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Tran N.,Vietnam National University, Ho Chi Minh City | Van T.,Vietnam National University, Ho Chi Minh City | Nguyen H.,Institute for Computational Science and Technology at Ho Chi Minh City | Le L.,Vietnam National University, Ho Chi Minh City
International Journal of Medical Sciences | Year: 2015

Influenza virus H7N9 foremost emerged in China in 2013 and killed hundreds of people in Asia since they possessed all mutations that enable them to resist to all existing influenza drugs, resulting in high mortality to human. In the effort to identify novel inhibitors combat resistant strains of influenza virus H7N9; we performed virtual screening targeting the Neuraminidase (NA) protein against natural compounds of traditional Chinese medicine database (TCM) and ZINC natural products. Compounds expressed high binding affinity to the target protein was then evaluated for molecular properties to determine drug-like molecules. 4 compounds showed their binding energy less than -11Kcal/mol were selected for molecular dynamics (MD) simulation to capture intermolecular interactions of ligand-protein complexes. The molecular mechan-ics/Poisson-Boltzmann surface area (MM/PBSA) method was utilized to estimate binding free energy of the complex. In term of stability, NA-7181 (IUPAC namely {9-Hydroxy-10-[3-(trifluoromrthyl) cyclohexyl]-4.8-diazatricyclo [,6]dodec-4-yl}(perhydro-1H-inden-5-yl) formaldehyde) achieved stable conformation after 20ns and 27ns for ligand and protein root mean square deviation, respectively. In term of binding free energy, 7181 gave the negative value of -30.031 (KJ/mol) indicating the compound obtained a favourable state in the active site of the protein. © Ivyspring International Publisher

Mai T.V.-T.,Institute for Computational Science and Technology at Ho Chi Minh City | Le X.T.,Institute for Computational Science and Technology at Ho Chi Minh City | Huynh L.K.,Vietnam National University, Ho Chi Minh City
Structural Chemistry | Year: 2014

Accurate description of reactions between methyl acetate (MA) radicals and molecular oxygen is an essential prerequisite for understanding as well as modeling low-temperature oxidation and/or ignition of MA, a small biodiesel surrogate, because their multiple reaction pathways either accelerate the oxidation process via chain branching or inhibit it by forming relatively stable products. The accurate composite CBS-QB3 level of theory was used to explore potential energy surfaces for MA radicals + O2 system. Using the electronic structure calculation results under the framework of canonical statistical mechanics and transition state theory, thermodynamic properties of all species as well as high-pressure rate constants of all reaction channels were derived with explicit corrections for tunneling and hindered internal rotations. Our calculated results are in good agreement with a limited number of scattered data in the literature. Furthermore, pressure- and temperature-dependent rate constants were then computed using the Quantum Rice-Ramsperger-Kassel and the modified strong collision theories. This procedure resulted in a thermodynamically consistent detailed kinetic mechanism for low-temperature oxidation of the title fuel. We also demonstrated that even the detailed mechanism consists of several reactions of different reaction types, only the addition of the reactants and the re-dissociation of the initially formed adducts are important for low-temperature combustion at engine-liked conditions. © 2014 Springer Science+Business Media New York.

Tran N.,Institute for Computational Science and Technology at Ho Chi Minh City | Tran L.,Institute for Computational Science and Technology at Ho Chi Minh City | Le L.,Ho Chi Minh City International University
Medicinal Chemistry Research | Year: 2013

The 2009 influenza A virus pandemic, with high level of drug resistance reported, has highlighted the urgent need of more effective anti-influenza drugs. M2 channel proteins on the influenza A virus membrane have emerged as an efficient structure-based drug design target since variety of M2 channel protein structures were constructed by different experiment methods to generate the high resolution of crystal, solution NMR and solid-state NMR structure. In an effort to facilitate the future design of M2 channel inhibitors, the binding modes of 200 Adamantane-based drugs in four different types of M2 channel protein structures were evaluated by the critical interactions in terms of ligand binding affinity. The molecular docking results and statistic testing of binding affinity showed that the effect of each representative type from M2 channel protein structures was significantly different. Moreover, pharmacophore analysis revealed that there are two mechanisms of binding interactions to critical residues, Ser31 in holo structures and Ala30 in apo structures, respectively. Molecular docking studies, drug-like filters, and structure-based pharmacophore approaches successfully led us identifying the final hits reduced the false positives and false negatives in strategy of designing new potential group of future M2 channel inhibitors. © 2013 Springer Science+Business Media New York.

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