Optimization of Class I Histone Deacetylase PROTACs Reveals thatHDAC1/2 Degradation is Critical to Induce Apoptosis and Cell Arrest in Cancer Cells

Class I histone deacetylase (HDAC) enzymes 1, 2, and 3 organize chromatin as the catalytic subunits within seven distinct multiprotein corepressorcomplexes and are established drug targets. We report optimization studies ofbenzamide-based Von Hippel-Lindau (VHL) E3-ligase proteolysis targeting chimeras(PROTACs) and for the first time describe transcriptome perturbations resulting from these degraders. By modifying the linker and VHL ligand, we identified PROTACs7,9, and22with submicromolar DC50values for HDAC1 and/or HDAC3 in HCT116cells. 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 HDAC1/2degraders correlated with greater total differentially expressed genes and enhanced apoptosis in HCT116 cells. We demonstrate thatHDAC1/2 degradation by PROTACs correlates with enhanced global gene expression and apoptosis, important for the development of more efficacious HDAC therapeutics with reduced side effects

Automated summary

This study optimized benzamide-based Von Hippel-Lindau (VHL) E3 ligase proteolysis targeting chimeras (PROTACs) and described the transcriptome perturbations caused by these degraders for the first time. By modifying the linker and VHL ligand, more potent degraders targeting HDAC1 and/or HDAC3 were identified with submicromolar DC50 values.