Probe Confined Dynamic Mapping for G Protein-Coupled Receptor Allosteric Site Prediction
journal contributionposted on 28.09.2021, 17:11 by Antonella Ciancetta, Amandeep Kaur Gill, Tianyi Ding, Dmitry S. Karlov, George Chalhoub, Peter J. McCormick, Irina G. Tikhonova
Targeting G protein-coupled receptors (GPCRs) through allosteric sites offers advantages over orthosteric sites in identifying drugs with increased selectivity and potentially reduced side effects. In this study, we developed a probe confined dynamic mapping protocol that allows the prediction of allosteric sites at both the GPCR extracellular and intracellular sides, as well as at the receptor–lipid interface. The applied harmonic wall potential enhanced sampling of probe molecules in a selected area of a GPCR while preventing membrane distortion in molecular dynamics simulations. The specific probes derived from GPCR allosteric ligand structures performed better in allosteric site mapping compared to commonly used cosolvents. The M2 muscarinic, β2 adrenergic, and P2Y1 purinergic receptors were selected for the protocol’s retrospective validation. The protocol was next validated prospectively to locate the binding site of [5-fluoro-4-(hydroxymethyl)-2-methoxyphenyl]-(4-fluoro-1H-indol-1-yl)methanone at the D2 dopamine receptor, and subsequent mutagenesis confirmed the prediction. The protocol provides fast and efficient prediction of key amino acid residues surrounding allosteric sites in membrane proteins and facilitates the structure-based design of allosteric modulators.
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yl ) methanonesubsequent mutagenesis confirmedspecific probes derivednext validated prospectivelymolecular dynamics simulationsmethoxyphenyl ]-( 4commonly used cosolventspreventing membrane distortionprotocol provides fast2 </ sub1 </ subh </membrane proteinsretrospective validationpurinergic receptorsprotocol ’probe moleculesorthosteric sitesintracellular sidesincreased selectivityidentifying drugsg proteindopamine receptorcoupled receptorsbinding sitebased designallosteric sitesallosteric modulators>- indol