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

[tetano]

Front Microbiol


. 2022 Jun 2;13:875840.
doi: 10.3389/fmicb.2022.875840. eCollection 2022.
Structural Characterization of a Neutralizing Nanobody With Broad Activity Against SARS-CoV-2 Variants


Tingting Li ¹ , Bingjie Zhou ^{2 3} , Zhipu Luo ⁴ , Yanling Lai ^{1 2} , Suqiong Huang ^{2 3 5} , Yuanze Zhou ⁶ , Yaning Li ^{1 2} , Anupriya Gautam ^{2 3} , Salome Bourgeau ^{2 3 7} , Shurui Wang ⁶ , Juan Bao ¹ , Jingquan Tan ⁶ , Dimitri Lavillette ^{3 8} , Dianfan Li ¹



Affiliations

• PMID: 35722331
• PMCID: PMC9201380
• DOI: 10.3389/fmicb.2022.875840

Abstract

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 IC₅₀ of 0.41 μg mL^-1. Neutralization assays with a panel of variants of concern (VOCs) reveal its wide-spectrum activity with IC₅₀ values ranging from 0.35 to 1.66 μg mL^-1 for the Alpha/Beta/Gamma/Delta and an IC₅₀ 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.

Keywords: COVID-19; SARS-CoV-2; conformation competition; coronavirus; crystal structure; nanobody; receptor-binding domain.