Histone deacetylases (HDACs) have proven to be promising targets for the development of anticancer
drugs. In this work, we report the design and synthesis of a series of 19 novel hydroxamic acid-based
histone deacetylase inhibitors conjugated to benzimidazole and benzoxazole core structures. Five
compounds showed anti-proliferative activity with an IC50 value of 2.9–70.9 mM. Compound 7 displayed
the highest efficacy against MCF-7 cells and exhibited antiproliferative effects against a panel of cancer
cell lines. Compound 7 was the most potent selective inhibitor of HDAC6 and had an IC50 value 8- to
4111.1-fold those of HDAC3, HDAC4, HDAC8, and HDAC11, and was a superior HDAC6 inhibitor to
belinostat. Its interaction with and inhibitory activity on HDAC enzymes were then explored in a
molecular docking study. The obtained data revealed the highest binding affinity (8.46 kcal mol1) of
compound 7 toward HDAC6, as it formed interactions with the key residues Cys584 and Asp612 within
the active site. Furthermore, the HDAC inhibitory activity of compound 7 was demonstrated from the
dose-dependent increase in the tubulin acetylation level. Together, our results indicated that compound
7 with a cap of benzimidazole and four carbon-chain-containing thioether linker is a potent anticancer
agent for selective HDAC6 inhibition and deserves further investigation.