Exploring Druggable Binding Sites on the Class A GPCRs Using the Residue Interaction Network and Site Identification by Ligand Competitive Saturation.

Abstract

G protein-coupled receptors (GPCRs) play a central role in cellular signaling and are linked to many diseases. Accordingly, computational methods to explore potential allosteric sites for this class of proteins to facilitate the identification of potential modulators are needed. Importantly, the availability of rich structural data providing the locations of the orthosteric ligands and allosteric modulators targeting different GPCRs allows for the validation of approaches to identify new allosteric binding sites. Here, we validate the combination of two computational techniques, the residue interaction network (RIN) model and the site identification by ligand competitive saturation (SILCS) method, to predict putative allosteric binding sites of class A GPCRs. RIN analysis identifies hub residues that mediate allosteric signaling within a receptor and have a high capacity to alter receptor dynamics upon ligand binding. The known orthosteric (and allosteric) binding sites of 18 distinct class A GPCRs were successfully predicted by RIN through a dataset of 105 crystal structures (91 ligand-bound, 14 unbound) with up to 77.8% (76.9%) sensitivity, 92.5% (95.3%) specificity, 51.9% (50%) precision, and 86.2% (92.4%) accuracy based on the experimental and theoretical binding site data. Moreover, graph spectral analysis of the residue networks revealed that the proposed sites were located at the interfaces of highly interconnected residue clusters with a high ability to coordinate the functional dynamics. Then, we employed the SILCS-Hotspots method to assess the druggability of the novel sites predicted for 7 distinct class A GPCRs that are critical for a variety of diseases. While the known orthosteric and allosteric binding sites are successfully explored by our approach, numerous putative allosteric sites with the potential to bind drug-like molecules are proposed. The computational approach presented here promises to be a highly effective tool to predict putative allosteric sites of GPCRs to facilitate the design of effective modulators.