Ranking docking poses by graph matching of protein–ligand interactions: lessons learned from the D3R Grand Challenge 2

A novel docking challenge has been set by the Drug Design Data Resource (D3R) in order to predict the pose and affinity ranking of a set of Farnesoid X receptor (FXR) agonists, prior to the public release of their bound X-ray structures and potencies. In a first phase, 36 agonists were docked to 26 Protein Data Bank (PDB) structures of the FXR receptor, and next rescored using the in-house developed GRIM method. GRIM aligns protein–ligand interaction patterns of docked poses to those of available PDB templates for the target protein, and rescore poses by a graph matching method. In agreement with results obtained during the previous 2015 docking challenge, we clearly show that GRIM rescoring improves the overall quality of top-ranked poses by prioritizing interaction patterns already visited in the PDB. Importantly, this challenge enables us to refine the applicability domain of the method by better defining the conditions of its success. We notably show that rescoring apolar ligands in hydrophobic pockets leads to frequent GRIM failures. In the second phase, 102 FXR agonists were ranked by decreasing affinity according to the Gibbs free energy of the corresponding GRIM-selected poses, computed by the HYDE scoring function. Interestingly, this fast and simple rescoring scheme provided the third most accurate ranking method among 57 contributions. Although the obtained ranking is still unsuitable for hit to lead optimization, the GRIM–HYDE scoring scheme is accurate and fast enough to post-process virtual screening data.     

Monitoring of selenium in water samples using dispersive liquid-liquid microextraction followed by iridium-modified tube graphite furnace atomic absorption spectrometry

A simple and powerful microextraction technique was used for determination of selenium in water samples using dispersive liquid-liquid microextraction (DLLME) followed by graphite furnace atomic absorption spectrometry (GF AAS). DLLME and simultaneous complex formation was performed with rapid injection of a mixture containing ethanol (disperser solvent), carbon tetrachloride (extraction solvent) and ammonium pyrrolidine dithiocarbamate (APDC, chelating agent) into water sample spiked with selenium. After centrifuging, fine droplets of carbon tetrachloride, which were dispersed among the solution and extracted Se-APDC complex, sediment at the bottom of the conical test tube. The concentration of enriched analyte in the sedimented phase was determined by iridium-modified pyrolitic tube graphite furnace atomic absorption spectrometry. The concentration of selenate was obtained as the difference between the concentration of selenite after and before pre-reduction of selenate to selenite. Some effective parameters on extraction and complex formation, such as extraction and disperser solvent type and their volume, extraction time, salt effect, pH and concentration of chelating agent were optimized. Under the optimum conditions, the enrichment factor of 70 was obtained from only 5.00 mL of water sample. The calibration graph was linear in the range of 0.1-3 μg L^− 1 with detection limit of 0.05 μg L^− 1. The relative standard deviation (RSDs) for ten replicate measurements of 2.00 μg L^− 1 of selenium was 4.5%. The relative recoveries of selenium in tap, river and sea water samples at spiking level of 2.00 μg L^− 1 were 106, 96 and 98%, respectively.     

Mono- and dinuclear bioxazoline-palladium complexes for the stereocontrolled synthesis of CO/styrene polyketones

The coordination chemistry of the chiral bioxazoline ligand (4S,4'S)-2,2'-bis(4-isopropyl-4,5-dihydrooxazole) to Pd(II) provides evidence that the ligand bonding can occur either through chelation of one Pd(II) ion leading to a mononuclear species with the expected cis geometry, or by double bridging of two Pd(II) ions giving a dinuclear complex with trans geometry. The species in solution are identified by 1H NMR spectroscopy. Both the mononuclear and the dinuclear complexes promote the CO/styrene copolymerization, yielding the corresponding polyketone with a fully or a predominantly isotactic microstructure, depending on the reaction medium. The nature of the anion present in the palladium precatalysts affects the polyketone stereochemistry. MALDI-TOF analysis of the copolymers synthesized reveals the presence of p-hydroxyphenolic end-groups, thus confirming and explaining the role of 1,4-hydroquinone as a molecular weight regulator.     

Determination of atenolol at a graphite-polyurethane composite electrode

A bare graphite-polyurethane composite was evaluated as an alternative electrode in the determination of atenolol (ATN) in pharmaceutical formulations. Using a DPV procedure, a linear analytical curve was observed in the 4-100 μmol L⁻¹ range with a LOD = 3.16 μmol L⁻¹, without need of surface renewing between successive runs, with recoveries between 95.5 and 108%. Interference of other antihypertensive drugs was observed, but not from the usual components of tablets. The results of the proposed method agreed with HPLC ones within 95% confidence level.     

Far-infrared and mid-infrared absorption in (Bi,Pb)-Sr-(Ca,Y)-Cu-O

The reflectivities of seven films belonging to the Bi-Sr-Ca-Cu-O family, with T_c ranging from 60 to 95 K, and of a single crystal of insulating Bi-Sr-Y-Cu-O, have been measured at room temperature in the normal phase. The optical conductivity has been analyzed in terms of Drude (D), mid-infrared (MIR), and charge-transfer (CT) contributions. As T_c increases, the spectral weight within the charge-transfer gap (D+MIR) increases. Meanwhile, the peak frequency of the MIR band moves towards the far-infrared and the optical conductivity becomes more similar to that of a normal metal.     

Spectroscopic studies of the intermolecular interactions of Congo red and tinopal CBS with modified cellulose fibers

The adsorption of Congo red and tinopal CBS dyes on cellulose fibers was investigated using electronic absorption and fluorescence spectroscopies. Hydrogen bonds appear to be relevant for the dye-fiber interactions as indicated by the solvatochromism of Congo red in water, methanol, and dimethyl sulfoxide solutions, and when adsorbed on cellulose fibers. We also demonstrate that electrostatic interactions play an important role in the dye-medium interaction, through the analysis of absorption spectra of Congo red and fluorescence spectra of tinopal in aqueous solutions containing salt and in layer-by-layer nanostructured films with poly(allylamine hydrochloride). For instance, dye adsorption was enhanced when salt was added to the dipping solution, which was explained by the synergistic effect between the conformational changes of the cellulose and changes in the solvation layer around the cellulose chains and around dye molecules. On the basis of the fluorescence results for tinopal CBS, we inferred that dye aggregation is not relevant for adsorption on the fibers. In addition, fluorescence spectroscopy is proven very sensitive for studying the organization of dye molecules in layer-by-layer films, particularly those undergoing irreversible structural changes.     

Photocatalytic activity of nanostructured TiO2 films produced by supersonic cluster beam deposition

The photocatalytic activity of thin, nanostructured films of titanium dioxide, synthesized by supersonic cluster beam deposition (SCBD) from the gas phase, has been investigated employing the photodegradation of salicylic acid as test reaction. Because of the low deposition energy, the so-deposited highly porous TiO₂ films are composed of nanoparticles maintaining their original properties in the film, which can be fully controlled by tuning the deposition and post-deposition treatment conditions. A systematic investigation on the evolution of light absorption properties and photoactivity of the films in relation to their morphology, determined by AFM analysis, and phase composition, determined by Raman spectroscopy, has been performed. The absorption and photocatalytic activity of the nanostructured films in the visible region could be enhanced either through post-deposition annealing treatment in ammonia containing atmosphere or employing mild oxidation conditions, followed by annealing in N₂ at 600 °C.     

Ettringite instability analysis in the hydration process of the supersulfated cement

Journal of Thermal Analysis and Calorimetry - The search for new materials to replace Portland cement (PC) has increased due to the high release of carbon dioxide (CO2) and the exploration of raw...