Atomic-Level Characterization of the Distinct Methadone-Induced Conformational Sampling and Activation Kinetics of the µ-Opioid Receptor by Molecular Simulations

Abstract

Although commonly associated with the treatment of opioid addiction, and structurally different from morphine, methadone is a synthetic opioid agonist of the µ-opioid receptor (MOR) with demonstrated efficiency in the management of chronic pain owing to its unique pharmacokinetics and pharmacodynamics properties. A recent biophysical study suggests that methadone's unique pharmacological features lie in its ability to stabilize distinct MOR active conformations from those induced by classical opioid drugs or G protein-biased agonists. However, the specific effects of methadone on the conformational sampling and activation kinetics of MOR remain largely uncharacterized at the atomic level. To shed light upon this matter, we explored the methadone-induced conformational space of MOR in an explicit lipid-water environment using ∼0.3 ms of enhanced molecular dynamics (MD) simulations, and compared it to the receptor conformational sampling of previously published ∼0.5 ms of high-throughput MD simulations of MOR bound to the classical opioid drug morphine or the G protein-biased ligand TRV-130. Markov State Models (MSMs) built using these large datasets revealed distinct ligand-induced conformational dynamics and activation kinetics of MOR. Predicted equilibrium probabilities from these MSMs suggest that the three explored ligand-bound MOR complexes differentially populate active, inactive, and metastable regions along their respective activation pathways. Finally, transfer entropy estimates based on information theory were used to identify the distinct structural features that most contribute to the activation-induced conformational changes in the three ligand-bound MOR complexes.