Design and evaluation of highly selective histone deacetylase 6 inhibitors derived from the natural product...

The development of isoform-selective histone deacetylase (HDAC) inhibitors offers a promising approach to minimize the adverse effects of nonselective HDAC inhibitors. HDAC6, due to its unique structural and functional properties, regulates critical cellular processes like gene expression, proliferation, senescence, and apoptosis. Inspired by a tryptoline-derived natural product, callophycin A, a series of compounds were synthesized and evaluated for HDAC6 selectivity. In the HDAC enzyme assay, compound 6a stood out as the lead, demonstrating 21-fold higher potency against HDAC6 compared with HDAC1 (HDAC6 IC₅₀ = 83.6 ± 1.1 nM vs HDAC1 IC₅₀ = 1790 ± 1.0 nM). In dose-dependent western blot experiments using H1975 lung cancer cells, a lower concentration of compound 6a (3 μM) induced significantly greater acetylation of α-tubulin compared with histone H3, indicating preferential inhibition of cytoplasmic HDAC6 over the nuclear HDAC1 isoform. Molecular docking of compound 6a at the HDAC6 active site (PDB code: 5EDU) revealed key interactions including π-alkyl contacts via the cap group, π-π stacking through the linker, hydrogen bonding involving the zinc-binding group, and Zn²⁺ chelation by the hydroxamic acid moiety that support its strong and selective binding, consistent with its HDAC6 inhibitory profile. Overall, compound 6a represents a promising prototype for the rational design of selective HDAC6 inhibitors, offering a structural framework for developing safer and more effective therapeutics aimed at HDAC6-driven cancers, thereby advancing targeted drug development in oncology. SIGNIFICANCE STATEMENT: Selective histone deacetylase 6 (HDAC6) inhibitors provide a safer alternative to nonselective HDAC inhibitors, with potential applications in cancer. This study identifies compound 6a as a promising lead with remarkable HDAC6 specificity, offering a foundation for developing targeted and efficient therapeutics.