Structural basis of nanobodies neutralizing SARS-CoV-2 variants

Zhenzhong Shi; Xiyang Li; Lu Wang; Zengchao Sun; Haiwei Zhang; Xiaochen Chen; Qianqian Cui; Huarui Qiao; Zhongyun Lan; Xin Zhang; Xianheng Li; Lingyun Li; Jianfeng Xu; Rui Gong; Chengpeng Fan; Yong Geng

doi:10.1016/j.str.2022.02.011

Structural basis of nanobodies neutralizing SARS-CoV-2 variants

Structure. 2022 May 5;30(5):707-720.e5. doi: 10.1016/j.str.2022.02.011. Epub 2022 Mar 10.

Authors

Zhenzhong Shi¹, Xiyang Li², Lu Wang³, Zengchao Sun¹, Haiwei Zhang⁴, Xiaochen Chen³, Qianqian Cui⁵, Huarui Qiao⁶, Zhongyun Lan⁶, Xin Zhang⁶, Xianheng Li⁶, Lingyun Li³, Jianfeng Xu⁷, Rui Gong⁸, Chengpeng Fan⁹, Yong Geng¹⁰

Affiliations

¹ The CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Department of Biopharmaceutics, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
² School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
³ The CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
⁴ Center for Emerging Infectious Diseases, CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan, Hubei 430071, P.R. China.
⁵ College of Science, Shanghai University, Shanghai 200444, China.
⁶ Department of Biopharmaceutics, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
⁷ Department of Biopharmaceutics, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China. Electronic address: jfxu@shou.edu.cn.
⁸ Center for Emerging Infectious Diseases, CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan, Hubei 430071, P.R. China. Electronic address: gongr@wh.iov.cn.
⁹ School of Basic Medical Sciences, Wuhan University, Wuhan 430071, P.R. China. Electronic address: chengpeng.fan@whu.edu.cn.
¹⁰ The CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: gengyong@simm.ac.cn.

Abstract

Because of the evolutionary variants of SARS-CoV-2, development of broad-spectrum neutralizing antibodies resilient to virus escape is urgently needed. We identified a group of high-affinity nanobodies from camels immunized with receptor-binding domain (RBD) of SARS-CoV-2 spike protein and resolved the structures of two non-competing nanobodies (NB1A7 and NB1B11) in complex with RBD using X-ray crystallography. The structures show that NB1A7 targets the highly conserved cryptic epitope shared by SARS-CoV-2 variants and some other coronaviruses and blocks ACE2 receptor attachment of the spike protein, and NB1B11 epitope overlaps with the contacting surface of ACE2 and is different from the binding site of NB1A7. These two nanobodies were covalently linked into multivalent and bi-paratopic formats, which significantly improved the avidity and neutralization potency and may further inhibit viral escape. The results contribute to the structure-guided design of antibodies against future variants of SARS-CoV-2 virus to combat coronavirus epidemics and pandemics.

Keywords: SARS-CoV-2 virus; bi-paratopic nanobodies; crystal structure; nanobody; receptor-binding domain.

Publication types

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

MeSH terms

Angiotensin-Converting Enzyme 2
Antibodies, Neutralizing
Broadly Neutralizing Antibodies
COVID-19*
Epitopes / metabolism
Humans
Protein Binding
SARS-CoV-2 / genetics
Single-Domain Antibodies* / chemistry
Single-Domain Antibodies* / genetics
Spike Glycoprotein, Coronavirus / chemistry

Substances

Antibodies, Neutralizing
Broadly Neutralizing Antibodies
Epitopes
Single-Domain Antibodies
Spike Glycoprotein, Coronavirus
spike protein, SARS-CoV-2
Angiotensin-Converting Enzyme 2

Supplementary concepts

SARS-CoV-2 variants