Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach

CXCR4 is a G-protein coupled receptor for CXCL12 that plays an important role in human immunodeficiency virus infection, cancer growth and metastasization, immune cell trafficking and WHIM syndrome. In the absence of an X-ray crystal structure, theoretical modeling of the CXCR4 receptor remains an important tool for structure–function analysis and to guide the discovery of new antagonists with potential clinical use. In this study, the combination of experimental data and molecular modeling approaches allowed the development of optimized ligand-receptor models useful for elucidation of the molecular determinants of small molecule binding and functional antagonism. The ligand-guided homology modeling approach used in this study explicitly re-shaped the CXCR4 binding pocket in order to improve discrimination between known CXCR4 antagonists and random decoys. Refinement based on multiple test-sets with small compounds from single chemotypes provided the best early enrichment performance. These results provide an important tool for structure-based drug design and virtual ligand screening of new CXCR4 antagonists.     

On the isothermal closed space sublimation growth of CdSe using a mixed source for selenium

The use of a selenium–tellurium (SeTe) mixed source in the isothermal close space sublimation growth of CdSe epilayers is considered. The epitaxial growth was performed in flowing helium by sequential exposures of the substrate to vapors of the mixed SeTe source and elemental cadmium at temperatures within 350–410 °C. In spite of the mixed source (proposed to decrease the partial pressure of Se), tellurium incorporation was small and CdSe_xTe_(1−x) (x∼0.98) epilayers were obtained. X-ray diffraction reciprocal space mapping shows the existence of hexagonal inclusions mainly on the (1 1 1) facets of the cubic phase. Material deposition on areas of the graphite crucible exposed to the sources, contamination of the Cd source and large growth rates suggest the existence of a selenium transport process via graphite. This transport might be the result of the combination of selenium deposition on graphite with a subsequent activated desorption of selenium under cadmium exposure. It affects Cd source purity and growth kinetic bringing on a modification of the usual atomic layer deposition regimen; however, a reproducible growth rate of the epilayers was obtained.     

Influence of polymerizing agent on structure and spectroscopic properties of nano‐crystalline La0.8Sr0.2MnO3 powders

Strontium‐doped lanthanum manganite (La_1‐xSr_xMnO₃ or LSM) is the material most widely used on solid oxide fuel cells cathode. In this work, nano‐scale La_0.8Sr_0.2MnO₃ powders have been synthesized by polymeric precursor‐based methods using different polymerizing agents with the aim of evaluating the influence of this change in the final powder. The powders calcined at 700 °C for 2 h have been characterized by X‐ray diffraction (XRD), scanning electron microscopy (FE‐SEM) and Fourier transform infrared spectroscopy (FTIR) in order to investigate the quality of both synthesis routes. It is shown that the crystal structure and morphology of the particles are significantly dependent on the preparation conditions. Single phase and La_0.8Sr_0.2MnO₃ nano‐crystalline particles less than 30 nm were obtained using ethylene glycol as polymerizing agent. FTIR results have been indicated that only the powder obtained using gelatin presented small traces of hydroxyl groups on its surface. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Strong Convergence in Hilbert Spaces via Γ-Duality

We analyze a primal-dual pair of problems generated via a duality theory introduced by Svaiter. We propose a general algorithm and study its convergence properties. The focus is a general primal-dual principle for strong convergence of some classes of algorithms. In particular, we give a different viewpoint for the weak-to-strong principle of Bauschke and Combettes and unify many results concerning weak and strong convergence of subgradient type methods.     

Low-Temperature Raman Spectra of l-Histidine Crystals

We present a Raman spectroscopy investigation of the vibrational properties of l-histidine crystals at low temperatures. The temperature dependence of the spectra show discontinuities at 165 K, which we identify with modifications in the bonds associated to both the NH₃ ⁺ and CO₂ ^? motifs indicative of a conformational phase transition that changes the intermolecular bonds. Additional evidence of such a phase transition is provided by differential scanning calorimetry measurements, which identified an enthalpic anomaly at ～165 K.     

A Combined Study of the Pion’s Static Properties and form Factors

We study consistently the pion’s static observables and the elastic and γ* γ → π ⁰ transition form factors within a light-front model. Consistency requires that all calculations are performed within a given model with the same and single adjusted length or mass-scale parameter of the associated pion bound-state wave function. Our results agree well with all extent data including recent Belle data on the γ* γ → π ⁰ form factor at large q ², yet the BaBar data on this transition form factor resists a sensible comparison. We relax the initial constraint on the bound-state wave function and show the BaBar data can partially be accommodated. This, however, comes at the cost of a hard elastic form factor not in agreement with experiment. Moreover, the pion charge radius is about 40 % smaller than its experimentally determined value. It is argued that a decreasing charge radius produces an ever harder form factor with a bound-state amplitude difficultly reconcilable with soft QCD. We also discuss why vector dominance type models for the photon-quark vertex, based on analyticity and crossing symmetry, are unlikely to reproduce the litigious transition form factor data.     

Biosurfactant production by Rhodococcus erythropolis grown on glycerol as sole carbon source

The production of biosurfactant by Rhodococcus erythropolis during the growth on glycerol was investigated. The process was carried out at 28 degrees C in a 1.5-L bioreactor using glycerol as carbon source. The bioprocess was monitored through measurements of biosurfactant concentration and glycerol consumption. After 51 h of cultivation, 1.7 g/L of biosurfactant, surface, and interfacial tensions values (with n-hexadecane) of 43 and 15 mN/m, respectively, 67% of Emulsifying Index (E (24)), and 94% of oil removal were obtained. The use of glycerol rather than what happens with hydrophobic carbon source allowed the release of the biosurfactant, originally associated to the cell wall.     

Unusual solvent effect on a SN2 reaction. A quantum-mechanical and kinetic study of the Menshutkin reaction between 2-amino-1-methylbenzimidazole and iodomethane in the gas phase and in acetonitrile

The quaternization reaction between 2-amino-1-methylbenzimidazole and iodomethane was investigated in the gas phase and in liquid acetonitrile. Both experimental and theoretical techniques were used in this study. In the experimental part of this work, accurate second-order rate constants were obtained for this reaction in acetonitrile from conductivity data in the 293-323 K temperature range and at ambient pressure. From two different empirical equations describing the effect of temperature on reaction rates, thermodynamic functions of activation were calculated. In the theoretical part of this work, the mechanism of this reaction was investigated in the gas phase and in acetonitrile. Two different quantum levels (B3LYP/[6-311++G(3df,3pd)/LanL2DZ]//B3LYP/[6-31G(d)/LanL2DZ] and B3LYP/[6-311++G(3df,3pd)/LanL2DZ]//B3LYP/[6-31+G(d)/LanL2DZ]) were used in the calculations, and the acetonitrile environment was modeled using the polarized continuum model (PCM). In addition, an atoms in molecules (AIM) analysis was made aiming to characterize possible hydrogen bonding. The results obtained by both techniques are in excellent agreement and lead to new insight into the mechanism of the reaction under examination. These include the identification and thermodynamic characterization of the relevant stationary species, the rationalization of the mechanistic role played by the solvent and the amine group adjacent to the nucleophile nitrogen atom, the proposal of alternative paths on the modeled potential energy surfaces, and the origin of the marked non-Arrhenius behavior of the kinetic data in solvent acetonitrile. In particular, the AIM analysis confirmed the operation of intermolecular hydrogen bonds between reactants and between products, both in the gas phase and in solution. It is also concluded that the unusual solvent effect on this Menshutkin reaction stems from the conjunction of a nucleophile possessing a relatively complex chemical structure with a dipolar aprotic solvent that is protophobic.     

A comparison of a gas chromatographic with electron-capture detection and a gas chromatographic with mass spectrometric detection screening methods for the analysis of famoxadone in grapes and wines

Famoxadone is a recent oxazolidinedione fungicide widely used in viticulture and in Integrated Pest Management strategies. In this work, after a simple and fast liquid-liquid extraction (LLE), two new gas chromatographic methods were developed to analyze famoxadone residues in grapes and wines, one with electron-capture detection (GC-ECD) and the other with mass spectrometry (GC-MS). Global uncertainties for validation parameters of both methods were compared. Limits of detection (LODs) were 0.06 and 0.02 mg/L, precision was not above 11.7 and 6.8% and recoveries were, on average, 103%+/-12 and 96%+/-12, respectively, for the GC-ECD and GC-MS methods. Similar expanded uncertainties in the range from 0.25 to 1.00 mg/L were below 35%, with increasing values for lower levels of famoxadone. GC-MS method had a lower LOD and a lower uncertainty if compared with the GC-ECD method.     

Aggregation of methyl orange probed by electrical impedance spectroscopy

We present results of an electrical impedance spectroscopy investigation of the evolution of the aggregation of methyl orange (MO) in pure aqueous solutions as the concentration of the dye is varied. By applying the constant phase element (CPE) approximation to model the electrical response of the MO solutions, we have verified that the formation of dimers and oligomers can be recognized by specific signatures in the loss and capacitive components of the dielectric response of the system. We interpret these well-defined changes in the dielectric properties of the solutions as a result of molecular rearrangements caused by the aggregation process that alter the current circulation pathways and the electric dipole distribution. The fact that these specific changes in the dielectric behavior coincide with critical concentrations where dimer and oligomer formation in pure aqueous MO solutions are known to occur suggests that electrical impedance spectroscopy can be a competitive technique for the investigation of aggregation behavior in dyes and surfactants.