Virtual Screening In Drug Discovery

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Virtual Screening In Drug Discovery

Author : Juan Alvarez
ISBN : 9781420028775
Genre : Medical
File Size : 84.85 MB
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Virtual screening can reduce costs and increase hit rates for lead discovery by eliminating the need for robotics, reagent acquisition or production, and compound storage facilities. The increased robustness of computational algorithms and scoring functions, the availability of affordable computational power, and the potential for timely structural determination of target molecules, have provided new opportunities for virtual screening, and made it more practical. Why then, isn’t everyone using virtual screening? Examining the scope and limitations of this method, Virtual Screening in Drug Discovery explores the algorithms involved and how to actually use them. Part I offers perspectives on both ligand-based and docking-based virtual screens. The authors of these chapters frame many of the challenges currently facing the field. Part II considers the choice of compounds that are best suited as drug leads. Part III discusses ligand-based approaches, including descriptor-based similarity, traditional pharmacophore searching, and similarity based 3D-pharmacophore fingerprints. The final two sections are devoted to molecular docking. Part IV outlines some important and practical considerations relating to the energetics of protein-ligand binding and target-site topography, whereas specific docking algorithms and strategies are discussed in Part V. Notwithstanding this list of subjects, the book does not overwhelm you with more information than you need—many of the strategies outlined will transcend the specifics of any given method. Nor does the book purport to offer single best ways to use the programs. What it does is provide a snapshot of virtual screening that gives you easy access to strategies and techniques for lead discovery. Daniel E. Levy, editor of the Drug Discovery Series, is the founder of DEL BioPharma, a consulting service for drug discovery programs. He also maintains a blog that explores organic chemistry.
Category: Medical

Virtual Screening

Author : Christoph Sotriffer
ISBN : 9783527633340
Genre : Medical
File Size : 38.3 MB
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Drug discovery is all about finding small molecules that interact in a desired way with larger molecules, namely proteins and other macromolecules in the human body. If the three-dimensional structures of both the small and large molecule are known, their interaction can be tested by computer simulation with a reasonable degree of accuracy. Alternatively, if active ligands are already available, molecular similarity searches can be used to find new molecules. This virtual screening can even be applied to compounds that have yet to be synthesized, as opposed to "real" screening that requires cost- and labor-intensive laboratory testing with previously synthesized drug compounds. Unique in its focus on the end user, this is a real "how to" book that does not presuppose prior experience in virtual screening or a background in computational chemistry. It is both a desktop reference and practical guide to virtual screening applications in drug discovery, offering a comprehensive and up-to-date overview. Clearly divided into four major sections, the first provides a detailed description of the methods required for and applied in virtual screening, while the second discusses the most important challenges in order to improve the impact and success of this technique. The third and fourth, practical parts contain practical guidelines and several case studies covering the most important scenarios for new drug discovery, accompanied by general guidelines for the entire workflow of virtual screening studies. Throughout the text, medicinal chemists from academia, as well as from large and small pharmaceutical companies report on their experience and pass on priceless practical advice on how to make best use of these powerful methods.
Category: Medical

Virtual Screening An Alternative Or Complement To High Throughput Screening

Author : Gerhard Klebe
ISBN : 9780306468834
Genre : Medical
File Size : 83.59 MB
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In the next couple of years the human genome will be fully sequenced. This will provide us with the sequence and overall function of all human genes as well as the complete genome for many micro-organisms. Subsequently it is hoped, by means of powerful bioinformatic tools, to determine the gene variants that contribute to various multifactorial diseases and genes that exist in certain infectious agents but not humans. As a consequence, this will allow us to define the most appropriate levels for drug intervention. It can be expected that the number of potential drug targets will increase, possibly by a factor of 10 or more. Nevertheless, sequencing the human genome or, for that matter, the genome of other species will only be the starting point for the understanding of their biological function. Structural genomics is a likely follow-up, combined with new techniques to validate the therapeutic relevance of such newly discovered targets. Accordingly, it can be expected that in the near future we will witness a substantial increase in novel putative targets for drugs. To address these new targets effectively, we require new approaches and innovative tools. At present, two alternative, yet complementary, techniques are employed: experimental high-throughput screening (HTS) of large compound libraries, increasingly provided by combinatorial chemistry, and computational methods for virtual screening and de novo design. As kind of status report on the maturity of virtual screening as a technique in drug design, the first workshop on new approaches in drug design and discovery was held in March 1999, at Schloß Rauischholzhausen, near Marburg in Germany. More than 80 scientists gathered and discussed their experience with the different techniques. The speakers were invited to summarize their contributions together with their impressions on the present applicability of their approach. Several of the speakers followed this request which is summarized in this publication.
Category: Medical

Chemoinformatics Approaches To Virtual Screening

Author : Alexandre Varnek
ISBN : 9780854041442
Genre : Science
File Size : 41.2 MB
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Chemoinformatics is broadly a scientific discipline encompassing the design, creation, organization, management, retrieval, analysis, dissemination, visualization and use of chemical information. It is distinct from other computational molecular modeling approaches in that it uses unique representations of chemical structures in the form of multiple chemical descriptors; has its own metrics for defining similarity and diversity of chemical compound libraries; and applies a wide array of statistical, data mining and machine learning techniques to very large collections of chemical compounds in order to establish robust relationships between chemical structure and its physical or biological properties. Chemoinformatics addresses a broad range of problems in chemistry and biology; however, the most commonly known applications of chemoinformatics approaches have been arguably in the area of drug discovery where chemoinformatics tools have played a central role in the analysis and interpretation of structure-property data collected by the means of modern high throughput screening. Early stages in modern drug discovery often involved screening small molecules for their effects on a selected protein target or a model of a biological pathway. In the past fifteen years, innovative technologies that enable rapid synthesis and high throughput screening of large libraries of compounds have been adopted in almost all major pharmaceutical and biotech companies. As a result, there has been a huge increase in the number of compounds available on a routine basis to quickly screen for novel drug candidates against new targets/pathways. In contrast, such technologies have rarely become available to the academic research community, thus limiting its ability to conduct large scale chemical genetics or chemical genomics research. However, the landscape of publicly available experimental data collection methods for chemoinformatics has changed dramatically in very recent years. The term "virtual screening" is commonly associated with methodologies that rely on the explicit knowledge of three-dimensional structure of the target protein to identify potential bioactive compounds. Traditional docking protocols and scoring functions rely on explicitly defined three dimensional coordinates and standard definitions of atom types of both receptors and ligands. Albeit reasonably accurate in many cases, conventional structure based virtual screening approaches are relatively computationally inefficient, which has precluded them from screening really large compound collections. Significant progress has been achieved over many years of research in developing many structure based virtual screening approaches. This book is the first monograph that summarizes innovative applications of efficient chemoinformatics approaches towards the goal of screening large chemical libraries. The focus on virtual screening expands chemoinformatics beyond its traditional boundaries as a synthetic and data-analytical area of research towards its recognition as a predictive and decision support scientific discipline. The approaches discussed by the contributors to the monograph rely on chemoinformatics concepts such as: -representation of molecules using multiple descriptors of chemical structures -advanced chemical similarity calculations in multidimensional descriptor spaces -the use of advanced machine learning and data mining approaches for building quantitative and predictive structure activity models -the use of chemoinformatics methodologies for the analysis of drug-likeness and property prediction -the emerging trend on combining chemoinformatics and bioinformatics concepts in structure based drug discovery The chapters of the book are organized in a logical flow that a typical chemoinformatics project would follow - from structure representation and comparison to data analysis and model building to applications of structure-property relationship models for hit identification and chemical library design. It opens with the overview of modern methods of compounds library design, followed by a chapter devoted to molecular similarity analysis. Four sections describe virtual screening based on the using of molecular fragments, 2D pharmacophores and 3D pharmacophores. Application of fuzzy pharmacophores for libraries design is the subject of the next chapter followed by a chapter dealing with QSAR studies based on local molecular parameters. Probabilistic approaches based on 2D descriptors in assessment of biological activities are also described with an overview of the modern methods and software for ADME prediction. The book ends with a chapter describing the new approach of coding the receptor binding sites and their respective ligands in multidimensional chemical descriptor space that affords an interesting and efficient alternative to traditional docking and screening techniques. Ligand-based approaches, which are in the focus of this work, are more computationally efficient compared to structure-based virtual screening and there are very few books related to modern developments in this field. The focus on extending the experiences accumulated in traditional areas of chemoinformatics research such as Quantitative Structure Activity Relationships (QSAR) or chemical similarity searching towards virtual screening make the theme of this monograph essential reading for researchers in the area of computer-aided drug discovery. However, due to its generic data-analytical focus there will be a growing application of chemoinformatics approaches in multiple areas of chemical and biological research such as synthesis planning, nanotechnology, proteomics, physical and analytical chemistry and chemical genomics.
Category: Science

Structure Based Drug Discovery

Author : Roderick E Hubbard
ISBN : 9781847552549
Genre : Medical
File Size : 63.87 MB
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Structure-based drug discovery is a collection of methods that exploits the ability to determine and analyse the three dimensional structure of biological molecules. These methods have been adopted and enhanced to improve the speed and quality of discovery of new drug candidates. After an introductory overview of the principles and application of structure-based methods in drug discovery, this book then describes the essential features of the various methods. Chapters on X-ray crystallography, NMR spectroscopy, and computational chemistry and molecular modelling describe how these particular techniques have been enhanced to support rational drug discovery, with discussions on developments such as high throughput structure determination, probing protein-ligand interactions by NMR spectroscopy, virtual screening and fragment-based drug discovery. The concluding chapters complement the overview of methods by presenting case histories to demonstrate the major impact that structure-based methods have had on discovering drug molecules. Written by international experts from industry and academia, this comprehensive introduction to the methods and practice of structure-based drug discovery not only illustrates leading-edge science but also provides the scientific background for the non-expert reader. The book provides a balanced appraisal of what structure-based methods can and cannot contribute to drug discovery. It will appeal to industrial and academic researchers in pharmaceutical sciences, medicinal chemistry and chemical biology, as well as providing an insight into the field for recent graduates in the biomolecular sciences.
Category: Medical

Virtual Drug Design

Author : Daniela Schuster
ISBN : 9782889633593
Genre :
File Size : 41.67 MB
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In the current drug research environment in academia and industry, cheminformatics and virtual screening methods are well established and integrated tools. Computational tools are used to predict a compound’s 3D structure, the 3D structure and function of a pharmacological target, ligand-target interactions, binding energies, and other factors essential for a successful drug. This includes molecular properties such as solubility, logP value, susceptibility to metabolism, cell permeation, blood brain barrier permeation, interaction with drug transporters and potential off-target effects. Given that approximately 40 million unique compounds are readily available for purchase, such computational modeling and filtering tools are essential to support the drug discovery and development process. The aim of all these calculations is to focus experimental efforts on the most promising candidates and exclude problematic compounds early in the project. In this Research Topic on virtual activity predictions, we cover several aspects of this research area such as historical perspectives, data sources, ligand treatment, virtual screening methods, hit list handling and filtering.
Category:

Computer Applications In Drug Discovery And Development

Author : Puratchikody, A.
ISBN : 9781522573272
Genre : Medical
File Size : 47.97 MB
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With more restrictions upon animal experimentations, pharmaceutical industries are currently focusing on a new generation of experiments and technologies that are considerably more efficient and less controversial. The integration of computational and experimental strategies has led to the identification and development of promising compounds. Computer Applications in Drug Discovery and Development is a pivotal reference source that provides innovative research on the application of computers for discovering and designing new drugs in modern molecular biology and medicinal chemistry. While highlighting topics such as chemical structure databases and dataset utilization, this publication delves into the current panorama of drug discovery, where high drug failure rates are a major concern and properly designed virtual screening strategies can be a time-saving, cost-effective, and productive alternative. This book is ideally designed for chemical engineers, pharmacists, molecular biologists, students, researchers, and academicians seeking current research on the unexplored avenues and future perspectives of drug design.
Category: Medical

Chemoinformatics Approaches To Structure And Ligand Based Drug Design

Author : Adriano D. Andricopulo
ISBN : 9782889457441
Genre :
File Size : 65.17 MB
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Chemoinformatics is paramount to current drug discovery. Structure- and ligand-based drug design strategies have been used to uncover hidden patterns in large amounts of data, and to disclose the molecular aspects underlying ligand-receptor interactions. This Research Topic aims to share with a broad audience the most recent trends in the use of chemoinformatics in drug design. To that end, experts in all areas of drug discovery have made their knowledge available through a series of articles that report state-of-the-art approaches. Readers are provided with outstanding contributions focusing on a wide variety of topics which will be of great value to those interested in the many different and exciting facets of drug design.
Category:

Virtual Screening For Bioactive Molecules

Author : Hans-Joachim Böhm
ISBN : 9783527613090
Genre : Science
File Size : 89.35 MB
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Recent progress in high-throughput screening, combinatorial chemistry and molecular biology has radically changed the approach to drug discovery in the pharmaceutical industry. New challenges in synthesis result in new analytical methods. At present, typically 100,000 to one million molecules have to be tested within a short period and, therefore, highly effective screening methods are necessary for today's researchers - preparing and characterizing one compound after another belongs to the past. Intelligent, computer-based search agents are needed and "virtual screening" provides solutions to many problems. Such screening comprises innovative computational techniques designed to turn raw data into valuable chemical information and to assist in extracting the relevant molecular features. This handbook is unique in bringing together the various efforts in the field of virtual screening to provide the necessary methodological framework for more effective research. Leading experts give a thorough introduction to the state of the art along with a critical assessment of both successful applications and drawbacks. The information collated here will be indispensable for experienced scientists, as well as novices, working in medicinal chemistry and related disciplines.
Category: Science

Virtual Screening

Author : Gerhard Klebe
ISBN : OCLC:59541176
Genre : Drugs
File Size : 48.1 MB
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Category: Drugs

Chemoinformatics In Drug Discovery

Author : Tudor I. Oprea
ISBN : 9783527604203
Genre : Science
File Size : 87.69 MB
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This handbook provides the first-ever inside view of today's integrated approach to rational drug design. Chemoinformatics experts from large pharmaceutical companies, as well as from chemoinformatics service providers and from academia demonstrate what can be achieved today by harnessing the power of computational methods for the drug discovery process. With the user rather than the developer of chemoinformatics software in mind, this book describes the successful application of computational tools to real-life problems and presents solution strategies to commonly encountered problems. It shows how almost every step of the drug discovery pipeline can be optimized and accelerated by using chemoinformatics tools -- from the management of compound databases to targeted combinatorial synthesis, virtual screening and efficient hit-to-lead transition. An invaluable resource for drug developers and medicinal chemists in academia and industry.
Category: Science

Platform Technologies In Drug Discovery And Validation

Author :
ISBN : 9780128130704
Genre : Medical
File Size : 60.31 MB
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Platform Technologies in Drug Discovery and Validation, Volume 50, the latest release in the Annual Reports in Medicinal Chemistry series, provides timely and critical reviews of important topics in medicinal chemistry, with an emphasis on emerging topics in the biological sciences. Topics covered in this new volume include DELT, Oligos: ASO, siRNA, CRISPR, Micro-fluidic chemistry, High throughput screening, Kinase-centric computational drug development, Virtual Screening, Phenotypic screening, PROTACS, Chemical Biology, Fragment-based lead generation, Antibody-Drug Conjugates, Antibody-recruiting small molecules, Deuteration, and Peptides. Unique for its treatment of platform technologies for medicinal chemistry and target validation Provides a single, rich volume that summaries a broad spectrum of expertise relevant to the field Presents state-of-the-art summaries of platform technologies
Category: Medical

Drug Design

Author : Royal Society of Chemistry (Great Britain)
ISBN : 0854048162
Genre : Medical
File Size : 77.84 MB
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Providing details of state-of-the-art research, Drug Design: Cutting Edge Approaches will be invaluable to all drug discovery scientists.
Category: Medical

Computational Drug Discovery And Design

Author : Mohini Gore
ISBN : 1493977555
Genre : Medical
File Size : 26.30 MB
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This volume details methods and techniques for identification of drug targets, binding sites prediction, high-throughput virtual screening,and prediction of pharmacokinetic properties using computer based methodologies. Chapters guide readers through techniques of the available computational tools, developing prediction models for drug target prediction and de novo design of ligands, structure based drug designing, fragment-based drug designing, molecular docking, and scoring functions for assessing protein-ligand docking protocols. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Drug Discovery and Design aims to provide protocols for the use of bioinformatics tools in drug discovery and design.
Category: Medical

Burger S Medicinal Chemistry And Drug Discovery Drug Discovery

Author : Donald J. Abraham
ISBN : 0471270903
Genre : Science
File Size : 46.12 MB
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This is Volume 1: Drug Discovery, of Burger's Medicinal Chemistry and Drug Discovery, 6th Edition. This new volume contains critical new chapters on Virtual Screening, Bioinformatics and Chemical Information Computing Systems in Drug Discovery. To purchase the entire 6 volume set, please refer to ISBN 0-471-37032-0. For a complete list of articles and contributors as well as FREE sample chapters from this new 6th Edition please visit: www.mrw.interscience.wiley.com/bmcdd
Category: Science

Small Molecule Drug Discovery

Author : Andrea Trabocchi
ISBN : 9780128183502
Genre : Science
File Size : 37.60 MB
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Small Molecule Drug Discovery: Methods, Molecules and Applications presents the methods used to identify bioactive small molecules, synthetic strategies and techniques to produce novel chemical entities and small molecule libraries, chemoinformatics to characterize and enumerate chemical libraries, and screening methods, including biophysical techniques, virtual screening and phenotypic screening. The second part of the book gives an overview of privileged cyclic small molecules and major classes of natural product-derived small molecules, including carbohydrate-derived compounds, peptides and peptidomimetics, and alkaloid-inspired compounds. The last section comprises an exciting collection of selected case studies on drug discovery enabled by small molecules in the fields of cancer research, CNS diseases and infectious diseases. The discovery of novel molecular entities capable of specific interactions represents a significant challenge in early drug discovery. Small molecules are low molecular weight organic compounds that include natural products and metabolites, as well as drugs and other xenobiotics. When the biological target is well defined and understood, the rational design of small molecule ligands is possible. Alternatively, small molecule libraries are being used for unbiased assays for complex diseases where a target is unknown or multiple factors contribute to a disease pathology. Outlines modern concepts and synthetic strategies underlying the building of small molecules and their chemical libraries useful for drug discovery Provides modern biophysical methods to screening small molecule libraries, including high-throughput screening, small molecule microarrays, phenotypic screening and chemical genetics Presents the most advanced chemoinformatics tools to characterize the structural features of small molecule libraries in terms of chemical diversity and complexity, also including the application of virtual screening approaches Gives an overview of structural features and classification of natural product-derived small molecules, including carbohydrate derivatives, peptides and peptidomimetics, and alkaloid-inspired small molecules
Category: Science

Structural Bioinformatics Applications In Preclinical Drug Discovery Process

Author : C. Gopi Mohan
ISBN : 9783030052829
Genre : Science
File Size : 44.55 MB
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This book reviews the advances and challenges of structure-based drug design in the preclinical drug discovery process, addressing various diseases, including malaria, tuberculosis and cancer. Written by internationally recognized researchers, this edited book discusses how the application of the various in-silico techniques, such as molecular docking, virtual screening, pharmacophore modeling, molecular dynamics simulations, and residue interaction networks offers insights into pharmacologically active novel molecular entities. It presents a clear concept of the molecular mechanism of different drug targets and explores methods to help understand drug resistance. In addition, it includes chapters dedicated to natural-product- derived medicines, combinatorial drug discovery, the CryoEM technique for structure-based drug design and big data in drug discovery. The book offers an invaluable resource for graduate and postgraduate students, as well as for researchers in academic and industrial laboratories working in the areas of chemoinformatics, medicinal and pharmaceutical chemistry and pharmacoinformatics.
Category: Science

Fragment Based Drug Discovery

Author : Edward R. Zartler
ISBN : 9780470721568
Genre : Science
File Size : 78.92 MB
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Fragment-based drug discovery (FBDD) is a new paradigm in drug discovery that utilizes very small molecules - fragments of larger molecules. It is a faster, cheaper, smarter way to do drug discovery, as shown by the number of pharmaceutical companies that have embraced this approach and the biotechnology companies who use fragments as their sole source of drug discovery. Fragment-Based Drug Discovery: A Practical Approach is a guide to the techniques and practice of using fragments in drug screening. The emphasis is on practical guidance, with procedures, case studies, practical tips, and contributions from industry. Topics covered include: an introduction to fragment based drug discovery, why using fragments is a more efficient process than predominant models, and what it means to have a successful FBDD effort. setting up an FBDD project library building and production NMR in fragment screening and follow up application of protein-ligand NOE matching to the rapid evaluation of fragment binding poses target immobilized NMR screening: validation and extension to membrane proteins in situ fragment-based medicinal chemistry: screening by mass spectrometry computational approaches to fragment and substructure discovery and evaluation virtual fragment scanning: current trends, applications and web based tools fragment-based lead discovery using covalent capture methods case study from industry: the identification of high affinity beta-secretase inhibitors using fragment-based lead generation With contributions from industry experts who have successfully set up an industrial fragment-based research program, Fragment-Based Drug Discovery: A Practical Approach offers essential advice to anyone embarking on drug discovery using fragments and those looking for a new approach to screening for drugs.
Category: Science

Chemoinformatics

Author : Jürgen Bajorath
ISBN : 9781592598021
Genre : Medical
File Size : 38.2 MB
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Well-recognized pioneers and investigators from diverse professional environments survey the key concepts in the field, describe cutting-edge methods, and provide exemplary pharmaceutical applications. The authors explain the theory behind the crucial concepts of molecular similarity and diversity, describe the challenging efforts to use chemoinformatics approaches to virtual and high-throughput screening, and illuminate the latest developments in multidimensional QSAR analysis. Other topics of interest include the use of partitioning algorithms and classification methods for analyzing large compound databases, screening sets, and virtual screening for active molecules; different approaches to target class-specific library design; and the generation of a novel class of molecular surface properties descriptors that can be readily calculated from 2D representations of molecular structures. Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery illuminates the conceptual and methodological diversity of this rapidly evolving field and offers instructive examples of cutting-edge applications in the drug discovery process. Understand the key concepts and novel methods behind chemoinformatics See cutting-edge chemoinformatic methods applied to the drug discovery process Appreciate the conceptual and methodological diversity of chemoinformatics Master the basics of machine learning, library design, and ADME modeling.
Category: Medical

Computational Chemogenomics

Author : Edgar Jacoby
ISBN : 9789814411400
Genre : Medical
File Size : 88.4 MB
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This book focuses on applications of compound library design and virtual screening to expand the bioactive chemical space, to target hopping of chemotypes to identify synergies within related drug discovery projects or to repurpose known drugs, to propose mechanism of action of compounds, or to identify off-target effects by cross-reactivity analysis. Both ligand-based and structure-based in silico approaches, as reviewed in this book, play important roles for all these applications. Computational chemogenomics is expected to increase the quality and productivity of drug discovery and lead to the discovery of new medicines.
Category: Medical