Network pharmacology to decipher the mechanism of Danggui Longhui Wan against chronic myeloid leukemia

Chronic myeloid leukemia(CML)is a hematopoietic myeloproliferative disorder.The Chinese prescription Danggui Longhui Wan(DGLHW)has been utilized in CML treatment,but its underlying mechanisms remain unclear.In this study,we gathered 794 constituents,1249 drug targets,1654 disease genes and 129 intersection genes.GO and KEGG were used to analyze the function of these genes.Compatibility of prescription study showed that monarch drug,minister drug,assistant and guide drug played a synergistic role in the treatment of CML.In addition,we obtained 20 hub genes and 12 key components.Molecular docking indicated that the main compounds and core proteins had good binding ability.The results of this study also showed that DGLHW might play a role in the treatment of CML by affecting MAPK,PI3K/AKT,FoxO and p53 signaling pathways.

Network pharmacology and molecular docking analysis reveal insights into the molecular mechanism of Gualou Qumai Wan in clear cell renal cell carcinoma

Background:To initially clarify the potential therapeutic targets and pharmacological mechanism regarding Gualou Qumai Wan(GQW),a kind of traditional Chinese medicine(TCM),in clear cell renal cell carcinoma(ccRCC)by virtue of the network pharmacology analysis and molecular docking analysis.Methods:The screening of bioactive components and targets of GQW was based on the Traditional Chinese Medicine System Pharmacology(TCMSP)and the UniProt platform served for standardizing their targets.Online Mendelian Inheritance in Man(OMIM),PharmGkb,TTD,DrugBank and GeneCards databases were searched to collect the disease targets of ccRCC.Cytoscape assisted in constructing herb-compound-target(H-C-T)networks.The STRING database was searched for constructing the target protein-protein interaction(PPI)networks,while the R programming language served for analyzing GO functional terms and the KEGG pathways related to potential targets.Analyses of core genes related to survival and tumor microenvironment(TME)were conducted respectively based on the GEPIA2 database and TIMER 2.0 database.Human Protein Atlas(HPA)and The Cancer Genome Atlas(TCGA)helped to obtain core genes’protein expression as well as transcriptome expression level.Autodock Vina software validated the molecular docking regarding GQW components and pivotal targets.Results:The constructed H-C-T networks mainly had 33 compounds and 65 targets.A topological analysis of the PPI network identified that ESR1,AKT1,HIF1A,PTGS2,TP53 and VEGFA serve as core targets in the way GQW affects ccRCC.According to the GO and KEGG pathway enrichment analyses,the effects of GQW are mediated by genes related to hypoxia and oxidative stress as well as the Chemical carcinogenesis-receptor activation and PI3K-Akt signaling pathways.AKT1 shows a close relation to the recruitment of various immune cells and can remarkably affect disease prognosis according to reports.Molecular docking and molecular dynamics simulations showed that diosgenin has higher affinity with core targets.Conclusion:The study makes a comprehensive explanation of the biological activity,potential targets,as well as molecular mechanism regarding GQW against ccRCC,which promisingly assists in revealing the action mechanism of TCM formulae in disease treatment and the respective and scientific basis.

Zuo Gui Wan Promotes Osteogenesis via PI3K/AKT Signaling Pathway:Network Pharmacology Analysis and Experimental Validation

Objective Osteogenesis is vitally important for bone defect repair,and Zuo Gui Wan(ZGW)is a classic prescription in traditional Chinese medicine(TCM)for strengthening bones.However,the specific mechanism by which ZGW regulates osteogenesis is still unclear.The current study is based on a network pharmacology analysis to explore the potential mechanism of ZGW in promoting osteogenesis.Methods A network pharmacology analysis followed by experimental validation was applied to explore the potential mechanisms of ZGW in promoting the osteogenesis of bone marrow mesenchymal stem cells(BMSCs).Results In total,487 no-repeat targets corresponding to the bioactive components of ZGW were screened,and 175 target genes in the intersection of ZGW and osteogenesis were obtained.And 28 core target genes were then obtained from a PPI network analysis.A GO functional enrichment analysis showed that the relevant biological processes mainly involve the cellular response to chemical stress,metal ions,and lipopolysaccharide.Additionally,KEGG pathway enrichment analysis revealed that multiple signaling pathways,including the phosphatidylinositol-3-kinase/protein kinase B(PI3K/AKT)signaling pathway,were associated with ZGW-promoted osteogensis.Further experimental validation showed that ZGW could increase alkaline phosphatase(ALP)activity as well as the mRNA and protein levels of ALP,osteocalcin(OCN),and runt related transcription factor 2(Runx 2).What’s more,Western blot analysis results showed that ZGW significantly increased the protein levels of p-PI3K and p-AKT,and the increases of these protein levels significantly receded after the addition of the PI3K inhibitor LY294002.Finally,the upregulated osteogenic-related indicators were also suppressed by the addition of LY294002.Conclusion ZGW promotes the osteogenesis of BMSCs via PI3K/AKT signaling pathway.

Simiao Wan alleviates obesity-associated insulin resistance via PKCε/IRS-1/PI3K/Akt signaling pathway based on network pharmacology analysis and experimental validation

Background:The purpose of the study was to investigatethe active ingredients and potential biochemicalmechanisms of Simiao Wan(SMW)in obesity-associated insulin resistance.Methods:An integrated network pharmacology method to screen the active compoundsand candidate targets,construct the protein-protein-interaction network,and ingredients-targets-pathways network was constructed for topological analysis to identify core targets and main ingredients.To find the possible signaling pathways,enrichment analysis was performed.Further,a model of insulin resistance in HL-7702 cells was established to verify the impact of SMW and the regulatory processes.Results:An overall of 63 active components and 151 candidate targets were obtained,in which flavonoids were the main ingredients.Enrichment analysis indicated that the PI3K-Akt signaling pathway was the potential pathway regulated by SMW in obesity-associated insulin resistance treatment.The result showed that SMW could significantly ameliorate insulin sensitivity,increase glucose synthesis and glucose utilization and reduce intracellular lipids accumulation in hepatocytes.Also,SMW inhibited diacylglycerols accumulation-induced PKCεactivity and decreased its translocation to the membrane.Conclusion:SMW ameliorated obesity-associated insulin resistance through PKCε/IRS-1/PI3K/Akt signaling axis in hepatocytes,providing a new strategy for metabolic disease treatment.

Discussion on the mechanism of Xiaoyao Wan in the treatment of depression and anxiety based on network pharmacology

In order to clarify the targets of Xiaoyao Wan in the treatment of depression and anxiety,the pharmacological database of traditional Chinese medicine system and the analysis platform(TCMSP)were used to search the chemical components and potential targets of Xiaoyao Wan.The databases of Malacards and Genecards were used to mine the targets related to depression and anxiety.With the help of Cytoscape3.2.1 software,the“Xiaoyao Wan-targets-diseases”network is constructed.The PPI network is constructed through String database.Common targets are enriched by cluster Profiler software package in R language.161 active components of Xiaoyao Wan were screened,and 247 targets related to Xiaoyao Wan were predicted(excluding repetitive targets).The related targets of depression and anxiety were 379,337 respectively.Through the intersection of Venny diagram,24 targets of Xiaoyao Wan,depression and anxiety were obtained.24 key targets were screened out by constructing the interaction network of Xiaoyao Wan,depression and anxiety.Pathway enrichment analysis showed that Xiaoyao Wan mainly acts on key targets involves D(2)dopamine receptor(DRD2),Interleukin-6(IL6),5-hydroxytryptamine receptor 2A(HTR2A),Interleukin-1 beta(IL1B),5-hydroxytryptamine receptor 3A(HTR3A),Sodium-dependent dopamine transporter(SLC6A3),D(1A)dopamine receptor(DRD1),Interleukin-10(IL10),Sodium-dependent noradrenaline transporterin(SLC6A2)and other key targets in the treatment of depression and anxiety,and participates in important pathway processes such as Serotonergic synapse,Dopaminergic synapse,Neuroactive ligand-receptor interaction and regulation of neurotransmitter levels.It is speculated that Xiaoyao Wan plays a role in the treatment of depression and anxiety by affecting neurotransmitters 5-HT and DA,participating in hypothalamic-pituitary-adrenal(HPA)and interfering in the process of inflammation.

Exploring the multicomponent synergy mechanism of Zuogui Wan(左归丸) on postmenopausal osteoporosis by a systems pharmacology strategy

OBJECTIVE: To explore the multi-component synergistic mechanism of Zuogui Wan(左归丸, ZGW) in treating postmenopausal osteoporosis(PMOP). METHODS: The main components and target genes of ZGW were screened via the Traditional Chinese Medicine Systems Pharmacology(TCMSP). In addition, the target gene sets of PMOP were derived from the Gene Cards and Online Mendelian Inheritance in Man databases. The search tool for recurring instances of neighbouring genes(STRING) 11.0 software was used to analyze the interaction among intersecting genes. Cytoscape 3.6.1 software and the Matthews correlation coefficient(MCC) algorithm were used to screen the core genes. Fifty Sprague-Dawley female rats were randomly divided into the sham-operated(Sham) group and the four ovariectomized(OVX) subgroups. Rats subjected to Sham or OVX were administered with the vehicle(OVX, 1 m L water/100 g weight), 17β-estradiol(E2, 50 μg·kg-1·d-1), and lyophilized powder of ZGW at a low dose of 2.3(ZGW-L) and high dose of 4.6(ZGW-H) g·kg-1·d-1 for three months. The bone density and bone strength were assessed using dual-energy X-ray and three-point bending tests, respectively. Furthermore, enzyme-linked immunosorbent assay, Hematoxylin-eosin staining, and western blot analysis were used to determine the potential pharmacological mechanisms of action of ZGW in PMOP. RESULTS: A total of 117 active compounds of ZGW were screened from the TCMSP. Furthermore, 108 intersecting genes of drugs and diseases were identified. Using STRING software and the MCC algorithm, ten core genes, including C-X-C chemokine living 8(CXCL8), C-C chemokine receptor type 2(CCR2), alpha-2a active receptor(ADRA2A), melatonin receptor type 1B(MTNR1B), and amyloid-beta A4 protein(APP), were identified. The anti-osteoporosis regulation network of ZGW was constructed using the Cytoscape software. The animal experiments demonstrated that ZGW groups significantly reduced the serum levels of β-C-terminal telopeptide of type I collagen(β-CTX) and increased serum levels of bone-specific alkaline phosphatase(BALP)(P < 0.05, P < 0.01). The OVX group exhibited a significant decrease in bone mineral density and bone strength compared with the Sham group(P < 0.01). Moreover, treatment with ZGW resulted in increased trabecular thickness, improved arrangement of trabecular structure, and reduced empty bone lacunae. Furthermore, treatment with ZGW significantly increased the protein expression of CXCL8, ADRA2A, and CCR2(P < 0.05, P < 0.01), and significantly decreased the protein expression of Runx2(P < 0.01). Furthermore, the ZGW and E2 groups demonstrated significantly increased BMD(P < 0.05, P < 0.01), improved bone strength(P < 0.05, P < 0.01), reduced expression of CXCL8, ADRA2A, and CCR2, and increased runt-related transcription factor 2 levels in bone tissue(P < 0.05, P < 0.01) compared with the OVX group. However, there were no significant differences in MTNR1B and APP expression among the groups. CONCLUSION: ZGW shows synergistic mechanisms in PMOP through multiple components, targets, and pathways.

Deciphering the mechanism of Liu Wei Di Huang Wan in treating premature ovarian failure:a comprehensive exploration through network pharmacology and molecular docking analysis

Premature ovarian failure(POF)is a prevalent gynecological disorder with significant implications for the physical and mental well-being of affected individuals.Liu Wei Di Huang Wan(LWDHW),a Chinese herbal compound,has demonstrated efficacy in alleviating the effects of POF.However,the underlying mechanism of action of LWDHW remains unclear.This study aimed to elucidate the potential molecular mechanism of LWDHW in treating POF using network pharmacology and molecular docking techniques.The active ingredients of LWDHW were initially screened through the TCMSP platform.At the same time,the relevant target genes associated with POF were identified using databases such as Disgenet,TTD,Drugbank,Gene Cards,OMIM,and Pharm GKB.Data analysis was conducted using the R language,Cytoscape,and STRING to construct and analyze the traditional Chinese medicine(TCM)regulatory network and protein-protein interaction(PPI)network maps.Subsequently,GO and KEGG enrichment analyses were performed using the R language.Finally,molecular docking was carried out between the protein receptors of the core genes and the corresponding small-molecule ligands.The study revealed 49 components and 189 predicted targets(after de-duplication)of LWDHW,along with 4524 targets(after de-duplication)associated with POF.Through comparative analysis,163 potential genes were identified as common targets of LWDHW and POF,participating in biological processes such as response to chemical substances,molecular function regulation,and signaling receptor binding.Key biological pathways implicated included the MAPK signaling pathway,IL-17 signaling pathway,and HIF-1 signaling pathway,among others.Molecular docking results demonstrated a robust binding ability between the core genes of LWDHW and their corresponding ingredients.In conclusion,this comprehensive analysis provided insights into the potential molecular mechanisms of LWDHW in treating POF.The identified common targets and associated pathways contributed to our understanding of how LWDHW exerted its therapeutic effects,paving the way for further research and clinical applications.It is worth noting that future studies with experimental validation and clinical trials are essential to confirm these findings and establish the safety and efficacy of LWDHW in the treatment of POF.

基于网络药理学、分子对接及细胞实验验证探讨二至丸治疗多发性骨髓瘤的作用机制

【目的】基于网络药理学、分子对接及细胞实验验证探讨二至丸治疗多发性骨髓瘤(MM)的潜在作用机制。【方法】应用网络药理学、分子对接筛选药物-疾病-靶标-通路关键指标。培养多发性骨髓瘤细胞株RPMI-8226,给予二至丸干预,采用膜联蛋白V(Annexin V)-异硫氰酸荧光素(FITC)染色法检测细胞凋亡,Transwell实验测定细胞侵袭能力,实时定量聚合酶链反应(qRT-PCR)法检测蛋白激酶B(Akt)、细胞周期蛋白D1(CCND1)、糖原合酶激酶3β(GSK-3β)、c-MycmRNA表达,Western Blot法检测细胞Akt、磷酸化蛋白激酶B(p-Akt)、CCND1、c-Myc、GSK-3β、磷酸化糖原合酶激酶3β(p-GSK-3β)蛋白表达。【结果】获得二至丸14个有效成分。二至丸治疗MM涉及靶点142个,通路富集分析结果显示关键靶点可能主要集中在癌症通路、脂质与动脉粥样硬化等。分子对接结果显示,木樨草素和槲皮素与GSK-3β有较好的结合活性及稳定性。进一步细胞实验验证发现,与空白组比较,二至丸低、中、高剂量组细胞凋亡率显著升高,细胞侵袭数减少,GSK-3β的mRNA和蛋白水平显著升高,CCND1、Akt和c-Myc的mRNA和蛋白水平显著降低,呈剂量依赖性,其中,中、高剂量组差异均有统计学意义(P<0.05或P<0.01)。【结论】二至丸对MM的治疗作用可能是通过木犀草素和槲皮素等关键活性成分,促进GSK-3β表达,并抑制Akt/GSK-3β/CCND1/c-Myc信号通路来实现的。

基于网络药理学和分子对接技术探析缩泉丸治疗膀胱过度活动症的作用机制

目的:通过网络药理学和分子对接技术探析缩泉丸治疗膀胱过度活动症(Overactive Bladder,OAB)的分子机制。方法:通过中药系统药理学数据库与分析平台(TCMSP)获得缩泉丸活性成分,利用Uniprot数据库获取缩泉丸活性成分对应的靶标基因。从OMIM、Gene Cards、Drug Bank数据库中检索得到OAB有关靶点,并取活性成分靶点和OAB相关靶点的交集以得出共同靶点。Cytoscape 3.9.1软件被用来绘制中药-活性成分-靶点网络图以直观显示活性成分与靶点之间的相互作用,并将共同靶点上传到STRING数据库用来挖掘网络中的核心靶点。采用Metascape数据库对共同靶点进行基因本体论(GO)功能富集分析和京都基因与基因组百科全书(KEGG)通路富集分析。最后运用Auto Dock Tools 1.5.7对缩泉丸的核心成分与核心靶点进行分子对接验证。结果:研究发现缩泉丸通过槲皮素、豆甾醇、β-谷甾醇等核心成分,作用于丝氨酸/苏氨酸蛋白激酶1(Akt Serine/Threonine Kinase1,AKT1)、白细胞介素(Interleukin,IL)-6、IL-1B、肿瘤坏死因子(Tumor Necrosis Factor,TNF)等核心靶点,调节缺氧诱导因子-1(Hypoxia Inducible Factor-1,HIF-1)信号通路、钙信号通路、环磷酸鸟苷(Cyclic Guanosine Monophosphate,c GMP)-蛋白激酶G(Protein Kinase G,PKG)信号通路等,并且参与对氮化合物、有机环化合物、蛋白质磷酸化等生物学过程以治疗OAB。分子对接结果表明缩泉丸中的豆甾醇、β-谷甾醇与AKT1、肿瘤蛋白p53(Tumor Protein p53,TP53)、IL-6、TNF等核心靶点均具有较好的结合活性。结论:本研究通过网络药理学和分子对接技术阐释了缩泉丸调节OAB的潜在成分、靶点及通路,为进一步研究缩泉丸治疗OAB的具体机制提供了方向。

基于网络药理学探讨桂枝茯苓丸治疗急性脑梗死的作用机制及体内验证

目的基于网络药理学的研究方法探讨桂枝茯苓丸治疗急性脑梗死的作用机制。方法在中药系统药理数据库及分析平台(TCMSP)数据库中收集桂枝茯苓丸的主要活性成分,设置口服利用度(OB)≥30%,类药性(DL)≥0.18为筛选条件;使用GeneCards、OMIM、DrugBank数据库收集急性脑梗死的作用靶点,获得桂枝茯苓丸与疾病的交集靶点,绘制交集韦恩图;利用BisoGenet构建PPI网络,通过Cytoscape提取核心靶点;获取关键靶点蛋白后利用Metascape进行GO功能及KEGG通路富集分析。结果利用TCMSP检索共获得桂枝茯苓丸有效成分65个,主要为槲皮素、β-谷甾醇、齿孔酸、猪苓酸C、白花素等;筛选出桂枝茯苓丸治疗急性脑梗死的关键靶点135个,包括TP53、MCM2、UBC等;涉及细胞周期信号通路、泛素介导的蛋白降解信号通路、PI3K-Akt信号通路等119条相关信号通路;分子对接结果显示多个化合物与蛋白的结合能≤8 kJ/moL;实验组的tp53、UBC基因表达量较模型组的低,PI3K、P-Akt蛋白表达量较模型组的高(P<0.05)。结论桂枝茯苓丸治疗急性脑梗死具有多通路、多靶点的特点,为今后研究桂枝茯苓丸治疗急性脑梗死的机制提供了科学的理论依据及研究思路。

六味地黄丸合四妙丸治疗股骨头坏死的网络药理学和分子对接机制研究

目的:运用网络药理学和分子对接技术探讨六味地黄丸合四妙丸治疗股骨头坏死的作用机制。方法:通过中药系统药理学数据库与分析平台(TCMSP)筛选出六味地黄丸合四妙丸的活性成分;利用UniProt数据库预测活性成分作用靶点,通过GeneCards和OMIM数据库预测股骨头坏死疾病靶点。通过STRING数据库构建潜在作用靶点和蛋白质-蛋白质相互作用网络并通过Cytoscape 3.10.1软件筛选出关键靶点。通过DAVID工具进行潜在靶点的基因本体论(GO)和京都基因与基因组百科全书(KEGG)富集分析。结果:六味地黄丸合四妙丸治疗股骨头坏死的有效成分主要为槲皮素、汉黄芩素、山柰酚;作用的核心靶点为白细胞介素(Interleukin,IL)-6、肿瘤坏死因子(Tumor Necrosis Factor,TNF)、IL-1B、肿瘤蛋白p53(Tumor Protein p53,TP53)、含半胱氨酸的天冬氨酸蛋白水解酶3(Caspase-3,CASP3)、表皮生长因子受体(Epidermal Growth Factor Receptor,EGFR)、雌激素受体1(Estrogen Receptor 1,ESR1)、基质金属蛋白酶(Matrix Metallopeptidase,MMP)9、缺氧诱导因子-1A(Hypoxia Inducible Factor-1A,HIF-1A)、过氧化物酶体增殖物激活受体重组蛋白(Peroxisome Proliferator Activated Receptor,PPAR)γ等。关键作用通路为晚期糖基化终末产物-受体(Advanced Glycation End-Products,AGE-RAGE)信号通路、IL-17信号通路、脂质与动脉粥样硬化通路、癌症信号通路等。分子对接显示核心成分与核心靶点有较好的结合活性。结论:本研究初步揭示了六味地黄丸合四妙丸的核心活性成分及其多成分、多靶点、多通路治疗股骨头坏死的作用机制,为临床上股骨头坏死保髋治疗提供用药思路和依据。

扶正感康丸治疗流行性感冒的网络药理学分析

目的:基于网络药理学方法探讨扶正感康丸治疗甲型流行性感冒、乙型流行性感冒的有效成分及作用机制。方法:通过中药系统药理学数据库与分析平台(TCMSP)获取扶正感康丸的有效成分及作用靶点。通过GeneCards、NCBI数据库检索甲型流行性感冒、乙型流行性感冒疾病基因,获取有效成分-疾病共同靶点,并通过STRING数据库获得蛋白质-蛋白质相互作用网络,再使用Cytoscape软件绘制网络图并筛选核心靶点。其后,使用Metascape数据库对核心靶点进行富集分析,进一步获取通路关键靶点,并结合BioGPS、DisGeNET、GeneCards网站获取关键靶点的组织定位、亚细胞分布的相关信息。结果:获得扶正感康丸6味主要药物的有效成分85个,与甲型流行性感冒的交集靶点有41个,与乙型流行性感冒的交集靶点有106个,其中槲皮素、山柰酚等是核心成分,肿瘤坏死因子(Tumor Necrosis Factor,TNF)、白细胞介素(Interleukin,IL)-6等是甲型流行性感冒关键靶点,丝氨酸/苏氨酸蛋白激酶1(Akt Serine/Threonine Kinase 1,AKT1)、IL-6等是乙型流行性感冒关键靶点。基因本体论(GO)富集分析显示,扶正感康丸主要参与细胞死亡的正调控、细胞分化的负调控等生物过程,膜筏、膜侧等细胞组分,RNA聚合酶II特异性DNA结合转录因子结合、蛋白质同源二聚化活性等分子功能。京都基因与基因组百科全书(KEGG)分析结果显示,扶正感康丸治疗甲型流行性感冒主要参与了肿瘤信号通路、糖尿病并发症中的晚期糖基化终末产物-糖基化终末产物受体(AGE-RAGE)信号通路、小细胞肺癌等通路;扶正感康丸治疗乙型流行性感冒主要参与了肿瘤信号通路、磷脂酰肌醇3激酶-蛋白激酶B(Phosphatidylinositol 3-kinase-Akt,PI3K-Akt)信号通路、核因子-κB信号通路等相关通路。根据扶正感康丸治疗甲型流行性感冒和乙型流行性感冒的靶点分布情况,推测免疫细胞在提高机体免疫功能、治疗此类疾病中发挥较大作用。结论:扶正感康丸可以调节核因子-κB、PI3K-Akt等信号通路的AKT1、TNF、基质金属蛋白酶(Matrix Metallopeptidase,MMP)9、IL-10、IL-6等疾病靶点干预生物进程,从而治疗流行性感冒。

基于网络药理学和分子对接探究金匮肾气丸治疗椎间盘退变的作用机制

目的:基于网络药理学和分子对接探究金匮肾气丸治疗椎间盘退变的作用机制。方法:通过中医药百科全书(ETCM)检索金匮肾气丸所含药物,得到活性成分和药物作用靶点。通过GeneCards数据库检索“椎间盘退变”相关靶点,取药物和疾病靶点的交集,绘制药物成分-靶点-通路网络图。利用STRING绘制蛋白质-蛋白质相互作用网络图,筛选核心靶点。通过基因本体论(GO)及京都基因和基因组百科全书(KEGG)通路富集分析分析核心靶点富集信息及潜在通路。使用MOE软件对药物活性成分及核心靶点进行分子对接预测。结果:(1)获得金匮肾气丸有效活性成分共125种,包括水苏糖、β-谷甾醇、泽泻醇A等;(2)金匮肾气丸与椎间盘退变的共同靶点共97个,关键靶点有丝氨酸/苏氨酸蛋白激酶1(Akt Serine/Threonine Kinase 1,AKT1)、半胱氨酸-天冬氨酸蛋白酶3(Caspase 3,CASP3)、白细胞介素(Interleukin,IL)-1β、IL-6、肿瘤坏死因子(Tumor Necrosis Factor,TNF)等;(3)金匮肾气丸治疗椎间盘退变主要涉及营养水平反应、胞外模拟反应、细菌来源分子的反应等生物学过程,膜筏、细胞质的囊泡腔、分泌颗粒腔等细胞组分,氧化还原反应、有机酸结合、羧基酸结合等分子功能,以及结核、美洲锥虫病、缺氧诱导因子-1等信号通路;(4)分子对接显示核心成分与关键靶点的结合能力稳定。结论:金匮肾气丸中的活性成分水苏糖、β-谷甾醇、泽泻醇A等,通过关键靶点AKT1、IL-6、IL-1β、TNF等参与结核、美洲锥虫病、缺氧诱导因子-1等信号通路的调控,从而治疗椎间盘退变。

基于网络药理学探究苏黄泻浊丸抗肾间质纤维化及其调控铁死亡的作用机制

目的:基于网络药理学探究苏黄泻浊丸治疗肾间质纤维化(Renal Interstitial Fibrosis,RIF)及调控铁死亡的作用机制。方法:通过中药系统药理学数据库与分析平台(TCMSP)、STRING、OMIM、Gene Cards、DisGeNet等筛选苏黄泻浊丸的中药活性成分及RIF关联靶标,借助Cytoscape 3.6.0软件构建苏黄泻浊丸活性成分-RIF靶标网络,结合STRING数据库构建方药与RIF关联靶点蛋白质-蛋白质相互作用网络,利用DAVID数据库进行京都基因与基因组百科全书(KEGG)通路富集分析;利用FerrDb数据库获取铁死亡调控基因,最终获取公共靶标基因,构建苏黄泻浊丸活性成分-RIF、铁死亡共同靶标网络,结合STRING数据库构建共同靶蛋白相互作用网络;利用DAVID数据库进行KEGG通路富集分析。结果:筛选出药物活性成分102个,与RIF关联的靶基因177个,经基因本体论(GO)、KEGG分析,苏黄泻浊丸治疗RIF的生物过程与RNA聚合酶Ⅱ促进转录的正调控、转录因子活性、序列特异性DNA结合等有关,通过调节脂质与动脉粥样硬化、白细胞介素(Interleukin,IL)-17信号通路、肿瘤坏死因子(Tumor Necrosis Factor,TNF)信号通路、磷脂酰肌醇3激酶(Phosphatidylinositol 3-kinase,PI3K)-蛋白激酶B(Akt)信号通路、辅助性T细胞17(T Helper Cells 17,Th17)细胞分化、细胞衰老发挥作用。调控铁死亡共同基因有34个,可能参与IL-17信号通路、缺氧诱导因子-1(Hypoxia Inducible Factor-1,HIF-1)信号通路、ErbB信号通路、脂质代谢、Th17细胞分化、C型凝集素受体信号通路、TNF信号通路等。结论:本研究预测了苏黄泻浊丸治疗RIF及其调控铁死亡的主要化合物、靶标及通路,为后续深入研究苏黄泻浊丸治疗RIF的作用机制提供理论参考。

《辅行诀》组方法则在仲景肾气丸中的体现与进展研究

《辅行诀》以“汤液经法图”为组方理论核心,以五脏虚实辨证,并基于五味体用化三义进行补泻治疗。《金匮要略》记载肾气丸的条文共有五条,分别治疗虚劳腰痛、少腹不仁、小便不利、痰饮、消渴、转胞等,文章旨在通过探讨《辅行诀》组方法则在仲景肾气丸中的体现,并结合肾气丸现代研究进展,以多角度理解和丰富经方的辨治思路,为理解仲景经方提供新的思路和方法,以期为临床遣方用药提供有益参考,为中医药科研提供新的思路。

桃仁膝康丸治疗骨性关节炎机制的网络药理学分析与验证

目的:以网络药理学方法探讨桃仁膝康丸治疗骨性关节炎的可能作用机制。方法:通过中药系统药理学数据库与分析平台(TCMSP)搜索和筛选出桃仁膝康丸活性成分及作用靶点,检索GeneCards、OMIM和CTD数据库获得与骨性关节炎相关的非重复靶点,取交集获取中药抗骨性关节炎相关的药物活性成分靶点,使用String软件构建蛋白质-蛋白质相互作用网络,利用Cytoscape 3.8.2软件构建蛋白质-蛋白质相互作用网络图,筛选核心靶点和构建药物-活性成分-骨性关节炎相关靶点网络;借助DAVID数据库进行基因本体论(GO)富集分析和京都基因与基因组百科全书(KEGG)通路富集分析;将活性成分与预测疾病核心靶点进行分子对接验证;免疫印迹法(Western Blot)验证对细胞凋亡效应蛋白半胱氨酸蛋白酶(Caspase,CASP)3靶点的干预。结果:从桃仁膝康丸中筛选出53个活性成分,主要作用于骨性关节炎相关55个的靶点,靶标作用主要涉及细胞凋亡、炎症、细胞自噬、细胞老化、活性氧代谢、免疫生物过程和通路;分子对接结果发现活性成分与核心靶标结合性能良好;Western Blot结果显示,桃仁膝康丸能显著抑制CASP3活化。结论:桃仁膝康丸治疗骨性关节炎是多靶点、多通路的复杂机制过程,可能主要与抗细胞凋亡、抗炎、诱导细胞自噬、阻滞细胞老化、抗氧化、抑制免疫相关。

六神丸治疗小鼠结肠炎相关性结直肠癌的作用机制:基于网络药理学和体内验证方法

目的通过网络药理学和体内实验探讨六神丸治疗结肠炎相关性结直肠癌(CAC)的潜在作用机制。方法运用TCMSP、BATMAN-TCM、CNKI、PubMed、Genecards、OMIM和TTD数据库获取六神丸和CAC相关靶点,利用Venny在线作图网站得到六神丸-CAC共同靶点。然后,通过Cytoscape 3.8.2构建PPI网络筛选六神丸治疗CAC的核心靶点,并利用DAVID数据库进行GO和KEGG富集分析。体内实验验证分析,将C57BL/6J小鼠随机分为3组:对照组(Ctrl)、模型组(AOM/DSS)和六神丸组(LSW),采用AOM/DSS构建CAC小鼠模型。通过小鼠体质量变化、疾病活动指数评分、结肠长度、肿瘤大小和肿瘤数量等评估六神丸对CAC的治疗作用;HE染色、RT-qPCR方法检测六神丸对CAC小鼠炎症介质的作用;免疫组织化学染色、TUNEL染色评估六神丸对AOM/DSS诱导结肠肿瘤细胞增殖和凋亡的影响;免疫组织化学、Westernblot方法检测六神丸对CAC小鼠TLR4蛋白表达的影响。结果通过网络药理学方法获得69个六神丸-CAC共同靶点,构建PPI网络进行核心靶点筛选,得到33个核心靶点。KEGG通路富集分析显示,六神丸可能通过Toll样受体信号通路作用于CAC。体内研究结果表明,与模型组相比,六神丸治疗能够显著抑制小鼠结肠炎相关肿瘤的发生,减少肿瘤数量和负荷(P<0.05),明显改善小鼠结肠组织病理学变化,下调促炎细胞因子mRNA水平,抑制结肠肿瘤细胞增殖(P<0.01)并促进其凋亡(P<0.001);同时,六神丸还显著降低了结肠组织中TLR4蛋白表达(P<0.05)。结论六神丸可能通过调控Toll样受体信号TLR4的表达,减轻小鼠肠道炎症,抑制结肠肿瘤细胞增殖并促进其凋亡来发挥抗CAC作用。

基于生物信息学联合网络药理学探讨四神丸治疗糖尿病肾病的作用机制

目的:整合网络药理学方法阐释四神丸治糖尿病肾病的潜在机制。方法:从中药系统药理学数据库与分析平台、中药分子机制的生物信息学分析数据库、Swiss Target Prediction、STITCH和ChEMBL数据库检索四神丸的药物成分及对应靶点。利用DisGeNET、GeneCards和CTD数据库识别糖尿病肾病的疾病基因;在GEO数据库获取糖尿病肾病的数据集,利用limma包和RRA方法筛选稳健差异表达基因,整合疾病数据得到疾病靶点。构建韦恩图,得到复合靶点。然后,基于STRING数据库构建蛋白质-蛋白质相互作用网络,根据拓扑学参数筛选四神丸治疗糖尿病肾病的核心靶点。通过Cytoscape软件构建成分-靶点网络和成分-靶点-通路网络。利用DAVID数据库对复合靶点进行基因本体(GO)功能富集分析和京都基因与基因组百科全书(KEGG)通路富集分析。最后,分子对接模拟验证主要活性成分与核心靶标之间的结合力。结果:筛选出有效成分121个,有效成分作用靶点542个,有关糖尿病肾病的靶点3832个。四神丸治疗糖尿病肾病的枢纽基因集为蛋白激酶B1、肿瘤坏死因子、白细胞介素1β等。活性成分为油酸、亚油酸、二氢吴茱萸卡品碱、吴茱萸酰胺等。分子对接模拟显示,核心活性化合物与枢纽基因具有较高的结合活性。结论:四神丸是通过多成分、多靶点和多途径发挥对糖尿病肾病的治疗作用,且作用机制集中体现在晚期糖基化终末产物(AGE)-AGE受体信号通路、TNF信号通路等通路上。

保和丸治疗食滞胃肠证泄泻合并肠道菌群失调的网络药理学分析

背景网络药理学整合了药物、靶点、疾病等信息,能够高效地阐明中药多组分和疾病多靶点之间的潜在作用关系.然而在许多网络药理学研究中,往往只注重中药对疾病靶点的作用,而忽视肠道菌群对疾病靶点的作用.将肠道菌群纳入网络药理学的研究中,可为中药多成分-多靶点-多途径贡献了一种新思路.目的采用网络药理学方法,探讨保和丸治疗食滞胃肠证泄泻合并肠道菌群失调的可能分子机制.方法通过TCMSP、BATMAN-TCM等数据库,结合文献筛选出保和丸活性成分及相应靶点.通过GeneCards数据库检索食滞胃肠证泄泻、肠道菌群的相关靶点,Venny平台筛选活性成分与疾病的共同靶点.Cytoscape 3.9.1软件构建疾病-靶点-化合物网络,筛选药物靶点、肠道菌群靶点和疾病靶点相互作用的有效靶点.STRING数据库构建蛋白质-蛋白质相互作用(protein-protein interaction,PPI)网络.利用DAVID数据库对有效靶点进行基因本体(Gene Ontology,GO)功能分析及京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)通路富集分析.结果共收集549种化学成分,根据OB≥30%及DL≥0.18,共得到45个活性成分,包括槲皮素、皮素、汉黄芩素、山奈酚、柚皮素等.Venn图显示保和丸活性成分中对应259个可能蛋白靶点,与食滞胃肠证泄泻存在作用的靶点有34个,与肠道菌群存在作用的有66个,三者共同的靶点数为11个,其过氧化物合酶2(peroxide synthase 2,PTGS2)、肿瘤坏死因子(tumor necrosis factor,TNF)、肿瘤蛋白P53(oncoprotein P53,TP53)、细胞间粘附分子-1(intercellular adhesion molecule-1,ICM1)、白介素10(interleukin-10,IL-10)为关键靶点.GO功能富集分析得到121个生物过程,KEGG通路富集筛选得到49条通路,包括TNF信号通路、白介素17(interleukin-17,IL-17)信号通路、NF-κB信号通路等.结论通过网络药理学的初步筛选及预测,保和丸可能通过多途径、多靶点改善食滞胃肠证泄泻合并肠道菌群失调.

基于网络药理学探讨益肾蠲痹丸治疗类风湿关节炎的作用机制

目的采用网络药理学方法探讨益肾蠲痹丸治疗类风湿关节炎(RA)的分子作用机制。方法采用中药系统药理学数据库与分析平台(TCMSP)、中医药整合药理学研究平台(TCMIP)、本草组鉴(HERB)和中医药百科全书数据库(ETCM)获取益肾蠲痹丸的有效成分,并借助SwissTargetPrediction数据库对有效成分的作用靶点进行预测;在人类基因综合数据库(GeneCards)、人类疾病相关基因与突变位点信息数据库(DisGeNET)、在线人类孟德尔遗传数据库(OMIM)、药物靶标数据库(TTD)中搜索RA相关基因。将益肾蠲痹丸的作用靶点和与RA相关靶点进行映射交集,获得二者的交集靶点,借助STRING数据库构建蛋白互作(PPI)网络;采用Cytoscape 3.7.2软件筛选出核心靶点,采用Cytoscape 3.9软件进行基因本体(GO)、京都基因与基因组百科全书(KEGG)信号通路分析。结果共获得益肾蠲痹丸治疗RA的有效成分185个,其中关键成分为山柰酚、木犀草素、槲皮素和黄藤素,核心作用靶点为肿瘤坏死因子(TNF)、白介素-6(IL-6)、白介素-1β(IL-1β)、血管内皮生长因子A(VEGFA)、信号转导及转录激活蛋白3(STAT3)基因等。KEGG信号通路主要涉及TNF、丝裂原活化蛋白激酶(MAPK)、白介素-17(IL-17)、VEGF、核因子-κB(NF-κB)信号通路及RA疾病信号通路等。结论益肾蠲痹丸治疗RA具有多成分、多靶点、多通路协同作用优势,可通过调控相关信号通路调节机体免疫功能、影响细胞凋亡、抑制炎症反应。