A synthetic nanobody targeting RBD protects hamsters from SARS-CoV-2 infection

Tingting Li, Hongmin Cai, Hebang Yao, Bingjie Zhou, Ning Zhang, Martje Fentener van Vlissingen, Thijs Kuiken, Wenyu Han, Corine H. GeurtsvanKessel, Yuhuan Gong, Yapei Zhao, Quan Shen, Wenming Qin, Xiao Xu Tian, Chao Peng, Yanling Lai, Yanxing Wang, Cedric A.J. Hutter, Shu Ming Kuo, Juan BaoCaixuan Liu, Yifan Wang, Audrey S. Richard, Hervé Raoul, Jiaming Lan, Markus A. Seeger, Yao Cong, Barry Rockx, Gary Wong*, Yuhai Bi*, Dimitri Lavillette*, Dianfan Li*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

63 Citations (Scopus)

Abstract

SARS-CoV-2, the causative agent of COVID-191, features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein1–6. Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics7–17. Llama-derived single-domain antibodies (nanobodies, ~15 kDa) offer advantages in bioavailability, amenability, and production and storage owing to their small sizes and high stability. Here, we report the rapid selection of 99 synthetic nanobodies (sybodies) against RBD by in vitro selection using three libraries. The best sybody, MR3 binds to RBD with high affinity (KD = 1.0 nM) and displays high neutralization activity against SARS-CoV-2 pseudoviruses (IC50 = 0.42 μg mL−1). Structural, biochemical, and biological characterization suggests a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency have been generated by structure-based design, biparatopic construction, and divalent engineering. Two divalent forms of MR3 protect hamsters from clinical signs after live virus challenge and a single dose of the Fc-fusion construct of MR3 reduces viral RNA load by 6 Log10. Our results pave the way for the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid development of targeted medical interventions during an outbreak.

Original languageEnglish
Article number4635
JournalNature Communications
Volume12
Issue number1
DOIs
Publication statusPublished - 30 Jul 2021

Bibliographical note

Funding Information:
We thank the staff members of the NCPSS Large-scale Protein Preparation System and the Electron Microscopy facility for equipment maintenance and management and staff scientists at the SSRF-BL19U1 beamline at National Facility for Protein Science (Shanghai), and the staff of BSL-3 in the Institute of Microbiology, Chinese Academy of Sciences for technical support and assistance. We thank Dr. Zhipu Luo at Soochow University (China) for helpful discussions regarding data processing. This work has been supported by the Strategic Priority Research Program of CAS (XDB37020204, D. Li; XDB29010102, Y.B.), Key Program of CAS Frontier Science (QYZDB-SSW-SMC037, D. Li), CAS Facility-based Open Research Program, the National Natural Science Foundation of China (31870726, D. Li; 31870153, D. Lavillette; 32041010, Y.B.), the One Belt and One Road major project for infectious diseases (2018ZX10101004-003, J.L., G.W.), National Key R&D Program of China (2020YFC0845900, D. Lavillette), CAS president’s international fellowship initiative (2020VBA0023, D. Lavillette), Natural Science Foundation of Shanghai (20ZR1466700, D. Li; 20ZR1463900, G.W.), Shanghai Municipal Science and Technology Major Project (20431900402, D. Lavillette), Science and Technology Commission of Shanghai Municipality (18DZ2210200), Funding for Construction and Operation of Zhangjiang Laboratory (II) (19DZ2260100), and the ERINHA-Advance project (funding from the European Union’s Horizon 2020 Research & Innovation program, grant agreement No. 824061). This project is included in RECOVER European Union’s Horizon 2020 research and innovation program under grant agreement No. 101003589. Y.B. is supported by the NSFC Outstanding Young Scholars (31822055) and Youth Innovation Promotion Association of CAS (2017122). G.W. is supported by a G4 grant from IP, FMX, and CAS.

Publisher Copyright:
© 2021, The Author(s).

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