Identification of a nanobody able to catalyze the destruction of the spike-trimer of SARS-CoV-2

Abstract

Neutralizing antibodies have been designed to specifically target and bind to the receptor binding domain (RBD) of spike (S) protein to block severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus from attaching to angiotensin converting enzyme 2 (ACE2). This study reports a distinctive nanobody, designated as VHH21, that directly catalyzes the S-trimer into an irreversible transition state through postfusion conformational changes. Derived from camels immunized with multiple antigens, a set of nanobodies with high affinity for the S1 protein displays abilities to neutralize pseudovirion infections with a broad resistance to variants of concern of SARS-CoV-2, including SARS-CoV and BatRaTG13. Importantly, a super-resolution screening and analysis platform based on visual fluorescence probes was designed and applied to monitor single proteins and protein subunits. A spontaneously occurring dimeric form of VHH21 was obtained to rapidly destroy the S-trimer. Structural analysis via cryogenic electron microscopy revealed that VHH21 targets specific conserved epitopes on the S protein, distinct from the ACE2 binding site on the RBD, which destabilizes the fusion process. This research highlights the potential of VHH21 as an abzyme-like nanobody (nanoabzyme) possessing broad-spectrum binding capabilities and highly effective anti-viral properties and offers a promising strategy for combating coronavirus outbreaks.

Keywords

nanobody / SARS-CoV-2 / spike-trimer / catalyzation / rapid destruction

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Acknowledgements

We thank Xiaojun Huang, Boling Zhu, Lihong Chen, Xujing Li, Dong Li, Zhensheng Xie at the Center for Biological Imaging, Core Facilities for protein Science and Yuanyuan Chen, Zhenwei Yang and Bingxue Zhou (IBP, CAS) for technical assistance, Wei Zhang, Dong Qi and Xuefen Zhang at the OptoFem Tech. Limited for the instrument demonstrations of Abberior STEDYCON nanoscopes. This work was supported by grants from National Natural Science Foundation of China (Nos. 92374206, 82225037, 31900871, and 32241027), National Key R&D Program of China (Nos. 2022YFA1303602 and 2021YFA1301402), the Strategic Priority Research Program of CAS (Nos. XDB37030206, XDB29040102, XDB37040101, and XDB29030103), Shanghai Municipal Science and Technology Major Project (No. ZD2021CY001), Basic Research Program Based on Major Scientific Infrastructures of CAS (No. JZHKYPT-2021-05), Key Laboratory of Biomacromolecules of CAS (No. ZGD-2023-05), Beijing Nova Program (No. 20230484239 to Duanfang Cao).

Compliance with ethics guidelines

Conflicts of interest Kai Wang, Duanfang Cao, Lanlan Liu, Xiaoyi Fan, Yihuan Lin, Wenting He, Yunze Zhai, Pingyong Xu, Xiyun Yan, Haikun Wang, Xinzheng Zhang, and Pengyuan Yang declare that no competing interests were involved in this work.

The experimental procedures for use and care of animals were approved by the ethics committee of Institute of Biophysics, Chinese Academy of Sciences. All institutional and national guidelines for the care and use of laboratory animals were followed.

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Supplementary material is available in the online version of this article at https://doi.org/10.1007/s11684-025-1128-4 and is accessible for authorized users.

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