Design, Synthesis, Molecular Docking, and Anticancer Activity Evaluation of Chalcone Derivatives as HDAC6 Inhibitors

Background: Histone deacetylase 6 (HDAC6) is a pivotal regulator of multiple cellular pathways in tumors, thereby rendering HDAC6 a potential target for anticancer therapy. Methods: A series of HDAC6 inhibitors containing chalcone scaffolds was designed based on the principle of molecular hybridization. The antiproliferative activities of K562 and SiHa cells were assessed using the Cell Counting Kit-8 (CCK-8) assay. Fluorogenic assay kits were used to evaluate the enzyme activities of HDAC1 and HDAC6 in vitro. Western blot analysis was employed to assess the acetylation levels of α-tubulin (Ac-α-tubulin) and histone H3. Molecular docking was performed to elucidate the binding modes of the compounds with HDAC1 and HDAC6. Results: In total, 23 novel HDAC6 inhibitors containing a chalcone scaffold were synthesized. Most compounds demonstrated low nanomolar IC50 values against HDAC6, with compound 3v exhibiting the greatest potency, an IC50 value of 4.3 nM and approximately 215-fold selectivity for HDAC6 over HDAC1. All target compounds exhibited strong antiproliferative effects against K562 and SiHa cells, with low micromolar IC50 values. Nonetheless, compound 3v demonstrated strong antiproliferative effects against both cell lines, with IC50 values of 1.16 μM in K562 cells and 1.28 μM in SiHa cells, respectively. In addition, compound 3v significantly upregulated the level of acetylated α-tubulin in K562 cells in a dose-dependent manner. Molecular docking analysis further revealed that compound 3v exhibited a stronger binding affinity for HDAC6 than for HDAC1. Additionally, flow cytometry analysis revealed that compound 3v induced apoptosis and the cell cycle arrest. Conclusions: Hydroxamic acid derivatives containing a chalcone fragment are potent HDAC6 inhibitors. These results indicate that chalcone substituents significantly affect enzyme and antiproliferative activities. Further studies are required to evaluate the anticancer potential and safety of these compounds.