New Design Rules for Developing Potent Cell-Active Inhibitors of the Nucleosome Remodeling Factor (NURF) via BPTF Bromodomain Inhibition

Abstract

The nucleosome remodeling factor (NURF) alters chromatin accessibility through interactions with its largest subunit,the bromodomain PHD finger transcription factor BPTF. BPTF is overexpressed in several cancers and is an emerging anticancer target. Targeting the BPTF bromodomain presents a potential strategy for its inhibition and the evaluation of its functional significance; however, inhibitor development for BPTF has lagged behind those of other bromodomains. Here we describe the development of pyridazinone-based BPTF inhibitors. The lead compound, BZ1, possesses a high potency (K d = 6.3 nM) and >350-fold selectivity over BET bromodomains. We identify an acidic triad in the binding pocket to guide future designs. We show that our inhibitors sensitize 4T1 breast cancer cells to doxorubicin but not BPTF knockdown cells, suggesting a specificity to BPTF. Given the high potency and good physicochemical properties of these inhibitors, we anticipate that they will be useful starting points for chemical tool development to explore the biological roles of BPTF.

Nucleosome conformation dictates the histone code

“…1b ). These are of interest for targeted therapeutics 30 , and so an understanding of their function is critical. In the context of histone peptides, the PHD finger (PHD) has been shown to associate with H3 tri-methylated at lysine 4 (H3K4me3) 28 , while the bromodomain (BD) binds to histone tails containing acetylated lysines, with a preference for the acetylated H4 tail 31–33 .…”

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

“…We further characterized our compounds for ternary complex formation and degradation of full-length BRD9 using NanoBRET. BRD9 is a reported offtarget for the pyridazinone scaffold 12,34 and TP-238. 25 Due to its smaller size (75 kDa) compared to full-length BPTF (~300 kDa), we expected full-length BRD9 (BRD9-FL) to be more amenable to transfection and easier to study in this assay compared to full-length BPTF.…”

“…11 However, for many non-BET bromodomains, it remains unclear whether bromodomain inhibition alone will be effective to induce a significant phenotypic effect. In the case of BPTF, we 12 and others 13 have shown that bromodomain inhibitors when used as single agents may be insufficient for anticancer therapeutic applications. We previously reported that BPTF inhibitors sensitize 4T1 breast cancer cells to the chemotherapeutic, doxorubicin.…”

“…Therefore, combination therapy may be a useful option in cases where bromodomain inhibition on its own proves to be ineffective. 12,14 An alternative pharmacological modality is targeted protein degradation which has progressed rapidly for BET bromodomains. 15 In contrast, only four non-BET bromodomain targeting degraders have been reported (Figure 1A).…”

“…Here we describe the design and evaluation of first-generation degraders for several class I bromodomains and BRD9 in class IV using two different scaffolds (Figure 1C). We use a pyridazinone-based scaffold featured in BZ1, previously developed for binding to PCAF/GCN5 24 and BPTF, 12 and a pyrimidine-based scaffold derived from TP-238, as a dual BPTF/CECR2 chemical probe. 25,26 We establish exit vectors for linker attachment and explore ternary complex formation through both invitro assays and in-cell NanoBRET.…”