Optimization of Class I Histone Deacetylase JPS0s Reveals HDAC1/2 Degradation is Critical to Induce Apoptosis and Cell Arrest in Cancer Cells

Class I Histone Deacetylase (HDAC) enzymes 1, 2 & 3 organize chromatin as the catalytic subunits within seven distinct multi-protein co-repressor complexes and are established drug targets. We report optimization studies of benzamide based Von Hippel-Lindau (VHL) E3-ligase Proteolysis Targeting Chimeras (JPS0s), and for the first time describe transcriptome perturbations resulting from these degraders. By modifying the linker and VHL ligand we identified JPS0s 7, 9 & 21 with submicromolar DC50 values for HDAC1 and/or HDAC3 in HCT116 cells. A hook effect was observed for HDAC3 that could be negated by modifying the position of attachment of the VHL ligand to the linker. The more potent HDAC1/2 degraders correlated with greater total differentially expressed genes and enhanced apoptosis in HCT116 cells. We demonstrate that HDAC1/2 degradation by JPS0s correlates with enhanced global gene expression and apoptosis, important for the development of more efficacious HDAC therapeutics with reduced side effects. Determining differential gene expression profiles upon treatment of HCT116 cells with JPS0s targeting class I HDACs