Functionality map analysis of the active site cleft of human thrombin

Summary The Multiple Copy Simultaneous Search methodology has been used to construct functionality maps for an extended region of human thrombin, including the active site. This method allows the determination of energetically favorable positions and orientations for functional groups defined by the user on the three-dimensional surface of a protein. The positions of 10 functional group sites are compared with those of corresponding groups of four thrombin-inhibitor complexes. Many, but not all features, of known thrombin inhibitors are reproduced by the method. The results indicate that certain aspects of the binding modes of these inhibitors are not optimal. In addition, suggestions are made for improving binding by interaction with functional group sites on the thrombin surface that are not used by the thrombin inhibitors. Abbreviations: MCSS, multiple copy simultaneous search; PPACK, d-phenylalanyl-l-propyl-l-arginine chloromethane; NAPAP, N -(2-naphthylsulfonylglycyl)-d-para-amidinophenylalanylpiperidine; argatroban, (2R,4R)-4-methyl-1-[N -(3-methyl-1,2,3,4-tetrahydro-8-quinolinylsulfonyl)-l-arginyl]-2-piperidine carboxylic acid; rms, root mean square. The thrombin residues are numbered according to the chymotrypsin-based numbering by Bode et al. [8]. P1, P2, P3, etc., denote the peptide inhibitor residues on the amino-terminal side of the scissile peptide bond, and S1, S2, S3, etc., the corresponding subsites of thrombin     

FRICTIONAL DISSIPATION AND NONLINEAR BAROTROPIC INSTABILITY

Based on the nonlinear quasi-geostrophic barotropic vorticity equation with Ekman friction, the criteria for nonlinear barotropic stability of the zonal basic flows are derived using Serrin-Joseph energy approach and through total energy, total enstrophy and their linear combination, separately, in terms of variational principle. Since the new transformation for Euler equation is utilized, the estimation of eigenvalue is more accurate, and the previous results of the author are improved very well.     

Structure and electronic structure of [(CF3)2PN]2NVCl2, a molecule involving a planar six-membered ring (N3P2V)

Summary The SCF method is applied to determine the (gas phase) structure of [(CF₃)₂PN]₂NVCl₂, which agrees with the solid-state X-ray structure within typical errors of 2 pm and 2° in bond distances and angles. The electronic structure of atoms forming the ring is best described in terms of divalent N^– and tetravlent P⁺ with appreciable declocalization of nitrogen lone pairs into low-lying empty orbitals of neighbouring atoms P and V. No evidence for aromaticity of the ring system is found.     

Assessment of Chemical Composition and Anti-Penicillium Activity of Vapours of Essential Oils from Abies Alba and Two Melaleuca Species in Food Model Systems

The possibilities of the practical utilization of essential oils (EOs) from various plant species in the food industry have attracted the attention of the scientific community. Following our previous studies, the antifungal activities of three further commercial EOs, Melaleuca armillaris subsp. armillaris (rosalina; REO), Melaleuca quinquenervia (niaouli; NEO), and Abies alba (fir; FEO), were evaluated in the present research in respect to their chemical profiles, over four different concentrations, 62.5 μL/L, 125 μL/L, 250 μL/L, and 500 μL/L. The findings revealed that the major compounds of REO, NEO, and FEO were linalool (47.5%), 1,8-cineole (40.8%), and α-pinene (25.2%), respectively. In vitro antifungal determinations showed that the inhibition zones of a Penicillium spp. mycelial growth ranged from no inhibitory effectiveness (00.00 ± 00.00 mm) to 16.00 ± 1.00 mm, indicating a very strong antifungal activity which was detected against P. citrinum after the highest REO concentration exposure. Furthermore, the in situ antifungal efficacy of all EOs investigated was shown to be dose-dependent. In this sense, we have found that the highest concentration (500 µL/L) of REO, NEO, and FEO significantly reduced (p < 0.05) the growth of all Penicillium strains inoculated on the bread, carrot, and potato models. These results indicate that the investigated EOs may be promising innovative agents in order to extend the shelf life of different types of food products, such as bread, carrot and potato.     

The Pharmacokinetics in Mice and Cell Uptake of Thymus Immunosuppressive Pentapeptide Using LC-MS/MS Analysis

Thymus immunosuppressive pentapeptide (TIPP) is a novel anti-inflammatory peptide with high efficacy and low toxicity. This study aims to establish a selective LC-MS/MS method for analyzing the analyte TIPP in biological samples, laying the foundation for further PK and PD studies of TIPP. Protein precipitation was conducted in acetonitrile supplemented with 2% formic acid and 25 mg/mL dithiothreitol as a stabilizer, which was followed by backwashing the organic phase using dichloromethane. The chromatographic separation of TIPP was achieved on a C18 column with a gradient elution method. During positive electrospray ionization, TIPP was analyzed via multiple-reaction monitoring. The linear relationships between the concentration of TIPP and peak area in murine plasma cell lysates, supernatants, and the final cell rinse PBS were established within the ranges of 20–5000 ng/mL, 1–200 ng/mL, 10–200 μg/mL, and 0.1–20 ng/mL, respectively (r² > 0.99). Validated according to U.S. FDA guidelines, the proposed method was proved to be acceptable. Such a method had been successfully applied to investigate the pharmacokinetics of TIPP in mice via subcutaneous injection. The plasma half-life in mice was 5.987 ± 1.824 min, suggesting that TIPP is swiftly eliminated in vivo. The amount of TIPP uptake by RBL-2H3 cells was determined using this method, which was also visually verified by confocal. Furthermore, the effective intracellular concentration of TIPP was deduced by comparing the intracellular concentration of TIPP and degrees of inflammation, enlightening further investigation on the intracellular target and mechanism of TIPP.     

The DI-SPME Method for Determination of Selected Narcotics and Their Metabolites,and Application to Bone Marrow and Whole Blood Analysis

The present investigation utilised the quick and easy SPME/LC-MS method to determine selected narcotic substances and their metabolites in whole blood. The study included qualitative analysis and validation of the method. Analytes were determined in the linearity range of 25–300 ng/mL. The precision during and between days (in general CV < 13.41%), and the LOD which results in between 0.36 and 11.08 ng/mL, and the LOQ between 1.20 and 36.90 ng/mL were investigated. The validation results obtained, as well as the results of subsequent in-laboratory tests, confirmed the applicability of the method in the analysis of blood samples. An attempt to apply the method to the analysis of bone marrow samples has yielded promising results; however, more detailed studies are needed in this area.     

Exploration of the Crystal Structure and Thermal and Spectroscopic Properties of Monoclinic Praseodymium Sulfate Pr2(SO4)3

Praseodymium sulfate was obtained by the precipitation method and the crystal structure was determined by Rietveld analysis. Pr₂(SO₄)₃ is crystallized in the monoclinic structure, space group C2/c, with cell parameters a = 21.6052 (4), b = 6.7237 (1) and c = 6.9777 (1) Å, β = 107.9148 (7)°, Z = 4, V = 964.48 (3) ų (T = 150 °C). The thermal expansion of Pr₂(SO₄)₃ is strongly anisotropic. As was obtained by XRD measurements, all cell parameters are increased on heating. However, due to a strong increase of the monoclinic angle β, there is a direction of negative thermal expansion. In the argon atmosphere, Pr₂(SO₄)₃ is stable in the temperature range of T = 30–870 °C. The kinetics of the thermal decomposition process of praseodymium sulfate octahydrate Pr₂(SO₄)₃·8H₂O was studied as well. The vibrational properties of Pr₂(SO₄)₃ were examined by Raman and Fourier-transform infrared absorption spectroscopy methods. The band gap structure of Pr₂(SO₄)₃ was evaluated by ab initio calculations, and it was found that the valence band top is dominated by the p electrons of oxygen ions, while the conduction band bottom is formed by the d electrons of Pr³⁺ ions. The exact position of ZPL is determined via PL and PLE spectra at 77 K to be at 481 nm, and that enabled a correct assignment of luminescent bands. The maximum luminescent band in Pr₂(SO₄)₃ belongs to the ³P₀ → ³F₂ transition at 640 nm.     

氦原子及类氦离子基态的二参数变分法研究

提出了一种计算氦原子及类氦离子基态能量和波函数的二参数变分法,包括试探波函数的设计和基态能量表达式的推导,并用Mathematica 5.0软件的优化计算功能方便快捷地计算出基态能量,将计算结果与实验结果和部分所列文献的结果进行对比.结果表明,本文所得精度较高,变分参数个数较少.同时强调交换对称性和量子态的交缠在双电子原子体系问题中的重要性.     

In Vitro and In Vivo Antibacterial Activity,Toxicity and Resistance Analysis of Pleuromutilin Derivative Z33 against Methicillin-Resistant Staphylococcus aureus

The novel pleuromutilin derivative, which showed excellent in vitro antibacterial activity against MRSA, 22-(2-(2-(4-((4-(4-nitrophenyl)piperazin-1-yl)methyl)-1H-1,2,3-triazol-1-yl)acetamido)phenyl)thioacety-l-yl-22-deoxypleuromutilin (Z33), was synthesized and characterized in our previous work. In this study, the preliminary pharmacodynamics and safety of Z33 were further evaluated. In in vitro antibacterial activity assays, Z33 was found to be a potent bactericidal antibiotic against MRSA that induced dose-dependent growth inhibition and long-term post-antibiotic effect (PAE). The drug-resistance test demonstrated that Z33 possessed a narrow mutant selection window and lower propensities to select resistance than that of tiamulin. Cytochrome P450 (CYP450) inhibition assay determined that the inhibitory effect of Z33 was similar to that of tiamulin against the activity of CYP3A4, and was lower than that of tiamulin on the activity of CYP2E1. Toxicity determination showed that both Z33 and tiamulin displayed low cytotoxicity of RAW264.7 cells. Furthermore, Z33 was found to be a high-security compound with a 50% lethal dose (LD₅₀) above 5000 mg/kg in the acute oral toxicity test in mice. In an in vivo antibacterial activity test, Z33 displayed better therapeutic effectiveness than tiamulin in the neutropenic mouse thigh infection model. In summary, Z33 was worthy of further development as a highly effective and safe antibiotic agent against MRSA infection.     

A New Trial Equation Method and Its Applications

As an improved version of trial equation method, a new trial equation method is proposed. Using this method, abundant new exact traveling wave solutions to a high-order KdV-type equation are obtained.