tetano
Editor, Senior Moderator
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[SUP] 1 [/SUP], Bingjie Zhou[SUP] 2 3 [/SUP], Zhipu Luo[SUP] 4 [/SUP], Yanling Lai[SUP] 1 2 [/SUP], Suqiong Huang[SUP] 2 3 5 [/SUP], Yuanze Zhou[SUP] 6 [/SUP], Yaning Li[SUP] 1 2 [/SUP], Anupriya Gautam[SUP] 2 3 [/SUP], Salome Bourgeau[SUP] 2 3 7 [/SUP], Shurui Wang[SUP] 6 [/SUP], Juan Bao[SUP] 1 [/SUP], Jingquan Tan[SUP] 6 [/SUP], Dimitri Lavillette[SUP] 3 8 [/SUP], Dianfan Li[SUP] 1 [/SUP]
Affiliations
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 [SUB]D[/SUB] of 1.56 nM and neutralizes the original SARS-CoV-2 strain with an IC[SUB]50[/SUB] of 0.41 μg mL[SUP]-1[/SUP]. Neutralization assays with a panel of variants of concern (VOCs) reveal its wide-spectrum activity with IC[SUB]50[/SUB] values ranging from 0.35 to 1.66 μg mL[SUP]-1[/SUP] for the Alpha/Beta/Gamma/Delta and an IC[SUB]50[/SUB] of 0.66 μg mL[SUP]-1[/SUP] 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.
. 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[SUP] 1 [/SUP], Bingjie Zhou[SUP] 2 3 [/SUP], Zhipu Luo[SUP] 4 [/SUP], Yanling Lai[SUP] 1 2 [/SUP], Suqiong Huang[SUP] 2 3 5 [/SUP], Yuanze Zhou[SUP] 6 [/SUP], Yaning Li[SUP] 1 2 [/SUP], Anupriya Gautam[SUP] 2 3 [/SUP], Salome Bourgeau[SUP] 2 3 7 [/SUP], Shurui Wang[SUP] 6 [/SUP], Juan Bao[SUP] 1 [/SUP], Jingquan Tan[SUP] 6 [/SUP], Dimitri Lavillette[SUP] 3 8 [/SUP], Dianfan Li[SUP] 1 [/SUP]
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 [SUB]D[/SUB] of 1.56 nM and neutralizes the original SARS-CoV-2 strain with an IC[SUB]50[/SUB] of 0.41 μg mL[SUP]-1[/SUP]. Neutralization assays with a panel of variants of concern (VOCs) reveal its wide-spectrum activity with IC[SUB]50[/SUB] values ranging from 0.35 to 1.66 μg mL[SUP]-1[/SUP] for the Alpha/Beta/Gamma/Delta and an IC[SUB]50[/SUB] of 0.66 μg mL[SUP]-1[/SUP] 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.