Long Time Scale GPU Dynamics Reveal the Mechanism of Drug Resistance of the Dual Mutant I223R/H275Y Neuraminidase from H1N1-2009 Influenza Virus

Multidrug resistance of the pandemic H1N1-2009 strain
of influenza has been reported due to widespread treatment using the
neuraminidase (NA) inhibitors, oseltamivir (Tamiflu), and zanamivir
(Relenza). From clinical data, the single I223R (IR) mutant of H1N1-2009 NA reduced efficacy of oseltamivir
and zanamivir by 45 and 10 times, respectively.
More seriously, the efficacy of these two inhibitors against the double
mutant I223R/H275Y (IRHY) was significantly
reduced by a factor of 12 374 and 21 times, respectively, compared
to the wild-type. This has led to the
question of why the efficacy of the NA inhibitors is reduced by the
occurrence of these mutations and, specifically, why the efficacy
of oseltamivir against the double mutant IRHY was significantly reduced,
to the point where oseltamivir has become an ineffective treatment.
In this study, 1 μs of molecular dynamics (MD) simulations was
performed to answer these questions. The simulations, run using graphical
processors (GPUs), were used to investigate the effect of conformational
change upon binding of the NA inhibitors oseltamivir and zanamivir
in the wild-type and the IR and IRHY mutant strains. These long time
scale dynamics simulations demonstrated that the mechanism of resistance
of IRHY to oseltamivir was due to the loss of key hydrogen bonds between
the inhibitor and residues in the 150-loop. This allowed NA to transition
from a closed to an open conformation. Oseltamivir binds weakly with
the open conformation of NA due to poor electrostatic interactions
between the inhibitor and the active site. The results suggest that
the efficacy of oseltamivir is reduced significantly because of conformational
changes that lead to the open form of the 150-loop. This suggests
that drug resistance could be overcome by increasing hydrogen bond
interactions between NA inhibitors and residues in the 150-loop, with
the aim of maintaining the closed conformation, or by designing inhibitors
that can form a hydrogen bond to the mutant R223 residue, thereby
preventing competition between R223 and R152.