An essential step for SARS-CoV-2 infection is the attachment to the host cell receptor by its Spike receptor-binding domain (RBD). Most of the existing RBD-targeting neutralizing antibodies block the receptor-binding motif (RBM), a mutable region with the potential to generate neutralization escape mutants. Here, we isolated and structurally characterized a non-RBM-targeting monoclonal antibody (FD20) from convalescent patients. FD20 engages the RBD at an epitope distal to the RBM with a KD of 5.6 nM, neutralizes SARS-CoV-2 including the current Variants of Concern such as B.1.1.7, B.1.351, P.1, and B.1.617.2 (Delta), displays modest cross-reactivity against SARS-CoV, and reduces viral replication in hamsters. The epitope coincides with a predicted “ideal” vulnerability site with high functional and structural constraints. Mutation of the residues of the conserved epitope variably affects FD20-binding but confers little or no resistance to neutralization. Finally, in vitro mode-of-action characterization and negative-stain electron microscopy suggest a neutralization mechanism by which FD20 destructs the Spike. Our results reveal a conserved vulnerability site in the SARS-CoV-2 Spike for the development of potential antiviral drugs.
Bibliographical noteFunding Information:
We thank Prof. Yao Cong at the authors? institute for providing the S plasmid, and Dr. Yanxing Wang and Mr. Yitian Luo for technical assistance on negative staining. We thank the staff members of the Large-scale Protein Preparation System for equipment maintenance and management, at the SSRF-BL18U1 and BL19U1 beamlines at National Facility for Protein Science (Shanghai) and of the electron microscope facility for technical support and assistance. 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 (2017), the National Natural Science Foundation of China (NSFC) (31870726, D. Li; 31870153, D. La; 31970880, F.L.M), Ministry of Science and Technology of China (2020YFC0845900, D. La.; 2017YFA0506700, F.L.M), CAS President's International Fellowship Initiative (2020VBA0023, DLa), the Key R & D Program of Jiangsu Province (Social Development) Project (BE2019625, DLa), Science and Technology Commission of Shanghai Municipality (STCSM) (20ZR1466700, D. Li; 20490760200, F.L.M), Shanghai Municipal Science and Technology Major Project (20431900402, D. La.), Innovation Capacity Building Project of Jiangsu province Nanjing Unicorn Academy of innovation (BM2020019, D. La.), the ERINHA-Advance project (funding from the European Union?s Horizon 2020 Research & Innovation program, grant agreement No. 824061), and Science and Technology Commission of Hangzhou Municipality (202013A02, J.C.). 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 the Chinese Academy of Sciences (Youth Innovation Promotion Association CAS) (2017122). F.L.M is supported by a CAS grant (JCTD-2020-17).
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