Simple structure descriptors quantifying the diffusion of ethene in small-pore zeolites: Insights from molecular dynamic simulations

Small-pore zeolites with 8-rings are pivotal catalytic materials to produce light olefins from non-petroleum resources employing methanol-to-olefins or syngas-to-olefins processes. The constraints of cage openings on the diffusion of light...

Molecular Dynamic Simulations of Bromodomain and Extra-Terminal Protein 4 Bonded to Potent Inhibitors

Bromodomain and extra-terminal domain (BET) subfamily is the most studied subfamily of bromodomain-containing proteins (BCPs) family which can modulate acetylation signal transduction and produce diverse physiological functions. Thus, the BET family can be treated as an alternative strategy for targeting androgen-receptor (AR)-driven cancers. In order to explore the effect of inhibitors binding to BRD4 (the most studied member of BET family), four 150 ns molecular dynamic simulations were performed (free BRD4, Cpd4-BRD4, Cpd9-BRD4 and Cpd19-BRD4). Docking studies showed that Cpd9 and Cpd19 were located at the active pocket, as well as Cpd4. Molecular dynamics (MD) simulations indicated that only Cpd19 binding to BRD4 can induce residue Trp81-Ala89 partly become α-helix during MD simulations. MM-GBSA calculations suggested that Cpd19 had the best binding effect with BRD4 followed by Cpd4 and Cpd9. Computational alanine scanning results indicated that mutations in Phe83 made the greatest effects in Cpd9-BRD4 and Cpd19-BRD4 complexes, showing that Phe83 may play crucial roles in Cpd9 and Cpd19 binding to BRD4. Our results can provide some useful clues for further BCPs family search.

Computational Screening of Isolated Compounds From Goniothalamus Species to Identify Potential Inhibitors for Dengue Virus

In this study, a set of 234 chemical constituents reported from Goniothalamus species were docked against envelope (E), NS2B/NS3, NS5 methyltransferase, and NS5 RdRp dengue virus (DENV) protein. As the result, compounds 95, 96, 97, 100, 149, 155, and 187 were identified as potential dengue protease inhibitors based on minimal docking energy values and multiple interactions with binding sites. The results from in-silico Lipinski’ rule and ADMET analysis showed that compound 149 was predicted as the most potential compound that fulfills the drug-likeness properties. Ligand 149 was found to be able to fit in well and remain stable in the binding site of proteins envelope, NS2B/NS3, NS5 methyltransferase and NS5 RdRp. The results from molecular dynamic simulations indicate that the ligand-protein complex of 149 in NS5 methyltransferase showed the most preferable, successfully interacted within the active sites and were able to reach convergence within 100 ns.

Carbon Nanotubes Use for the Semiconductors ZnSe and ZnS Material Surface Modification via the Laser-Oriented Deposition Technique

It is known that a material’s volume and the surface structuring by the nanoparticles causes a significant change in the material’s basic properties. In this aspect, the structuration of the surface of semiconductors is of interest, because their wide potential application in optoelectronics can extend the products’ transparency, hardness, wettability, and other important parameters. This paper presents possible methods for the surface modification of zinc selenide and zinc sulfide when carbon nanotubes are deposited on the surface by the application of the laser-oriented technique. It also shows changes of the spectral, mechanical, and wetting characteristics of the considered materials. Using the molecular dynamic simulations, the possible process of the carbon nanotubes penetration into the considered surfaces is presented. The simulation results are partially supported by the obtained experimental data.