Thermal denaturation of a coronavirus envelope (CoVE) protein by a coarse-grained Monte Carlo simulation

Thermal response of an envelope protein conformation from coronavirus-2 (CoVE) is studied by a coarse-grained Monte Carlo simulation. Three distinct segments, the N-terminal, Trans-membrane, and C-terminal are verified from its specific contact profile. The radius of gyration (Rg) reveals a non-monotonic sub-universal thermal response: Rg decays substantially on heating in native phase under low-temperature regime in contrast to a continuous increase on further raising the temperature prior to its saturation to a random-coil in denature phase. The globularity index which is a measure of effective dimension of the protein, decreases as the protein denatures from a globular to a random-coil conformation

Phase separation dynamics and morphologies prediction of PEO-b-PMMA copolymer by atomistic and mesoscopic simulations

Atomistic and mesoscopic simulations are the most important tools to predict the morphologies of block copolymers. In this study, inter-bead interactions and essential parameters for meso-structure polymeric models were optimized for poly(ethylene oxide)-block-poly(methyl methacrylate) (PEO-b-PMMA; O-b-M) binary systems. A coarse-grained model in a mesoscopic dynamic was used to represent polymeric chain. Gaussian chain is calculated from polymer chain length concerning its characteristic properties. Free energy density was considered by setting suitable time steps and inter-bead interactions for meso-structure simulations. The interaction energies of 1:1, 2:1 and 4:1 molar ratio of O to M segments were 3.67, 4.66, and 5.92, respectively. These values are obtained from Flory-Huggins parameters in atomistic simulations. Morphology at equilibrium was obtained in five different types: worm-like micelle, defected lamellar, lamellar, spherical micelle and bicontinuous at 400 K from M5-1M2-O5, O4-O4M6, M4-M5O5, O10-2M122-O10 and M11-1M2-O10, respectively. The obtained morphologies correlate with order parameter developed from the simulations

3D-QSAR modelling dataset of bioflavonoids for predicting the potential modulatory effect on P-glycoprotein activity

The data is obtained from exploring the modulatory activities of bioflavonoids on P-glycoprotein function by ligand-based approaches. Multivariate Linear-QSAR models for predicting the induced/inhibitory activities of the flavonoids were created. Molecular descriptors were initially used as independent variables and a dependent variable was expressed as pFAR. The variables were then used in MLR analysis by stepwise regression calculation to build the linear QSAR data. The entire dataset consisted of 23 bioflavonoids was used as a training set. Regarding the obtained MLR QSAR model, R of 0.963, R2=0.927, Radj2=0.900, SEE=0.197, F=33.849 and q2=0.927 were achieved. The true predictabilities of QSAR model were justified by evaluation with the external dataset (Table 4). The pFARs of representative flavonoids were predicted by MLR QSAR modelling. The data showed that internal and external validations may generate the same conclusion

Tentative Peptide‒Lipid Bilayer Models Elucidating Molecular Behaviors and Interactions Driving Passive Cellular Uptake of Collagen-Derived Small Peptides

Collagen contains hydroxyproline (Hyp), which is a unique amino acid. Three collagen-derived small peptides (Gly-Pro-Hyp, Pro-Hyp, and Gly-Hyp) interacting across a lipid bilayer (POPC model membrane) for cellular uptakes of these collagen-derived small peptides were studied using accelerated molecular dynamics simulation. The ligands were investigated for their binding modes, hydrogen bonds in each coordinate frame, and mean square displacement (MSD) in the Z direction. The lipid bilayers were evaluated for mass and electron density profiles of the lipid molecules, surface area of the head groups, and root mean square deviation (RMSD). The simulation results show that hydrogen bonding between the small collagen peptides and plasma membrane plays a significant role in their internalization. The translocation of the small collagen peptides across the cell membranes was shown. Pro-Hyp laterally condensed the membrane, resulting in an increase in the bilayer thickness and rigidity. Perception regarding molecular behaviors of collagen-derived peptides within the cell membrane, including their interactions, provides the novel design of specific bioactive collagen peptides for their applications

Multitarget-Based Virtual Screening for Identification of Herbal Substances toward Potential Osteoclastic Targets

Osteoporosis is a complex bone disease indicating porous bone with low bone mass density and fragility. Cathepsin K, V-ATPase, and αVβ3 integrin are exhibited as novel targets for osteoporosis treatment. Our preliminary study uses a state-of-the-art method, including target-based virtual screening and clustering methods to determine promising candidates with multitarget properties. Phytochemicals with osteoprotective properties from the literature are used to elucidate the molecular interactions toward three targets. The binding scores of compounds are normalized and rescored. The K-means and hierarchical clustering methods are applied to filter and define the promising compounds, and the silhouette analysis is supposed to validate the clustering method. We explore 108 herbal compounds by virtual screening and the cluster approach, and find that rutin, sagittatoside A, icariin, and kaempferitrin showed strong binding affinities against Cathepsin K, V-ATPase, and αVβ3 integrin. Dockings of candidates toward three targets also provide the protein-ligand interactions and crucial amino acids for binding. Our study provides a straightforward and less time-consuming approach to exploring the new multitarget candidates for further investigations, using a combination of in silico methods

Synthesis of BiVO4 photocatalyst via cyclic microwave irradiation method

Visible light-active BiVO4 photocatalyst was successfully synthesized through a cyclic microwave irradiation method without further calcination process. The synthesized powder was characterized by X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), and UV-Vis diffuse reflectance spectroscopy (UV-Vis DRS). The BiVO4 powder revealed an excellent photocatalytic degradation of methylene blue under visible light irradiation. The degraded methylene blue was monitored by both UV-Vis spectrophotometer and absorbance in RGB channels. Similar decolorization percentage as well as pseudo first-order rate constant were achieved with high accuracy and sensitivity. The light absorption in RGB channels is an alternative simple and cartable way requiring lower amount of sample for detecting the dye degradation photocatalytic activity

Enhanced catalysis of CO2 cycloaddition at ambient pressure through rational design of interpenetrating ZnII/LnIII heterometallic coordination polymers

The major obstacle in using CO2 in the cycloaddition reactions with epoxides can be subdued through the use of high performance catalysts particularly those efficient at or near ambient temperature and pressure. Performances of heterogeneous catalysts are, however, subpar compared to the homogeneous counterparts although being preferable from practical viewpoint. Heterometallic 3d-4f coordination polymers have offered the best opportunity to date and their best possible performances is not yet achieved. Through rational use of 2,2′-bipyridine-4,4′-dicarboxylic acid (H2bipydc), new series of interpenetrating coordination polymers, i.e. [ZnIILnIII(bipydc)2(HCOO)(H2O)3]∙2H2O where LnIII = PrIII (I), NdIII (II), SmIII (III) and EuIII (IV), were synthesized and characterized. Their single crystal structures were elucidated, and potential functioning sites were identified. Their performances in catalyzing the reactions of allyl glycidyl ether were evaluated. The aid of tetrabutylammonium bromide was notably necessary. The unparallel performances were disclosed. The percentage yields of over 80 %, percentage conversion of 85–90 %, turn-over number of 2088 - 2260, and turn-over frequencies of 522 - 565 h−1 could be achieved from the reactions conducted at 90 °C for 4 h at ambient pressure. Synergistic contribution from various structural features is postulated. Viability of IV in catalyzing the reactions of other monosubstituted epoxides was also studied. Taking advantage of the single crystal structure, the preferential and influential interactions of selected epoxides at different metal sites and the prime motivation of their interactions were investigated using computational calculations