Prediction of Rhizoma Drynariae Targets in the Treatment of Osteoarthritis Based on Network Pharmacology and Experimental Verification

Rhizoma Drynariae has been widely used for the treatment of osteoarthritis (OA), but its potential targets and molecular mechanisms remain to be further explored. Targets of Rhizoma Drynariae and OA were predicted by relevant databases, and a protein-protein interaction (PPI) network was constructed to identify key targets. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed to obtain related pathways and then select significant pathways associated with OA. The OA chondrocyte model was established by inflammatory factor-induced SW1353 chondrocytes, and molecular docking was conducted to verify the above theoretical prediction. The results showed that a total of 86 Rhizoma Drynariae-OA interaction targets were identified, among which IL-6 and AKT1 were the key targets in the PPI network. Luteolin was the most critical component of Rhizoma Drynariae. KEGG results indicated that the effects of Rhizoma Drynariae on OA are associated with the PI3K/AKT, TNF, IL-17, apoptosis, and HIF-1 signaling pathway. The PI3K/AKT pathway can activate the downstream NF-κB pathway and further regulate the transcription and expression of downstream IL-6, IL-17, HIF-1α, Bax, and TNF, suggesting that the PI3K/AKT/NF-κB pathway is the critical pathway in the treatment of OA with Rhizoma Drynariae. Active components of Rhizoma Drynariae and key proteins of the PI3K/AKT/NF-κB signaling pathway were subjected to molecular docking, whose results showed that luteolin and IKK-α played a critical role. In vitro experiments indicated that both aqueous extracts of Rhizoma Drynariae (AERD) and luteolin inhibited the expression of IL-6 and HIF-1α and suppressed the activation of PI3K/AKT/NF-κB, IL-17, and TNF pathways. The measurement of mitochondrial membrane potential (Δψm) indicated that AERD and luteolin can decrease the LPS-induced early apoptotic cells. Luteolin had a more prominent inhibitory effect than AERD in the abovementioned in vitro experiments. In conclusion, the therapeutic mechanism of Rhizoma Drynariae against OA may be closely related to the inhibition of the PI3K/AKT/NF-κB pathway and downstream pathways, and luteolin plays a vital role in the treatment.

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Network Pharmacology-Based Prediction of the Active Ingredients and Potential Targets of Chinese Herbal Danyu Gukang Pills for Application to Osteonecrosis of the Femoral Head Disease

10.21203/rs.3.rs-143355/v1 ◽

2021 ◽

Author(s):

Yongchang Guo ◽

Dapeng Zhang ◽

Yuju Cao ◽

Xiaoyan Feng ◽

Caihong Shen ◽

...

Keyword(s):

Molecular Docking ◽

Femoral Head ◽

Signaling Pathway ◽

Molecular Mechanisms ◽

Enrichment Analysis ◽

Network Pharmacology ◽

Pathway Enrichment Analysis ◽

In Vitro Experiments ◽

Active Components

Abstract Ethnopharmacological relevanceOsteonecrosis of the femoral head (ONFH) is still a challenge for orthopedists worldwide, which may lead to disability in patients without effective treatment. A newly developed formula of Chinese medicine, Danyu Gukang Pills (DGP), was recognized to be effective for ONFH. Nevertheless, its molecular mechanisms remain to be clarified. MethodsNetwork pharmacology was adopted to detect the mechanism of DGP on ONFH. The compounds of DGP were collected from the online databases, and active components were selected based on their OB and DL index. The potential proteins of DGP were acquired from TCMSP database, while the potential genes of ONFH were obtained from Gene Cards and Pubmed Gene databases. The function of Gene and potential pathways were researched by GO and KEGG pathway enrichment analysis. The compounds-targets and targets-pathways network were constructed in an R and Cytosacpe software. The mechanism was further investigated via molecular docking. Finally, in-vitro experiments were validated in the BMSCs. ResultsA total of 2305 compounds in DGP were gained, among which, 370 were selected as active components for which conforming to criteria. Combined the network analysis, molecular docking and in-vitro experiments, the results firstly demonstrated that the treatment effect of DGP on ONFH may be closely related to HIF-1α, VEGFA and HIF-1 signaling pathway. ConclusionThe current study firstly researched the molecular mechanism of DGP on ONFH based on network pharmacology. The results indicated that DGP may exert the effect on ONFH targeting on HIF-1α and VEGFA via HIF-1 signaling pathway.

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Network Pharmacology Prediction and Molecular Docking-Based Strategy to Discover the Potential Pharmacological Mechanism of Wen-yu-jin Against Pulmonary Fibrosis in Mouse Model

10.21203/rs.3.rs-923117/v1 ◽

2021 ◽

Author(s):

lu wang ◽

Wenxiang Zhu ◽

Rui Sun ◽

Jing Liu ◽

Qihong Ma ◽

...

Keyword(s):

Molecular Docking ◽

Pulmonary Fibrosis ◽

Signaling Pathway ◽

Lung Fibrosis ◽

Mapk Signaling ◽

Mapk Signaling Pathway ◽

Network Pharmacology ◽

In Vitro Experiments

Abstract Background Pulmonary fibrosis (PF) is a devastating lung disease. The two drugs approved by the FDA, pirfenidone and nintedanib, can only delay the progression of the disease but cannot cure the disease. These drugs also present adverse effects. Wen-yu-jin (WYJ) obtained from steamed roots of Curcuma wenyujin showed a variety of pharmacological activities. In this study we investigated whether WYJ present anti-lung fibrosis effects. Methods Ultra-high pressure liquid chromatography combined with linear ion trap-orbital tandem mass spectrometry (UHPLC-LTQ-orbital trap) was used to identify chemical composition of WYJ. PF-related and WYJ-related targets were obtained from public databases. Network pharmacological was performed to acquire potential targets and major signaling pathways. The binding activity of composition with core targets was predicted by molecular docking. Based on the predicted results, the anti-lung fibrosis effect of WYJ was verified in vivo and in vitro experiments. Results 23 major compositions of WYJ were identified based on UHPLC-LTQ-Orbitrap. According to the results of network pharmacology, MAPK signaling pathway might play an important role in WYJ against lung fibrosis and STAT3 also could be the potential therapeutic targets. Molecular docking results indicated that most of the compositions have good binding activities with core targets. In vivo and in vitro experiments showed that WYJ alleviated process of fibrosis by inhibiting MAPK signaling pathway and the levels of phosphorylated STAT3 (p-STAT3). Conclusion According to the results of network pharmacology and molecular docking, in vivo and in vitro experiments further verified potential targets and molecular mechanism of WYJ against lung fibrosis. Our study provided a novel approach to explain the pharmacological basis of other herbs.

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Systematic Elucidation of the Mechanism of Action of Curcumin Against Colorectal Cancer via Network Pharmacology Approach

10.21203/rs.3.rs-535607/v1 ◽

2021 ◽

Author(s):

Xinyue Han ◽

Yimin Xu ◽

Xiaoqiang Liu ◽

Yuan Li ◽

Cui Guo ◽

...

Keyword(s):

Colorectal Cancer ◽

Molecular Docking ◽

Signaling Pathways ◽

Signaling Pathway ◽

Mechanism Of Action ◽

Experimental Verification ◽

Enrichment Analysis ◽

Network Pharmacology ◽

In Vitro Experiments

Abstract Background: Curcumin is a potential drug for the treatment of colorectal cancer (CRC). Its mechanism of action has not been elucidated.Aim: To investigate the mechanism of action of curcumin in the treatment of CRC via network pharmacology, molecular docking and experimental verification.Methods: The targets of curcumin and CRC were obtained from the public databases. The component-targets network of curcumin in the treatment of CRC was constructed by Cytoscape v3.7.2. Through protein-protein interaction (PPI), the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), important targets and signaling pathways related to CRC treatment were identified. Finally, the results were verified by molecular docking and in vitro experiments.Results: A total of 30 potential targets of curcumin for CRC treatment were collectedThe core targets included AKT1, EGFR and STAT3 were identified. GO function enrichment analysis showed 140 items, and KEGG pathway enrichment analysis showed 61 signaling pathways, that were related to the regulation of protein kinase activity, negative regulation of apoptosis process, cancer signaling pathway and PI3K-Akt signali-ng pathway. In vitro experimental verification showed that curcumin could promote the apoptosis of CRC cells, and the key proteins of these signaling pathways were differentially expressed.Conclusion: This study explored the targets and pathways of curcumin in the treatment of colorectal cancer. In vitro experiments showed that curcumin has a therapeutic effect against CRC by inhibiting PI3K-Akt signaling pathway. Our results will lay a foundation for subsequent clinical research and drug development.

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Capn4 Enhances Osteopontin Expression through Activation of the Wnt/β-Catenin Pathway to Promote Epithelial Ovarian Carcinoma Metastasis

Cellular Physiology and Biochemistry ◽

10.1159/000477310 ◽

2017 ◽

Vol 42 (1) ◽

pp. 185-197 ◽

Cited By ~ 12

Author(s):

Xiaoming Yang ◽

Jing Sun ◽

Dandan Xia ◽

Xupei Can ◽

Lei Liu ◽

...

Keyword(s):

Ovarian Carcinoma ◽

Signaling Pathway ◽

Cell Lines ◽

Western Blotting ◽

Molecular Mechanisms ◽

Critical Role ◽

Epithelial Ovarian Carcinoma ◽

Regulatory Subunit ◽

Epithelial Tissue

Background and Aim: Increasing evidence shows that the calpain regulatory subunit Capn4 can modulate the proliferation and metastasis of cancer cells, and plays an important role in the development of malignant tumors. However, there is no information on the clinical significance of Capn4 in epithelial ovarian carcinoma (EOC) or the molecular mechanisms by which Capn4 promotes the growth and metastasis of EOC. Therefore, the aim of this study was to clarify the role of Capn4 in EOC. Methods: We evaluated Capn4 and osteopontin (OPN) expression in EOC cell lines and tissues from patients with ovarian cancer by western blotting and immunohistochemical analysis. We then created cell lines with downregulated and upregulated Capn4 expression, using Capn4-targeting small interfering RNA and a pcDNA3.1-Capn4 overexpression vector, respectively, to investigate its function in EOC in vitro. In addition, we investigated the potential mechanism underlying the function of Capn4 by examining the effect of modifying Capn4 expression on Wnt/β-catenin signaling pathway-related genes by western blotting. Results: Capn4 was overexpressed in clinical EOC tissues compared with that in normal ovarian epithelial tissue, and was associated with poor clinical outcomes. Upon silencing or overexpressing Capn4 in EOC cells, we concluded that Capn4 promotes cell proliferation and migration in vitro. Furthermore, Capn4 promoted EOC metastasis by interacting with the Wnt/β-catenin signaling pathway to upregulate OPN expression. Conclusion: Our study indicates that Capn4 plays a critical role in the progression and metastasis of EOC, and could be a potential therapeutic target for EOC management.

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Investigation of Active Ingredients and Mechanism of Sanao Decoction in the Treatment of Chronic Cough by Network Pharmacology

10.21203/rs.3.rs-127466/v1 ◽

2020 ◽

Author(s):

Mengke Sheng ◽

Xing Liu ◽

Qingsong Qu ◽

Xiaowen Wu ◽

Yuyao Liao ◽

...

Keyword(s):

Molecular Docking ◽

Signaling Pathway ◽

Chronic Cough ◽

Fluid Shear Stress ◽

Oxidant Stress ◽

Network Pharmacology ◽

Ppi Network ◽

Active Ingredients ◽

Active Components ◽

Pathway Network

Abstract Background: Chronic cough significantly affects human health and quality of life. Studies have shown that Sanao Decoction（SAD）can clinically treat chronic cough. To investigate its mechanisms, we used the method of network pharmacology to conduct research at the molecular level.Methods: The active ingredients and their targets were screened by pharmacokinetics parameters from the traditional Chinese medicine system pharmacology analysis platform (TCMSP). The relevant targets of chronic cough were obtained from two databases: GeneCards and DrugBank. Take the intersection to get potential targets of SAD to treat chronic cough and establish the component-target regulatory network by CytoScape3.7.2 and protein-protein interaction (PPI) network by STRING 1.0. The function of the target gene and related pathways were analyzed by the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) in the Database for Annotation, Visualization, and Integrated Discovery (DAVID). The significant pathways and their relevant targets were obtained and the target-pathway network was established by CytoScape3.7.2. Finally, molecular docking of the core active components and relevant targets was performed.Results: A total of 98 active components, 113 targets were identified. The component-target and target-pathway network of SAD and PPI network were established. Enrichment analysis of DAVID indicated that 2062 terms were in biological processes, 77 in cellular components, 142 in molecular functions and 20 significant pathways. In addition, the molecular docking showed that quercetin and luteolin had a good combination with the corresponding targets.Conclusions: It indicates that the active compounds of SAD, such as quercetin, luteolin, may act on AKT1, MAPK1, RELA, EGFR, BCL2 and regulate PI3K-Akt signaling pathway, AGE-RAGE signaling pathway in diabetic complications and Fluid shear stress and atherosclerosis pathway to exert the effects of anti-inflammatory, anti-airway remodeling, anti-oxidant stress and repair airway damage to treat chronic cough.

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Exploring the Mechanisms Underlying the Therapeutic Effect of Xixin Decoction on Alzheimer's Disease Based on Network Pharmacology and Molecular Docking

10.21203/rs.3.rs-562321/v1 ◽

2021 ◽

Author(s):

Zhuo Zhang ◽

Jiang-lin Xu ◽

Ming-qing Wei ◽

Ting Li ◽

Jing Shi

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Molecular Docking ◽

Signaling Pathway ◽

Therapeutic Effect ◽

Mapk Signaling ◽

Network Pharmacology ◽

Receptor Interaction ◽

Ppi Network ◽

Active Compounds

Abstract Background and objective: Alzheimer’s disease (AD) has been a worldwide problem, not only the treatment but also the prevention. As a commonly used Chinese Herbal Formula, Xixin Decoction (XXD) has significant therapeutic effect on AD but without clear mechanism. This study was aimed to predict the main active compounds and targets of XXD in the treatment of AD and to explore the potential mechanism by using network pharmacology and molecular docking. Methods: The compounds of XXD were searched in the TCMSP and the TCMID database, and the active compounds were screened based on the ADME model and SwissADME platform. SwissTargetPrediction platform was used to search for the primary candidate targets of XXD. The common targets related to AD obtained by two databases (GeneCards and DisGeNET) were determined as candidate proteins involved in AD. To acquire the related targets of XXD in the treatment of AD, the target proteins related to AD were intersected with the predicted targets of XXD. Then these overlapping targets were imported into the STRING database to build PPI network including hub targets; Cytoscape 3.7.2 software was used to construct the topology analysis for the herb-compound-target network diagram while one of it’s plug-in called CytoNCA was used to calculate degree value to screen the main active compounds of XXD. GO and KEGG pathway enrichment analyses were conducted to explore the core mechanism of action and biological pathways associated with the decoction via Metascape platform. We used AutoDock Vina and PyMOL 2.4.0 softwares for molecular docking of hub targets and main compounds.Results: We determined 114 active compounds which meet the conditions of ADME screening, 973 drug targets, and 973 disease targets. However, intersection analysis screened out 208 shared targets. PPI network identified 9 hub targets, including TP53, PIK3CA, MAPK1, MAPK3, STAT3, AKT1, etc. The 10 main active compounds play a major role in treatment of AD by XXD. Hub targets were found to be enriched in 10 KEGG pathways, involving the Pathways in cancer, AGE-RAGE signaling pathway in diabetic complications, Alzheimer's disease, Neuroactive ligand-receptor interaction, Dopaminergic synapse, Serotonergic synapse and MAPK signaling pathway. The docking results indicated that the 8 hub targets exhibit good binding activity with the 9 main active compounds of XXD.Conclusions: We found the advantages of multi-compounds-multi-targets-multi-pathways regulation to reveal the mechanism of XXD for treating AD based on network pharmacology and molecular docking. Our study provided a theorical basis for further clinical application and experimental research of XXD for anti-AD in the future.

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Elucidating the Effects of Curcumin against Influenza Using In Silico and In Vitro Approaches

Pharmaceuticals ◽

10.3390/ph14090880 ◽

2021 ◽

Vol 14 (9) ◽

pp. 880

Author(s):

Minjee Kim ◽

Hanul Choi ◽

Sumin Kim ◽

Lin Woo Kang ◽

Young Bong Kim

Keyword(s):

Influenza Virus ◽

Molecular Docking ◽

Mdck Cells ◽

Influenza Infection ◽

Network Pharmacology ◽

Therapeutic Effects ◽

In Vitro Experiments ◽

Target Interaction ◽

Ppi Networks

The influenza virus is a constantly evolving pathogen that challenges medical and public health systems. Traditionally, curcumin has been used to treat airway inflammatory diseases, such as bronchitis and pneumonia. To elucidate common targets of curcumin and influenza infection and underlying mechanisms, we employed network pharmacology and molecular docking approaches and confirmed results using in vitro experiments. Biological targets of curcumin and influenza were collected, and potential targets were identified by constructing compound–disease target (C-D) and protein–protein interaction (PPI) networks. The ligand–target interaction was determined using the molecular docking method, and in vitro antiviral experiments and target confirmation were conducted to evaluate curcumin’s effects on influenza. Our network and pathway analyses implicated the four targets of AKT1, RELA, MAPK1, and TP53 that could be involved in the inhibitory effects of curcumin on influenza. The binding energy calculations of each ligand–target interaction in the molecular docking showed that curcumin bound to AKT1 with the highest affinity among the four targets. In vitro experiments, in which influenza virus-infected MDCK cells were pre-, co-, or post-treated with curcumin, confirmed curcumin’s prophylactic and therapeutic effects. Influenza virus induction increased the level of mRNA expression of AKT in MDCK cells, and the level was attenuated by curcumin treatment. Collectively, our findings identified potential targets of curcumin against influenza and suggest curcumin as a potential therapy for influenza infection.

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Network Pharmacology-Based Systematic Analysis of Molecular Mechanisms of Dingji Fumai Decoction for Ventricular Arrhythmia

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2021/5535480 ◽

2021 ◽

Vol 2021 ◽

pp. 1-12

Author(s):

Yi Liang ◽

Bo Liang ◽

Xin-Rui Wu ◽

Wen Chen ◽

Li-Zhi Zhao

Keyword(s):

Molecular Docking ◽

Ventricular Arrhythmia ◽

Molecular Mechanisms ◽

Mendelian Inheritance ◽

Network Pharmacology ◽

Ppi Network ◽

Systematic Analysis ◽

Chemical Structures ◽

Function Modules ◽

Underlying Mechanisms

Background. Dingji Fumai Decoction (DFD), a traditional herbal mixture, has been widely used to ventricular arrhythmia (VA) in clinical practice in China. However, research on the bioactive components and underlying mechanisms of DFD in VA is still scarce. Methods. Components of DFD were collected from TCMSP, ETCM, and literature. The chemical structures of each component were obtained from PubChem. Next, SwissADME and SwissTargetPrediction were applied for compounds screening and targets prediction of DFD; meanwhile, targets of VA were collected from DrugBank and Online Mendelian Inheritance in Man (OMIM). Then, the H-C-T-D network and the protein-protein interaction (PPI) network were constructed based on the data obtained above. CytoNCA was utilized to filter hub genes and VarElect was used to analyze the relationship between genes and diseases. At last, Metascape was employed for systematic analysis on the potential targets of herbals against VA, and AutoDock was applied for molecular docking to verify the results. Results. A total of 434 components were collected, 168 of which were qualified, and there were 28 shared targets between DFD and VA. Three function modules of DFD were found from the PPI network. Further systematic analysis of shared genes and function modules explained the potential mechanism of DFD in the treatment of VA; molecular docking has verified the interactions. Conclusions. DFD could be employed for VA through mechanisms, including complex interactions between related components and targets, as predicted by network pharmacology and molecular docking. This work confirmed that DFD could apply to the treatment of VA and promoted the explanation of DFD for VA in the molecular mechanisms.

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Exploring the effect of Polyphyllin I on hepatitis B virus-related liver cancer through network pharmacology and in vitro experiments

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207324666210816141436 ◽

2021 ◽

Vol 24 ◽

Author(s):

Shuxian Yu ◽

Wenhui Gao ◽

Puhua Zeng ◽

Chenglong Chen ◽

Zhuo Liu ◽

...

Keyword(s):

Molecular Docking ◽

Liver Cancer ◽

Mechanism Of Action ◽

Active Ingredient ◽

Vehicle Group ◽

Network Pharmacology ◽

Dependent Manner ◽

In Vitro Experiments ◽

Concentration Dependent Manner

Aim and Objective: To investigate the effect of Polyphyllin I (PPI) on HBV-related liver cancer through network pharmacology and in vitro experiments, and to explore its mechanism of action. Materials and Methods: Use bioinformatics software to predict the active ingredient target of PPI and the disease target of liver cancer, and perform active ingredient-disease target analysis. The results of network pharmacology through molecular docking and in vitro experiments can be further verified. The HepG2 receptor cells (HepG2. 2. 15) were transfected with HBV plasmid for observation, with the human liver cancer HepG2 being used as the control. Results: Bioinformatics analysis found that PPI had totally 161 protein targets, and the predicted target and liver cancer targets were combined to obtain 13 intersection targets. The results of molecular docking demonstrated that PPI had good affinity with STAT3, PTP1B, IL2, and BCL2L1. The results of the in vitro experiments indicated that the PPI inhibited cell proliferation and metastasis in a concentration-dependent manner (P<0.01). Compared with the vehicle group, the PPI group of 1.5, 3, and 6 μmol/L can promote the apoptosis of liver cancer to different degrees (P<0.01). Conclusion: The present study revealed the mechanism of PPI against liver cancer through network pharmacology and in vitro experiments. Its mechanism of action is related to the inhibition of PPI on the proliferation of HBV-related liver cancer through promoting the apoptosis of liver cancer cells. Additionally, in vitro experiments have also verified that PPI can promote the apoptosis of HepG2 and HepG2.2.15 cells.

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Exploring the Antiglioma Mechanisms of Luteolin Based on Network Pharmacology and Experimental Verification

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2021/7765658 ◽

2021 ◽

Vol 2021 ◽

pp. 1-18

Author(s):

Renxuan Huang ◽

Rui Dong ◽

Nan Wang ◽

Beiwu Lan ◽

Hongyang Zhao ◽

...

Keyword(s):

Molecular Docking ◽

Signaling Pathway ◽

Fruits And Vegetables ◽

Docking Simulation ◽

Underlying Mechanism ◽

Venn Diagram ◽

Network Pharmacology ◽

Discovery Studio ◽

Inorganic Substances

Luteolin, a natural flavone compound, exists in a variety of fruits and vegetables, and its anticancer effect has been shown in many studies. However, its use in glioma treatment is hampered due to the fact that the underlying mechanism of action has not been fully explored. Therefore, we elucidated the potential antiglioma targets and pathways of luteolin systematically with the help of network pharmacology and molecular docking technology. The druggability of luteolin, including absorption, excretion, distribution, and metabolism, was assessed via the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). The potential targets of luteolin and glioma were extracted from public databases, and the intersecting targets between luteolin and glioma were integrated and visualized by a Venn diagram. In addition, GO and KEGG pathway analysis was engaged in Metascape. The network of the luteolin-target-pathway was visualized by Cytoscape. Ultimately, the interactions between luteolin and predicted key targets were confirmed by Discovery studio software. According to the ADME results, luteolin shows great potential for development into a drug. 4860 glioma-associated targets and 280 targets of luteolin were identified, of which 205 were intersection targets. 6 core targets of luteolin against glioma, including AKT1, JUN, ALB, MAPK3, MAPK1, and TNF, were identified via PPI network analysis of which AKT1, JUN, ALB, MAPK1, and TNF harbor diagnostic value. The biological processes of luteolin are mainly involved in the response to inorganic substances, response to oxidative stress, and apoptotic signaling pathway. The essential pathways of luteolin against glioma involve pathways in cancer, the PI3K-Akt signaling pathway, the TNF signaling pathway, and more. Meanwhile, luteolin’s interaction with six core targets was verified by molecular docking simulation and its antiglioma effect was verified by in vitro experiments. This study suggests that luteolin has a promising potential for development into a drug and, moreover, it displays preventive effects against glioma by targeting various genes and pathways.

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