Synthesis of SAM‐Adenosine Conjugates for the Study of m⁶A‐RNA Methyltransferases

Abstract

RNA methyltransferases (RNMTs) catalyze the methylation of RNA using S‐adenosyl‐l‐methionine (SAM) as the methyl donor. Methylation at the N‐6 position of adenosine is the most abundant modification found in nearly all classes of RNAs and contributes to the regulation of many biological processes in the three domains of life. However, this family of enzymes remains relatively unexplored by the medicinal chemistry community and new molecules are needed for their studies. Since RNMTs are suitable for bisubstrate binding, we report here the synthesis of SAM‐adenosine conjugates as bisubstrate analogues for RNMTs responsible for methylation of the N6‐position of adenosine. Six compounds were synthesized by connecting an analogue of SAM to an adenosine unit chosen to mimic the RNA substrate, via alkyl and urea linkers.

Synthesis of adenine dinucleosides SAM analogs as specific inhibitors of SARS-CoV nsp14 RNA cap guanine-N7-methyltransferase

“…This modification presents the advantage of increasing the chemical stability of the linker and offers a possible variability of compounds due to the Nsubstitution by any chain susceptible to interact with additional protein residues (Scheme 1). It is noteworthy that bisubstrate dinucleosides with N-containing linkers have already been reported in transition state analogs of DNA methylation [15] and of RNA methylation at N6 position of adenosine [16,17]. However, till our work, none viral 2 0 O-MTase or N7-MTase have been targeted by bisubstrate adenine dinucleosides.…”

“…The major advantage of this N-containing linker is the possibility to functionalize the secondary amine with a large variety of groups which may lead to additional binding with specific sites of RNA 2 0 -O-MTases. According to the schematic representation of the transition state of the 2 0 -O-methylation (Scheme 1), an accurate mimic was represented by compound 2 with the a-amino acid chain of the SAM branched to the nitrogen atom [16]. We further modified this side chain under a-amino-ester form or a-amino-amide form to result in compounds 3 and 4, respectively.…”

Synthesis of Triazole-Linked SAM-Adenosine Conjugates: Functionalization of Adenosine at N-1 or N-6 Position without Protecting Groups

“…In this context, we recently described the synthesis of SAM-adenosine conjugates as first transition state analogues for m 6 A RNA MTases and their use as tools for structural study [ 25 , 26 ]. We showed that a SAM-adenosine conjugate containing a three-carbon linker tethering the analogue of SAM to the N-6 atom of the adenosine binds the bacterial RNA MTase RlmJ with a conformation close to the real transition state.…”

Synthesis of Adenine Dinucleosides 2′,5′‐Bridged by Sulfur‐Containing Linkers as Bisubstrate SAM Analogues for Viral RNA 2′‐O‐Methyltransferases

“…Moreover, the first bisubstrates targeting RNA methyltransferases have been described in 1986 and one compound designed with the SAM moiety linked to the C6 of a guanine derivative demonstrated an inhibitory activity against vaccinia RNA N 7‐guanine MTase for the N 7‐methylation of the 5′‐cap structure . More recently, in the context of deciphering the roles of N 6m‐A RNA modifications and consequently exploring the functions of N 6‐A RNA MTases, SAM‐adenosine conjugates mimicking the transition state of methylation at N 6 were synthesized by connecting a SAM analogue to the N 6‐position of an adenosine unit via alkyl and urea linkers . The binding of these bisubstrate analogues for Ribosomal RNA large subunit MTase J (RlmJ) has been studied and they were shown to be useful as starting scaffolds for inhibitor design against m6A RNA MTases .…”

“…[13] More recently, in the context of deciphering the roles of N6m-A RNA modifications and consequently exploring the functions of N6-A RNA MTases, SAM-adenosine conjugates mimicking the transition state of methylation at N6 were synthesized by connecting a SAM analogue to the N6-position of an adenosine unit via alkyl and urea linkers. [14] The binding of these bisubstrate analogues for Ribosomal RNA large subunit MTase J (RlmJ) has been studied and they were shown to be useful as starting scaffolds for inhibitor design against m6A RNA MTases. [15] Beside these few examples, none other RNA MTases have been targeted by bisubstrate analogues.…”