Substrate and oseltamivir binding into influenza virus neuraminidase by molecular dynamics simulations

Abstract

Neuraminidase (NA), a glycoprotein on influenza virus membrane, attachs to the terminal sialic acid (SIA) then cleaves the glycosidic linkage from the subsequent sugar of host cell receptor to release new virions. Types of receptor based on glycosidic linkage are SIA-2,3-GAL-1,4-NAG (3SL) and SIA-2,6-GAL-1,4-NAG (6SL). NA has been an important target for developing anti-influenza agents; however, the substrate binding and specificity of NA are not well understood. In addition, the widespread use of NA inhibitor leads to the mutation of gene. For instance, the pandemic of novel H7N9 virus has a R292K substitution of NA conferring oseltamivir resistance. Therefore, this work aims to understand the substrate binding into NAs from H1N1, H2N2 and H3N2 human viruses and H5N1, H7N9 avian viruses as well as to elucidate insight into oseltamivir resistance of H7N9 substitution using MD simulations and binding free energy predictions. QM/MM-GBSA binding free energies predicted that NAs of human viruses show strong binding to 6SL, whereas avian NAs have preference for 3SL. Although SIA is the main part of glycan for binding into NA, the difference of binding patterns is caused by the diversity of 6SL revealing the rotation of torsion angles between GAL and NAG. The prediction of oseltamivir susceptibilities of H7N9 NA using MM/PB(GB)SA and MM/3D-RISM is in good agreement with the experimental data. The primary source of oseltamivir resistance is due to the decrease of drug-target interaction. The shorter side chain of lysine at mutated residue results in the loss of hydrogen bond forming with carboxylate group and increasing of water molecules.