Comparative Study of Allosteric GPCR Binding Sites\nand Their Ligandability Potential

The steadily growing\nnumber of experimental G-protein-coupled receptor\n(GPCR) structures has revealed diverse locations of allosteric modulation,\nand yet few drugs target them. This gap highlights the need for a\ndeeper understanding of allosteric modulation in GPCR drug discovery.\nThe current work introduces a systematic annotation scheme to structurally\nclassify GPCR binding sites based on receptor class, transmembrane\nhelix contacts, and, for membrane-facing sites, membrane sublocation.\nThis GPCR specific annotation scheme was applied to 107 GPCR structures\nbound by small molecules contributing to 24 distinct allosteric binding\nsites for comparative evaluation of three binding site detection methods\n(BioGPS, SiteMap, and FTMap). BioGPS identified the most in 22 of\n24 sites. In addition, our property analysis showed that extrahelical\nallosteric ligands and binding sites represent a distinct chemical\nspace characterized by shallow pockets with low volume, and the corresponding\nallosteric ligands showed an enrichment of halogens. Furthermore,\nwe demonstrated that combining receptor and ligand similarity can\nbe a viable method for ligandability assessment. One challenge regarding\nsite prediction is the ligand shaping effect on the observed binding\nsite, especially for extrahelical sites where the ligand-induced effect\nwas most pronounced. To our knowledge, this is the first study presenting\na binding site annotation scheme standardized for GPCRs, and it allows\na comparison of allosteric binding sites across different receptors\nin an objective way. The insight from this study provides a framework\nfor future GPCR binding site studies and highlights the potential\nof targeting allosteric sites for drug development.