Discovery of an H3K36me3-Derived Peptidomimetic Ligand with Enhanced Affinity for Plant Homeodomain Finger Protein 1 (PHF1)

Plant homeodomain finger protein
1 (PHF1) is an accessory component
of the gene silencing complex polycomb repressive complex 2 and recognizes
the active chromatin mark, trimethylated lysine 36 of histone H3 (H3K36me3).
In addition to its role in transcriptional regulation, PHF1 has been
implicated as a driver of endometrial stromal sarcoma and fibromyxoid
tumors. We report the discovery and characterization of UNC6641, a
peptidomimetic antagonist of the PHF1 Tudor domain which was optimized
through in silico modeling and incorporation of non-natural amino
acids. UNC6641 binds the PHF1 Tudor domain with a Kd value of 0.96 ± 0.03 μM while also binding
the related protein PHF19 with similar potency. A crystal structure
of PHF1 in complex with UNC6641, along with NMR and site-directed
mutagenesis data, provided insight into the binding mechanism and
requirements for binding. Additionally, UNC6641 enabled the development
of a high-throughput assay to identify small molecule binders of PHF1.