Insilico analysis

  • 文章类型: Journal Article
    复发性妊娠丢失(RPL)是一种以妊娠20周前失去两次或更多次妊娠为特征的疾病。RPL的原因是复杂的,可能是由于多种因素,包括遗传,免疫学,荷尔蒙,和环境因素。使用Insilco方法进行了这项转录组数据挖掘研究,以探索负责RPL发病机理的差异表达基因(DEGs)和相关途径。来自基因表达综合(GEO)数据库的RNAseq数据集用于提取RPL的RNAseq数据集。Meta分析由ExpressAnalyst进行。使用Cytoscape软件的KEGG和BINGO插件进行DEGs的功能和途径富集分析。使用STRING进行蛋白质-蛋白质相互作用,并鉴定hub基因。总共确定了91个DEG,其中10个下调,81个上调。通路分析表明,大多数DEGs在免疫通路中富集(IL-17信号通路,TLR信号通路,自身免疫性甲状腺疾病),血管生成VEGF信号通路和细胞周期信号通路。其中,选择了10个高连通性的hub基因(CXCL8、CCND1、FOS、PTGS2,CTLA4,THBS1,MMP2,KDR,和CD80)。这些基因中的大多数参与维持母胎界面的免疫应答。Further,在功能富集分析中揭示了在调节生物过程之后是细胞过程的最高节点大小,它们对多细胞组织过程的调控。这种计算机转录组学荟萃分析结果可能有助于识别RPL的新型生物标志物和治疗靶标。这可能导致针对这种情况的新诊断和治疗策略的开发。
    Recurrent pregnancy loss (RPL) is a condition characterized by the loss of two or more pregnancies before 20 weeks of gestation. The causes of RPL are complex and can be due to a variety of factors, including genetic, immunological, hormonal, and environmental factors. This transcriptome data mining study was done to explore the differentially expressed genes (DEGs) and related pathways responsible for pathogenesis of RPL using an Insilco approach. RNAseq datasets from the Gene Expression Omnibus (GEO) database was used to extract RNAseq datasets of RPL. Meta-analysis was done by ExpressAnalyst. The functional and pathway enrichment analysis of DEGs were performed using KEGG and BINGO plugin of Cytoscape software. Protein-protein interaction was done using STRING and hub genes were identified. A total of 91 DEGs were identified, out of which 10 were downregulated and 81 were upregulated. Pathway analysis indicated that majority of DEGs were enriched in immunological pathways (IL-17 signalling pathway, TLR-signalling pathway, autoimmune thyroid disease), angiogenic VEGF-signalling pathway and cell-cycle signalling pathways. Of these, 10 hub genes with high connectivity were selected (CXCL8, CCND1, FOS, PTGS2, CTLA4, THBS1, MMP2, KDR, and CD80). Most of these genes are involved in maintenance of immune response at maternal-fetal interface. Further, in functional enrichment analyses revealed the highest node size in regulation of biological processes followed by cellular processes, their regulation and regulation of multicellular organismal process. This in-silico transcriptomics meta-analysis findings could potentially contribute in identifying novel biomarkers and therapeutic targets for RPL, which could lead to the development of new diagnostic and therapeutic strategies for this condition.
    导出

    更多引用

    收藏

    翻译标题摘要

    我要上传

    求助全文

  • 文章类型: Journal Article
    L.edodes(L.edodes)是世界上消耗最多的蘑菇,以其作为可食用和药用候选物的治疗潜力而闻名,它含有膳食纤维,维生素,蛋白质,矿物,和碳水化合物。在目前的研究中,蘑菇的丁醇提取物用于形成半固体丁醇提取物。本研究旨在利用FT-IR、GC-MS和LC-MS等方法探索香菇正丁醇提取物中可能具有生物活性的生物代谢物。生物活性化合物的协同性能进一步通过进行不同的生物测定,如抗氧化剂,抗炎和抗糖尿病。红外光谱显示不同的官能团包括酰胺N-H基团,烷烃(C-H拉伸),和(C=C拉伸)组分别在500cm-1至5000cm-1范围内的不同光谱峰。正丁醇提取物的GC-MS分析描绘了二甲基中的34种有效生物分子;吗啡,2TMS衍生物;苯甲酸,甲基酯1-(2-甲氧基-1-甲基乙氧基)-2-丙醇被点样在最高范围。结果表明,香菇正丁醇提取物在300mg/mL时显示出91.4%的最大抗炎潜力。通过测量自由基清除活性观察到抗氧化活性,在最佳浓度下为64.6%,并具有良好的抗糖尿病活性。计算机研究执行了活性成分吗啡的生物电势,该生物电势证明了针对醛糖还原酶的最佳对接得分(-7.0kJ/mol)。对通过GC-MS检测到的生物代谢物进行了计算机药物设计分析,这可能是硫酸酯酶2治疗反刍性关节炎的潜在靶标。吗啡比所示的其他生物活性成分结合更强(~7.9kJ/mol)。QSAR和ADMET分析表明,吗啡是抗反刍性关节炎的良好候选药物。目前的研究表明,香菇可能被用作治疗多种疾病的有效药物分子。由于蘑菇具有很高的生物活性,它们可以用于治疗不同的疾病,并根据世界上由于滥用抗生素而导致耐药性增加的现状开发抗菌药物,因此需要新的和新的生物活性化合物来克服这种情况。
    L. edodes (L. edodes) is the most consumed mushroom in the world and has been well known for its therapeutic potential as an edible and medicinal candidate, it contains dietary fibers, vitamins, proteins, minerals, and carbohydrates. In the current study butanolic extract of mushroom was used to form semisolid butanol extract. The current study aimed to explore biometabolites that might have biological activities in n-butanol extract of L. edodes using FT-IR and GC-MS and LC-MS. The synergistic properties of bioactive compounds were futher assessed by performing different biological assays such as antioxidant, anti-inflammatory and antidiabetic. FTIR spectra showed different functional groups including amide N-H group, Alkane (C-H stretching), and (C = C stretching) groups at different spectrum peaks in the range of 500 cm-1 to 5000 cm-1 respectively. GC-MS profiling of n-butanol extract depicted 34 potent biomolecules among those dimethyl; Morphine, 2TMS derivative; Benzoic acid, methyl ester 1-(2-methoxy-1-methylethoxy)-2-propanol were spotted at highest range. Results indicate that L. edodes n-butanol extract showed a maximum anti-inflammatory potential 91.4% at 300 mg/mL. Antioxidant activity was observed by measuring free radical scavenging activity which is 64.6% at optimized concentration along with good antidiabetic activity. In-silico study executed the biopotential of active ingredient morphine which proved the best docking score (- 7.0 kJ/mol) against aldose reductase. The in-silico drug design analysis was performed on biometabolites detected through GC-MS that might be a potential target for sulfatase-2 to treat ruminated arthritis. Morphine binds more strongly (- 7.9 kJ/mol) than other bioactive constituents indicated. QSAR and ADMET analysis shown that morphine is a good candidates against ruminated arthritis. The current study showed that L. edodes might be used as potent drug molecules to cure multiple ailments. As mushrooms have high bioactivity, they can be used against different diseases and to develop antibacterial drugs based on the current situation in the world in which drug resistance is going to increase due to misuse of antibiotics so new and noval biological active compounds are needed to overcome the situation.
    导出

    更多引用

    收藏

    翻译标题摘要

    我要上传

       PDF(Pubmed)

  • 文章类型: Journal Article
    根据世卫组织的估计,2021年约有160万人因结核病丧生。尽管存在针对因果因素的强化治疗计划,结核分枝杆菌,病原体的多药耐药菌株的进化使大量全球人群处于危险之中。可以诱导长期保护的疫苗仍在制造中,许多候选物目前处于临床试验的不同阶段。COVID-19大流行通过影响早期结核病的诊断和治疗进一步加剧了逆境。然而,世卫组织坚持其“终结结核病”战略,并致力于到2035年大幅减少结核病发病率和死亡人数。这样一个雄心勃勃的目标将需要一个多部门的方法,这将大大受益于最新的计算进步。为了突出这些工具对抗结核病的进展,通过这次审查,我们总结了使用先进的计算工具和算法进行早期结核病诊断的最新研究,抗分枝杆菌药物的发现和下一代结核病疫苗的设计。最后,我们对其他计算工具和机器学习方法进行了深入的了解,这些工具和方法已成功应用于生物医学研究,并讨论了它们对结核病的前景和应用。
    Around 1.6 million people lost their life to Tuberculosis in 2021 according to WHO estimates. Although an intensive treatment plan exists against the causal agent, Mycobacterium Tuberculosis, evolution of multi-drug resistant strains of the pathogen puts a large number of global populations at risk. Vaccine which can induce long-term protection is still in the making with many candidates currently in different phases of clinical trials. The COVID-19 pandemic has further aggravated the adversities by affecting early TB diagnosis and treatment. Yet, WHO remains adamant on its \"End TB\" strategy and aims to substantially reduce TB incidence and deaths by the year 2035. Such an ambitious goal would require a multi-sectoral approach which would greatly benefit from the latest computational advancements. To highlight the progress of these tools against TB, through this review, we summarize recent studies which have used advanced computational tools and algorithms for-early TB diagnosis, anti-mycobacterium drug discovery and in the designing of the next-generation of TB vaccines. At the end, we give an insight on other computational tools and Machine Learning approaches which have successfully been applied in biomedical research and discuss their prospects and applications against TB.
    导出

    更多引用

    收藏

    翻译标题摘要

    我要上传

       PDF(Pubmed)

  • 文章类型: Journal Article
    Staphylococcus epidermidis is the most common cause of medical device-associated infections and is an opportunistic biofilm former. Among hospitalized patients, S. epidermidis infections are the most prevalent, and resistant to most antibiotics. In order to overcome this resistance, it is imperative to treat the infection at a cellular level. The present study aims to identify inhibitors of the prokaryotic cell division protein FtsZ a widely conserved component of bacterial cytokinesis. Two substrate binding sites are present on the FtsZ protein; the nucleotide-binding domain and the inter-domain binding sites. Molecular modeling was used to identify potential inhibitors against the binding sites of the FtsZ protein. One hundred thirty-eight chemical entities were virtually screened for the binding sites and revealed ten molecules, each with good binding affinities (docking score range -9.549 to -4.290 kcal/mol) compared to the reference control drug, i.e., Dacomitinib (-4.450 kcal/mol) and PC190723 (-4.694 kcal/mol) at nucleotide and inter-domain binding sites respectively. These top 10 hits were further analyzed for their ADMET properties and molecular dynamics simulations. The Chloro-derivative of GTP, naphthalene-1,3-diyl bis(3,4,5-trihydroxybenzoate), Guanosine triphosphate (GTP), morpholine and methylpiperazine derivative of GTP were identified as the lead molecules for nucleotide binding site whereas for inter-domain binding site, 1-(((amino(iminio)methyl)amino)methyl)-3-(3-(tert-butyl)phenyl)-6,7-dimethoxyisoquinolin-2-ium, and Chlorogenic acidwere identified as lead molecules. Molecular dynamics simulation and post MM/GBSA analysis of the complexes revealed good protein-ligand stability predicting them as potential inhibitors of FtsZ (Figure 1). Thus, identified FtsZ inhibitors are a promising lead compounds for S. epidermidis related infections.
    导出

    更多引用

    收藏

    翻译标题摘要

    我要上传

       PDF(Pubmed)

  • 文章类型: Journal Article
    糖尿病是一种多因素疾病,其特征在于血糖水平的慢性升高。目前,抗糖尿病药物可用于抵消相关的病症。它们的伴随作用需要研究一种有效和安全的药物,目的是降低血糖水平,副作用少。一些研究人员正在采取新的举措来探索植物来源,因为已知它们含有各种各样的活性剂。因此,本研究是利用硅相互作用研究来研究天然产物的作用。选择存在于地衣中的赤霉素化合物作为潜在的抗糖尿病药物。使用14种靶蛋白进行分子对接研究以评估其抗糖尿病潜力。分子对接分析导致有利的相互作用结合能范围低至-119.676至-92.9545kcal/mol的红蛋白,模拟显示与3C45(-119.676kcal/mol)的相互作用最高,其次是2Q5S(-118.398kcal/mol),1XU7(-117.341kcal/mol),3K35(-114.267kcal/mol)。研究发现,赤霉素比三种临床使用的抗糖尿病化合物更好,二甲双胍,瑞格列奈和西格列汀。Further,通过分析与相关氨基酸的相互作用,建立了红蛋白与糖尿病相关靶蛋白之间的分子相互作用。使用admetSAR软件的红藻素的计算机药代动力学和毒性谱预测红藻素是非致癌和非诱变的。使用摩尔软件遵循Lipinski的5条规则计算药物的可能性。发现该化合物符合Lipinksi规则,仅违反一个过滤器标准。研究表明,红藻素可能是一种潜在的抗糖尿病药物。
    Diabetes mellitus is a multifactorial disorder characterized by a chronic elevation in blood glucose levels. Currently, antidiabetic drugs are available to counteract the associated pathologies. Their concomitant effects necessitate the investigation for an effective and safe drug aimed to diminish blood glucose levels with fewer side effects. Several researchers are taking new initiatives to explore plant sources as they are known to contain a wide variety of active agents. Hence, the present study was undertaken to study the role of natural products using in silico interaction studies. Erythrin a compound present in lichens was selected as a potential anti-diabetic agent. Molecular docking studies were carried out with 14 target proteins to evaluate its antidiabetic potential. Molecular docking analysis resulted in favourable binding energy of interaction ranging as low as - 119.676 to - 92.9545 kcal/mol for erythrin, Analogue showed the highest interactions with 3C45 (- 119.676 kcal/mol) followed by 2Q5S (- 118.398 kcal/mol), 1XU7 (- 117.341 kcal/mol), 3K35 (- 114.267 kcal/mol). Erythrin was found to fare better than the three clinically used antidiabetic compounds, metformin, repaglinide and sitagliptin. Further, the molecular interactions between erythrin and the diabetes related target proteins was established by analysing the interactions with associated amino acids. In silico pharmacokinetics and toxicity profile of erythrin using admetSAR software predicted erythrin as non-carcinogenic and non-mutagenic. The drug-likeliness was calculated using molsoft software respecting Lipinski\'s rule of five. The compound was found to comply with Lipinksi rules violating only one filter criterion. The study suggested that erythrin could be a potential anti-diabetic agent.
    导出

    更多引用

    收藏

    翻译标题摘要

    我要上传

       PDF(Sci-hub)

       PDF(Pubmed)

  • 文章类型: Journal Article
    Extracellular matrix is a dynamic meshwork of macromolecules that plays an important role in biological processes such as tissue remodeling and various developmental processes. Collagen is the chief component of ECM. Upon hydrolysis, it forms an irreversible left-handed helical structure which is further hydrolyzed by a specialized group of MMP family i.e. Gelatinases (MMP2 and MMP9). Present study was carried to figure out deleterious SNPs associated with MMP9 gene. Our results showed that two nsSNP (rs8125581 and rs41529445) that are present in catalytic domain are highly conserved and affect the protein structure and function.7 SNPs located in UTRs were found to alter miRNA seed region 13 SNPs of splice site were predicted to affect splice signals thereby affecting the post translational expression of MMP9. Most of the SNPs are still uncharacterized thereby present study provides a direction that can help to validate the relation between the altered expressions and functions of MMP9 protein in terms of disease susceptibility.
    导出

    更多引用

    收藏

    翻译标题摘要

    我要上传

    求助全文

  • 文章类型: Journal Article
    To investigate the role of Peroxidase and its physiological significance under Karnal Bunt (KB) were determined in resistant (HD-29) and susceptible genotype (WH-542) of wheat during different developmental stages. The enzymes were expressed constitutively in both the susceptible and resistant genotype. In gel assay and differential expression analysis of POD was significantly higher (p >0.05) in Sv and S2, than the S1 and S3 stages. in silico analysis of Peroxidase for eg. physico-chemical properties, secondary structural features and phylogenetic classification for comparative analysis. Motif and Domain analysis of Peroxidase by MEME, to be important for the biological functions, and studies of evolution. Our results clearly indicate that the enhanced expression of POD at the WS2 stage, which reinforces its role in stage dependent immunity against Karnal bunt and role of POD metabolism provides genotype and stage dependant structural barrier resistance in wheat against KB.
    导出

    更多引用

    收藏

    翻译标题摘要

    我要上传

    求助全文

公众号