Calculation of the Absolute Free Energy of Binding and Related Entropies with the HSMD-TI Method: The FKBP12-L8 Complex

The hypothetical scanning molecular dynamics (HSMD) method is used here for calculating the absolute free energy of binding, ΔA(0) of the complex of the protein FKBP12 with the ligand SB2 (also denoted L8) - a system that has been studied previously for comparing the performance of different methods. Our preliminary study suggests that considering long-range electrostatics is imperative even for a hydrophobic ligand such as L8. Therefore the system is modeled by the AMBER force field using Particle Mesh Ewald (PME). HSMD consists of three stages applied to both the ligand-solvent and ligand-protein systems. (1) A small set of system configurations (frames) is extracted from an MD trajectory. (2) The entropy of the ligand in each frame is calculated by a reconstruction procedure. (3) The contribution of water and protein to ΔA(0) is calculated for each frame by gradually increasing the ligand-environment interactions from zero to their full value using thermodynamic integration (TI). Unlike the conventional methods, the structure of the ligand is kept fixed during TI, and HSMD is thus free from the end-point problem encountered with the double annihilation method (DAM); therefore, the need for applying restraints is avoided. Furthermore, unlike the conventional methods, the entropy of the ligand and water is obtained directly as a byproduct of the simulation. In this paper, in addition to the difference in the internal entropies of the ligand in the two environments, we calculate for the first time the external entropy of the ligand, which provides a measure for the size of the active site. We obtain ΔA(0) = -10.7 ±1.0 as compared to the experimental values -10.9 and -10.6 kcal/mol. However, a protein/water system treated by periodic boundary conditions grows significantly with increasing protein size and the computation of ΔA(0) would become expensive by all methods. Therefore, we also apply HSMD to FKBP12-L8 described by the GSBP/SSBP model of Roux's group (implemented in the software CHARMM) where only part of the protein and water around the active site are considered and long-range electrostatic effects are taken into account. For comparison this model was also treated by the double decoupling method (DDM). The two methods have led to comparable results for ΔA(0) which are somewhat lower than the experimental value. The ligand was found to be more confined in the active site described by GSBP/SSBP than by PME where its entropy in solvent is larger than in the active site by 1.7 and by 5.5 kcal/mol, respectively.     

EPR study of free radicals in non- and gamma-irradiated nutritive supplements containing anthocyanins concentrate from lyophilized red wine

Nutritive supplements Enoviton, Enoviton C and Enoviton CE containing standardized anthocyanins from lyophilized red wine, vitamins (some of them) and excipients were investigated by EPR spectrometry before and after gamma-irradiation. Non-irradiated samples exhibit one singlet line with g=2.0039±0.0002, most probably due to free radicals from anthocyanins. After irradiation with 10 kGy gamma-rays, tablets of Еnoviton, Еnoviton С and Еnoviton СЕ, all exhibit complex EPR signals centered at a g-value of g=2.0034. The EPR spectrum of irradiated Enoviton is different from that of Еnoviton С or Еnoviton СЕ due to the overlap of the spectra of microcrystalline cellulose and the background singlet spectrum present in all tablets with the EPR resonance due to irradiated ascorbic acid (in Еnoviton С and Еnoviton СЕ). Gamma-induced free radicals exhibit long time stability—for a six months period the intensity of central peak decrease with 30–40%.     

Synthesis,characterization and adsorption properties of nanostructured hybrid materials modified by boron and zirconium

The adsorption properties of two new nanostructured hybrid materials containing B₂O₃ and ZrO₂ were studied. The new organic-inorganic materials were synthesized via a sol-gel method. As a modifying agent, a quantity of 10 wt.% Zr(OPr)₄ or B(OCH₃)₃ was added. The structure of the hybrid materials was investigated by means of (Fourier transform infrared spectroscopy (FTIR), x-ray diffractometry (XRD), scanning electron microscopy (SEM), (atomic force microscopy (AFM) and nuclear magnetic resonance spectroscopy (NMR). Based on the obtained data, the most probable cross-linking mechanism for the derived gels was proposed. The characterization of texture parameters of both materials was carried out with the use of low-temperature adsorption of nitrogen. Adsorption of Cu(II), Fe(III), Cr(III), Cd(II) and Pb(II) ions on both materials was investigated using multi-component solutions with different concentrations and acidity by means of the batch method. Kinetics of adsorption was also investigated. Pseudo-first order, pseudo-second order and intraparticle diffusion models were used to analyze kinetic data. The adsorption was significantly affected by the pH value. Equilibrium data were fitted to linear Langmuir, Freundlich and Dubinin-Radushkevich models and maximum adsorption capacities were calculated.      

Antimicrobial Triterpenoids and Ingol Diterpenes from Propolis of Semi-Arid Region of Morocco

The chemical composition and antimicrobial activity of propolis from a semi-arid region of Morocco were investigated. Fifteen compounds, including triterpenoids (1, 2, 7–12), macrocyclic diterpenes of ingol type (3–6) and aromatic derivatives (13–15), were isolated by various chromatographic methods. Their structures were elucidated by a combination of spectroscopic and chiroptical methods. Compounds 1 and 3 are new natural compounds, and 2, 4–6, and 9–11 are newly isolated from propolis. Moreover, the full nuclear magnetic resonance (NMR) assignments of three of the known compounds (2, 4 and 5) were reported for the first time. Most of the compounds tested, especially the diterpenes 3, 4, and 6, exhibited very good activity against different strains of bacteria and fungi. Compound 3 showed the strongest activity with minimum inhibitory concentrations (MICs) in the range of 4–64 µg/mL. The combination of isolated triterpenoids and ingol diterpenes was found to be characteristic for Euphorbia spp., and Euphorbia officinarum subsp. echinus could be suggested as a probable and new plant source of propolis.     

Chemical Profile and Antioxidant Capacity of Propolis from Tetragonula,Lepidotrigona, Lisotrigona and Homotrigona Stingless Bee Species in Vietnam

The present study aimed to analyze and compare the chemical profile and antioxidant capacity of propolis from different bee species and different regions. The chemical profiles of propolis from six stingless bee species (Tetragonula iridipennis, T. laeviceps, Lepidotrigona terminata, L. ventralis, Lisotrigona carpenteri and Homotrigona apicalis) collected from a total of eight locations in Vietnam were investigated by gas chromatography–mass spectrometry (GC-MS). More than 70 compounds were identified, amongst which phenolic lipids (cardanols, resorcinols and anacardic acids), aromatic acids, triterpenes and xanthones. Taxonomic markers for Mangifera indica (phenolic lipids and cycloartane triterpenes) were detected in propolis from bees of the genera Tetragonula and Lepidotrigona, although in different amounts, whereas propolis from H. apicalis was characterized by triterpenes of the amyrine type, typical of dipterocarp trees. A clear discrimination between both groups was observed by principal component analysis (PCA) and partial least squares–discriminant analysis (PLS-DA). Propolis from Tetragonula and Lepidotrigona spp. and from Lisotrigona carpenteri, which is rich in xanthones, possesses higher radical scavenging and ferric-reducing capacity than that from H. apicalis. Propolis produced by all six stingless bee species in Vietnam was analyzed for the first time. In addition, this is the first report on L. carpenteri propolis.     

EPR study of free radicals in bread

The features of the recorded EPR spectra of paramagnetic species formed in bread and rusk are reported. The appearance of free radicals in them is only connected with their thermal treatment since the starting materials (flour and grains) exhibit very weak EPR signal. The obtained EPR spectra are complex and indicate that: (i) the relative number of paramagnetic species depends on the temperature and treating time of the raw product; (ii) the g-values are strongly temperature dependent with a tendency to coincide at t > or = 220 degrees C. Because of the relatively low (150-220 degrees C) temperature of thermal treatment, the studied free radicals can be assumed to appear in the course of the browning (Maillard) reaction and not to the carbonization of the material.     

Chemical and technological characterization of medieval glass bracelets from South-East Bulgaria

The present paper deals with chemical and physicochemical characterization of seven glass fragments of medieval glass bracelets from South-East Bulgaria. Samples were investigated by Fourier-transform infrared spectroscopy (FT-IR), transmission electron microscopy (TEM) and differential thermal analysis (DTA). Gravimetric chemical analysis was used for silica assessment. Flame photometry was applied to determine sodium and potassium content while aluminium, calcium and magnesium were determined by flame atomic absorption spectrometry after dissolution using a mixture of acids. All investigated artefacts are soda-lime-silica glasses and when produced two different recipe norms were used. Important technological parameters of glass manufacturing were determined and discussed. This investigation throws light on the technological development and production of glass during medieval times.      

The Solubilization of Rock Phosphate by Organic Acids

Bases of the production of phosphoric fertilizers are classical methods involving acid dissolution of rock phosphates. The development of new methods applicable both to high-quality and low-quality phosphates is important for solving technological and ecological problems and to increase the economical effectiveness of phosphorus fertilizer technologies. In this respect, the bioconversion of rock phosphates in order to obtain phosphorus fertilizers is very promising. The basic principle of the biotechnological processing of natural phosphates is the production of organic acids, mainly citric, oxalic, and gluconic acid, that attack and dissolve the phosphates, converting the phosphorus to a form utilizable for the plants. The aim of this research is to optimize the process of Tunisian phosphorite solubilization with citric, oxalic, and gluconic acids in relation to the following main factors: the acid concentration, reaction time, solid/liquid phases ratio, and natural phosphate fraction. Two objective functions have been investigated: the quantity of the available acid in the system and the extent of phosphate dissolution. The research data has been processed according to the standard statistical tests. A mathematical model describing the phosphate decomposition process by organic acids has been obtained. A multicriteria optimization has been performed to determine the optimum levels of the examined factors. It was established that the different factors have a different effect on the goal parameters. A maximum degree of 91.89% of phosphorus extraction has been reached at phosphate solubilization by citric acid.     

Effect of gamma irradiation on antiradical activity of goji berry fruits (Lycium barbarum) evaluated by EPR spectroscopy

Antiradical activity of goji berry (Lycium barbarum) was evaluated by means of electron paramagnetic resonance spectroscopy. The goji berry samples were exposed to gamma-irradiation at doses 0.05, 2 and 10 kGy. The characteristic satellite lines from cellulose radicals can prove irradiation treatment. Their intensity increase after alcohol washing and lyophilization. The fading property of satellite lines show that identification of radiation treatment is possible for 50 days. The effect of irradiation on antiradical properties of goji berry extracts was investigated by radical scavenging activity using the stable free radical 1,1-diphenyl-2-picrylhydrazyl (DPPH). The percentages of scavenged DPPH radicals and IC₅₀ of the extracts of goji berry before and after irradiation were calculated. The antioxidant capacity was presented in Trolox Equivalents as well. It was found out that gamma irradiation of goji berry fruits increases its antiradical activity.

     

A new 8,14-dihydropromorphinane alkaloid from Papaver nudicaule L

A racem. 8,14-dihydroamurine is a new promorphinane alkaloid isolated from the aerial parts of Papaver nudicaule L. (Papaveraceae) of Mongolian origin. The known promorphinane and isopavine alkaloids (+)-amurine, (-)-amurensinine, (-)-O-methylthalisopavine, (-)-flavinantine and (-)-amurensine were also described. All structures were established by physical and spectral analysis. Flavinantine has been found for the first time in the species.