Abstract / Summary
Bladder cancer (BCa) remains a therapeutically challenging malignancy with limited targeted treatment options. Natural products from food–medicine homology resources offer a promising reservoir for discovering bioactive compounds with favorable safety profiles, yet their mechanisms of action often remain incompletely characterized. A multi‑omics strategy integrating computational ADMET profiling, network pharmacology, single‑cell transcriptomics, and multi‑layer experimental validation was employed to systematically evaluate the anti‑BCa potential of twelve metabolites from Myrica rubra. Target identification was performed through reverse virtual screening, protein–protein interaction network analysis, and molecular docking. The core target was validated by gene dependency analysis, and its cell‑type‑specific expression pattern was examined using public scRNA‑seq datasets. Anti‑proliferative, pro‑apoptotic, and anti‑metastatic effects were assessed in UM‑UC‑3 and T24 cells in vitro, and tumor growth inhibition was evaluated in a subcutaneous xenograft model in vivo. Myricetin was identified as the top candidate compound, directly binding to the ATP‑binding pocket of HSP90AA1 with a Vina score of − 8.9 kcal/mol through hydrogen bonds with TYR‑139, ASP‑93, and ASN‑51. Myricetin treatment significantly suppressed BCa cell viability, reduced colony formation, inhibited migration and invasion, and induced apoptosis in a concentration‑dependent manner, accompanied by downregulation of CCND1 and BCL‑2, upregulation of BAX, and activation of caspase‑3. Flow cytometric analysis further confirmed that myricetin induces G1 phase cell cycle arrest in BCa cells. Mechanistically, myricetin reduced HSP90AA1 expression and selectively suppressed PI3K and AKT phosphorylation without affecting total protein levels. Rescue experiments using tamoxifen confirmed that these effects were mediated at least in part through HSP90AA1 engagement. In vivo, myricetin (60 mg/kg) significantly suppressed UM‑UC‑3 xenograft growth without causing body weight loss. Single‑cell transcriptomic analysis revealed that HSP90AA1 is preferentially enriched in BC_3 and BC_4 subpopulations, which occupy the root of the developmental trajectory and exhibit elevated PI3K–Akt pathway activity, suggesting a potential subpopulation‑specific vulnerability that warrants further investigation. Myricetin directly targets HSP90AA1 and suppresses PI3K–Akt signaling to inhibit BCa progression. These findings provide a mechanistic framework for myricetin as a lead compound from food–medicine homology resources, warranting further pharmacokinetic optimization and clinical investigation.