1
|
Modhiran N, Lauer SM, Amarilla AA, Hewins P, Lopes van den Broek SI, Low YS, Thakur N, Liang B, Nieto GV, Jung J, Paramitha D, Isaacs A, Sng JD, Song D, Jørgensen JT, Cheuquemilla Y, Bürger J, Andersen IV, Himelreichs J, Jara R, MacLoughlin R, Miranda-Chacon Z, Chana-Cuevas P, Kramer V, Spahn C, Mielke T, Khromykh AA, Munro T, Jones ML, Young PR, Chappell K, Bailey D, Kjaer A, Herth MM, Jurado KA, Schwefel D, Rojas-Fernandez A, Watterson D. A nanobody recognizes a unique conserved epitope and potently neutralizes SARS-CoV-2 omicron variants. iScience 2023; 26:107085. [PMID: 37361875 PMCID: PMC10251734 DOI: 10.1016/j.isci.2023.107085] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/12/2023] [Accepted: 06/06/2023] [Indexed: 06/28/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) Omicron variant sub-lineages spread rapidly worldwide, mostly due to their immune-evasive properties. This has put a significant part of the population at risk for severe disease and underscores the need for effective anti-SARS-CoV-2 agents against emergent strains in vulnerable patients. Camelid nanobodies are attractive therapeutic candidates due to their high stability, ease of large-scale production, and potential for delivery via inhalation. Here, we characterize the receptor binding domain (RBD)-specific nanobody W25 and show superior neutralization activity toward Omicron sub-lineages in comparison to all other SARS-CoV2 variants. Structure analysis of W25 in complex with the SARS-CoV2 spike glycoprotein shows that W25 engages an RBD epitope not covered by any of the antibodies previously approved for emergency use. In vivo evaluation of W25 prophylactic and therapeutic treatments across multiple SARS-CoV-2 variant infection models, together with W25 biodistribution analysis in mice, demonstrates favorable pre-clinical properties. Together, these data endorse W25 for further clinical development.
Collapse
Affiliation(s)
- Naphak Modhiran
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
| | - Simon Malte Lauer
- Institute of Medical Physics and Biophysics, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Alberto A. Amarilla
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Peter Hewins
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Sara Irene Lopes van den Broek
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100 Copenhagen, Denmark
| | - Yu Shang Low
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Nazia Thakur
- The Pirbright Institute, Ash Road, Guildford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benjamin Liang
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Guillermo Valenzuela Nieto
- Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile, Valdivia, Chile
| | - James Jung
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Devina Paramitha
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Ariel Isaacs
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - Julian D.J. Sng
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
| | - David Song
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jesper Tranekjær Jørgensen
- Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
- Cluster for Molecular Imaging, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Yorka Cheuquemilla
- Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile, Valdivia, Chile
| | - Jörg Bürger
- Institute of Medical Physics and Biophysics, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Ida Vang Andersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100 Copenhagen, Denmark
- Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Johanna Himelreichs
- Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile, Valdivia, Chile
| | - Ronald Jara
- Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile, Valdivia, Chile
| | - Ronan MacLoughlin
- Research and Development, Science and Emerging Technologies, Aerogen Limited, Galway Business Park, H91 HE94 Galway, Ireland
| | | | - Pedro Chana-Cuevas
- CETRAM & Faculty of Medical Science Universidad de Santiago de Chile, Chile
| | - Vasko Kramer
- PositronPharma SA, Rancagua 878, 7500921 Providencia, Santiago, Chile
| | - Christian Spahn
- Institute of Medical Physics and Biophysics, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Alexander A. Khromykh
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| | - Trent Munro
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
| | - Martina L. Jones
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
| | - Paul R. Young
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| | - Keith Chappell
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| | - Dalan Bailey
- The Pirbright Institute, Ash Road, Guildford, UK
| | - Andreas Kjaer
- Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
- Cluster for Molecular Imaging, Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Matthias Manfred Herth
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100 Copenhagen, Denmark
- Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Kellie Ann Jurado
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - David Schwefel
- Institute of Medical Physics and Biophysics, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Alejandro Rojas-Fernandez
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Berking Biotechnology, Valdivia, Chile
| | - Daniel Watterson
- School of Chemistry and Molecular Bioscience, the University of Queensland, Brisbane, QLD, Australia
- Australian Institute for Bioengineering and Nanotechnology, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| |
Collapse
|
2
|
Valenzuela Nieto G, Jara R, Watterson D, Modhiran N, Amarilla AA, Himelreichs J, Khromykh AA, Salinas-Rebolledo C, Pinto T, Cheuquemilla Y, Margolles Y, López González Del Rey N, Miranda-Chacon Z, Cuevas A, Berking A, Deride C, González-Moraga S, Mancilla H, Maturana D, Langer A, Toledo JP, Müller A, Uberti B, Krall P, Ehrenfeld P, Blesa J, Chana-Cuevas P, Rehren G, Schwefel D, Fernandez LÁ, Rojas-Fernandez A. Potent neutralization of clinical isolates of SARS-CoV-2 D614 and G614 variants by a monomeric, sub-nanomolar affinity nanobody. Sci Rep 2021; 11:3318. [PMID: 33558635 PMCID: PMC7870875 DOI: 10.1038/s41598-021-82833-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/25/2021] [Indexed: 02/06/2023] Open
Abstract
Despite unprecedented global efforts to rapidly develop SARS-CoV-2 treatments, in order to reduce the burden placed on health systems, the situation remains critical. Effective diagnosis, treatment, and prophylactic measures are urgently required to meet global demand: recombinant antibodies fulfill these requirements and have marked clinical potential. Here, we describe the fast-tracked development of an alpaca Nanobody specific for the receptor-binding-domain (RBD) of the SARS-CoV-2 Spike protein with potential therapeutic applicability. We present a rapid method for nanobody isolation that includes an optimized immunization regimen coupled with VHH library E. coli surface display, which allows single-step selection of Nanobodies using a simple density gradient centrifugation of the bacterial library. The selected single and monomeric Nanobody, W25, binds to the SARS-CoV-2 S RBD with sub-nanomolar affinity and efficiently competes with ACE-2 receptor binding. Furthermore, W25 potently neutralizes SARS-CoV-2 wild type and the D614G variant with IC50 values in the nanomolar range, demonstrating its potential as antiviral agent.
Collapse
Affiliation(s)
| | - Ronald Jara
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia, Chile
| | - Daniel Watterson
- School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Australia
- The Australian Institute for Biotechnology and Nanotechnology, The University of Queensland, Brisbane, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia
| | - Naphak Modhiran
- School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Australia
- The Australian Institute for Biotechnology and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Alberto A Amarilla
- School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Johanna Himelreichs
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Alexander A Khromykh
- School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia
| | | | - Teresa Pinto
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Yorka Cheuquemilla
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
- Berking Biotechnology, Valdivia, Chile
| | - Yago Margolles
- Department of Microbial Biotechnology, National Biotechnology Center, Superior Council of Scientific Research, Madrid, Spain
| | | | - Zaray Miranda-Chacon
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Alexei Cuevas
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | | | - Camila Deride
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
- Institute of Veterinary Clinical Sciences, Faculty of Veterinary Sciences, Universidad Austral de Chile, Valdivia, Chile
| | | | - Héctor Mancilla
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Daniel Maturana
- NanoTemper Technologies GmbH, Floessergasse 4, 81369, Munich, Germany
| | - Andreas Langer
- NanoTemper Technologies GmbH, Floessergasse 4, 81369, Munich, Germany
| | - Juan Pablo Toledo
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Ananda Müller
- Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
- Institute of Veterinary Clinical Sciences, Faculty of Veterinary Sciences, Universidad Austral de Chile, Valdivia, Chile
| | - Benjamín Uberti
- Institute of Veterinary Clinical Sciences, Faculty of Veterinary Sciences, Universidad Austral de Chile, Valdivia, Chile
| | - Paola Krall
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
- Department of Pediatrics and Children's Surgery Oriente, Universidad de Chile, Valdivia, Chile
| | - Pamela Ehrenfeld
- Institute of Anatomy, Histology, and Pathology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
- Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile, Valdivia, Chile
| | - Javier Blesa
- HM CINAC, Hospital Universitario HM Puerta del Sur, Mostoles, 28938, Madrid, Spain
| | - Pedro Chana-Cuevas
- CETRAM & Faculty of Medical Science, Universidad de Santiago de Chile, Santiago, Chile
| | - German Rehren
- Technology Transfer and Licensing Office, Universidad Austral de Chile, Valdivia, Chile
| | - David Schwefel
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Luis Ángel Fernandez
- Department of Microbial Biotechnology, National Biotechnology Center, Superior Council of Scientific Research, Madrid, Spain
| | - Alejandro Rojas-Fernandez
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.
- Berking Biotechnology, Valdivia, Chile.
- Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile, Valdivia, Chile.
- Institute of Philosophy and Complexity Sciences, Santiago, Chile.
| |
Collapse
|