in drug discovery.
Download or read book Biophysical and Computational Tools in Drug Discovery written by Anil Kumar Saxena and published by Springer Nature. This book was released on 2021-10-18 with total page 405 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews recent physicochemical and biophysical techniques applied in drug discovery research, and it outlines the latest advances in computational drug design. Divided into 10 chapters, the book discusses about the role of structural biology in drug discovery, and offers useful application cases of several biophysical and computational methods, including time-resolved fluorometry (TRF) with Förster resonance energy transfer (FRET), X-Ray crystallography, nuclear magnetic resonance spectroscopy, mass spectroscopy, generative machine learning for inverse molecular design, quantum mechanics/molecular mechanics (QM/MM,ONIOM) and quantum molecular dynamics (QMT) methods. Particular attention is given to computational search techniques applied to peptide vaccines using novel mathematical descriptors and structure and ligand-based virtual screening techniques in drug discovery research. Given its scope, the book is a valuable resource for students, researchers and professionals from pharmaceutical industry interested in drug design and discovery.
Download or read book Biophysical Methods for Biotherapeutics written by Tapan K. Das and published by John Wiley & Sons. This book was released on 2014-04-28 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt: With a focus on practical applications of biophysical techniques, this book links fundamental biophysics to the process of biopharmaceutical development. • Helps formulation and analytical scientists in pharma and biotech better understand and use biophysical methods • Chapters organized according to the sequential nature of the drug development process • Helps formulation, analytical, and bioanalytical scientists in pharma and biotech better understand and usestrengths and limitations of biophysical methods • Explains how to use biophysical methods, the information obtained, and what needs to be presented in a regulatory filing, assess impact on quality and immunogenicity • With a focus on practical applications of biophysical techniques, this book links fundamental biophysics to the process of biopharmaceutical development.
Download or read book Biophysics for Therapeutic Protein Development written by Linda O. Narhi and published by Springer Science & Business Media. This book was released on 2013-02-26 with total page 299 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book can be used to provide insight into this important application of biophysics for those who are planning a career in protein therapeutic development, and for those outside this area who are interested in understanding it better. The initial chapters describe the underlying theory, and strengths and weaknesses of the different techniques commonly used during therapeutic development. The majority of the chapters discuss the applications of these techniques, including case studies, across the product lifecycle from early discovery, where the focus is on identifying targets, and screening for potential drug product candidates, through expression and purification, large scale production, formulation development, lot-to-lot comparability studies, and commercial support including investigations.
Download or read book Structural Biology in Drug Discovery written by Jean-Paul Renaud and published by John Wiley & Sons. This book was released on 2020-01-09 with total page 1367 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book Biochemistry Biophysics and Molecular Chemistry written by Francisco Torrens and published by CRC Press. This book was released on 2020-04-07 with total page 211 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biochemistry, Biophysics, and Molecular Chemistry: Applied Research and Interactions provides the background needed in biophysics and molecular chemistry and offers a great deal of advanced biophysical knowledge. It emphasizes the growing interrelatedness of molecular chemistry and biochemistry, and acquaints one with experimental methods of both disciplines. This book addresses some of the enormous advances in biochemistry, particularly in the areas of structural biology and bioinformatics, by providing a solid biochemical foundation that is rooted in chemistry. Topics include scientific integrity and ethics in the field; clinical translational research in cancer, diabetes, and cardiovascular disease; emerging drugs to treat neurodegenerative diseases; swine, avian, and human flu; the use of big data in artificial knowledge in the field; bioinformatic insights on molecular chemistry; and much more.
Download or read book Structure based Drug Discovery written by Harren Jhoti and published by Springer Science & Business Media. This book was released on 2007-05-24 with total page 255 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes some of the most exciting developments for the discovery of new drugs, such as Fragment-based methods. It contains the latest developments in technologies that can be used to obtain the 3-D structures. This book includes experimental approaches using X-ray crystallography and NMR for Fragment-based screening as well as other biophysical methods for studying protein/ligand interactions.
Download or read book Biophysical and Computational Tools in Drug Discovery written by Anil Kumar Saxena and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews recent physicochemical and biophysical techniques applied in drug discovery research, and it outlines the latest advances in computational drug design. Divided into 10 chapters, the book discusses about the role of structural biology in drug discovery, and offers useful application cases of several biophysical and computational methods, including time-resolved fluorometry (TRF) with Förster resonance energy transfer (FRET), X-Ray crystallography, nuclear magnetic resonance spectroscopy, mass spectroscopy, generative machine learning for inverse molecular design, quantum mechanics/molecular mechanics (QM/MM,ONIOM) and quantum molecular dynamics (QMT) methods. Particular attention is given to computational search techniques applied to peptide vaccines using novel mathematical descriptors and structure and ligand-based virtual screening techniques in drug discovery research. Given its scope, the book is a valuable resource for students, researchers and professionals from pharmaceutical industry interested in drug design and discovery.
Download or read book Introduction to Modern Biophysics written by Mohammad Ashrafuzzaman and published by CRC Press. This book was released on 2023-12-15 with total page 603 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook provides an introduction to the fundamental and applied aspects of biophysics for advanced undergraduate and graduate students of physics, chemistry, and biology. The application of physics principles and techniques in exploring biological systems has long been a tradition in scientific research. Biological systems hold naturally inbuilt physical principles and processes which are popularly explored. Systematic discoveries help us understand the structures and functions of individual biomolecules, biomolecular systems, cells, organelles, tissues, and even the physiological systems of animals and plants. Utilizing a physics- based scientific understanding of biological systems to explore disease is at the forefront of applied scientific research. This textbook covers key breakthroughs in biophysics whilst looking ahead to future horizons and directions of research. It contains models based on both classical and quantum mechanical treatments of biological systems. It explores diseases related to physical alterations in biomolecular structures and organizations alongside drug discovery strategies. It also discusses the cutting- edge applications of nanotechnologies in manipulating nanoprocesses in biological systems. Key Features: • Presents an accessible introduction to how physics principles and techniques can be used to understand biological and biochemical systems. • Addresses natural processes, mutations, and their purposeful manipulation. • Lays the groundwork for vitally important natural scientific, technological, and medical advances. Mohammad Ashrafuzzaman, a biophysicist and condensed matter scientist, is passionate about investigating biological and biochemical processes utilizing physics principles and techniques. He is a professor of biophysics at King Saud University’s Biochemistry Department in the College of Science, Riyadh, Saudi Arabia; the co- founder of MDT Canada Inc., and the founder of Child Life Development Institute, Edmonton, Canada. He has authored Biophysics and Nanotechnology of Ion Channels, Nanoscale Biophysics of the Cell, and Membrane Biophysics. He has also published about 50 peer- reviewed articles and several patents, edited two books, and has been serving on the editorial boards of Elsevier and Bentham Science journals. Dr. Ashrafuzzaman has held research and academic ranks at Bangladesh University of Engineering & Technology, University of Neuchatel (Switzerland), Helsinki University of Technology (Finland), Weill Medical College of Cornell University (USA), and University of Alberta (Canada). During 2013– 2018 he also served as a Visiting Professor at the Departments of Oncology, and Medical Microbiology and Immunology, of the University of Alberta. Dr. Ashrafuzzaman earned his highest academic degree, Doctor of Science (D.Sc.) in condensed matter physics from the University of Neuchatel, Switzerland in 2004.
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 2015-07-28 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 Contemporary Aspects of Biomedical Research written by S. J. Enna and published by . This book was released on 2009 with total page 501 pages. Available in PDF, EPUB and Kindle. Book excerpt: Each volume of Advances in Pharmacology provides a rich collection of reviews on timely topics. Emphasis is placed on the molecular basis of drug action, both applied and experimental. Articles written by leading investigators in the field Informs and updates on all the latest developments
Download or read book Quantum Mechanics in Drug Discovery written by Alexander Heifetz and published by . This book was released on 2020 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume looks at applications of quantum mechanical (QM) methods in drug discovery. The chapters in this book describe how QM approaches can be applied to address key drug discovery issues, such as characterizing protein-water-ligand and protein-protein interactions, providing estimates of binding affinities, determining ligand energies and bioactive conformations, refinement of molecular geometries, scoring docked protein-ligand poses, describing molecular similarity, structure-activity-relationship (SAR) analysis, and ADMET prediction. 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 modeling protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and unique, Quantum Mechanics in Drug Discovery is a valuable resource for structural and molecular biologists, computational and medicinal chemists, pharmacologists, and drug designers.
Download or read book Deep Learning for the Life Sciences written by Bharath Ramsundar and published by O'Reilly Media. This book was released on 2019-04-10 with total page 236 pages. Available in PDF, EPUB and Kindle. Book excerpt: Deep learning has already achieved remarkable results in many fields. Now it’s making waves throughout the sciences broadly and the life sciences in particular. This practical book teaches developers and scientists how to use deep learning for genomics, chemistry, biophysics, microscopy, medical analysis, and other fields. Ideal for practicing developers and scientists ready to apply their skills to scientific applications such as biology, genetics, and drug discovery, this book introduces several deep network primitives. You’ll follow a case study on the problem of designing new therapeutics that ties together physics, chemistry, biology, and medicine—an example that represents one of science’s greatest challenges. Learn the basics of performing machine learning on molecular data Understand why deep learning is a powerful tool for genetics and genomics Apply deep learning to understand biophysical systems Get a brief introduction to machine learning with DeepChem Use deep learning to analyze microscopic images Analyze medical scans using deep learning techniques Learn about variational autoencoders and generative adversarial networks Interpret what your model is doing and how it’s working
Download or read book Current Methods In Medicinal Chemistry And Biological Physics written by Carlton A. Taft and published by . This book was released on 2008-01-01 with total page 247 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is aimed at, from students to advanced researchers, for anyone that is interested or works with current experimental and theoretical methods in medicinal chemistry and biological physics, with particular interest in chemoinformatics, bioinformatics, molecular modeling, QSAR, spectrometry, molecular biology and combinatorial chemistry for many therapeutic purposes. This book attempts to convey something of the fascination of working in these multidisciplinar areas, which overlap knowledge of chemistry, physics, biochemistry, biology and pharmacology. This second volume, in particular, contains 11 chapters, of which 6 are related to theoretical methods in medicinal chemistry and at least 5 deal with experimental/mixed methods. In the modern computational medicinal chemistry, quantum mechanics (QM) plays an important role since the associated methods can describe molecular energies, bond breaking or forming, charge transfer and polarization effects. Historically in drug design, QM ligand-based applications were devoted to investigations of electronic features, and they have also been routinely used in the development of quantum descriptors in quantitative structure-activity relationships (QSAR) approaches. In chapter 1, we present an overview of the state-of-the-art of quantum methods currently used in medicinal chemistry. Molecular Dynamics (MD) simulation is a sophisticated molecular modeling technique useful to describe molecular structures and macroscopic properties in very large molecular systems comprising hundreds or even thousands of atoms. In the field of drug discovery, MD simulation has been widely used to understand the biomolecule structure, drug and biomolecule interactions. The chapter 2 outlines the theory and practical details of MD approach and focuses on its application in studies of prediction of binding affinities for putative receptor-ligand complexes. In chapter 3 we discuss the important role of the homology modeling procedure in the drug discovery process. This strategy, associated with computational power and more sophisticated and robust algorithms, has been used to predict properties, energies, conformations and support the binding modes of ligands inside their receptor sites. This approach is vital in structure-based drug design (SBBD), since it can quickly predict the tertiary structure of the target whose structure has not been experimentally solved. In drug discovery research, a massive dataset of information is involved and the high throughput screening of typically millions of compounds plays an important role. Different docking protocols can be combined in order to predict binding models and affinities of a ligand with a target receptor, selecting as example the best drug-like compound candidates to further experimental assays, leading to a reduction in the time and cost of the drug discovery process. In the chapter 4, we discuss the general basis and aspects of this approach, presenting some successful cases in drug discovery. Structure-based approaches have increasingly demonstrated their value in drug design. The impact of these technologies on early discovery and lead optimization is significant. Although there is a multiplicity of different approaches being employed in early stages of drug discovery, structure-based drug design (SBDD) is one of the most powerful techniques, and has been used quite frequently by scientists in the pharmaceutical industry as well as in academic laboratories over the past twenty years. The evolution of medicinal chemistry has resulted in an increase in the number of successful applications of structure-based approaches. Some case studies are presented in chapter 5, exploring the value of structure-based virtual screening (SBVS) approaches in drug design, highlighting the identification of novel, potent and selective receptor modulators with drug like properties. Drug discovery has moved toward more rational strategies based on our increasing understanding of the fundamental principles of protein-ligand interactions. The combination of available knowledge of several 3D protein structures with hundreds of thousands of commercially available small molecules has attracted the attention of scientists from all over the world for the application of structure-based pharmacophore strategies. Pharmacophore approaches offer timely and cost-effective ways to identify new drug-like ligands for a variety of biological targets, and their utility in drug design is unquestionable. In the chapter 6, the understanding and limitations of this approach in drug R&D are discussed. Modern molecular biology has inundated drug discovery organizations with countless potential novel drug targets. A foremost challenge for the researchers is to validate this asset of targets with bioactive small molecules (bioproducts can also be included). Eventually, they will be developed into drugs for the more promising targets. The difficulty of finding a good small-molecule starting point is at the beginning of the searching for a proper chemical space that is well related to biological space. Drugs that are small molecules and act at enzyme targets account for over 50% of all medicines in therapeutically use in the marketplace. It is for this reason that chapter 7 take thermodynamics of the small molecule-target enzyme interactions into account to a limited scope. So far, the main purpose of this chapter is to provide a guidance profile of biocalorimetry and its role in drug discovery and development. The chapter 8 intends to describe how proteomes can be analyzed and studied. It addresses some available databases and bioinformatics tools. The description of certain instrumentation, such as mass spectrometry is also presented, but not highly detailed. The aim of chapter 9 is to introduce the reader to the wide spectrum of tools currently available in the drug validation process. With the conclusion of the human genome sequencing, an increase demand for target validation follows the development of high throughput techniques used in the identification of potential new drugs. In vitro technology as the RNA interference (RNAi) and recombinant protein array together with advances on the in vivo technology as the development of transgenic animals, including here the humanized ones, will certainly improve the safety of future clinical trials processes and ultimately play an important role in the treatment of several human diseases. A therapeutically significant drug may have limited utilization in clinical practice because of various shortcomings like poor organoleptic properties (chloranphenicol), poor bioavailability (ampicilin), lack of site specificity (antineoplastic agents), incomplete absorption (epinephrine), poor aqueous solubility (corticosteroids), high first-pass metabolism (propranolol), low chemical stability (penicillin), high toxicity (thalidomide) or other adverse effects. Sometimes, an adequate pharmaceutical formulation can overcome these drawbacks, but often the galenic formulation is inoperant and a chemical modification of active molecule is necessary to correct its pharmacokinetic profile. This chemical formulation process, whose objective is to convert an interesting active molecule into a clinically acceptable drug, often involves the so-called prodrug design , which is extensively discussed in chapter 10. The dominant role of synthetic chemistry has been increasingly challenged by knowledge of the structure and functions of enzymes, receptors, channels, membrane pumps, nucleic acids and by the exponential growth of information about biology, genetics and pathology, giving paramount importance to the dialogue between chemists and biologists. Nevertheless, as in the old days, the development of new chemical entities is still highly dependent on the ability of chemists to obtain, with simple, reliable, fast and possibly inexpensive methods, the molecules that have been designed. Even if it is an undisputed fact that biology has become exceedingly important in drug research, it is reasonable to imagine that chemistry, and in particular synthetic organic chemistry, will continue to play a fundamental role in academic research and in the R&D departments of drug companies of the third millennium. In chapter 11, we describe synthetic routes that have been used to synthesize the structures of top drugs in current usage. This provides an ideal way of introducing students to a wide range of applied chemistry with brief descriptions of the modes of action of these drugs. Some contents of this book therefore reflect our own ideas and personal experiences, which are presented in reviews of different topics here investigated. It is interesting to consider the information described in this book as the starting point to access available and varied knowledge in Medicinal Chemistry and Biological Physics or related areas.
Download or read book Chemical Epigenetics written by Antonello Mai and published by Springer Nature. This book was released on 2020-03-31 with total page 569 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an authoritative review of the most significant findings about all the epigenetic targets (writers, readers, and erasers) and their implication in physiology and pathology. The book also covers the design, synthesis and biological validation of epigenetic chemical modulators, which can be useful as novel chemotherapeutic agents. Particular attention is given to the chemical mechanisms of action of these molecules and to the drug discovery prose which allows their identification. This book will appeal to students who want to know the extensive progresses made by epigenetics (targets and modulators) in the last years from the beginning, and to specialized scientists who need an instrument to quickly search and check historical and/or updated notices about epigenetics.
