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Computational Methods for GPCR Drug Discovery

  • Book
  • © 2018

Overview

Editors:
  1. Alexander Heifetz

    1. Evotec (UK) Ltd., Abingdon, United Kingdom

    View editor publications

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1705)

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Table of contents (21 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Current and Future Challenges in GPCR Drug Discovery

    • Sid Topiol
    Pages 1-21

  3. Characterization of Ligand Binding to GPCRs Through Computational Methods

    • Silvana Vasile, Mauricio Esguerra, Willem Jespers, Ana Oliveira, Jessica Sallander, Johan Åqvist et al.
    Pages 23-44

  4. Breakthrough in GPCR Crystallography and Its Impact on Computer-Aided Drug Design

    • Antonella Ciancetta, Kenneth A. Jacobson
    Pages 45-72

  5. A Structural Framework for GPCR Chemogenomics: What’s In a Residue Number?

    • Márton Vass, Albert J. Kooistra, Stefan Verhoeven, David Gloriam, Iwan J. P. de Esch, Chris de Graaf
    Pages 73-113

  6. GPCR Homology Model Generation for Lead Optimization

    • Christofer S. Tautermann
    Pages 115-131

  7. GPCRs: What Can We Learn from Molecular Dynamics Simulations?

    • Naushad Velgy, George Hedger, Philip C. Biggin
    Pages 133-158

  8. Methods of Exploring Protein–Ligand Interactions to Guide Medicinal Chemistry Efforts

    • Paul Labute
    Pages 159-177

  9. Exploring GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method

    • Ewa I. Chudyk, Laurie Sarrat, Matteo Aldeghi, Dmitri G. Fedorov, Mike J. Bodkin, Tim James et al.
    Pages 179-195

  10. Molecular Basis of Ligand Dissociation from G Protein-Coupled Receptors and Predicting Residence Time

    • Dong Guo, Adriaan P. IJzerman
    Pages 197-206

  11. Methodologies for the Examination of Water in GPCRs

    • Andrea Bortolato, Benjamin G. Tehan, Robert T. Smith, Jonathan S. Mason
    Pages 207-232

  12. Methods for Virtual Screening of GPCR Targets: Approaches and Challenges

    • Jason B. Cross
    Pages 233-264

  13. Approaches for Differentiation and Interconverting GPCR Agonists and Antagonists

    • Przemysław Miszta, Jakub Jakowiecki, Ewelina Rutkowska, Maria Turant, Dorota Latek, Sławomir Filipek
    Pages 265-296

  14. Opportunities and Challenges in the Discovery of Allosteric Modulators of GPCRs

    • Damian Bartuzi, Agnieszka A. Kaczor, Dariusz Matosiuk
    Pages 297-319

  15. Challenges and Opportunities in Drug Discovery of Biased Ligands

    • Ismael Rodríguez-Espigares, Agnieszka A. Kaczor, Tomasz Maciej Stepniewski, Jana Selent
    Pages 321-334

  16. Synergistic Use of GPCR Modeling and SDM Experiments to Understand Ligand Binding

    • Andrew Potterton, Alexander Heifetz, Andrea Townsend-Nicholson
    Pages 335-343

  17. Computational Support of Medicinal Chemistry in Industrial Settings

    • Daniel F. Ortwine
    Pages 345-350

  18. Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations

    • Kristen A. Marino, Marta Filizola
    Pages 351-364

  19. Ligand-Based Methods in GPCR Computer-Aided Drug Design

    • Paul C. D. Hawkins, Gunther Stahl
    Pages 365-374

  20. Computational Methods Used in Hit-to-Lead and Lead Optimization Stages of Structure-Based Drug Discovery

    • Alexander Heifetz, Michelle Southey, Inaki Morao, Andrea Townsend-Nicholson, Mike J. Bodkin
    Pages 375-394
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Keywords

About this book

This volume looks at modern computational strategies and techniques used in GPCR drug discovery including structure and ligand-based approaches and cheminformatics. The chapters in this book describe how these approaches can be applied to address key drug discovery issues, such as receptor structure modelling, function and dynamics, prediction of protein-water-ligand interactions and binding kinetics, free energy of binding, interconversion between agonists and antagonists, deorphanization of GPCRs, and the discovery of biased and allosteric modulators. 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 modelling protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and unique,Computational Methods for GPCR Drug Discovery is a valuable resource for structural and molecular biologists, computational and medicinal chemists, pharmacologists, and drug designers.


Editors and Affiliations

  • Evotec (UK) Ltd., Abingdon, United Kingdom

    Alexander Heifetz

Bibliographic Information

  • Book Title: Computational Methods for GPCR Drug Discovery

  • Editors: Alexander Heifetz

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7465-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2018

  • Hardcover ISBN: 978-1-4939-7464-1Published: 30 November 2017

  • Softcover ISBN: 978-1-4939-8494-7Published: 30 August 2018

  • eBook ISBN: 978-1-4939-7465-8Published: 28 November 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 436

  • Number of Illustrations: 9 b/w illustrations, 102 illustrations in colour

  • Topics: Pharmacology/Toxicology

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