Discovery of a New-Generation S‑Adenosylmethionine-Noncompetitive Covalent Inhibitor Targeting the Lysine Methyltransferase Enhancer of Zeste Homologue 2

The
first-generation enhancer of zeste homologue 2 (EZH2) inhibitors
suffer from several limitations, such as high dosage, cofactor S-adenosylmethionine
(SAM) competition, and acquired drug resistance. Development of covalent
EZH2 inhibitors that are noncompetitive with cofactor SAM offers an
opportunity to overcome these disadvantages. The structure-based design
of compound 16 (BBDDL2059) as a highly potent and selective
covalent inhibitor of EZH2 is presented in this context. 16 inhibits EZH2 enzymatic activity at sub-nanomolar concentrations
and achieves low nanomolar potencies in cell growth inhibition. The
kinetic assay revealed that 16 is noncompetitive with
the cofactor SAM, providing the basis for its superior activity over
noncovalent and positive controls by reducing competition with cofactor
SAM and offering a preliminary proof for its covalent inhibition nature.
Mass spectrometric analysis and washout experiments firmly establish
its covalent inhibition mechanism. This study demonstrates that covalent
inhibition of EZH2 can offer a new opportunity for the development
of promising new-generation drug candidates.