Computational Methods for GPCR Drug Discovery

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.

Current and Future Challenges in GPCR Drug Discovery.- Characterization of Ligand Binding to GPCRs through Computational Methods.- Breakthrough in GPCR Crystallography and its Impact on Computer-Aided Drug Design.- A Structural Framework for GPCR Chemogenomics: What’s in a Residue Number?.- GPCR Homology Model Generation for Lead Optimization.- GPCRs: What Can We Learn from Molecular Dynamics Simulations?.- Methods of Exploring Protein-Ligand Interactions to Guide Medicinal Chemistry Efforts.- Exploring GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method.- Molecular Basis of Ligand Dissociation from G Protein-Coupled Receptors and Predicting Residence Time.- Methodologies for the Examination of Water in GPCRs.- Methods for Virtual Screening of GPCR Targets: Approaches and Challenges.- Approaches for Differentiation and Interconverting GPCR Agonists and Antagonists.- Opportunities and Challenges in the Discovery of Allosteric Modulators of GPCRs.- Challenges andOpportunities in Drug Discovery of Biased Ligands.- Synergistic Use of GPCR Modeling and SDM Experiments to Understand Ligand Binding.- Computational Support of Medicinal Chemistry Effort in Industrial Setting.- Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations.- Ligand-Based Methods in GPCR Computer-Aided Drug Design.- Computational Methods Used in Hit-to-Lead and Lead Optimization Stages of Structure-Based Drug Discovery.- Cheminformatics in the Service of GPCR Drug Discovery.- Modeling and Deorphanization of Orphan GPCRs.