Structural and functional determination of peptide versus small molecule ligand binding at the apelin receptor

Abstract We describe a structural and functional study of the apelin receptor, a G protein-coupled receptor (GPCR) that binds two endogenous peptide ligands, apelin and Elabela/Toddler (ELA), to regulate cardiovascular development and function. Characterisation of novel, naturally occurring apelin receptor variants from the UK Genomics England 100,000 Genomes Project, in combination with AlphaFold2 modelling, identified T892.64 as an important residue in the ELA binding site, and R1684.64 as forming extensive interactions with the C-termini of both peptides. Base editing to introduce an R/H1684.64 variant into stem cell-derived cardiomyocytes demonstrated that this residue is critical for receptor binding and function in a clinically relevant setting. Additionally, we present a novel apelin receptor crystal structure bound to the G protein-biased, small molecule agonist, CMF-019, which revealed a deeper binding mode versus peptides at lipophilic pockets between transmembrane helices associated with GPCR activation. Overall, the data provide proof-of-principle for using genetic variation to fast-track the identification and characterisation of key sites that regulate receptor-ligand engagement, potentially informing future drug design.