Probe Confined Dynamic Mapping for G Protein-Coupled Receptor Allosteric Site Prediction

Antonella Ciancetta, Amandeep Kaur Gill, Tianyi Ding, Dmitry S. Karlov, George Chalhoub, Peter J. McCormick, Irina G. Tikhonova

Research output: Contribution to journalArticlepeer-review

14 Citations (Scopus)
127 Downloads (Pure)


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.
Original languageEnglish
JournalACS Central Science
Early online date28 Sept 2021
Publication statusEarly online date - 28 Sept 2021


  • General Chemical Engineering
  • General Chemistry


Dive into the research topics of 'Probe Confined Dynamic Mapping for G Protein-Coupled Receptor Allosteric Site Prediction'. Together they form a unique fingerprint.

Cite this