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Detection of Brain Tumor Employing Residual Network-based Optimized Deep Learning 利用基于残差网络的优化深度学习检测脑肿瘤
IF 1.5 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2024-08-06 DOI: 10.2174/1573409920666230816090626
Saransh Rohilla, Shruti Jain

Background: Diagnosis and treatment planning play a very vital role in improving the survival of oncological patients. However, there is high variability in the shape, size, and structure of the tumor, making automatic segmentation difficult. The automatic and accurate detection and segmentation methods for Brain tumors are proposed in this paper.

Methods: A modified ResNet50 model was used for tumor detection, and a ResUNetmodel-based convolutional neural network for segmentation is proposed in this paper. The detection and segmentation were performed on the same dataset consisting of pre-contrast, FLAIR, and postcontrast MRI images of 110 patients collected from the Cancer Imaging Archive. Due to the use of Residual Networks, the authors observed improvement in evaluation parameters, such as accuracy for tumor detection and dice similarity coefficient for tumor segmentation.

Results: The accuracy of tumor detection and Dice Similarity Coefficient achieved by the segmentation model were 96.77% and 0.893, respectively, for the TCIA dataset. The results were compared based on manual segmentation and existing segmentation techniques. The tumor mask was also individually compared to the ground truth using the SSIM value. The proposed detection and segmentation models were validated on BraTS2015 and BraTS2017 datasets, and the results were consensus.

Conclusion: The use of residual networks in both the detection and the segmentation model resulted in improved accuracy and DSC score. DSC score was increased by 5.9% compared to the UNet model, and the accuracy of the model was increased from 92% to 96.77% for the test set.

背景:诊断和治疗计划对提高肿瘤患者的生存率起着至关重要的作用。然而,肿瘤的形状、大小和结构变化很大,给自动分割带来了困难。本文提出了自动、准确的脑肿瘤检测和分割方法:方法:本文使用改进的 ResNet50 模型进行肿瘤检测,并提出了基于 ResUNetmodel 的卷积神经网络进行分割。检测和分割是在同一数据集上进行的,该数据集由癌症影像档案馆收集的 110 名患者的对比前、FLAIR 和对比后 MRI 图像组成。由于使用了残差网络,作者观察到了评估参数的改进,如肿瘤检测的准确性和肿瘤分割的骰子相似系数:结果:在 TCIA 数据集上,分割模型的肿瘤检测准确率和骰子相似系数分别为 96.77% 和 0.893。在人工分割和现有分割技术的基础上对结果进行了比较。此外,还使用 SSIM 值将肿瘤掩膜与地面实况进行了单独比较。在 BraTS2015 和 BraTS2017 数据集上对所提出的检测和分割模型进行了验证,结果达成了共识:结论:在检测和分割模型中使用残差网络提高了准确性和 DSC 分数。与 UNet 模型相比,DSC 分数提高了 5.9%,模型在测试集上的准确率从 92% 提高到 96.77%。
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引用次数: 0
Computer-Aided Drug Discovery Approaches in the Identification of Anticancer Drugs from Natural Products: A Review 从天然产品中鉴定抗癌药物的计算机辅助药物发现方法:综述
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2024-05-03 DOI: 10.2174/0115734099283410240406064042
M. Gnana Ruba Priya, Jessica Manisha, Lal Prasanth M.L, Seema S. Rathore, Raja Solomon Viswas
: Natural plant sources are essential in the development of several anticancer drugs, such as vincristine, vinblastine, vinorelbine, docetaxel, paclitaxel, camptothecin, etoposide, and teniposide. However, various chemotherapies fail due to adverse reactions, drug resistance, and target specificity. Researchers are now focusing on developing drugs that use natural compounds to overcome these issues. These drugs can affect multiple targets, have reduced adverse effects, and are effective against several cancer types. Developing a new drug is a highly complex, expensive, and time-consuming process. Traditional drug discovery methods take up to 15 years for a new medicine to enter the market and cost more than one billion USD. However, recent Computer Aided Drug Discovery (CADD) advancements have changed this situation. This paper aims to comprehensively describe the different CADD approaches in identifying anticancer drugs from natural products. Data from various sources, including Science Direct, Elsevier, NCBI, and Web of Science, are used in this review. In-silico techniques and optimization algorithms can provide versatile solutions in drug discovery ventures. The structure-based drug design technique is widely used to understand chemical constituents' molecular-level interactions and identify hit leads. This review will discuss the concept of CADD, in-silico tools, virtual screening in drug discovery, and the concept of natural products as anticancer therapies. Representative examples of molecules identified will also be provided.
:天然植物资源对开发多种抗癌药物至关重要,如长春新碱、长春碱、长春瑞滨、多西他赛、紫杉醇、喜树碱、依托泊苷和替尼泊苷。然而,由于不良反应、耐药性和靶向特异性等原因,各种化疗均告失败。目前,研究人员正致力于开发利用天然化合物来克服这些问题的药物。这些药物可以影响多个靶点,减少不良反应,并对多种癌症类型有效。研发新药是一个非常复杂、昂贵和耗时的过程。传统的药物发现方法需要长达 15 年的时间才能让一种新药进入市场,成本超过 10 亿美元。然而,近年来计算机辅助药物发现(CADD)的发展改变了这一局面。本文旨在全面介绍从天然产物中发现抗癌药物的不同 CADD 方法。本综述使用了来自不同来源的数据,包括 Science Direct、Elsevier、NCBI 和 Web of Science。硅学技术和优化算法可以为药物研发提供多种解决方案。基于结构的药物设计技术被广泛应用于了解化学成分的分子级相互作用和确定新药线索。这篇综述将讨论 CADD 的概念、水下工具、药物发现中的虚拟筛选以及天然产品作为抗癌疗法的概念。此外,还将提供已确定分子的代表性实例。
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引用次数: 0
Study on the Mechanism of Competing Endogenous Network of 'Scutellaria barbata D.Don-Houttuynia cordata- Radix Scutellariae' in the Treatment of NSCLC based on Bioinformatics, Molecular Dynamics and Experimental Verification 基于生物信息学、分子动力学和实验验证的黄芩内源网络竞争治疗 NSCLC 的机制研究
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2024-04-30 DOI: 10.2174/0115734099288771240419110716
Lulu Wu, Bo Xu, Yu Qi, Changjin Yuan
Introduction: Non-small cell lung cancer (NSCLC) is the most common type of lung cancer. Traditional Chinese medicine, known for its multi-target and multi-pathway characteristics, offers a potential treatment approach for NSCLC. Objective: This study aimed to explore the mechanism of the competitive endogenous network of 'Scutellaria barbata D.Don-Houttuynia cordata-Radix Scutellariae' in treating NSCLC through bioinformatics analysis and in vitro experiments. objective: This study aimed to explore the mechanism of the competitive endogenous network of 'Scutellaria barbata D.Don-Houttuynia cordata-Radix Scutellariae' in treating NSCLC through bioinformatics analysis and in vitro experiments. Materials and Methods: Various databases and ceRNA networks were utilized to collect and screen components and target genes, molecular docking and molecular dynamics simulations to determine the binding ability of ligand-receptor complexes. In vitro experiments were conducted to validate the effects of active ingredients of 'Scutellaria barbata D.Don-Houttuynia cordata- Radix Scutellariae' on non-small cell lung cancer cell line A549. method: Various databases and ceRNA networks were utilized to collect and screen components and target genes, molecular docking and molecular dynamics simulations to determine the binding ability of ligand-receptor complexes. In vitro experiments were conducted to validate the effects of active ingredients of 'Scutellaria barbata D.Don-Houttuynia cordata-Radix Scutellariae' on non-small cell lung cancer cell line A549. Results: The key target proteins CCL2, EDN1, MMP9, PPARG, and SPP1 were docked well with their corresponding TCM ligands. Among the ligand-receptor complexes, MMP9-Luteolin and MMP9-Quercetin demonstrated the weaking binding force, while the SPP1-Quercetin complex, associated with NSCLC prognosis, exhibited stable structure formation through hydrogen bond interaction during MD simulation. In vitro experiments confirmed the inhibitory effect of Quercetin on SPP1 expression, as well as the proliferation and migration of A549 cells. Conclusion: The findings suggest that 'Scutellaria barbata D.Don-Houttuynia cordata-Radix Scutellariae' may potentially treat lung cancer by suppressing the expression of SPP1. This study provides valuable insights and novel research directions for understanding the mechanism of traditional Chinese medicine in combating lung cancer.
简介:非小细胞肺癌(NSCLC)是最常见的肺癌类型:非小细胞肺癌(NSCLC)是最常见的肺癌类型。中医药具有多靶点、多途径的特点,为治疗非小细胞肺癌提供了一种潜在的方法。研究目的本研究旨在通过生物信息学分析和体外实验,探索'黄芩-D.Don-蕺菜-Radix Scutellariae'竞争性内源性网络治疗 NSCLC 的机制:本研究旨在通过生物信息学分析和体外实验,探讨 "黄芩 D.Don-Houttuynia cordata-Radix Scutellariae "治疗 NSCLC 的竞争性内源性网络机制。材料与方法:利用各种数据库和 ceRNA 网络收集和筛选成分和靶基因,通过分子对接和分子动力学模拟确定配体-受体复合物的结合能力。体外实验验证了 "黄芩 "有效成分对非小细胞肺癌细胞株 A549 的影响:利用各种数据库和 ceRNA 网络收集和筛选成分和靶基因,通过分子对接和分子动力学模拟确定配体-受体复合物的结合能力。体外实验验证了 "Scutellaria barbata D.Don-Houttuynia cordata-Radix Scutellariae "有效成分对非小细胞肺癌细胞系 A549 的影响。结果主要靶蛋白CCL2、EDN1、MMP9、PPARG和SPP1与相应的中药配体对接良好。在配体-受体复合物中,MMP9-木犀草素和MMP9-槲皮素的结合力较弱,而与NSCLC预后相关的SPP1-槲皮素复合物在MD模拟过程中通过氢键相互作用形成了稳定的结构。体外实验证实了槲皮素对 SPP1 表达的抑制作用,以及对 A549 细胞增殖和迁移的抑制作用。结论研究结果表明,"Scutellaria barbata D.Don-Houttuynia cordata-Radix Scutellariae "可通过抑制 SPP1 的表达来治疗肺癌。本研究为了解中药防治肺癌的机制提供了有价值的见解和新的研究方向。
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引用次数: 0
An Enhanced Computational Approach Using Multi-kernel Positive Unlabeled Learning for Predicting Drug-target Interactions 利用多核正向无标记学习预测药物靶标相互作用的增强型计算方法
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2024-04-30 DOI: 10.2174/0115734099288803240416103536
Mohammad Reza Keyvanpour, Soheila Mehrmolaei, Faraneh Haddadi
Background:: In recent years, analyzing complex biological networks to predict future links in such networks has attracted the attention of many medical and computer science researchers. The discovery of new drugs is one of the application cases for predicting future connections in biological networks. The operation of drug-target interactions prediction (DTIP) can be considered a fundamental step in identifying potential interactions between drug and target to identify new drugs. Objective:: The previous studies reveal that predictions are made based on known interactions using computational methods to solve the cost problem and avoid blind study of all interactions. But, there seem to be challenges such as the lack of confirmed negative samples and the low accuracy in some computational methods. Thus, we have proposed an efficient and hybrid approach called MKPUL-BLM to manage some of the aforementioned challenges for predicting drug-target interactions. Methods:: The MKPUL-BLM combins multi-kernel and positive unlabeled learning (PUL) approaches. Our method uses more information to increase accuracy, in addition to minimizing small similarities using network information. Also, potential negative samples are produced using a PUL approach because of lacking negative laboratory samples. Finally, labels are expanded via a semi-supervised. Results:: Our method improved to 0.98 and 0.94 in the old interactions set for the ROCAUC and AUPR criteria, respectively. Also, this method enhanced ROCAUC and AUPR criteria by 0.89 and 0.77 for the new interactions set. Conclusion:: The MKPUL-BLM can be considered an efficient alternative to achieve more reliable predictions in the field of DTIP.
背景近年来,通过分析复杂的生物网络来预测这些网络中未来的联系吸引了许多医学和计算机科学研究人员的关注。发现新药是预测生物网络未来联系的应用案例之一。药物与靶点相互作用预测(DTIP)的操作可视为识别药物与靶点之间潜在相互作用以发现新药的基本步骤。目标:.....:以往的研究表明,预测是基于已知的相互作用,利用计算方法来解决成本问题,并避免对所有相互作用进行盲目研究。但是,目前似乎还存在一些挑战,例如缺乏确证的阴性样本,以及一些计算方法的准确性较低。因此,我们提出了一种名为 MKPUL-BLM 的高效混合方法来应对上述预测药物-靶点相互作用的挑战。方法MKPUL-BLM 结合了多核和正向无标记学习(PUL)方法。除了利用网络信息最小化微小相似性外,我们的方法还利用更多信息来提高准确性。此外,由于缺乏实验室负样本,因此使用 PUL 方法会产生潜在的负样本。最后,通过半监督方式扩展标签。结果我们的方法将旧交互集的 ROCAUC 和 AUPR 标准分别提高到 0.98 和 0.94。此外,在新的交互集上,该方法的 ROCAUC 和 AUPR 标准分别提高了 0.89 和 0.77。结论在 DTIP 领域,MKPUL-BLM 可被视为实现更可靠预测的有效替代方法。
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引用次数: 0
Designing a Novel di-epitope Diphtheria Vaccine: A Rational Structural Immunoinformatics Approach 设计新型二表位白喉疫苗:合理的结构免疫信息学方法
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2024-04-27 DOI: 10.2174/0115734099294259240411073449
Mahsa Shadmani, Atefeh Ghasemnejad, Samira Bazmara, Kamran Pooshang Bagheri
Background: The design of an epitope-based vaccine against diphtheria toxin (DT) originated from the idea that many strong binder epitopes may be structurally located in the depth of DT. Subsequently, many ineffective antibodies may be produced by the presentation of those epitopes to T and B lymphocytes. The other critical issue is the population coverage of a vaccine that has been neglected in traditional vaccines. Objective: Given the issues above, our study aimed to design a peptide-based diphtheria vaccine, considering the issues of unwanted epitopes and population coverage. Methods: The frequencies of pre-determined HLA alleles were listed. A country in which almost all HLA alleles had been determined in almost all geographical distribution was selected. The epitopes within the sequence of diphtheria toxin were predicted by the NetMHCIIPan server based on the selected HLA alleles. Strong binder epitopes on the surface of diphtheria toxin were selected by structural epitope mapping. The epitopes, which cover almost all the human population for each of the HLA alleles in the candidate country, were then selected as epitopebased vaccines. Results: At first, 793 strong binder epitopes were predicted, of which 82 were surface epitopes. Nine surface epitopes whose amino acids had extruding side chains were selected. Finally, 2 epitopes had the most population coverage and were suggested as a di-epitope diphtheria vaccine. The population coverage of the di-epitope vaccine in France and the world was 100 and 99.24 %, respectively. HLA-DP had the most roles in epitope presentation.
背景:设计基于表位的白喉毒素(DT)疫苗源于这样一种想法,即许多强粘合剂表位可能在结构上位于 DT 的深处。随后,这些表位可能会在 T 淋巴细胞和 B 淋巴细胞中产生许多无效抗体。另一个关键问题是疫苗的人群覆盖率,而这正是传统疫苗所忽视的。研究目的鉴于上述问题,我们的研究旨在设计一种基于多肽的白喉疫苗,同时考虑到不需要的表位和人群覆盖问题。研究方法列出预先确定的 HLA 等位基因的频率。我们选择了一个几乎所有 HLA 等位基因都已确定的国家。根据所选的 HLA 等位基因,NetMHCIIPan 服务器对白喉毒素序列中的表位进行了预测。通过结构表位图谱筛选出白喉毒素表面的强粘合剂表位。这些表位几乎覆盖了候选国中每个 HLA 等位基因的所有人群,因此被选为表位疫苗。结果:首先预测出了 793 个强粘合剂表位,其中 82 个是表面表位。筛选出 9 个氨基酸具有挤出侧链的表面表位。最后,2个表位的人群覆盖率最高,被推荐作为二表位白喉疫苗。二表位疫苗在法国和全球的人群覆盖率分别为 100% 和 99.24%。HLA-DP在表位呈现中的作用最大。
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引用次数: 0
Hedyotis diffusa Willd and Astragalus membranaceus May Exert Anti-colon Cancer Effects by Affecting AKTI Expression, as Determined by Network Pharmacology and Molecular Docking 通过网络药理学和分子对接确定黄花菜和黄芪可通过影响 AKTI 表达发挥抗结肠癌作用
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2024-04-19 DOI: 10.2174/0115734099282388240405055003
Jianwei Ren, Zhiting Mo, Zhengsha Huang, Shangze Li
Background: Network pharmacology is a novel approach that uses bioinformatics to predict multitarget drugs and ingredient-target interactions in various diseases. A thorough search of previously published studies revealed that Hedyotis diffusa Willd (HDW) and Astragalus membranaceus (AM) possess anticancer activity. Colon cancer (CC) is one of the most common malignant tumors of the digestive tract and occurs in the colon. Herein, we explored the effect of two drugs in the treatment of CC. Objective: The present study aimed to predict and verify the effect of these two drugs in the treatment of CC. Methods: To explore the molecular mechanisms of the “HDW-AM” drug in the treatment of CC, we analyzed its principal efficiency in terms of ingredients, target spots, and pathways via network pharmacology, molecular docking, and experimental verification. The ingredients and their gene target sites were searched and screened through the TCMSP platform according to specific filtering conditions. Subsequently, components corresponding to the gene targets were chosen to construct the drug component-target network. The GEO (Gene Expression Omnibus) dataset was used to collect and screen for gene chips under CC and normal conditions, obtain differential genes, and construct a volcano map. The intersection genes between drug and disease targets were screened, the “.tsv” file was downloaded from the STRING platform and imported into Cytoscape 3.8.0 for visualization, a protein-protein interaction (PPI) network was constructed, the core targets were identified, and the common components with core targets were docked through Autodock Tools-1.5.6. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were carried out through the Metascape platform to determine the major pathways. The CCK-8 (Cell Counting Kit-8) assay verified the effect of AKT1 on cell proliferation after treatment with quercetin. Results: After the screening, 3658 DEGs (1841 downregulated and 1817 upregulated) were obtained from the GSE75970 gene chip; 21 active components and 220 targets were identified from the drugs. Subsequently, ten core genes (including AKT1, P53, and CASP3) and six major components were screened. GO functional analysis and KEGG analysis revealed that “HDWAM” regulates cell migration and motility through the combination of a transcription regulator complex, membrane rafts, vesicle lumen, and protein kinases via the MAPK, PI3K-Akt, and IL17 signaling pathways. The molecular docking results suggested that quercetin binds to AKT1, TP53, TNF, and CASP3. HDW-AM may exert a therapeutic effect on CC by modulating AKT1, TP53, TNF, and CASP3 and through signaling pathways. A CCK-8 cytotoxicity assay verified that quercetin affects cell viability through AKT1. Conclusions: The current study provides a theoretical basis for an in-depth investigation into the molecular mechanism of the “HDW-AM” drug in CC treatment via network pharmacology, molecular
背景:网络药理学是一种利用生物信息学预测各种疾病中多靶点药物和成分-靶点相互作用的新方法。对以前发表的研究进行彻底搜索后发现,白花蛇舌草(Hedyotis diffusa Willd,HDW)和黄芪(Astragalus membranaceus,AM)具有抗癌活性。结肠癌(CC)是消化道最常见的恶性肿瘤之一,好发于结肠。在此,我们探讨了两种药物治疗结肠癌的效果。研究目的本研究旨在预测和验证这两种药物治疗 CC 的效果。方法为了探索 "HDW-AM "药物治疗CC的分子机制,我们通过网络药理学、分子对接和实验验证,从成分、靶点和途径等方面分析了其主要功效。根据特定的筛选条件,通过 TCMSP 平台对药物成分及其基因靶点进行了检索和筛选。随后,选择与基因靶点相对应的成分构建药物成分-靶点网络。利用GEO(Gene Expression Omnibus)数据集收集和筛选CC和正常条件下的基因芯片,获得差异基因并构建火山图。筛选出药物靶点与疾病靶点之间的交叉基因,从STRING平台下载".tsv "文件并导入Cytoscape 3.8.0进行可视化,构建蛋白-蛋白相互作用(PPI)网络,确定核心靶点,并通过Autodock Tools-1.5.6对接与核心靶点的共同成分。通过 Metascape 平台进行了基因本体(GO)分析和京都基因组百科全书(KEGG)分析,以确定主要通路。CCK-8(细胞计数试剂盒-8)检测验证了槲皮素处理后 AKT1 对细胞增殖的影响。结果经过筛选,从 GSE75970 基因芯片中获得了 3658 个 DEGs(1841 个下调,1817 个上调);从药物中确定了 21 个活性成分和 220 个靶点。随后,筛选出 10 个核心基因(包括 AKT1、P53 和 CASP3)和 6 个主要成分。GO功能分析和KEGG分析表明,"HDWAM "通过转录调控因子复合物、膜筏、囊泡腔和蛋白激酶的结合,通过MAPK、PI3K-Akt和IL17信号通路调控细胞迁移和运动。分子对接结果表明,槲皮素能与 AKT1、TP53、TNF 和 CASP3 结合。HDW-AM可能通过调节AKT1、TP53、TNF和CASP3以及信号通路对CC产生治疗作用。CCK-8 细胞毒性试验证实,槲皮素通过 AKT1 影响细胞活力。结论:本研究通过网络药理学、分子对接和实验验证,为深入研究 "HDW-AM "药物治疗 CC 的分子机制提供了理论依据。
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引用次数: 0
Comprehensive Analysis and Experimental Validation of FOXD2 as a Novel Potential Prognostic Biomarker Associated with Immune Infiltration in Head and Neck Squamous Cell Carcinoma 将 FOXD2 作为与头颈部鳞状细胞癌免疫渗透相关的新型潜在预后生物标记物的综合分析和实验验证
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2024-04-17 DOI: 10.2174/0115734099302492240405065505
Hanping He, Feng Yuan, Ying Li, Guoliang Pi, Hongwei Shi, Yanping Li, Guang Han
Background: The role of Forkhead Box D2 (FOXD2) in head and neck squamous cell carcinoma (HNSC) has never been studied. Object: Our object was to explore the role of FOXD2 in HNSC. Methods: Clinical data for patients with HNSC was obtained from TCGA. Our study examined the atypical expression of FOXD2 in both HNSC and pan-cancer, along with its diagnostic and prognostic implications, as well as the association between FOXD2 expression and clinical characteristics, immune infiltration, immune checkpoint genes, and MSI. Gene set enrichment analysis (GESA) was used to investigate the potential regulation network of FOXD2 in HNSC. We analyze the genomic alterations of FOXD2 in HNSC. GSE13397 and qRT-PCR were used for the validation of FOXD2 expression. Results: FOXD2 was aberrantly expressed in 24 tumors. FOXD2 was significantly up-regulated in HNSC compared to normal head and neck tissue (p < 0.001). High FOXD2 expression was associated with the histologic grade of the patient with HNSC (p < 0.001), lymphovascular infiltration (p = 0.002) and lymph node neck dissection (p = 0.002). In HNSC, an autonomous correlation between FOXD2 expression and OS was observed (HR: 1.36; 95% CI: 1.04-1.78; p = 0.026). FOXD2 was associated with the neuronal system, neuroactive ligand-receptor interaction, and retinoblastoma gene in cancer. FOXD2 was associated with immune infiltration, immune checkpoints, and MSI. The somatic mutation rate of FOXD2 in HNSC was 0.2%. FOXD2 was significantly up-regulated in HNSC cell lines. Conclusion: Our findings suggest that FOXD2 has the potential to serve as a prognostic biomarker and immunotherapeutic target for individuals with HNSC.
背景:从未研究过叉头盒 D2(FOXD2)在头颈部鳞状细胞癌(HNSC)中的作用。研究目的我们的目的是探索 FOXD2 在 HNSC 中的作用。研究方法从 TCGA 获取 HNSC 患者的临床数据。我们的研究考察了FOXD2在HNSC和泛癌症中的非典型表达及其对诊断和预后的影响,以及FOXD2表达与临床特征、免疫浸润、免疫检查点基因和MSI之间的关联。基因组富集分析(GESA)用于研究 FOXD2 在 HNSC 中的潜在调控网络。我们分析了FOXD2在HNSC中的基因组改变。GSE13397 和 qRT-PCR 被用于验证 FOXD2 的表达。结果24 例肿瘤中 FOXD2 存在异常表达。与正常头颈部组织相比,FOXD2在HNSC中明显上调(p < 0.001)。FOXD2 的高表达与 HNSC 患者的组织学分级(p < 0.001)、淋巴管浸润(p = 0.002)和颈部淋巴结清扫(p = 0.002)有关。在 HNSC 中,观察到 FOXD2 表达与 OS 之间存在自主相关性(HR:1.36;95% CI:1.04-1.78;p = 0.026)。FOXD2与癌症中的神经元系统、神经活性配体-受体相互作用和视网膜母细胞瘤基因有关。FOXD2 与免疫浸润、免疫检查点和 MSI 有关。FOXD2在HNSC中的体细胞突变率为0.2%。FOXD2 在 HNSC 细胞系中明显上调。结论我们的研究结果表明,FOXD2 有可能成为 HNSC 患者的预后生物标志物和免疫治疗靶点。
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引用次数: 0
Mechanism of Shenfu Injection in Treating Ischemic Stroke Elucidated using Network Pharmacology and Experimental Validation 利用网络药理学和实验验证阐明神浮注射液治疗缺血性中风的机制
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2024-04-17 DOI: 10.2174/0115734099292513240404091734
Xuecheng Yu, Kun Shi, Bin Wu, Zengxiang Gao, Jiyuan Tu, Yan Cao, Linlin Chen, Guosheng Cao
Background: Shenfu injection was derived from the classical Chinese medicine formula ‘Shenfu decoction’, which was widely used in the treatment of cardiovascular and cerebrovascular diseases in clinical practice. background: Shenfu injection is derived from the classical Chinese medicine formula ‘shenfu decoction’, which is widely used in the treatment of cardiovascular and cerebrovascular diseases in clinical practice. Objectives: Predict the main active ingredients, core targets, and related signaling pathways of Shenfu injection in the treatment of ischemic stroke. objective: Predicting the main active ingredients, core targets, and related signaling pathways of shenfu injection in the treatment of ischemic stroke. Methods: Databases were used to collect the active ingredients and target information of Shenfu injection; GO and KEGG pathway enrichment analyses were performed using the David database. The effects of Shenfu injection on core targets were verified using molecular docking and in vivo experiments. method: Databases were used to collect the active ingredients and target information of shenfu injection; GO and KEGG pathway enrichment analysis were performed using David database.The effects of shenfu injection on core targets were verified using molecular docking and in vivo experiments. Results: The predicted results identified 44 active ingredients and 635 targets in Shenfu injection, among which 418 targets, including TNF, IL-6, MAPK1, and MAPK14, were potential targets for the treatment of ischemic stroke. Molecular docking revealed that the active ingredients had good binding to IL-6, MAPK1, and MAPK14. In vivo experiments demonstrated that Shenfu injection significantly improved the pathological damage due to ischemic stroke, promoted the expression of tight junction proteins, and inhibited MMP-2 and MMP-9 expressions, thereby reducing BBB permeability. Animal experiments revealed that Shenfu injection could inhibit p38、JNK and ERK phosphorylation. Conclusions: Mechanism of Shenfu injection in treating ischemic stroke may be via inhibition of the inflammatory factors levels and protecting the BBB, thereby warranting subsequent studies and highlighting its potential as a reference for new drug development.
背景介绍神府注射液源于中医经典名方 "神府煎",在临床上被广泛应用于心脑血管疾病的治疗。 背景:神府注射液源于中医经典名方 "神府煎",在临床上被广泛应用于心脑血管疾病的治疗:神衰注射液源自中医经典名方 "神衰汤",临床上广泛用于心脑血管疾病的治疗。研究目的预测参附注射液治疗缺血性中风的主要有效成分、核心靶点及相关信号通路:预测神扶注射液治疗缺血性脑卒中的主要活性成分、核心靶点及相关信号通路。方法利用数据库收集神浮注射液的有效成分和靶点信息;利用David数据库进行GO和KEGG通路富集分析。通过分子对接和体内实验验证神府注射液对核心靶点的作用:利用David数据库收集神府注射液的有效成分和靶点信息,进行GO和KEGG通路富集分析,利用分子对接和体内实验验证神府注射液对核心靶点的作用。结果预测结果表明,神府注射液中含有44种有效成分和635个靶点,其中包括TNF、IL-6、MAPK1和MAPK14在内的418个靶点是治疗缺血性脑卒中的潜在靶点。分子对接显示,其活性成分与IL-6、MAPK1和MAPK14具有良好的结合力。体内实验表明,神衰注射液能明显改善缺血性脑卒中的病理损伤,促进紧密连接蛋白的表达,抑制MMP-2和MMP-9的表达,从而降低BBB的通透性。动物实验表明,神甫注射液可抑制p38、JNK和ERK磷酸化。结论神浮注射液治疗缺血性脑卒中的机制可能是通过抑制炎症因子水平和保护BBB,因此值得后续研究,并突出了其作为新药开发参考的潜力。
{"title":"Mechanism of Shenfu Injection in Treating Ischemic Stroke Elucidated using Network Pharmacology and Experimental Validation","authors":"Xuecheng Yu, Kun Shi, Bin Wu, Zengxiang Gao, Jiyuan Tu, Yan Cao, Linlin Chen, Guosheng Cao","doi":"10.2174/0115734099292513240404091734","DOIUrl":"https://doi.org/10.2174/0115734099292513240404091734","url":null,"abstract":"Background: Shenfu injection was derived from the classical Chinese medicine formula ‘Shenfu decoction’, which was widely used in the treatment of cardiovascular and cerebrovascular diseases in clinical practice. background: Shenfu injection is derived from the classical Chinese medicine formula ‘shenfu decoction’, which is widely used in the treatment of cardiovascular and cerebrovascular diseases in clinical practice. Objectives: Predict the main active ingredients, core targets, and related signaling pathways of Shenfu injection in the treatment of ischemic stroke. objective: Predicting the main active ingredients, core targets, and related signaling pathways of shenfu injection in the treatment of ischemic stroke. Methods: Databases were used to collect the active ingredients and target information of Shenfu injection; GO and KEGG pathway enrichment analyses were performed using the David database. The effects of Shenfu injection on core targets were verified using molecular docking and in vivo experiments. method: Databases were used to collect the active ingredients and target information of shenfu injection; GO and KEGG pathway enrichment analysis were performed using David database.The effects of shenfu injection on core targets were verified using molecular docking and in vivo experiments. Results: The predicted results identified 44 active ingredients and 635 targets in Shenfu injection, among which 418 targets, including TNF, IL-6, MAPK1, and MAPK14, were potential targets for the treatment of ischemic stroke. Molecular docking revealed that the active ingredients had good binding to IL-6, MAPK1, and MAPK14. In vivo experiments demonstrated that Shenfu injection significantly improved the pathological damage due to ischemic stroke, promoted the expression of tight junction proteins, and inhibited MMP-2 and MMP-9 expressions, thereby reducing BBB permeability. Animal experiments revealed that Shenfu injection could inhibit p38、JNK and ERK phosphorylation. Conclusions: Mechanism of Shenfu injection in treating ischemic stroke may be via inhibition of the inflammatory factors levels and protecting the BBB, thereby warranting subsequent studies and highlighting its potential as a reference for new drug development.","PeriodicalId":10886,"journal":{"name":"Current computer-aided drug design","volume":"38 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140614136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Network Pharmacology and Molecular Docking to Explore the Mechanism of Compound Qilian Tablets in Treating Diabetic Retinopathy 通过网络药理学和分子对接探索复方芪连片治疗糖尿病视网膜病变的机制
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2024-04-13 DOI: 10.2174/0115734099298932240308104437
Jiangwei Jia, Bo Liu, Xin Wang, Fenglan Ji, Fuchun Wen, Lianlian Song, Huibo Xu, Tao Ding
Background: Diabetic Retinopathy (DR) is one of the common chronic complications of diabetes mellitus, which has developed into the leading cause of irreversible visual impairment in adults worldwide. The Compound Qilian Tablets (CQLT) were developed in China for the treatment and prevention of DR, but their mechanism of action is still unclear. Objective: In the present study, network pharmacology, molecular docking, and in vivo validation experiments were used to investigate the active components and molecular mechanisms of CQLT against DR. Methods: The active components and targets of CQLT were collected through the TCSMP database, and the targets of DR were obtained from GeneCards, OMIM, and Drugbank databases. We established a protein-protein interaction network using the STRING database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted using the Metascape database. Molecular docking using AutoDock Vina was performed to investigate the interactions between components of CQLT and core targets. Moreover, we selected ZDF rats to establish a DR model for the experimental studies. Results: 39 active components and 448 targets in CQLT were screened, among which 90 targets were shared with DR. KEGG pathway enrichment analysis identified 181 pathways. The molecular docking results demonstrated that the main active components had strong binding ability to the core targets. The results from animal experiments indicate that the mechanism of CQLT against DR is associated with inhibiting the retinal mTOR/HIF-1α/VEGF signaling pathway, alleviating the inflammatory response, suppressing retinal neovascularization, and protecting the function and morphology of the retina. Conclusion: The present study preliminarily explored the mechanism of CQLT in treating DR and demonstrated that CQLT exerts anti-DR effects through multiple components, multiple targets, and multiple pathways. These findings suggest that CQLT shows promise as a potential therapeutic agent for DR and could contribute to developing novel treatments.
背景:糖尿病视网膜病变(DR)是糖尿病常见的慢性并发症之一,已发展成为全球成人不可逆视力损伤的主要原因。中国开发了复方芪连片(CQLT)用于治疗和预防 DR,但其作用机制仍不清楚。研究目的本研究采用网络药理学、分子对接和体内验证实验研究复方芪连片对 DR 的活性成分和分子机制。研究方法通过TCSMP数据库收集CQLT的活性成分和靶点,通过GeneCards、OMIM和Drugbank数据库获得DR的靶点。我们利用 STRING 数据库建立了蛋白质-蛋白质相互作用网络。使用 Metascape 数据库进行了基因本体(GO)和京都基因组百科全书(KEGG)通路富集分析。使用 AutoDock Vina 进行了分子对接,以研究 CQLT 成分与核心靶标之间的相互作用。此外,我们还选择了 ZDF 大鼠建立 DR 模型进行实验研究。结果筛选了 CQLT 中的 39 个活性成分和 448 个靶点,其中 90 个靶点与 DR 共享。KEGG 通路富集分析确定了 181 条通路。分子对接结果表明,主要活性成分与核心靶点有很强的结合能力。动物实验结果表明,CQLT 抗 DR 的机制与抑制视网膜 mTOR/HIF-1α/VEGF 信号通路、减轻炎症反应、抑制视网膜新生血管、保护视网膜功能和形态有关。结论本研究初步探讨了CQLT治疗DR的机制,证明CQLT通过多成分、多靶点、多途径发挥抗DR作用。这些研究结果表明,CQLT有望成为一种潜在的DR治疗药物,并有助于开发新型治疗方法。
{"title":"Network Pharmacology and Molecular Docking to Explore the Mechanism of Compound Qilian Tablets in Treating Diabetic Retinopathy","authors":"Jiangwei Jia, Bo Liu, Xin Wang, Fenglan Ji, Fuchun Wen, Lianlian Song, Huibo Xu, Tao Ding","doi":"10.2174/0115734099298932240308104437","DOIUrl":"https://doi.org/10.2174/0115734099298932240308104437","url":null,"abstract":"Background: Diabetic Retinopathy (DR) is one of the common chronic complications of diabetes mellitus, which has developed into the leading cause of irreversible visual impairment in adults worldwide. The Compound Qilian Tablets (CQLT) were developed in China for the treatment and prevention of DR, but their mechanism of action is still unclear. Objective: In the present study, network pharmacology, molecular docking, and in vivo validation experiments were used to investigate the active components and molecular mechanisms of CQLT against DR. Methods: The active components and targets of CQLT were collected through the TCSMP database, and the targets of DR were obtained from GeneCards, OMIM, and Drugbank databases. We established a protein-protein interaction network using the STRING database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted using the Metascape database. Molecular docking using AutoDock Vina was performed to investigate the interactions between components of CQLT and core targets. Moreover, we selected ZDF rats to establish a DR model for the experimental studies. Results: 39 active components and 448 targets in CQLT were screened, among which 90 targets were shared with DR. KEGG pathway enrichment analysis identified 181 pathways. The molecular docking results demonstrated that the main active components had strong binding ability to the core targets. The results from animal experiments indicate that the mechanism of CQLT against DR is associated with inhibiting the retinal mTOR/HIF-1α/VEGF signaling pathway, alleviating the inflammatory response, suppressing retinal neovascularization, and protecting the function and morphology of the retina. Conclusion: The present study preliminarily explored the mechanism of CQLT in treating DR and demonstrated that CQLT exerts anti-DR effects through multiple components, multiple targets, and multiple pathways. These findings suggest that CQLT shows promise as a potential therapeutic agent for DR and could contribute to developing novel treatments.","PeriodicalId":10886,"journal":{"name":"Current computer-aided drug design","volume":"33 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140580535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Functional Investigation and Two-sample Mendelian Randomization Study of Inguinal Hernia Hub Genes Obtained by Bioinformatics Analysis 通过生物信息学分析获得的腹股沟疝枢纽基因的功能调查和双样本孟德尔随机化研究
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2024-04-09 DOI: 10.2174/0115734099282407240325054745
De Kun Lu, Zheng Chang Guo, Jia Jia zhang, Xin Yu, Zong Yao Zhang
Background: Inguinal hernia in adults is a common and frequent disease in surgery, prone to occur in the elderly or in those with a weak abdominal wall. Despite its prevalence, Molecular mechanisms underlying inguinal hernia formation are unclear. Objective: This study aims to identify potential gene markers for inguinal hernia and available drugs. objective: This study aims to identify potential gene markers for inguinal hernia and available drugs. Methods: Pubmed2Ensembl text mining was used to identify genes related to "inguinal hernia" keywords. The GeneCodis system was used to specify GO biological process terms and KEGG pathways defined in the Kyoto Encyclopedia of Genes and Genomes (KEGG). The STRING tool was used to construct protein-protein interaction networks, which were then visualized using Cytoscape.CytoHubba and Molecular Complex Detection were utilized to analyze the module (MCODE). A GO and KEGG analysis of gene modules was conducted using the DAVID platform database. Hub genes are those that are concentrated in prominent modules. The druggene interaction database was also used to identify potential drugs for inguinal hernia patients based on their interactions between the hub genes. Finally, a Mendelian randomization study was conducted based on genome-wide association studies to determine whether hub genes cause inguinal hernias. Results: The identification of 96 genes associated with inguinal hernia was carried out using text mining techniques. It was constructed using PPI networks with 80 nodes and 476 edges, and the sequence of the genes was performed using CytoHubba. MCODE analysis identified three gene modules. Three modules contain 37 genes clustered as hub candidate genes associated with inguinal hernia patients. The PI3K-Akt, MAPK, AGE-RAGE, and HIF-1 pathways were found to be enriched in signaling pathways. Sixteen of the 37 genes were found to be targetable by 30 existing drugs. The relationship between hub genes and inguinal hernia was examined using Mendelian randomization. The research revealed nine genes that may be connected with inguinal hernia, such as POMC, CD40LG, TFRC, VWF, LOX, IGF2, BRCA1, TNF, and HGF in the plasma. By inverse variance weighting, ALB was associated with an increased risk of inguinal hernia with an OR of 1.203 (OR [95%] = 1,04 [1.012 to 1.089], p = 0.008). Conclusion: We identified potential hub genes for inguinal hernia, predicted potential drugs for inguinal hernia, and reverse-validated potential genes by Mendelian randomization. This may provide further insights into asymptomatic pre-diagnostic methods and contribute to studies to understand the molecular mechanisms of risk genes associated with inguinal hernia.
背景:成人腹股沟疝是外科常见病和多发病,易发生于老年人或腹壁薄弱者。尽管腹股沟疝很常见,但其形成的分子机制尚不清楚。研究目的本研究旨在确定腹股沟疝的潜在基因标记和可用药物:本研究旨在确定腹股沟斜疝的潜在基因标记和可用药物。研究方法使用 Pubmed2Ensembl 文本挖掘技术识别与 "腹股沟疝 "关键词相关的基因。GeneCodis 系统用于指定京都基因组百科全书(KEGG)中定义的 GO 生物过程术语和 KEGG 通路。使用 STRING 工具构建蛋白质-蛋白质相互作用网络,然后使用 Cytoscape.CytoHubba 和 Molecular Complex Detection 对模块(MCODE)进行可视化分析。利用 DAVID 平台数据库对基因模块进行了 GO 和 KEGG 分析。枢纽基因是那些集中在突出模块中的基因。此外,还利用药物基因相互作用数据库,根据枢纽基因之间的相互作用来确定腹股沟疝患者的潜在药物。最后,在全基因组关联研究的基础上进行了孟德尔随机化研究,以确定枢纽基因是否会导致腹股沟疝。研究结果利用文本挖掘技术确定了 96 个与腹股沟疝相关的基因。利用有 80 个节点和 476 条边的 PPI 网络构建了基因序列,并利用 CytoHubba 进行了基因序列分析。MCODE 分析确定了三个基因模块。三个模块包含 37 个基因,这些基因被聚类为与腹股沟疝患者相关的中枢候选基因。发现信号通路中富含 PI3K-Akt、MAPK、AGE-RAGE 和 HIF-1 通路。在这 37 个基因中,有 16 个基因可被 30 种现有药物靶向。研究人员使用孟德尔随机化方法检验了枢纽基因与腹股沟疝之间的关系。研究发现 9 个基因可能与腹股沟疝有关,如血浆中的 POMC、CD40LG、TFRC、VWF、LOX、IGF2、BRCA1、TNF 和 HGF。通过逆方差加权,ALB 与腹股沟疝风险增加有关,OR 值为 1.203(OR [95%] = 1,04 [1.012 至 1.089],P = 0.008)。结论我们发现了腹股沟斜疝的潜在枢纽基因,预测了腹股沟斜疝的潜在药物,并通过孟德尔随机法反向验证了潜在基因。这可能为无症状预诊断方法提供进一步的见解,并有助于研究了解与腹股沟疝相关的风险基因的分子机制。
{"title":"Functional Investigation and Two-sample Mendelian Randomization Study of Inguinal Hernia Hub Genes Obtained by Bioinformatics Analysis","authors":"De Kun Lu, Zheng Chang Guo, Jia Jia zhang, Xin Yu, Zong Yao Zhang","doi":"10.2174/0115734099282407240325054745","DOIUrl":"https://doi.org/10.2174/0115734099282407240325054745","url":null,"abstract":"Background: Inguinal hernia in adults is a common and frequent disease in surgery, prone to occur in the elderly or in those with a weak abdominal wall. Despite its prevalence, Molecular mechanisms underlying inguinal hernia formation are unclear. Objective: This study aims to identify potential gene markers for inguinal hernia and available drugs. objective: This study aims to identify potential gene markers for inguinal hernia and available drugs. Methods: Pubmed2Ensembl text mining was used to identify genes related to \"inguinal hernia\" keywords. The GeneCodis system was used to specify GO biological process terms and KEGG pathways defined in the Kyoto Encyclopedia of Genes and Genomes (KEGG). The STRING tool was used to construct protein-protein interaction networks, which were then visualized using Cytoscape.CytoHubba and Molecular Complex Detection were utilized to analyze the module (MCODE). A GO and KEGG analysis of gene modules was conducted using the DAVID platform database. Hub genes are those that are concentrated in prominent modules. The druggene interaction database was also used to identify potential drugs for inguinal hernia patients based on their interactions between the hub genes. Finally, a Mendelian randomization study was conducted based on genome-wide association studies to determine whether hub genes cause inguinal hernias. Results: The identification of 96 genes associated with inguinal hernia was carried out using text mining techniques. It was constructed using PPI networks with 80 nodes and 476 edges, and the sequence of the genes was performed using CytoHubba. MCODE analysis identified three gene modules. Three modules contain 37 genes clustered as hub candidate genes associated with inguinal hernia patients. The PI3K-Akt, MAPK, AGE-RAGE, and HIF-1 pathways were found to be enriched in signaling pathways. Sixteen of the 37 genes were found to be targetable by 30 existing drugs. The relationship between hub genes and inguinal hernia was examined using Mendelian randomization. The research revealed nine genes that may be connected with inguinal hernia, such as POMC, CD40LG, TFRC, VWF, LOX, IGF2, BRCA1, TNF, and HGF in the plasma. By inverse variance weighting, ALB was associated with an increased risk of inguinal hernia with an OR of 1.203 (OR [95%] = 1,04 [1.012 to 1.089], p = 0.008). Conclusion: We identified potential hub genes for inguinal hernia, predicted potential drugs for inguinal hernia, and reverse-validated potential genes by Mendelian randomization. This may provide further insights into asymptomatic pre-diagnostic methods and contribute to studies to understand the molecular mechanisms of risk genes associated with inguinal hernia.","PeriodicalId":10886,"journal":{"name":"Current computer-aided drug design","volume":"62 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140580453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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Current computer-aided drug design
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