Background: Microtubules are attractive targets for anticancer drugs. However, the microtubule-targeting agents (MTAs) currently in clinical use exhibit inevitable drug resistance. Therefore, there is an urgent need to discover novel MTAs for the clinical treatment of cancer. Methods: Bioactive compounds extracted from Lithospermum erythrorhizon were assessed for in vitro anti-proliferative activities against a panel of human cancer cell lines using cell counting kit-8 (CCK-8) assay. Tubulin polymerization inhibition assay, colchicine competitive binding site assay, and immunofluorescence were used to validate the tubulin inhibition effect of acetylshikonin. Flow cytometry, Hoechst staining, and caspase-3 activity evaluation were performed to assess cell cycle arrest and cell apoptosis. 5,5',6,6'-tetrachloro-1,1',3,3'-tetramethylbenzimidazolylcarbocyanine iodide (JC-1) staining and dichloro-dihydro-fluorescein diacetate (DCFH-DA) staining were used to evaluate mitochondrial membrane potential (MMP) and reactive oxygen species (ROS), respectively. Results: Acetylshikonin exhibited potent anti-proliferative activities against a panel of human cancer cell lines (IC₅₀ values: 1.09–7.26 µM) and displayed comparable cytotoxicity against several drug-resistant cell lines. Further mechanism studies revealed that acetylshikonin induced cell cycle arrest of MHCC-97H cells at G₂/M phase, and significantly promoted apoptosis marked by a collapse of MMP and abnormal ROS accumulation. Conclusions: In this study, acetylshikonin was identified as MTA against hepatocellular carcinoma and can serve as a promising lead compound for further development of anti-cancer drug, underscoring its potential clinical significance.

G-quadruplex (G4) structures are important in both biological and medical fields. A unique G4 type containing G vacancies allowing stabilization by guanine or guanine derivatives is widely used in the treatment of diseases, such as cancer. However, the identification of ligands with suitable affinities and specificities for G4 structures remains challenging. This study investigated the assisting effect of guanine derivatives in the formation of G-vacancy G4 structures. Focusing on the EAD2 sequence, we designed EAD2 sequences with one or two missing G bases. Circular dichroism (CD) assays revealed negligible impact of guanine and its derivatives on intact EAD2 structures but notable alterations in single-G-base-deficient EAD2 sequences. The formation of G4 structures in the EAD2 sequence lacking two G bases was difficult, even with the assistance of guanine derivatives. Moreover, experimental results demonstrated that the guanine derivatives M2 had better auxiliary effects on base-deficient sequences than other compounds, which may be due to the enhanced pairing capability of G4 caused by M2. Lastly, the experiment demonstrates that the hemin/G4 DNAzyme-catalyzed ABTS confirmed the auxiliary role of the guanine derivatives in the formation of G4 in G base-deficient sequences. Overall, the findings indicated the significant impact of G base deficiency on G4 assembly, with the guanine derivative M2 effectively aiding stable G4 formation in G base-deficient sequences.