A network pharmacology analysis on drug-like compounds from Ganoderma lucidum for alleviation of Atherosclerosis

Abstract Background: Ganoderma lucidum (GL) is known as a potent alleviator against chronic inflammatory disease like atherosclerosis (AS), but its critical bioactive compounds and their mechanisms against AS have not been unveiled. This research aimed to identify the key compounds(s) and mechanism(s) of GL against AS through network pharmacology.Methods: The compounds from GL were identified by gas chromatography-mass spectrum (GC-MS), and SwissADME screened their physicochemical properties. Then, the gene(s) associated with the screened compound(s) or AS related genes were identified by public databases, and we selected the overlapping genes using a Venn diagram. The networks between overlapping genes and compounds were visualized, constructed, and analyzed by RStudio. Finally, we performed molecular docking test (MDT) to identify key gene(s), compound(s) on AutoDockVina.Results: A total of 35 compounds in GL was detected via GC-MS, and 34 compounds (accepted by the Lipinski's rule) were selected as drug-like compounds (DLCs). A total of 34 compounds were connected to the number of 785 genes and 2,606 AS-related genes were identified by DisGeNET and Online Mendelian Inheritance in Man (OMIM). The final 98 overlapping genes were extracted between the compounds-genes network and AS-related genes. On Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, the number of 27 signaling pathways were sorted out, and a hub signaling pathway (MAPK signaling pathway), a core gene (PRKCA), and a key compound (Benzamide, 4-acetyl-N-(2,6-dimethylphenyl)) were selected among the 27 signaling pathways via MDT. Conclusion: Overall, we found that the identified 3 DLCs from GL have potent anti-inflammatory efficacy, improving AS by inactivating the MAPK signaling pathway.

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Network Pharmacology Identifies the Mechanisms of Sang-Xing-Zhi-Ke-Fang against Pharyngitis

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2020/2421916 ◽

2020 ◽

Vol 2020 ◽

pp. 1-12

Author(s):

Yinhe Deng ◽

Quanjiang Li ◽

Menglin Li ◽

Tiantian Han ◽

Guixian Li ◽

...

Keyword(s):

Signaling Pathway ◽

Influenza A ◽

Molecular Mechanisms ◽

Mapk Signaling ◽

Venn Diagram ◽

Network Pharmacology ◽

Pathway Enrichment Analysis ◽

Ras Signaling ◽

Clinical Effects ◽

Overlapping Genes

Background. Sang-Xing-Zhi-Ke-Fang (SXZKF) demonstrates good therapeutic effect against pharyngitis. Nevertheless, the pharmacological mechanism underlying its effectiveness is still unclear. Objective. To investigate the underlying mechanisms of SXZKF against pharyngitis using network pharmacology method. Methods. Bioactive ingredients of SXZKF were collected and screened using published literature and two public databases. Using four public databases, the overlapping genes between these bioactive compound-related and pharyngitis-related genes were identified by Venn diagram. Protein-protein interaction (PPI) was obtained using “Search Tool for the Retrieval of Interacting Genes (STRING)” database. “Database for Annotation, Visualization, and Integrated Discovery ver. 6.8 (DAVID 6.8)” was used to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis to explore the molecular mechanisms of SXZKF against pharyngitis. Finally, Cytoscape 3.7.2 software was used to construct and visualize the networks. Result. A total of 102 bioactive compounds were identified. Among them, 886 compounds-related and 6258 pharyngitis-related genes were identified, including 387 overlapping genes. Sixty-three core targets were obtained, including ALB, PPARγ, MAPK3, EGF, and PTGS2. Signaling pathways closely related to mechanisms of SXZKF for pharyngitis were identified, including serotonergic synapse, VEGF signaling pathway, Fc epsilon RI signaling pathway, Ras signaling pathway, MAPK signaling pathway, and influenza A. Conclusion. This is the first identification of in-depth study of SXZKF against pharyngitis using network pharmacology. This new evidence could be informative in providing new support on the clinical effects of SXZKF on pharyngitis and for the development of personalized medicine for pharyngitis.

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Therapeutic mechanism of Toujie Quwen granules in COVID-19 based on network pharmacology

BioData Mining ◽

10.1186/s13040-020-00225-8 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Ying Huang ◽

Wen-jiang Zheng ◽

Yong-shi Ni ◽

Mian-sha Li ◽

Jian-kun Chen ◽

...

Keyword(s):

Chinese Medicine ◽

Signaling Pathways ◽

Signaling Pathway ◽

Mapk Signaling ◽

Venn Diagram ◽

Network Pharmacology ◽

Active Ingredients ◽

Integrated Network ◽

Therapeutic Mechanism ◽

The World

Abstract Background Chinese medicine Toujie Quwen granule (TJQW) has proven to be effective in the treatment of mild coronavirus disease 2019 (COVID-19) cases by relieving symptoms, slowing the progression of the disease, and boosting the recovery of patients. But the bioactive compounds and potential mechanisms of TJQW for COVID-19 prevention and treatment are unclear. This study aimed to explore the potential therapeutic mechanism of TJQW in coronavirus disease 2019 (COVID-19) based on an integrated network pharmacology approach. Methods TCMSP were used to search and screen the active ingredients in TJQW. The Swiss TargetPrediction was used to predict the potential targets of active ingredients. Genes co-expressed with ACE2 were considered potential therapeutic targets on COVID-19. Venn diagram was created to show correlative targets of TJQW against COVID-19. Cytoscape was used to construct a “drug-active ingredient-potential target” network, STRING were used to construct protein-protein interaction network, and cytoHubba performed network topology analysis. Enrichment of biological functions and signaling pathways of core targets was performed by using the clusterProfiler package in R software and ClueGO with CluePedia plugins in Cytoscape. Results A total of 156 active ingredients were obtained through oral bioavailability and drug-likeness screenings. Two hundred twenty-seven potential targets of TJQW were related to COVID-19. The top ten core targets are EGFR, CASP3, STAT3, ESR1, FPR2, F2, BCL2L1, BDKRB2, MPO, and ACE. Based on that, we obtained 19 key active ingredients: umbelliprenin, quercetin, kaempferol, luteolin, praeruptorin E, stigmasterol, and oroxylin A. And the enrichment analysis obtained multiple related gene ontology functions and signaling pathways. Lastly, we constructed a key network of “drug-component-target-biological process-signaling pathway”. Our findings suggested that TJQW treatment for COVID-19 was associated with elevation of immunity and suppression of inflammatory stress, including regulation of inflammatory response, viral process, neutrophil mediated immunity, PI3K-Akt signaling pathway, MAPK signaling pathway, Jak-STAT signaling pathway, Complement and coagulation cascades, and HIF-1 signaling pathway. Conclusions Our study uncovered the pharmacological mechanism underlying TJQW treatment for COVID-19. These results should benefit efforts for people around the world to gain more knowledge about Chinese medicine TJQW in the treatment of this vicious epidemic COVID-19, and help to address this pressing problem currently facing the world.

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Targeting ERK-Hippo Interplay in Cancer Therapy

International Journal of Molecular Sciences ◽

10.3390/ijms21093236 ◽

2020 ◽

Vol 21 (9) ◽

pp. 3236 ◽

Cited By ~ 2

Author(s):

Karel Vališ ◽

Petr Novák

Keyword(s):

Cancer Therapy ◽

Signaling Pathways ◽

Signaling Pathway ◽

Cross Talk ◽

Mapk Signaling ◽

Mapk Signaling Pathway ◽

Mitogen Activated Protein Kinase ◽

Cancer Therapies ◽

Anti Cancer ◽

Targeted Inhibition

Extracellular signal-regulated kinase (ERK) is a part of the mitogen-activated protein kinase (MAPK) signaling pathway which allows the transduction of various cellular signals to final effectors and regulation of elementary cellular processes. Deregulation of the MAPK signaling occurs under many pathological conditions including neurodegenerative disorders, metabolic syndromes and cancers. Targeted inhibition of individual kinases of the MAPK signaling pathway using synthetic compounds represents a promising way to effective anti-cancer therapy. Cross-talk of the MAPK signaling pathway with other proteins and signaling pathways have a crucial impact on clinical outcomes of targeted therapies and plays important role during development of drug resistance in cancers. We discuss cross-talk of the MAPK/ERK signaling pathway with other signaling pathways, in particular interplay with the Hippo/MST pathway. We demonstrate the mechanism of cell death induction shared between MAPK/ERK and Hippo/MST signaling pathways and discuss the potential of combination targeting of these pathways in the development of more effective anti-cancer therapies.

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Identification of the Crucial Gene in Overflow Arteriovenous Fistula by Bioinformatics Analysis

Frontiers in Physiology ◽

10.3389/fphys.2021.621830 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhengde Zhao ◽

Qining Fu ◽

Liangzhu Hu ◽

Yangdong Liu

Keyword(s):

Signaling Pathways ◽

Signaling Pathway ◽

Intimal Hyperplasia ◽

Enrichment Analysis ◽

Mapk Signaling ◽

Mapk Signaling Pathway ◽

Biological Processes ◽

Hub Genes ◽

Av Fistula ◽

Core Genes

Objective: The aim was to study the preliminary screening of the crucial genes in intimal hyperplasia in the venous segment of arteriovenous (AV) fistula and the underlying potential molecular mechanisms of intimal hyperplasia with bioinformatics analysis.Methods: The gene expression profile data (GSE39488) was analyzed to identify differentially expressed genes (DEGs). We performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of DEGs. Gene set enrichment analysis (GSEA) was used to understand the potential activated signaling pathway. The protein–protein interaction (PPI) network was constructed with the STRING database and Cytoscape software. The Venn diagram between 10 hub genes and gene sets of 4 crucial signaling pathways was used to obtain core genes and relevant potential pathways. Furthermore, GSEAs were performed to understand their biological functions.Results: A total of 185 DEGs were screened in this study. The main biological function of the 111 upregulated genes in AV fistula primarily concentrated on cell proliferation and vascular remodeling, and the 74 downregulated genes in AV fistula were enriched in the biological function mainly relevant to inflammation. GSEA found four signaling pathways crucial for intimal hyperplasia, namely, MAPK, NOD-like, Cell Cycle, and TGF-beta signaling pathway. A total of 10 hub genes were identified, namely, EGR1, EGR2, EGR3, NR4A1, NR4A2, DUSP1, CXCR4, ATF3, CCL4, and CYR61. Particularly, DUSP1 and NR4A1 were identified as core genes that potentially participate in the MAPK signaling pathway. In AV fistula, the biological processes and pathways were primarily involved with MAPK signaling pathway and MAPK-mediated pathway with the high expression of DUSP1 and were highly relevant to cell proliferation and inflammation with the low expression of DUSP1. Besides, the biological processes and pathways in AV fistula with the high expression of NR4A1 similarly included the MAPK signaling pathway and the pathway mediated by MAPK signaling, and it was mainly involved with inflammation in AV fistula with the low expression of NR4A1.Conclusion: We screened four potential signaling pathways relevant to intimal hyperplasia and identified 10 hub genes, including two core genes (i.e., DUSP1 and NR4A1). Two core genes potentially participate in the MAPK signaling pathway and might serve as the therapeutic targets of intimal hyperplasia to prevent stenosis after AV fistula creation.

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Deciphering the Active Ingredients and Molecular Mechanisms of Tripterygium hypoglaucum (Levl.) Hutch against Rheumatoid Arthritis Based on Network Pharmacology

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2020/2361865 ◽

2020 ◽

Vol 2020 ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Yunbin Jiang ◽

Mei Zhong ◽

Fei Long ◽

Rongping Yang

Keyword(s):

Rheumatoid Arthritis ◽

Signaling Pathways ◽

Molecular Mechanisms ◽

Venn Diagram ◽

Network Pharmacology ◽

Pathway Enrichment Analysis ◽

Clinical Effects ◽

Overlapping Genes ◽

Active Ingredients ◽

Tripterygium Hypoglaucum

Tripterygium hypoglaucum (Levl.) Hutch (THH) shows well clinical effect on rheumatoid arthritis (RA), but the active ingredients and molecular mechanisms remain unclear. This work was designed to explore these issues by network pharmacology. Compounds from THH were gathered by retrieving literatures. Compound-related and RA-related genes were identified using databases, and the overlapping genes were identified by Venn diagram. The active ingredients and genes of THH against RA were confirmed by dissecting interactions between overlapping genes and compounds using Cytoscape. SystemsDock website was used to further verify the combining degree of key genes with active ingredients. Pathway enrichment analysis was performed to decipher the mechanisms of THH against RA by Database for Annotation, Visualization and Integrated Discovery. A total of 123 compounds were collected, and 110 compounds-related and 1871 RA-related genes were identified, including 64 overlapping genes. The target genes and active ingredients of THH against RA comprised 64 genes and 17 compounds, the focus of which was PTGS2, triptolide, and celastrol. SystemsDock website indicated that the combing degree of PTGS2 with triptolide or celastrol was very good. The mechanisms of THH against RA were linked to 31 signaling pathways, and the key mechanism was related to inhibition of inflammation response through inactivating TNF and NF-kappa B signaling pathways. This work firstly explored the active ingredients and mechanisms of THH against RA by network pharmacology and provided evidence to support clinical effects of THH on RA.

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Cross-talk of Signaling Pathways in the Pathogenesis of Allergic Asthma and Cataract

Protein and Peptide Letters ◽

10.2174/0929866527666200207113439 ◽

2020 ◽

Vol 27 (9) ◽

pp. 810-822

Author(s):

Yang Zhao ◽

Sumei Liu ◽

Xiangsheng Li ◽

Zhenzhen Xu ◽

Lifang Hao ◽

...

Keyword(s):

Signaling Pathways ◽

Allergic Asthma ◽

Signaling Pathway ◽

Academic Research ◽

Notch Signaling Pathway ◽

Mapk Signaling ◽

Chronic Inflammatory Disease ◽

Smad Signaling Pathway ◽

Immune Imbalance ◽

Cellular Components

: Allergic asthma is a chronic inflammatory disease, which involves many cellular and cellular components. Cataract is a condition that affects the transparency of the lens, which the opacity of the lens caused by any innate or acquired factor degrades its transparency or changes in color. Both of them belong to diseases induced by immune disorders or inflammation. We want to confirm the signaling pathways involved in the regulation of asthma and cataract simultaneously, and provide reference for the later related experiments. So we conducted a scoping review of many databases and searched for studies (Academic research published in Wiley, Springer and Bentham from 2000 to 2019) about the possible relationship between asthma and cataract. It was found that during the onset of asthma and cataract, Rho/Rock signaling pathway, Notch signaling pathway, Wnt/β-catenin signaling pathway, PI3K/AKT signaling pathway, JAK/STAT signaling pathway, MAPK signaling pathway, TGF-β1/Smad signaling pathway and NF-κB signaling pathway are all active, so they may have a certain correlation in pathogenesis. Asthma may be associated with cataract through the eight signaling pathways, causing inflammation or immune imbalance based on allergy that can lead to cataract. According to these studies, we speculated that the three most likely signaling pathways are PI3K/AKT, MAPK and NF-κB signaling pathway.

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A Bioinformatics Investigation into the Pharmacological Mechanisms of Sodium-Glucose Co-transporter 2 Inhibitors on Diabetes Mellitus and Heart Failure based on Network Pharmacology

10.21203/rs.3.rs-231920/v1 ◽

2021 ◽

Author(s):

Ziling Mai ◽

Huanqiang Li ◽

Guanzhong Chen ◽

Enzhao Chen ◽

Liwei Liu ◽

...

Keyword(s):

Heart Failure ◽

Signaling Pathway ◽

Drug Target ◽

Kinase Inhibitor ◽

Target Prediction ◽

Mapk Signaling ◽

Mendelian Inheritance ◽

Sglt2 Inhibitors ◽

Network Pharmacology ◽

Pharmacological Mechanism

Abstract BackgroundDiabetes mellitus (DM) is a major risk factor for the development of heart failure (HF). Sodium-glucose co-transporter 2 (SGLT2) inhibitors have been demonstrated consistent benefits in the reduction of hospitalization for HF in patients with DM. However, the pharmacological mechanism is not clear. To investigate the mechanisms of SGLT2 inhibitors on HF and DM, we performed target prediction and network analysis by network pharmacology method.Material/MethodsWe selected targets of SGLT2 inhibitors according to SwissTargetPrediction and DrugBank databases and collected therapeutic targets on HF and DM from the Human Gene (GeneCards) and Human Mendelian Inheritance (OMIM) databases. The “Drug-Target” and “Drug-Target-Disease” networks were constructed by using Cytoscape_v3.6.1. Then the protein-protein interaction (PPI) was analyzed by using the String database. Gene Ontology (GO) biological functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were performed to investigate by using Bioconductor tool for analysis.ResultsThere were 125 effective targets among SGLT2 inhibitors, HF and DM. Through further screening and analyzing, 33 core targets were obtained, such as SRC, MAPK1, NARS, MAPK3 and EGFR. And it is predicted that Rap1 signaling pathway, MAPK signaling pathway, EGFR tyrosine kinase inhibitor resistance, AGE-RAGE signaling pathway in diabetic complications and other signaling pathways were involved in the treatment of HF and DM by SGLT2 inhibitors.ConclusionsOur study elucidated the possible mechanisms of SGLT2 inhibitors from a systemic and holistic perspective based on pharmacological networks. The key targets and pathways will provide new insights for further research on the pharmacological mechanism of SGLT2 inhibitors in the therapy of HF and DM.

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Network Pharmacology Study Reveals the Mechanism of Astragali Radix in Treatment of Diabetic Nephropathy

10.21203/rs.3.rs-42374/v1 ◽

2020 ◽

Author(s):

Chongmei Tian ◽

Jing-bai Chen ◽

Xiang Chen ◽

Dao-zong Xia

Keyword(s):

Diabetic Nephropathy ◽

Signaling Pathway ◽

Mapk Signaling ◽

Mapk Signaling Pathway ◽

Network Pharmacology ◽

Signal Pathways ◽

Therapeutic Effects ◽

Disease Network ◽

Astragali Radix ◽

Target Disease

Abstract Background Diabetic nephropathy (DN), a unique complication of diabetes, could contribute to an increase in mortality. In this study, we predicted and proved the molecular pharmacological mechanism concerning the protective effects of Astragali Radix on DN. Methods The same potential target genes from Astragali Radix and DN were analyzed and constructed the protein interaction network. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment-related major targets and signal pathways were performed. The drug-ingredients-target-disease network was visually built using Cytoscape 3.6.1. The beneficial pharmacological activities of quercetin from Astragali Radix were confirmed by CCK-8 assay, determination of antioxidant parameters and Western blotting analysis. Results There are 12 bioactive components from Astragali Radix and 56 same targets between Astragali Radix and DN. The GO analysis results showed that the biological processes mainly included protein homodimerization activity. KEGG analysis indicate that the screened targets were most closely linked to the mitogen-activated protein kinase (MAPK) signaling pathway. The drug-ingredients-target-disease network results revealed that the therapeutic effects of Astragali Radix mainly included oxidative stress, inflammatory reaction and apoptosis. During the verification process, quercetin from Astragali Radix could attenuate cytotoxicity, enhance catalase (CAT) and superoxide dismutase (SOD) activities and suppress MAPK signaling pathway. Conclusions In the current study, network pharmacology with experimental analysis predicted and proved the therapeutic function of Astragali Radix by improving antioxidant capacity and suppressing MAPK signaling pathway, these investigations could provide a new perspective for further exploration of Astragali Radix on DN treatment.

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Huanglian Jiedu Decoction Exerts Antipyretic Effect by Inhibiting MAPK Signaling Pathway

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2021/2209574 ◽

2021 ◽

Vol 2021 ◽

pp. 1-13

Author(s):

Xing Li ◽

Shizhang Wei ◽

Xiao Ma ◽

Haotian Li ◽

Manyi Jing ◽

...

Keyword(s):

Signaling Pathway ◽

Western Blotting ◽

Mapk Signaling ◽

Mapk Signaling Pathway ◽

Network Pharmacology ◽

Potential Mechanism ◽

Model Group ◽

Rat Serum ◽

Antipyretic Effect ◽

Tnf Α

Aim. The aim of this study was to explore the antipyretic effect and potential mechanism of Huanglian Jiedu Decoction (HLJDD) on LPS-induced fever in rats. Materials and Methods. The fever rat model was established by LPS. Anal temperature of rats was measured every 1 hour after modeling. TNF-α, IL-6, PGE2, and cAMP in rat serum or hypothalamus tissue were detected by ELISA kit. In order to explore the potential active ingredients and mechanism of antipyretic effect of HLJDD, we predicted the underlying antipyretic mechanism by using network pharmacology and then verified its mechanism by Western Blotting. Results. The results showed that HLJDD can alleviate LPS-induced fever in rats. The expression levels of TNF-α, IL-6, PGE2, and cAMP in the treatment group were significantly lower than those in the model group. Western Blotting results showed that the protein expression of p-ERK, p-JNK, and p-P38 was significantly inhibited. Conclusion. The findings suggest that HLJDD has a good antipyretic effect on LPS-induced fever in rats, which may be closely related to the inhibition of MAPK signaling pathway.

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A network pharmacology approach to explore the mechanisms of action of Epimrdii Herba-Coicis Semen for treatment of Alzheimer's disease

10.21203/rs.3.rs-20651/v1 ◽

2020 ◽

Author(s):

Yuxuan Zhou

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Signaling Pathways ◽

Mapk Signaling ◽

Venn Diagram ◽

Network Pharmacology ◽

Pharmacokinetic Parameters ◽

Neuron Death

Abstract Background: Traditional Chinese medicine (TCM) can treat diseases through its “multi-component, multi-target, multi-pathway” mechanisms. Especially have advantages in the treatment of diseases with complicated pathogenesis, such as Alzheimer’s disease (AD). Tonifying the kidney and strengthening the spleen is one of the common methods of Chinese Medicine to treat AD. The TCM combination of Epimrdii Herba and Coicis Semen can be used as the main drugs of a prescription for tonifying the kidney and strengthening the spleen. However, the mechanisms for Epimrdii Herba-Coicis Semen (EH-CS) to treat AD is vague. The purpose of this study was to explore the mechanisms of EH-CS on AD using a network pharmacological method.Methods: We retrieved the chemical compounds and targets of Epimrdii Herba-Coicis Semen from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). We screened the active ingredients based on the pharmacokinetic parameters (ADME). The Human Gene Database (GeenCards) was used to obtain disease targets of Alzheimer’s disease. Then we drew a venn diagram to obtain common targets of Chinese medicine and disease. Based on the topological properties, we screened the key targets. The protein-protein interaction (PPI) network was constructed using the STRING database, and the "Traditional Chinese Medicine-active ingredient-target" network was constructed using Cytoscape software. The key targets were respectively uploaded to the Metascape and DAVID database for GO and KEGG pathway analysis.Results: We obtained 31 active compounds for EH-CS. Flavonoids play important roles in the treatment of AD. A total of 29 key targets, including AKT1, MAPK1, and TP53, etc. The biological processes involve response to lipopolysaccharide, neuron death, neuroinflammatory response, etc. The main pathways include TNF signaling pathways, MAPK signaling pathways, PI3K-Akt signaling pathways and other signaling pathways.Conclusion: The network pharmacology method is an effective tool for exploring the mechanisms of TCM. Based on network pharmacology, this study systematically explained the potential mechanisms of EH-CS on AD. It provides a valuable reference for the development of AD drugs.

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