Impact of Intracellular Proteins on μ‑Opioid Receptor Structure and Ligand Binding

Chronic pain is a prevalent problem affecting approximately
one
out of every five adults in the U.S. The most effective way to treat
chronic pain is with opioids, but they cause dangerous side effects
such as tolerance, addiction, and respiratory depression, which makes
them quite deadly. Opioids, such as fentanyl, target the μ-opioid
receptor (MOR), which can then bind to the intracellular Gi protein or the β-arrestin protein. The Gi pathway
is primarily responsible for pain relief and potential side effects,
but the β-arrestin pathway is chiefly responsible for the unwanted
side effects. Ideally, an effective pain medication without side effects
would bind to MOR, which would bias signaling solely through the Gi pathway. We used the Bio3D library to conduct principal component
analysis to compare the cryo-electron microscopy MOR structure in
complex with the Gi versus an X-ray crystallography MOR
structure with a nanobody acting as a Gi mimic. Our results
agree with a previous study by Munro, which concluded that nanobody-bound
MOR is structurally different than Gi-bound MOR. Furthermore,
we investigated the structural diversity of opioids that can bind
to MOR. Quantum mechanical calculations show that the low energy solution
structures of fentanyl differ from the one bound to MOR in the experimental
structure, and pKa calculations reveal
that fentanyl is protonated in aqueous solution. Glide docking studies
show that higher energy structures of fentanyl in solution form favorable
docking complexes with MOR. Our calculations show the relative abundance
of each fentanyl conformation in solution as well as the energetic
barriers that need to be overcome to bind to MOR. Docking studies
confirm that multiple fentanyl conformations can bind to the receptor.
Perhaps a variety of conformations of fentanyl can stabilize multiple
conformations of the MOR, which can explain why fentanyl can induce
different intracellular signaling and multiple physiological effects.