Molecular Docking of SP40 Peptide towards Cellular Receptors for Enterovirus 71 (EV-A71)

Enterovirus 71 (EV-A71) is one of the predominant etiological agents of hand, foot and mouth disease (HMFD), which can cause severe central nervous system infections in young children. There is no clinically approved vaccine or antiviral agent against HFMD. The SP40 peptide, derived from the VP1 capsid of EV-A71, was reported to be a promising antiviral peptide that targeted the host receptor(s) involved in viral attachment or entry. So far, the mechanism of action of SP40 peptide is unknown. In this study, interactions between ten reported cell receptors of EV-A71 and the antiviral SP40 peptide were evaluated through molecular docking simulations, followed by in vitro receptor blocking with specific antibodies. The preferable binding region of each receptor to SP40 was predicted by global docking using HPEPDOCK and the cell receptor-SP40 peptide complexes were refined using FlexPepDock. Local molecular docking using GOLD (Genetic Optimization for Ligand Docking) showed that the SP40 peptide had the highest binding score to nucleolin followed by annexin A2, SCARB2 and human tryptophanyl-tRNA synthetase. The average GoldScore for 5 top-scoring models of human cyclophilin, fibronectin, human galectin, DC-SIGN and vimentin were almost similar. Analysis of the nucleolin-SP40 peptide complex showed that SP40 peptide binds to the RNA binding domains (RBDs) of nucleolin. Furthermore, receptor blocking by specific monoclonal antibody was performed for seven cell receptors of EV-A71 and the results showed that the blocking of nucleolin by anti-nucleolin alone conferred a 93% reduction in viral infectivity. Maximum viral inhibition (99.5%) occurred when SCARB2 was concurrently blocked with anti-SCARB2 and the SP40 peptide. This is the first report to reveal the mechanism of action of SP40 peptide in silico through molecular docking analysis. This study provides information on the possible binding site of SP40 peptide to EV-A71 cellular receptors. Such information could be useful to further validate the interaction of the SP40 peptide with nucleolin by site-directed mutagenesis of the nucleolin binding site.     

Study of hydrogen-bonded clusters of 2-methoxyphenol–water

Various hydrogen-bonded clusters of 2-methoxyphenol (2MP) with water have been analyzed using ab initio methods and Atoms in Molecules (AIM) theory. The intramolecular hydrogen bond energy (and enthalpy) for 2MP was evaluated from two different methods. The results of rotational barriers method are in better agreement with experimental data. Binding energies, vibrational frequencies and geometrical parameters were examined and compared for these complexes. It was shown that in the most stable complex, water acts both as a donor and an acceptor. The “bifurcated” complex was shown to be relatively stable based on energy values. Atoms in Molecules and Natural Bond Orbital (NBO) analysis were used to confirm the existence of hydrogen bonds and to compare the strengths of them. The results obtained from quantum mechanical, AIM and NBO calculations are in agreement with each other.     

Mercury(II) selective sensors based on AlGaN/GaN transistors

This work presents the first polymer approach to detect metal ions using AlGaN/GaN transistor-based sensor. The sensor utilised an AlGaN/GaN high electron mobility transistor-type structure by functionalising the gate area with a polyvinyl chloride (PVC) based ion selective membrane. Sensors based on this technology are portable, robust and typically highly sensitive to the target analyte; in this case Hg²⁺. This sensor showed a rapid and stable response when it was introduced to solutions of varying Hg²⁺ concentrations. At pH 2.8 in a 10⁻² M KNO₃ ion buffer, a detection limit below 10⁻⁸ M and a linear response range between 10⁻⁸ M-10⁻⁴ M were achieved. This detection limit is an order of magnitude lower than the reported detection limit of 10⁻⁷ M for thioglycolic acid monolayer functionalised AlGaN/GaN HEMT devices. Detection limits of approximately 10⁻⁷ M and 10⁻⁶ M in 10⁻² M Cd(NO₃)₂ and 10⁻² M Pb(NO₃)₂ ion buffers were also achieved, respectively. Furthermore, we show that the apparent gate response was near-Nernstian under various conditions. X-ray photoelectron spectroscopy (XPS) experiments confirmed that the sensing membrane is reversible after being exposed to Hg²⁺ solution and rinsed with deionised water. The success of this study precedes the development of this technology in selectively sensing multiple ions in water with use of the appropriate polymer based membranes on arrays of devices.     

Dark Matter Density from Heavy Neutrino Decays

As we know the heavy neutrino decays is a successful model for describing dark matter and also is origin of the universe entropy. In this paper we use heavy neutrino decays to calculate time-dependent dark matter density. In that case we use observational data to fixing our solutions.     

Highly selective transport of lead cation through bulk liquid membrane by macrocyclic ligand of decyl-18-crown-6 as carrier

The liquid membrane transport of Pb²⁺ cation using decyl-18-crown-6 as selective ion carrier was studied. The transport of lead ion across the liquid membrane in the presence of S₂O ₃ ^2? , P₂O ₇ ^4? , CN^?, SCN^?, and DDC^? as stripping agents in the receiving phase shows that the nature and the concentration of the stripping agents affect on Pb²⁺ cation transport and the maximum transport occurs when the sodium thiosulfate (Na₂S₂O₃) was used. The effects of various parameters influencing the transport efficiency such as the pH of the source and receiving phases, the concentration of picrate ion as counter ion in the source phase were also studied. Five replicated experiments show that a value 82.12 ± 2.09% of the initial concentration of the Pb²⁺ cation in the source phase is extracted into the receiving phase after 4 hours. Also the selectivity and efficiency of lead ion transport from the source phase containing equimolar mixtures of Na⁺, K⁺, Ca²⁺, Ni²⁺, Cu²⁺, Cd²⁺ and Ag⁺ metal cations were investigated.     

Pyridazine-based Schiff base ligands with N4OxS2 (x = 2, 4) donor set atoms: Synthesis,characterization, spectral studies and 13C chemical shifts computed by the GIAO-DFT and CSGT-DFT methodologies

Six pyridazine-based Schiff base ligands, H₂Lⁿ (n = 1–5) and H₄L, with N₄O₂S₂ and N₄O₄S₂ donor set atoms, respectively, were prepared by condensation reaction of 3,6-bis-((2-aminoethyl)thio)pyridazine with various salicyladehyde derivatives in ethanol and under solvent-free polyphosphate ester catalyzed conditions. The acid–base properties of H₂L² and H₂L³ in DMSO/water (1:1) solution have been studied by spectrophotometric method at 25 °C. Optimized geometries of all compounds were also obtained at the B3LYP level of theory. Additionally, the ¹³C chemical shielding of gas phase H₂L¹ and H₂L² were studied by the gauge independent atomic orbital (GIAO) and continuous set of gauge transformations (CSGT) methods at the level of density functional theory (DFT). The 6-311++G* basis set was utilized for all of the atoms.     

Electrocatalytic determination of L-cysteine using a modified carbon nanotube paste electrode:Application to the analysis of some real samples

The electrooxidation of L-cysteine(L-Cys) was studied using a benzoylferrocene(BF) modified multi-wall carbon nanotube paste electrode(BFCNPE) using cyclic voltammetry(CV),square wave voltammetry(SWV) and chronoamperometry(CHA).Under optimum pH in CV the oxidation of L-Cys occurs at a potential about 215 mV less positive than that at the surface of unmodified carbon paste electrode.The catalytic oxidation peak currents were dependent on the L-Cys concentration and a linear calibration curve was obtained in the range 0.7-350.0 mmol/L of L-Cys with SWV method.The detection limit(3s) was determined as 0.1 mmol/L.This method was also used for the determination of L-Cys in some real samples.     

Nanostructure-based electrochemical sensor for determination of glutathione in hemolysed erythrocytes and urine

A sensitive and selective electrochemical method was developed for the determination of glutathione (GSH) in hemolysed erythrocyte using vinylferocene modified carbon nanotubes paste electrode (VFMCNTPE). The results indicate that the electrode is efficient in terms of its electrocatalytic activity for the oxidation of GSH, leading to a reduced overpotential by more than 470 mV. Also, the values of catalytic rate constant (k), and diffusion coefficient (D) for GSH were calculated. The electrocatalytic oxidation peak current of GSH showed two linear dynamic ranges with a detection limit of 0.09 μM GSH. The linear calibration ranges were obtained between 0.2–4.0 and 4.0–250.0 μM GSH using square wave voltammetry (SWV) method. The proposed method was also examined as a selective, simple and precise electrochemical sensor for the determination of GSH in real samples such as urine and hemolysed erythrocyte.     

Preparation and characterization of polyvinyl alcohol/β‐cyclodextrin/GO‐Ag nanocomposite with improved antibacterial and strength properties

In this work, new hydrogel films based on polyvinyl alcohol (PVA) and β‐cyclodextrin (β‐CD) were prepared with the aim of studying their ability as an antibacterial and drug carrier system. Gallic acid (GA) was used as an antibacterial drug which was encapsulated into the β‐CD cavity, and finally, β‐CD inclusion complex (GA/βCD‐IC) was prepared. On the other hand, silver nanoparticles (AgNPs) were synthesized on the graphene oxide (GO) surface (GO‐Ag), and the obtained GO‐Ag was used to enhance the antibacterial properties and mechanical strength of their films. FT‐IR and DSC analysis approved the formation of cross‐linking with glutaraldehyde between the PVA and β‐CD. Hydrogel films were characterized using XRD and SEM. The disc diffusion method showed the antibacterial activity for the films containing GO‐Ag and GA. Due to the good strength, elasticity, WVP, and swelling ability, PVA/GA/βCD‐IC/GO‐Ag can be proposed as a potential antibacterial drug delivery system.     

A Cheap and Efficient Methodology for the Solvent‐Free,One‐pot and Multi‐component Synthesis of 3,4‐Dihydropyrimidin‐2(1H)‐ones Catalyzed by Mesoporous NH4H2PO4/MCM‐48 and Comparison of Its Catalytic Efficacy with NH4H2PO4/MCM‐41

The catalytic efficiency of ammonium dihydrogenphosphate was evaluated in the two heterogeneous forms of NH₄H₂PO₄/MCM‐48 and NH₄H₂PO₄/MCM‐41, as mesoporous catalysts, in the solvent free synthesis of 3,4‐dihydropyrimidin‐2(1H)‐ones through one‐pot three‐component condensation of ethyl acetoacetate, an aryl aldehyde and urea. Different reaction parameters including catalytic efficacy, solvent effect, and urea concentration are considered.