Improvement of S_NAr Reaction Rate by an Electron‐Withdrawing Group in the Crosslinking of DNA Cytosine‐5 Methyltransferase by a Covalent Oligodeoxyribonucleotide Inhibitor

Abstract

DNA cytosine 5-methyltransferase (DNMT) catalyzes methylation at the C5 position of the cytosine residues in the CpG sequence. Aberrant DNA methylation patterns are found in cancer cells. Therefore, inhibition of human DNMT is an effective strategy for treating various cancers. The inhibitors of DNMT have an electron-deficient nucleobase because this group facilitates attack by the catalytic Cys residue in DNMTs. Recently, we reported the synthesis and properties of mechanism-based modified nucleosides, 2-amino-4-halopyridine-C-nucleosides (d P), as inhibitors of DNMT. To develop a more efficient inhibitor of DNMT for oligonucleotide therapeutics, oligodeoxyribonucleotides (ODNs) containing other nucleoside analogues, which react more quickly with DNMT, are needed. Herein, we describe the design, synthesis, and evaluation of the properties of 2-amino-3-cyano-4-halopyridine-C-nucleosides (d P ) and ODNs containing d P , as more reactive inhibitors of DNMTs. Nucleophilic aromatic substitution (S Ar) of the designed nucleosides, d P , was faster than that of d P, and the ODN containing d P effectively formed a complex with DNMTs. This study suggests that the incorporation of an electron-withdrawing group would be an effective method to increase reactivity toward the nucleophile of the DNMTs, while maintaining high specificity.

Emerging and Re-Emerging Warheads for Targeted Covalent Inhibitors: Applications in Medicinal Chemistry and Chemical Biology

“…If a properly positioned nucleophile is present in the binding site, such a ligand might be readily turned into an irreversible modifier simply by the installation of suitable leaving groups. Besides the efforts discussed above, it is worth mentioning that an elegant approach to target DNA cytosine-5-methyltransferases covalently via an S N Ar mechanism has very recently been reported in two studies by Akira Matsuda, Satoshi Ichikawa, and co-workers. , However, their approach addressing an active site cysteine via a suicide mechanism is beyond the scope of this Perspective. The interested reader is therefore referred to the original articles.…”

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

“…The latter might be complicated by the concomitant removal of the positive charge, which may also play an important role for the reversible recognition of these hit fragments. Beyond this, several additional examples of heteroaromatic scaffolds with sulfonyl/sulfinyl moieties 215,216 or halides 217 acting as S N Ar LGs in a biological context have been described. Compounds with (non-hetero) aryl-based S N Ar warheads, including the chloronitrobenzamide GW9662 (102, Figure 35A), 218 have previously been described as covalent modulators of the peroxisome-proliferator activated receptor (PPAR) family of nuclear receptors (see the discussion in our previous Perspective 46 ).…”