Large-scale virtual screening for the identification of new Helicobacter pylori urease inhibitor scaffolds

Here, we report a structure-based virtual screening of the ZINC database (containing about five million compounds) by computational docking and the analysis of docking energy calculations followed by in vitro screening against H. pylori urease enzyme. One of the compounds selected showed urease inhibition in the low micromolar range. Barbituric acid and compounds 1a, 1d, 1e, 1f, 1g, 1h were found to be more potent urease inhibitors than the standard inhibitor hydroxyurea, yielding IC(50) values of 41.6, 83.3, 66.6, 50, 58.8, and 60 μM, respectively (IC(50) of hydroxyurea = 100 μM). 5-Benzylidene barbituric acid has enhanced biological activities compared to barbituric acid. Furthermore, the results indicated that among the substituted 5-benzylidene barbiturates, those with para substitution have higher urease inhibitor activities. This may be because the barbituric acid moiety is closer to the bimetallic nickel center in unsubstituted or para-substituted than in ortho- or meta-substituted analogs, so it has greater chelating ability.     

Long-lasting depression-like behavior and epigenetic changes of BDNF gene expression induced by perinatal exposure to methylmercury

Substantial evidence indicates that predisposition to diseases can be acquired during early stages of development and interactions between environmental and genetic factors may be implicated in the onset of many pathological conditions. Data collected over several decades have shown that chemicals are among the relevant factors that can endanger CNS. We previously showed that perinatal exposure to methylmercury (MeHg) causes persistent changes in learning and motivational behavior in mice. In this study, we report that the depression-like behavior in MeHg-exposed male mice is reversed by chronic treatment with the antidepressant fluoxetine. Behavioral alterations are associated with a decrease in brain-derived neurotrophic factor (BDNF) mRNA in the hippocampal dentate gyrus and fluoxetine treatment restores BDNF mRNA expression. We also show that MeHg-exposure induces long-lasting repressive state of the chromatin structure at the BDNF promoter region, in particular DNA hypermethylation, an increase in histone H3-K27 tri-methylation and a decrease in H3 acetylation at the promoter IV. While fluoxetine treatment does not alter hypermethylation of H3-K27, it significantly up-regulates H3 acetylation at the BDNF promoter IV in MeHg-exposed mice. Our study shows that developmental exposure to low levels of MeHg predisposes mice to depression and induces epigenetic suppression of BDNF gene expression in the hippocampus.     

Groups IV, V, and X phospholipases A2s in human neutrophils: role in eicosanoid production and gram-negative bacterial phospholipid hydrolysis.

The bacterial tripeptide formyl-Met-Leu-Phe (fMLP) induces the secretion of enzyme(s) with phospholipase A(2) (PLA(2)) activity from human neutrophils. We show that circulating human neutrophils express groups V and X sPLA(2) (GV and GX sPLA(2)) mRNA and contain GV and GX sPLA(2) proteins, whereas GIB, GIIA, GIID, GIIE, GIIF, GIII, and GXII sPLA(2)s are undetectable. GV sPLA(2) is a component of both azurophilic and specific granules, whereas GX sPLA(2) is confined to azurophilic granules. Exposure to fMLP or opsonized zymosan results in the release of GV but not GX sPLA(2) and most, if not all, of the PLA(2) activity in the extracellular fluid of fMLP-stimulated neutrophils is due to GV sPLA(2). GV sPLA(2) does not contribute to fMLP-stimulated leukotriene B(4) production but may support the anti-bacterial properties of the neutrophil, because 10-100 ng per ml concentrations of this enzyme lead to Gram-negative bacterial membrane phospholipid hydrolysis in the presence of human serum. By use of a recently described and specific inhibitor of cytosolic PLA(2)-alpha (group IV PLA(2)alpha), we show that this enzyme produces virtually all of the arachidonic acid used for the biosynthesis of leukotriene B(4) in fMLP- and opsonized zymosan-stimulated neutrophils, the major eicosanoid produced by these pro-inflammatory cells.     

Effects of different Sertoli cell types on the maintenance of adult spermatogonial stem cells in vitro

Spermatongonial stem cells (SSCs) are unique testis cells that are able to proliferate, differentiate, and transmit genetic information to the next generation. However, the effect of different Sertoli cell types on the expression of specific SSC genes is not yet well understood. In this study, we compare the in vitro effect of adult Sertoli cells, embryonic Sertoli cells, and TM4 (a Sertoli cell line) as feeder layers on the expression of SSC genes. SSCs were isolated from the testis of adult male mice and purified by differential plating. Following enrichment, SSCs were cultivated for 1 and 2 wk in the presence of various feeders. The expression of SSC-specific genes (Mvh, ZBTB, and c-kit) was evaluated by real-time polymerase chain reaction. Our results revealed that expression of the specific SSC genes was significantly higher in the embryonic Sertoli cells after 1 and 2 wk compared to the adult Sertoli cells and the TM4 group. Our finding suggest that co-culturing of SSCs with embryonic Sertoli cells is helpful for in vitro cultivation of SSCs and might improve the self-renewal of these stem cells.     

Cytokine single nucleotide polymorphisms in Iranian populations

Cytokines are important immunomodulatory molecules involved in immune responses against microorganisms; they also have an important role in the setting of immune system disorders. Cytokine single nucleotide polymorphisms have been extensively studied in different, normal populations as well as in association with disease. Cytokine gene polymorphisms are potentially important as genetic predictors of disease susceptibility, clinical outcome, and as a tool for anthropological studies. In this study, samples have been collected from 455 healthy individuals located in different regions of Iran (Tehran, Yazd, Sistan and Balochistan). Allele and genotype frequencies of cytokine SNP, including: IL-1alpha, IL-1beta, IL-1R, IL-1RA, IL-2, IL-4, IL-4RA, IL-6, IL-10, IL-12, TNF-alpha, TGF-beta and IFN-gamma were investigated, using the PCR-SSP method. Allele frequencies in Tehran and Yazd populations were similar, except for TGF-beta. Allele frequencies in Sistani & Baloch populations were similar at all positions, except for IL-1beta at position of -511 and IFN-gamma genes at position UTR5644; there were some differences in allele frequencies comparing these populations with the Yazd population, including: IL-4, IL-6, IL-10, TGF-beta and TNF-alpha. Although some significant differences were observed for some cytokines, it seems that the cytokine gene polymorphism profile of the Iranian population is similar to that of Caucasians, particularly the Italian population.     

Mercury(II) complex formation with glutathione in alkaline aqueous solution

The structure and speciation of the complexes formed between mercury(II) ions and glutathione (GSH = L-glutamyl-L-cysteinyl-glycine) have been studied for a series of alkaline aqueous solutions (\( C_{{{\text{Hg}}^{{2 + }}}}\,{\sim18\,{\rm{mmol}}\,{\rm{{dm^{-3}}}}}\) and C _GSH = 40–200 mmol dm^?3 at pH ～10.5) by means of extended X-ray absorption fine structure (EXAFS) and ¹⁹⁹Hg NMR spectroscopy at ambient temperature. The dominant complexes are [Hg(GS)₂]^4? and [Hg(GS)₃]^7?, with mean Hg–S bond distances of 2.32(1) and 2.42(2) Å observed in digonal and trigonal Hg–S coordination, respectively. The proportions of the Hg²⁺–glutathione complexes were evaluated by fitting linear combinations of model EXAFS oscillations representing each species to the experimental EXAFS spectra. The [Hg(GS)₄]^10? complex, with four sulfur atoms coordinated at a mean Hg–S bond distance of 2.52(2) Å, is present in minor amounts (<30%) in solutions containing a large excess of glutathione (C _GSH ≥ 160 mmol dm^?3). Comparable alkaline mercury(II) cysteine (H₂Cys) solutions were also investigated and a reduced tendency to form higher complexes was observed, because the deprotonated amino group of Cys^2? allows the stable [Hg(S,N-Cys)₂]^2? chelate to form. The effect of temperature on the distribution of the Hg²⁺–glutathione complexes was studied by comparing the EXAFS spectra at ambient temperature and at 25 K of a series of glycerol/water (33/67, v/v) frozen glasses with \( C_{{{\text{Hg}}^{{2 + }} }} \,{\sim7\,{\rm{mmol}}\,{\rm{{dm^{-3}}}}} \) and C _GSH = 16–81 mmol dm^?3. Complexes with high Hg–S coordination numbers, [Hg(GS)₃]^7? and [Hg(GS)₄]^10?, became strongly favored when just a moderate excess of glutathione (C _GSH ≥28 mmol dm^?3) was used in the glassy samples, as expected for a stepwise exothermic bond formation. Addition of glycerol had no effect on the Hg(II)–glutathione speciation, as shown by the similarity of the EXAFS spectra obtained at room temperature for two parallel series of Hg(II)-glutathione solutions with \( C_{{{\text{Hg}}^{{2 + }} }} \,{\sim7\,{\rm{mmol}}\,{\rm{{dm^{-3}}}}},\) with and without 33% glycerol. Also, the ¹⁹⁹Hg NMR chemical shifts of a series of ～18 mmol dm^?3 mercury(II) glutathione solutions with 33% glycerol were not significantly different from those of the corresponding series in aqueous solution.     

Unusual mode of binding of human group IIA secreted phospholipase A2 to anionic interfaces as studied by continuous wave and time domain electron paramagnetic resonance spectroscopy

Human group IIA phospholipase A(2) (hGIIA) is secreted from a number of cells during inflammation and is known to interact strongly with anionic membranes and to exhibit potent Gram-positive bactericidal activity. This protein contains 23 cationic residues, which are scattered over its entire surface, resulting in a high pI of 9.39. To understand the molecular basis for the selective binding of hGIIA to anionic membranes, 14 single-site, spin-labeled hGIIA proteins were analyzed in the presence and absence of vesicles of anionic phospholipid by time domain and continuous wave electron paramagnetic resonance (EPR) spin relaxant techniques. Surprisingly, for hGIIA bound to anionic vesicles, all of the spin labels were highly protected from water-soluble spin relaxants. Together with light scattering studies, these EPR results suggest the formation of a supramolecular aggregate involving clusters of hGIIA molecules bridging together multiple vesicles. This anomalous mode of binding of hGIIA to anionic phospholipid explains previous data in which charge reversal mutation of a few cationic residues on multiple faces of hGIIA leads to a comparable and modest reduction in affinity of the protein for anionic vesicles. In the presence of mixed micelles composed of 10% anionic phospholipids in Triton X-100 a monodisperse protein-lipid complex is formed. Under these conditions, the EPR methods were used to map the surface of hGIIA that constitutes the interfacial binding site (IBS). The IBS of hGIIA consists of the highly hydrophobic surface that surrounds the opening to the active site slot.