Mutation-Induced Loop Opening and Energetics for Binding of Tamiflu to Influenza N8 Neuraminidase

Tamiflu, also known as oseltamivir (OTV), binds to influenza
A
neuraminidase (H5N1) with very high affinity (0.32 nM). However, this
inhibitor binds to other neuraminidases as well. In the present work,
a systematic computational study is performed to investigate the mechanism
underlying the binding of oseltamivir to N8 neuraminidase (NA) in
“open” and “closed” conformations of the
150-loop through molecular dynamics simulations and the popular and
well established molecular mechanics Poisson–Boltzmann (MM-PBSA)
free energy calculation method. Whereas the closed conformation is
stable for wild type N8, it transforms into the open conformation
for the mutants Y252H, H274Y, and R292K, indicating that bound to
oseltamivir these mutants are preferentially in the open conformation.
Our calculations show that the binding of wild type oseltamivir to
the closed conformation of N8 neuraminidase is energetically favored
compared to the binding to the open conformation. We observe water
mediated binding of oseltamivir to the N8 neuraminidase in both conformations
which is not seen in the case of binding of the same drug to the H5N1
neuraminidase. The decomposition of the binding free energy reveals
the mechanisms underlying the binding and changes in affinity due
to mutations. Considering the mutant N8 variants in the open conformation
adopted during the simulations, we observe a significant loss in the
size of the total binding free energy for the N8Y252H–OTV,
N8H274Y–OTV, and N8R292K–OTV complexes
compared to N8WT–OTV, mainly due to the decrease
in the size of the intermolecular electrostatic energy. For R292K,
an unfavorable shift in the van der Waals interactions also contributes
to the drug resistance. The mutations cause a significant expansion
in the active site cavity, increasing its solvent accessible surface
compared to the crystal structures of both the open and closed conformations.
Our study underscores the need to consider dynamics in rationalizing
the structure–function relationships of various antiviral inhibitor–NA
complexes.