Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands

Abstract

The bromodomain-containing protein BRD9, a subunit of the human BAF (SWI/SNF) nucleosome remodeling complex, has emerged as an attractive therapeutic target in cancer. Despite the development of chemical probes targeting the BRD9 bromodomain, there is a limited understanding of BRD9 function beyond acetyl-lysine recognition. We have therefore created the first BRD9-directed chemical degraders, through iterative design and testing of heterobifunctional ligands that bridge the BRD9 bromodomain and the cereblon E3 ubiquitin ligase complex. Degraders of BRD9 exhibit markedly enhanced potency compared to parental ligands (10 to 100 fold). Parallel study of degraders with divergent BRD9-binding chemotypes in models of acute myeloid leukemia resolves bromodomain polypharmacology in this emerging drug class. Together, these findings reveal the tractability of non-BET bromodomain containing proteins to chemical degradation, and highlight lead compound 6 (dBRD9) as a tool for the study of BRD9. Graphical abstractWith structural guidance alongside comparative biochemical and biological assays, an iterative design strategy resulted in the development of targeted small molecule degraders that rapidly, potently, and selectively eliminate BAF complex member BRD9. These first in class non-BET bromodomain degraders offer dramatic potency improvements over existing BRD9 probes in models of acute myloid leukemia.* james_bradner@dfci.harvard.edu; james.bradner@novartis.com.Supporting information for this article is given via a link at the end of the document. [4][5][6] Further, significant research effort has contributed a number of high quality chemical probes for bromodomain-containing proteins beyond the BET family. [7,8] The bromodomain-containing protein BRD9 has garnered particular attention as a component of the human ATP-dependent chromatin remodeling BAF complex (also known as SWI/SNF). Meta-analyses of whole-genome sequencing efforts have recently identified a high frequency of recurrent somatic mutations in BAF factors in diverse human cancers. [9] Within several subsets of these genetically defined malignancies, components of the BAF complex have emerged as context-specific dependencies, either supporting growth within a residual complex following loss of function mutation, or as novel oncogenes such as the SS18-SSX fusion. [10] These observations have generated interest in therapeutic strategies to target BAF. HHS Public AccessBeyond its presence in the BAF complex, a lack of functional annotation for BRD9 has provided incentive for development of BRD9 selective inhibitors to interrogate its biological role and to assess any therapeutic potential. Several BRD9-dircted efforts in discovery chemistry have been reported, [11][12][13][14][15] developing chemotypes for BRD9-specific engagement. A recent study further suggested BRD9 as a dependency in acute myeloid leukemia (AML), where bromodomain inhibition prompted a cytostatic response. [16] Beyond the bromodomain, the function of BRD9 remains unclear, and chemi...

Cereblon versus VHL: Hijacking E3 ligases against each other using PROTACs

“…alkylic versus polyethylene glycol (PEG) as well as mixtures thereof, are known to impact degradation activity and selectivity in often unpredictable ways. 21 , 22 , 31 We therefore decided to explore different linkers, focusing on varying lengths and ratio between carbon and oxygen atoms, as we and others have found that these modifications can have a profound impact on PROTAC structure-activity relationships. 21 , 22 , 23 , 31 As a result, the designed compounds explore diversity in the derivatization point, linker length and chemical properties.…”

“… 8 , 11 , 12 , 15 , 16 , 17 Within the past four years, potent and selective PROTACs have been designed to hijack either the von Hippel-Lindau (VHL) or cereblon (CRBN) E3 ligase against a target protein of interest. 18 , 19 Targets that have been shown to be degraded by PROTACs include members of bromodomain-containing proteins such as the BET proteins (Brd2, Brd3 and Brd4), 7 , 8 , 9 , 14 , 15 , 17 , 20 , 21 amongst other epigenetic protein classes; 22 , 23 , 24 , 25 , 26 protein kinases; 10 , 12 , 27 , 28 , 29 , 30 , 31 as well as non-bromodomain and non-kinase target proteins. 32 , 33 , 34 , 35 Recent progress in understanding principles of PROTAC mode of action, and demonstration of applicability across different target classes, suggest that PROTACs have the potential to target new protein families, including proteins that are difficult to block using current approaches.…”

Spliceosomal disruption of the non-canonical BAF complex in cancer

“…3e). Chemical degradation of BRD9 (dBRD9) 19 or BRD9 knockout similarly reduced BRG1-GLTSCR1 interaction (Fig. 3c, Extended Data Fig.…”

Advancements in the Development of non‐BET Bromodomain Chemical Probes

“…Bradner and co‐workers have disclosed dBRD9 ( 73 ) the first BRD9 PROTAC (Figure c) . A selection of BRD9 PROTACs were synthesized based around three different BRD9 chemical probes, LP99, I‐BRD9, both of which were reviewed previously, and 58 discussed above.…”