A Study Of Prediction On Drug Resistance Of H1N1 Influenza Virus With Mutated Neuraminidase

In late April 2009, the outbreak of a new strain of influenza A (H1N1) had cause a global concern of the risk of a flu epidemic. Oseltamivir was recommended for the most effective antiviral drug for treating the infected patients by The World Health Organization (WHO) and The Centers for Disease Control and Prevention (CDC). However, WHO announced that more than 200 cases confer resistance to oseltamivir in February 2010.Oseltamivir is an antiviral drug against neuraminidase (NA) which plays a major role in influenza virus propagation for cleaving a terminal sialic acid and releasing viral progeny from infected cells. It is converted to oseltamivir phosphate, which is a active metabolite by hepatic and intestinal esterases after oral administration. Oseitamivir is an acetamido cyclohexene that is a structure homolog of sialic acid and can directly interact with the amino acid residues of the NA active sites. NA is divided into two groups according to genetic and structural relationships:one group includes N1, N4, N5 and N8, the other group includes N2, N3, N6, N7, and N9. Based on the crystal structures, the difference of two groups is that the first group has a large cavity close to the active site on the 150-loop, at residues 147-152. However, the active site of the NA is conserved in all NA subtypes. The catalytic sites (R118, D151, D152, R224, E276, R292, R371 and Y406) were found to directly contact to the sialic acid and the framework sites (E119, R156, W178, S179, D198,1222, E227, H274, E277, N294, and E425) were supposed to stabilize the active site structure. Two mutations, H274Y and N294S, in the mutated framework, residues were indentified in N1 subtype. In the new H1N1 subtypes virus strains, the H274Y mutant strains demonstrated on average a 1466-fold reduction in oseltamivir susceptibility. Therefore, mutation at the conserved residues of the NA active sites may affect the sensitivity of oseltamivir.In the article, we found six mutations(N294S, E119K, D151G, S179P, D198G, R292W and Y406H) in the active sites. In order to understand whether these mutated NA strains confer resistance, homology modeling, molecular docking and molecular dynamics simulation were performed. MM-GBSA method was performed to calculate the binding free energy of NA with oseltamivir, and the binding free energy was decomposed into inhibitor-residue pairs interaction using the MM-GBSA energy decomposition analysis. The results showed the binding free energy of S179P and R292W complexes is increased by 9.5 and 11.88 kcal/mol with respect to the WT complex, which elucidated that this two NA exhibit drug resistance to oseltamivir. In the S179P mutation, the polar solvation energy of the prolin is reduced by 2.28kcal/mol because of the serine replaced by the proline, and the loss of the hydrogen bonds are the main cause of the resistance of S179P to oseltamivir. In the R292W mutation, the size of the arginine is narrowed because of the arginine replaced by tryptophan, which may increase binding cavity space and reduce the affinity of the NA and oseltamivir.