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Structural basis for SARS-CoV-2 neutralizing antibodies with novel binding epitopes
Authors:Dan Fu  Guangshun Zhang  Yuhui Wang  Zheng Zhang  Hengrui Hu  Shu Shen  Jun Wu  Bo Li  Xin Li  Yaohui Fang  Jia Liu  Qiao Wang  Yunjiao Zhou  Wei Wang  Yufeng Li  Zhonghua Lu  Xiaoxiao Wang  Cui Nie  Yujie Tian  Da Chen  Yuan Wang  Xingdong Zhou  Qisheng Wang  Feng Yu  Chen Zhang  Changjing Deng  Liang Zhou  Guangkuo Guan  Na Shao  Zhiyong Lou  Fei Deng  Hongkai Zhang  Xinwen Chen  Manli Wang  Louis Liu  Zihe Rao  Yu Guo
Abstract:The ongoing Coronavirus Disease 2019 (COVID-19) pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) threatens global public health and economy unprecedentedly, requiring accelerating development of prophylactic and therapeutic interventions. Molecular understanding of neutralizing antibodies (NAbs) would greatly help advance the development of monoclonal antibody (mAb) therapy, as well as the design of next generation recombinant vaccines. Here, we applied H2L2 transgenic mice encoding the human immunoglobulin variable regions, together with a state-of-the-art antibody discovery platform to immunize and isolate NAbs. From a large panel of isolated antibodies, 25 antibodies showed potent neutralizing activities at sub-nanomolar levels by engaging the spike receptor-binding domain (RBD). Importantly, one human NAb, termed PR1077, from the H2L2 platform and 2 humanized NAb, including PR953 and PR961, were further characterized and subjected for subsequent structural analysis. High-resolution X-ray crystallography structures unveiled novel epitopes on the receptor-binding motif (RBM) for PR1077 and PR953, which directly compete with human angiotensin-converting enzyme 2 (hACE2) for binding, and a novel non-blocking epitope on the neighboring site near RBM for PR961. Moreover, we further tested the antiviral efficiency of PR1077 in the Ad5-hACE2 transduction mouse model of COVID-19. A single injection provided potent protection against SARS-CoV-2 infection in either prophylactic or treatment groups. Taken together, these results shed light on the development of mAb-related therapeutic interventions for COVID-19.

This study characterizes novel neutralizing antibodies against the SARS-CoV-2 spike protein. Co-crystal structures of the spike protein receptor-binding domain and humanised mouse antibodies identify novel epitopes on the spike protein; binding to these epitopes competes with the ACE2 receptor, and one of the antibodies provides protection against SARS-CoV-2 infection in a mouse model of COVID-19.
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