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In-silico structural analysis of the influenza A subtype H7N9 neuraminidase and molecular docking with different neuraminidase inhibitors.

ABSTRACT: Human infection with H7 influenza subtypes usually resulted in mild disease with a rare mortalities, however, human infection with the avian low pathogenic H7N9 influenza virus resulted in about 38.6 % human fatality. Due to the new cross-species barrier of this virus subtype, there is an urgent need to better understand the susceptibility to commercially available antivirals and their relation to the structural changes of the viral neuraminidase. Neuraminidases derived from 2013 H7N9, H5N1 and H1N1 were subjected to a structural analysis of their catalytic and framework binding sites. The modeling structure of selected neuraminidases from H7N9 and influenza A subtypes were solved and the docking studies with oseltamivir, zanamivir, laninamivir and peramivir were conducted. The active site residues that are responsible for both binding and cleavage of the terminally linked sialic acid receptors were found conserved. Docking studies with oseltamivir, zanamivir, laninamivir and peramivir revealed that the laninamivir and peramivir showed superior energy binding activities in comparison to the commonly used oseltamivir and zanamivir. The results presented in the current study provide data that are useful for the future treatment of different influenza A subtypes including the recently emerged H7N9.

SUBMITTER: Eweas AF

PROVIDER: S-EPMC4585053 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature

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In-silico structural analysis of the influenza A subtype H7N9 neuraminidase and molecular docking with different neuraminidase inhibitors.

Eweas Ahmad F AF Abdel-Moneim Ahmed S AS

Virusdisease 20150205 1-2

Human infection with H7 influenza subtypes usually resulted in mild disease with a rare mortalities, however, human infection with the avian low pathogenic H7N9 influenza virus resulted in about 38.6 % human fatality. Due to the new cross-species barrier of this virus subtype, there is an urgent need to better understand the susceptibility to commercially available antivirals and their relation to the structural changes of the viral neuraminidase. Neuraminidases derived from 2013 H7N9, H5N1 and ...[more]

PMID: 26436118

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Project description:Influenza virus disease is one of the most infectious diseases responsible for many human deaths, and the high mutability of the virus causes drug resistance effects in recent times. As such, it became necessary to explore more inhibitors that could avert future influenza pandemics. The present research utilized some in-silico modelling concepts such as 2D-QSAR, 3D-QSAR, molecular docking simulation, and ADMET predictions on some 5-benzyl-4-thiazolinone derivatives as influenza neuraminidase (NA) inhibitors. The 2D-QSAR modelling results revealed GFA-MLR ( Rtrain2 =0.8414, Q2 = 0.7680) and GFA-ANN ( Rtrain 2 =0.8754, Q2 = 0.8753) models with the most relevant descriptors (MATS3i, SpMax5_Bhe, minsOH and VE3_D) for predicting the inhibitory activities of the molecules which has passed the global criteria of accepting QSAR models. The results of the 3D-QSAR modelling results showed that CoMFA_ES ( Rtrain 2 =0.9030, Q2 = 0.5390) and CoMSIA_EA ( Rtrain2 =0.880, Q2 = 0.547) models are having good predicting ability among other developed models. The molecules were virtually screened via molecular docking simulation with the active site of NA protein receptor (pH1N1) which confirms their resilient potency when compared with zanamivir standard drug. Molecule 11 as the most potent molecule formed more H-bond interactions with the key residues such as TRP178, ARG152, ARG292, ARG371, and TYR406 that triggered the catalytic reactions for NA inhibition. Furthermore, six (6) molecules (9, 10, 11, 17, 22, and 31) with relatively high inhibitory activities and docking scores were identified as the possible leads for in-silico exploration of novel NA inhibitors. The drug-likeness and ADMET predictions of the lead molecules revealed non-violation of Lipinski's rule and good pharmacokinetic profiles respectively, which are important guidelines for rational drug design. Hence, the outcome of this study overlaid a solid foundation for the in-silico design and exploration of novel NA inhibitors with improved potency.

Project description:BACKGROUND: Since late March 2013, there has been another global health concern with a sudden wave of flu infections by a novel strain of avian influenza A (H7N9) virus in China. To-date, there have been more than 100 infections with 23 deaths. It is more worrying as this viral strain has never been detected in humans and only been found to be of low-pathogenicity. Currently, there are 3 effective neuraminidase inhibitors for this H7N9 virus strain, i.e. oseltamivir, zanamivir, and peramivir. These drugs have been used for treatment of the H7N9 influenza in China. However, how these inhibitors work and affect the binding cavity of the novel H7N9 neuraminidase in the presence of potential mutations has not been disclosed. In our study, we investigate steric effects and subsequently show the conformational restraints of the inhibitor-binding site of the non-mutated and mutated H7N9 neuraminidase structures to different drug compounds. RESULTS: Combination of molecular docking and Molecular Dynamics simulation reveal that zanamivir forms more favorable and stable complex than oseltamivir and peramivir when binding to the active site of the H7N9 neuraminidase. And it is likely that the novel influenza A (H7N9) virus adopts a higher probability to acquire resistance to peramivir than the other two inhibitors. Conformational changes induced by the mutation R289K causes loss of number of hydrogen bonds between the inhibitors and the H7N9 viral neuraminidase in 2 out of 3 complexes. In addition, our results of binding-affinity relationships of the 3 inhibitors with the viral neuraminidase proteins of previous pandemics (H1N1, H5N1) and the current novel H7N9 reflected the extent of binding effectiveness of the 3 inhibitors to the novel H7N9 neuraminidase. CONCLUSIONS: The results are novel and specific for the A/Hangzhou/1/2013(H7N9) influenza strain. Furthermore, the protocol could be useful for further drug-binding analysis and prediction of future viral mutations to which the virus evolves through adaptation and acquires resistance to the current available drugs.

Dataset Information

In-silico structural analysis of the influenza A subtype H7N9 neuraminidase and molecular docking with different neuraminidase inhibitors.

Publications

In-silico structural analysis of the influenza A subtype H7N9 neuraminidase and molecular docking with different neuraminidase inhibitors.

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