PROTAC Linkerology Leads to an Optimized Bivalent Chemical Degrader of Polycomb Repressive Complex 2 (PRC2) Components

Abstract

Bivalent chemical degraders, otherwise known as proteolysis-targeting chimeras (PROTACs), have proven to be an efficient strategy for targeting overexpressed or mutated proteins in cancer. PROTACs provide an alternative approach to small-molecule inhibitors, which are restricted by occupancy-driven pharmacology, often resulting in acquired inhibitor resistance via compensatory increases in protein expression. Despite the advantages of bivalent chemical degraders, they often have suboptimal physicochemical properties and optimization for efficient degradation remains highly unpredictable. Herein, we report the development of a potent EED-targeted PRC2 degrader, UNC7700. UNC7700 contains a unique cis-cyclobutane linker and potently degrades PRC2 components EED (DC50 = 111 nM; D max = 84%), EZH2WT/EZH2Y641N (DC50 = 275 nM; D max = 86%), and to a lesser extent SUZ12 (D max = 44%) after 24 h in a diffuse large B-cell lymphoma DB cell line. Characterization of UNC7700 and related compounds for ternary complex formation and cellular permeability to provide a rationale for the observed improvement in degradation efficiency remained challenging. Importantly, UNC7700 dramatically reduces H3K27me3 levels and is anti-proliferative in DB cells (EC50 = 0.79 ± 0.53 μM).

Harmony of Protein Tags and Chimeric Molecules Empowers Targeted Protein Ubiquitination and Beyond

“…The estimated rate constant for the reaction between HaloTag and its chloroalkane substrate is 2.7 × 10 6 M −1 s −1 [ 76 ]. Finally, the cell penetration efficiency of HaloTag-targeted molecules can be easily assessed through competitive assay against a chloroalkane-modified fluorophore [ 78 ].…”

Degraders in epigenetic therapy: PROTACs and beyond

“…It can also reduce the levels of H3K27me3 and potently inhibit the proliferation of diffuse large B-cell lymphoma (DB) and Pfeiffer cells (DLBCL-related cell lines bearing mutated EZH2). Recently, they further reported a novel potent EED-targeting PRC2 degrader, UNC7700 (compound 85) (Figure 17 B), which features a rigidity cis -cyclobutane linker in contrast to the flexible propyl linker of UNC6852 78 . UNC7700 exhibited a strong degradation activity against EED (DC 50 = 111 nM; D max = 84%) and EZH2 WT /EZH2 Y641N (DC 50 = 275 nM; D max = 86%) in a diffuse large B-cell lymphoma DB cell line.…”

Targeting reversible post-translational modifications with PROTACs: a focus on enzymes modifying protein lysine and arginine residues

“…The optimization of 62 led to the development of UNC7700 ( 63 ), a second-generation EED-targeted PRC2 degrader using a cis -cyclobutane linker instead of the propyl linker of 62 77 . In diffuse large B-cell lymphoma DB cells, 63 degraded EED 15-fold more potently than 62 and could efficiently degrade the main PRC2 components.…”