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A selective inhibitor of EZH2 blocks H3K27 methylation and kills mutant lymphoma cells

Abstract

EZH2 catalyzes trimethylation of histone H3 lysine 27 (H3K27). Point mutations of EZH2 at Tyr641 and Ala677 occur in subpopulations of non-Hodgkin's lymphoma, where they drive H3K27 hypertrimethylation. Here we report the discovery of EPZ005687, a potent inhibitor of EZH2 (Ki of 24 nM). EPZ005687 has greater than 500-fold selectivity against 15 other protein methyltransferases and has 50-fold selectivity against the closely related enzyme EZH1. The compound reduces H3K27 methylation in various lymphoma cells; this translates into apoptotic cell killing in heterozygous Tyr641 or Ala677 mutant cells, with minimal effects on the proliferation of wild-type cells. These data suggest that genetic alteration of EZH2 (for example, mutations at Tyr641 or Ala677) results in a critical dependency on enzymatic activity for proliferation (that is, the equivalent of oncogene addiction), thus portending the clinical use of EZH2 inhibitors for cancers in which EZH2 is genetically altered.

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Figure 1: Chemical structures of PRC2 inhibitors.
Figure 2: EPZ005687 is a SAM-competitive inhibitor of EZH2 enzyme activity.
Figure 3: Ligand affinity maps of EPZ005687 across the family trees of human lysine methyltransferases and arginine methyltransferase enzymes show EPZ005687 is a selective and potent inhibitor of EZH2 and EZH1 enzymes.
Figure 4: EPZ005687 specifically inhibits H3K27 methylation in lymphoma cells.
Figure 5: EPZ005687 decreases proliferation in mutant but not wild-type EZH2 lymphoma cells.
Figure 6: Inhibition of EZH2 by EPZ005687 results in accumulation in the G1 phase of the cell cycle in an EZH2 Tyr641 mutant lymphoma cell line.

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Acknowledgements

We thank D. Johnston and A. Basavapathruni for performing DOT1L and WHSC1 enzyme selectivity assays, K. Kuplast for help with the LCC calculations, A. Santospago for preparation of assay plates and R. Gould for helpful discussions.

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Contributions

L.J. made the enzymes. K.W.K. and E.J.O. designed compounds including EPZ005687. T.J.W., C.R.M. and C.J.S. performed the enzyme inhibition assays, and T.J.W. performed substrate competitions, Yonetani-Theorell analysis and the in vitro EZH2 pull-down assay. S.K.K., N.M.W., C.J.A., C.R.K., J.S. and J.D.S. performed the intracellular inhibition of H3K27 methylation ELISA. S.K.K. and N.M.W. performed the western blotting of all methyl marks and proliferation assays. S.K.K., N.M.W. and J.J.S. performed gene expression and cell cycle experiments. S.K.K., T.J.W., K.W.K., A.R., J.J.S., M.P.S., R.M.P., R.C., M.P.M., V.M.R., R.A.C. and H.K. designed studies and interpreted results. S.K.K., T.J.W., K.W.K. and R.A.C. wrote the paper.

Corresponding author

Correspondence to Kevin W Kuntz.

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All of the authors are employees and shareholders of Epizyme, Inc.

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Supplementary Dataset 1.xlsx (XLS 140 kb)

Supplementary Data Set 2

Supplementary Dataset 2.xlsx (XLS 94 kb)

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Knutson, S., Wigle, T., Warholic, N. et al. A selective inhibitor of EZH2 blocks H3K27 methylation and kills mutant lymphoma cells. Nat Chem Biol 8, 890–896 (2012). https://doi.org/10.1038/nchembio.1084

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