Structure-based virtual screening of influenza virus RNA polymerase inhibitors from natural compounds: Molecular dynamics simulation and MM-GBSA calculation

The resistances of matrix protein 2 (M2) protein inhibitors and neuraminidase inhibitors for influenza virus have attracted much attention and there is an urgent need for new drug. The antiviral drugs that selectively act on RNA polymerase are less prone to resistance and possess fewer side effects on the patient. Therefore, there is increased interest in screening compounds that can inhibit influenza virus RNA polymerase. Three natural compounds were found by using molecular docking-based virtual screening, which could bind tightly within the polymerase acidic protein-polymerase basic protein 1 (PA-PB1) subunit of influenza virus polymerase. Firstly, their drug likeness properties were evaluated, which showed that the hepatotoxicity values of all the three compounds indicating they had less or no hepatotoxicity, and did not have the plasma protein biding (PPB) ability, the three compounds needed to be modified in some aspects, like bulky molecular size. The stability of the complexes of PA-hits was validated through molecular dynamics (MD) simulation, revealing compound 2 could form more stable complex with PA subunit. The torsional conformations of each rotatable bond of the ligands in PA subunit were also monitored, to investigate variation in the ligand properties during the simulation, compound 3 had fewer rotatable bonds, indicating that the molecule had stronger rigidity. The bar charts of protein–ligand contacts and contacts over the course of trajectory showed that four key residues (Glu623, Lys643, Asn703 and Trp706) of PA subunit that participated in hydrogen-bond, water bridge and hydrophobic interactions with the hit compounds. Finally, the binding free energy and contributed energies were calculated by using MM-GBSA method. Out of the three compounds, compound 1 showed the lowest total binding free energy. Among all the interactions, the contribution of the covalent binding and the van der Waals energy were more than other items, compound 1 formed more stable hydrogen bonds with the residues of PA subunit binding pocket. This study smoothed the path for the development of novel lead compounds with improved binding properties, high drug likeness, and low toxicity to humans for the treatment of influenza, which provided a good basis for further research on novel and effective influenza virus PA-PB1 interaction inhibitors.     

Antiferromagnetic ordering and metamagnetism in PrCuSi

A variety of physical properties measured on the hexagonal rare-earth intermetallic compound PrCuSi are presented. We provide compelling evidence for antiferromagnetic ordering at T_N = 5.1 K in this compound, in contrast to the former claim of ferromagnetic ordering at 14 K. The antiferromagnetic order is, however, found to be unstable in applied magnetic fields, becoming ferromagnetic beyond a metamagnetic transition at a field of 0.7 T at 2 K. It is argued that the magnetism in PrCuSi has the ingredients of a tricritical phase transition at the intersection of paramagnetism, ferromagnetism, and antiferromagnetism.     

Synthesis and Anti-inflammatory Activity of a Novel Series of 9,10-Dihydro-4H,8H-chromeno[8,7-e][1,3]oxazin-4-one Derivatives

Flavonoids exhibit a wide range of biological activities including anti-inflammatory activity,while some 1,3-benzoxazine derivatives show anti-inflammatory activity.In order to explore the novel anti-inflammatory agents,based on the principles of bioisosterism and hybridization,ten novel chromeno[8,7-e][1,3]oxazin-4-ones were synthesized and characterized with IR,1H NMR,MS and elemental analyses.The anti-inflammatory activities of the target compounds were evaluated via the croton oil-induced ear oedema tes...     

银杏叶化学组分群动态FTIR指纹图谱研究

比较了相同产地不同月份与相同月份不同产地银杏叶的FTIR图谱,研究了银杏叶化学组分群随气候、季节、地域等的差异而呈现出的动态分布规律。结果表明,从4月份到10月份,银杏叶内化学组分群呈现动态分布与变化,其变化在6月16日,9月1日,10月4日3个时段。5月份所采集的不同产地银杏叶的化学组分群分布基本一致。这在银杏叶药材种植质量管理规范(GAP)基地的建设、确保银杏叶原料的稳定性以及其后各类相关指纹图谱的研究及制定等方面具有重要意义。     

Chemically shortened multi-walled carbon nanotubes used as anode materials for lithium-ion batteries

An easy chemically cutting process, modified Hummers' method, was proposed to treat multi-walled carbon nanotubes, successfully cutting pristine long, entangled carbon nanotubes into hydrosoluble pieces, mostly less than 200 nm. This short, chemically oxidized carbon nanotube was then applied as an anode material for lithium-ion batteries. The as-prepared material possessed higher reversible capacity and coulombic efficiency. The intrinsic factors were explored by X-ray photoelectron spectroscopy and cyclic voltammetry.     

Structures, phase transition, elastic properties of SnO2 from first-principles analysis

We investigate the structural, phase transition and elastic properties of SnO₂ in the rutile-type, pyrite-type, ZrO₂-type and cotunnite-type phases by the plane-wave pseudopotential density functional theory method. The lattice constants, bulk modulus and its pressure derivative are well consistent with the available experimental and other theoretical data. Also, we find that the rutile→pyrite, pyrite→ZrO₂ and ZrO₂→cotunnite phase transition occur at 12.9, 59.1 and 111.1 GPa, which are in better agreement with the experimental results than those of Gracia et al. (2007). Moreover, we obtain the pressure dependences of elastic constants for the four structures.     

Ab initio study for the intermolecular interaction potential surface of Ar-N2 complex

The intermolecular interaction potentials of van der Waals Ar-N2 complex have been studied by ab initio calculations using the single and double excitation coupled cluster [CCSD(T)] theory with perturbative triples correction. The full counterpoise method is applied to correct the basis set superposition error (BSSE). It is found that the T-shaped structure is the most stable conformation with the well depth De of 12.40 meV at the minimum distance Rm of 3.70 Å. The calculated anisotropic values for Rm, R0 and De are 0.56 Å, 0.54 Å and 2.68 meV, respectively. Compared with those obtained by others, our calculated PES seems to be in better agreement with experiments.     

New insight into the solid electrolyte interphase with use of a focused ion beam

The formation and evolution of the solid electrolyte interphase (SEI) film on the surface of natural graphite spheres in the electrolyte of 1 M LiPF6 in ethylene carbonate (EC) and dimethyl carbonate (DMC) (volume ratio 1:1) were investigated with use of focused ion beam (FIB) technology. Secondary electron FIB images clearly show the surface and cross-section morphology of the SEI film. The composition variation along the surface and cross section of the SEI film was also explored by the elemental line scan analysis (ELSA). The initial SEI film with an apparent thickness range of approximately 450 to approximately 980 nm is rough in morphology and nonuniform in composition, and contains small splits. After certain electrochemical cycles, the thickened SEI film displays microscale holes and obvious cracks on the surface, and the content of organic compounds increases. In addition, the concept of "internal SEI film" is first proposed based on the characterization of the cross section of the natural graphite spheres with the aid of FIB. Finally, the capacity fading mechanisms of the natural graphite spheres corresponding to different electrochemical stages are discussed.     

Determination of mangiferin, jateorrhizine, palmatine, berberine, cinnamic acid, and cinnamaldehyde in the traditional Chinese medicinal preparation Zi-Shen pill by high-performance liquid chromatography

High-performance liquid chromatography is employed to determine the contents of six marker components such as mangiferin, jateorrhizine, palmatine, berberine, cinnamic acid, and cinnamaldehyde in the traditional Chinese medicinal preparation Zi-Shen pill. The separation is performed on a C(18) column by stepwise gradient elution with water (0.2%, v/v, triethylamine adjusted to pH 4 with phosphoric acid)-methanol-acetonitrile (0.01 min, 98:0:2; 20 min, 80:5:15; 30 min, 65:13:22; and 55 min, 65:13:22) as the mobile phase at a flow rate of 0.9 mL/min, with UV detection at 280 nm. Six regression equations show good linear relationships between the peak area of each marker and concentration. The recoveries of the markers listed are 95.5%, 98.3%, 96.8%, 99.5%, 101.7%, and 102.1%, respectively. The repeatability and reproducibility (relative standard deviation) of the method are less than 2.5% and 3.3%, respectively.     

Pulsed-laser-deposited epitaxial aluminum nitride films on (111) Si for surface acoustic-wave applications

Epitaxial (001) aluminum nitride (AlN) thin films on (111) Si substrates are prepared using pulsed-laser deposition. The epitaxial structure of the as-prepared thin films is characterized by checking the X-ray-diffraction θ-2 θ scan and pole-figure, using scanning electron microscopy, infrared radiation (IR) spectroscopy and Raman spectroscopy. The surface acoustic-wave resonance at 345 MHz for a 1.5 μm thick AlN film on a (111) Si substrate is observed using an inter-digital electrode. Received: 18 September 2001 / Accepted: 29 January 2002 / Published online: 3 June 2002 RID="*" ID="*"Corresponding author. Fax: +86-25/359-5535, E-mail: liujm@nju.edu.cn