Protein-primed RNA synthesis in SARS-CoVs and structural basis for inhibition by AT-527

Shannon, A.; Fattorini, V.; Sama, B.; Selisko, B.; Feracci, M.; Falcou, C.; Gauffre, P.; El Kazzi, P.; Decroly, E.; Rabah, N.; Toulon, K.; Eydoux, C.; Guillemot, J.-C.; Noel, M.; Debart, F.; Vasseur, J.-J.; Moussa, A.; Good, S.; Lin, K.; Sommadossi, J.-P.; Zhu, Y.; Yan, X.; Shi, H.; Ferron, F.; Canard, B.

doi:10.1101/2021.03.23.436564

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bioRxiv · 10.1101/2021.03.23.436564

Protein-primed RNA synthesis in SARS-CoVs and structural basis for inhibition by AT-527

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Abstract

How viruses from the Coronaviridae family initiate viral RNA synthesis is unknown. Here we show that the SARS-CoV-1 and -2 Nidovirus RdRp-Associated Nucleotidyltransferase (NiRAN) domain on nsp12 uridylates the viral cofactor nsp8, forming a UMP-Nsp8 covalent intermediate that subsequently primes RNA synthesis from a poly(A) template; a protein-priming mechanism reminiscent of Picornaviridae enzymes. In parallel, the RdRp active site of nsp12 synthesizes a pppGpU primer, which primes (-)ssRNA synthesis at the precise genome-poly(A) junction. The guanosine analogue 5-triphosphate AT-9010 (prodrug: AT-527) tightly binds to the NiRAN and inhibits both nsp8-labeling and the initiation of RNA synthesis. A 2.98 [A] resolution Cryo-EM structure of the SARS-CoV-2 nsp12-nsp7-(nsp8)2 /RNA/NTP quaternary complex shows AT-9010 simultaneously binds to both NiRAN and RdRp active site of nsp12, blocking their respective activities. AT-527 is currently in phase II clinical trials, and is a potent inhibitor of SARS-CoV-1 and -2, representing a promising drug for COVID-19 treatment.

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Shannon, A., Fattorini, V., Sama, B., Selisko, B., Feracci, M., Falcou, C., Gauffre, P., El Kazzi, P., Decroly, E., Rabah, N., Toulon, K., Eydoux, C., Guillemot, J.-C., Noel, M., Debart, F., Vasseur, J.-J., Moussa, A., Good, S., Lin, K., Sommadossi, J.-P., Zhu, Y., Yan, X., Shi, H., Ferron, F., Canard, B.. 2021-03-23. Protein-primed RNA synthesis in SARS-CoVs and structural basis for inhibition by AT-527. https://doi.org/10.1101/2021.03.23.436564

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