[New studies on inhibition of tRNA N2 guanine methyltransferase by S-adenosyl-homocysteine and S-adenosyl-methionine analogs]

Chemical biology and medicinal chemistry of RNA methyltransferases

RNA methyltransferases (MTases) are ubiquitous enzymes whose hitherto low profile in medicinal chemistry, contrasts with the surging interest in RNA methylation, the arguably most important aspect of the new field of epitranscriptomics. As MTases become validated as drug targets in all major fields of biomedicine, the development of small molecule compounds as tools and inhibitors is picking up considerable momentum, in academia as well as in biotech. Here we discuss the development of small molecules for two related aspects of chemical biology. Firstly, derivates of the ubiquitous cofactor S-adenosyl-l-methionine (SAM) are being developed as bioconjugation tools for targeted transfer of functional groups and labels to increasingly visible targets. Secondly, SAM-derived compounds are being investigated for their ability to act as inhibitors of RNA MTases. Drug development is moving from derivatives of cosubstrates towards higher generation compounds that may address allosteric sites in addition to the catalytic centre. Progress in assay development and screening techniques from medicinal chemistry have led to recent breakthroughs, e.g. in addressing human enzymes targeted for their role in cancer. Spurred by the current pandemic, new inhibitors against coronaviral MTases have emerged at a spectacular rate, including a repurposed drug which is now in clinical trial.

Expanding the chemical scope of RNA:methyltransferases to site-specific alkynylation of RNA for click labeling

This work identifies the combination of enzymatic transfer and click labeling as an efficient method for the site-specific tagging of RNA molecules for biophysical studies. A double-activated analog of the ubiquitous co-substrate S-adenosyl-l-methionine was employed to enzymatically transfer a five carbon chain containing a terminal alkynyl moiety onto RNA. The tRNA:methyltransferase Trm1 transferred the extended alkynyl moiety to its natural target, the N2 of guanosine 26 in tRNA^Phe. LC/MS and LC/MS/MS techniques were used to detect and characterize the modified nucleoside as well as its cycloaddition product with a fluorescent azide. The latter resulted from a labeling reaction via Cu(I)-catalyzed azide-alkyne 1,3-cycloaddition click chemistry, producing site-specifically labeled RNA whose suitability for single molecule fluorescence experiments was verified in fluorescence correlation spectroscopy experiments.

Affinity chromatography of an S-adenosylmethionine-dependent methyltransferase using immobilized S-adenosylhomocysteine. Purification of the indolethylamine N-methyltransferases of phalaris tuberosa

In the cases that have been studied so far, S-adenosylhomocysteine (SAH) is a powerful inhibitor of S-adenosylmethionine (SAM) binding to SAM-dependent methyltransferases. We deduced, from the available data on the binding of SAM and SAH analogues to SAM dependent methyltransferases, that linkage of SAH through the carboxyl group to an immobilized support would lead to a more general affinity adsorbent for SAM-dependent methyltransferases than linkage through other functional groups. This paper describes the synthesis of this affinity adsorbent and its use to purify the two indolethylamine N-methyltransferases of Phalaris tuberosa.

S-adenosylhomocysteine analogues as inhibitors of specific tRNA methylation

Of 17 base- or amino acid-modified analogues of S-adenosylhomocysteine, six were found to produce at least 50% inhibition of the activity of an unfractionated tRNA methyltransferase extract at concentrations of 200 micron. The inhibitory effects of these six analogues on five purified rat liver tRNA methyltransferases were examined. The purified enzymes differed greatly in their sensitivity to the analogues. Ki values for the inhibitory analogues were determined for the three most highly purified methyltransferases. The kinetic analyses indicated that inhibition is competitive for nearly all enzyme/inhibitor combinations. The Ki values for good enzyme/inhibitor pairs were in the range of 0.11--2 micron. Each analogue appears to inhibit one methylation more strongly than others; e.g. the Ki values obtained for N6-methyl-S-adenosyl-L-homocysteine are approx. 0.4 micron for guanine-1 tRNA methyltransferase, 6 micron for adenine-1 tRNA methyltransferase and 100 micron for N2-guanine tRNA methyltransferase I. Structural features which are important for inhibitory activity are presence of a terminal amino group on the amino acid and the presence of adenosine rather than any other base. Ring nitrogens, a terminal carboxyl group and conformation at the asymmetric carbon appear to be important for some but not all of the tRNA methyltransferases examined.

[New syntheses of S-adenosylhomocysteine and S-adenosylmethionine analogs]

With the aim of studying analogues of S adenosyl homocysteine and S adenosyl methionine as potential inhibitors of methyl-transferases, we describe the syntheses of such analogues, in which either the amino-acid chain is replaced by various aliphatic radicals of the N 6 amino group of adenine is substituted.