Degradation of Polycomb Repressive Complex 2 with an EED-Targeted Bivalent Chemical Degrader

Abstract

Protein degradation via the use of bivalent chemical degraders provides an alternative strategy to block protein function and assess the biological roles of putative drug targets. This approach capitalizes on the advantages of small-molecule inhibitors while moving beyond the restrictions of traditional pharmacology. Here, we report a chemical degrader (UNC6852) that targets polycomb repressive complex 2 (PRC2). UNC6852 contains an EED226derived ligand and a ligand for VHL which bind to the WD40 aromatic cage of EED and CRL2 VHL , respectively, to induce proteasomal degradation of PRC2 components, EED, EZH2, and SUZ12. Degradation of PRC2 with UNC6852 blocks the histone methyltransferase activity of EZH2, decreasing H3K27me3 levels in HeLa cells and diffuse large B cell lymphoma (DLBCL) cells containing EZH2 gain-of-function mutations. UNC6852 degrades both wild-type and mutant EZH2, and additionally displays anti-proliferative effects in this cancer model system.

Current strategies for the design of PROTAC linkers: a critical review

“…It is well documented that the identification of appropriate vectors from the warhead and anchor is critical to devise a suitable strategy for their conjugation to the linker and access potent degraders [128]. The availability of high-resolution co-crystal structures for warheads bound to the POIs is an invaluable tool and often a prerequisite for PROTAC design and assembly, in particular to identify solvent-exposed exit vectors on the warhead where a linker can be conjugated with minimal effect on POI binding [129][130][131][132]. As an illustrative example, Maniaci et al [133], utilised the co-crystal structure (PDB 5LLI) of VHL in complex with VH298 (87) for the development of "Homo-PROTACs" for the self-induced degradation of VHL.…”

Proteolysis‐targeting chimeras in drug development: A safety perspective

“…Many studies have shown that PROTACs are not entirely selective and can degrade proteins other than the primary target (Bai et al, ; Bondeson et al, ; Brand et al, ; Matyskiela et al, ; Yang et al, ; Zorba et al, ). Degradation of a protein that is not directly bound by the PROTAC can arise as a consequence of “bystander degradation” where the degradation of a protein that is not directly bound by the PROTAC becomes ubiquitinated and hence degraded as part of the same complex with the PROTAC POI (Hsu et al, ; Maniaci et al, ; Potjewyd et al, ). In other instances, this is an off‐target effect due to the neo‐morphic interactions with so‐called neosubstrates, which become ubiquitinated by the E3 ligase and subsequently degraded (Figure ).…”

Proteolysis targeting chimeras (PROTACs) are emerging therapeutics for hematologic malignancies

“…In 2020, two separate research groups successfully converted the EED inhibitors into PROTACs [47,161]. Interestingly, both groups used the VHL ligand to design the PROTACs, but used different EED inhibitors as the warhead, as well as different strategies for linker optimization.…”

“…The most potent compound named PROTAC2 developed by Bloecher’s group selectively degraded EED, EZH2, and SUZ12, and reduced the proliferation of EZH-dependent tumor cells Karpas422 [ 161 ]. The most potent compounds named UNC6852 developed by James’ group also selectively degraded EED, EZH2, and SUZ12, and potently inhibited the proliferation of DLBCL cell lines with a wild-type and Y641N mutant EZH2 [ 47 ]. Although the EED-based PROTACs could degrade EZH2, so far no selective PROTACs based on EZH2 inhibitors were reported, until 2019 when Jian et al developed MS1943, an EZH2 inhibitor-based degrader, via hydrophobic tagging strategy, which was designed by linking an EZH2 inhibitor to a bulky adamantyl group [ 162 ].…”