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TitleA potent synthetic nanobody with broad-spectrum activity neutralizes SARS-CoV-2 virus and the Omicron variant BA.1 through a unique binding mode.
Journal, issue, pagesJ Nanobiotechnology, Vol. 20, Issue 1, Page 411, Year 2022
Publish dateSep 15, 2022
AuthorsDongping Zhao / Liqin Liu / Xinlin Liu / Jinlei Zhang / Yuqing Yin / Linli Luan / Dingwen Jiang / Xiong Yang / Lei Li / Hualong Xiong / Dongming Xing / Qingbing Zheng / Ningshao Xia / Yuyong Tao / Shaowei Li / Haiming Huang /
PubMed AbstractThe major challenge to controlling the COVID pandemic is the rapid mutation rate of the SARS-CoV-2 virus, leading to the escape of the protection of vaccines and most of the neutralizing antibodies ...The major challenge to controlling the COVID pandemic is the rapid mutation rate of the SARS-CoV-2 virus, leading to the escape of the protection of vaccines and most of the neutralizing antibodies to date. Thus, it is essential to develop neutralizing antibodies with broad-spectrum activity targeting multiple SARS-CoV-2 variants. Here, we report a synthetic nanobody (named C5G2) obtained by phage display and subsequent antibody engineering. C5G2 has a single-digit nanomolar binding affinity to the RBD domain and inhibits its binding to ACE2 with an IC of 3.7 nM. Pseudovirus assays indicated that monovalent C5G2 could protect the cells from infection with SARS-CoV-2 wild-type virus and most of the viruses of concern, i.e., Alpha, Beta, Gamma and Omicron variants. Strikingly, C5G2 has the highest potency against Omicron BA.1 among all the variants, with an IC of 4.9 ng/mL. The cryo-EM structure of C5G2 in complex with the spike trimer showed that C5G2 binds to RBD mainly through its CDR3 at a conserved region that does not overlap with the ACE2 binding surface. Additionally, C5G2 binds simultaneously to the neighboring NTD domain of the spike trimer through the same CDR3 loop, which may further increase its potency against viral infection. Third, the steric hindrance caused by FR2 of C5G2 could inhibit the binding of ACE2 to RBD as well. Thus, this triple-function nanobody may serve as an effective drug for prophylaxis and therapy against Omicron as well as future variants.
External linksJ Nanobiotechnology / PubMed:36109732 / PubMed Central
MethodsEM (single particle)
Resolution3.51 - 3.88 Å
Structure data

EMDB-33415: Cryo-EM structure of SARS-CoV-2 spike protein in complex with nanobody C5G2
Method: EM (single particle) / Resolution: 3.51 Å

33416

7xrp

EMDB-33416, PDB-7xrp:
Cryo-EM structure of SARS-CoV-2 spike protein in complex with nanobody C5G2 (localized refinement)
Method: EM (single particle) / Resolution: 3.88 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

Source
  • severe acute respiratory syndrome coronavirus 2
  • camelus dromedarius (Arabian camel)
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Neutralizing nanobody / Cryo-EM / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex

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