Targeted Degradation of BET Proteins in Triple-Negative Breast Cancer

Abstract

Triple-negative breast cancers (TNBC) remain clinically challenging with a lack of options for targeted therapy. In this study, we report the development of a second-generation BET bromodomain (BRD) inhibitor, BETd-246, which exhibits superior selectivity, potency and antitumor activity. In human TNBC cells, BETd-246 induced degradation of BET transcription factors at low nanomolar concentrations within 1 hr of exposure, resulting in robust growth inhibition and apoptosis. BETd-246 was more potent and effective in TNBC cells than its parental BET inhibitor compound BETi-211. RNA-seq analysis revealed predominant downregulation of a large number of genes involved in proliferation and apoptosis in cells treated with BETd-246, as compared to BETi-211 treatment which upregulated and downregulated a similar number of genes. Functional investigations identified the MCL1 gene as a critical downstream effector of these BET degraders, which synergized with small molecule inhibitors of BCL-xL in triggering apoptosis. In multiple murine xenograft models of human breast cancer, BETd-246 and a further optimized analogue BETd-260 effectively depleted BET proteins in tumors and exhibited strong antitumor activities at well-tolerated dosing schedules. Overall, our findings show how specific targeting of BET proteins for degradation yields an effective therapeutic strategy for TNBC treatment.

Targeted Protein Degradation: from Chemical Biology to Drug Discovery

“…This potency translates into mouse models of CRPC leading to tumor regression of enzalutamide-resistant 22Rv1 xenografts and advancing the scope of PROTAC technology to solid tumors. Superior efficacy compared to BET inhibition was also observed for a pomalidomide based PROTAC comprising a second generation BET inhibitor which induces growth inhibition and apoptosis in triple-negative breast cancers (TNBC) (Bai et al, 2017). Tethering this second generation BET inhibitor to lenalidomide resulted in PROTACs degrading BET proteins at picomolar concentration which caused >90% tumor regression in acute leukemia mouse xenograft models (Zhou et al, 2017).…”

Chemically induced degradation of CDK9 by a proteolysis targeting chimera (PROTAC)

“…This results in the poly-ubiquitination of that target protein, which is then proteosomally degraded (Figure 1). 22–24, 26, 27, 29–37 FKBP12, 23 BET, 23, 26, 28 BCR-ABL, 34 and Sirt2 37 proteins have been successfully targeted for degradation using small molecule bifunctional degraders that bind cereblon/Cullin4A E3 ubiquitin ligase. Degradation of the target protein makes this a catalytic process.…”

“…Furthermore, studies with BET degraders demonstrated potent inhibition of cancer cell growth and the induction of apoptosis when compared to the corresponding BET inhibitors. 24, 25, 27, 38 …”

Proteolysis‐targeting chimeras in drug development: A safety perspective

“…Many studies have shown that PROTACs are not entirely selective and can degrade proteins other than the primary target (Bai et al, 2017;Bondeson et al, 2018;Brand et al, 2019;Matyskiela et al, 2016;Yang et al, 2019;Zorba et al, 2018). Degradation of a protein that is not directly bound by the PROTAC can arise as a consequence of "bystander degradation" where the degradation of a protein that is not directly bound by the PROTAC becomes ubiquitinated and hence degraded as part of the same complex with the PROTAC POI (Hsu et al, 2019;Maniaci et al, 2017;Potjewyd et al, 2019).…”