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Hannula L, Kuivanen S, Lasham J, Kant R, Kareinen L, Bogacheva M, Strandin T, Sironen T, Hepojoki J, Sharma V, Saviranta P, Kipar A, Vapalahti O, Huiskonen JT, Rissanen I. Nanobody engineering for SARS-CoV-2 neutralization and detection. Microbiol Spectr 2024; 12:e0419922. [PMID: 38363137 PMCID: PMC10986514 DOI: 10.1128/spectrum.04199-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/03/2024] [Indexed: 02/17/2024] Open
Abstract
In response to the ongoing COVID-19 pandemic, the quest for coronavirus inhibitors has inspired research on a variety of small proteins beyond conventional antibodies, including robust single-domain antibody fragments, i.e., "nanobodies." Here, we explore the potential of nanobody engineering in the development of antivirals and diagnostic tools. Through fusion of nanobody domains that target distinct binding sites, we engineered multimodular nanobody constructs that neutralize wild-type SARS-CoV-2 and the Alpha and Delta variants at high potency, with IC50 values as low as 50 pM. Despite simultaneous binding to distinct epitopes, Beta and Omicron variants were more resistant to neutralization by the multimodular nanobodies, which highlights the importance of accounting for antigenic drift in the design of biologics. To further explore the applications of nanobody engineering in outbreak management, we present an assay based on fusions of nanobodies with fragments of NanoLuc luciferase that can detect sub-nanomolar quantities of the SARS-CoV-2 spike protein in a single step. Our work showcases the potential of nanobody engineering to combat emerging infectious diseases. IMPORTANCE Nanobodies, small protein binders derived from the camelid antibody, are highly potent inhibitors of respiratory viruses that offer several advantages over conventional antibodies as candidates for specific therapies, including high stability and low production costs. In this work, we leverage the unique properties of nanobodies and apply them as building blocks for new therapeutic and diagnostic tools. We report ultra-potent SARS-CoV-2 inhibition by engineered nanobodies comprising multiple modules in structure-guided combinations and develop nanobodies that carry signal molecules, allowing rapid detection of the SARS-CoV-2 spike protein. Our results highlight the potential of engineered nanobodies in the development of effective countermeasures, both therapeutic and diagnostic, to manage outbreaks of emerging viruses.
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Affiliation(s)
- Liina Hannula
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Suvi Kuivanen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jonathan Lasham
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Ravi Kant
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Gdynia, Poland
| | - Lauri Kareinen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Mariia Bogacheva
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tomas Strandin
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Jussi Hepojoki
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Vivek Sharma
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Petri Saviranta
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Anja Kipar
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Olli Vapalahti
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Juha T. Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Ilona Rissanen
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
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