Selective inhibition mechanism of nitroxoline to the BET family: Insight from molecular simulations.

Although the proteins in bromodomain and extra-terminal domain (BET) family are promising therapy drug targets for numerous human diseases, the binding effectiveness is interfered by the competition from non-BET protein BRD9. In this study, molecular docking, molecular dynamics simulations, binding free energy calculations and per-residue energy decomposition methods were employed to clarify the selective inhibition mechanism of nitroxoline. The results showed that the different cavity volume of effective embedding inhibitor and the changes in conserved residues were associated with the significant higher selectivity of inhibitor nitroxoline for BET family than non-BET protein (BRD9). In addition, the non-polar interactions occurred in Phe83, Val87 at ZA loop, and the polar interaction appeared in Met132, Asn135 at BC loop. Therefore, when designing a new inhibitor, it could better improve the inhibitor activity by introducing the heteroatom conjugated pyridine-like moiety and the strong electron-withdrawing nitro-like moiety. Overall, this study not only clarified the molecular mechanism of the selective inhibition of nitroxoline, but also provided insight into designing more effective BET inhibitors in next step.

The binding mechanism of nitroreductase fluorescent probe: Active pocket deformation and intramolecular hydrogen bonds.

Nitroreductase (NTR), a member of the flavoenzyme family, could react with nicotinamide adenine dinucleotide by reducing nitro to amino at hypoxic tumor, which can be monitored by some fluorescent probes in vivo. Here, molecular docking and molecular dynamics simulation techniques were used to explore the molecular mechanisms between NTR and probes. The results showed that formation of hydrogen bond in 1F5V-13 between A@His215 and B@Ser41 with 74.53% occupancy might be the main reason for the decrease of probe fluorescence emission in experiment. Moreover, Probe 16 was rotated by nearly 60 degrees with respect to the position of other probes in protein binding pocket, deforming the protein active pocket, changing the hydrogen bond formation, which leads to the fluorescence performance of 16 with electron donor and electron acceptor groups was superior to other probes in experiment. The deformation of protein active pocket and the formation of intramolecular hydrogen bonds revealed the difference in performance of NTR fluorescent probe at molecular level, which provide theoretical guidance for latter design of fluorescent probes with better performance.

In situ preparation of multilayer coated capillary column with HKUST-1 for separation of neutral small organic molecules by open tubular capillary electrochromatography.

The popularity of novel nanoparticles coated capillary column has aroused widespread attention of researchers. Metal organic frameworks (MOFs) with special structure and chemical properties have received great interest in separation sciences. This work presents the investigation of HKUST-1 (Hong Kong University of Science and Technology-1, called Cu3(BTC)2 or MOF-199) nanoparticles as a new type of coating material for capillary electrochromatography. For the first time, three layers coating (3-LC), five layers coating (5-LC), ten layers coating (10-LC), fifteen layers coating (15-LC), twenty layers coating(20-LC) and twenty-five layers coating (25-LC) capillary columns coated with HKUST-1 nanoparticles were synthesized by covalent bond with in situ, layer-by-layer self-assembly approach. The results of scanning electron microscopy (SEM), X-ray diffraction (XRD) and plasma atomic emission spectrometry (ICP-AES) indicated that HKUST-1 was successfully grafted on the inner wall of the capillary. The separating performances of 3-LC, 5-LC, 10-LC, 15-LC, 20-LC and 25-LC open tubular (OT) capillary columns were studied with some neutral small organic molecules. The results indicated that the neutral small organic molecules were separated successfully with 10-LC, 15-LC and 20-LC OT capillary columns because of the size selectivity of lattice aperture and hydrophobicity of organic ligands. In addition, 10-LC and 15-LC OT capillary columns showed better performance for the separation of certain phenolic compounds. Furthermore, 10-LC, 15-LC and 20-LC OT capillary columns exhibited good intra-day repeatability with the relative standard deviations (RSDs; %) of migration time and peak areas lying in the range of 0.3-1.2% and 0.5-4.2%, respectively. For inter-day reproducibility, the RSDs of the three OT capillary columns were found to be lying in the range of 0.3-5.5% and 0.3-4.5% for migration time and peak area, respectively. The RSDs of retention times for column-to-column for three batches of 10-LC, 15-LC and 20-LC OT capillary columns were in the range from 2.3% to 7.2%. Moreover, the fabricated 10-LC, 15-LC and 20-LC OT capillary columns exhibited good repeatability and stability for separation, which could be used successively for more than 120 runs with no observable changes on the separation efficiency.

Aqueous synthesis of CdTe/CdSe core/shell quantum dots as pH-sensitive fluorescence probe for the determination of ascorbic acid.

By controlling the reflux time and the quantity of the shell materials, different sizes of thioglycollic acid (TGA) modified CdTe/CdSe core/shell quantum dots were synthesized in aqueous solution. This type of QDs was used for sensitive and selective determination of ascorbic acid in commercial tablets. Under optimal conditions, a good linearity was observed between the relative fluorescence (FL) intensity and the concentration of ascorbic acid in the range of 4.0 to 64.0 µg/mL with a correlation coefficient of 0.9968. The limit of detection was 2.4 µg/mL. This method was applied to the determination of the ascorbic acid in Vitamin C tablets and Vitamin C Yinqiao pills, and satisfactory results were obtained.

Thousand fold concentration of an alkaloid in capillary zone electrophoresis by micelle to solvent stacking.

In this paper, the co-solvent of methanol-water was used to facilitate the sodium dodecyl sulfate (SDS) micelles collapse, thereby inducing the on-line sample focusing technique of micelle to solvent stacking (MSS). To demonstrate this stacking method, the mechanism of micelles collapse in co-solvent was discussed. The details of the required conditions were investigated and the optimized conditions were: running buffer, 20mM H(3)BO(3) and 20mM NaH(2)PO(4) solution (pH 4.0); micellar sample matrix, 20mM SDS, 20mM H(3)BO(3) and 20mM NaH(2)PO(4) solution (pH 4.0); co-solvent buffer, 20mM H(3)BO(3) and 20mM NaH(2)PO(4) in methanol/water (90:10, v/v). The validity of the developed method was tested using cationic alkaloid compounds (ephedrine and berberine) as model analytes. Under the optimized conditions, this proposed method afforded limits of detection (LODs) of 0.5 and 1.1ng/mL with 300 and 1036-fold improvements in sensitivity for ephedrine and berberine, respectively, within 15min.