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

Abstract

Class I histone deacetylase (HDAC) enzymes 1, 2, and 3 organize chromatin as the catalytic subunits within seven distinct multiprotein corepressor complexes and are established drug targets. We report optimization studies of benzamide-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 PROTACs 7 , 9 , and 22 with submicromolar DC 50 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 PROTACs correlates with enhanced global gene expression and apoptosis, important for the development of more efficacious HDAC therapeutics with reduced side effects.

Collateral lethality between HDAC1 and HDAC2 exploits cancer-specific NuRD complex vulnerabilities

“…Our findings provide further motivation for the ongoing effort to develop direct-acting HDAC1/2 PROTACs 47,63 . To effectively capitalize on this synthetic lethality therapeutically, it will be necessary to develop selective degraders that only target one paralog or the other, thereby avoiding the toxicity associated with combined HDAC1/2 loss of function.…”

Developing HDAC4-Selective Protein Degraders To Investigate the Role of HDAC4 in Huntington’s Disease Pathology

“…While several bifunctional degraders of HDAC proteins have been developed, − none target HDAC4. Here we describe the design, synthesis, and in vitro characterization of the first generation of highly isoform-selective HDAC4 protein degraders.…”

Design of a Fluorogenic Probe Based on Intramolecular Condensation for Specific Detection of HDAC3

“…[9] These side effects are attributed to the inhibition of several or all types of HDAC isoenzymes in normal cells and tissues. [10][11][12] Thus, it is crucial to focus on selective targeting and detection of individual HDAC family member in a given tumour type for future drug development. [13][14][15] Fluorescence detection is a powerful approach for the analysis of biorelevant substances, enzyme activity investigation and drug selection.…”

“…However, HDAC inhibitors act unselectively against several or all HDAC family members and cause numerous side effects such as diarrhea, [5] thrombocytopenia, [6] cardiotoxicity, [7] neutropenia, [8] and vomiting [9] . These side effects are attributed to the inhibition of several or all types of HDAC isoenzymes in normal cells and tissues [10–12] . Thus, it is crucial to focus on selective targeting and detection of individual HDAC family member in a given tumour type for future drug development [13–15] …”