Computational Study On Natural Compound Inhibitors Of Type A H1N1Influenza Virus Neuraminidase

The prevention and treatment of influenza are the major issues for human health.Neuraminidase (NA) encoded by the influenza virus plays an important role in theprocess of viral infection, maturity, and release. Therefore, influenza virusneuraminidase inhibitors are used as the most effective antiviral drugs. However, theemergence of drug-resistant NA variants and drug side effects are the major problemsof antiviral therapy. Thus, research and discovery of new NA inhibitor is ofparticularly importance. Natural compounds have been the mainstay of traditionalmedicine for thousands of years and have shown significant treatment effect towardsinfluenza. In recent years, natural products have been increasing reported showinganti-influenza virus activities. Identification and characterization of NA inhibitoryactive ingredient from natural compounds is a major focus and important field for theanti-influenza research of natural compounds. This dissertation focuses on naturalproducts specifically targeting the viral surface protein NA, as do currently availablefirst-line drugs stockpiled worldwide in the case of a pandemic.In this dissertation, homology modeling, virtual screening and molecular dockingapproach was used to find effective inhibitor of NA, we study on the development ofeffective inhibitors of NA. First, using BLAST to search the similarity template of NAsequence, four template were found with high identity (41.1%) and high similarity(56.0%). Then use the MODELER program to generate three-dimensional structuralmodel of the template sequence NA. After evaluating of the three-dimensionalstructure of NA, it suggests that finds that the modeling structure of NA was credible.Finally, we defined the active site, Arg118, Glu119, Asp151, Arg152, Glu278, Arg292,Arg293, Asn344, Arg368, Arg371of NA, with theoretical predictions andexperimental data. Upon application of virtual screening technique with AutoDock Vina software,34hydrophobic polycyclic compounds from Natural ProductsDatabase (NPD) were found as the favorable affinity energy with NA (<-11kcal/mol).The molecular docking was carried out with Flexible Docking program of theDiscovery Studio software, the compounds was finally predicted to have inhibitoryactivity, after analyzed the precise binding mode and the energy score. Moreover,docking results showed that the compounds bound not only in the active pocket, butalso in a new hydrophobic cave which contains Arg368, Trp399, Ile427, Pro431andLys432of NA. The compounds also formed Pi-Pi interaction with the newhydrophobic cave of NA, which brings a strong conjugation effect. However, thecontrol inhibitor zanamivir did not have this effect. Then, the Estimated Free Energyof Binding was calculated with AutoDock software. To analyzing the different energyscore from the different program, it could find that no apparent correspondencebetween the CDOCKER energy score and the Estimated Free Energy, but they have aconsistent trend. That is the energy score of all34compounds were lower than that ofzanamivir. And the compounds screening by means of theoretical studies had thebetter efficacy than the positive control drug zanamivir. The ADMET module inDiscovery Studio software was used to study on the good permeation ability, highprotein binding affinity, volume distribution and metabolic stability of34compoundsand the positive control drug. Moreover, the TOPKAT module in Discovery Studiosoftware was used to study on the toxicological properties of compounds, especiallythe developmental toxicity potential, the ames mutagenicity and the rodentcarcinogenicity. All the results shown that the compounds, ZINC02090662,ZINC0425922, ZINC0427057, ZINC0427058, ZINC05433942, ZINC05433944,ZINC08918259, ZINC08918445, ZINC12863203, had the favorable inhibition of NAactivity and had not carcinogenic, mutagenic and reproductive toxicity as zanamivirdid, furthermore they had good ADMET properties. These results greatly narrowedthe scope of the experiment, reduced the huge experiment funding, and saved a lot oftime for future drug discovery. The details of NA-compound binding structureobtained will be valuable for the development of a new anti-influenza virus agent.