Prime editor-mediated functional reshaping of ACE2 prevents the entry of multiple human coronaviruses, including SARS-CoV-2 variants

Wenwen Zhao; Jifang Li; Xiao Wang; Wei Xu; Bao-Qing Gao; Jiangchao Xiang; Yaofeng Hou; Wei Liu; Jing Wu; Qilian Qi; Jia Wei; Xiaoyu Yang; Lu Lu; Li Yang; Jia Chen; Bei Yang

doi:10.1002/mco2.356

Prime editor-mediated functional reshaping of ACE2 prevents the entry of multiple human coronaviruses, including SARS-CoV-2 variants

MedComm (2020). 2023 Sep 10;4(5):e356. doi: 10.1002/mco2.356. eCollection 2023 Oct.

Authors

Wenwen Zhao^{1

2

3}, Jifang Li^{1

2

3}, Xiao Wang^{1

2

4}, Wei Xu^{5

6

7}, Bao-Qing Gao⁸, Jiangchao Xiang^{1

2

3}, Yaofeng Hou^{1

3}, Wei Liu⁹, Jing Wu^{1

2}, Qilian Qi¹, Jia Wei^{10

11}, Xiaoyu Yang⁹, Lu Lu⁵, Li Yang^{10

11}, Jia Chen^{1

2

3

4}, Bei Yang^{1

3}

Affiliations

¹ Shanghai Frontiers Science Center for Biomacromolecules and Precision Medicine Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology ShanghaiTech University Shanghai China.
² Gene Editing Center School of Life Science and Technology ShanghaiTech University Shanghai China.
³ Shanghai Clinical Research and Trial Center Shanghai China.
⁴ Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai China.
⁵ Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS) School of Basic Medical Sciences Fudan University Shanghai China.
⁶ Shanghai Institute of Infectious Disease and Biosecurity, Fudan University Shanghai China.
⁷ Biosafety Level 3 Laboratory Shanghai Medical College Shanghai Frontiers Science Center of Pathogenic Microbes and Infection Fudan University Shanghai China.
⁸ Shanghai Institute of Nutrition and Health University of Chinese Academy of Sciences Chinese Academy of Sciences Shanghai China.
⁹ School of Physical Science and Technology ShanghaiTech University Shanghai China.
¹⁰ Center for Molecular Medicine Children's Hospital Fudan University Shanghai China.
¹¹ Shanghai Key Laboratory of Medical Epigenetics International Laboratory of Medical Epigenetics and Metabolism Ministry of Science and Technology Institutes of Biomedical Sciences Fudan University Shanghai China.

Abstract

The spike protein of SARS-CoV-2 hijacks the host angiotensin converting enzyme 2 (ACE2) to meditate its entry and is the primary target for vaccine development. Nevertheless, SARS-CoV-2 keeps evolving and the latest Omicron subvariants BQ.1 and XBB have gained exceptional immune evasion potential through mutations in their spike proteins, leading to sharply reduced efficacy of current spike-focused vaccines and therapeutics. Compared with the fast-evolving spike protein, targeting host ACE2 offers an alternative antiviral strategy that is more resistant to viral evolution and can even provide broad prevention against SARS-CoV and HCoV-NL63. Here, we use prime editor (PE) to precisely edit ACE2 at structurally selected sites. We demonstrated that residue changes at Q24/D30/K31 and/or K353 of ACE2 could completely ablate the binding of tested viruses while maintaining its physiological role in host angiotensin II conversion. PE-mediated ACE2 editing at these sites suppressed the entry of pseudotyped SARS-CoV-2 major variants of concern and even SARS-CoV or HCoV-NL63. Moreover, it significantly inhibited the replication of the Delta variant live virus. Our work investigated the unexplored application potential of prime editing in high-risk infectious disease control and demonstrated that such gene editing-based host factor reshaping strategy can provide broad-spectrum antiviral activity and a high barrier to viral escape or resistance.

Keywords: HCoV‐NL63; SARS‐CoV; SARS‐CoV‐2 VOCs; broad spectrum; host factor reshaping; prime editing.