Covalent S-Adenosylhomocysteine-Based DNA Methyltransferase 2 Inhibitors with a New Type of Aryl Warhead

Abstract

The DNA methyltransferase 2 (DNMT2) is an RNA modifying enzyme associated with pathophysiological processes, such as mental and metabolic disorders or cancer. Although the development of methyltransferase inhibitors remains challenging, DNMT2 is not only a promising target for drug discovery, but also for the development of activity-based probes. Here, we present covalent SAH-based DNMT2 inhibitors decorated with a new type of aryl warhead. Based on a noncovalent DNMT2 inhibitor with N-benzyl substituent, the Topliss scheme was followed for optimization. The results showed that electrondeficient benzyl moieties highly increased affinity. By decorating the structures with strong electron-withdrawing moieties and leaving groups, we adjusted the electrophilicity to create covalent DNMT2 inhibitors. A 4-bromo-3-nitrophenylsulfonamide-decorated SAH derivative (80) turned out to be the most potent (IC 50 = 1.2 ± 0.1 μM) and selective inhibitor. Protein mass spectrometry confirmed the covalent reaction with the catalytically active cysteine-79.

Emerging and Re-emerging Warheads for Targeted Covalent Inhibitors: An Update

“…The Schirmeister group recently developed an S N Ar-based covalent inhibitor for the DNA methyl­transferase 2 (DNMT2), an RNA-modifying enzyme linked to mental and metabolic disorders as well as cancer. Based on their previous work, molecular modifications using a Topliss scheme were performed to decorate the N -benzyl moiety of the (non-covalent) low-affinity prototype 111 (57% inhibition at 100 μM, Figure ) with different substituents, where EWGs performed best.…”

Substitution-Induced Mechanistic Switching in SNAr-Warheads for Cysteine Proteases

“…The anion can be oxidized, yielding the so-called Zimmermann product; the substitution reaction can take place by elimination of a leaving group, or the addition can revert back to the original reactants via the π-complex. The application of electron-deficient arenes in the context of addressing (non-)catalytic cysteines irreversibly through a substitution reaction has been described on different targets, e.g., peroxisome proliferator-activated receptors (PPARs) [ 19 ], the bacterial enzyme sortase A (SrtA) [ 20 ], the fibroblast growth factor receptor 4 (FGFR4) [ 21 ], S6 kinase β2 (S6K2) [ 22 ], and DNA methyltransferase 2 (DNMT2) [ 23 ]. While the electrophiles look similar to the ones described for rhodesain, the inhibition mechanism differs substantially.…”