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TitleA novel nanobody broadly neutralizes SARS-CoV-2 via induction of spike trimer dimers conformation.
Journal, issue, pagesExploration (Beijing), Vol. 4, Issue 3, Page 20230086, Year 2024
Publish dateDec 15, 2023
AuthorsYang Yang / Junfang Zhang / Shengnan Zhang / Chenhui Zhang / Chenguang Shen / Shuo Song / Yanqun Wang / Yun Peng / Xiaohua Gong / Jun Dai / Chongwei Xie / Tatyana Aleksandrovna Khrustaleva / Vladislav Victorovich Khrustalev / Yongting Huo / Di Lu / Da Yao / Jincun Zhao / Yingxia Liu / Hongzhou Lu /
PubMed AbstractThe ongoing mutations of the SARS-CoV-2 pose serious challenges to the efficacy of the available antiviral drugs, and new drugs with fantastic efficacy are always deserved investigation. Here, a ...The ongoing mutations of the SARS-CoV-2 pose serious challenges to the efficacy of the available antiviral drugs, and new drugs with fantastic efficacy are always deserved investigation. Here, a nanobody called IBT-CoV144 is reported, which exhibits broad neutralizing activity against SARS-CoV-2 by inducing the conformation of spike trimer dimers. IBT-CoV144 was isolated from an immunized alpaca using the RBD of wild-type SARS-CoV-2, and it showed strong cross-reactive binding and neutralizing potency against diverse SARS-CoV-2 variants, including Omicron subvariants. Moreover, the prophylactically and therapeutically intranasal administration of IBT-CoV144 confers fantastic protective efficacy against the challenge of Omicron BA.1 variant in BALB/c mice model. The structure analysis of the complex between spike (S) protein, conducted using Cryo-EM, revealed a special conformation known as the trimer dimers. This conformation is formed by two trimers, with six RBDs in the "up" state and bound by six VHHs. IBT-CoV144 binds to the lateral region of the RBD on the S protein, facilitating the aggregation of S proteins. This aggregation results in steric hindrance, which disrupts the recognition of the virus by ACE2 on host cells. The discovery of IBT-CoV144 will provide valuable insights for the development of advanced therapeutics and the design of next-generation vaccines.
External linksExploration (Beijing) / PubMed:38939869 / PubMed Central
MethodsEM (single particle)
Resolution3.96 - 4.5 Å
Structure data

36730

8jys

EMDB-36730, PDB-8jys:
SARS-CoV-2 Spike RBD (dimer) in complex with two 2S-1244 nanobodies
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-36735: Dimer of SARS-CoV-2 BA.2 spike and IBT-CoV144(C3 symmetry)
Method: EM (single particle) / Resolution: 3.96 Å

EMDB-36740: Dimer of SARS-CoV-2 BA.2 spike and IBT-CoV144(C1 symmetry)
Method: EM (single particle) / Resolution: 4.3 Å

Source
  • camelus bactrianus (Bactrian camel)
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / Spike / nanobody / dimer / local

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