Investigating small-molecule ligand binding to g protein-coupled receptors with biased or unbiased molecular dynamics simulations

Kristen A. Marino, Marta Filizola

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

11 Scopus citations

Abstract

An increasing number of G protein-coupled receptor (GPCR) crystal structures provide important—albeit static—pictures of how small molecules or peptides interact with their receptors. These high-resolution structures represent a tremendous opportunity to apply molecular dynamics (MD) simulations to capture atomic-level dynamical information that is not easy to obtain experimentally. Understanding ligand binding and unbinding processes, as well as the related responses of the receptor, is crucial to the design of better drugs targeting GPCRs. Here, we discuss possible ways to study the dynamics involved in the binding of small molecules to GPCRs, using long timescale MD simulations or metadynamics-based approaches.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages351-364
Number of pages14
DOIs
StatePublished - 2018

Publication series

NameMethods in Molecular Biology
Volume1705
ISSN (Print)1064-3745

Keywords

  • Allosteric communication
  • Enhanced-sampling methods
  • GPCRs
  • Interaction fingerprints
  • Ligand binding
  • Molecular dynamics
  • Small-molecule drugs

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