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Applied biophysics for drug discovery

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Title (user) : Applied biophysics for drug discoveryISBN : 9781119099499,1119099498,9781119099512,111909951XDOI : 10.1002/9781119099512GoogleBook ID : kuMsDwAAQBAJAuthors (user) : Donald Preston Huddler, Edward ZartlerAuthors (google) : Donald Huddler,Edward R. ZartlerPublisher : John Wiley & Sons LtdLanguage : EnglishPublicat...
Description

Title (user) : Applied biophysics for drug discovery

ISBN : 9781119099499,1119099498,9781119099512,111909951X

DOI : 10.1002/9781119099512

GoogleBook ID : kuMsDwAAQBAJ

Authors (user) : Donald Preston Huddler, Edward Zartler

Authors (google) : Donald Huddler,Edward R. Zartler

Publisher : John Wiley & Sons Ltd

Language : English

Publication Date : 2017

File Format : pdf

Categories : Science


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Description (user) :
"This book 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 Read more...


Abstract:
Applied Biophysics for Drug Discovery is a guide to new techniques and approaches to identifying and characterizing small molecules in early drug discovery. Read more...


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Description (google) :
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.


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Table of contents :
Content: Title Page
Copyright Page
Contents
List of Contributors
Chapter 1 Introduction
References
Chapter 2 Thermodynamics in Drug Discovery
2.1 Introduction
2.2 Methods for Measuring Thermodynamics of Biomolecular Interactions
2.2.1 Direct Method: Isothermal Titration Calorimetry
2.2.2 Indirect Methods: van't Hoff Analysis
2.2.2.1 Enthalpy Measurement Using van't Hoff Analysis
2.3 Thermodynamic-Driven Lead Optimization
2.3.1 The Thermodynamic Rules of Thumb
2.3.2 Enthalpy-Entropy Compensation
2.3.3 Enthalpy-Entropy Transduction
2.3.4 The Role of Water 2.4 Enthalpy as a Probe for Binding2.4.1 Thermodynamics in Fragment-Based Drug Design (FBDD)
2.4.2 Experimental Considerations and Limitations When Working with Fragments
2.4.3 Enthalpic Screening
2.5 Enthalpy as a Tool for Studying Complex Interactions
2.5.1 Identifying and Handling Complexity
2.6 Current and Future Prospects for Thermodynamics in Decision-Making Processes
References
Chapter 3 Tailoring Hit Identification and Qualification Methods for Targeting Protein-Protein Interactions
3.1 Introduction
3.2 Structural Characteristics of PPI Interfaces 3.3 Screening Library Properties3.3.1 Standard/Targeted Libraries/DOS
3.3.2 Fragment Libraries
3.3.3 Macrocyclic and Constrained Peptides
3.3.4 DNA-Encoded Libraries
3.4 Hit-Finding Strategies
3.4.1 Small-Molecule Approaches
3.4.2 Peptide-Based Approaches
3.4.3 In Silico Approaches
3.5 Druggability Assessment
3.5.1 Small Molecule: Ligand-Based Approaches
3.5.2 Small Molecule: Protein Structure-Based Approaches
3.6 Allosteric Inhibition of PPIs
3.7 Stabilization of PPIs
3.8 Case Studies
3.8.1 Primary Peptide Epitopes
3.8.1.1 Bromodomains
3.8.2 Secondary Structure Epitopes 3.8.2.1 Bcl-2 3.8.2.2 p53/MDM2
3.8.3 Tertiary Structure Epitopes
3.8.3.1 CD80-CD28
3.8.3.2 IL-17A
3.9 Summary
References
Chapter 4 Hydrogen-Deuterium Exchange Mass Spectrometry in Drug Discovery --
Theory, Practice and Future
4.1 General Principles
4.2 Parameters Affecting Deuterium Incorporation
4.2.1 Primary Sequence
4.2.2 Intramolecular Hydrogen Bonding
4.2.3 Solvent Accessibility
4.2.4 pH Value
4.3 Utilization of HDX MS
4.3.1 Binding Site and Structural Changes Characterization upon Ligand Binding
4.3.1.1 Protein Stability --
Biosimilar Characterization 4.4 Practical Aspects of HDX MS4.4.1 Labeling
4.4.1.1 Deuterium Oxide and Protein Concentration
4.4.1.2 Ligand/Protein Ratio
4.4.1.3 Incubation-Labeling Time
4.4.1.4 Careful Preparation of the Control Sample
4.4.2 Sample Analysis
4.4.3 Data Analysis
4.5 Advantages of HDX MS
4.6 Perspectives and Future Application of HDX MS
References
Chapter 5 Microscale Thermophoresis in Drug Discovery
5.1 Microscale Thermophoresis
5.1.1 Theoretical Background
5.1.2 Added Values for Small-Molecule Interaction Studies
5.1.2.1 Size-Change Independent Binding Signals

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