Dataset on biochemical inhibiting activities of selected phytochemicals in Azadirachta indica L as potential NS2B-NS3 proteases inhibitors.

The anti-NS2B-NS3 proteases activities of Azadirachta indica L. were investigated via the data obtained from selected bioactive compounds from Azadirachta indica L. The work was investigated using insilico approach and the series of computational software were used to execute the task. The software used were Spartan 14, material studio, Padel, Pymol, Autodock tool, Autodock vina and discovery studio. The obtained descriptors from 2D and 3D of the optimized compounds were screened and they were used to develop QSAR model using material studio software. Also, biological interaction between the selected bioactive compounds from Azadirachta indica L. and NS2B-NS3 proteases (PDB ID: 2fom) were accomplished using docking method and the calculated binding affinity as well as the residues involved in the interaction were reported. More so, the ADMET features for [(5S,6R,7S,8R,9S,10R,11S,12R,13S,17R)-17-(2,5-dihydroxy-2,5-dihydrofuran-3-yl)-11,12-dihydroxy-6­methoxy-4,4,8,10,13-pentamethyl-1,16-dioxo-6,7,9,11,12,17-hexahydro-5H-cyclopenta[a]phenanthren-7-yl] 3-methylbut-2-enoate (Compound 6) and (10R,13S,14S,17S)-17-[1-(3,4-dihydroxy-5,5-dimethyloxolan-2-yl)ethyl]-4,4,10,13,14-pentamethyl-1,2,5,6,9,11,12,15,16,17-decahydrocyclopenta[a]phenanthren-3-one (compound 12) with lowest binding affinity were investigated and reported.

Solar-Light-Responsive Titanium-Sheet-Based Carbon Nanoparticles/B-BiVO4/WO3 Photoanode for the Photoelectrocatalytic Degradation of Orange II Dye Water Pollutant.

We report the preparation and application of a heterostructured photoelectrocatalyst comprising carbon nanoparticles (CNPs) and boron codoped BiVO4 and WO3 for the removal of an organic dye pollutant in water. The materials, synthesized by hydrothermal method, were characterized by X-ray diffraction, diffuse reflectance UV-visible spectroscopy, energy-dispersive X-ray spectroscopy, and electron microscopy. The catalysts were immobilized on treated titanium sheets by drop-casting. The fabricated electrodes were characterized by linear sweep voltammetry (LSV) and chronoamperometry. Diffuse reflectance spectroscopy of the catalysts reveals that the incorporation of CNPs and B into the structure of monoclinic BiVO4 enhanced its optical absorption in both UV and visible regions. The LSV measurements carried out in 0.1 M Na2SO4 showed that the BiVO4- and WO3-based photoelectrode demonstrated significant photoactivity. CNP/B-BiVO4 and CNP/B-BiVO4/WO3 photoanodes gave photocurrent densities of approximately 0.83 and 1.79 mA/cm2, respectively, at 1.2 V (vs 3 M Ag/AgCl). The performance of the electrodes toward degradation of orange II dye was in the order BiVO4 < B-BiVO4 < WO3 < CNP-BiVO4 < CNP/B-BiVO4 < CNP/B-BiVO4/WO3, and the apparent rate constants obtained by fitting the experimental data into the Langmuir Hinshelwood kinetic model are 0.0924, 0.1812, 0.254, and 0.845 h-1 for BiVO4, WO3, CNP/B-BiVO4, and CNP/B-BiVO4/WO3, respectively. The chemical oxygen demand abatement after 3 h of electrolysis at the best performing photoanode was 58%. The study showed that BiVO4 and WO3 are promising anodic materials for photoelectrocatalytic water treatment plant.

Acid sphingomyelinase activity is regulated by membrane lipids and facilitates cholesterol transfer by NPC2.

During endocytosis, membrane components move to intraluminal vesicles of the endolysosomal compartment for digestion. At the late endosomes, cholesterol is sorted out mainly by two sterol-binding proteins, Niemann-Pick protein type C (NPC)1 and NPC2. To study the NPC2-mediated intervesicular cholesterol transfer, we developed a liposomal assay system. (Abdul-Hammed, M., B. Breiden, M. A. Adebayo, J. O. Babalola, G. Schwarzmann, and K. Sandhoff. 2010. Role of endosomal membrane lipids and NPC2 in cholesterol transfer and membrane fusion. J. Lipid Res. 51: 1747-1760.) Anionic lipids stimulate cholesterol transfer between liposomes while SM inhibits it, even in the presence of anionic bis(monoacylglycero)phosphate (BMP). Preincubation of vesicles containing SM with acid sphingomyelinase (ASM) (SM phosphodiesterase, EC 3.1.4.12) results in hydrolysis of SM to ceramide (Cer), which enhances cholesterol transfer. Besides SM, ASM also cleaves liposomal phosphatidylcholine. Anionic phospholipids derived from the plasma membrane (phosphatidylglycerol and phosphatidic acid) stimulate SM and phosphatidylcholine hydrolysis by ASM more effectively than BMP, which is generated during endocytosis. ASM-mediated hydrolysis of liposomal SM was also stimulated by incorporation of diacylglycerol (DAG), Cer, and free fatty acids into the liposomal membranes. Conversely, phosphatidylcholine hydrolysis was inhibited by incorporation of cholesterol, Cer, DAG, monoacylglycerol, and fatty acids. Our data suggest that SM degradation by ASM is required for physiological secretion of cholesterol from the late endosomal compartment, and is a key regulator of endolysosomal lipid digestion.

Hybrid materials from agro-waste and nanoparticles: implications on the kinetics of the adsorption of inorganic pollutants.

This study is a first-hand report of the immobilization of Nauclea diderrichii seed waste biomass (ND) (an agro-waste) with eco-friendly mesoporous silica (MS) and graphene oxide-MS (GO + MS) nanoparticles, producing two new hybrid materials namely: MND adsorbent for agro-waste modified with MS and GND adsorbent for agro-waste modified with GO + MS nanoparticles showed improved surface area, pore size and pore volume over those of the agro-waste. The abstractive potential of the new hybrid materials was explored for uptake of Cr(III) and Pb(II) ions. Analysis of experimental data from these new hybrid materials showed increased initial sorption rate of Cr(III) and Pb(II) ions uptake. The amounts of Cr(III) and Pb(II) ions adsorbed by MND and GND adsorbents were greater than those of ND. Modification of N. diderrichii seed waste significantly improved its rate of adsorption and diffusion coefficient for Cr(III) and Pb(II) more than its adsorption capacity. The rate of adsorption of the heavy metal ions was higher with GO + MS nanoparticles than for other adsorbents. Kinetic data were found to fit well the pseudo-second-order and the diffusion-chemisorption kinetic models suggesting that the adsorption of Cr(III) and Pb(II) onto these adsorbents is mainly through chemisorption mechanism. Analysis of kinetic data with the homogeneous particle diffusion kinetic model suggests that particle diffusion (diffusion of ions through the adsorbent) is the rate-limiting step for the adsorption process.

Role of the subunit interactions in the conformational transitions in adult human hemoglobin: an explicit solvent molecular dynamics study.

Hemoglobin exhibits allosteric structural changes upon ligand binding due to the dynamic interactions between the ligand binding sites, the amino acids residues and some other solutes present under physiological conditions. In the present study, the dynamical and quaternary structural changes occurring in two unligated (deoxy-) T structures and two fully ligated (oxy-) R, R2 structures of adult human hemoglobin were investigated with molecular dynamics. It is shown that, in the submicrosecond time scale, there is no marked difference in the global dynamics of the amino acid residues in both the oxy- and the deoxy-forms of the individual structures. In addition, the R, R2 are relatively stable and do not present quaternary conformational changes within the time scale of our simulations, while the T structure is dynamically more flexible and exhibited the T → R quaternary conformational transition, which is propagated by the relative rotation of the residues at the α(1)ß(2) and α(2)ß(1) interface.

Kinetics and thermodynamics of heavy metal ions sequestration onto novel Nauclea diderrichii seed biomass.

This study reports the sequestration of Cd(II) and Hg(II) using a new biosorbent, Nauclea diderrichii seed biomass. Experimental data obtained were fitted into kinetic and thermodynamic models. Experimental data fitted best into pseudo-second order kinetic model among others. Results obtained kinetically revealed that the biosorption of Cd(II) and Hg(II) using N. diderrichii seed biosorbent increased with increase in temperature. At the highest temperature, which was 333 K, the highest amount of metal biosorbed, q(e), for Cd(II) and Hg(II) obtained were 6.30 and 6.15 mg/g respectively. The biosorption of Cd(II) was kinetically faster than that of Hg(II), the highest initial biosorption rates for Cd(II) and Hg(II) were 56.19 and 4.39 mg/g min respectively. Thermodynamic parameters obtained by Erying equation from this study revealed that the biosorption process was spontaneous, feasible, endothermic with a decrease in the degree of chaos in the biosorption system.

Role of endosomal membrane lipids and NPC2 in cholesterol transfer and membrane fusion.

We examined the effect of Niemann-Pick disease type 2 (NPC2) protein and some late endosomal lipids [sphingomyelin, ceramide and bis(monoacylglycero)phosphate (BMP)] on cholesterol transfer and membrane fusion. Of all lipid-binding proteins tested, only NPC2 transferred cholesterol at a substantial rate, with no transfer of ceramide, GM3, galactosylceramide, sulfatide, phosphatidylethanolamine, or phosphatidylserine. Cholesterol transfer was greatly stimulated by BMP, little by ceramide, and strongly inhibited by sphingomyelin. Cholesterol and ceramide were also significantly transferred in the absence of protein. This spontaneous transfer of cholesterol was greatly enhanced by ceramide, slightly by BMP, and strongly inhibited by sphingomyelin. In our transfer assay, biotinylated donor liposomes were separated from fluorescent acceptor liposomes by streptavidin-coated magnetic beads. Thus, the loss of fluorescence indicated membrane fusion. Ceramide induced spontaneous fusion of lipid vesicles even at very low concentrations, while BMP and sphingomyelin did so at about 20 mol% and 10 mol% concentrations, respectively. In addition to transfer of cholesterol, NPC2 induced membrane fusion, although less than saposin-C. In this process, BMP and ceramide had a strong and mild stimulating effect, and sphingomyelin an inhibiting effect, respectively. Note that the effects of the lipids on cholesterol transfer mediated by NPC2 were similar to their effect on membrane fusion induced by NPC2 and saposin-C.

Development of an assay for the intermembrane transfer of cholesterol by Niemann-Pick C2 protein.

Niemann-Pick type C disease is an inherited fatal disorder characterized by the accumulation of unesterified cholesterol and other lipids in the endosomal/lysosomal compartment. Two independent genes responsible for this neurodegenerative disorder have been identified, but the precise functions of the encoded Niemann-Pick C1 (NPC1) and C2 (NPC2) proteins are not yet known. We developed a cell-free assay for measuring intermembrane lipid transport and examined the ability of bovine NPC2 (bNPC2) for intermembrane cholesterol transfer. NPC2 specifically extracts cholesterol from phospholipid bilayers and catalyzes intermembrane transfer to acceptor vesicles in a dose- and time-dependent manner. This transfer activity is dependent on temperature, pH, ionic strength, lipid composition of the model membranes, and the ratio of donor to acceptor vesicles. In model membranes, the presence of the lysosomal anionic phospholipids bis(monooleoylglycero)phosphate and phosphatidyl inositol significantly stimulated cholesterol transfer by NPC2, whereas bis(monomyristoylglycero)phosphate, phosphatidyl serine, and phosphatidic acid had no effect. Moreover, ceramide stimulated cholesterol transfer slightly, whereas sphingomyelin reduced cholesterol transfer rates. With our assay system we identified for the first time the ability of other lysosomal proteins, most notably the GM2-activator protein, to mediate intermembrane cholesterol transfer. This assay system promises to be a valuable tool for further quantitative and mechanistic studies of protein-mediated lipid transfer.

Varying apparent rate constant: determination of uptake and release of protons during tetramer-dimer dissociation in human hemoglobin A.

The effect of association-dissociation on the sulphydryl reactivity of human hemoglobin A is reported. The reactivity of CysF9(93)beta towards the sulphydryl reagent, 5,5'-dithiobis(2-nitrobenzoate), is higher at lower concentrations of hemoglobin at all pH values. This is because hemoglobin dimers have higher sulphydryl reactivity than tetramers and it is known that the proportion of dimers increases as the hemoglobin concentration decreases. This study takes advantage of this observation to determine the tetramer-dimer dissociation constant, K(4,2), of hemoglobin A and subsequently the proton uptake and the proton release during this process. The concentration dependence profiles of the apparent second-order rate constants, k(app), show that (between 2 and 20 microM heme) k(app) decreases with increasing hemoglobin concentration. Above 30 M heme k(app) remains fairly constant for all hemoglobin derivatives (oxy, carbonmonoxy and aquomethemoglobin) used. The pH dependence of the negative logarithm of tetramer-dimer dissociation constant, pK(4,2), for oxy- (and for carbonmonoxy-) hemoglobin exhibits a biphasic character with a maximum near pH 7.4 (and 6.6). For aquomethemoglobin, pK(4,20 decreases with increasing pH. The tetramer-dimer dissociation of human oxyhemoglobin A at an ionic strength of 200 mM uptakes 0.87 +/- 0.09 mole of protons between pH 6.2 to 7.4 phase and releases 0.84 0.09 mole of protons between pH 7.4 and 9.0 phase. Under a similar condition carbonmonoxyhemoglobin uptakes 0.54 +/- 0.05 mole of protons between pH 5.8 and 6.6 phase and releases 0.48 +/- 0.05 mole of protons between pH 6.6 and 9.0 phase. Aquomethemoglobin has only a single phase, it releases 0.39 +/- 0.05 mole of protons during tetramer-dimer dissociation.