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J Chem Inf Model. 2014 Jan 27;54(1):169-83. doi: 10.1021/ci400532b. Epub 2014 Jan 8.

Bridging molecular docking to membrane molecular dynamics to investigate GPCR-ligand recognition: the human A₂A adenosine receptor as a key study.

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  • 1Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova , via Marzolo 5, 35131 Padova, Italy.

Abstract

G protein-coupled receptors (GPCRs) represent the largest family of cell-surface receptors and about one-third of the actual targets of clinically used drugs. Following the progress made in the field of GPCRs structural determination, docking-based screening for novel potent and selective ligands is becoming an increasingly adopted strategy in the drug discovery process. However, this methodology is not yet able to anticipate the "bioactive" binding mode and discern it among other conformations. In the present work, we present a novel approach consisting in the integration of molecular docking and membrane MD simulations with the aim to merge the rapid sampling of ligand poses into in the binding site, typical of docking algorithms, with the thermodynamic accuracy of MD simulations in describing, at the molecular level, the stability a GPCR-ligand complex embedded into explicit lipid-water environment. To validate our approach, we have chosen as a key study the human A(2A) adenosine receptor (hA(2A) AR) and selected four receptor-antagonist complexes and one receptor-agonist complex that have been recently crystallized. In light of the obtained results, we believe that our novel strategy can be extended to other GPCRs and might represent a valuable tool to anticipate the "bioactive" conformation of high-affinity ligands.

PMID:
24359090
DOI:
10.1021/ci400532b
[PubMed - indexed for MEDLINE]
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