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.     

Sensitive voltammetric determination of paracetamol by poly (4-vinylpyridine)/multiwalled carbon nanotubes modified glassy carbon electrode

A novel glassy carbon electrode (GCE) modified with a composite film of poly (4-vinylpyridine) (P4VP) and multiwalled carbon nanotubes (P4VP/MWCNT GCE) was used for the voltammetric determination of paracetamol (PCT). This novel electrode displayed a combined effect of P4VP and MWCNT on the electro-oxidation of PCT in a solution of phosphate buffer at pH 7. Hence, conducting properties of P4VP along with the remarkable physical properties of MWCNTs might have combined effects in enhancing the kinetics of PCT oxidation. The P4VP/MWCNT GCE has also demonstrated excellent electrochemical activity toward PCT oxidation compared to that with bare GCE and MWCNT GCE. The anodic peak currents of PCT on the P4VP/MWCNT GCE were about 300 fold higher than that of the non-modified electrodes. By applying differential pulse voltammetry technique under optimized experimental conditions, a good linear ratio of oxidation peak currents and concentrations of PCT over the range of 0.02–450 μM with a limit of detection of 1.69 nM were achieved. This novel electrode was stable for more than 60 days and reproducible responses were obtained at 99% of the initial current of PCT without any influence of physiologically common interferences such as ascorbic acid and uric acid. The application of this electrode to determine PCT in tablets and urine samples was proposed.     

On the numerical range in tropical algebra

ABSTRACT

We introduce the concept of numerical range in tropical linear algebra, explore its properties and show in particular that it contains all the tropical eigenvalues. An explicit formula is obtained for the tropical numerical range and an application in the asymptotic analysis of condition number of symmetric matrices is proposed.     

Ultrasound-assisted temperature-controlled ionic-liquid dispersive liquid-phase microextraction method for simultaneous determination of anethole,estragole, and para-anisaldehyde in different plant extracts and human urine: a comparative study

In this study, the performances of four ionic-liquid-based microextraction methods, ionic-liquid-based dispersive liquid–liquid microextraction (IL-DLLME), ionic-liquid-based ultrasound-assisted emulsification microextraction (IL-USA-ME), temperature-controlled ionic-liquid dispersive liquid-phase microextraction (TC-IL-DLME), and ultrasound-assisted temperature-controlled ionic-liquid dispersive liquid-phase microextraction (USA-TC-IL-DLME), were investigated for extraction of three bioactive compounds (anethole, estragole, and anisaldehyde) from different plant extracts and human urine. Anethole and estragole were chosen because they can alter cellular processes positively or negatively, and an efficient method is needed for their extraction and sensitive determination in the samples mentioned. Because there is no previous report on the separation of anethole and estragole (structural isomers), first, simultaneous gradient elution and flow programming were used. The microextraction methods were then applied and compared for analysis of these compounds in plant extracts and human urine by use of high-performance liquid chromatography (HPLC). The effect of conditions on extraction efficiency was studied and under the optimum conditions, the best enrichment factors (58–64), limits of detection (14–18 ng mL^?1), limits of quantification (47–60 ng mL^?1), and recovery (94.4–101.7 %) were obtained by use of USA-TC-IL-DLME. The optimized conditions were used to determine anethole, estragole, and para-anisaldehyde in fennel, anise, and tarragon extracts and in human urine.     

Regioselective synthesis of highly-substituted biaryls by reaction of vinyl malononitriles with acetylenic esters

The one-pot procedure for synthesis of highly-substituted biaryl derivatives has been described via cyclocondensation reaction between vinyl malononitriles and acetylenic esters. A series of complex biaryls containing one-donor and three-acceptor moieties was obtained with good yields.