Selective Small Molecule Induced Degradation of the BET Bromodomain Protein BRD4

TLDR

BET proteins BRD2, BRD3, and BRD4 are key regulators of transcription, epigenetics, and cancer, yet pan‑BET inhibitors such as JQ1 lack intra‑BET selectivity, limiting their use as probes and raising concerns about off‑target toxicity. The authors sought to create PROTACs that link JQ1 to a VHL ligand to induce selective degradation of BET proteins. They engineered PROTACs that recruit the E3 ligase VHL to JQ1‑bound BET proteins, triggering ubiquitination and proteasomal degradation. The resulting compound MZ1 potently and selectively removes BRD4 over BRD2/3 in a VHL‑dependent, low‑concentration, reversible manner, producing distinct transcriptional changes that highlight BRD4’s unique cellular roles.

Abstract

The Bromo- and Extra-Terminal (BET) proteins BRD2, BRD3, and BRD4 play important roles in transcriptional regulation, epigenetics, and cancer and are the targets of pan-BET selective bromodomain inhibitor JQ1. However, the lack of intra-BET selectivity limits the scope of current inhibitors as probes for target validation and could lead to unwanted side effects or toxicity in a therapeutic setting. We designed Proteolysis Targeted Chimeras (PROTACs) that tether JQ1 to a ligand for the E3 ubiquitin ligase VHL, aimed at triggering the intracellular destruction of BET proteins. Compound MZ1 potently and rapidly induces reversible, long-lasting, and unexpectedly selective removal of BRD4 over BRD2 and BRD3. The activity of MZ1 is dependent on binding to VHL but is achieved at a sufficiently low concentration not to induce stabilization of HIF-1α. Gene expression profiles of selected cancer-related genes responsive to JQ1 reveal distinct and more limited transcriptional responses induced by MZ1, consistent with selective suppression of BRD4. Our discovery opens up new opportunities to elucidate the cellular phenotypes and therapeutic implications associated with selective targeting of BRD4.