Insight into the binding modes and inhibition mechanisms of adamantyl-based 1,3-disubstituted urea inhibitors in the active site of the human soluble epoxide hydrolase

Soluble epoxide hydrolase (sEH) is a promising new target for treating hypertension and inflammation. Considerable efforts have been devoted to develop novel inhibitors. In this study, the binding modes and interaction mechanisms of a series of adamantyl-based 1,3-disubstituted urea inhibitors were investigated by molecular docking, molecular dynamics simulations, binding free energy calculations, and binding energy decomposition analysis. Based on binding affinity, the most favorable binding mode was determined for each inhibitor. The calculation results indicate that the total binding free energy (ΔG_TOT, the sum of enthalpy ΔG_MM-GB/SA, and entropy ?TΔS) presents a good correlation with the experimental inhibitory activity (IC₅₀, r²?=?.99). The van der Waals energy contributes most to the total binding free energy (ΔG_TOT). A detailed discussion on the interactions between inhibitors and those residues located in the active pocket is made based on hydrogen bond and binding modes analysis. According to binding energy decomposition, the residues Asp333 and Trp334 contribute the most to binding free energy in all systems. Furthermore, Hip523 plays a major role in determining this class of inhibitor-binding orientations. Combined with the results of hydrogen bond analysis and binding free energy, we believe that the conserved hydrogen bonds play a role only in anchoring the inhibitors to the exact site for binding and the number of hydrogen bonds may not directly relate to the binding free energy. The results we obtained will provide valuable information for the design of high potency sEH inhibitors.     

封闭循环养殖系统中β变形菌亚纲氨氧化细菌的引物特异性

摘要:【目的】为探讨4 对不同的引物对封闭循环养殖系统生物膜中β 变形菌亚纲氨氧化细菌(β-AOB) 的特异性差异。【方法】采用16S rDNA 文库克隆技术对β-AOB 的多样性进行了分析。【结果】以引物CTO189f/CTO654r 扩增构建的文库中所含β-AOB 比例最高,可达67. 3%。不同封闭循环养殖系统的生物膜对引物的扩增效率有明显的影响,其中以养殖尼罗罗非鱼的封闭循环养殖系统生物膜为DNA 来源的,引物均有较高的扩增效率。【结论】针对封闭循环养殖系统生物膜中的β-AOB,特异性最高的是CTO189f /CTO654r 引物。     

HDL mimetic peptide ATI-5261 forms an oligomeric assembly in solution that dissociates to monomers upon dilution

ATI-5261 is a 26-mer peptide that stimulates cellular cholesterol efflux with high potency. This peptide displays high aqueous solubility, despite having amphipathic α-helix structure and a broad nonpolar surface. These features suggested to us that ATI-5261 may adopt a specific form in solution, having favorable structural characteristics and dynamics. To test this, we subjected ATI-5261 to a series of biophysical studies and correlated self-association with secondary structure and activity. Gel-filtration chromatography and native gel electrophoresis indicated ATI-5261 adopted a discrete self-associated form of low molecular weight at concentrations >1 mg/mL. Formation of a discrete molecular species was verified by small-angle X-ray scattering (SAXS), which further revealed the peptide formed a tetrameric assembly having an elongated shape and hollow central core. This assembly dissociated to individual peptide strands upon dilution to concentrations required for promoting high-affinity cholesterol efflux from cells. Moreover, the α-helical content of ATI-5261 was exceptionally high (74.1 ± 6.8%) regardless of physical form and concentration. Collectively, these results indicate ATI-5261 displays oligomeric behavior generally similar to native apolipoproteins and dissociates to monomers of high α-helical content upon dilution. Optimizing self-association behavior and secondary structure may prove useful for improving the translatability and efficacy of apolipoprotein mimetic peptides.     

Fungal associates of the lodgepole pine beetle, <Emphasis Type="Italic">Dendroctonus murrayanae</Emphasis>

Bark beetles are well known vectors of ophiostomatoid fungi including species of Ophiostoma, Grosmannia and Ceratocystis. In this study, the most common ophiostomatoid fungi associated with the lodgepole pine beetle, Dendroctonus murrayanae, were characterized. Pre-emergent and post-attack adult beetles were collected from lodgepole pines at four sites in British Columbia, Canada. Fungi were isolated from these beetles and identified using a combination of morphology and DNA sequence comparisons of five gene regions. In all four populations, Grosmannia aurea was the most common associate (74–100% of all beetles) followed closely by Ophiostoma abietinum (29–75%). Other fungi isolated, in order of their relative prevalence with individual beetles were an undescribed Leptographium sp. (0–13%), Ophiostoma ips (0–15%), Ophiostoma piliferum (0–11%), a Pesotum sp. (0–11%) and Ophiostoma floccosum (0–1%). Comparisons of the DNA sequences of Leptographium strains isolated in this study, with ex-type isolates of G. aurea, Grosmannia robusta, Leptographium longiclavatum, and Leptographium terebrantis, as well as with sequences from GenBank, revealed a novel lineage within the Grosmannia clavigera complex. This lineage included some of the D. murrayane isolates as well as several isolates from previous studies referred to as L. terebrantis. However, the monophyly of this lineage is not well supported and a more comprehensive study will be needed to resolve its taxonomic status as one or more novel taxa.     

Altered substrate specificity of the gluco‐oligosaccharide oxidase from Acremonium strictum

A gluco‐oligosaccharide oxidase (GOOX) from Acremonium strictum type strain CBS 346.70 was cloned and expressed in Pichia pastoris. The recombinant protein, GOOX‐VN, contained fifteen amino acid substitutions compared with the previously reported A. strictum GOOX. These two enzymes share 97% sequence identity; however, only GOOX‐VN oxidized xylose, galactose, and N‐acetylglucosamine. Besides monosaccharides, GOOX‐VN oxidized xylo‐oligosaccharides, including xylobiose and xylotriose with similar catalytic efficiency as for cello‐oligosaccharides. Of three mutant enzymes that were created in GOOX‐VN to improve substrate specificity, Y300A and Y300N doubled k_cat values for monosaccharide and oligosaccharide substrates. With this novel substrate specificity, GOOX‐VN and its variants are particularly valuable for oxidative modification of cello‐ and xylo‐oligosaccharides. Biotechnol. Bioeng. 2011;108: 2261–2269. © 2011 Wiley Periodicals, Inc.     

Necessary role for intracellular Ca2+ transients in initiating the apical-basolateral thinning of enveloping layer cells during the early blastula period of zebrafish development

During the early blastula period of zebrafish embryos, the outermost blastomeres begin to undergo a significant thinning in the apical/basolateral dimension to form the first distinct cellular domain of the embryo, the enveloping layer (EVL). During this shape transformation, only the EVL-precursor cells generate a coincidental series of highly restricted Ca(2+) transients. To investigate the role of these localized Ca(2+) transients in this shape-change process, embryos were treated with a Ca(2+) chelator (5,5'-difluoro BAPTA AM; DFB), or the Ca(2+) ionophore (A23187), to downregulate and upregulate the transients, respectively, while the shape-change of the forming EVL cells was measured. DFB was shown to significantly slow, and A23187 to significantly facilitate the shape change of the forming EVL cells. In addition, to investigate the possible involvement of the phosphoinositide and Wnt/Ca(2+) signaling pathways in the Ca(2+) transient generation and/or shape-change processes, embryos were treated with antagonists (thapsigargin, 2-APB and U73122) or an agonist (Wnt-5A) of these pathways. Wnt-5A upregulated the EVL-restricted Ca(2+) transients and facilitated the change in shape of the EVL cells, while 2-APB downregulated the Ca(2+) transients and significantly slowed the cell shape-change process. Furthermore, thapsigargin and U73122 also both inhibited the EVL cell shape-change. We hypothesize, therefore, that the highly localized and coincidental Ca(2+) transients play a necessary role in initiating the shape-change of the EVL cells.     

Autophagy inhibition via Becn1 downregulation improves the mesenchymal stem cells antifibrotic potential in experimental liver fibrosis

Liver fibrosis (LF) is the result of a vicious cycle between inflammation-induced chronic hepatocyte injury and persistent activation of hepatic stellate cells (HSCs). Mesenchymal stem cell (MSC)-based therapy may represent a potential remedy for treatment of LF. However, the fate of transplanted MSCs in LF remains largely unknown. In the present study, the fate and antifibrotic effect of MSCs were explored in a LF model induced by CCl₄ in mouse. Additionally, MSCs were stimulated in vitro with LF-associated factors, tumor necrosis factor-α (TNF-α), interferon-γ (IFN-γ), and transforming growth factor-β1 (TGF-β1), to mimic the LF microenvironment. We unveiled that MSCs exhibited autophagy in response to the LF microenvironment through Becn1 upregulation both in vivo and in vitro. However, autophagy suppression induced by Becn1 knockdown in MSCs resulted in enhanced antifibrotic effects on LF. The improved antifibrotic potential of MSCs may be attributable to their inhibitory effects on T lymphocyte infiltration, HSCs proliferation, as well as production of TNF-α, IFN-γ, and TGF-β1, which may be partially mediated by elevated paracrine secretion of PTGS2/PGE₂. Thus, autophagy manipulation in MSCs may be a novel strategy to promote their antifibrotic efficacy.     

单增李斯特菌溶血素O的PEST序列激活ERK1/2磷酸化的作用

[目的]本研究旨在构建单核细胞增多性李斯特菌(Listeria monocytogenes,简称单增李斯特菌)溶血素O(Listeriolysin O,LLO)的关键结构域PEST序列(包含S44、S48和T51关键磷酸化位点)突变体,并针对其生物学功能展开研究。[方法]以李斯特菌参考菌株EGD-e为模板扩增编码LLO的hly基因,克隆至pET30a(+)原核表达载体,在此基础上利用氨基酸突变技术获得表达PEST突变体(LLO△PEST、LLOS44A、LLOS48A和LLOT51A)的重组质粒,转入E.coli Rosetta感受态细胞中,诱导表达重组蛋白经镍离子亲和层析纯化后进行SDS-PAGE分析。利用红细胞裂解试验检测重组蛋白的溶血活性,并通过Western blotting检测重组突变蛋白刺激Caco-2细胞后对MAPK关键信号分子ERK1/2磷酸化水平变化的影响。[结果]结果显示,本研究成功获得重组LLO及其突变体蛋白LLO△PEST、LLOS44A、LLOS48A和LLOT51A。在pH5.5和7.4条件下,LLO△PEST、LLOS44A、LLOS48A和LLOT51A均具有和LLO相当的溶血活性,说明PEST序列缺失或突变并不影响LLO的膜裂解活性。研究进一步发现,重组LLO及其突变蛋白刺激Caco-2细胞后均能激活ERK1/2的磷酸化。[结论]研究表明LLO的关键结构域PEST序列对于维持该蛋白的膜裂解能力及穿孔活性并非必需,且该结构域的缺失不影响李斯特菌在感染宿主时依赖LLO介导ERK1/2磷酸化的生物学过程。本研究将为进一步探索细菌感染过程中PEST序列对于LLO发挥生物学功能的潜在作用及分子机制奠定基础。     

A review of the genus Strophidon (Anguilliformes: Muraenidae), with description of a new species

Strophidon McClelland is a muraenid genus with characteristic appearance of a very elongated body, a large mouth cleft and anteriorly placed eyes. The nomenclature and taxonomic history of species within Strophidon are contentious and its members are easily misidentified. In the present study, species of the genus Strophidon are revised based on morphological and molecular data, and five species are considered valid, including S. dawydoffi Prokofiev, S. dorsalis (Seale), S. sathete (Hamilton), S. ui Tanaka and a new species, S. tetraporus. Strophidon tetraporus sp. nov. is described based on 15 specimens from Indonesia, the Philippines, Taiwan and Vietnam with the unique characteristic of the constant presence of the fourth infraorbital pore among species of Strophidon. The intraspecific variation of vertebral formula within S. dorsalis is discussed based on molecular data. Muraena macrurus Bleeker and Thyrsoidea longissima Kaup are synonyms of S. sathete that can be distinguished from the most similar congener S. ui by a longer tail, smaller eyes and more inner maxillary and inner dentary teeth. A key to identify species of Strophidon is provided. The distribution and maximum size of each species are also re-evaluated.