Structure-Guided Design of EED Binders Allosterically Inhibiting the Epigenetic Methyltransferase PRC2

PRC2is a multisubunit methyltransferaseinvolved in epigenetic regulation of early embryonic development and cell growth. The catalytic subunit EZH2methylates primarily lysine 27 of histone H3, leading to chromatin compaction and repression of tumor suppressor genes. Inhibiting this activity by small moleculestargeting EZH2was shown to result in anti-tumor efficacy. Here, we describe the identification and optimization of a new class of small molecule PRC2inhibitors that acts allosterically via the trimethyllysine pocket of the non-catalytic EED subunit. Deconstruction of a larger screening hit to a fragment-sized molecule followed by structure-guided regrowth and careful property modulation were employed to achieve sub-micromolar inhibition in functional assays and cellular activity.