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

PRC2 is a multisubunit methyltransferase involved in epigenetic regulation of early embryonic development and cell growth. The catalytic subunit EZH2 methylates primarily lysine 27 of histone H3, leading to chromatin compaction and repression of tumor suppressor genes. Inhibiting this activity by small molecules targeting EZH2 was shown to result in anti-tumor efficacy. Here, we describe the identification and optimization of a new class of small molecule PRC2 inhibitors 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.