Narrow Results

The latest influenza A (H7N9) virus attracted a worldwide attention due to the first report of human infections and the continuing reported cases in China. In this work, homology modeling, docking and molecular dynamics simulations were combined to study the interactions between neuraminidase (N9_2013, from novel A/H7N9 virus) and agents zanamivir, oseltamivir, peramivir. It was found that N9_2013 protein is structurally close to the template (PDB code: 1F8B), especially the active site. The binding properties of N9_2013 protein were nearly identical to those of template. As a result, the three available drugs should be still efficacious for the new emerging A (H7N9) virus. However, the stabilities of docked complexes and binding affinities (E_int) were slightly reduced, in contrast to the corresponding inhibitor-template complexes, with the values of -82.27 (-84.30), -78.84 (-80.28) and -77.52 (-81.94) kcal mol^-1, respectively. Besides, R292K mutation might induce the resistance of the novel virus to the commercial inhibitors. Thus, it arouses the need for continuous monitoring of antiviral drug susceptibilities.

The surface protein of Influenza virus, Neuraminidase (NA), is believed to play a critical role in the release of new viral particle and thus spreads infection. It has been recognized as a valid drug target for anti-influenza therapy. Despite the number of available approved drugs for the influenza infection treatment, the emergence of resistant variants with novel mutations are the foremost challenges for the currently used NA inhibitors. Thus, the current investigation was carried out to ascertain potent inhibitors using computational strategies such as e-pharmacophore based virtual screening and docking approach. A three-dimensional e-pharmacophore hypothesis was generated based on the chemical features of complexes of the drugs and NA protein using PHASE module of Schrödinger suite. The generated hypothesis consisted of one hydrogen bond acceptor (A), two hydrogen bond donors (D), one negatively charged group (N) and one aromatic ring (R), ADDNR. The hypothesis was further evaluated for its integrity using enrichment analysis and used to filter out molecules with similar pharmacophoric features from approved, investigational and experimental subsets of DrugBank and ZINC database. In addition, ligand filtration was performed to curb down the molecules to an efficient collection of hit molecules by using Lipinski “rule of five and ADME analysis by using Qikprop module. Overall, the results from our analysis suggest that compound lisinopril and formoterol could serve as potent antiviral compounds for the treatment of influenza A virus infection. It is worth mentioning that the results correlate well with literature evidences.

Interactions between integral membrane proteins hemagglutinin (HA), neuraminidase (NA), M2 and membrane-associated matrix protein M1 of influenza A virus are thought to be crucial for assembly of functionally competent virions. We hypothesized that the amino acid residues located at the interface of two different proteins are under physical constraints and thus probably co-evolve. To predict co-evolving residue pairs, the EvFold (http://evfold.org) program searching the (nontransitive) Direct Information scores was applied for large samplings of amino acid sequences from Influenza Research Database (http://www.fludb.org/). Having focused on the HA, NA, and M2 cytoplasmic tails as well as C-terminal domain of M1 (being the less conserved among the protein domains) we captured six pairs of correlated positions. Among them, there were one, two, and three position pairs for HA–M2, HA–M1, and M2–M1 protein pairs, respectively. As expected, no co-varying positions were found for NA–HA, NA–M1, and NA–M2 pairs obviously due to high conservation of the NA cytoplasmic tail. The sum of frequencies calculated for two major amino acid patterns observed in pairs of correlated positions was up to 0.99 meaning their high to extreme evolutionary sustainability. Based on the predictions a hypothetical model of pair-wise protein interactions within the viral envelope was proposed.

Avian infectious bronchitis virus (IBV) has been reported to acquire haemagglutination (HA) activity after treatment with neuraminidase, which depends on the IBV S1 protein. The purpose of this study was to test the IBV HA activity and its relationship to the S1 sequences. A wild strain of IBV, 2575/98 possessed HA activity after neuraminidase treatment. On the contrary, its attenuated strain through 75 chicken embryo passages did not. The nucleotide sequence differences in S1 genes before and after attenuation were C166A and G280T, resulting in amino acid changes of P56T and A94S. The S1 and S genes of the wild strain were cloned and expressed in a baculovirus (B) expression system. To test the relationship between HA activity and the S sequence changes after attenuation, the two nucleotide residues were mutated. The HA activity of those recombinant baculoviruses (rBs) was tested. The results showed that rB containing S gene from wild strain possesses the HA activity, that containing S gene with C166A mutation shows partial HA but that containing G280T mutation shows no any HA activity. Thus, a Taiwan IBV strain 2575/98 loses its HA activity after attenuation and this loss might be related to amino acid changes of P56T and A94S in the IBV S protein.