Paper

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

Selisko, Barbara, Falcou, Camille, Rabah, Nadia, Feracci, Mikael, Shannon, Ashleigh, Yan, Xiaodong, Gauffre, Pierre, Moussa, Adel, Lin, Kai, Good, Steven, Sommadossi, Jean-Pierre, Zhu, Yingxiao, Mathieu, Noel, Alvarez, Karine, Eydoux, Cécilia, Debart, Françoise, Shi, Hui, Fattorini, Véronique, Canard, Bruno, Vasseur, Jean-Jacques, Sama, Bhawna, Priscila El Kazzi, Decroly, Etienne, Guillemot, Jean-Claude, Ferron, François

2021

Overview

Summary 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 Å 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. Competing Interest Statement S.G., A.M., K.L. and J.P.S. are employees of ATEA Pharmaceuticals, Inc. The other authors declare no competing interests.

• Publisher: Cold Spring Harbor Laboratory Press,Cold Spring Harbor Laboratory
• Subject: Biochemistry / Clinical trials / COVID-19 / Genomes / Poly(A) / Protein biosynthesis / Severe acute respiratory syndrome coronavirus 2 / Transcription