Selective Peptidomimetic Inhibitors of NTMT1/2: Rational Design, Synthesis, Characterization, and Crystallographic Studies

Protein N-terminal methyltransferases
(NTMTs) methylate the α-N-terminal
amines of proteins starting with the canonical X-P-K/R motif. Genetic
studies imply that NTMT1 regulates cell mitosis and DNA damage repair.
Herein, we report the rational design and development of the first
potent peptidomimetic inhibitor for NTMT1/2. Biochemical and cocrystallization
studies manifest that BM30 (with a half-maximal inhibitory
concentration of 0.89 ± 0.10 μM) is a competitive inhibitor
to the peptide substrate and noncompetitive to the cofactor S-adenosylmethionine. BM30 exhibits over 100-fold selectivity to NTMT1/2 among a
panel of 41 MTs, indicating its potential to achieve high selectivity
when targeting the peptide substrate binding site of NTMT1/2. Its
cell-permeable analogue DC432 (IC50 of 54
± 4 nM) decreases the N-terminal methylation level of the regulator
of chromosome condensation 1 and SET proteins in HCT116 cells. This
proof-of principle study provides valuable probes for NTMT1/2 and
highlights the opportunity to develop more cell-potent inhibitors
to elucidate the function of NTMTs in the future.