A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors

Liming Yan; Yucen Huang; Ji Ge; Zhenyu Liu; Pengchi Lu; Bo Huang; Shan Gao; Junbo Wang; Liping Tan; Sihan Ye; Fengxi Yu; Weiqi Lan; Shiya Xu; Feng Zhou; Lei Shi; Luke W Guddat; Yan Gao; Zihe Rao; Zhiyong Lou

doi:10.1016/j.cell.2022.09.037

A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors

Cell. 2022 Nov 10;185(23):4347-4360.e17. doi: 10.1016/j.cell.2022.09.037. Epub 2022 Oct 4.

Authors

Liming Yan¹, Yucen Huang², Ji Ge³, Zhenyu Liu⁴, Pengchi Lu⁵, Bo Huang⁶, Shan Gao¹, Junbo Wang¹, Liping Tan¹, Sihan Ye¹, Fengxi Yu⁷, Weiqi Lan⁸, Shiya Xu¹, Feng Zhou⁶, Lei Shi⁶, Luke W Guddat⁹, Yan Gao¹⁰, Zihe Rao¹¹, Zhiyong Lou¹²

Affiliations

¹ MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China.
² MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
³ MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; Innovation Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China.
⁴ MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
⁵ Division of Biosciences, University College London, London, UK.
⁶ Beijing StoneWise Technology Co Ltd., Beijing, China.
⁷ Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
⁸ Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
⁹ School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
¹⁰ Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China. Electronic address: gaoyan@shanghaitech.edu.cn.
¹¹ MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; Innovation Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. Electronic address: raozh@tsinghua.edu.cn.
¹² MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China. Electronic address: louzy@mail.tsinghua.edu.cn.

Abstract

Decoration of cap on viral RNA plays essential roles in SARS-CoV-2 proliferation. Here, we report a mechanism for SARS-CoV-2 RNA capping and document structural details at atomic resolution. The NiRAN domain in polymerase catalyzes the covalent link of RNA 5' end to the first residue of nsp9 (termed as RNAylation), thus being an intermediate to form cap core (GpppA) with GTP catalyzed again by NiRAN. We also reveal that triphosphorylated nucleotide analog inhibitors can be bonded to nsp9 and fit into a previously unknown "Nuc-pocket" in NiRAN, thus inhibiting nsp9 RNAylation and formation of GpppA. S-loop (residues 50-KTN-52) in NiRAN presents a remarkable conformational shift observed in RTC bound with sofosbuvir monophosphate, reasoning an "induce-and-lock" mechanism to design inhibitors. These findings not only improve the understanding of SARS-CoV-2 RNA capping and the mode of action of NAIs but also provide a strategy to design antiviral drugs.

Keywords: SARS-CoV-2; capping; cryo-EM; nucleotide analog inhibitor.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Antiviral Agents / chemistry
COVID-19*
Humans
Nucleotides / chemistry
RNA, Viral / metabolism
RNA-Dependent RNA Polymerase
SARS-CoV-2*
Viral Nonstructural Proteins / metabolism

Substances

RNA, Viral
RNA-Dependent RNA Polymerase
Antiviral Agents
Nucleotides
Viral Nonstructural Proteins