(PDF) Computational Methods for GPCR Drug Discovery by Alexander Heifetz

This is the PDF eBook version for Computational Methods for GPCR Drug Discovery by Alexander Heifetz

Table of Contents

Preface…
Table of Contents…
Contributing Authors…

1. Current and Future Challenges in GPCR Drug Discovery
Sid Topiol

2. Characterization of Ligand Binding to GPCRs through Computational Methods
Silvana Vasile, Mauricio Esguerra, Willem Jespers, Ana Oliveira, Jessica Sallander, Johan Åqvist, and Hugo Gutiérrez-de-Terán

3. Breakthrough in GPCR Crystallography and its Impact on Computer-Aided Drug Design
Antonella Ciancetta and Kenneth A. Jacobson

4. 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, and Chris de Graaf

5. GPCR Homology Model Generation for Lead Optimization
Christofer S. Tautermann

6. GPCRs: What Can We Learn from Molecular Dynamics Simulations?
Naushad Velgy, George Hedger, and Philip C. Biggin

7. Methods of Exploring Protein-Ligand Interactions to Guide Medicinal Chemistry Efforts

Paul Labute
8. 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, Michelle Southey, Roger Robinson, Inaki Morao, and Alexander Heifetz

9. Molecular Basis of Ligand Dissociation from G Protein-Coupled Receptors and Predicting Residence Time
Dong Guo and Adriaan P. IJzerman

10. Methodologies for the Examination of Water in GPCRs
Andrea Bortolato, Benjamin G. Tehan, Robert T. Smith, and Jonathan S. Mason

11. Methods for Virtual Screening of GPCR Targets: Approaches and Challenges
Jason B. Cross

12. Approaches for Differentiation and Interconverting GPCR Agonists and Antagonists
Przemyslaw Miszta, Jakub Jakowiecki, Ewelina Rutkowska, Maria Turant, Dorota Latek, and Slawomir Filipek

13. Opportunities and Challenges in the Discovery of Allosteric Modulators of GPCRs
Damian Bartuzi, Agnieszka A. Kaczor, and Dariusz Matosiuk

14. Challenges and Opportunities in Drug Discovery of Biased Ligands
Ismael Rodríguez-Espigares, Agnieszka A. Kaczor, Tomasz Maciej Stepniewski, and Jana Selent

15. Synergistic Use of GPCR Modeling and SDM Experiments to Understand Ligand Binding
Andrew Potterton, Alexander Heifetz, and Andrea Townsend-Nicholson

16. Computational Support of Medicinal Chemistry Effort in Industrial Setting
Daniel F. Ortwine

17. Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations
Kristen A. Marino and Marta Filizola

18. Ligand-Based Methods in GPCR Computer-Aided Drug Design
Paul C. D. Hawkins and Gunther Stahl

19. 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, and Mike J. Bodkin

20. Cheminformatics in the Service of GPCR Drug Discovery
Tim James

21. Modeling and Deorphanization of Orphan GPCRs
Constantino Diaz, Patricia Angelloz-Nicoud, and Emilie Pihan