New potent bisubtrate inhibitors of SARS-CoV-2 nsp14 N7-Methyltransferase
The CARE partner Aix-Marseille University (AMU), in collaboration with other research groups, has published two articles pertaining to the development of new bisubstrate inhibitors against the SARS-CoV-2 nsp14 (N7-guanine)-methyltransferase (N7-MTase). This enzyme, which catalyses the transfer of the methyl group from the S-adenosyl-L-methionine (SAM) cofactor to the N7-guanosine cap, plays a key role in the translation of viral RNA into proteins.
As a first step, AMU designed and synthetized nucleoside-derived inhibitors with the goal to improve interactions with the SARS-CoV-2 N7-MTase nsp14. In a biochemical assay, seven out of the 39 compounds showed remarkable double-digit nanomolar inhibitory activity against the N7-MTase nsp14. The three most potent inhibitors significantly stabilized nsp14 and the best inhibitor demonstrated high selectivity for nsp14 over human RNA N7-MTase.
Structure-Activity Relationship studies reveal an effective bisubstrate structure of the inhibitors, which occupy both the SAM-binding site and the cap RNA substrate binding site of the enzyme. Moreover, based on docking studies, the particular scaffold of these compounds interacts with two key conserved residues – Arg310 and Phe426 in SARS-CoV nsp14 – of the catalytic pocket that has been identified as critical for N7-MTase nsp14 activity and consequently for SARS-CoV-2 replication. Click here for the publication or here for a repository access.
As a second step, a structure-guided drug design approach was applied to design a new series of inhibitors with the aim of increasing the interaction with the SAM binding pocket. 26 novel adenosine mimetics were synthesized with eight of them inhibiting the N7-MTases of coronaviruses with subnanomolar to nanomolar activity, while sparing the cognate human N7-MTase. Moreover, the best compounds inhibit SARS-CoV, SARS-CoV-2 and MERS-CoV nsp14 N7-MTase activity, three viruses which share a similar structure organisation of the nsp14 protein. Click here for the publication. The activity of the developed compounds remains at a moderate level in infected cells at this stage. We are currently analyzing the delivery of the compounds into cells, and work on the synthesis of prodrugs is also currently underway.
These promising results strengthen the emerging status of the N7-MTase nsp14 as a valid target for antiviral rational-designed pancoronavirus inhibitors.