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TitleA panel of nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants including Omicron.
Journal, issue, pagesCommun Biol, Vol. 5, Issue 1, Page 669, Year 2022
Publish dateJul 6, 2022
AuthorsRyota Maeda / Junso Fujita / Yoshinobu Konishi / Yasuhiro Kazuma / Hiroyuki Yamazaki / Itsuki Anzai / Tokiko Watanabe / Keishi Yamaguchi / Kazuki Kasai / Kayoko Nagata / Yutaro Yamaoka / Kei Miyakawa / Akihide Ryo / Kotaro Shirakawa / Kei Sato / Fumiaki Makino / Yoshiharu Matsuura / Tsuyoshi Inoue / Akihiro Imura / Keiichi Namba / Akifumi Takaori-Kondo /
PubMed AbstractWe are amid the historic coronavirus infectious disease 2019 (COVID-19) pandemic. Imbalances in the accessibility of vaccines, medicines, and diagnostics among countries, regions, and populations, ...We are amid the historic coronavirus infectious disease 2019 (COVID-19) pandemic. Imbalances in the accessibility of vaccines, medicines, and diagnostics among countries, regions, and populations, and those in war crises, have been problematic. Nanobodies are small, stable, customizable, and inexpensive to produce. Herein, we present a panel of nanobodies that can detect the spike proteins of five SARS-CoV-2 variants of concern (VOCs) including Omicron. Here we show via ELISA, lateral flow, kinetic, flow cytometric, microscopy, and Western blotting assays that our nanobodies can quantify the spike variants. This panel of nanobodies broadly neutralizes viral infection caused by pseudotyped and authentic SARS-CoV-2 VOCs. Structural analyses show that the P86 clone targets epitopes that are conserved yet unclassified on the receptor-binding domain (RBD) and contacts the N-terminal domain (NTD). Human antibodies rarely access both regions; consequently, the clone buries hidden crevasses of SARS-CoV-2 spike proteins that go undetected by conventional antibodies.
External linksCommun Biol / PubMed:35794202 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.6 - 3.29 Å
Structure data

32078

7vq0

EMDB-32078, PDB-7vq0:
Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) bound to neutralizing nanobodies P86
Method: EM (single particle) / Resolution: 3.03 Å

EMDB-32079: Cryo-EM structure of the SARS-CoV-2 spike protein (3-up RBD) bound to neutralizing nanobodies P86
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-32080: Cryo-EM structure of the SARS-CoV-2 spike protein (1-up RBD) bound to neutralizing nanobodies P17
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-32081: Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) bound to neutralizing nanobodies P17
Method: EM (single particle) / Resolution: 3.29 Å

PDB-7vpy:
Crystal structure of the neutralizing nanobody P86 against SARS-CoV-2
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

Chemicals

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-HOH:
WATER / Water

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

Source
  • severe acute respiratory syndrome coronavirus 2
  • vicugna pacos (alpaca)
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / VIRAL PROTEIN/IMMUNE SYSTEM / spike / nanobody / VHH / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex

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