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Roberts SE, Martin HL, Al-Qallaf D, Tang AA, Tiede C, Gaule TG, Dobon-Alonso A, Overman R, Shah S, Peyret H, Saunders K, Bon R, Manfield IW, Bell SM, Lomonossoff GP, Speirs V, Tomlinson DC. Affimer reagents enable targeted delivery of therapeutic agents and RNA via virus-like particles. iScience 2024; 27:110461. [PMID: 39104409 PMCID: PMC11298639 DOI: 10.1016/j.isci.2024.110461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 05/09/2024] [Accepted: 07/02/2024] [Indexed: 08/07/2024] Open
Abstract
Monoclonal antibodies have revolutionized therapies, but non-immunoglobulin scaffolds are becoming compelling alternatives owing to their adaptability. Their ability to be labeled with imaging or cytotoxic compounds and to create multimeric proteins is an attractive strategy for therapeutics. Focusing on HER2, a frequently overexpressed receptor in breast cancer, this study addresses some limitations of conventional targeting moieties by harnessing the potential of these scaffolds. HER2-binding Affimers were isolated and characterized, demonstrating potency as binding reagents and efficient internalization by HER2-overexpressing cells. Affimers conjugated with cytotoxic agent achieved dose-dependent reductions in cell viability within HER2-overexpressing cell lines. Bispecific Affimers, targeting HER2 and virus-like particles, facilitated efficient internalization of virus-like particles carrying enhanced green fluorescent protein (eGFP)-encoding RNA, leading to protein expression. Anti-HER2 affibody or designed ankyrin repeat protein (DARPin) fusion constructs with the anti-VLP Affimer further underscore the adaptability of this approach. This study demonstrates the versatility of scaffolds for precise delivery of cargos into cells, advancing biotechnology and therapeutic research.
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Affiliation(s)
- Sophie E. Roberts
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Heather L. Martin
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Danah Al-Qallaf
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Anna A. Tang
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - Christian Tiede
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - Thembaninkosi G. Gaule
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
- Institutue of Cardiovascular & Metabolic Medicine, University of Leeds, Leeds, UK
| | | | - Ross Overman
- Leaf Expression Systems, Norwich Research Park, Norwich, UK
| | - Sachin Shah
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Hadrien Peyret
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Keith Saunders
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Robin Bon
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - Iain W. Manfield
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - Sandra M. Bell
- Leeds Institute of Medical Research at St James’s, St James’s University Hospital, University of Leeds, Leeds, UK
| | - George P. Lomonossoff
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Valerie Speirs
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Darren C. Tomlinson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
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2
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Debski-Antoniak O, Flynn A, Klebl DP, Rojas Rechy MH, Tiede C, Wilson IA, Muench SP, Tomlinson D, Fontana J. Exploiting the Affimer platform against influenza A virus. mBio 2024; 15:e0180424. [PMID: 39037231 PMCID: PMC11323568 DOI: 10.1128/mbio.01804-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024] Open
Abstract
Influenza A virus (IAV) is well known for its pandemic potential. While current surveillance and vaccination strategies are highly effective, therapeutic approaches are often short-lived due to the high mutation rates of IAV. Recently, monoclonal antibodies (mAbs) have emerged as a promising therapeutic approach, both against current strains and future IAV pandemics. In addition to mAbs, several antibody-like alternatives exist, which aim to improve upon mAbs. Among these, Affimers stand out for their short development time, high expression levels in Escherichia coli, and animal-free production. In this study, we utilized the Affimer platform to isolate and produce specific and potent inhibitors of IAV. Using a monomeric version of the IAV trimeric hemagglutinin (HA) fusion protein, we isolated 12 Affimers that inhibit IAV infection in vitro. Two of these Affimers were characterized in detail and exhibited nanomolar-binding affinities to the target H3 HA protein, specifically binding to the HA1 head domain. Cryo-electron microscopy (cryo-EM), employing a novel spray approach to prepare cryo-grids, allowed us to image HA-Affimer complexes. Combined with functional assays, we determined that these Affimers inhibit IAV by blocking the interaction of HA with the host-cell receptor, sialic acid. Furthermore, these Affimers inhibited IAV strains closely related to the one used for their isolation. Overall, our results support the use of Affimers as a viable alternative to existing targeted therapies for IAV and highlight their potential as diagnostic reagents. IMPORTANCE Influenza A virus is one of the few viruses that can cause devastating pandemics. Due to the high mutation rates of this virus, annual vaccination is required, and antivirals are short-lived. Monoclonal antibodies present a promising approach to tackle influenza virus infections but are associated with some limitations. To improve on this strategy, we explored the Affimer platform, which are antibody-like proteins made in bacteria. By performing phage-display against a monomeric version of influenza virus fusion protein, an established viral target, we were able to isolate Affimers that inhibit influenza virus infection in vitro. We characterized the mechanism of inhibition of the Affimers by using assays targeting different stages of the viral replication cycle. We additionally characterized HA-Affimer complex structure, using a novel approach to prepare samples for cryo-electron microscopy. Overall, these results show that Affimers are a promising tool against influenza virus infection.
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Affiliation(s)
- Oliver Debski-Antoniak
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Alex Flynn
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - David P. Klebl
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Moisés H. Rojas Rechy
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Christian Tiede
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Stephen P. Muench
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Darren Tomlinson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Juan Fontana
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
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3
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Farokhinejad F, Lane RE, Lobb RJ, Edwardraja S, Wuethrich A, Howard CB, Trau M. Generation of Nanoyeast Single-Chain Variable Fragments as High-Avidity Biomaterials for Dengue Virus Detection. ACS Biomater Sci Eng 2021; 7:5850-5860. [PMID: 34738789 DOI: 10.1021/acsbiomaterials.1c01001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bioengineered yeast bio-nanomaterials termed nanoyeasts displaying antibody single-chain variable fragments (scFvs) against diagnostic targets are a promising alternative to monoclonal antibodies (mAbs). A potential limitation for translating nanoyeasts into diagnostic tools is batch-to-batch variability. Herein, we demonstrate a systematic approach for cost-efficient production of highly specific nanoyeasts that enabled accurate dengue virus (DENV) detection by immunoassay (2.5% CV). Yeasts bioengineered to surface express DENV-specific scFvs (up to 66% of the total cell population) were fragmented into nanoyeast fractions trialing sonication, bead beating, and high-pressure disruption methods. Nanoyeast fractions from sonication had optimal target binding, uniform particle size (±89 nm), were stable, and retained diagnostic activity for 7 days at 37 °C compared to traditional mAbs that lost activity after 1 day at 37 °C. We engineered a panel of nanoyeast scFvs targeting DENV nonstructural protein 1 (NS1): (i) specific for serotyping DENV 1-4 and (ii) cross-reactive anti-DENV scFvs that are suitable for "yes/no" diagnostic applications. We demonstrate highly specific nanoyeast scFvs for serotyping DENV. We show that nanoyeast scFvs specifically detect NS1 in simulated patient plasma with a limit of detection of 250 ng/mL, the concentration found in infected patients.
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Affiliation(s)
- Fahimeh Farokhinejad
- Centre of Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rebecca E Lane
- Centre of Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Richard J Lobb
- Centre of Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Selvakumar Edwardraja
- Centre of Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alain Wuethrich
- Centre of Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Christopher B Howard
- Centre of Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Matt Trau
- Centre of Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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POLArIS, a versatile probe for molecular orientation, revealed actin filaments associated with microtubule asters in early embryos. Proc Natl Acad Sci U S A 2021; 118:2019071118. [PMID: 33674463 DOI: 10.1073/pnas.2019071118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Biomolecular assemblies govern the physiology of cells. Their function often depends on the changes in molecular arrangements of constituents, both in the positions and orientations. While recent advancements of fluorescence microscopy including super-resolution microscopy have enabled us to determine the positions of fluorophores with unprecedented accuracy, monitoring the orientation of fluorescently labeled molecules within living cells in real time is challenging. Fluorescence polarization microscopy (FPM) reports the orientation of emission dipoles and is therefore a promising solution. For imaging with FPM, target proteins need labeling with fluorescent probes in a sterically constrained manner, but because of difficulties in the rational three-dimensional design of protein connection, a universal method for constrained tagging with fluorophore was not available. Here, we report POLArIS, a genetically encoded and versatile probe for molecular orientation imaging. Instead of using a direct tagging approach, we used a recombinant binder connected to a fluorescent protein in a sterically constrained manner that can target specific biomolecules of interest by combining with phage display screening. As an initial test case, we developed POLArISact, which specifically binds to F-actin in living cells. We confirmed that the orientation of F-actin can be monitored by observing cells expressing POLArISact with FPM. In living starfish early embryos expressing POLArISact, we found actin filaments radially extending from centrosomes in association with microtubule asters during mitosis. By taking advantage of the genetically encoded nature, POLArIS can be used in a variety of living specimens, including whole bodies of developing embryos and animals, and also be expressed in a cell type/tissue specific manner.
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Sung KJ, Jabbour Al Maalouf Y, Johns QR, Miller EA, Sikes HD. Functional comparison of paper-based immunoassays based on antibodies and engineered binding proteins. Analyst 2020; 145:2515-2519. [PMID: 32163071 DOI: 10.1039/d0an00299b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Binding protein scaffolds, such as rcSso7d, have been investigated for use in diagnostic tests; however, the functional performance of rcSso7d has not yet been studied in comparison to antibodies. Here, we assessed the analyte-binding capabilities of rcSso7d and antibodies on cellulose with samples in buffer and 100% human serum.
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Affiliation(s)
- Ki-Joo Sung
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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Adamson H, Ajayi MO, Campbell E, Brachi E, Tiede C, Tang AA, Adams TL, Ford R, Davidson A, Johnson M, McPherson MJ, Tomlinson DC, Jeuken LJC. Affimer-Enzyme-Inhibitor Switch Sensor for Rapid Wash-free Assays of Multimeric Proteins. ACS Sens 2019; 4:3014-3022. [PMID: 31578863 DOI: 10.1021/acssensors.9b01574] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Robust technology is required to underpin rapid point-of-care and in-field diagnostics to improve timely decision making across broad sectors. An attractive strategy combines target recognition and signal generating elements into an "active" enzyme-switch that directly transduces target-binding into a signal. However, approaches that are broadly applicable to diverse targets remain elusive. Here, an enzyme-inhibitor switch sensor was developed by insertion of non-immunoglobulin Affimer binding proteins, between TEM1-β-lactamase and its inhibitor protein, such that target binding disrupts the enzyme-inhibitor complex. Design principles for a successful switch architecture are illustrated by the rapid (min), simple (wash-free), and sensitive (pM) quantification of multimeric target analytes in biological samples (serum, plasma, leaf extracts), across three application areas. A therapeutic antibody (Herceptin), protein biomarker (human C-reactive protein), and plant virus (cow pea mosaic virus) were targeted, demonstrating assays for therapeutic drug monitoring, health diagnostics, and plant pathogen detection, respectively. Batch-to-batch reproducibility, shelf-life stability, and consistency with validated enzyme-linked immunosorbent assay analysis confirm that the principle of an Affimer-enzyme-inhibitor switch provides a platform for point-of-care and in-field diagnostics.
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Affiliation(s)
| | | | | | | | | | | | | | - Robert Ford
- Avacta Life Sciences Limited, Unit 20, Ash Way, Thorp Arch Estate, Wetherby LS23 7FA, U.K
| | - Alex Davidson
- Avacta Life Sciences Limited, Unit 20, Ash Way, Thorp Arch Estate, Wetherby LS23 7FA, U.K
| | - Matt Johnson
- Avacta Life Sciences Limited, Unit 20, Ash Way, Thorp Arch Estate, Wetherby LS23 7FA, U.K
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