Mechanism of Astragalus mongholicus Bunge ameliorating cerebral ischemia-reperfusion injury: Based on network pharmacology analysis and experimental verification.

ETHNOPHARMACOLOGICAL RELEVANCE: Astragalus mongholicus Bunge (AMB) is a herb with wide application in traditional Chinese medicine, exerting a wealth of pharmacological effects. AMB has been proven to have an evident therapeutic effect on ischemic cerebrovascular diseases, including cerebral ischemia-reperfusion injury (CIRI). However, the specific mechanism underlying AMB in CIRI remains unclear. AIM OF THE STUDY: This study aimed to investigate the potential role of AMB in CIRI through a comprehensive approach of network pharmacology and in vivo experimental research. METHODS: The intersection genes of drugs and diseases were obtained through analysis of the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database and Gene Expression Omnibus (GEO) database. The protein-protein interaction (PPI) network was created through the string website. Meanwhile, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was carried out using R studio, and thereafter the key genes were screened. Then, the molecular docking prediction was made between the main active ingredients and target genes, and hub genes with high binding energy were obtained. In addition, molecular dynamic (MD) simulation was used to validate the result of molecular docking. Based on the results of network pharmacology, we used animal experiments to verify the predicted hub genes. First, the rat middle cerebral artery occlusion and reperfusion (MACO/R) model was established and the effective dose of AMB in CIRI was determined by behavioral detection and 2,3,5-Triphenyltetrazolium chloride (TTC) staining. Then the target proteins corresponding to the hub genes were measured by Western blot. Moreover, the level of neuronal death was measured using hematoxylin and eosin (HE) and Nissl staining. RESULTS: Based on the analysis of the TCMSP database and GEO database, a total of 62 intersection target genes of diseases and drugs were obtained. The KEGG enrichment analysis showed that the therapeutic effect of AMB on CIRI might be realized through the advanced glycation endproduct-the receptor of advanced glycation endproduct (AGE-RAGE) signaling pathway in diabetic complications, nuclear factor kappa-B (NF-κB) signaling pathway and other pathways. Molecular docking results showed that the active ingredients of AMB had good binding potential with hub genes that included Prkcb, Ikbkb, Gsk3b, Fos and Rela. Animal experiments showed that AWE (60 g/kg) could alleviate CIRI by regulating the phosphorylation of PKCß, IKKß, GSK3ß, c-Fos and NF-κB p65 proteins. CONCLUSION: AMB exerts multi-target and multi-pathway effects against CIRI, and the underlying mechanism may be related to anti-apoptosis, anti-inflammation, anti-oxidative stress and inhibiting calcium overload.

Identification and analysis of a prognostic ferroptosis and iron-metabolism signature for esophageal squamous cell carcinoma.

Background: The role of ferroptosis in esophageal squamous cell carcinoma (ESCC) is still unclear. Methods: The association of iron metabolism and ferroptosis-related genes with the prognosis, copy number variation (CNV), TMB, and immune cell infiltration of ESCC was explored using data from the GEO and TCGA database and validated by immunofluorescence in 112 ESCC patients from our center. The potential anti-cancer drugs and compounds from the GDSC and the Connectivity Map database were also screened. Results: A total of 117 iron metabolism and ferroptosis-related genes were identified. We found the expressions of PRNP, SLC3A2, SLC39A8, and SLC39A14 negatively related to the prognosis of ESCC patients, while ATP6V0A1 and LCN2 were opposite, which was validated in 112 ESCC samples from our center. And a prognostic signature was constructed based on their expressions and Cox regression coefficient (ß). The low-score group exhibited a significantly worse OS. Besides, analysis of 179 ESCC samples from GSE53625 revealed that patients of poorly differentiation, more than 60 years, T4 stage, advanced N stage, advanced stage, and adjuvant therapy also exhibited a significantly shorter OS, based on which a nomogram to predict the OS was established. Moreover, the low-score group exhibited significantly higher CNV and TMB and more frequent mutations of TP53, MUC16, and NOTCH1. Higher proportion of Macrophages M2, and lower proportion of T cells follicular helper were observed in the low-score group. We discovered that AZD7762, Sunitinib, Cytarabine, Docetaxel, Vinblastine, and Elesclomol exhibited lower IC50 in the low-score group. And 20 potential compounds were identified from the CMap database. Conclusions: Six iron metabolism and ferroptosis-related genes were associated with the prognosis, CNV, TMB, and immune cell infiltration of ESCC. Some potential anti-cancer drugs and compounds may be helpful for OS.

Action mechanism of Roman chamomile in the treatment of anxiety disorder based on network pharmacology.

Anxiety disorder is a common psychiatric disease. Roman chamomile as medicine or tea has long been used as a mild tranquilizer to reduce anxiety, but the mechanism is unclear. This research is based on network pharmacology combined with database mining to find the ingredients, action pathways and key targets of Roman chamomile for the treatment of anxiety. About 126 common targets related to chamomile and anxiety were obtained, and these targets were involved in 56 KEGG pathways. GEO screened LRRK2 as a key protein, and molecular docking showed that the protein could stably bind to drug components. Roman chamomile has the characteristics of multi-target and multi-pathway in the treatment of anxiety disorder. Its possible mechanism is to intervene anxiety disorder in the process of disease development, such as neuroactive ligand-receptor interaction, serotonin synapse, and cAMP signaling pathway. LRRK2 may be an important gene for Roman chamomile in the treatment of anxiety disorder. PRACTICAL APPLICATIONS: Roman chamomile is well known for its use in medicine and tea making. It contains many nutrients, which can relieve people's anxiety, help sleep, antibacterial and anti-inflammatory. In this article, through network pharmacology combined with Gene Expression Omnibus data mining and molecular docking, the target and mechanism of Roman chamomile in the treatment of anxiety were discussed, and its efficacy was verified by model animals, which not only clarified its mechanism at the systematic level, but also proved to be effective at the biological level. It provides a reference for the further development and utilization of Roman chamomile.

Systematic Pharmacology and GEO Database Mining Revealed the Therapeutic Mechanism of Xuefu Zhuyu Decoration for Atherosclerosis Cardiovascular Disease.

Background: Xuefu Zhuyu decoration (XFZYD), as a traditional Chinese compound recipe, has been used to treat atherosclerosis cardiovascular disease (ASCVD) for thousands of years in China, but its effective compounds and underlying treatment molecular mechanism remains promiscuous, which severely limits its clinical application. Methods: The effective components and their targets of XFZYD were predicted and screened based on the Traditional Chinese Medicine System Pharmacology (TCMSP) database. The candidate therapeutic targets of ASCVD were screened by Pharmacogenomics Knowledgebase (PharmGKB) and Comparative Toxicogenomics Database (CTD). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses for target proteins were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) database. Differentially expressed genes were identified using the GEO2R online tool. Molecular docking was performed by Schrodinger software. To assess the efficacy of the prediction, human umbilical vein endothelial cells (HUVECs) treated with the effective compound of XFZYD were used as the in vitro model. Results: A total of 108 effective compounds (including quercetin) and 137 candidate therapeutic targets were identified. Analyzing the relationships among effective compounds, candidate therapeutic targets, and signaling pathways, the therapy mechanisms of XFZYD were mainly reflected in the protection of vascular endothelium, anti-inflammatory, antioxidant stress, etc. Accordingly, we found the effective compound of XFZYD (quercetin) decreased intracellular adhesion molecule 1 (ICAM-1) and vascular cell adhesion molecule 1 (VCAM-1) expressions and pro-inflammatory cytokines in HUVECs treated with lipopolysaccharide (LPS), and reduced the adhesion function of HUVECs with monocytes. The inhibitor of the predicted target protein (PTGS2) could further reduce the expressions of VCAM-1, ICAM-1, and TNF-α induced by LPS, and inhibit the adhesion function of HUVECs with monocytes, while PTGS2 agonists partially counteracted the protective effect of quercetin. Conclusions: In this study, the effective components and potential therapeutic targets of XFZYD for ASCVD treatment were explored from the perspective of systemic pharmacology. The effective component quercetin was verified to protect endothelial cells by reducing endothelial inflammatory response and impeding the attachment of monocytes against the predicted therapeutic target PTGS2.

Mechanism of anti-hepatoma of Rhei Radix et Rhizoma based on integrative pharmacology platform, GEO database chip and molecular docking / 中草药

Objective: To investigate the anti-hepatoma active components of Rhei Radix et Rhizoma and their molecular mechanisms through GEO database, integrative pharmacology platform and molecular docking technology. Method: The active ingredients of Rhei Radix et Rhizoma were screened by TCMIP and the corresponding targets of these components were predicted through TCMIP and Swisstarget databases. The hepatoma gene chip database was downloaded from GEO databases, and the differentially expressed genes between hepatocellular carcinoma (HCC) and normal liver tissue were analyzed by GEO2R. Based on the matching results of potential targets of Rhei Radix et Rhizoma and the targets of hepatoma, the key targets of Rhei Radix et Rhizoma against hepatoma were screened, and GO function enrichment and KEGG pathway enrichment analysis of the key targets were performed. Main components and core targets of Rhei Radix et Rhizoma against hepatoma were analyzed and screened by constructing PPI network, component-target network and traditional Chinese medicine-component-target-pathway network. Furthermore, the molecular docking between the core targets and the main active components was performed by Schrodinger-Maestro software to virtually verify their binding ability and analyze their binding mode. Result: A total of 20 anti-hepatoma active components of Rhei Radix et Rhizoma were collected and related 86 targets were obtained, including CDK1, AKR1C3, PTGS2, AR and CCNB1, etc. The results of GO functional enrichment mainly focused on the cell cycle, G2/M transition of mitotic cell cycle, oxidation-reduction process, drug reactions and steroid metabolism processes, etc. The results of KEGG pathway enrichment mainly involved cell cycle, cell senescence, complement system, arachidonic acid metabolism and bile metabolism, and these metabolic pathways were related to cell apoptosis, metastasis, inflammation and immunity. The results of molecular docking showed that 92.2% of the active components had good binding ability with the 10 core proteins, and the main combination forms mainly were hydrogen bonds, hydrophobic bonds, π-π bonds and cation-π. Conclusion: The active components of Rhei Radix et Rhizoma including rhein, emodin, chrysophanol-8-O-β-D-glucopyranoside, chrysophanol-1-O-β-D-glucoside and rhapontigenin can act on multiple targets such as CDK1, CCNB1, CYP2C9, MMP9 and PTGS2, by regulating signaling pathways related to cell apoptosis, metastasis, inflammation and immunity to play an anti-hepatoma effect.

Identification of possible molecular markers and functional gene modules associated with lung adenocarcinoma based on weighted co-expression network analysis method / 中草药

Objective: The potential biological targets for anti-lung adenocarcinoma of Solanum nigrum were scored using the weighted co-expression network analysis (WGCNA) method. Methods: A database of chemical components of S. nigrum was established through oral bioavailability (OB), drug-likeness (DL) based on Traditional Chinese Medicine Systems Pharmacology (TCMSP) and literature retrieval. The targets of active ingredients of S. nigrum were predicted based on reverse docking with DRAR-CPI server, and combined with WGCNA to mine GSE10072 dataset in Gene Expression Omnibus (GEO) database to obtain coexpression gene module. Furthermore, the potential anti-lung adenocarcinoma targets of S. nigrum were confirmed under intersected with predicted targets and coexpression genes. The GO terms of biological processes and KEGG pathway enrichment analysis of predicted targets and anti-lung adenocarcinoma targets were performed by Metascape database, respectively. Using the targets-pathways networks to study the mechanisms of S. nigrum in the fight against cancer. The transcriptional level expression of key String database combined with Cytoscape software to draw the proteins-proteins interactions (PPI), and active ingredients-targets-pathways networks to study the mechanisms of S. nigrum in the fight against cancer. The transcriptional level expression of key genes in lung adenocarcinoma cancer tissues and normal lung tissues was assessed based on UALCAN dataset. And the correlation between key genes and prognosis of lung cancer patients was calculated by KM plotter analysis. Results: This study collected nine active components of S. nigrum, including medioresinol, sitosterol, diosgenin, solanocapsine, quercetin, α-chaconine, solasonin, solamargine, and solasodine. Totally 271 targets were predicted, and 41 potential anticancer targets were confirmed. The potential regulatory pathways included pathway in cancer, PI3K-Akt signaling pathway, chemical carcinogenesis, central carbon metabolism in cancer and so on. From the PPI network, we found that hub genes EGFR, CASP8, HPGDS, FYN, and high expression of EGFR and CASP8 were related to the poor overall survival in patient with lung adenocarcinoma. Oncontrary, lower expression of HPGDS and FYN were also associated with poor overall survival. Conclusion: This study reflects the multi-component, multi-target and multi-pathway features of S. nigrum, and provides a scientific basis for anticancer substance and elucidating the mechanisms of action of S. nigrum, as well as a reference for the study of mechanisms.