QM/MM based 3D QSAR models for potent B-Raf inhibitors

Three dimensional (3D) quantitative structure-activity relationship studies of 37 B-Raf inhibitors, pyrazole-based derivatives, were performed. Based on the co-crystallized compound (PDB ID: 3D4Q), several alignment methods were utilized to derive reliable comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models. Receptor-guided alignment with quantum mechanics/molecular mechanics (QM/MM) minimization led to the best CoMFA model (q ² = 0.624, r ² = 0.959). With the same alignment, a statistically reliable CoMSIA model with steric, H-bond acceptor, and hydrophobic fields was also derived (q ² = 0.590, r ² = 0.922). Both models were validated with an external test set, which gave satisfactory predictive r ² values of 0.926 and 0.878, respectively. Contour maps from CoMFA and CoMSIA models revealed important structural features responsible for increasing biological activity within the active site and explained the correlation between biological activity and receptor-ligand interactions. New fragments were identified as building blocks which can replace R1-3 groups through combinatorial screening methods. By combining these fragments a compound with a high bioactivity level prediction was found. These results can offer useful information for the design of new B-Raf inhibitors.     

First synthesis of 2′-oxabicyclo[3.1.0]hexyl nucleosides with a north conformation

The first synthesis of 2′-oxabicyclo[3.1.0]hexyl nucleosides, a novel class of bicyclonucleosides, with a north conformation was successfully accomplished starting from (S)-epichlorohydrin via a tandem alkylation-lactonization, a less steric hindrance-dependent silylation in equilibrium and a coupling reaction with nucleobases under Vorbruggen conditions. Addition of acetic acid prevented a benzoyl group from migrating during desilylation with TBAF. ¹H NMR and X-ray crystallographic analysis indicated that the anomeric effect worked on the β-2′-oxabicyclo[3.1.0]hexyl nucleosides.     

Polymerase Chain Reaction-based Detection of Total and Specific Vibrio Species

The polymerase chain reaction (PCR) technique is widely used for efficient detection of food-borne pathogens because of speed and specificity. However, PCR methods have focused mostly on species-specific detection. In the present work, we describe a PCR-based method for the simultaneous detection of all Vibrio species because lots of them are notorious food-borne human pathogens. We then combined this total detection method with specific detection of Vibrio cholerae pathogen. Using a degenerate primer set based on the sequence of the potassium uptake gene, trkA, we were able to successfully detect all Vibrio species. Specific detection of V. cholerae was also possible using primer sets based on putative flagellin sequence. Importantly, simultaneous total and species-specific Vibrio detection was possible using all two primer sets in a multiplexed PCR strategy. Thus, the PCR method we have developed is applicable to both simultaneous and two-step detection of total and specific Vibrio species.     

Electrospinning fabrication and characterization of poly(vinyl alcohol)/montmorillonite/silver hybrid nanofibers for antibacterial applications

Poly(vinyl alcohol) (PVA)/montmorillonite clay (MMT)/silver (Ag) nanoparticles have been electrospun for fabricating PVA/MMT/Ag nanofiber in aqueous solutions. Since PVA is a water-soluble and biocompatible polymer, it is one of the best materials for preparation of antibacterial nanofiber. MMT has been used as an inorganic filler to enhance properties of homopolymeric nanofiber. The PVA/MMT/Ag nanofiber diameter increases with increasing contents of MMT clay and Ag nanoparticles. In preservation test, the PVA/MMT/Ag nanofiber confirms an excellent antibacterial performance, elucidating for practical uses as a new preservative. Moreover, the PVA/MMT/Ag nanofiber shows improved thermal properties.     

Gas chromatography‐mass spectrometric method for the screening and quantification of illicit drugs and their metabolites in human urine using solid‐phase extraction and trimethylsilyl derivatization

A simple and rapid GC‐MS method has been developed for the screening and quantification of many illicit drugs and their metabolites in human urine by using automatic SPE and trimethylsilylation. Sixty illicit drugs, including parent drugs and their metabolites that are possibly abused in Korea, can be monitored by this method. Among them, 24 popularly abused illicit drugs were selected for quantification. Very delicate optimizations were carried out in SPE, trimethylsilylation derivatization, and GC/MS to enable such remarkable achievements. Trimethylsilylated analytes were well separated within 21 min by GC‐MS. In the validation results, the LOD of all the analytes were in the range of 2–75 ng/mL. The LOQ of the quantified analytes were in the range of 5–98 ng/mL. The linearity (r²) of the quantified analytes ranged 0.990–1.000 in each concentration range between 10 and 1000 ng/mL. The mean recoveries ranged from 62 to 126% at three different concentrations of each analyte. The inter‐day and inter‐person accuracies were within ?13.3～14.9%, and ?10.1～13.0%, respectively, and the inter‐day and inter‐person precisions were less than 12.9%. The method was reliable and efficient for the screening and quantification of abused illicit drugs in routine urine analysis.     

Two new phenolic amides from the seeds of Pharbitis nil

Two new phenolic amides, pharnilatins A (1) and B (2), were isolated from the seeds of Pharbitis nil. These new compounds possess a p-coumaroyl unit with a structurally unique side chain, (2S,3S)-2,3-dihydroxyputrescine. The chemical structures and absolute stereochemistries of the new compounds were determined on the basis of spectroscopic analyses including 1D- and 2D-NMR experiments and chemical reactions. Compounds 1 and 2 exhibited cytotoxicity against A549, SK-OV-3, SK-MEL-2, and HCT-15 human tumor cells. However, none of the compounds inhibited nitric oxide (NO) production in lipopolysaccharide (LPS)-activated microglia cells.     

Integrated chemical process for exothermic wave synthesis of high luminance YAG:Ce phosphors

In this paper, high-luminance yellow-emitting Y₃Al₅O₁₂:Ce³⁺ phosphor (YAG:Ce) microparticles were prepared in a solid flame using a 1.425Y₂O₃+2.5Al₂O₃+0.15CeO₂+k(KClO₃+urea)+mNH₄F precursor mixture (here k is the number of moles of the KClO₃+urea red-ox mixture, and m is the number of moles of NH₄F). The self-sustaining combustion process for the entire reaction sample was provided by the heat generated from the KClO₃+urea mixture. Parametric studies demonstrated that the maximum temperature in the combustion wave varied from 885 to 1200 °C for k=2.0-3.0 mole and m=0-1.5 mole. X-ray analysis results showed that the product obtained in the solid flame consisted of Y₃Al₅O₁₂:Ce³⁺ and KCl phases. Therefore, after dissolving potassium chloride in distillated water, pure-phase YAG:Ce phosphor powder was obtained. The as-prepared YAG:Ce phosphor particles had diameters of 10-25 μm and good dispersity and exhibited luminescence properties comparable to those of YAG:Ce phosphor powders prepared by conventional high-temperature processing.     

Comparison of catalytic activities for photocatalytic and sonocatalytic degradation of methylene blue in present of anatase TiO2-CNT catalysts

Anatase TiO(2)-CNT catalysts with high specific surface areas were prepared by depositing TiO(2) particles on the surface of carbon nanotubes (CNTs) using a modified sol-gel technique. These catalysts prepared with different amounts of CNTs were characterized by nitrogen adsorption, Fourier Transform infrared (FT-IR) spectroscopy, scanning electron microscope (SEM), Transmission Electron Microscope (TEM), X-ray diffraction (XRD), Raman spectroscopy, energy dispersive X-ray (EDX) and ultraviolet-visible (UV-Vis) spectroscopy. The catalytic activity of the anatase TiO(2)-CNT catalysts was assessed by examining the degradation of methylene blue (MB) from model aqueous solutions as a probe reaction under visible light and ultrasonic irradiation. The synergistic effect of the greater surface area and catalytic activities of the composite catalysts was examined in terms of the strong adsorption ability and interphase interaction by comparing the different amounts and roles of CNTs in the catalysts.     

Development of optical fiber-based respiration sensor for noninvasive respiratory monitoring

In this study, two types of nasal-cavity-attached fiber-optic respiration sensors have been fabricated for noninvasive respiratory monitoring. One is a silver halide optical-fiber-based respiration sensor that can measure the variations of infrared radiation generated by the respiratory airflow from a nasal cavity. The other is a thermochromic-pigment-based fiber-optic respiration sensor that can measure the intensity of reflected light which changes owing to color variations of the temperature-sensing film according to the temperature difference between inspiratory and expiratory air. We have demonstrated the similarities of the respiratory signals using the fiber-optic respiration sensors and the temperature transducer of the BIOPAC? system. In addition, we verified that respiratory signals without the deterioration of the MR image can be obtained using the fiber-optic respiration sensors. It is anticipated that the proposed noninvasive fiberoptic respiration sensors will be highly effective for respiratory monitoring of a patient during MRI procedures.