ct8b00173_si_001.pdf (1.77 MB)
Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways
journal contribution
posted on 2018-05-01, 00:00 authored by J. Rydzewski, R. Jakubowski, W. Nowak, H. GrubmüllerThe dissociation of huperzine A (hupA)
from Torpedo californica acetylcholinesterase
(TcAChE) was investigated by 4 μs unbiased
and biased all-atom molecular dynamics (MD) simulations in explicit
solvent. We performed our study using memetic sampling (MS) for the
determination of reaction pathways (RPs), metadynamics to calculate
free energy, and maximum-likelihood estimation (MLE) to recover kinetic
rates from unbiased MD simulations. Our simulations suggest that the
dissociation of hupA occurs mainly via two RPs: a front door along
the axis of the active-site gorge (pwf) and through a new transient
side door (pws), i.e., formed by the Ω-loop (residues 67–94
of TcAChE). An analysis of the inhibitor unbinding
along the RPs suggests that pws is opened transiently after hupA and
the Ω-loop reach a low free-energy transition state characterized
by the orientation of the pyridone group of the inhibitor directed
toward the Ω-loop plane. Unlike pws, pwf does not require large
structural changes in TcAChE to be accessible. The
estimated free energies and rates agree well with available experimental
data. The dissociation rates along the unbinding pathways are similar,
suggesting that the dissociation of hupA along pws is likely to be
relevant. This indicates that perturbations to hupA-TcAChE interactions could potentially induce pathway hopping. In summary,
our results characterize the slow-onset inhibition of TcAChE by hupA, which may provide the structural and energetic bases
for the rational design of the next-generation slow-onset inhibitors
with optimized pharmacokinetic properties for the treatment of Alzheimer’s
disease.