Study of drug resistance of chicken influenza A virus (H5N1) from homology-modeled 3D structures of neuraminidases.

The spread of highly pathogenic H5N1 influenza virus in many Asian and European countries as well as its drug-resistance have raised serious worldwide concerns. In this paper, the structure-activity relationship between NA (neuraminidase) and its three inhibitors (DANA, zanamivir, and oseltamivir) was investigated. A homology model of H5N1-NA (BAE46950), which is the first reported oseltamivir-resistance virus strain, and the 108 homology-modeled 3D structures of chicken influenza H5N1 NAs downloaded from the website at , formed the molecular structural basis for the drug-resistance study. The multiple sequence and structure alignment for these NAs indicated that 11 functional residues were highly conserved except for AAF02313 with the mutated virus strain. However, the framework residues have remarkable mutations from N9-NA to H5N1-NA, and a few mutated residues were observed in different H5N1-NAs. A partially hydrophobic site S5 (formed by Ala246 and Thr247) in N9-NA is changed to a hydrophilic site (formed by Ala227 and Asn228) in H5N1-NA, while a hydrophilic site S6 (formed by Asn346 and Asn347) in N9-NA was replaced by a hydrophobic site (formed by Ala323 and Tyr324). All these mutations might be the reason for the oseltamivir-resistance by some H5N1 viruses. In order to find the possible drug-resistant H5N1 virus, similarity analysis was performed using the BAE46950 sequence as the benchmark template, and 21 sequences were found from the database of the 108 H5N1 NAs that had over 95% sequence similarity with BAE46950.