Identification of ligand-specific G-protein coupled receptor states and prediction of downstream efficacy via data-driven modeling [article]

Oliver Fleetwood, Jens Carlsson, Lucie Delemotte
2020 bioRxiv   pre-print
G protein-coupled receptors (GPCRs) shift between inactive non-signalling states and active signalling states, to which intracellular binding partners can bind. Extracellular binding of ligands stabilizes different receptor states and modulates the intracellular response via a complex and not well understood allosteric process. Despite the recent advances in structure determination and spectroscopy techniques, a comprehensive view of the ligand-protein interplay remains a challenge. We derived
more » ... he activation free energy of the β2 adrenergic receptor (β2AR) bound to ligands with different efficacy profiles using enhanced sampling molecular dynamics (MD) simulations. The resulting free energy landscapes reveal clear shifts towards active-like states at the G protein binding site for receptors bound to partial and full agonists compared to antagonists and inverse agonists. Not only do the ligands control the population of states, they also modulate the receptors conformational ensemble by flipping allosteric protein microswitches. We find an excellent correlation between the conformation of the microswitches close to the ligand binding site and in the transmembrane region and experimentally reported cAMP signaling responses, highlighting the predictive power of our approach. Using dimensionality reduction techniques, we could further assess the similarity between the unique states induced by different ligands. Two hotspots governing agonism on transmembrane helix 5 (TM5) and TM7, including the conserved NPxxY motif, formed the endpoints of an allosteric pathway between the binding sites. Our results demonstrate that computational methods can be used to assess GPCR drug candidates with specific efficacy profiles.
doi:10.1101/2020.07.06.186601 fatcat:w4fwbh3p7nhm5eurbwn4wml3fu