Pharmacological proximities in the GPCR family discovered using contact-informed amino-acid and binding pocket similarities

Understanding protein proximities in the theoretical ligand space is essential for developing therapeutics with desirable polypharmacology, predicting off-targets, and discovering surrogate ligands for poorly characterized proteins. This is especially important for G protein-coupled receptors (GPCRs) - a major class of drug targets, many of which still lack known ligands. Circumventing this limitation, we present GPCR-CoINPocket v2, a contact-informed metric for detecting GPCR pharmacological similarities from amino-acid sequences alone. We first establish a “gold standard” of pharmacological relatedness using ChEMBL-derived ligand sets. We then replace traditional evolutionary amino acid similarity matrices with a chemically-informed matrix derived from protein:ligand interaction patterns across 3,306 structures, significantly improving early detection of shared pharmacology between distantly homologous receptors. An additional unconstrained, contact-informed matrix further enhances predictive performance. Pilot application of the method revealed previously unrecognized similarities between the β ₂ adrenoceptor and three Class A peptide GPCRs, which we confirmed experimentally by demonstrating the binding of select ligands of these receptors to the β ₂ . Dimensionality reduction of similarity scores recapitulates known receptor relationships and predicts neighbors of orphan GPCRs later confirmed experimentally. Overall, GPCR-CoINPocket v2 provides a powerful sequence-based framework to prioritize ligand space, predict polypharmacology, and accelerate GPCR drug discovery and deorphanization.