Development of an N-Terminal BRD4 Bromodomain-Targeted Degrader

Abstract

Targeted protein degradation is a powerful induced-proximity tool to control cellular protein concentrations using small molecules. However, the design of selective degraders remains empirical. Among bromodomain and extra-terminal (BET) family proteins, BRD4 is the primary therapeutic target over family members BRD2/3/T. Existing strategies for selective BRD4 degradation use pan-BET inhibitors optimized for BRD4:E3 ubiquitin ligase (E3) ternary complex formation, but these result in residual inhibition of undegraded BET-bromodomains by the pan-BET ligand, obscuring BRD4-degradation phenotypes. Using our selective inhibitor of the first BRD4 bromodomain, iBRD4-BD1 (IC 50 = 12 nM, 23-to 6200-fold intra-BET selectivity), we developed dBRD4-BD1 to selectively degrade BRD4 (DC 50 = 280 nM). Notably, dBRD4-BD1 upregulates BRD2/3, a result not observed with degraders using pan-BET ligands. Designing BRD4 selectivity up front enables analysis of BRD4 biology without wider BET-inhibition and simplifies designing BRD4-selective heterobifunctional molecules, such as degraders with new E3 recruiting ligands or for additional probes beyond degraders.

Design of Class I/IV Bromodomain-Targeting Degraders for Chromatin Remodeling Complexes

“…The resulting residue was purified by column chromatography (CombiFlash Rf system: 24 g of silica, hexanes/ethyl acetate, 0−100% ethyl acetate, 16 min) (Scheme 4). (21). Following the general procedure C, sulfone 17 was alkylated with bromide 19, sulfone 17 29 (280 mg, 0.822 mmol, 1.0 eq), bromide 19 43 (258 mg, 1.03 mmol, 1.5 eq), K 2 CO 3 (227 mg, 1.64 mmol, 1.5 eq), and DMF (8.0 mL).…”

Precise Conformational Control Yielding Highly Potent and Exceptionally Selective BRD4 Degraders with Strong Antitumor Activity

“…In the last few years, selective BD1 or BD2 inhibitors were discovered − and have enabled elucidation of the differential roles played by these two domains in gene transcription and human diseases. In addition, BRD4 inhibitors with >10-fold binding selectivity over BRD2 and BRD3 have been reported. , …”

“…In addition to the development of bromodomain inhibitors, the major advancement in induced target protein degradation using the PROTAC technology − has enabled the discovery of highly potent degraders of the BET proteins. ,− While most of the reported BET degraders induce degradation of BRD2, BRD3, and BRD4 with similar potencies, compounds displaying selective degradation of BRD4 over BRD2 and BRD3 have been reported. ,, MZ1, reported by Ciulli et al, was the first selective BRD4 degrader and was designed using JQ1, a pan BET inhibitor, and a VHL-1 ligand. A subsequent study showed that MZ1 induced de novo contacts between BRD4 protein and VHL-1, forming a stable ternary complex and causing the selective degradation of BRD4 over that of BRD2 or BRD3 .…”

“…ZXH-3-26 was shown to engage in unique interactions with BRD4 to achieve selective degradation of BRD4 over that of BRD2 or BRD3 . dBRD4-BD1 was recently reported as another BRD4 selective degrader . In addition to these BRD4 selective PROTAC degraders, “molecular glue” degraders that demonstrate selectivity for BRD4/2 over BRD3 have been reported. , …”

“…In addition, BRD4 inhibitors with >10-fold binding selectivity over BRD2 and BRD3 have been reported. 13,14 In addition to the development of bromodomain inhibitors, the major advancement in induced target protein degradation using the PROTAC technology 15−19 has enabled the discovery of highly potent degraders of the BET proteins. 16,20−28 BRD2, BRD3, and BRD4 with similar potencies, compounds displaying selective degradation of BRD4 over BRD2 and BRD3 have been reported.…”