From three-dimensional GPCR structure to rational ligand discovery

Albert J. Kooistra, Rob Leurs, Iwan J.P. De Esch, Chris de Graaf*

*Corresponding author for this work

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Abstract

This chapter will focus on G protein-coupled receptor structure-based virtual screening and ligand design. A generic virtual screening workflow and its individual elements will be introduced, covering amongst others the use of experimental data to steer the virtual screening process, ligand binding mode prediction, virtual screening for novel ligands, and rational structure-based virtual screening hit optimization. An overview of recent successful structure-based ligand discovery and design studies shows that receptor models, despite structural inaccuracies, can be efficiently used to find novel ligands for GPCRs.Moreover, the recently solved GPCR crystal structures have further increased the opportunities in structure-based ligand discovery for this pharmaceutically important protein family. The current chapter will discuss several challenges in rational ligand discovery based on GPCR structures including: (i) structure-based identification of ligands with specific effects on GPCR mediated signaling pathways, and (ii) virtual screening and structure-based optimization of fragment-like molecules.

Original languageEnglish
Title of host publicationG Protein-Coupled Receptors - Modeling and Simulation
EditorsMarta Filizola
PublisherSpringer New York LLC
Chapter7
Pages129-157
Number of pages29
ISBN (Electronic)9789400774230
ISBN (Print)9789400774223
DOIs
Publication statusPublished - 2014

Publication series

NameAdvances in Experimental Medicine and Biology
PublisherSpringer New York
Volume796
ISSN (Print)00652598

Keywords

  • Crystal structures
  • Docking
  • Drug design
  • In silico methods
  • Virtual screening

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