Bioinformatics prediction of siRNAs as potential antiviral agents against dengue viruses

Dengue virus (DENV 1-4) represents the major emerging arthropod-borne viral infection in the world. Currently, there is neither an available vaccine nor a specific treatment. Hence, there is a need of antiviral drugs for these viral infections; we describe the prediction of short interfering RNA (siRNA) as potential therapeutic agents against the four DENV serotypes. Our strategy was to carry out a series of multiple alignments using ClustalX program to find conserved sequences among the four DENV serotype genomes to obtain a consensus sequence for siRNAs design. A highly conserved sequence among the four DENV serotypes, located in the encoding sequence for NS4B and NS5 proteins was found. A total of 2,893 complete DENV genomes were downloaded from the NCBI, and after a depuration procedure to identify identical sequences, 220 complete DENV genomes were left. They were edited to select the NS4B and NS5 sequences, which were aligned to obtain a consensus sequence. Three different servers were used for siRNA design, and the resulting siRNAs were aligned to identify the most prevalent sequences. Three siRNAs were chosen, one targeted the genome region that codifies for NS4B protein and the other two; the region for NS5 protein. Predicted secondary structure for DENV genomes was used to demonstrate that the siRNAs were able to target the viral genome forming double stranded structures, necessary to activate the RNA silencing machinery.     

Crystal Structure of the Complex of Concanavalin A and Hexapeptide

The X-ray structure analysis of a cross-linked crystal of concanavalin A soaked with a hexapeptide molecule as a probe molecule showed an electron density corresponding to full occupation in the binding pocket. The site lies on the surface of concanavalin A and is surrounded by three symmetry-related molecules. The crystal structure of the hexapeptide complex was refined at 1.93- resolution, to an R-factor of 19% (R _free factor of 25%), with an RMS deviation in bond distances of 0.01 . The model includes all 237 residues of concanavalin A, one manganese ion, one calcium ion, 95 water molecules, one glutaraldehyde molecule, one isopropanol molecule, and one hexapeptide molecule. This X-ray structure analysis also provides an approach to mapping the binding surface of crystalline protein with a probe molecule that is dissolved in the mixture of organic solvent with water or in neat organic solvent but is hardly dissolved in aqueous solution.     

登革病毒ADE发生机制的研究进展

在登革病毒致病机理中,抗体依赖增强感染效应(Antibody-dependent enhancement,ADE)占据重要地位,可能在人体二次感染登革病毒后引起严重疾病。对近年来重症登革病毒感染作用机制研究中常用的细胞系、动物模型、ADE对于病毒进入宿主细胞的促进作用以及ADE引起的细胞因子变化等方面的研究进展进行了综述。     

雷公藤甲素对Con A诱导小鼠急性肝损伤的保护作用及机制

摘要 目的：探究雷公藤甲素（Triptolide）对刀豆蛋白A（Concanavalin, Con A）诱导的小鼠急性肝损伤的保护机制。方法：雄性BALB/c小鼠30只,随机等分为正常对照组、Con A模型组和雷公藤甲素治疗组。通过尾静脉注射Con A构建小鼠急性肝损伤模型。微孔板法检测血清谷丙转氨酶（ALT）和谷草转氨酶（AST）水平,HE染色观察肝组织病理变化,免疫组化、实时荧光定量PCR（RT-qPCR）和酶联免疫吸附试验（ELISA）检测肝组织及血清中细胞因子水平。结果：与正常对照组比较,Con A诱导急性肝损伤小鼠血清ALT、AST水平显著增高（P<0.05）,肝组织呈局灶性炎性浸润、坏死。与Con A模型组比较,雷公藤甲素治疗组小鼠血清ALT、AST水平显著下降（P<0.05）;肝组织病理程度明显减轻;肝组织中CD4⁺T细胞的浸润降低,促炎细胞因子（IFN-γ、TNF-α、IL-1β、IL-2）的水平显著降低（P<0.05）。结论：雷公藤甲素可以通过抑制CD4⁺T细胞向肝脏募集,下调IFN-γ、TNF-α、IL-1β、IL-2的表达,有效防治Con A诱导的急性免疫性肝损伤。     

Membrane mobility and the Concanavalin A binding system of the plasmalemma of higher plant protoplasts

The binding of a colloidal gold-Concanavalin A (ConA) complex to the plasmalemma of tobacco leaf protoplasts has been investigated using scanning electron microscopy. At 5° C the particles of gold-ConA appear to be randomly distributed over the surface of the protoplast. If the temperature is raised, the particles associate into clusters. Saturation of the membrane with particles can only occur when the weight of ConA in solution exceeds 1 g/10⁴ protoplasts in suspension, and when its concentration exceeds 15 g/ml. These results are discussed in terms of the properties of the ConA binding site and the mobility of such sites within the membrane surface.Abbreviations ConA Concanavalin A - AuConA Colloidal gold-Concanavalin A complex     

曲霉菌半乳甘露聚糖单克隆抗体的制备及初步应用

目的:制备抗曲霉菌半乳甘露聚糖的单克隆抗体,并基于获得的抗体建立用于快速准确检测曲霉菌感染的双抗体夹心酶联免疫吸附法(ELISA),以期可用于侵袭性曲霉菌病的临床诊断。方法:提取曲霉菌半乳甘露聚糖后免疫BALB/c小鼠,筛选与制备抗曲霉菌半乳甘露聚糖的单克隆抗体,通过间接ELISA法与Western Blot方法开展单克隆抗体检测性能分析,使用获得的单克隆抗体建立双抗体夹心ELISA方法,并初步应用于曲霉菌感染血清检测。结果:获得抗曲霉菌半乳甘露聚糖单克隆抗体5株,均可特异性识别曲霉菌半乳甘露聚糖,以其中性能最佳的3C9抗体和辣根过氧化物酶标记的3C9抗体配对为基础,建立了双抗体夹心ELISA方法,通过初步评价确定该方法可应用于临床侵袭性曲霉菌病血清检测,并且该方法与现有商品化试剂盒相比检测背景值较低,可更有效区分曲霉菌感染阴阳性血清。结论:本研究筛选获得针对曲霉菌半乳甘露聚糖的特异性单克隆抗体,以该抗体为基础建立双抗体夹心ELISA方法具有潜在转化应用前景,可为侵袭性曲霉菌病的临床诊断提供支持。     

Asymmetric distribution of Concanavalin A binding sites on yeast plasmalemma and vacuolar membrane

Isolated vacuoles of Saccharomyces cerevisiae did not bind Concanavalin A (labelled with tritium or with a fluorescent dye) unless the vacuoles were rendered permeable and their inner membrane surface made accessible. Yeast protoplasts, on the other hand, bound large amounts of Concanavalin A on their surface, and the number of binding sites was not increased after a gentle lysis expected to expose also the inner surface of the plasmalemma. It is concluded that both the plasmalemma and the vacuolar membrane carry Concanavalin A binding sites exclusively on the surface opposite to the cytoplasmic matrix.Non-Standard Abbreviations ConA concanavalin A - MDPF 2-methoxy-2,4-diphenyl-3(2H)-furanone - -MM -methyl-D-mannopyranoside - Pipes piperazine-N,N-bis-2-ethanesulfonic acid - DNP potassium dinitrophenolate     

Reactive thin polymer films as platforms for the immobilization of biomolecules

Spin-coated thin films of poly(N-hydroxysuccinimidyl methacrylate) (PNHSMA) on oxidized silicon and gold surfaces were investigated as reactive layers for obtaining platforms for biomolecule immobilization with high molecular loading. The surface reactivity of PNHSMA films in coupling reactions with various primary amines, including amine-terminated poly(ethylene glycol) (PEG-NH2) and fluoresceinamine, was determined by Fourier transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), fluorescence microscopy, and ellipsometry measurements, respectively. The rate constants of PEG-NH2 attachment on the PNHSMA films were found to be significantly increased compared to the coupling on self-assembled monolayers (SAMs) of 11,11'-dithiobis(N-hydroxysuccinimidylundecanoate) (NHS-C10) on gold under the same conditions. More significantly, the PEG loading observed was about 3 times higher for the polymer thin films. These data indicate that the coupling reactions are not limited to the very surface of the polymer films, but proceed into the near-surface regions of the films. PNHSMA films were shown to be stable in contact with aqueous buffer; the swelling analysis, as performed by atomic force microscopy (AFM), indicated a film thickness independent swelling of approximately 2 nm. An increased loading was also observed by surface plasmon resonance for the covalent immobilization of amino-functionalized probe DNA. Hybridization of fluorescently labeled target DNA was successfully detected by fluorescence microscopy and surface plasmon resonance enhanced fluorescence spectroscopy (SPFS), thereby demonstrating that thin films of PNHSMA comprise an attractive and simple platform for the immobilization of biomolecules with high densities.     

Transport and processing of the glycosylated precursor of Concanavalin A in jack-bean

Concanavalin A (ConA) is a tetrameric lectin which is synthesized in the developing cotyledons of jack bean (Canavalia ensiformis L.) as a glycosylated precursor, pro-concanavalin A (pro-ConA). The processing of pro-ConA involves the excision of a small glycopeptide from the center of the pro-ConA molecule, and the ligation of the two polypeptides. In this paper, we show that pro-ConA is associated with the endoplasmic reticulum/Golgi fraction of the cells, and that the processing of pro-ConA occurs in the protein bodies. Processing is a complex process and different intermediate-sized polypeptides appear at different times during cotyledon development. The ConA-related polypeptides which accumulate during seed development may be the products of alternate processing events or breakdown products of ConA, rather than precursors of ConA. When glycosylation is prevented by tunicamycin, there is very little transport of pro-ConA out of the endoplasmic reticulum/Golgi system to the protein bodies; the unglycosylated pro-ConA which is transported is slowly processed. Tunicamycin does not prevent the transport of canavalin (a protein which is not glycosylated) or the transport and processing of the small amounts of glycosylated pro-ConA synthesized in the presence of the drug. This is, to our knowledge, the first demonstration that the transport of a glycoprotein in plant cells is dependent on the presence of the glycan.Abbreviations ConA concanavalin A - ER endoplasmic reticulum - GlcN glucosamine - M_r relative molecular mass - SDS-PAGE sodium dodecyl sulfate-polyacrylamide gel electrophoresis supported by a grant from NATO     

Identification of a 48kDa tubulin or tubulin-like C6/36 mosquito cells protein that binds dengue virus 2 using mass spectrometry

Binding of dengue virus 2 (DENV-2) to C6/36 mosquito cells protein was investigated. A 48 kDa DENV-2-binding C6/36 cells protein (D2BP) was detected in a virus overlay protein-binding assay. The binding occurred only to the C6/36 cells cytosolic protein fraction and it was inhibited by free D2BP. D2BP was shown to bind to DENV-2 E in the far-Western-binding studies and using mass spectrometry (MS) and MS/MS, peptide masses of the D2BP that matched to beta-tubulin and alpha-tubulin chains were identified. These findings suggest that DENV-2 through DENV-2 E binds directly to a 48 kDa tubulin or tubulin-like protein of C6/36 mosquito cells.     

Concanavalin A binding sites on the plasma membrane of leek stem protoplasts

The binding of concanavalin A (con A) to leek (Allium porrum L.) stem protoplasts has been investigated using sequential treatment with con A and haemocyanin and using con A covalently linked to ferritin. Prefixed protoplasts were evenly labelled. Unfixed protoplasts showed a clustered distribution of label. Low temperature and lanthanum reduced the clustering. Bound con A was lost from unfixed protoplasts incubated for 5 h after treatment, but con A/haemocyanin was not bound to nascent wall materials. Prefixed protoplasts treated with wall-removing enzymes before labelling showed only a small reduction of con A binding. These results indicate that con A is bound to plasma membrane components, but that binding is reduced by competition of nascent wall precursors.Abbreviations con A concanavalin A - con A-H sequential treatment with con A and haemocyanin - con A-F con A covalently linked to ferritin     

Searching for drug leads targeted to the hydrophobic cleft of dengue virus capsid protein

We synthesised and screened 18 aromatic derivatives of guanylhydrazones and oximes aromatic for their capacity to bind to dengue virus capsid protein (DENVC). The intended therapeutic target was the hydrophobic cleft of DENVC, which is a region responsible for its anchoring in lipid droplets in the infected cells. The inhibition of this process completely suppresses virus infectivity. Using NMR, we describe five compounds able to bind to the α1-α2 interface in the hydrophobic cleft. Saturation transfer difference experiments showed that the aromatic protons of the ligands are important for the interaction with DENVC. Fluorescence binding isotherms indicated that the selected compounds bind at micromolar affinities, possibly leading to binding-induced conformational changes. NMR-derived docking calculations of ligands showed that they position similarly in the hydrophobic cleft. Cytotoxicity experiments and calculations of in silico drug properties suggest that these compounds may be promising candidates in the search for antivirals targeting DENVC.     

A structural comparison of concanavalin a and tomato bushy stunt virus protein

Summary Significant structural equivalence has been found among the polypeptide folds of the two tomato bushy stunt virus (TBSV) subunit domains and concanavalin A. This suggests gene duplication in the TBSV coat protein and leads to speculation on common functional properties of concanavalin A and viral coat proteins.Non-standard abbreviations TBSV tomato bushy stunt virus - SBMV southern bean mosaic virus     

A Study on the Comparative Stability of Insoluble Complexes of Glucose Oxidase Obtained with Concanavalin A and Specific Polyclonal Antibodies

Summary The formation of insoluble complexes of glycoenzymes with lectins and antibodies is one of the simplest methods of enzyme immobilization. Insoluble complexes of glucose oxidase were simply obtained by mixing the enzyme with concanavalin A or a specific polyclonal antibodies solution. The concanavalin A and immunocomplexes of glucose oxidase retained more than 80% of the original enzyme activity. Expression of very high enzyme activity in insoluble complexes suggested that these aggregates were quite porous and easily accessible to substrates. Insoluble complexes of glucose oxidase showed very high stability against denaturation induced by pH, temperature, urea and water-miscible organic solvents. Complexes of glucose oxidase obtained with concanavalin A and glycosyl-specific antiglucose oxidase polyclonal antibodies were quite comparable in stability while complexes prepared using polyclonal antibodies raised against the native glucose oxidase were slightly less stable. The complexes of glucose oxidase obtained with glycosyl-specific antiglucose oxidase polyclonal antibodies showed very high stability against inactivation mediated by exposure to water-miscible organic solvents. Insoluble complexes of glucose oxidase were cross-linked with glutaraldehyde to maintain their integrity in the presence of substrates. The cross-linking of complexes resulted in a slight decrease in enzyme activity but showed a pronounced enhancement in stability against various forms of denaturation.     

Development of robust in vitro RNA-dependent RNA polymerase assay as a possible platform for antiviral drug testing against dengue

NS5 is the largest and most conserved protein among the four dengue virus (DENV) serotypes. It has been the target of interest for antiviral drug development due to its major role in replication. NS5 consists of two domains, the N-terminal methyltransferase domain and C-terminal catalytic RNA-dependent RNA polymerase (RdRp) domain. It is an unstable protein and is prone to inactivation upon prolonged incubation at room temperature, thus affecting the inhibitor screening assays. In the current study, we expressed and purified DENV RdRp alone in Esherichia coli (E. coli) cells. The N-terminally His-tagged construct of DENV RdRp was transformed into E. coli expression strain BL-21 (DE3) pLysS cells. Protein expression was induced with isopropyl-β-D-thiogalactopyranoside (IPTG) at a final concentration of 0.4 mM. The induced cultures were then grown for 20 h at 18 °C and cells were harvested by centrifugation at 6000 x g for 15 min at 4 °C. The recombinant protein was purified using HisTrap affinity column (Ni-NTA) and then the sample was subjected to size exclusion chromatography, which successfully removed the degradation product obtained during the previous purification step. The in vitro polymerase activity of RdRp was successfully demonstrated using homopolymeric polycytidylic acid (poly(rC)) RNA template. This study describes the high level production of enzymatically active DENV RdRp protein which can be used to develop assays for testing large number of compounds in a high-throughput manner. RdRp has the de novo initiation activity and the in vitro polymerase assays for the protein provide a platform for highly robust and efficient antiviral compound screening systems.     

Concanavalin A-binding glycoproteins in the subcommissural and the pineal organ of the sheep (Ovis aries)

Summary Glycoproteins rich in mannosyl or glucosyl residues were analyzed in the subcommissural organ (SCO) and the pineal organ of the sheep (Ovis aries). By use of concanavalin A labelled with fluorescein isothiocyanate, fluorescent material was found both in ependymal and hypendymal cells of the SCO. In the pineal organ, either isolated or grouped parenchymal cells showed a marked fluorescence. These cells may correspond to ependymal elements also called interstitial cells or supporting cells. In addition, scarce slender, fluorescent processes were observed in the pineal parenchyma. The techniques of electrophoresis and electrotransfer on nitrocellulose paper have been applied to analyze the glycopeptide content of the SCO and the pineal organ in comparison to cerebellar and cerebral fractions solubilized by use of Triton X 100. Approximately 30 different concanavalin A-reactive glycopeptides were revealed in each fraction. In the SCO extract four glycopeptides (30, 54, 72, 100 kd) might correspond to subunits of the glycoprotein(s) characteristically stored in the ependymal cells of the SCO. In addition, two glycopeptides (32/33, 115 kd) are specific to the pineal organ extract. The possible similarity of the concanavalin A-reactive material in both organs is discussed and a putative secretory activity of the pineal ependymal cells is postulated.     

Design,synthesis and biological evaluation of spiropyrazolopyridone derivatives as potent dengue virus inhibitors

The effective treatment for dengue virus infection continues to be a challenge. We herein reported our continued SAR exploration on the spiropyrazolopyridone scaffold. Introducing different substituents at the 3́- or 5́-site of the pyrazolopyridone core or moving the benzyl chain to the adjacent nitrogen led to a significant loss of potency on DENV-2. While a narrow range of substitutions were tolerated at the para-position of the phenyl ring, di-substitution on the phenyl ring is beneficial for DENV-2 potency and has variable influences on DENV-3 potency depending on the exact compound. Among these molecules, compounds 22 (JMX0376) with 4-chloro-3-fluorobenzyl and 24 (JMX0395) with 2,4-bis(trifluoromethyl)benzyl showed the most potent and broadest inhibitory activities against DENV-1 to −3 with nanomolar to low micromolar EC₅₀ values.     

乙脑/登革4型嵌合病毒的构建及其小鼠神经毒力测定

目的构建以乙型脑炎病毒(Japanese encephalitis virus,JEV)疫苗株SA14-14-2为基因骨架的乙脑/登革4型嵌合病毒,并分析该嵌合病毒对小鼠的神经毒力。方法通过重叠PCR方法扩增含有登革病毒4型(DENV-4)H241株pr ME基因序列和乙型脑炎病毒疫苗株SA14-14-2的NS1蛋白前177个核苷酸的融合片段,用Nar I和Bgl II双酶切后替换乙型脑炎病毒疫苗株SA14-14-2全长克隆中的相应区域,构建成乙脑/登革4型嵌合全长克隆,通过体外转录和转染BHK21细胞获得嵌合病毒(JEV/DENV-4 chimeric virus,JD4)。通过测定嵌合病毒JD4和2个母本株JEV SA14-14-2株及DENV-4 H241株蚀斑大小、小鼠脑内神经毒力和皮下感染入脑能力、乳鼠脑内神经毒力,比较JD4和母本株之间的差异。通过将JD4在原代地鼠肾(primary hamster kidney,PHK)细胞传代30次,分析传代后嵌合病毒的神经毒力是否减弱及减弱的程度。结果测序结果表明,构建的嵌合病毒JD4基因组序列和预期一致,没有产生新的位点突变。JD4蚀斑较SA14-14-2明显偏小,但和DENV-4 H241株没有明显区别。JD4对3周龄小鼠具有较强的脑内神经毒力,和母本株DENV-4 H241没有差异,对小鼠没有神经侵袭力。乳鼠实验结果表明,嵌合病毒JD4脑内神经毒力虽然略低于母本株DENV-4 H241,但两者之间没有明显差异,都明显强于乙脑疫苗株SA14-14-2。在PHK细胞传代30次后,小鼠神经毒力虽然有所减低,但并不明显。结论成功构建了嵌合病毒JD4,通过测定并比较JD4与母本株的蚀斑特征、小鼠及乳鼠神经毒力等试验,为分析登革疫苗候选株安全性研究奠定了基础。     

Calcium alginate–starch hybrid support for both surface immobilization and entrapment of bitter gourd (Momordica charantia) peroxidase

Calcium alginate–starch hybrid gel was employed as an enzyme carrier both for surface immobilization and entrapment of bitter gourd peroxidase. Entrapped crosslinked concanavalin A–bitter gourd peroxidase retained 52% of the initial activity while surface immobilized and glutaraldehyde crosslinked enzyme showed 63% activity. A comparative stability of both forms of immobilized bitter gourd peroxidase was investigated against pH, temperature and chaotropic agent; like urea, heavy metals, water-miscible organic solvents, detergent and inhibitors. Entrapped peroxidase was significantly more stable as compared to surface immobilized form of enzyme. The pH and temperature-optima for both immobilized preparations were the same as for soluble bitter gourd peroxidase. Entrapped crosslinked concanavalin A–bitter gourd peroxidase showed 75% of the initial activity while the surface immobilized and crosslinked bitter gourd peroxidase retained 69% of the original activity after its seventh repeated use.