Improved Cell-Potent and Selective Peptidomimetic Inhibitors of Protein N-Terminal Methyltransferase 1

Abstract

Protein N-terminal methyltransferase 1 (NTMT1) recognizes a unique N-terminal X-P-K/R motif (X represents any amino acid other than D/E) and transfers 1–3 methyl groups to the N-terminal region of its substrates. Guided by the co-crystal structures of NTMT1 in complex with the previously reported peptidomimetic inhibitor DC113, we designed and synthesized a series of new peptidomimetic inhibitors. Through a focused optimization of DC113, we discovered a new cell-potent peptidomimetic inhibitor GD562 (IC50 = 0.93 ± 0.04 µM). GD562 exhibited improved inhibition of the cellular N-terminal methylation levels of both the regulator of chromosome condensation 1 and the oncoprotein SET with an IC50 value of ~50 µM in human colorectal cancer HCT116 cells. Notably, the inhibitory activity of GD562 for the SET protein increased over 6-fold compared with the previously reported cell-potent inhibitor DC541. Furthermore, GD562 also exhibited over 100-fold selectivity for NTMT1 against several other methyltransferases. Thus, this study provides a valuable probe to investigate the biological functions of NTMT1.

Structure–Activity Relationship Studies of Venglustat on NTMT1 Inhibition

“…Compound 3 was synthesized by following our previously reported method. 26 4.1.4. (S)-Piperidin-3-yl (2-(2-(4-Fluorophenyl)thiazol-4-yl)propan-2-yl)carbamate (4).…”

“…Different approaches have been applied to discover cell-potent NTMT1/2 inhibitors as chemical probes to dissect their biological function (Figure ). Among them, bisubstrate inhibitors selectively inhibit recombinant NTMT1 at 140 pM but are impermeable to cell membranes. − Compared to bisubstrate inhibitors, peptidomimetic inhibitors inhibit both NTMT1 and 2 (NTMT1/2), displaying modest cellular potency in the micromolar range. − Following up on our recent discovery of venglustat as the first cell-potent and small-molecule inhibitor of NTMT1 (Figure ), we describe here our efforts to systematically examine the structure–activity relationship (SAR) of venglustat to boost its potency and selectivity, as well as demonstrating its applicability for inhibiting Nα methylation that is catalyzed by NTMT1/2.…”

Unlocking the mysteries of alpha-N-terminal methylation and its diverse regulatory functions

“…5 ). A recent study reported the development of a novel inhibitor in this class, GD562, which improves the inhibition of cellular N-terminal methylation by 6-fold compared with DC541 ( 118 ). Overall, NTMT1 inhibitors have steadily improved in cell potency and are staged to be further employed for mechanistic and cellular studies.…”

Venglustat Inhibits Protein N-Terminal Methyltransferase 1 in a Substrate-Competitive Manner

“…Although there are potent and selective NTMT1 bisubstrate inhibitors, − their intrinsic properties restrict them for cell-based studies. Meanwhile, selective peptidomimetic inhibitors only exhibited modest cellular inhibition with an IC 50 ≈ 50 μM. − Therefore, cell-active small-molecule inhibitors of NTMT1 are in demand. Here, we report the identification of venglustat as a cell-potent inhibitor of NTMT1 resulting from a quantitative high-throughput screening (qHTS).…”