A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase

Abstract

A worldwide effort is ongoing to discover drugs against the Severe Acute Respiratory Syndrome coronavirus type 2 (SARS-CoV-2), which has so far caused >3.5 million fatalities (https://covid19.who.int/). The virus essential RNA-dependent RNA polymerase complex is targeted by several nucleoside/tide analogues whose mechanisms of action and clinical potential are currently evaluated. The guanosine analogue AT-527, a double prodrug of its 5'-triphosphate AT-9010, is currently in phase III clinical trials as a COVID19 treatment. Here we report the cryo-EM structure at 2.98 Å resolution of the SARS-CoV-2 nsp12-nsp7-(nsp8)2 complex with RNA showing AT-9010 bound at three sites of nsp12. At the RdRp active-site, one AT-9010 is incorporated into the RNA product. Its 2'-methyl group prevents correct alignment of a second AT-9010 occupying the incoming NTP pocket. The 2'-F, 2'-methyl 3'-OH ribose scaffold explains the non-obligate RNA chain-termination potency of this NA series for both HCV NS5 and SARS-CoV RTCs. A third AT-9010 molecule 5'-diphosphate binds to a coronavirus-specific pocket in the nsp12 N-terminus NiRAN domain, a SelO pseudo-kinase structural and functional homologue. This unique binding mode impedes NiRAN-mediated UMPylation of SARS-CoV-2 nsp8 and nsp9 proteins. Our results suggest a mechanism of action for AT-527 in line with a therapeutic use for COVID19.

Mechanism of Action of Small-Molecule Agents in Ongoing Clinical Trials for SARS-CoV-2: A Review

“…Besides, the 5'diphosphate of AT-9010 stably binds to the specific NSP12 N-terminal NiRAN domain of SARS-CoV-2, a structural and functional homolog of selenoprotein-O pseudokinase. This unique binding mode blocks the NiRANmediated UMPylation of SARS-CoV-2 NSP8 and NSP9 (Canard et al, 2021). The results indicate that AT-9010, the active form of AT-527, may exert anti-SARS-CoV-2 activity through a dual mechanism of inhibition via binding to both RdRp and NiRAN active sites.…”

“…Since AT-511 is a double prodrug requiring multiple enzymes for activation, it may be more susceptible to different experimental conditions (Do et al, 2021). To explore the mechanism of action of AT-527/AT-511 against SARS-CoV-2, Canard et al (2021) determined the structure of the SARS-CoV-2 RdRp:RNA:AT-9010 complex via cryoelectron microscopy reconstruction and identified three sites of AT-9010 binding to NSP12. The compound is inserted into the nascent RNA strand at the activation site, and its 2'-methyl group blocks the accurate positioning of the second AT-9010 inserted into the following NTP site.…”