Chemoproteomics reveals Ailanthone directly binds to PKM2 to inhibit the progression of Hepatocellular carcinoma

Background

Hepatocellular Carcinoma (HCC) is a widely recognized aggressive tumor, owing primarily to its high recurrence and metastasis risk. On the other hand, Ailanthone (AIL), a natural plant derivative, has demonstrated diverse pharmacological properties and a capacity to induce cell death among other mechanisms. Consequently, it could be employed to suppress HCC proliferation. Nonetheless, AIL’s precise targets and mechanisms of action in inhibiting HCC cell growth remain unclear, forming the basis of this study.

Purpose

To investigate the role and molecular mechanisms of AIL in inducing SMMC-7721 cell apoptosis and identify its key action targets.

Methods

First, the potential pathways and targets of AIL-induced cell death were identified via transcriptomics sequencing analyses. The impact of AIL on HCC cell growth was then evaluated both in vivo and in vitro, with the underlying mechanisms validated further. Finally, molecular docking, Molecular Dynamics (MD) simulation techniques, and Surface Plasmon Resonance (SPR) experiments were employed to elucidate AIL’s binding target.

Results

Our findings revealed that AIL could inhibit Pyruvate Kinase M2 (PKM2) expression, thus suppressing the aerobic glycolysis level of HCC cells. Mechanistically, AIL induced SMMC-7721 cell apoptosis via the PKM2/HSP90/HIF-1α signaling pathway. Furthermore, molecular docking, MD simulation, and SPR experiments confirmed AIL’s direct binding to PKM2. Specifically, AIL formed hydrogen bonds with PKM2 residues Lys311B, Leu353B, and Asp354A, accompanied by hydrophobic interactions with Phe26A/B and Leu353B.

Conclusion

By binding directly to PKM2, AIL exerts anti-tumor effects in SMMC-7721 cells, with glycolysis inhibition via PKM2/HSP90/HIF-1α signaling axis suppression as the potential mechanism, which could be leveraged in HCC treatment.