Biology subjects

Vo, Q. N.

Publications and source records attributed to Vo, Q. N..

2 recordsLinked to original sources

bioRxiv2021

Mechanism and Kinetics of Fentanyl Dissociation from the mu-Opioid Receptor

Driven by illicit fentanyl, opioid related deaths have reached the highest level in 2020. Currently, an opioid over-dose is resuscitated by the use of naloxone, which competitively binds and antagonizes the {micro}-opioid receptor (mOR). Thus, knowledge of the residence times of opioids at mOR and the unbinding mechanisms is valuable for assessing the effectiveness of naloxone. In the present study we calculate the fentanyl-mOR dissociation time and elucidate the mechanism by applying an enhanced sampling molecular dynamics (MD) technique. Two sets of metadynamics simulations with different initial structures were performed while accounting for the protonation state of the conserved H2976.52, which has been suggested to modulate the ligand-mOR affinity and binding mode. Surprisingly, with the N{delta}-protonated H2976.52, fentanyl can descend as much as 10 [A] below the level of the conserved D1473.32 before escaping the receptor, and has a calculated residence time{tau} of 38 s. In contrast, with the N - and doubly protonated H2976.52, the calculated{tau} are 2.6 s and 0.9 s, respectively. Analysis suggests that formation of the piperidine-Hid297 hydrogen bond strengthens the hydrophobic contacts with the transmembrane helix (TM) 6, allowing fentanyl to explore a deep pocket. Considering the experimental{tau} of [~]4 min for fentanyl and the role of TM6 in mOR activation, we suggest that the deep insertion mechanism may be biologically relevant. The work paves the way for large-scale computational predictions of opioid dissociation rates to inform the regulatory decision. The profound role of the histidine protonation state found here may shift the paradigm in computational studies of ligand-receptor kinetics.

biophysics↗

bioRxiv2020

How mu-Opioid Receptor Recognizes Fentanyl

In 2019, drug overdose has claimed over 70,000 lives in the United States. More than half of the deaths are related to synthetic opioids represented by fentanyl which is a potent agonist of mu-opioid receptor (mOR). In recent years, the crystal structures of mOR in complex with morphine derivatives have been determined; however, structural basis of mOR activation by fentanyl-like synthetic opioids remains lacking. Exploiting the X-ray structure of mOR bound to a morphinan ligand and several state-of-the-art simulation techniques, including weighted ensemble and continuous constant pH molecular dynamics, we elucidated the detailed binding mechanism of fentanyl with mOR. Surprisingly, in addition to forming a salt-bridge with Asp1473.32 in the orthosteric site common to morphinan opiates, fentanyl can move deeper and bind mOR through hydrogen bonding with a conserved histidine His2976.52, which has been shown to modulate mORs ligand affinity and pH dependence in mutagenesis experiments, but its precise role remains unclear. Intriguingly, the secondary binding mode is only accessible when His297 adopts a neutral HID tautomer. Alternative binding modes and involvement of tautomer states may represent general mechanisms in G protein-coupled receptor (GPCR)-ligand recognition. Our work provides a starting point for understanding the molecular basis of mOR activation by fentanyl which has many analogs emerging at a rapid pace. The knowledge may also inform the design of safer analgesics to combat the opioid crisis. Current protein simulation studies employ standard protonation and tautomer states; our work demonstrates the need to move beyond the practice to advance our understanding of protein-ligand recognition.

biophysics↗