Discovery of Small-Molecule Antagonists of PHF1 and 19 Demonstrates the Ligandability of PRC2 Accessory Proteins

PHF1 and PHF19 are key accessory components of polycomb repressive complex 2 (PRC2) which is responsible for trimethylation at histone H3 lysine 27, ultimately leading to gene repression. PHF1 and 19 are known for their methyl-lysine reader Tudor domains that recognize methylated lysine 36 on H3, and they have also been implicated as drivers of a range of cancers, including multiple myeloma. Here, we describe the first small-molecule antagonist of the Tudor domains of PHF1 and 19. We screened an internal library of ∼ 1 K compounds against the Tudor domains using a TR-FRET assay. Upon validation of a hit compound, we performed structure–activity relationship (SAR) studies to better understand the binding mode and improve the affinity of the compound for the PHF1 and 19 Tudor domains. One such compound, UNC7242, which binds PHF1 with a Kd of 1.13 ± 0.04 μM and PHF19 with a Kd of 0.64 ± 0.14 μM, emerged as a lead compound. UNC7242 clearly demonstrates the ligandability of these disease-relevant proteins and serves as a starting point for the future development of potent and selective PHF1 and 19 chemical probes.