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pmid:32714406
Study on the Selection of the Targets of Esophageal Carcinoma and Interventions of Ginsenosides Based on Network Pharmacology and Bioinformatics.
Xin Yang · Yahui Li · Haibing Qian
Evidence-based complementary and alternative medicine : eCAM · 2020 doi:10.1155/2020/4821056
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Complete file
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Then, data associated with ESCA samples are downloaded from The Cancer Genome Atlas (TCGA) database for integrated analysis. Moreover, the effect of epithelial cell adhesion molecule (EpCAM) expression on the survival of patients with ESCA is evaluated by Kaplan-Meier and Cox analyses. The virtual screening is carried out using a Suflex-Dock molecular docking module. The chemical components, which have been well bound to EpCAM, are screened out based on a total score >5 as a threshold. Ginsenosides and EpCAM are analyzed by LigPlot + v.2.2 software to identify the binding sites.\nRESULTS: Four ESCA targets are obtained from GeneCards, DisGeNET, and GEO databases. In this study, it is found that high EpCAM expression is associated with histologic grade, stage, patient age, N classification, T classification, and radiation therapy. The Kaplan-Meier curves for overall survival also show that the higher expression of EpCAM is associated with worse outcomes in patients with ESCA. Univariate and multivariate Cox analyses indicate that EpCAM mRNA expression might be a useful biomarker for ESCA(P < 0.05). Molecular docking technology suggests that ginsenoside Rg3 and ginsenoside Rh2 can easily establish good docking modes and have a high affinity with EpCAM. The 6'-hydroxyl and 6″-hydroxyl on the 3-glycosyl of ginsenoside Rg3 are prone to form hydrogen bonds (Lys151 and Lys221) with the active sites of EpCAM ligand binding domain. The hydroxyl groups on the 12 sites of the ginsenoside Rh2 glycoside framework are found to have hydrogen bonding with Leu240. The formation of hydrogen bonds plays an important role in binding of ginsenoside Rg3 and ginsenoside Rh2 to EpCAM, as well as the stability of EpCAM conformation.\nCONCLUSION: EpCAM may be determined as a potential biomarker for early diagnosis and prognosis of ESCA. Ginsenoside Rg3 and ginsenoside Rh2 have potential antiesophageal cancer activities. 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High EpCAM Expression Is an Independent Risk Factor for Overall Survival among ESCA Patients", "row_count": 10, "column_count": 7}, "table": {"label": "Table 3", "caption": "Univariate analysis and multivariate analysis of the correlation of EpCAM expression with OS among ESCA patients.", "rows": [["Parameter", "Univariate analysis", "Multivariate analysis"], ["HR", "95% CI", "P", "HR", "95% CI", "P"], ["Age", "1.00", "0.98–1.03", "0.731", "1.02", "0.98–1.05", "0.323"], ["Gender", "4.23", "1.02–17.47", "0.046", "2.15", "0.49–9.46", "0.310"], ["Histologic grade", "1.48", "0.92–2.36", "0.102", "0.94", "0.53–1.66", "0.821"], ["Stage", "2.51", "1.68–3.75", "7.40E 06", "1.73", "0.57–5.27", "0.336"], ["T classification", "1.32", "0.90–1.94", "0.159", "1.14", "0.66–1.96", "0.633"], ["M classification", "3.64", "1.60–8.28", "0.002", "1.87", "0.27–13.09", "0.529"], ["N classification", "1.74", "1.27–2.39", "0.001", "1.34", "0.72–2.46", "0.363"], ["EpCAM", "1.00", "1.00–1.01", "0.004", "1.00", "1.00–1.01", "0.010"]], "row_count": 10, "column_count": 7, "numeric_cells": 50, "header_rows": 2, "locator": "section[14]/table-wrap[1]#tab3"}}, {"id": "asset:table:pmid:32714406:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b9621487032e985ae14d03fabd3b57152a43770b247b25b0e680c95c18e2df44", "bytes": 900, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#tab4", "version": null, "note": "The 2D protein-ligand interaction.", "structure": {"pmcid": "PMC7333027", "section_index": 15, "section_title": "3.6. Molecular Docking and Interaction", "row_count": 5, "column_count": 6}, "table": {"label": "Table 4", "caption": "The 2D protein-ligand interaction.", "rows": [["No.", "Compound name", "CAS", "Score", "Hydrogen bond", "Hydrophobic interactions"], ["1", "Ginsenoside Rg3", "14197-60-5", "5.91", "Lys151, Lys221", "Asp232, Leu242, Val220, Pro244, Gly222,Asp219, Phe216, Ile193, Glu169, Ile170,Leu166, Tyr174, Leu233"], ["2", "Ginsenoside Rh2", "78214-33-2", "5.24", "Leu240", "Glu169, Ile170, Leu233, Asp232, Asp241,Leu242, Pro244, Val220, Lys229, Asp219,Arg173, Phe216, Tye174, Leu166"], ["3", "Ginsenoside Rg5", "186763-78-0", "4.10", "Lys151, Asp241", "Tyr174, Glu169, Leu233, Leu242, Asp219,Asp232, Arg173, Pro244, Val220, Leu240,Ile170, Phe216, Leu148"], ["4", "Ginsenoside Rk3", "364779-15-7", "3.59", "Lys151, Asp241", "Gly222, Lys229, Arg173, Asp219, Asp232,Leu240, Leu233, Val220, Leu242, Pro244"]], "row_count": 5, "column_count": 6, "numeric_cells": 20, "header_rows": 1, "locator": "section[15]/table-wrap[1]#tab4"}}], "gaps": ["asset:data:geo:GSE1420 not downloaded", "asset:data:geo:GSE1420 licence not read", "asset:data:geo:GSE20347 not downloaded", "asset:data:geo:GSE20347 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-2", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "chi-square"}}, {"id": "method-3", "family": "contingency_analysis", "specific": "fisher_exact", "label": "Categorical (contingency table) analysis", "dsl_operations": ["contingency_table", "chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Fisher's exact"}}, {"id": "method-4", "family": null, "specific": null, "label": "Univariate and multivariate Cox analyses", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "A univariate Cox analysis is performed to select potential prognostic factors. A multivariate Cox analysis is conducted to verify the correlation between EpCAM expression and survival along with other clinical features. Univariate and multivariate Cox (Figure S2) analyses show that EpCAM expression is an independent risk factor for overall survival (OS) among ESCA patients (hazard ratio [HR] = 1.00, 95% confidence interval (CI): 1.00–1.01, P=0.01; Table 3). 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