Network pharmacology and transcriptomic analysis reveal wogonin as a key bioactive compound of Scutellaria baicalensis Georgi in suppressing glioma progression via PI3K-Akt pathway suppression.

Glioblastoma (GBM) remains one of the most lethal brain tumors due to pronounced heterogeneity and persistent activation of oncogenic signaling. This study aimed to identify bioactive constituents of Scutellaria baicalensis Georgi (SBG) with anti-GBM potential and to elucidate their molecular mechanisms. An integrated multi-layered strategy combining network pharmacology, molecular docking, molecular dynamics simulations, transcriptomic profiling, and in vitro functional assays was employed. Wogonin, a top-ranked SBG-derived flavonoid, was selected for experimental validation. Functional and mechanistic studies were primarily conducted in U251 cells, including proliferation, migration, clonogenicity, cell-cycle distribution, apoptosis, and pathway interrogation. U87MG cells were used as an independent validation model. Sub-cytotoxic concentrations were applied to distinguish specific anti-migratory effects from general cytotoxicity. Rescue experiments using the AKT activator SC79 were performed to establish mechanistic causality. Clinical relevance was assessed using TCGA‑GBM transcriptomic datasets. Network pharmacology analysis identified 32 active SBG compounds targeting 362 GBM-associated proteins, with enrichment in the PI3K-Akt signaling pathway. Functional screening demonstrated that wogonin exhibited the most potent anti-GBM activity among candidate compounds. In U251 cells, wogonin significantly suppressed proliferation, migration, and clonogenicity, induced G2/M cell-cycle arrest, and promoted apoptosis. Transcriptomic profiling revealed extensive gene expression reprogramming, with coordinated downregulation of PI3K-Akt pathway components, which was further confirmed by reduced phosphorylation of PI3K and AKT. Importantly, these effects were partially reversed by SC79-mediated AKT activation, establishing a causal role of AKT inhibition in wogonin-induced phenotypes. Low-dose assays demonstrated that wogonin inhibited migration under sub-cytotoxic conditions, excluding non-specific cytotoxicity as the primary driver. These findings were further validated in U87MG cells, confirming the reproducibility of both phenotypic and mechanistic effects across GBM models. Molecular docking and molecular dynamics simulations supported stable binding of wogonin to AKT1 and PIK3CA, providing mechanistic plausibility for the observed pathway inhibition. TCGA‑GBM analysis identified AKT1 as a clinically relevant prognostic factor. This study demonstrates that wogonin acts as a key bioactive constituent of SBG and suppresses GBM progression through AKT1-centered PI3K-Akt pathway inhibition, with rescue experiments supporting a causal contribution of AKT suppression to the observed phenotypes. By integrating multi-omics analysis with functional and rescue-based validation, this work provides mechanistic evidence supporting wogonin as a promising compound for further preclinical evaluation in GBM.