Discovery of cyanocarbonimidodithioates as novel non-hydroxamate zinc-binding groups for selective HDAC8 inhibition: Design, synthesis, biological evaluation, anticancer activity, and in silico studies.

Histone deacetylase 8 (HDAC8) is a promising therapeutic target in cancer; however, the clinically approved hydroxamate-based inhibitors exhibit weak selectivity and undesirable toxicity due to binding at multiple sites. In this work, we report the design and synthesis of a new class of non-hydroxamate HDAC8 inhibitors with an unexplored cyanocarbonimidodithioate zinc-binding group (ZBG). A series of new compounds (SHC 1-3 and AC 1-14) were synthesized by the optimization of the cap groups and linker. SHC-1 and SHC-2 were found to be the most potent and selective HDAC8 inhibitors, with IC50 values of 0.036 μM and 0.041 μM, respectively, and high selectivity for HDAC8 over other HDAC isoforms. SHC-1 showed promising antiproliferative activity in IMR-32 neuroblastoma cells, colony formation inhibition, cell migration inhibition, caspase 3/7 assay and western blot. Mechanistic studies indicated increased SMC3 acetylation, suggesting HDAC8 inhibition. Molecular docking, molecular dynamics simulation, and MM-GBSA showed that SHC-2 binds stably to the HDAC8 active pocket via strong zinc coordination and critical interactions in the enzyme sub-pocket. ADMET predictions indicated good drug-likeness for the new compounds. A crystal of AC-4 was grown, and the structure was confirmed through SC-XRD. In summary, we have developed cyanocarbonimidodithioates as a new non-hydroxamate ZBG. These inhibitors demonstrated encouraging activity and a robust association with reported phenotypic changes, suggesting they could be further developed as cancer therapeutic agents.