Hybrid Molecular Mechanics/Coarse-Grained Simulations for Structural Prediction of G-Protein Coupled Receptor/Ligand Complexes

Michael Leguèbe, Chuong Nguyen, Luciana Capece, Zung Hoang, Alejandro Giorgetti and Paolo Carloni

PLOS ONE, 2012, vol. 7, issue 10, 1-7

Abstract: Understanding how ligands bind to G-protein coupled receptors (GPCRs) provides insights into a myriad of cell processes and is crucial for drug development. Here we extend a hybrid molecular mechanics/coarse-grained (MM/CG) approach applied previously to enzymes to GPCR/ligand complexes. The accuracy of this method for structural predictions is established by comparison with recent atomistic molecular dynamics simulations on the human β2 adrenergic receptor, a member of the GPCRs superfamily. The results obtained with the MM/CG methodology show a good agreement with previous all-atom classical dynamics simulations, in particular in the structural description of the ligand binding site. This approach could be used for high-throughput predictions of ligand poses in a variety of GPCRs.

Date: 2012
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0047332

DOI: 10.1371/journal.pone.0047332

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