Protein–ligand docking using FFT based sampling: D3R case study

Fast Fourier transform (FFT) based approaches have been successful in application to modeling of relatively rigid protein–protein complexes. Recently, we have been able to adapt the FFT methodology to treatment of flexible protein–peptide interactions. Here, we report our latest attempt to expand the capabilities of the FFT approach to treatment of flexible protein–ligand interactions in application to the D3R PL-2016-1 challenge. Based on the D3R assessment, our FFT approach in conjunction with Monte Carlo minimization off-grid refinement was among the top performing methods in the challenge. The potential advantage of our method is its ability to globally sample the protein–ligand interaction landscape, which will be explored in further applications.     

Ag3[PMo12O40]: An efficient and green catalyst for the synthesis of highly functionalized pyran‐annulated heterocycles via multicomponent reaction

A facile, efficient and eco‐friendly catalytic protocol was developed for the synthesis of medicinally important pyran‐annulated heterocycles via multicomponent reaction (MCR). Cyclocondensation of differently substituted aromatic aldehydes, malononitrile/ethyl cyanoacetate and various β‐dicarbonyl compounds in the presence of Ag₃[PMo₁₂O₄₀]?nH₂O as heterogeneous catalyst, in EtOH–H₂O, afforded diverse pyran‐fused chromene analogues. The merits observed for this approach were it being conducted via MCR, using commercially available or easily accessible starting materials in the presence of a green and easily separable heterogeneous and reusable catalyst, and affording high yields of desired products in very short reaction times with high purity in one‐pot fashion, thus providing a superior alternative approach for the synthesis of pyran‐annulated heterocycles.     

Finely dispersed palladium on silk‐fibroin as an efficient and ligand‐free catalyst for Heck cross‐coupling reaction

A palladium–fibroin complex (Pd/Fib.) was prepared by the addition of sonicated fibroin fiber in water to palladium acetate solution. Pd (OAc)₂ was absorbed by fibroin and reduced with NaBH₄ at room temperature to the Pd(0) nanoparticles. Powder‐X‐ray diffraction, scanning electron microscopy–energy‐dispersive X‐ray spectroscopy, Fourier transform‐infrared, CHN elemental analysis and inductively coupled plasma‐atomic emission spectroscopy were carried out to characterize the Pd/Fib. catalyst. Catalytic activity of this finely dispersed palladium was examined in the Heck coupling reaction. The catalytic coupling of aryl halides (‐Cl, ‐Br, ‐I) and olefins led to the formation of the corresponding coupled products in moderate to high yields under air atmosphere. A variety of substrates, including electron‐rich and electron‐poor aryl halides, were converted smoothly to the targeted products in simple procedure. Heterogeneous supported Pd catalyst can be recycled and reused several times.     

KAl(SO4)2 · 12H2O (alum) a reusable catalyst for the synthesis of some 4-substituted coumarins via Pechmann reaction under solvent-free conditions

A simple, efficient, and practical procedure for the Pechmann condensation using KAl(SO₄)₂ · 12H₂O (alum) as a non-toxic, reusable, inexpensive, and easily available catalyst is described under solvent-free condition at 65°C. These improved reaction conditions allow the preparation of a wide variety of some new substituted coumarins in high yields (86–96%) and purity under mild reaction conditions. Compared to the classical Pechmann condensation, this new method consistently has the advantage of high yields. Correspondence: Ali A. Mohammadi, Department of Chemistry, Shahid Beheshti University, P.O. Box 19839-4716, Tehran, Iran.     

Density and viscosity of 1-butyl-3-methylimidazolium nitrate with ethanol, 1-propanol, or 1-butanol at several temperatures

Densities and viscosities of 1-butyl-3-methylimidazolium nitrate [Bmim][NO₃], and its binaries with alcohol (ethanol, 1-propanol, or 1-butanol) were measured at different temperatures. The densities and viscosities of pure ionic liquid were correlated successfully by empirical equations. The Vogel–Fulcher–Tammann equations can fit the experimental data of viscosities for pure IL. Excess molar volume and viscosity deviations were calculated for the binaries. The excess molar volumes have negative deviations from the ideal solution.     

Potentiometric PVC membrane sensor for the determination of phenylephrine hydrochloride in some pharmaceutical products

A new PVC membrane electrode for the determination of phenylephrine hydrochloride based on the formation of an ionassociation complex of phenylephrine hydrochloride with the phosphotungstate counter anion as an electroactive material dispersed in a PVC matrix is described. The sensor shows a fast, stable, near-Nernstian response for 1.0 × 10^?5 to 1.0 × 10^?1 M phenylephrine hydrochloride at 25 °C over the pH range of 3.5–8.0 with a cationic slope of 58.1 ± 0.6 mV decade^?1. The electrode was successfully used for potentiometric determination of phenylephrine hydrochloride in some pharmaceutical drugs.     

Novel and versatile methodology for synthesis of β-aryl-β-mercapto ketone derivatives as potential urease inhibitors

The objective was to obtain new scaffold of compounds possessing anti-urease activity. For this new and simple method for the synthesis of β-aryl-β-mercapto ketone derivatives based on Michael addition of thiophenol to chalcones in an ionic liquid as a solvent was improved. The products were obtained in good to moderate yields with high purity and characterized by spectral and elemental analyses. The activities of synthesized compounds were investigated as new inhibitors of jack bean urease. Among 22 synthesized compounds, all of them have shown inhibitory effect in micromolar range, and the most potent one has IC₅₀ = 6 μM compared to hydroxyurea IC₅₀ = 100 μM as a reference inhibitor. A docking study was performed using Autodock 4.2 in parallel to in vitro experiments to illustrate the corresponded binding affinities as well as binding site, and involved residues in interaction. These computational results complimented the experimental inhibition activity and enabled us to report a potent urease inhibitors based on β-aryl-β-mercapto ketone scaffold.     

Application of gold-labeled antibody biosensor in simultaneous determination of total aflatoxins using artificial neural network

Preparation of antibody-coated gold nanoparticles (GNPs) specific to aflatoxins B1, B2, G1 and G2 and its use in developing aflatoxins diagnostic method were presented in this paper. The formation of gold-labeled antibodies was accomplished at optimal condition. Due to severe overlapping between the emission profiles for the aflatoxins, they cannot be determined by direct inspection of data. The strategy used in this study, constituted by artificial neural network (ANN), was easy to implement and to originate reliable results. ANN can be successfully applied to spectrofluorimetric spectra matrices to simultaneous determination of total aflatoxins. Quantitative results obtained using ANN method for aflatoxins in pistachio nuts samples were compared to those obtained using the HPLC method. Obtained results using these two methods did not show significant differences.     

Evaluation of the corrosion inhibition effect of micro/nanocapsulated polymeric coatings: a comparative study by use of EIS and Tafel experiments and the area under the Bode plot

In this paper we propose an approach for ranking self-healing polymeric coatings containing micro/nanocapsules in order of corrosion-protection effectiveness on exposure to 3.5 % (w/w) NaCl solution. The results indicated that development of electrochemical cells was inhibited by the active components of the ruptured embedded inhibitor micro/nanocapsules which were released into a scratch inflicted in the polymeric coating on steel surface. Undamaged surface film of test and control specimens exposed to the solution had excellent corrosion-inhibition performance, as reflected by results from both electrochemical impedance spectroscopy and polarization tests. Moreover, three coatings containing capsules synthesized at three different agitation rates with the same thickness were compared to determine the optimum rate. For the optimum rate the optimum thickness was then determined. The areas under Bode plots were determined and used as useful values for evaluation and ranking the coatings. It was found that the area under the Bode plot is a good criterion for evaluating polymeric coating degradation during immersion. There was good agreement between the results of this work and those from electrochemical tests.     

Catalytic behaviors of Co-Mn/TiO2 catalysts for Fischer-Tropsch synthesis

The 15%(Co-Mn)/TiO₂,(Co/Mn=1/6) catalyst was prepared using fusion procedure and studied for the conversion of synthesis gas to C_2~4 olefins. The effects of calcination conditions and operation conditions such as the H₂/CO molar feed ratio at different temperatures, gas hourly space velocity (GHSV) and total reaction pressure on the catalytic performance of catalyst were investigated. The stability of the catalyst during 150 h at optimal operation conditions (t=250 ℃ H₂/CO=2/1, GHSV=1 500 h^-1 and p=0.3 MPa) has been investigated. It is found that this catalyst is high stable for production C_2~4 olefins. Characterizations of both precursors and calcined catalysts by powder X-ray diffraction, scanning electron microscopy (SEM), Brunauer-Emmett-Teller (BET) specific surface area measurement and thermal analysis methods such as thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC) show that the different preparation method influences the catalyst precursor structure and morphology.