Mapping partial agonism of mitragynine at the µ-opioid receptor through molecular dynamics and Markov state modelling...

Area of Science:

• Pharmacology and Molecular Biophysics
• Computational Chemistry and Molecular Dynamics

Background:

• Mitragynine, a key alkaloid from Mitragyna speciosa (kratom), is a partial agonist at the µ-opioid receptor (µOR).
• The structural and dynamic basis for mitragynine's submaximal efficacy and biased signaling at the µOR remains poorly understood.

Purpose of the Study:

• To elucidate the molecular mechanisms underlying mitragynine's partial agonism and G-protein biased signaling at the µOR.
• To compare the conformational dynamics and kinetics of the µOR bound to mitragynine versus morphine using advanced computational methods.

Main Methods:

• Microsecond-scale all-atom molecular dynamics (MD) simulations in explicit lipid bilayers.
• Markov State Modelling (MSM) to analyze conformational landscapes and kinetics.
• Molecular mechanics/Poisson-Boltzmann surface area (MMPBSA) calculations for binding free energy estimation.

Main Results:

• MMPBSA calculations showed favorable binding for both mitragynine and morphine, with a more negative binding free energy for mitragynine.
• MSMs revealed distinct µOR conformational ensembles: morphine stabilized an active-like state, while mitragynine broadened sampling of intermediate states.
• Kinetic analysis indicated significantly longer microsecond-scale transitions to the open state for mitragynine compared to morphine's nanosecond-scale transitions.

Conclusions:

• Mitragynine's partial agonism and biased signaling arise from its ability to stabilize intermediate µOR conformations, reducing the population of fully active states.
• This study provides a mechanistic explanation for mitragynine's unique pharmacological profile at the µOR.
• The findings offer a quantitative framework for designing novel biased µOR ligands with tailored signaling properties.