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1.
基于生物信息学方法发现潜在药物靶标   总被引:2,自引:0,他引:2       下载免费PDF全文
药物靶点通常是在代谢或信号通路中与特定疾病或病理状态有关的关键分子.通过绑定到特定活动区域抑制这个关键分子进行药物设计.确定特定疾病有关的靶标分子是现代新药开发的基础.在药物靶标发现的过程中,生物信息学方法发挥了不可替代的重要的作用,尤其适用于大规模多组学数据的分析.目前,已涌现了许多与疾病相关的数据库资源,基于生物网络特征、多基因芯片、蛋白质组、代谢组数据等建立了多种生物信息学方法发现潜在的药物靶标,并预测靶标可药性和药物副作用.  相似文献   

2.
目的:对人幽门螺杆菌(Helicobacter pylori,H.pylori)36ku(OMP36)外膜蛋白进行基因克隆表达,探索研制H.pylori疫苗的新途径。方法:培养H.pylori菌株NCTC11637,采用酚:氯仿抽提和纯化基因组DNA。设计上下游引物,并以该基因组为模板,采用聚合酶链反应(PCR)扩增目的基因片断。将目的基因和PET32a( )同时经HindⅢ和KpnⅠ双酶切,纯化,连接后,转化含有目的基因的重组载体,酶切鉴定后进行序列分析。结果:经酶切,测序分析表明,插入的基因片断为987bp,与GenBank公布的H.pylori 26695、ATCC43504及J99序列相比较,同源性高达94%-96%,推测的氨基酸序列同源性为97%-99%,GenBank登录号059968。结论:成功克隆了H.pylori 36ku的外膜蛋白的编码基因,其表达产物OMP36有望成为新的Hp疫苗候选分子,为H.pylori疫苗的研制和试剂盒的开发奠定了基础。  相似文献   

3.
化学基因组技术是药物作用靶标确认、药物分子在通路中的作用的确证等方面有重要应用,可为新药研发和老药新用提供理论依据,并可降低药物发现中的高额成本.精氨酸-甘氨酸-天冬氨酸(RGD)三肽被证明是与细胞粘附受体特异性结合的特征序列,在生理学上扮演者重要角色.本研究利用化学基因组学中的其中一种方法即基于反向对接和药效团反向匹配搜索技术来研究RGD三肽的潜在作用靶标,并进行计算机模拟分析.反向匹配搜索结果发现计算得到的关键性靶标及其涉及的相关疾病与实验报道的RGD的药理活性相吻合,包括具有抗凝血、抗肿瘤作用,与肾及心血管作用有关等,而且还发现RGD可能是一个潜在的神经氨酸酶的抑制剂.  相似文献   

4.
2-甲基柠檬酸循环广泛分布于细菌中,参与丙酸或丙酰-CoA的分解代谢。我们一直致力于微生物代谢调控方面的研究,并以苏云金芽胞杆菌为研究对象在2-甲基柠檬酸循环的代谢调控及生理功能方面取得了新的进展。本文将从2-甲基柠檬酸循环关键酶基因的组成、关键酶基因的转录调控和该循环参与的生理功能3个方面介绍细菌中2-甲基柠檬酸循环的研究进展。同时,对该循环研究中存在的相关科学问题和未来的研究重点作简要评述,并对该循环关键酶作为药物靶标在病原菌感染防治方面的应用进行展望。  相似文献   

5.
偏头痛相关酶和KEGG通路分析   总被引:1,自引:0,他引:1       下载免费PDF全文
黄瑞  郑珩 《生物信息学》2014,12(3):218-226
搜集与偏头痛相关的编码酶的基因,利用KEGG通路分析目标基因的分布和功能,促进偏头痛遗传学研究和新药靶点研究。以"gene name"AND migraine检索PUBMED数据库,从原始文献中搜集并整理偏头痛相关酶基因数据,用DAVID在线分析工具对数据进行处理。搜索得到31个偏头痛酶基因,对7条KEGG代谢通路进行了分析:色氨酸代谢通路、酪氨酸代谢通路、精氨酸和脯氨酸代谢通路、叶酸一碳单位循环代谢通路、药物代谢通路、外源物质细胞色素P450代谢通路、肾素血管紧张素代谢通路。其中药物代谢通路包括9个药物,又以高选择性5-羟色胺重摄取抑制剂西酞普兰的应用前景最大。DDC、DBH、MTHFD1等6个偏头痛相关基因需要完善多态性研究。CYP450和单胺氧化酶在偏头痛的病理和治疗中都占有重要的地位。通过分析疾病相关酶基因的代谢通路,有助于了解疾病的分子病理基础,并为新药设计提供可靠靶点。  相似文献   

6.
幽门螺旋杆菌(Helicobacter pylori, H. pylori)选择性地在人的胃黏膜中定植,是引发胃癌的最强危险因素之一。多胺是一类广泛存在于真核细胞中带高密度正电荷的烷基类小分子化合物,参与细胞增殖、分化、凋亡等重要的生理过程,多种疾病的发生发展与多胺代谢紊乱相关。近期研究发现,H.pylori感染能诱导宿主胃黏膜上皮细胞和巨噬细胞中多胺代谢异常。特别是该菌对多胺代谢途径中的关键酶ARG2(arginase 2,精氨酸酶2)、ODC(ornithine decarboxylase,鸟氨酸脱羧酶)和SMO(soermine oxidase,精胺氧化酶)的激活作用,与H. pylori免疫逃逸,慢性炎症维持、DNA损伤和胃癌的发生发展密切相关,提示多胺代谢途径可能成为H. pylori相关胃癌防治的新靶点。  相似文献   

7.
胃内定植是引起幽门螺杆菌(Helicobacter pylori,H.pylori)感染的先决条件。H.pylori可穿过胃黏液层并与胃上皮细胞相互作用。这个定植过程主要受到H.pylori动力和尿素酶的影响。同时H.pylori形态、胃内pH、外膜蛋白及益生菌等也在其中扮演重要角色。该研究主要对H.pylori胃内定植过程中的相关影响因素进行综述。  相似文献   

8.
幽门螺杆菌(Helicobacter pylori,H.pylori)是导致活动性胃炎、消化性溃疡、胃癌、胃黏膜相关淋巴组织淋巴瘤等消化系统疾病的重要病因之一,已被世界卫生组织确认为Ⅰ类致癌因子,根除H.pylori对防治上述疾病有重要意义。目前临床上主要采用含抗生素的三联或四联药物进行H.pylori的根除,虽然取得一定的疗效,但随着抗生素耐药率逐年增加,根除率持续下降,限制了其广泛应用。此外,初次或多次治疗失败后再治疗可选择的药物很少。近年来人们开始尝试将益生菌应用在H.pylori根除治疗中,并取得一定疗效。本文就益生菌在辅助根除幽门螺杆菌方面的研究进展作一简单综述。  相似文献   

9.
基于结核分枝杆菌国际标准强毒株H37Rv菌株的基因组尺度代谢网络模型iNJ661进行分析,以寻找代谢网络中培养基的关键成分和必要基因.该研究在Matlab平台上利用COBRA工具箱,采用基于约束的建模方法进行动态生长模拟、解空间抽样在酶活性水平上的具体化和基因删除模拟实验.结果发现培养基成分中铵盐、三价铁盐、磷酸盐、硫酸盐、甘油等可影响H37Rv的生长;培养基中去除磷酸盐后十种酶均在不同程度上受到抑制,其中丙糖磷酸异构酶、3-磷酸甘油醛脱氢酶、磷酸甘油酸变位酶、烯醇酶受限明显.通过基因删除得出188个必要基因以及非必要基因中的16个致死基因对.基于约束建模分析可初步了解结核杆菌H37Rv菌株代谢网络的性质,可为后续相关研究提供参考和借鉴.  相似文献   

10.
【背景】幽门螺杆菌(Helicobacter pylori,H.pylori)是胃癌的主要致病因素,其分泌的细胞毒素相关基因A蛋白(Cytotoxin associated gene A,CagA)是目前已知唯一能被H.pylori注入胃上皮细胞并模拟细胞内蛋白发挥作用的癌蛋白,参与胃癌的发生发展。【目的】比较H.pylori东亚株和西方株CagA结构差异,初步探讨H.pylori-CagA对胃癌细胞增殖与凋亡的影响。【方法】对H.pylori东亚株和西方株CagA的核酸及氨基酸序列进行生物信息学分析,构建含东亚株和西方株cagA基因的真核表达载体,转染胃癌细胞AGS,用Western blot法检测CagA蛋白的表达,用CCK8法测定细胞的生长曲线,流式细胞术检测细胞凋亡。【结果】生物信息学分析发现H.pylori东亚、西方菌株CagA的核酸序列和氨基酸序列均存在特征性差异。构建了含东亚、西方菌株cagA基因的表达载体[命名为GZ7/cagA(东亚株)和26695/cagA(西方株)]。与空载体组比较,GZ7/cagA和26695/cagA转染组均表达CagA蛋白,两组比较表达量无显著性差异,GZ7/cagA转染组细胞生长显著增加,而26695/cagA转染组细胞生长显著降低(P0.05)。GZ7/cagA转染组、26695/cagA转染组细胞的凋亡率分别为7.23±0.96及9.17±1.40,均高于空载体组(5.03±0.63),差异有统计学意义(P0.05)。【结论】东亚株与西方株CagA之间有结构和功能的差异,东亚株CagA能促进细胞增殖,而西方株CagA却抑制细胞增殖,但两者均能促进细胞凋亡。  相似文献   

11.
In host-parasite diseases like tuberculosis, non-homologous proteins (enzymes) as drug target are first preference. Most potent drug target can be identified among large number of non-homologous protein through protein interaction network analysis. In this study, the entire promising dimension has been explored for identification of potential drug target. A comparative metabolic pathway analysis of the host Homo sapiens and the pathogen M. tuberculosis H37Rv has been performed with three level of analysis. In first level, the unique metabolic pathways of M. tuberculosis have been identified through its comparative study with H. sapiens and identification of non-homologous proteins has been done through BLAST similarity search. In second level, choke-point analysis has been performed with identified non-homologous proteins of metabolic pathways. In third level, two type of analysis have been performed through protein interaction network. First analysis has been done to find out the most potential metabolic functional associations among all identified choke point proteins whereas second analysis has been performed to find out the functional association of high metabolic interacting proteins to pathogenesis causing proteins. Most interactive metabolic proteins which have highest number of functional association with pathogenesis causing proteins have been considered as potential drug target. A list of 18 potential drug targets has been proposed which are various stages of progress at the TBSGC and proposed drug targets are also studied for other pathogenic strains.As a case study, we have built a homology model of identified drug targets histidinol-phosphate aminotransferase (HisC1) using MODELLER software and various information have been generated through molecular dynamics which will be useful in wetlab structure determination. The generated model could be further explored for insilico docking studies with suitable inhibitors.  相似文献   

12.
He C  Wu Y  Lai Y  Cai Z  Liu Y  Lai L 《Molecular bioSystems》2012,8(5):1585-1594
The arachidonic acid (AA) metabolic network produces key inflammatory mediators which have been considered as hallmark contributors in various inflammatory related diseases. Enzymes in this network, such as 5-lipoxygenase (5-LOX), cyclooxygenase (COX), leukotriene A(4) hydrolase (LTA4H) and prostaglandin E synthase (PGES), have been used as targets for anti-inflammatory drug discovery. Multi-target drugs and drug combinations have also been developed for this network. However, how the inhibitors alter the dynamics of metabolite production and which combinatorial target intervention solutions are better needs further exploration. We did a system based intervention analysis on the AA metabolic network. Using an LC-MS/MS method, we quantitatively studied the eicosanoid metabolites responses of AA metabolic network during stimulation of Sprague Dawley rat blood samples with the calcium ionophore. Our results indicate that inhibiting the upstream rather than the downstream target of 5-LOX pathway will simultaneously alter the AA metabolism to the COX pathway (and vice versa). Therefore, single-target inhibitors cannot control all the inflammatory mediators at the same time. We also suggest that in the case of multiple-target anti-inflammatory solutions, the combination of inhibitors of the downstream enzymes may have stronger inhibition efficiency and cause less side-effects compared to the other solutions. One therapeutic strategy, LTA4H/COX inhibition solution, was found promising for the intervention of inflammatory mediator biosynthesis and at the same time stimulating the production of anti-inflammatory agents.  相似文献   

13.
Helicobacter pylori is a major etiological agent in gastroduodenal disorders. The adhesion of H. pylori to gastric epithelial cells is the initial step of H. pylori infection. Inhibition of H. pylori adhesion is thus a therapeutic target in the prevention of H. pylori infection. We have reported that rebamipide and ecabet sodium, mucoprotective antiulcer agents, independently inhibit H. pylori adhesion. However, the antiadhesion activity of each antiulcer agent was incomplete. Experiments were performed to evaluate the combined effect of rebamipide and ecabet sodium on H. pylori adhesion to gastric epithelial cells. MKN-28 and MKN-45 cells, derived from human gastric carcinomas, were used as target cells. Twelve clinical isolates of H. pylori were used in this study. We evaluated the effects of rebamipide and ecabet sodium, individually and in combination, on H. pylori adhesion to target cells quantitatively using our previously established enzyme-linked immunosorbent assay. Rebamipide and ecabet sodium each partially inhibited H. pylori adhesion. In contrast, adhesion was almost completely inhibited by pretreating target cells and H. pylori with the combination of rebamipide and ecabet sodium. Our studies suggest that the synergistic antiadhesion activity of rebamipide and ecabet sodium is greater than that of each antiulcer agent alone.  相似文献   

14.
Helicobacter pylori, a microaerophilic Gram-negative bacterium, is known to cause chronic gastritis, peptic ulcer and gastric cancer. Genes that are present in certain isolates may determine strain-specific traits such as disease association and drug resistance. In order to understand the pathogenic mechanisms of gastric diseases, identify molecular markers of the diseases associated with H. pylori strains and provide clues for target treatment of H. pylori-related diseases, a subtracted DNA library was constructed from a gastric cancer-associated H. pylori strain and a superficial gastritis-associated H. pylori strain by suppression subtractive hybridization. The presence of gastric cancer-specific genes was identified by dot blot hybridization, DNA sequencing and PCR-based screening. Twelve gastric cancer-specific high-copy genes and nine low-copy genes were found in gastric cancer compared with the superficial gastritis strain. These genes were confirmed by PCR analysis of H. pylori isolates. Notably, peptidyl-prolyl cis-trans isomerase (PPIase) was detected positively in 11 out of 22 (50%) gastric cancer-associated H. pylori strains. In contrast, <24% of the H. pylori strains from superficial gastritis showed positive results. Given the potential role of PPIases in cell growth, apoptosis and oncogenic transformation, our results suggest that PPIase may represent a novel marker and potential therapeutic target for gastric cancer.  相似文献   

15.
During this review period, we have definitely entered into the genomic era. The Helicobacter pylori studies reported here illustrate the use of most of the technologies currently available to globally interrogate the genome of a pathogen. Global analysis of the gene content of H. pylori strains gives insight into the extent of its genetic diversity and its in vivo evolution. Our understanding of the particularities of H. pylori as a gastric pathogen colonizing a unique niche has been improved by studies aimed at: (i) the identification of H. pylori-specific genes; (ii) the establishment of correlations between the presence of one or a group of genes (or proteins) with clinical outcome; and (iii) the analysis of global regulatory circuits or responses to the extracellular signals. The response of host cells to H. pylori infection will be developed in the chapter 'H. pylori and gastric malignancies' by Sepulveda and Coehlo. Despite our knowledge of the H. pylori genome, the function of about one third of its total proteins is still unknown. Functional genomics are straightforward approaches for the identification of new gene functions or metabolic pathways as well as for the understanding of cellular processes and the detection of new virulence factors. In silico studies combined with experimental work will undoubtedly continue to develop. To date, the expansion of proteomics with refinements in mass spectrometry technology has illustrated that through immunoproteomics and comparative studies, relevant novel antigens can be identified. Genomics not only provides invaluable information on H. pylori but also opens new perspectives for diagnostic or therapeutic applications.  相似文献   

16.
17.
Colonization of human stomach by the bacterium Helicobacter pylori is a major causative factor for gastrointestinal illnesses and gastric cancer. However, the discovery of anti-H. pylori agents is a difficult task due to lack of mature protein targets. Therefore, identifying new molecular targets for developing new drugs against H. pylori is obviously necessary. In this study, the in-house potential drug target database (PDTD, http://www.dddc.ac.cn/tarfisdock/) was searched by the reverse docking approach using an active natural product (compound 1) discovered by anti-H. pylori screening as a probe. Homology search revealed that, among the 15 candidates discovered by reverse docking, only diaminopimelate decarboxylase (DC) and peptide deformylase (PDF) have homologous proteins in the genome of H. pylori. Enzymatic assay demonstrated compound 1 and its derivative compound 2 are the potent inhibitors against H. pylori PDF (HpPDF) with IC50 values of 10.8 and 1.25 microM, respectively. X-ray crystal structures of HpPDF and the complexes of HpPDF with 1 and 2 were determined for the first time, indicating that these two inhibitors bind well with HpPDF binding pocket. All these results indicate that HpPDF is a potential target for screening new anti-H. pylori agents. In addition, compounds 1 and 2 were predicted to bind to HpPDF with relatively high selectivity, suggesting they can be used as leads for developing new anti-H. pylori agents. The results demonstrated that our strategy, reverse docking in conjunction with bioassay and structural biology, is effective and can be used as a complementary approach of functional genomics and chemical biology in target identification.  相似文献   

18.
Gao XX  Ge HM  Zheng WF  Tan RX 《Helicobacter》2008,13(2):103-111
Background:  Helicobacter pylori , the human pathogenic gram-negative microaerophilic bacterium, causes chronic gastric infection in more than half of the human population regardless of race. The infection of microbe is not yet controllable to pose a substantial public health impact and a growing social burden. The management of H. pylori infection primarily necessitates accurate and timely diagnosis at case level, on-demand supervision of pathologic progression, and reliable evaluation of the impact of pharmacologic interventions on the patients' population.
Methods:  The characterization of H. pylori infection on gerbils model was performed by metabolic profiling, employing 1H NMR spectroscopy compounding multivariate pattern recognition strategies. In the same manner, urine samples were individually collected from 10 gerbils infected with H. pylori GS13, and from 10 uninfected control animals equally accessible to feed and water.
Results:  The resultant metabolic profiles indicate that H. pylori infection disturbs carbohydrate metabolism to elevate the levels of α- and β-glucose, and cis -aconitate (a TCA cycle intermediate). In addition to the energy metabolism alteration, the colonization of H. pylori in gerbil stomach generates a remarkable deviation of amino acid metabolism as indicated by depletion of taurine and arginine, and elevation of proline and glutamine in the animal urine. Moreover, the H. pylori infection modifies the gut microbiota as highlighted by a range of microbial-related metabolites such as indoxyl sulfate and hippurate.
Conclusions:  These findings demonstrate that the 1H NMR-based urine metabolic profiling is a promising technique capable of providing an accurate, noninvasive, and rapid diagnosis of H. pylori infection.  相似文献   

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