An allosteric PRC2 inhibitor targeting the H3K27me3 binding pocket of EED

Abstract

Polycomb repressive complex 2 (PRC2) consists of three core subunits, EZH2, EED and SUZ12, and plays pivotal roles in transcriptional regulation. The catalytic subunit EZH2 methylates histone H3 lysine 27 (H3K27), and its activity is further enhanced by the binding of EED to trimethylated H3K27 (H3K27me3). Small-molecule inhibitors that compete with the cofactor S-adenosylmethionine (SAM) have been reported. Here we report the discovery of EED226, a potent and selective PRC2 inhibitor that directly binds to the H3K27me3 binding pocket of EED. EED226 induces a conformational change upon binding EED, leading to loss of PRC2 activity. EED226 shows similar activity to SAM-competitive inhibitors in blocking H3K27 methylation of PRC2 target genes and inducing regression of human lymphoma xenograft tumors. Interestingly, EED226 also effectively inhibits PRC2 containing a mutant EZH2 protein resistant to SAM-competitive inhibitors. Together, we show that EED226 inhibits PRC2 activity via an allosteric mechanism and offers an opportunity for treatment of PRC2-dependent cancers.

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Figure 1: EED226 selectively inhibits the PRC2 activity via binding to EED.
Figure 2: Crystal structure of EED–EBD–EED226 ternary complex.
Figure 3: EED226 specifically decreases cellular global and loci-specific H3K27 methylation and regulates gene expression.
Figure 4: EED226 inhibits the proliferation of DLBCL cell lines and leads to tumor regression in mouse xenograph model.
Figure 5: EED226 is effective on EZH2 inhibitor resistant mutations and synergize with EZH2 inhibitors.

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Acknowledgements

We thank the following colleagues for their help with this manuscript: J.-H. Zhang for HTS screening; L. Zhong for cellular assay development; Y. Wei for LC–MS/MS sample analysis; M. Dillon for medicinal chemistry; L. Liu for protein expression, purification and characterization; Z. Chen for animal studies; Y. Fan for bioinformatics data handling; X. Luo and H. Liu for assistance in structural studies; Zhenting Gao for modeling analysis; Zhenhai Gao for PRC2 biology discussion; staff at SSRF for data collection.

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W.Q., K.Z., J.G., Y.H. and E.L. designed the study and interpreted data. K.Z., J.G., H.Z., M. Zhang, L.L., M. Zhao, Z.C., Leying F., Lijian F., Y.G., G.L., Y. Lin, M.S., Z.W., Y.Y., C. Zeng and S.Z. performed the biochemical, biophysical and structure-related experiments and data analysis. W.Q., Y.W., J.Z., L.T., S.C., C. Zhang, H.C., D.F., Q.F., H.G., X.G., Y. Liu, F.L., J.Z. and L.Z. are involved in the cellular and animal studies and data analysis. Y.H., Z.Y., A.L., L.W. and Q.Z. designed, synthesized and characterized the chemical compounds. P.A., C.O. and E.L. guided multiple aspects of this study and team collaboration. K.Z., J.G., W.Q. and E.L. wrote the manuscript with input from co-authors.

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Correspondence to En Li.

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All authors performed the work herein as employees of the Novartis Institutes for Biomedical Research, Inc.

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Supplementary Results, Supplementary Tables 1–5 and Supplementary Figures 1–7. (PDF 1890 kb)

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Qi, W., Zhao, K., Gu, J. et al. An allosteric PRC2 inhibitor targeting the H3K27me3 binding pocket of EED. Nat Chem Biol 13, 381–388 (2017). https://doi.org/10.1038/nchembio.2304

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