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TitleA potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses, including all major Omicron strains.
Journal, issue, pagesMedComm (2020), Vol. 4, Issue 6, Page e397, Year 2023
Publish dateOct 26, 2023
AuthorsHebang Yao / Hongyang Wang / Zhaoyong Zhang / Yuchi Lu / Zhiying Zhang / Yu Zhang / Xinyi Xiong / Yanqun Wang / Zhizhi Wang / Haitao Yang / Jincun Zhao / Wenqing Xu /
PubMed AbstractSARS-CoV-2 viruses are highly transmissible and immune evasive. It is critical to develop broad-spectrum prophylactic and therapeutic antibodies for potential future pandemics. Here, we used the ...SARS-CoV-2 viruses are highly transmissible and immune evasive. It is critical to develop broad-spectrum prophylactic and therapeutic antibodies for potential future pandemics. Here, we used the phage display method to discover nanobodies (Nbs) for neutralizing SARS-CoV-2 viruses especially Omicron strains. The leading nanobody (Nb), namely, Nb4, with excellent physicochemical properties, can neutralize Delta and Omicron subtypes, including BA.1, BA.1.1 (BA.1 + R346K), BA.2, BA.5, BQ.1, and XBB.1. The crystal structure of Nb4 in complex with the receptor-binding domain (RBD) of BA.1 Spike protein reveals that Nb4 interacts with an epitope on the RBD overlapping with the receptor-binding motif, and thus competes with angiotensin-converting enzyme 2 (ACE2) binding. Nb4 is expected to be effective for neutralizing most recent Omicron variants, since the epitopes are evolutionarily conserved among them. Indeed, trivalent Nb4 interacts with the XBB1.5 Spike protein with low nM affinity and competes for ACE2 binding. Prophylactic and therapeutic experiments in mice indicated that Nb4 could reduce the Omicron virus loads in the lung. In particular, in prophylactic experiments, intranasal administration of multivalent Nb4 completely protected mice from Omicron infection. Taken together, these results demonstrated that Nb4 could serve as a potent and broad-spectrum prophylactic and therapeutic Nb for COVID-19.
External linksMedComm (2020) / PubMed:37901798 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.43 - 3.66 Å
Structure data

36877

8k45

EMDB-36877, PDB-8k45:
A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major Omicron strains
Method: EM (single particle) / Resolution: 3.66 Å

36878

8k46

EMDB-36878, PDB-8k46:
A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major Omicron strains
Method: EM (single particle) / Resolution: 3.37 Å

36879

8k47

EMDB-36879, PDB-8k47:
A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major Omicron strains
Method: EM (single particle) / Resolution: 3.54 Å

PDB-8k3k:
The crystal structure of nanobody Nb4 in complex with receptor binding domain (RBD) of BA.1 Spike protein
Method: X-RAY DIFFRACTION / Resolution: 2.43 Å

Chemicals

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)
  • synthetic construct (others)
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Nanobody / Receptor binding domain / SARS-CoV-2 / Complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex / COVID-19 / spike glycoprotein / virus / antibody

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