Chemoproteomic study uncovers HemK2/KMT9 as a new target for NTMT1 bisubstrate inhibitors

Understanding the selectivity of methyltransferase inhibitors is important to dissect the functions of each methyltransferase target. From this perspective, here we report a chemoproteomic study to profile the selectivity of a potent protein N-terminal methyltransferase 1 (NTMT1) bisubstrate inhibitor NAH-C3-GPKK (Ki, app = 7{+/-}1 nM) in endogenous proteomes. First, we describe the rational design, synthesis, and biochemical characterization of a new chemical probe 6, a biotinylated analogue of NAH-C3-GPKK. Next, we systematically analyze protein networks that may selectively interact with the biotinylated probe 6 in concert with the competitor NAH-C3-GPKK. Besides NTMT1, the designated NTMT1 bisubstrate inhibitor NAH-C3-GPKK was found to also potently inhibit a methyltransferase complex HemK2-Trm112 (also known as KMT9-Trm112), highlighting the importance of systematic selectivity profiling. Furthermore, this is the first potent inhibitor for HemK2/KMT9 reported to date. Thus, our studies lay the foundation for future efforts towards the development of selective inhibitors for NTMT1 and HemK2/KMT9. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/439666v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@1bedeb5org.highwire.dtl.DTLVardef@f58a4org.highwire.dtl.DTLVardef@1847a17org.highwire.dtl.DTLVardef@6ba9eb_HPS_FORMAT_FIGEXP M_FIG C_FIG