Probing the Plasticity in the Active Site of Protein N‑terminal Methyltransferase 1 Using Bisubstrate Analogues

The bisubstrate analogue
strategy is a promising approach to develop
potent and selective inhibitors for protein methyltransferases. Herein,
the interactions of a series of bisubstrate analogues with protein
N-terminal methyltransferase 1 (NTMT1) were examined to probe the
molecular properties of the active site of NTMT1. Our results indicate
that a 2-C to 4-C atom linker enables its respective bisubstrate analogue
to occupy both substrate- and cofactor-binding sites of NTMT1, but
the bisubstrate analogue with a 5-C atom linker only interacts with
the substrate-binding site and functions as a substrate. Furthermore,
the 4-C atom linker is the optimal and produces the most potent inhibitor
(Ki,app = 130 ± 40 pM) for NTMT1
to date, displaying more than 3000-fold selectivity for other methyltransferases
and even for its homologue NTMT2. This study reveals the molecular
basis for the plasticity of the active site of NTMT1. Additionally,
our study outlines general guidance on the development of bisubstrate
inhibitors for any methyltransferases.