Integrating Network Pharmacology and Experimental Verification to Explore the Pharmacological Mechanisms of Radix Paeoniae Rubra Against Glioma.
Glioma has a high mortality and can hardly be completely cured. Radix Paeoniae Rubra (RPR) is a prevalent component in traditional Chinese medicine used for tumor treatments. We explored the mechanism of RPR in treating glioma using network pharmacology and experiments. A network pharmacology approach was used to screen active ingredients, targets of RPR and glioma. We then constructed a herb-active ingredient-target-pathway network and conducted protein-protein interaction (PPI) network analysis, as well as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Molecular docking was also performed. Using CCK-8, colony formation, and xenograft experiments, we evaluated the effect of RPR on glioma. The involved pathway and proteins were identified by Western blot. From public databases, we identified nine active RPR ingredients and 40 overlapping targets among 109 RPR targets and 1360 glioma-associated targets. The PPI analysis revealed ten targets, such as AKT1, TP53, and VEGFA, which were identified as hub genes. The results from GO and KEGG analysis highlighted the involvement of the PI3K/AKT pathway. A herb-active ingredient-target-pathway network was constructed. By docking molecular structures, six suitable conformations have been identified. The RPR extract demonstrated anti-tumor properties by inhibiting glioma cell proliferation in vitro and in vivo, likely achieved by suppressing the phosphorylation of the PI3K/AKT signaling pathway. RPR concurrently downregulated the phosphorylation level of AKT1 and the protein expression level of VEGFA, while upregulating the expression of P53 in the U251 cell line. Utilizing network pharmacology and molecular docking, our study not only predicted the impact of RPR on glioma but also delineated the herb-active ingredient-target-pathway network. Experimentally, we confirmed that RPR may exert its anti-tumor properties by inhibiting the phosphorylation of the PI3K/AKT pathway, including AKT1, and by regulating the expression levels of VEGFA and P53.
Pubmed ID: 38381309 RIS Download
Research resources used in this publication
- GraphPad Prism (RRID:SCR_002798) (software resource)
- Odyssey CLx (RRID:SCR_014579) (software resource)
- ImageJ (RRID:SCR_003070) (software resource)
- U-251MG (RRID:CVCL_0021) (cell line)
- AutoDock (RRID:SCR_012746) (software resource)
- PyMOL (RRID:SCR_000305) (software resource)
- Open Babel (RRID:SCR_014920) (data processing software)
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) (data repository)
- Metascape (RRID:SCR_016620) (software resource)
- DAVID (RRID:SCR_001881) (software resource)
- Cytoscape (RRID:SCR_003032) (software resource)
- STRING (RRID:SCR_005223) (data or information resource)
- GeneCards (RRID:SCR_002773) (data or information resource)
- DisGeNET (RRID:SCR_006178) (data or information resource)
- UniProtKB (RRID:SCR_004426) (data repository)
- PubChem (RRID:SCR_004284) (data repository)
Additional research tools detected in this publication
None foundAntibodies used in this publication
- Goat anti-Rabbit IgG H&L (IRDye® 800CW) preadsorbed (RRID:AB_2925189)
- VEGF antibody (RRID:AB_2212642)
- p53 antibody (RRID:AB_11155283)
- AKT1 (phospho S473) antibody [EP2109Y] (RRID:AB_2224551)
- Rabbit Anti-AKT Polyclonal Antibody, Unconjugated (RRID:AB_940188)
- Phospho-PI3 Kinase p85 (Tyr458)/p55 (Tyr199) Antibody (RRID:AB_659940)
- Anti-PI3 Kinase p85 Antibody, Unconjugated (RRID:AB_329869)
- pan-AKT (phospho T308) antibody (RRID:AB_722678)
- pan-AKT antibody (RRID:AB_722674)
- GAPDH antibody [6C5] (RRID:AB_2107448)
Associated grants
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Goat anti-Rabbit IgG H&L (IRDye® 800CW) preadsorbed (antibody)
RRID:AB_2925189
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This monoclonal targets Akt1
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This polyclonal targets
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This polyclonal targets AKT1 (phospho T308)
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RRID:AB_722674
This polyclonal targets pan-AKT antibody
View all literature mentionsGAPDH antibody [6C5] (antibody)
RRID:AB_2107448
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RRID:SCR_014579
A data analysis software developed to simplify and record data from fluorescent related assays such as Western Blots, EMSAs, and Western Assays. This software will consolidate all of the resulting data into one easy-to-track image, and thus removes the need for multiple exposures, as well as standardizing the resulting fluorescent bands without image saturation, blowout, or removed sensitivity. Odyssey CLx is capable of scanning multiple mini-blots, microplates, or slides at the same time.
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RRID:CVCL_0021
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RRID:SCR_012746
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RRID:SCR_000305
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RRID:SCR_003032
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RRID:SCR_005223
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RRID:SCR_002773
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RRID:SCR_004426
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RRID:SCR_004284
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