Structural Characterization of a Neutralizing Nanobody With Broad Activity Against SARS-CoV-2 Variants

作者：Tingting Li, Bingjie Zhou, Zhipu Luo, Yanling Lai, Suqiong Huang, Yuanze Zhou, Yaning Li, Anupriya Gautam, Salomé Bourgeau, Shurui Wang, Juan Bao, Jingquan Tan, Dimitri Lavillette, Dianfan Li · 发表于：Frontiers in Microbiology · 年份：2022 · DOI：10.3389/fmicb.2022.875840 · 被引用次数：14 · 研究领域：SARS-CoV-2 and COVID-19 Research、Bacteriophages and microbial interactions、SARS-CoV-2 detection and testing

SARS-CoV-2 and its variants, such as the Omicron continue to threaten public health. The virus recognizes the host cell by attaching its Spike (S) receptor-binding domain (RBD) to the host receptor, ACE2. Therefore, RBD is a primary target for neutralizing antibodies and vaccines. Here, we report the isolation and biological and structural characterization of a single-chain antibody (nanobody) from RBD-immunized alpaca. The nanobody, named DL28, binds to RBD tightly with a K D of 1.56 nM and neutralizes the original SARS-CoV-2 strain with an IC 50 of 0.41 μg mL −1 . Neutralization assays with a panel of variants of concern (VOCs) reveal its wide-spectrum activity with IC 50 values ranging from 0.35 to 1.66 μg mL −1 for the Alpha/Beta/Gamma/Delta and an IC 50 of 0.66 μg mL −1 for the currently prevalent Omicron. Competition binding assays show that DL28 blocks ACE2-binding. However, structural characterizations and mutagenesis suggest that unlike most antibodies, the blockage by DL28 does not involve direct competition or steric hindrance. Rather, DL28 may use a “conformation competition” mechanism where it excludes ACE2 by keeping an RBD loop in a conformation incompatible with ACE2-binding.