Polycomb repressive complex 2 structure with inhibitor reveals a mechanism of activation and drug resistance

Abstract

Polycomb repressive complex 2 (PRC2) mediates gene silencing through chromatin reorganization by methylation of histone H3 lysine 27 (H3K27). Overexpression of the complex and point mutations in the individual subunits of PRC2 have been shown to contribute to tumorigenesis. Several inhibitors of the PRC2 activity have shown efficacy in EZH2-mutated lymphomas and are currently in clinical development, although the molecular basis of inhibitor recognition remains unknown. Here we report the crystal structures of the inhibitor-bound wild-type and Y641N PRC2. The structures illuminate an important role played by a stretch of 17 residues in the N-terminal region of EZH2, we call the activation loop, in the stimulation of the enzyme activity, inhibitor recognition and the potential development of the mutation-mediated drug resistance. The work presented here provides new avenues for the design and development of next-generation PRC2 inhibitors through establishment of a structure-based drug design platform.

Structure of the PRC2 complex and application to drug discovery

“…Recently, three PRC2 structures were determined: PRC2 of the thermophilic fungus Chaetomium thermophilum (ctPRC2) in a stimulated and basal state [93] , human PRC2 in a stimulated state [94] and a human/chameleon (Anolis carolinensis) hybrid PRC2 [Hs/AcPRC2] in complex with a pyridine-based PRC2 inhibitor [95] . Although human and fungal PRC2 have low sequence conservation, they share a similar overall structure.…”

“…The N-terminal 29 residues (561-589) of the SUZ12(VEFS) form a random coil that is sandwiched between the EED and EZH2 SET domain, serving as the glue that holds them together [95] . Residues 590-685 of SUZ12(VEFS) form a helical bundle with exclusive interactions with different parts of EZH2 [95] .…”

“…Residues 590-685 of SUZ12(VEFS) form a helical bundle with exclusive interactions with different parts of EZH2 [95] . The first four helices interact intimately with the EZH2 MSCC subdomain, and the C-terminal two helices provide an interaction surface for the two N-terminal helices of the EZH2 SANT2 subdomain [94,95] (Figure 2).…”

“…Residues 590-685 of SUZ12(VEFS) form a helical bundle with exclusive interactions with different parts of EZH2 [95] . The first four helices interact intimately with the EZH2 MSCC subdomain, and the C-terminal two helices provide an interaction surface for the two N-terminal helices of the EZH2 SANT2 subdomain [94,95] (Figure 2). Asp652, Gln648, Leu666, Asn668 and Tyr726 of human EZH2 interact with the H3 (22-31) K27M peptide ( Figure 3A), while Ala622, Trp624, Ser664, Asn688, His689 and Asp725 form hydrogen bonds with the co-factor SAH ( Figure 3C).…”

“…Overlay of the active and inhibitory states of human PRC2. The structure of active (PDB ID: 5HYN) [94] and inhibited PRC2 (PDB ID: 5IJ7) [95] . Green: active PRC2, magenta: inhibitory PRC2, red: JARID2K116me2 peptide, cyan: H3K27M peptide, orange: SAH, wheat: Inhibitor 1 from structure 5IJ7.…”