A potent neutralizing human antibody reveals the N-terminal domain of the Spike protein of SARS-CoV-2 as a site of vulnerability

Chi, Xiangyang; Yan, Renhong; Zhang, Jun; Zhang, Guanying; Zhang, Yuanyuan; Hao, Meng; Zhang, Zhe; Fan, Pengfei; Dong, Yunzhu; Yang, Yilong; Chen, Zhengshan; Guo, Yingying; Zhang, Jinlong; Li, Yaning; Song, Xiaohong; Chen, Yi; Xia, Lu; Fu, Ling; Hou, Lihua; Xu, Junjie; Yu, Changming; Li, Jianmin; Zhou, Qiang; Chen, Wei

The pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a global public health threat. Most research on therapeutics against SARS-CoV-2 focused on the receptor binding domain (RBD) of the Spike (S) protein, whereas the vulnerable epitopes and functional mechanism of non-RBD regions are poorly understood. Here we isolated and characterized monoclonal antibodies (mAbs) derived from convalescent COVID-19 patients. An mAb targeting the N-terminal domain (NTD) of the SARS-CoV-2 S protein, named 4A8, exhibits high neutralization potency against both authentic and pseudotyped SARS-CoV-2, although it does not block the interaction between angiotensin-converting enzyme 2 (ACE2) receptor and S protein. The cryo-EM structure of the SARS-CoV-2 S protein in complex with 4A8 has been determined to an overall resolution of 3.1 Angstrom and local resolution of 3.4 Angstrom for the 4A8-NTD interface, revealing detailed interactions between the NTD and 4A8. Our functional and structural characterizations discover a new vulnerable epitope of the S protein and identify promising neutralizing mAbs as potential clinical therapy for COVID-19.