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Broggini L, Barzago MM, Speranzini V, Schulte T, Sonzini F, Giono M, Romeo M, Milani P, Caminito S, Mazzini G, Rognoni P, Merlini G, Pappone C, Anastasia L, Nuvolone M, Palladini G, Diomede L, Ricagno S. Nanobodies counteract the toxicity of an amyloidogenic light chain by stabilizing a partially open dimeric conformation. J Mol Biol 2023; 435:168320. [PMID: 37865287 DOI: 10.1016/j.jmb.2023.168320] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/18/2023] [Accepted: 10/16/2023] [Indexed: 10/23/2023]
Abstract
Light chain amyloidosis (AL) is a systemic disease where fibrillar deposition of misfolded immunoglobulin light chains (LCs) severely affects organ function and results in poor prognosis for patients, especially when heart involvement is severe. Particularly relevant in this context is the cardiotoxicity exerted by still uncharacterized soluble LC species. Here, with the final goal of identifying alternative therapeutic strategies to tackle AL amyloidosis, we produced five llama-derived nanobodies (Nbs) specific against H3, a well-characterized amyloidogenic and cardiotoxic LC from an AL patient with severe cardiac involvement. We found that Nbs are specific and potent agents capable of abolishing H3 soluble toxicity in C. elegans in vivo model. Structural characterization of H3-Nb complexes revealed that the protective effect of Nbs is related to their ability to bind to the H3 VL domain and stabilise an unexpected partially open LC dimer in which the two VL domains no longer interact with each other. Thus, while identifying potent inhibitors of LC soluble toxicity, we also describe the first non-native structure of an amyloidogenic LC that may represent a crucial step in toxicity and aggregation mechanisms.
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Affiliation(s)
- Luca Broggini
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097 San Donato Milanese, Italy
| | - Maria Monica Barzago
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, Milano 20156, Italy
| | | | - Tim Schulte
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097 San Donato Milanese, Italy
| | - Federica Sonzini
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097 San Donato Milanese, Italy; Department of Biosciences, Università degli Studi di Milano, Milan 20133, Italy
| | - Matteo Giono
- Department of Biosciences, Università degli Studi di Milano, Milan 20133, Italy
| | - Margherita Romeo
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, Milano 20156, Italy
| | - Paolo Milani
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia 27100, Italy
| | - Serena Caminito
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia 27100, Italy
| | - Giulia Mazzini
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia 27100, Italy
| | - Paola Rognoni
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia 27100, Italy
| | - Giampaolo Merlini
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia 27100, Italy
| | - Carlo Pappone
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097 San Donato Milanese, Italy; Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, San Donato, Milan 20097, Italy; Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Luigi Anastasia
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097 San Donato Milanese, Italy; Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Mario Nuvolone
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia 27100, Italy
| | - Giovanni Palladini
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo, Università Degli Studi di Pavia, Pavia 27100, Italy
| | - Luisa Diomede
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, Milano 20156, Italy
| | - Stefano Ricagno
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097 San Donato Milanese, Italy; Department of Biosciences, Università degli Studi di Milano, Milan 20133, Italy.
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2
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Nakada-Masuta T, Takeda H, Uchida K. Novel Approach for Obtaining Variable Domain of New Antigen Receptor with Different Physicochemical Properties from Japanese Topeshark ( Hemitriakis japanica). Mar Drugs 2023; 21:550. [PMID: 37999374 PMCID: PMC10672104 DOI: 10.3390/md21110550] [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: 09/30/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023] Open
Abstract
Diverse candidate antibodies are needed to successfully identify therapeutic and diagnostic applications. The variable domain of IgNAR (VNAR), a shark single-domain antibody, has attracted attention owing to its favorable physicochemical properties. The phage display method used to screen for optimal VNARs loses sequence diversity because of the bias caused by the differential ease of protein expression in Escherichia coli. Here, we investigated a VNAR selection method that combined panning with various selection pressures and next-generation sequencing (NGS) analyses to obtain additional candidates. Drawing inspiration from the physiological conditions of sharks and the physicochemical properties of VNARs, we examined the effects of NaCl and urea concentrations, low temperature, and preheating at the binding step of panning. VNAR phage libraries generated from Japanese topeshark (Hemitriakis japanica) were enriched under these conditions. We then performed NGS analysis and attempted to select clones that were specifically enriched under each panning condition. The identified VNARs exhibited higher reactivity than those obtained by panning without selection pressure. Additionally, they possess physicochemical properties that reflect their respective selection pressures. These results can greatly enhance our understanding of VNAR properties and offer guidance for the screening of high-quality VNAR clones that are present at low frequencies.
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Affiliation(s)
- Tomofumi Nakada-Masuta
- Graduate School of Science, Technology and Innovation, Kobe University, 7-1-49 Minatojimaminamimachi Chuo-ku, Kobe 650-0047, Japan;
- Bio-Diagnostic Reagent Technology Center, Sysmex Corporation, 4-3-2 Nishi-ku Takatsukadai, Kobe 651-2271, Japan
| | - Hiroyuki Takeda
- Division of Proteo-Drug-Discovery Sciences, Ehime University Proteo-Science Center, Bunkyocho 3, Matsuyama 790-8577, Japan;
| | - Kazuhisa Uchida
- Graduate School of Science, Technology and Innovation, Kobe University, 7-1-49 Minatojimaminamimachi Chuo-ku, Kobe 650-0047, Japan;
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3
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Kourelis J, Marchal C, Posbeyikian A, Harant A, Kamoun S. NLR immune receptor-nanobody fusions confer plant disease resistance. Science 2023; 379:934-939. [PMID: 36862785 DOI: 10.1126/science.abn4116] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/01/2023] [Indexed: 03/04/2023]
Abstract
Plant pathogens cause recurrent epidemics, threatening crop yield and global food security. Efforts to retool the plant immune system have been limited to modifying natural components and can be nullified by the emergence of new pathogen strains. Made-to-order synthetic plant immune receptors provide an opportunity to tailor resistance to pathogen genotypes present in the field. In this work, we show that plant nucleotide-binding, leucine-rich repeat immune receptors (NLRs) can be used as scaffolds for nanobody (single-domain antibody fragment) fusions that bind fluorescent proteins (FPs). These fusions trigger immune responses in the presence of the corresponding FP and confer resistance against plant viruses expressing FPs. Because nanobodies can be raised against most molecules, immune receptor-nanobody fusions have the potential to generate resistance against plant pathogens and pests delivering effectors inside host cells.
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Affiliation(s)
- Jiorgos Kourelis
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Clemence Marchal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Andres Posbeyikian
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
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4
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Stokstad E. Antibody-based defense may protect plants from disease. Science 2023; 379:867. [PMID: 36862778 DOI: 10.1126/science.adh3913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
A "creative" strategy to keep crops healthy borrows key pathogen detectors from the animal immune system.
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5
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Sang Z, Xiang Y, Bahar I, Shi Y. Llamanade: An open-source computational pipeline for robust nanobody humanization. Structure 2022; 30:418-429.e3. [PMID: 34895471 DOI: 10.1016/j.str.2021.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 07/29/2021] [Revised: 09/21/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022]
Abstract
Nanobodies (Nbs) have emerged as a promising class of biologics. Despite having marked physicochemical properties, Nbs are derived from camelids and may require humanization to improve translational potentials. By systematically analyzing the sequence and structural properties of Nbs, we found substantial framework diversities and revealed the key differences between Nbs and human immunoglobulin G antibodies. We identified conserved residues that may contribute to enhanced solubility, structural stability, and antigen binding, providing insights into Nb humanization. Based on big data analysis, we developed "Llamanade," an open-source software to facilitate rational humanization of Nbs. Using sequence as input, Llamanade can rapidly extract sequence features, model structures, and optimize solutions to humanize Nbs. Finally, we used Llamanade to successfully humanize a cohort of structurally diverse and potent SARS-CoV-2 neutralizing Nbs. Llamanade is freely available and will be easily accessible on a server to support the development of therapeutic Nbs into safe and effective trials.
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Affiliation(s)
- Zhe Sang
- Department of Cell Biology, Pittsburgh, PA, USA; Department Computational and Systems Biology, Pittsburgh, PA, USA; University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA
| | - Yufei Xiang
- Department of Cell Biology, Pittsburgh, PA, USA
| | - Ivet Bahar
- Department Computational and Systems Biology, Pittsburgh, PA, USA; University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA
| | - Yi Shi
- Department of Cell Biology, Pittsburgh, PA, USA; University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA.
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6
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Liu B, Yang D. Easily Established and Multifunctional Synthetic Nanobody Libraries as Research Tools. Int J Mol Sci 2022; 23:ijms23031482. [PMID: 35163405 PMCID: PMC8835997 DOI: 10.3390/ijms23031482] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023] Open
Abstract
Nanobodies, or VHHs, refer to the antigen-binding domain of heavy-chain antibodies (HCAbs) from camelids. They have been widely used as research tools for protein purification and structure determination due to their small size, high specificity, and high stability, overcoming limitations with conventional antibody fragments. However, animal immunization and subsequent retrieval of antigen-specific nanobodies are expensive and complicated. Construction of synthetic nanobody libraries using DNA oligonucleotides is a cost-effective alternative for immunization libraries and shows great potential in identifying antigen-specific or even conformation-specific nanobodies. This review summarizes and analyses synthetic nanobody libraries in the current literature, including library design and biopanning methods, and further discusses applications of antigen-specific nanobodies obtained from synthetic libraries to research.
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7
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Wang J, Kang G, Yuan H, Cao X, Huang H, de Marco A. Research Progress and Applications of Multivalent, Multispecific and Modified Nanobodies for Disease Treatment. Front Immunol 2022; 12:838082. [PMID: 35116045 PMCID: PMC8804282 DOI: 10.3389/fimmu.2021.838082] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [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: 12/17/2021] [Accepted: 12/30/2021] [Indexed: 12/22/2022] Open
Abstract
Recombinant antibodies such as nanobodies are progressively demonstrating to be a valid alternative to conventional monoclonal antibodies also for clinical applications. Furthermore, they do not solely represent a substitute for monoclonal antibodies but their unique features allow expanding the applications of biotherapeutics and changes the pattern of disease treatment. Nanobodies possess the double advantage of being small and simple to engineer. This combination has promoted extremely diversified approaches to design nanobody-based constructs suitable for particular applications. Both the format geometry possibilities and the functionalization strategies have been widely explored to provide macromolecules with better efficacy with respect to single nanobodies or their combination. Nanobody multimers and nanobody-derived reagents were developed to image and contrast several cancer diseases and have shown their effectiveness in animal models. Their capacity to block more independent signaling pathways simultaneously is considered a critical advantage to avoid tumor resistance, whereas the mass of these multimeric compounds still remains significantly smaller than that of an IgG, enabling deeper penetration in solid tumors. When applied to CAR-T cell therapy, nanobodies can effectively improve the specificity by targeting multiple epitopes and consequently reduce the side effects. This represents a great potential in treating malignant lymphomas, acute myeloid leukemia, acute lymphoblastic leukemia, multiple myeloma and solid tumors. Apart from cancer treatment, multispecific drugs and imaging reagents built with nanobody blocks have demonstrated their value also for detecting and tackling neurodegenerative, autoimmune, metabolic, and infectious diseases and as antidotes for toxins. In particular, multi-paratopic nanobody-based constructs have been developed recently as drugs for passive immunization against SARS-CoV-2 with the goal of impairing variant survival due to resistance to antibodies targeting single epitopes. Given the enormous research activity in the field, it can be expected that more and more multimeric nanobody molecules will undergo late clinical trials in the next future. Systematic Review Registration.
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Affiliation(s)
- Jiewen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Guangbo Kang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Haibin Yuan
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Xiaocang Cao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Nova Gorica, Slovenia
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8
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Hanke L, Das H, Sheward DJ, Perez Vidakovics L, Urgard E, Moliner-Morro A, Kim C, Karl V, Pankow A, Smith NL, Porebski B, Fernandez-Capetillo O, Sezgin E, Pedersen GK, Coquet JM, Hällberg BM, Murrell B, McInerney GM. A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo. Nat Commun 2022; 13:155. [PMID: 35013189 PMCID: PMC8748511 DOI: 10.1038/s41467-021-27610-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [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: 04/20/2021] [Accepted: 11/30/2021] [Indexed: 01/04/2023] Open
Abstract
Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the beta variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes an uncommon strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Egon Urgard
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vivien Karl
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alec Pankow
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Natalie L Smith
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Bartlomiej Porebski
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oscar Fernandez-Capetillo
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel K Pedersen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jonathan M Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska Institutet VR-RÅC, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany.
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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9
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Hanke L, Das H, Sheward DJ, Perez Vidakovics L, Urgard E, Moliner-Morro A, Kim C, Karl V, Pankow A, Smith NL, Porebski B, Fernandez-Capetillo O, Sezgin E, Pedersen GK, Coquet JM, Hällberg BM, Murrell B, McInerney GM. A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo. Nat Commun 2022. [PMID: 35013189 DOI: 10.1101/2021.03.20.436243v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the beta variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes an uncommon strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Egon Urgard
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vivien Karl
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alec Pankow
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Natalie L Smith
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Bartlomiej Porebski
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oscar Fernandez-Capetillo
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel K Pedersen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jonathan M Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska Institutet VR-RÅC, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany.
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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10
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Yuan TZ, Garg P, Wang L, Willis JR, Kwan E, Hernandez AGL, Tuscano E, Sever EN, Keane E, Soto C, Mucker EM, Fouch ME, Davidson E, Doranz BJ, Kailasan S, Aman MJ, Li H, Hooper JW, Saphire EO, Crowe JE, Liu Q, Axelrod F, Sato AK. Rapid discovery of diverse neutralizing SARS-CoV-2 antibodies from large-scale synthetic phage libraries. MAbs 2022; 14:2002236. [PMID: 34967699 PMCID: PMC8726723 DOI: 10.1080/19420862.2021.2002236] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 07/04/2021] [Revised: 10/12/2021] [Accepted: 11/01/2021] [Indexed: 12/22/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an evolving global public health crisis in need of therapeutic options. Passive immunization of monoclonal antibodies (mAbs) represents a promising therapeutic strategy capable of conferring immediate protection from SARS-CoV-2 infection. Herein, we describe the discovery and characterization of neutralizing SARS-CoV-2 IgG and VHH antibodies from four large-scale phage libraries. Each library was constructed synthetically with shuffled complementarity-determining region loops from natural llama and human antibody repertoires. While most candidates targeted the receptor-binding domain of the S1 subunit of SARS-CoV-2 spike protein, we also identified a neutralizing IgG candidate that binds a unique epitope on the N-terminal domain. A select number of antibodies retained binding to SARS-CoV-2 variants Alpha, Beta, Gamma, Kappa and Delta. Overall, our data show that synthetic phage libraries can rapidly yield SARS-CoV-2 S1 antibodies with therapeutically desirable features, including high affinity, unique binding sites, and potent neutralizing activity in vitro, and a capacity to limit disease in vivo.
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MESH Headings
- Animals
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Antibodies, Neutralizing/pharmacology
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Antibody Specificity
- Binding Sites, Antibody
- COVID-19/immunology
- COVID-19/metabolism
- COVID-19/prevention & control
- COVID-19/virology
- Cell Surface Display Techniques
- Chlorocebus aethiops
- Disease Models, Animal
- Epitopes
- Female
- Host-Pathogen Interactions
- Immunoglobulin G/genetics
- Immunoglobulin G/immunology
- Immunoglobulin G/metabolism
- Immunoglobulin G/pharmacology
- Mesocricetus
- Peptide Library
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Single-Domain Antibodies/genetics
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/metabolism
- Single-Domain Antibodies/pharmacology
- Spike Glycoprotein, Coronavirus/immunology
- Vero Cells
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Affiliation(s)
- Tom Z. Yuan
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | | | - Linya Wang
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | - Jordan R. Willis
- IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, USA
| | - Eric Kwan
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | | | - Emily Tuscano
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | - Emily N. Sever
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | - Erica Keane
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Cinque Soto
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric M. Mucker
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | | | | | | | | | | | - Haoyang Li
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jay W. Hooper
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiang Liu
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | - Fumiko Axelrod
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
| | - Aaron K. Sato
- Twist Biopharma, Twist Bioscience, South San Francisco, CA, USA
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11
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Zebardast A, Hosseini P, Hasanzadeh A, latifi T. The role of single-domain antibodies (or nanobodies) in SARS-CoV-2 neutralization. Mol Biol Rep 2022; 49:647-656. [PMID: 34648139 PMCID: PMC8514607 DOI: 10.1007/s11033-021-06819-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/08/2021] [Indexed: 01/06/2023]
Abstract
The severe acute respiratory syndrome (SARS-CoV-2), a newly emerging of coronavirus, continues to infect humans in the absence of a viable treatment. Neutralizing antibodies that disrupt the interaction of RBD and ACE2 has been under the spotlight as a way of developing the COVID-19 treatment. Some animals, such as llamas, manufacture heavy-chain antibodies that have a single variable domain (VHH) instead of two variable domains (VH/VL) as opposed to typical antibodies. Nanobodies are antigen-specific, single-domain, changeable segments of camelid heavy chain-only antibodies that are recombinantly produced. These types of antibodies exhibit a wide range of strong physical and chemical properties, like high solubility, and stability. The VHH's high-affinity attachment to the receptor-binding domain (RBD) allowed the neutralization of SARS-CoV-2. To tackle COVID-19, some nanobodies are being developed against SARS-CoV-2, some of which have been recently included in clinical trials. Nanobody therapy may be useful in managing the COVID-19 pandemic as a potent and low-cost treatment. This paper describes the application of nanobodies as a new class of recombinant antibodies in COVID-19 treatment.
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Affiliation(s)
- Arghavan Zebardast
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Parastoo Hosseini
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Hasanzadeh
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Golestan, Iran
| | - Tayebeh latifi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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12
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Robinson SA, Raybould MIJ, Schneider C, Wong WK, Marks C, Deane CM. Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies. PLoS Comput Biol 2021; 17:e1009675. [PMID: 34898603 PMCID: PMC8700021 DOI: 10.1371/journal.pcbi.1009675] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 12/23/2021] [Accepted: 11/22/2021] [Indexed: 12/30/2022] Open
Abstract
Identifying the epitope of an antibody is a key step in understanding its function and its potential as a therapeutic. Sequence-based clonal clustering can identify antibodies with similar epitope complementarity, however, antibodies from markedly different lineages but with similar structures can engage the same epitope. We describe a novel computational method for epitope profiling based on structural modelling and clustering. Using the method, we demonstrate that sequence dissimilar but functionally similar antibodies can be found across the Coronavirus Antibody Database, with high accuracy (92% of antibodies in multiple-occupancy structural clusters bind to consistent domains). Our approach functionally links antibodies with distinct genetic lineages, species origins, and coronavirus specificities. This indicates greater convergence exists in the immune responses to coronaviruses than is suggested by sequence-based approaches. Our results show that applying structural analytics to large class-specific antibody databases will enable high confidence structure-function relationships to be drawn, yielding new opportunities to identify functional convergence hitherto missed by sequence-only analysis. Antibodies are a key component of the immune system that combat pathogens by binding to a defined region of their molecular surface (known as an ‘epitope’). The ability to map which antibodies target the same epitopes is crucial when designing non-competing antibody therapeutics or predicting the influence of pathogen mutation on population immunity. While one can use laboratory experiments to deduce when pairs of antibodies engage the same epitope, such experiments are very expensive and time consuming if used to compare on the order of thousands of antibodies. In this work, we report a new computational algorithm (SPACE) that clusters antibodies that target the same epitope based on their predicted 3D structure, as binding site structure is a property often conserved between binders complementary to the same epitope. Unlike existing antibody epitope profiling tools which assume two antibodies must share a high sequence identity/similar genetic basis to engage the same region, our orthogonal method can detect broader patterns of convergent evolution across binders to different pathogen strains, and between antibodies with different genetic and even species origins.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/metabolism
- Antibody Specificity
- Antigen-Antibody Complex/chemistry
- Antigen-Antibody Complex/genetics
- Antigen-Antibody Reactions/genetics
- Antigen-Antibody Reactions/immunology
- Antigens, Viral/chemistry
- COVID-19/immunology
- COVID-19/virology
- Computational Biology
- Coronavirus/chemistry
- Coronavirus/genetics
- Coronavirus/immunology
- Databases, Chemical
- Epitope Mapping
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/genetics
- Humans
- Mice
- Models, Molecular
- Pandemics
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Single-Domain Antibodies/immunology
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Affiliation(s)
- Sarah A Robinson
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Matthew I J Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Constantin Schneider
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Wing Ki Wong
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Claire Marks
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
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13
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Tang Q, Owens RJ, Naismith JH. Structural Biology of Nanobodies against the Spike Protein of SARS-CoV-2. Viruses 2021; 13:v13112214. [PMID: 34835020 PMCID: PMC8625641 DOI: 10.3390/v13112214] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 10/06/2021] [Revised: 10/27/2021] [Accepted: 10/30/2021] [Indexed: 12/28/2022] Open
Abstract
Nanobodies are 130 amino acid single-domain antibodies (VHH) derived from the unique heavy-chain-only subclass of Camelid immunogloblins. Their small molecular size, facile expression, high affinity and stability have combined to make them unique targeting reagents with numerous applications in the biomedical sciences. The first nanobody agent has now entered the clinic as a treatment against a blood disorder. The spread of the SARS-CoV-2 virus has seen the global scientific endeavour work to accelerate the development of technologies to try to defeat a pandemic that has now killed over four million people. In a remarkably short period of time, multiple studies have reported nanobodies directed against the viral Spike protein. Several agents have been tested in culture and demonstrate potent neutralisation of the virus or pseudovirus. A few agents have completed animal trials with very encouraging results showing their potential for treating infection. Here, we discuss the structural features that guide the nanobody recognition of the receptor binding domain of the Spike protein of SARS-CoV-2.
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Affiliation(s)
- Qilong Tang
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot OX11 0FA, UK;
- The Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Raymond J. Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot OX11 0FA, UK;
- The Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, UK
- Correspondence: (R.J.O.); (J.H.N.)
| | - James H. Naismith
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot OX11 0FA, UK;
- The Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, UK
- Correspondence: (R.J.O.); (J.H.N.)
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14
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Golcuk M, Hacisuleyman A, Erman B, Yildiz A, Gur M. Binding Mechanism of Neutralizing Nanobodies Targeting SARS-CoV-2 Spike Glycoprotein. J Chem Inf Model 2021; 61:5152-5160. [PMID: 34581563 PMCID: PMC8491549 DOI: 10.1021/acs.jcim.1c00695] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Indexed: 12/25/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters human cells upon binding of its spike (S) glycoproteins to ACE2 receptors. Several nanobodies neutralize SARS-CoV-2 infection by binding to the receptor-binding domain (RBD) of the S protein, but how their binding antagonizes S-ACE2 interactions is not well understood. Here, we identified interactions between the RBD and nanobodies H11-H4, H11-D4, and Ty1 by performing all-atom molecular dynamics simulations. H11-H4 and H11-D4 can bind to RBD without overlapping with ACE2. H11-H4, and to a lesser extent H11-D4, binding dislocates ACE2 from its binding site due to electrostatic repulsion. In comparison, Ty1 overlaps with ACE2 on RBD and has a similar binding strength to ACE2. Mutations in the Alpha variant of SARS-CoV-2 had a minor effect in RBD binding strengths of ACE2 and nanobodies, but reduced the ability of H11-H4 and H11-D4 to dislocate ACE2 from RBD. In comparison, the Beta variant weakened the RBD binding strengths of H11-H4 and H11-D4, which were less effective to dislocate ACE2 binding. Unexpectedly, mutations in Beta strengthened Ty1 binding to RBD, suggesting that this nanobody may be more effective to neutralize the Beta variant of SARS-CoV-2.
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Affiliation(s)
- Mert Golcuk
- Department of Mechanical Engineering,
Istanbul Technical University (ITU), 34437 Istanbul,
Turkey
| | - Aysima Hacisuleyman
- Institute of Bioengineering, Swiss
Federal Institute of Technology (EPFL), 1015 Lausanne,
Switzerland
| | - Burak Erman
- Chemical and Biological Engineering Department,
Koc University, 34450 Istanbul,
Turkey
| | - Ahmet Yildiz
- Physics Department, University of
California, Berkeley, California 94720, United
States
- Department of Molecular and Cell Biology,
University of California, Berkeley, California 94720,
United States
| | - Mert Gur
- Department of Mechanical Engineering,
Istanbul Technical University (ITU), 34437 Istanbul,
Turkey
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15
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Chen G, Kong Y, Li Y, Huang A, Wang C, Zhou S, Yang Z, Wu Y, Ren J, Ying T. A Promising Intracellular Protein-Degradation Strategy: TRIMbody-Away Technique Based on Nanobody Fragment. Biomolecules 2021; 11:biom11101512. [PMID: 34680146 PMCID: PMC8533776 DOI: 10.3390/biom11101512] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/03/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022] Open
Abstract
Most recently, a technology termed TRIM-Away has allowed acute and rapid destruction of endogenous target proteins in cultured cells using specific antibodies and endogenous/exogenous tripartite motif 21 (TRIM21). However, the relatively large size of the full-size mAbs (150 kDa) results in correspondingly low tissue penetration and inaccessibility of some sterically hindered epitopes, which limits the target protein degradation. In addition, exogenous introduction of TRIM21 may cause side effects for treated cells. To tackle these limitations, we sought to replace full-size mAbs with the smaller format of antibodies, a nanobody (VHH, 15 kDa), and construct a new type of fusion protein named TRIMbody by fusing the nanobody and RBCC motif of TRIM21. Next, we introduced enhanced green fluorescent protein (EGFP) as a model substrate and generated αEGFP TRIMbody using a bispecific anti-EGFP (αEGFP) nanobody. Remarkably, inducible expression of αEGFP TRIMbody could specifically degrade intracellular EGFP in HEK293T cells in a time-dependent manner. By treating cells with inhibitors, we found that intracellular EGFP degradation by αEGFP TRIMbody relies on both ubiquitin-proteasome and autophagy-lysosome pathways. Taken together, these results suggested that TRIMbody-Away technology could be utilized to specifically degrade intracellular protein and could expand the potential applications of degrader technologies.
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Affiliation(s)
- Gang Chen
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; (G.C.); (Y.K.); (Y.L.); (A.H.); (C.W.); (S.Z.)
| | - Yu Kong
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; (G.C.); (Y.K.); (Y.L.); (A.H.); (C.W.); (S.Z.)
| | - You Li
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; (G.C.); (Y.K.); (Y.L.); (A.H.); (C.W.); (S.Z.)
| | - Ailing Huang
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; (G.C.); (Y.K.); (Y.L.); (A.H.); (C.W.); (S.Z.)
| | - Chunyu Wang
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; (G.C.); (Y.K.); (Y.L.); (A.H.); (C.W.); (S.Z.)
| | - Shanshan Zhou
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; (G.C.); (Y.K.); (Y.L.); (A.H.); (C.W.); (S.Z.)
| | - Zhenlin Yang
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China;
| | - Yanling Wu
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; (G.C.); (Y.K.); (Y.L.); (A.H.); (C.W.); (S.Z.)
- Correspondence: (Y.W.); (J.R.); (T.Y.); Tel.: +86-021-54237761 (Y.W.); +86-021-54920668 (J.R.); +86-021-54237761 (T.Y.)
| | - Jianke Ren
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Correspondence: (Y.W.); (J.R.); (T.Y.); Tel.: +86-021-54237761 (Y.W.); +86-021-54920668 (J.R.); +86-021-54237761 (T.Y.)
| | - Tianlei Ying
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; (G.C.); (Y.K.); (Y.L.); (A.H.); (C.W.); (S.Z.)
- Correspondence: (Y.W.); (J.R.); (T.Y.); Tel.: +86-021-54237761 (Y.W.); +86-021-54920668 (J.R.); +86-021-54237761 (T.Y.)
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16
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Hrynchak I, Santos L, Falcão A, Gomes CM, Abrunhosa AJ. Nanobody-Based Theranostic Agents for HER2-Positive Breast Cancer: Radiolabeling Strategies. Int J Mol Sci 2021; 22:ijms221910745. [PMID: 34639086 PMCID: PMC8509594 DOI: 10.3390/ijms221910745] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 02/07/2023] Open
Abstract
The overexpression of human epidermal growth factor 2 (HER2) in breast cancer (BC) has been associated with a more aggressive tumor subtype, poorer prognosis and shorter overall survival. In this context, the development of HER2-targeted radiotracers is crucial to provide a non-invasive assessment of HER2 expression to select patients for HER2-targeted therapies, monitor response and identify those who become resistant. Antibodies represent ideal candidates for this purpose, as they provide high contrast images for diagnosis and low toxicity in the therapeutic setting. Of those, nanobodies (Nb) are of particular interest considering their favorable kinetics, crossing of relevant biological membranes and intratumoral distribution. The purpose of this review is to highlight the unique characteristics and advantages of Nb-based radiotracers in BC imaging and therapy. Additionally, radiolabeling methods for Nb including direct labeling, indirect labeling via prosthetic group and indirect labeling via complexation will be discussed, reporting advantages and drawbacks. Furthermore, the preclinical to clinical translation of radiolabeled Nbs as promising theranostic agents will be reported.
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Affiliation(s)
- Ivanna Hrynchak
- ICNAS-Produção Unipessoal, Lda.—University of Coimbra, 3000-548 Coimbra, Portugal; (I.H.); (L.S.)
- CIBIT/ICNAS—Institute for Nuclear Sciences Applied to Health, University of Coimbra, 3000-548 Coimbra, Portugal;
| | - Liliana Santos
- ICNAS-Produção Unipessoal, Lda.—University of Coimbra, 3000-548 Coimbra, Portugal; (I.H.); (L.S.)
- CIBIT/ICNAS—Institute for Nuclear Sciences Applied to Health, University of Coimbra, 3000-548 Coimbra, Portugal;
| | - Amílcar Falcão
- CIBIT/ICNAS—Institute for Nuclear Sciences Applied to Health, University of Coimbra, 3000-548 Coimbra, Portugal;
| | - Célia M. Gomes
- iCBR—Coimbra Institute for Clinical and Biomedical Research, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal;
- CIBB—Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3000-548 Coimbra, Portugal
- CACC—Clinical Academic Center of Coimbra, 3000-075 Coimbra, Portugal
| | - Antero J. Abrunhosa
- ICNAS-Produção Unipessoal, Lda.—University of Coimbra, 3000-548 Coimbra, Portugal; (I.H.); (L.S.)
- CIBIT/ICNAS—Institute for Nuclear Sciences Applied to Health, University of Coimbra, 3000-548 Coimbra, Portugal;
- Correspondence:
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17
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Ahmad J, Jiang J, Boyd LF, Zeher A, Huang R, Xia D, Natarajan K, Margulies DH. Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction. J Biol Chem 2021; 297:101202. [PMID: 34537245 PMCID: PMC8444450 DOI: 10.1016/j.jbc.2021.101202] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 12/15/2022] Open
Abstract
Combating the worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the emergence of new variants demands understanding of the structural basis of the interaction of antibodies with the SARS-CoV-2 receptor-binding domain (RBD). Here, we report five X-ray crystal structures of sybodies (synthetic nanobodies) including those of binary and ternary complexes of Sb16-RBD, Sb45-RBD, Sb14-RBD-Sb68, and Sb45-RBD-Sb68, as well as unliganded Sb16. These structures reveal that Sb14, Sb16, and Sb45 bind the RBD at the angiotensin-converting enzyme 2 interface and that the Sb16 interaction is accompanied by a large conformational adjustment of complementarity-determining region 2. In contrast, Sb68 interacts at the periphery of the SARS-CoV-2 RBD-angiotensin-converting enzyme 2 interface. We also determined cryo-EM structures of Sb45 bound to the SARS-CoV-2 spike protein. Superposition of the X-ray structures of sybodies onto the trimeric spike protein cryo-EM map indicates that some sybodies may bind in both "up" and "down" configurations, but others may not. Differences in sybody recognition of several recently identified RBD variants are explained by these structures.
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Affiliation(s)
- Javeed Ahmad
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Lisa F Boyd
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Allison Zeher
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rick Huang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - David H Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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18
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Jiang C, Zhang L, Xu X, Qi M, Zhang J, He S, Tian Q, Song S. Engineering a Smart Agent for Enhanced Immunotherapy Effect by Simultaneously Blocking PD-L1 and CTLA-4. Adv Sci (Weinh) 2021; 8:e2102500. [PMID: 34473430 PMCID: PMC8529437 DOI: 10.1002/advs.202102500] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/04/2021] [Indexed: 05/06/2023]
Abstract
Combinations of immune checkpoint therapies show encouraging results in the treatment of many human cancers. However, the higher costs and greater side effects of such combinations compared with single-agent immunotherapies limit their further applications. In this work, a novel smart agent, KN046@19 F-ZIF-8, is developed to overcome these limitations. KN046 is a novel recombinant humanized PD-L1/CTLA-4 bispecific single-domain antibody-Fc fusion protein, which can bind to both PD-L1 and CTLA-4 effectively. ZIF-8 is a smart delivery system, which can safely and effectively deliver KN406 to a tumor. In vitro and in vivo results demonstrate that the smart agent KN046@19 F-ZIF-8 not only improves the immune response rate of the antibody drug in treatment of tumors but also reduces its toxic side effects, thereby achieving excellent antitumor efficacy. This study provides an engineering strategy for clinical applications of a more effective immunotherapy.
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Affiliation(s)
- Chunjuan Jiang
- Department of Nuclear MedicineFudan University Shanghai Cancer CenterShanghai200032China
- Center for Biomedical ImagingFudan UniversityShanghai200032China
- Shanghai Engineering Research Center of Molecular Imaging ProbesShanghai200032China
| | - Le Zhang
- Department of Nuclear MedicineFudan University Shanghai Cancer CenterShanghai200032China
- Center for Biomedical ImagingFudan UniversityShanghai200032China
- Shanghai Engineering Research Center of Molecular Imaging ProbesShanghai200032China
- Department of Research and DevelopmentShanghai Proton and Heavy Ion CenterShanghai201321China
| | - Xiaoping Xu
- Department of Nuclear MedicineFudan University Shanghai Cancer CenterShanghai200032China
- Center for Biomedical ImagingFudan UniversityShanghai200032China
- Shanghai Engineering Research Center of Molecular Imaging ProbesShanghai200032China
| | - Ming Qi
- Department of Nuclear MedicineFudan University Shanghai Cancer CenterShanghai200032China
- Center for Biomedical ImagingFudan UniversityShanghai200032China
- Shanghai Engineering Research Center of Molecular Imaging ProbesShanghai200032China
| | - Jianping Zhang
- Department of Nuclear MedicineFudan University Shanghai Cancer CenterShanghai200032China
- Center for Biomedical ImagingFudan UniversityShanghai200032China
- Shanghai Engineering Research Center of Molecular Imaging ProbesShanghai200032China
| | - Simin He
- Department of Nuclear MedicineFudan University Shanghai Cancer CenterShanghai200032China
- Center for Biomedical ImagingFudan UniversityShanghai200032China
- Shanghai Engineering Research Center of Molecular Imaging ProbesShanghai200032China
| | - Qiwei Tian
- Shanghai Key Laboratory of Molecular ImagingShanghai University of Medicine and Health SciencesShanghai201318China
| | - Shaoli Song
- Department of Nuclear MedicineFudan University Shanghai Cancer CenterShanghai200032China
- Center for Biomedical ImagingFudan UniversityShanghai200032China
- Shanghai Engineering Research Center of Molecular Imaging ProbesShanghai200032China
- Department of Research and DevelopmentShanghai Proton and Heavy Ion CenterShanghai201321China
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19
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Huo J, Mikolajek H, Le Bas A, Clark JJ, Sharma P, Kipar A, Dormon J, Norman C, Weckener M, Clare DK, Harrison PJ, Tree JA, Buttigieg KR, Salguero FJ, Watson R, Knott D, Carnell O, Ngabo D, Elmore MJ, Fotheringham S, Harding A, Moynié L, Ward PN, Dumoux M, Prince T, Hall Y, Hiscox JA, Owen A, James W, Carroll MW, Stewart JP, Naismith JH, Owens RJ. A potent SARS-CoV-2 neutralising nanobody shows therapeutic efficacy in the Syrian golden hamster model of COVID-19. Nat Commun 2021; 12:5469. [PMID: 34552091 PMCID: PMC8458290 DOI: 10.1038/s41467-021-25480-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [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: 05/27/2021] [Accepted: 08/12/2021] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 remains a global threat to human health particularly as escape mutants emerge. There is an unmet need for effective treatments against COVID-19 for which neutralizing single domain antibodies (nanobodies) have significant potential. Their small size and stability mean that nanobodies are compatible with respiratory administration. We report four nanobodies (C5, H3, C1, F2) engineered as homotrimers with pmolar affinity for the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Crystal structures show C5 and H3 overlap the ACE2 epitope, whilst C1 and F2 bind to a different epitope. Cryo Electron Microscopy shows C5 binding results in an all down arrangement of the Spike protein. C1, H3 and C5 all neutralize the Victoria strain, and the highly transmissible Alpha (B.1.1.7 first identified in Kent, UK) strain and C1 also neutralizes the Beta (B.1.35, first identified in South Africa). Administration of C5-trimer via the respiratory route showed potent therapeutic efficacy in the Syrian hamster model of COVID-19 and separately, effective prophylaxis. The molecule was similarly potent by intraperitoneal injection.
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MESH Headings
- Administration, Intranasal
- Animals
- Antibodies, Neutralizing/administration & dosage
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/pharmacology
- Cryoelectron Microscopy
- Crystallography, X-Ray
- Disease Models, Animal
- Dose-Response Relationship, Immunologic
- Epitopes/chemistry
- Epitopes/metabolism
- Female
- Male
- Mesocricetus
- Neutralization Tests
- SARS-CoV-2/drug effects
- Single-Domain Antibodies/administration & dosage
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/metabolism
- Single-Domain Antibodies/pharmacology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/metabolism
- COVID-19 Drug Treatment
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Affiliation(s)
- Jiandong Huo
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
| | | | - Audrey Le Bas
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
| | - Jordan J Clark
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Parul Sharma
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Anja Kipar
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Joshua Dormon
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
| | - Chelsea Norman
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
| | - Miriam Weckener
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
| | - Daniel K Clare
- Diamond Light Source Ltd, Harwell Science Campus, Didcot, UK
| | - Peter J Harrison
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
- Diamond Light Source Ltd, Harwell Science Campus, Didcot, UK
| | - Julia A Tree
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Karen R Buttigieg
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | | | - Robert Watson
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Daniel Knott
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Oliver Carnell
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Didier Ngabo
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Michael J Elmore
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Susan Fotheringham
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Adam Harding
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lucile Moynié
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
| | - Philip N Ward
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK
| | - Maud Dumoux
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
| | - Tessa Prince
- Diamond Light Source Ltd, Harwell Science Campus, Didcot, UK
| | - Yper Hall
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Julian A Hiscox
- Diamond Light Source Ltd, Harwell Science Campus, Didcot, UK
- Department of Preventive Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
- Infectious Diseases Horizontal Technology Centre (ID HTC), A*STAR, Singapore, Singapore
| | - Andrew Owen
- Department of Pharmacology and Therapeutics, Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, Liverpool, UK
| | - William James
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Miles W Carroll
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James P Stewart
- Diamond Light Source Ltd, Harwell Science Campus, Didcot, UK
- Department of Preventive Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
- Department of Infectious Disease, University of Georgia, Georgia, USA
| | - James H Naismith
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK.
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK.
| | - Raymond J Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK.
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Protein Production UK, The Rosalind Franklin Institute - Diamond Light Source, The Research Complex at Harwell, Science Campus, Didcot, UK.
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20
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Orlando M, Fortuna S, Oloketuyi S, Bajc G, Goldenzweig A, de Marco A. CDR1 Composition Can Affect Nanobody Recombinant Expression Yields. Biomolecules 2021; 11:biom11091362. [PMID: 34572576 PMCID: PMC8465892 DOI: 10.3390/biom11091362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 01/03/2023] Open
Abstract
The isolation of nanobodies from pre-immune libraries by means of biopanning is a straightforward process. Nevertheless, the recovered candidates often require optimization to improve some of their biophysical characteristics. In principle, CDRs are not mutated because they are likely to be part of the antibody paratope, but in this work, we describe a mutagenesis strategy that specifically addresses CDR1. Its sequence was identified as an instability hot spot by the PROSS program, and the available structural information indicated that four CDR1 residues bound directly to the antigen. We therefore modified the loop flexibility with the addition of an extra glycine rather than by mutating single amino acids. This approach significantly increased the nanobody yields but traded-off with moderate affinity loss. Accurate modeling coupled with atomistic molecular dynamics simulations enabled the modifications induced by the glycine insertion and the rationale behind the engineering design to be described in detail.
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Affiliation(s)
- Marco Orlando
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100 Varese, Italy;
| | - Sara Fortuna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy;
| | - Sandra Oloketuyi
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia;
| | - Gregor Bajc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia;
| | - Adi Goldenzweig
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia;
- Correspondence: ; Tel.: +386-(05)-3315295
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21
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Donà MG, Di Bonito P, Chiantore MV, Amici C, Accardi L. Targeting Human Papillomavirus-Associated Cancer by Oncoprotein-Specific Recombinant Antibodies. Int J Mol Sci 2021; 22:ijms22179143. [PMID: 34502053 PMCID: PMC8431386 DOI: 10.3390/ijms22179143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
In recent decades, recombinant antibodies against specific antigens have shown great promise for the therapy of infectious diseases and cancer. Human papillomaviruses (HPVs) are involved in the development of around 5% of all human cancers and HPV16 is the high-risk genotype with the highest prevalence worldwide, playing a dominant role in all HPV-associated cancers. Here, we describe the main biological activities of the HPV16 E6, E7, and E5 oncoproteins, which are involved in the subversion of important regulatory pathways directly associated with all known hallmarks of cancer. We then review the state of art of the recombinant antibodies targeted to HPV oncoproteins developed so far in different formats, and outline their mechanisms of action. We describe the advantages of a possible antibody-based therapy against the HPV-associated lesions and discuss the critical issue of delivery to tumour cells, which must be addressed in order to achieve the desired translation of the antibodies from the laboratory to the clinic.
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Affiliation(s)
| | - Paola Di Bonito
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (P.D.B.); (M.V.C.)
| | - Maria Vincenza Chiantore
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (P.D.B.); (M.V.C.)
| | - Carla Amici
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy;
| | - Luisa Accardi
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (P.D.B.); (M.V.C.)
- Correspondence:
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22
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Abstract
A newly-emergent beta-coronavirus, SARS-CoV-2, rapidly has become a pandemic since 2020. It is a serious respiratory disease and caused more than 100 million of deaths in the world. WHO named it COVIA-19 and there is no effective targeted drug for it. The main treatment strategies include chemical medicine, traditional Chinese medicine (TCM) and biologics. Due to SARS-CoV-2 uses the spike proteins (S proteins) on its envelope to infect human cells, monoclonal antibodies that neutralize the S protein have become one of the hot research areas in the current research and treatment of SARS-CoV-2. In this study, we reviewed the antibodies that have been reported to have neutralizing activity against the SARS-CoV-2 infection. According to their different binding epitope regions in RBD or NTD, they are classified, and the mechanism of the representative antibodies in each category is discussed in depth, which provides potential foundation for future antibody and vaccine therapy and the development of antibody cocktails against SARS-CoV-2 mutants.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibodies, Viral/therapeutic use
- COVID-19/immunology
- COVID-19/therapy
- COVID-19/virology
- COVID-19 Vaccines/immunology
- Epitopes/immunology
- Humans
- Models, Molecular
- Neutralization Tests
- Pandemics
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Single-Domain Antibodies/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- Dongfu Jin
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Jing Wei
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China.
| | - Jian Sun
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China; Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China.
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23
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Sun D, Sang Z, Kim YJ, Xiang Y, Cohen T, Belford AK, Huet A, Conway JF, Sun J, Taylor DJ, Schneidman-Duhovny D, Zhang C, Huang W, Shi Y. Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting diverse and conserved epitopes. Nat Commun 2021; 12:4676. [PMID: 34344900 PMCID: PMC8333356 DOI: 10.1038/s41467-021-24963-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [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: 03/18/2021] [Accepted: 07/19/2021] [Indexed: 01/07/2023] Open
Abstract
Interventions against variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgently needed. Stable and potent nanobodies (Nbs) that target the receptor binding domain (RBD) of SARS-CoV-2 spike are promising therapeutics. However, it is unknown if Nbs broadly neutralize circulating variants. We found that RBD Nbs are highly resistant to variants of concern (VOCs). High-resolution cryoelectron microscopy determination of eight Nb-bound structures reveals multiple potent neutralizing epitopes clustered into three classes: Class I targets ACE2-binding sites and disrupts host receptor binding. Class II binds highly conserved epitopes and retains activity against VOCs and RBDSARS-CoV. Cass III recognizes unique epitopes that are likely inaccessible to antibodies. Systematic comparisons of neutralizing antibodies and Nbs provided insights into how Nbs target the spike to achieve high-affinity and broadly neutralizing activity. Structure-function analysis of Nbs indicates a variety of antiviral mechanisms. Our study may guide the rational design of pan-coronavirus vaccines and therapeutics.
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Affiliation(s)
- Dapeng Sun
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhe Sang
- The University of Pittsburgh and Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA, USA
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yong Joon Kim
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine and Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tomer Cohen
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of 6, Jerusalem, Israel
| | - Anna K Belford
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alexis Huet
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - James F Conway
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ji Sun
- Department of Structure Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of 6, Jerusalem, Israel.
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA.
| | - Yi Shi
- The University of Pittsburgh and Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA, USA.
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA.
- Medical Scientist Training Program, University of Pittsburgh School of Medicine and Carnegie Mellon University, Pittsburgh, PA, USA.
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24
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Sander CL, Sears AE, Pinto AF, Choi EH, Kahremany S, Gao F, Salom D, Jin H, Pardon E, Suh S, Dong Z, Steyaert J, Saghatelian A, Skowronska-Krawczyk D, Kiser PD, Palczewski K. Nano-scale resolution of native retinal rod disk membranes reveals differences in lipid composition. J Cell Biol 2021; 220:e202101063. [PMID: 34132745 PMCID: PMC8240855 DOI: 10.1083/jcb.202101063] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/26/2021] [Accepted: 05/18/2021] [Indexed: 02/07/2023] Open
Abstract
Photoreceptors rely on distinct membrane compartments to support their specialized function. Unlike protein localization, identification of critical differences in membrane content has not yet been expanded to lipids, due to the difficulty of isolating domain-specific samples. We have overcome this by using SMA to coimmunopurify membrane proteins and their native lipids from two regions of photoreceptor ROS disks. Each sample's copurified lipids were subjected to untargeted lipidomic and fatty acid analysis. Extensive differences between center (rhodopsin) and rim (ABCA4 and PRPH2/ROM1) samples included a lower PC to PE ratio and increased LC- and VLC-PUFAs in the center relative to the rim region, which was enriched in shorter, saturated FAs. The comparatively few differences between the two rim samples likely reflect specific protein-lipid interactions. High-resolution profiling of the ROS disk lipid composition gives new insights into how intricate membrane structure and protein activity are balanced within the ROS, and provides a model for future studies of other complex cellular structures.
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Affiliation(s)
- Christopher L. Sander
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Avery E. Sears
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Antonio F.M. Pinto
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA
| | - Elliot H. Choi
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Shirin Kahremany
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Fangyuan Gao
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - David Salom
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Hui Jin
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
| | - Els Pardon
- Vlaams Instituut voor Biotechnologie–Vrije Universiteit Brussel Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Susie Suh
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Zhiqian Dong
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Jan Steyaert
- Vlaams Instituut voor Biotechnologie–Vrije Universiteit Brussel Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA
| | - Dorota Skowronska-Krawczyk
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA
| | - Philip D. Kiser
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA
- Research Service, VA Long Beach Healthcare System, Long Beach, CA
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA
- Department of Chemistry, University of California, Irvine, Irvine, CA
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25
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Li T, Cai H, Yao H, Zhou B, Zhang N, van Vlissingen MF, Kuiken T, Han W, GeurtsvanKessel CH, Gong Y, Zhao Y, Shen Q, Qin W, Tian XX, Peng C, Lai Y, Wang Y, Hutter CAJ, Kuo SM, Bao J, Liu C, Wang Y, Richard AS, Raoul H, Lan J, Seeger MA, Cong Y, Rockx B, Wong G, Bi Y, Lavillette D, Li D. A synthetic nanobody targeting RBD protects hamsters from SARS-CoV-2 infection. Nat Commun 2021; 12:4635. [PMID: 34330908 PMCID: PMC8324831 DOI: 10.1038/s41467-021-24905-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [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: 09/10/2020] [Accepted: 07/15/2021] [Indexed: 01/15/2023] Open
Abstract
SARS-CoV-2, the causative agent of COVID-191, features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein1-6. Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics7-17. Llama-derived single-domain antibodies (nanobodies, ~15 kDa) offer advantages in bioavailability, amenability, and production and storage owing to their small sizes and high stability. Here, we report the rapid selection of 99 synthetic nanobodies (sybodies) against RBD by in vitro selection using three libraries. The best sybody, MR3 binds to RBD with high affinity (KD = 1.0 nM) and displays high neutralization activity against SARS-CoV-2 pseudoviruses (IC50 = 0.42 μg mL-1). Structural, biochemical, and biological characterization suggests a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency have been generated by structure-based design, biparatopic construction, and divalent engineering. Two divalent forms of MR3 protect hamsters from clinical signs after live virus challenge and a single dose of the Fc-fusion construct of MR3 reduces viral RNA load by 6 Log10. Our results pave the way for the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid development of targeted medical interventions during an outbreak.
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Affiliation(s)
- Tingting Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Hongmin Cai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Hebang Yao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Bingjie Zhou
- University of CAS, Beijing, China
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China
| | - Ning Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), CAS, Beijing, China
| | - Martje Fentener van Vlissingen
- Erasmus Laboratory Animal Science Center, Erasmus University Medical Center, Rotterdam, Netherlands
- European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Paris, France
| | - Thijs Kuiken
- European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Paris, France
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Wenyu Han
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
- University of CAS, Beijing, China
| | - Corine H GeurtsvanKessel
- European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Paris, France
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Yuhuan Gong
- University of CAS, Beijing, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), CAS, Beijing, China
| | - Yapei Zhao
- University of CAS, Beijing, China
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China
| | - Quan Shen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), CAS, Beijing, China
| | - Wenming Qin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), CAS, Shanghai, China
| | - Xiao-Xu Tian
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), CAS, Shanghai, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), CAS, Shanghai, China
| | - Yanling Lai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
- University of CAS, Beijing, China
| | - Yanxing Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Shu-Ming Kuo
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China
| | - Juan Bao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Caixuan Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
- University of CAS, Beijing, China
| | - Yifan Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
- University of CAS, Beijing, China
| | - Audrey S Richard
- European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Paris, France
| | - Hervé Raoul
- European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Paris, France
| | - Jiaming Lan
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Yao Cong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Barry Rockx
- European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Paris, France
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Gary Wong
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China.
- Département de microbiologie-infectiologie et d'immunologie, Université Laval, Québec, QC, Canada.
| | - Yuhai Bi
- University of CAS, Beijing, China.
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), CAS, Beijing, China.
| | - Dimitri Lavillette
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China.
- Pasteurien College, Soochow University, Jiangsu, China.
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China.
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26
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Lin J, Lee SL, Russell AM, Huang RF, Batt MA, Chang SS, Ferrante A, Verdino P. A structure-based engineering approach to abrogate pre-existing antibody binding to biotherapeutics. PLoS One 2021; 16:e0254944. [PMID: 34297759 PMCID: PMC8301669 DOI: 10.1371/journal.pone.0254944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 07/06/2021] [Indexed: 01/12/2023] Open
Abstract
Development of biotherapeutics is hampered by the inherent risk of immunogenicity, which requires extensive clinical assessment and possible re-engineering efforts for mitigation. The focus in the pre-clinical phase is to determine the likelihood of developing treatment-emergent anti-drug antibodies (TE-ADA) and presence of pre-existing ADA in drug-naïve individuals as risk-profiling strategies. Pre-existing ADAs are routinely identified during clinical immunogenicity assessment, but their origin and impact on drug safety and efficacy have not been fully elucidated. One specific class of pre-existing ADAs has been described, which targets neoepitopes of antibody fragments, including Fabs, VH, or VHH domains in isolation from their IgG context. With the increasing number of antibody fragments and other small binding scaffolds entering the clinic, a widely applicable method to mitigate pre-existing reactivity against these molecules is desirable. Here is described a structure-based engineering approach to abrogate pre-existing ADA reactivity to the C-terminal neoepitope of VH(H)s. On the basis of 3D structures, small modifications applicable to any VH(H) are devised that would not impact developability or antigen binding. In-silico B cell epitope mapping algorithms were used to rank the modified VHH variants by antigenicity; however, the limited discriminating capacity of the computational methods prompted an experimental evaluation of the engineered molecules. The results identified numerous modifications capable of reducing pre-existing ADA binding. The most efficient consisted of the addition of two proline residues at the VHH C-terminus, which led to no detectable pre-existing ADA reactivity while maintaining favorable developability characteristics. The method described, and the modifications identified thereby, may provide a broadly applicable solution to mitigate immunogenicity risk of antibody-fragments in the clinic and increase safety and efficacy of this promising new class of biotherapeutics.
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Affiliation(s)
- Joanne Lin
- Eli Lilly & Co, Lilly Biotechnology Center, San Diego, California, United States of America
| | - Stacey L. Lee
- Eli Lilly & Co, Lilly Biotechnology Center, San Diego, California, United States of America
| | - Anna M. Russell
- Eli Lilly & Co, Lilly Biotechnology Center, San Diego, California, United States of America
| | - Rong Fong Huang
- Eli Lilly & Co, Lilly Biotechnology Center, San Diego, California, United States of America
| | - Micheal A. Batt
- Eli Lilly & Co, Lilly Biotechnology Center, San Diego, California, United States of America
| | - Shawn S. Chang
- Eli Lilly & Co, Lilly Biotechnology Center, San Diego, California, United States of America
| | - Andrea Ferrante
- Eli Lilly & Co, Lilly Biotechnology Center, San Diego, California, United States of America
| | - Petra Verdino
- Eli Lilly & Co, Lilly Biotechnology Center, San Diego, California, United States of America
- * E-mail:
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27
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Brilhante-da-Silva N, de Oliveira Sousa RM, Arruda A, Dos Santos EL, Marinho ACM, Stabeli RG, Fernandes CFC, Pereira SDS. Camelid Single-Domain Antibodies for the Development of Potent Diagnosis Platforms. Mol Diagn Ther 2021; 25:439-456. [PMID: 34146333 DOI: 10.1007/s40291-021-00533-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2021] [Indexed: 11/26/2022]
Abstract
The distinct biophysical and pharmaceutical properties of camelid single-domain antibodies, referred to as VHHs or nanobodies, are associated with their nanometric dimensions, elevated stability, and antigen recognition capacity. These biomolecules can circumvent a number of diagnostic system limitations, especially those related to the size and stability of conventional immunoglobulins currently used in enzyme-linked immunosorbent assays and point-of-care, electrochemical, and imaging assays. In these formats, VHHs are directionally conjugated to different molecules, such as metallic nanoparticles, small peptides, and radioisotopes, which demonstrates their comprehensive versatility. Thus, the application of VHHs in diagnostic systems range from the identification of cancer cells to the detection of degenerative disease biomarkers, viral antigens, bacterial toxins, and insecticides. The improvements of sensitivity and specificity are among the central benefits resulting from the use of VHHs, which are indispensable parameters for high-quality diagnostics. Therefore, this review highlights the main biotechnological advances related to camelid single-domain antibodies and their use in in vitro and in vivo diagnostic approaches for human health.
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Affiliation(s)
- Nairo Brilhante-da-Silva
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, Fiocruz, Unidade Rondônia, Porto Velho, RO, 76812-245, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, IOC, Rio de Janeiro, Brazil
| | - Rosa Maria de Oliveira Sousa
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, Fiocruz, Unidade Rondônia, Porto Velho, RO, 76812-245, Brazil
| | - Andrelisse Arruda
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, Fiocruz, Unidade Rondônia, Porto Velho, RO, 76812-245, Brazil
| | - Eliza Lima Dos Santos
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, Fiocruz, Unidade Rondônia, Porto Velho, RO, 76812-245, Brazil
| | - Anna Carolina Machado Marinho
- Plataforma de Desenvolvimento de Anticorpos e Nanocorpos, Fundação Oswaldo Cruz, Fiocruz Ceará, Eusebio, Brazil
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Rodrigo Guerino Stabeli
- Plataforma Bi-institucional de Medicina Translacional.Fundação Oswaldo Cruz-USP, Ribeirão Preto, São Paulo, Brazil
| | - Carla Freire Celedonio Fernandes
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, IOC, Rio de Janeiro, Brazil
- Plataforma de Desenvolvimento de Anticorpos e Nanocorpos, Fundação Oswaldo Cruz, Fiocruz Ceará, Eusebio, Brazil
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Soraya Dos Santos Pereira
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, Fiocruz, Unidade Rondônia, Porto Velho, RO, 76812-245, Brazil.
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, IOC, Rio de Janeiro, Brazil.
- Programa de Pós-graduação em Biologia Experimental, Universidade Federal de Rondônia, Porto Velho, Brazil.
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28
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Lu Q, Liu J, Zhao S, Gomez Castro MF, Laurent-Rolle M, Dong J, Ran X, Damani-Yokota P, Tang H, Karakousi T, Son J, Kaczmarek ME, Zhang Z, Yeung ST, McCune BT, Chen RE, Tang F, Ren X, Chen X, Hsu JCC, Teplova M, Huang B, Deng H, Long Z, Mudianto T, Jin S, Lin P, Du J, Zang R, Su TT, Herrera A, Zhou M, Yan R, Cui J, Zhu J, Zhou Q, Wang T, Ma J, Koralov SB, Zhang Z, Aifantis I, Segal LN, Diamond MS, Khanna KM, Stapleford KA, Cresswell P, Liu Y, Ding S, Xie Q, Wang J. SARS-CoV-2 exacerbates proinflammatory responses in myeloid cells through C-type lectin receptors and Tweety family member 2. Immunity 2021; 54:1304-1319.e9. [PMID: 34048708 PMCID: PMC8106883 DOI: 10.1016/j.immuni.2021.05.006] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [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: 10/14/2020] [Revised: 03/12/2021] [Accepted: 05/05/2021] [Indexed: 02/07/2023]
Abstract
Despite mounting evidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) engagement with immune cells, most express little, if any, of the canonical receptor of SARS-CoV-2, angiotensin-converting enzyme 2 (ACE2). Here, using a myeloid cell receptor-focused ectopic expression screen, we identified several C-type lectins (DC-SIGN, L-SIGN, LSECtin, ASGR1, and CLEC10A) and Tweety family member 2 (TTYH2) as glycan-dependent binding partners of the SARS-CoV-2 spike. Except for TTYH2, these molecules primarily interacted with spike via regions outside of the receptor-binding domain. Single-cell RNA sequencing analysis of pulmonary cells from individuals with coronavirus disease 2019 (COVID-19) indicated predominant expression of these molecules on myeloid cells. Although these receptors do not support active replication of SARS-CoV-2, their engagement with the virus induced robust proinflammatory responses in myeloid cells that correlated with COVID-19 severity. We also generated a bispecific anti-spike nanobody that not only blocked ACE2-mediated infection but also the myeloid receptor-mediated proinflammatory responses. Our findings suggest that SARS-CoV-2-myeloid receptor interactions promote immune hyperactivation, which represents potential targets for COVID-19 therapy.
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Affiliation(s)
- Qiao Lu
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Jia Liu
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Shuai Zhao
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | | | - Maudry Laurent-Rolle
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | | | - Xiaojuan Ran
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Payal Damani-Yokota
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Hongzhen Tang
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Triantafyllia Karakousi
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Juhee Son
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Maria E Kaczmarek
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ze Zhang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Stephen T Yeung
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Broc T McCune
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rita E Chen
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Fei Tang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xianwen Ren
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xufeng Chen
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jack C C Hsu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Marianna Teplova
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | | | - Haijing Deng
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Zhilin Long
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Tenny Mudianto
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Shumin Jin
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Peng Lin
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Jasper Du
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ruochen Zang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tina Tianjiao Su
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Alberto Herrera
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ming Zhou
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Renhong Yan
- Joint Research Center of Hangzhou First Hospital Group and Westlake University, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Jia Cui
- Kactus Biosystems Co., Ltd., Shanghai 201114, China
| | - James Zhu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qiang Zhou
- Joint Research Center of Hangzhou First Hospital Group and Westlake University, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jianzhu Ma
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Sergei B Koralov
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Zemin Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Iannis Aifantis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Leopoldo N Segal
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Michael S Diamond
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kamal M Khanna
- The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA; Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Kenneth A Stapleford
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Peter Cresswell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Yue Liu
- Ab Studio, Inc., Hayward, CA 94545, USA
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Qi Xie
- Westlake Laboratory of Life Sciences and Biomedicine, Center for Infectious Diseases Research, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China; Institute of Basics Medical Sciences, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China.
| | - Jun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA.
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29
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Pymm P, Adair A, Chan LJ, Cooney JP, Mordant FL, Allison CC, Lopez E, Haycroft ER, O'Neill MT, Tan LL, Dietrich MH, Drew D, Doerflinger M, Dengler MA, Scott NE, Wheatley AK, Gherardin NA, Venugopal H, Cromer D, Davenport MP, Pickering R, Godfrey DI, Purcell DFJ, Kent SJ, Chung AW, Subbarao K, Pellegrini M, Glukhova A, Tham WH. Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Proc Natl Acad Sci U S A 2021; 118:e2101918118. [PMID: 33893175 PMCID: PMC8126837 DOI: 10.1073/pnas.2101918118] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [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] [Indexed: 12/27/2022] Open
Abstract
Neutralizing antibodies are important for immunity against SARS-CoV-2 and as therapeutics for the prevention and treatment of COVID-19. Here, we identified high-affinity nanobodies from alpacas immunized with coronavirus spike and receptor-binding domains (RBD) that disrupted RBD engagement with the human receptor angiotensin-converting enzyme 2 (ACE2) and potently neutralized SARS-CoV-2. Epitope mapping, X-ray crystallography, and cryo-electron microscopy revealed two distinct antigenic sites and showed two neutralizing nanobodies from different epitope classes bound simultaneously to the spike trimer. Nanobody-Fc fusions of the four most potent nanobodies blocked ACE2 engagement with RBD variants present in human populations and potently neutralized both wild-type SARS-CoV-2 and the N501Y D614G variant at concentrations as low as 0.1 nM. Prophylactic administration of either single nanobody-Fc or as mixtures reduced viral loads by up to 104-fold in mice infected with the N501Y D614G SARS-CoV-2 virus. These results suggest a role for nanobody-Fc fusions as prophylactic agents against SARS-CoV-2.
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Affiliation(s)
- Phillip Pymm
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Amy Adair
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Li-Jin Chan
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - James P Cooney
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Francesca L Mordant
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Cody C Allison
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Ester Lopez
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Ebene R Haycroft
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Matthew T O'Neill
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Li Lynn Tan
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Melanie H Dietrich
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Damien Drew
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Marcel Doerflinger
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Michael A Dengler
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
- Australian Research Council Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Nicholas A Gherardin
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Hariprasad Venugopal
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Deborah Cromer
- Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
- Department of Mathematics and Statistics, University of New South Wales, Sydney, NSW 2052, Australia
| | - Miles P Davenport
- Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Raelene Pickering
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Damian F J Purcell
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
- Australian Research Council Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Amy W Chung
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Marc Pellegrini
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Alisa Glukhova
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Drug Discovery Biology, Monash Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Wai-Hong Tham
- Infectious Diseases and Immune Defences Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
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30
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Bolli E, Scherger M, Arnouk SM, Pombo Antunes AR, Straßburger D, Urschbach M, Stickdorn J, De Vlaminck K, Movahedi K, Räder HJ, Hernot S, Besenius P, Van Ginderachter JA, Nuhn L. Targeted Repolarization of Tumor-Associated Macrophages via Imidazoquinoline-Linked Nanobodies. Adv Sci (Weinh) 2021; 8:2004574. [PMID: 34026453 PMCID: PMC8132149 DOI: 10.1002/advs.202004574] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/14/2021] [Indexed: 05/06/2023]
Abstract
Tumor-associated macrophages (TAMs) promote the immune suppressive microenvironment inside tumors and are, therefore, considered as a promising target for the next generation of cancer immunotherapies. To repolarize their phenotype into a tumoricidal state, the Toll-like receptor 7/8 agonist imidazoquinoline IMDQ is site-specifically and quantitatively coupled to single chain antibody fragments, so-called nanobodies, targeting the macrophage mannose receptor (MMR) on TAMs. Intravenous injection of these conjugates result in a tumor- and cell-specific delivery of IMDQ into MMRhigh TAMs, causing a significant decline in tumor growth. This is accompanied by a repolarization of TAMs towards a pro-inflammatory phenotype and an increase in anti-tumor T cell responses. Therefore, the therapeutic benefit of such nanobody-drug conjugates may pave the road towards effective macrophage re-educating cancer immunotherapies.
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Affiliation(s)
- Evangelia Bolli
- Lab of Cellular and Molecular ImmunologyVrije Universiteit BrusselPleinlaan 2Brussels1050Belgium
- Myeloid Cell Immunology LabVIB Center for Inflammation ResearchBrussels1050Belgium
| | | | - Sana M. Arnouk
- Lab of Cellular and Molecular ImmunologyVrije Universiteit BrusselPleinlaan 2Brussels1050Belgium
- Myeloid Cell Immunology LabVIB Center for Inflammation ResearchBrussels1050Belgium
| | - Ana Rita Pombo Antunes
- Lab of Cellular and Molecular ImmunologyVrije Universiteit BrusselPleinlaan 2Brussels1050Belgium
- Myeloid Cell Immunology LabVIB Center for Inflammation ResearchBrussels1050Belgium
| | - David Straßburger
- Department of ChemistryJohannes Gutenberg‐University MainzDuesbergweg 10‐14Mainz55128Germany
| | - Moritz Urschbach
- Department of ChemistryJohannes Gutenberg‐University MainzDuesbergweg 10‐14Mainz55128Germany
| | - Judith Stickdorn
- Max Planck Institute for Polymer ResearchAckermannweg 10Mainz55128Germany
| | - Karen De Vlaminck
- Lab of Cellular and Molecular ImmunologyVrije Universiteit BrusselPleinlaan 2Brussels1050Belgium
- Myeloid Cell Immunology LabVIB Center for Inflammation ResearchBrussels1050Belgium
| | - Kiavash Movahedi
- Lab of Cellular and Molecular ImmunologyVrije Universiteit BrusselPleinlaan 2Brussels1050Belgium
- Myeloid Cell Immunology LabVIB Center for Inflammation ResearchBrussels1050Belgium
| | - Hans Joachim Räder
- Max Planck Institute for Polymer ResearchAckermannweg 10Mainz55128Germany
| | - Sophie Hernot
- Laboratory of In Vivo Cellular and Molecular ImagingVrije Universiteit BrusselLaarbeeklaan 103Brussels1090Belgium
| | - Pol Besenius
- Department of ChemistryJohannes Gutenberg‐University MainzDuesbergweg 10‐14Mainz55128Germany
| | - Jo A. Van Ginderachter
- Lab of Cellular and Molecular ImmunologyVrije Universiteit BrusselPleinlaan 2Brussels1050Belgium
- Myeloid Cell Immunology LabVIB Center for Inflammation ResearchBrussels1050Belgium
| | - Lutz Nuhn
- Max Planck Institute for Polymer ResearchAckermannweg 10Mainz55128Germany
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31
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Affiliation(s)
- Ram Sasisekharan
- From the Koch Institute for Integrative Cancer Research, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge
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32
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Xi X, Sun W, Li H, Fan Q, Zhang X, Sun F. A comparative study and evaluation of anti-EGFR nanobodies expressed in Pichia pastoris and Escherichia coli as antitumor moieties. Protein Expr Purif 2021; 184:105888. [PMID: 33857600 DOI: 10.1016/j.pep.2021.105888] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/23/2021] [Accepted: 04/07/2021] [Indexed: 11/17/2022]
Abstract
Anti-EGFR nanobodies have been successfully applied as antitumor moieties in the photodynamic therapy and drug delivery systems. But the yields of nanobodies were still limited due to the volumetric capacity of the periplasmic compartments and inclusion bodies of Escherichia coli. A comparative study of Pichia pastoris and Escherichia coli was done through characterizing their products. Nanobody 7D12 and 7D12-9G8 were successfully expressed in Pichia pastoris with 6-13.6-fold higher yield. Both two types of nanobodies had internalization ability to be developed as antitumor moieties.
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Affiliation(s)
- Xi Xi
- Department of Biopharmacy, School of Pharmaceutical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Weihan Sun
- Department of Biopharmacy, School of Pharmaceutical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Hongrui Li
- Institute of Frontier Medical Science, Jilin University, No. 1163 Xinmin Street, Changchun, 130021, Jilin, People's Republic of China
| | - Qingjie Fan
- Department of Biopharmacy, School of Pharmaceutical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Xitian Zhang
- Changchun Intellicrown Pharmaceutical Co., Ltd, No. 1688 Jichang Road, Changchun, 130507, Jilin, People's Republic of China
| | - Fei Sun
- Institute of Frontier Medical Science, Jilin University, No. 1163 Xinmin Street, Changchun, 130021, Jilin, People's Republic of China.
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33
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Liu Y, Tiruthani K, Wang M, Zhou X, Qiu N, Xiong Y, Pecot CV, Liu R, Huang L. Tumor-targeted gene therapy with lipid nanoparticles inhibits tumor-associated adipocytes and remodels the immunosuppressive tumor microenvironment in triple-negative breast cancer. Nanoscale Horiz 2021; 6:319-329. [PMID: 33587080 PMCID: PMC8638658 DOI: 10.1039/d0nh00588f] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Adipocytes are the primary cellular components within the tumor microenvironment (TME) of triple-negative breast cancer (TNBC). Increasing evidence suggests that tumor-associated adipocytes (TAAs) can aggravate tumor progression, exacerbate the immunosuppressive TME and compromise therapeutic efficacy. In this study, the biological effect of TAAs within the breast cancer TME is first investigated, and the C-C Motif Chemokine Ligand 2 (CCL2) which is mainly secreted by TAAs in the extracellular environment is identified as the key mediator. CCL2 recruits immune cells such as monocytes and macrophages that further differentiated into immunosuppressive myeloid-derived suppressor cells (MDSCs) and M2 macrophages. To manipulate CCL2-mediated immune response, a protein trap that binds with CCL2 with high affinity and specificity is designed. The plasmid DNA encoding the CCL2 trap (pCCL2) is specifically delivered to the TME by using targeted lipid-protamine-DNA (LPD) nanoparticles to locally express the CCL2 trap and ameliorate the immunosuppressive TME. Significantly, compared with the commercially available CCL2 antibody, this strategy shows enhanced therapeutic efficacy and appreciable tumor growth inhibition. Furthermore, the pCCL2 trap treatment successfully suppresses TAAs, increases T cell infiltration and decreases the population of immunosuppressive M2 macrophages and MDSCs. Further studies show that the pCCL2 trap could facilitate PD-L1 blockade immunotherapy, demonstrating its translation potential.
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Affiliation(s)
- Yun Liu
- Division of Pharmacoengineering and Molecular Pharmaceutics and Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karthik Tiruthani
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Menglin Wang
- Division of Pharmacoengineering and Molecular Pharmaceutics and Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xuefei Zhou
- Division of Pharmacoengineering and Molecular Pharmaceutics and Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nasha Qiu
- Division of Pharmacoengineering and Molecular Pharmaceutics and Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yang Xiong
- Division of Pharmacoengineering and Molecular Pharmaceutics and Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chad V. Pecot
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rihe Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Leaf Huang
- Division of Pharmacoengineering and Molecular Pharmaceutics and Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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34
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Dhaouadi S, Ben Abderrazek R, Loustau T, Abou-Faycal C, Ksouri A, Erne W, Murdamoothoo D, Mörgelin M, Kungl A, Jung A, Ledrappier S, Benlasfar Z, Bichet S, Chiquet-Ehrismann R, Hendaoui I, Orend G, Bouhaouala-Zahar B. Novel Human Tenascin-C Function-Blocking Camel Single Domain Nanobodies. Front Immunol 2021; 12:635166. [PMID: 33790905 PMCID: PMC8006918 DOI: 10.3389/fimmu.2021.635166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/19/2021] [Indexed: 01/05/2023] Open
Abstract
The extracellular matrix (ECM) molecule Tenascin-C (TNC) is well-known to promote tumor progression by multiple mechanisms. However, reliable TNC detection in tissues of tumor banks remains limited. Therefore, we generated dromedary single-domain nanobodies Nb3 and Nb4 highly specific for human TNC (hTNC) and characterized the interaction with TNC by several approaches including ELISA, western blot, isothermal fluorescence titration and negative electron microscopic imaging. Our results revealed binding of both nanobodies to distinct sequences within fibronectin type III repeats of hTNC. By immunofluroescence and immunohistochemical imaging we observed that both nanobodies detected TNC expression in PFA and paraffin embedded human tissue from ulcerative colitis, solid tumors and liver metastasis. As TNC impairs cell adhesion to fibronectin we determined whether the nanobodies abolished this TNC function. Indeed, Nb3 and Nb4 restored adhesion of tumor and mesangial cells on a fibronectin/TNC substratum. We recently showed that TNC orchestrates the immune-suppressive tumor microenvironment involving chemoretention, causing tethering of CD11c+ myeloid/dendritic cells in the stroma. Here, we document that immobilization of DC2.4 dendritic cells by a CCL21 adsorbed TNC substratum was blocked by both nanobodies. Altogether, our novel TNC specific nanobodies could offer valuable tools for detection of TNC in the clinical practice and may be useful to inhibit the immune-suppressive and other functions of TNC in cancer and other diseases.
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Affiliation(s)
- Sayda Dhaouadi
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Rahma Ben Abderrazek
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Thomas Loustau
- Université Strasbourg, INSERM U1109 – The Tumor Microenvironment group, Hôpital Civil, Institut d'Hématologie et d'Immunologie, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Chérine Abou-Faycal
- Université Strasbourg, INSERM U1109 – The Tumor Microenvironment group, Hôpital Civil, Institut d'Hématologie et d'Immunologie, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Ayoub Ksouri
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - William Erne
- Université Strasbourg, INSERM U1109 – The Tumor Microenvironment group, Hôpital Civil, Institut d'Hématologie et d'Immunologie, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Devadarssen Murdamoothoo
- Université Strasbourg, INSERM U1109 – The Tumor Microenvironment group, Hôpital Civil, Institut d'Hématologie et d'Immunologie, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | | | - Andreas Kungl
- Institute of Pharmaceutical Sciences, Karl Franzens University Graz, Graz, Austria
- Antagonis Biotherapeutics GmbH, Graz, Austria
| | - Alain Jung
- Tumor Bank Centre Paul Strauss, Strasbourg, France
| | | | - Zakaria Benlasfar
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Sandrine Bichet
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Ismaïl Hendaoui
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Gertraud Orend
- Université Strasbourg, INSERM U1109 – The Tumor Microenvironment group, Hôpital Civil, Institut d'Hématologie et d'Immunologie, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Balkiss Bouhaouala-Zahar
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
- Faculté de Médecine de Tunis, Université Tunis el Manar, Tunis, Tunisia
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35
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Tung Yep A, Takeuchi Y, Engelhardt OG, Hufton SE. Broad Reactivity Single Domain Antibodies against Influenza Virus and Their Applications to Vaccine Potency Testing and Immunotherapy. Biomolecules 2021; 11:biom11030407. [PMID: 33802072 PMCID: PMC8001348 DOI: 10.3390/biom11030407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/11/2022] Open
Abstract
The antigenic variability of influenza presents many challenges to the development of vaccines and immunotherapeutics. However, it is apparent that there are epitopes on the virus that have evolved to remain largely constant due to their functional importance. These more conserved regions are often hidden and difficult to access by the human immune system but recent efforts have shown that these may be the Achilles heel of the virus through development and delivery of appropriate biological drugs. Amongst these, single domain antibodies (sdAbs) are equipped to target these vulnerabilities of the influenza virus due to their preference for concave epitopes on protein surfaces, their small size, flexible reformatting and high stability. Single domain antibodies are well placed to provide a new generation of robust analytical reagents and therapeutics to support the constant efforts to keep influenza in check.
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Affiliation(s)
- Andrew Tung Yep
- Biotherapeutics Division, National Institute for Biological Standards and Control (NIBSC), Potters Bar, Hertfordshire EN6 3QG, UK;
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK;
| | - Yasu Takeuchi
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK;
- Advanced Therapies Division, NIBSC, Potters Bar, Hertfordshire EN6 3QG, UK
| | | | - Simon E. Hufton
- Biotherapeutics Division, National Institute for Biological Standards and Control (NIBSC), Potters Bar, Hertfordshire EN6 3QG, UK;
- Correspondence:
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36
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Yao H, Cai H, Li T, Zhou B, Qin W, Lavillette D, Li D. A high-affinity RBD-targeting nanobody improves fusion partner's potency against SARS-CoV-2. PLoS Pathog 2021; 17:e1009328. [PMID: 33657135 PMCID: PMC7959386 DOI: 10.1371/journal.ppat.1009328] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 03/15/2021] [Accepted: 01/21/2021] [Indexed: 02/06/2023] Open
Abstract
A key step to the SARS-CoV-2 infection is the attachment of its Spike receptor-binding domain (S RBD) to the host receptor ACE2. Considerable research has been devoted to the development of neutralizing antibodies, including llama-derived single-chain nanobodies, to target the receptor-binding motif (RBM) and to block ACE2-RBD binding. Simple and effective strategies to increase potency are desirable for such studies when antibodies are only modestly effective. Here, we identify and characterize a high-affinity synthetic nanobody (sybody, SR31) as a fusion partner to improve the potency of RBM-antibodies. Crystallographic studies reveal that SR31 binds to RBD at a conserved and 'greasy' site distal to RBM. Although SR31 distorts RBD at the interface, it does not perturb the RBM conformation, hence displaying no neutralizing activities itself. However, fusing SR31 to two modestly neutralizing sybodies dramatically increases their affinity for RBD and neutralization activity against SARS-CoV-2 pseudovirus. Our work presents a tool protein and an efficient strategy to improve nanobody potency.
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Affiliation(s)
- Hebang Yao
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongmin Cai
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bingjie Zhou
- University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Wenming Qin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), Chinese Academy of Sciences, Shanghai, China
| | - Dimitri Lavillette
- University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- Pasteurien College, Soochow University, Jiangsu, China
| | - Dianfan Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
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37
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Abstract
Camelid-derived and synthetic single-domain antibodies (sdAbs) are emerging as potent weapons against the novel coronavirus, SARS-CoV-2. sdAbs are small, compact, thermostable immunoglobulin elements capable of binding targets with subnanomolar affinities. By leveraging the power of phage- and yeast surface-display technologies, rare sdAbs can be isolated from highly diverse and complex antibody libraries. Once in hand, sdAbs can be engineered to improve binding affinity, avidity, target specificities, and biodistribution. In this Opinion piece we highlight a series of sophisticated studies describing the identification of ultrapotent sdAbs directed against the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein. We discuss the possible applications of these antibodies in the global fight against COVID-19.
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Affiliation(s)
- Timothy F Czajka
- Department of Biomedical Sciences, University at Albany, Albany, NY 12201, USA
| | - David J Vance
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Nicholas J Mantis
- Department of Biomedical Sciences, University at Albany, Albany, NY 12201, USA; Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA.
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38
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Zare H, Aghamollaei H, Hosseindokht M, Heiat M, Razei A, Bakherad H. Nanobodies, the potent agents to detect and treat the Coronavirus infections: A systematic review. Mol Cell Probes 2021; 55:101692. [PMID: 33358936 PMCID: PMC7832525 DOI: 10.1016/j.mcp.2020.101692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/15/2022]
Abstract
The newly emerged coronavirus (SARS-CoV-2) continues to infect humans, and no effective treatment has yet been found. Antibody therapy is one way to control infection caused by COVID-19. However, the use of classical antibodies raises complex issues. Heavy chain antibodies (HCAbs) are single-domain antibodies derived from the Camelidae family. The variable part of these antibodies (Nanobodies or VHH) has interesting properties such as small size, cost-effective production, and good tissue permeability, causing VHH to be regarded as an antiviral therapeutics. However, the small size of nanobodies may lead to low antigen binding affinity and rapid renal clearance. In this systematic review, the application of nanobodies in the treatment of COVID-19 infection and other similar infections (MERS and SARS) was reviewed.
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Affiliation(s)
- Hamed Zare
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Hossein Aghamollaei
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Maryam Hosseindokht
- Department of Molecular Medicine, School of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Mohammad Heiat
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Razei
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Science, Tehran, Iran
| | - Hamid Bakherad
- Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
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39
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Ruano-Gallego D, Fernández LÁ. Identification of Nanobodies Blocking Intimate Adherence of Shiga Toxin-Producing Escherichia coli to Epithelial Cells. Methods Mol Biol 2021; 2291:253-272. [PMID: 33704757 DOI: 10.1007/978-1-0716-1339-9_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Therapeutic antibodies (Abs) inhibiting bacterial adhesion to host epithelia are an attractive option to reduce the load of Shiga toxin-producing E. coli (STEC) in the intestine of the patient and also in the bovine reservoir, thereby minimizing the risk of STEC contamination in the food chain. Of particular interest are recombinant single-domain Ab fragments called nanobodies (Nbs) derived from the variable domain of camelid heavy chain-only antibodies (VHH). The outer membrane adhesin intimin and the translocated intimin receptor (Tir) are essential for the attachment of STEC to host epithelia. In addition, EspA filaments of the bacterial type III protein secretion system are needed for Tir translocation into the host cell. Given their importance for bacterial adhesion and colonization, we developed Nbs against intimin, Tir and EspA proteins of STEC serotype O157:H7. Here, we report the screening methods used to isolate inhibitory Nbs blocking intimin-Tir protein-protein interaction, actin-pedestal formation, and intimate adhesion of STEC to epithelial cells in vitro. First, we describe how VHH gene repertoires can be produced as Nbs secreted by E. coli using the α-hemolysin (HlyA) protein secretion system. Next, we report the methods for identification of inhibitors of intimin-Tir protein-protein interaction and of STEC intimate adhesion to HeLa cells in culture. These methods can be adapted for the screening of Nbs against different adhesin-receptor complexes to block the adhesion of other pathogens to host cells.
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Affiliation(s)
- David Ruano-Gallego
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain.
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40
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Abstract
Immuno-PCR (IPCR) is a sensitive antigen detection by means of specific antibody-DNA conjugates. To ensure the successful conjugation of a protein (an antibody) with a reporter DNA, immuno-PCR method based on cDNA display (cD-IPCR) has been introduced. The cDNA display molecule is a 1:1 covalent complex of a polypeptide and its encoding cDNA at the single molecule level, which is directly used for antigen detection and subsequent qPCR. This method can be applied to detect various antigens in biological samples, if sequences of their single-domain antibodies (VHHs) or peptide aptamers are known.
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Affiliation(s)
| | - Naoto Nemoto
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan.
- Epsilon Molecular Engineering, Inc., Saitama, Japan.
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41
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Abstract
Present review summarizes the current applications of nanobodies in plant science and biotechnology, including plant expression of nanobodies, plant biotechnological applications, nanobody-based immunodetection, and nanobody-mediated resistance against plant pathogens. Nanobodies (Nbs) are variable domains of heavy chain-only antibodies (HCAbs) isolated from camelids. In spite of their single domain structure, nanobodies display many unique features, such as small size, high stability, and cryptic epitopes accessibility, which make them ideal for sophisticated applications in plants and animals. In this review, we summarize the current applications of nanobodies in plant science and biotechnology, focusing on nanobody expression in plants, plant biotechnological applications, determination of plant toxins and pathogens, and nanobody-mediated resistance against plant pathogens. Prospects and challenges of nanobody applications in plants are also discussed.
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Affiliation(s)
- Wenyi Wang
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, Hubei, China.
- Precision Medicine R&D Center, Zhuhai Institute of Advanced Technology, Chinese Academy of Sciences, Zhuhai, Guangdong Province, China.
- Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China.
| | - Jumao Yuan
- Precision Medicine R&D Center, Zhuhai Institute of Advanced Technology, Chinese Academy of Sciences, Zhuhai, Guangdong Province, China
- Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China
| | - Changan Jiang
- Precision Medicine R&D Center, Zhuhai Institute of Advanced Technology, Chinese Academy of Sciences, Zhuhai, Guangdong Province, China
- Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China
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Khan I, O'Bryan JP. Probing RAS Function with Monobodies. Methods Mol Biol 2021; 2262:281-302. [PMID: 33977484 PMCID: PMC8121162 DOI: 10.1007/978-1-0716-1190-6_17] [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] [Indexed: 10/21/2022]
Abstract
RAS is frequently mutated in human cancers with nearly 20% of all cancers harboring mutations in one of three RAS isoforms (KRAS, HRAS, or NRAS). Furthermore, RAS proteins are critical oncogenic drivers of tumorigenesis. As such, RAS has been a prime focus for development of targeted cancer therapeutics. Although RAS is viewed by many as undruggable, the recent development of allele-specific covalent inhibitors to KRAS(G12C) has provided significant hope for the eventual pharmacological inhibition of RAS (Ostrem et al., Nature 503(7477):548-551, 2013; Patricelli et al., Cancer Discov 6(3):316-329, 2016; Janes et al., Cell 172(3):578-589.e17, 2018; Canon et al., Nature 575(7781):217-223, 2019; Hallin et al., Cancer Discov 10(1):54-71, 2020). Indeed, these (G12C)-specific inhibitors have elicited promising responses in early phase clinical trials (Canon et al., Nature 575(7781):217-223, 2019; Hallin et al., Cancer Discov 10(1):54-71, 2020). Despite this success in pharmacologically targeting KRAS(G12C), the remaining RAS mutants lack readily tractable chemistries for development of covalent inhibitors. Thus, alternative approaches are needed to develop broadly efficacious RAS inhibitors. We have utilized Monobody (Mb) technology to identify vulnerabilities in RAS that can potentially be exploited for development of novel RAS inhibitors. Here, we describe the methods used to isolate RAS-specific Mbs and to define their inhibitory activity.
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Affiliation(s)
- Imran Khan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
- Ralph H. Johnson VA Medical Center, Charleston, SC, USA
| | - John P O'Bryan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA.
- Ralph H. Johnson VA Medical Center, Charleston, SC, USA.
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Xiang Y, Nambulli S, Xiao Z, Liu H, Sang Z, Duprex WP, Schneidman-Duhovny D, Zhang C, Shi Y. Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2. Science 2020; 370:1479-1484. [PMID: 33154108 PMCID: PMC7857400 DOI: 10.1126/science.abe4747] [Citation(s) in RCA: 236] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022]
Abstract
Cost-effective, efficacious therapeutics are urgently needed to combat the COVID-19 pandemic. In this study, we used camelid immunization and proteomics to identify a large repertoire of highly potent neutralizing nanobodies (Nbs) to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein receptor binding domain (RBD). We discovered Nbs with picomolar to femtomolar affinities that inhibit viral infection at concentrations below the nanograms-per-milliliter level, and we determined a structure of one of the most potent Nbs in complex with the RBD. Structural proteomics and integrative modeling revealed multiple distinct and nonoverlapping epitopes and indicated an array of potential neutralization mechanisms. We bioengineered multivalent Nb constructs that achieved ultrahigh neutralization potency (half-maximal inhibitory concentration as low as 0.058 ng/ml) and may prevent mutational escape. These thermostable Nbs can be rapidly produced in bulk from microbes and resist lyophilization and aerosolization.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Animals
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibody Affinity
- COVID-19/therapy
- Camelids, New World
- Escherichia coli
- Humans
- Neutralization Tests
- Protein Binding
- Protein Domains
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/immunology
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- SARS-CoV-2/immunology
- Single-Domain Antibodies/chemistry
- Single-Domain Antibodies/genetics
- Single-Domain Antibodies/immunology
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Affiliation(s)
- Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sham Nambulli
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhengyun Xiao
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Heng Liu
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhe Sang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
- University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA
| | - W Paul Duprex
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA.
- University of Pittsburgh-Carnegie Mellon University Program in Computational Biology, Pittsburgh, PA, USA
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Soetens E, Ballegeer M, Saelens X. An Inside Job: Applications of Intracellular Single Domain Antibodies. Biomolecules 2020; 10:biom10121663. [PMID: 33322697 PMCID: PMC7764588 DOI: 10.3390/biom10121663] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Sera of camelid species contain a special kind of antibody that consists only of heavy chains. The variable antigen binding domain of these heavy chain antibodies can be expressed as a separate entity, called a single domain antibody that is characterized by its small size, high solubility and oftentimes exceptional stability. Because of this, most single domain antibodies fold correctly when expressed in the reducing environment of the cytoplasm, and thereby retain their antigen binding specificity. Single domain antibodies can thus be used to target a broad range of intracellular proteins. Such intracellular single domain antibodies are also known as intrabodies, and have proven to be highly useful tools for basic research by allowing visualization, disruption and even targeted degradation of intracellular proteins. Furthermore, intrabodies can be used to uncover prospective new therapeutic targets and have the potential to be applied in therapeutic settings in the future. In this review we provide a brief overview of recent advances in the field of intracellular single domain antibodies, focusing on their use as research tools and potential therapeutic applications. Special attention is given to the available methods that allow delivery of single domain antibodies into cells.
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Affiliation(s)
- Eline Soetens
- VIB-UGent Center for Medical Biotechnology, VIB, B-9052 Ghent, Belgium; (E.S.); (M.B.)
- Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
| | - Marlies Ballegeer
- VIB-UGent Center for Medical Biotechnology, VIB, B-9052 Ghent, Belgium; (E.S.); (M.B.)
- Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, B-9052 Ghent, Belgium; (E.S.); (M.B.)
- Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
- Correspondence:
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Moliner-Morro A, J. Sheward D, Karl V, Perez Vidakovics L, Murrell B, McInerney GM, Hanke L. Picomolar SARS-CoV-2 Neutralization Using Multi-Arm PEG Nanobody Constructs. Biomolecules 2020; 10:biom10121661. [PMID: 33322557 PMCID: PMC7764822 DOI: 10.3390/biom10121661] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 12/29/2022] Open
Abstract
Multivalent antibody constructs have a broad range of clinical and biotechnological applications. Nanobodies are especially useful as components for multivalent constructs as they allow increased valency while maintaining a small molecule size. We here describe a novel, rapid method for the generation of bi- and multivalent nanobody constructs with oriented assembly by Cu-free strain promoted azide-alkyne click chemistry (SPAAC). We used sortase A for ligation of click chemistry functional groups site-specifically to the C-terminus of nanobodies before creating C-to-C-terminal nanobody fusions and 4-arm polyethylene glycol (PEG) tetrameric nanobody constructs. We demonstrated the viability of this approach by generating constructs with the SARS-CoV-2 neutralizing nanobody Ty1. We compared the ability of the different constructs to neutralize SARS-CoV-2 pseudotyped virus and infectious virus in neutralization assays. The generated dimers neutralized the virus similarly to a nanobody-Fc fusion variant, while a 4-arm PEG based tetrameric Ty1 construct dramatically enhanced neutralization of SARS-CoV-2, with an IC50 in the low picomolar range.
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Affiliation(s)
- Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (A.M.-M.); (D.J.S.); (V.K.); (L.P.V.); (B.M.); (G.M.M.)
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (A.M.-M.); (D.J.S.); (V.K.); (L.P.V.); (B.M.); (G.M.M.)
- Division of Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, 7925 Cape Town, South Africa
| | - Vivien Karl
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (A.M.-M.); (D.J.S.); (V.K.); (L.P.V.); (B.M.); (G.M.M.)
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (A.M.-M.); (D.J.S.); (V.K.); (L.P.V.); (B.M.); (G.M.M.)
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (A.M.-M.); (D.J.S.); (V.K.); (L.P.V.); (B.M.); (G.M.M.)
| | - Gerald M. McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (A.M.-M.); (D.J.S.); (V.K.); (L.P.V.); (B.M.); (G.M.M.)
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden; (A.M.-M.); (D.J.S.); (V.K.); (L.P.V.); (B.M.); (G.M.M.)
- Correspondence:
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Gavira-O’Neill CE, Dong JX, Trimmer JS. Development, Screening, and Validation of Camelid-Derived Nanobodies for Neuroscience Research. Curr Protoc Neurosci 2020; 94:e107. [PMID: 33185319 PMCID: PMC7673645 DOI: 10.1002/cpns.107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Nanobodies (nAbs) are recombinant antigen-binding variable domain fragments obtained from heavy-chain-only immunoglobulins. Among mammals, these are unique to camelids (camels, llamas, alpacas, etc.). Nanobodies are of great use in biomedical research due to their efficient folding and stability under a variety of conditions, as well as their small size. The latter characteristic is particularly important for nAbs used as immunolabeling reagents, since this can improve penetration of cell and tissue samples compared to conventional antibodies, and also reduce the gap distance between signal and target, thereby improving imaging resolution. In addition, their recombinant nature allows for unambiguous definition and permanent archiving in the form of DNA sequence, enhanced distribution in the form of sequences or plasmids, and easy and inexpensive production using well-established bacterial expression systems, such as the IPTG induction method described here. This article will review the basic workflow and process for developing, screening, and validating novel nAbs against neuronal target proteins. The protocols described make use of the most common nAb development method, wherein an immune repertoire from an immunized llama is screened via phage display technology. Selected nAbs can then be taken through validation assays for use as immunolabels or as intrabodies in neurons. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Total RNA isolation from camelid leukocytes Basic Protocol 2: First-strand cDNA synthesis; VH H and VH repertoire PCR Basic Protocol 3: Preparation of the phage display library Basic Protocol 4: Panning of the phage display library Basic Protocol 5: Small-scale nAb expression Basic Protocol 6: Sequence analysis of selected nAb clones Basic Protocol 7: Nanobody validation as immunolabels Basic Protocol 8: Generation of nAb-pEGFP mammalian expression constructs Basic Protocol 9: Nanobody validation as intrabodies Support Protocol 1: ELISA for llama serum testing, phage titer, and screening of selected clones Support Protocol 2: Amplification of helper phage stock Support Protocol 3: nAb expression in amber suppressor E. coli bacterial strains.
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Affiliation(s)
- Clara E. Gavira-O’Neill
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA 95616
| | | | - James S. Trimmer
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA 95616
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Abstract
Antibodies represent a well-established class of clinical diagnostics for medical applications as well as essential research and biotechnological tools. Although both polyclonal and monoclonal antibodies are indispensable reagents in basic research and diagnostics but both of them have their limitations. Hence, there is urgent need to develop strategies aimed at production of alternative scaffolds and recombinant antibodies of smaller dimensions that could be easily produced, selected and manipulated. Unlike conventional antibodies, members of Camelidae and sharks produce antibodies composed only of heavy chains with small size, high solubility, thermal stability, refolding capacity and good tissue penetration in vivo. The discovery of these naturally occurring antibodies having only heavy-chain in Camelidae family and their further development into small recombinant nanobodies represents an attractive alternative in drug delivery, diagnostics and imaging. Nanobody derivatives are soluble, stable, versatile, have unique refolding capacities, reduced aggregation tendencies and high-target binding capabilities. They can be genetically customized to target enzymes, transmembrane proteins or molecular interactions. Their ability to recognize recessed antigenic sites has been attributed to their smaller size and the ability of the extended CDR3 loop to quickly penetrate into such epitopes. With the advent of molecular engineering and phage display technology, they can be of potential use in molecular imaging, drug delivery and therapeutics for several major diseases. In this review we present the recent advances in nanobodies for modulating immune functions, for targeting cancers, viruses, toxins and microbes as well as their utility as diagnostic and biosensor tools.
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48
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Lai JY, Lim TS. Infectious disease antibodies for biomedical applications: A mini review of immune antibody phage library repertoire. Int J Biol Macromol 2020; 163:640-648. [PMID: 32650013 PMCID: PMC7340592 DOI: 10.1016/j.ijbiomac.2020.06.268] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/21/2020] [Accepted: 06/28/2020] [Indexed: 12/18/2022]
Abstract
Antibody phage display is regarded as a critical tool for the development of monoclonal antibodies for infectious diseases. The different classes of antibody libraries are classified based on the source of repertoire used to generate the libraries. Immune antibody libraries are generated from disease infected host or immunization against an infectious agent. Antibodies derived from immune libraries are distinct from those derived from naïve libraries as the host's in vivo immune mechanisms shape the antibody repertoire to yield high affinity antibodies. As the immune system is constantly evolving in accordance to the health state of an individual, immune libraries can offer more than just infection-specific antibodies but also antibodies derived from the memory B-cells much like naïve libraries. The combinatorial nature of the gene cloning process would give rise to a combination of natural and un-natural antibody gene pairings in the immune library. These factors have a profound impact on the coverage of immune antibody libraries to target both disease-specific and non-disease specific antigens. This review looks at the diverse nature of antibody responses for immune library generation and discusses the extended potential of a disease-specified immune library in the context of phage display.
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Affiliation(s)
- Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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Abstract
Reagents that bind tightly and specifically to biomolecules of interest remain essential in the exploration of biology and in their ultimate application to medicine. Besides ligands for receptors of known specificity, agents commonly used for this purpose are monoclonal antibodies derived from mice, rabbits, and other animals. However, such antibodies can be expensive to produce, challenging to engineer, and are not necessarily stable in the context of the cellular cytoplasm, a reducing environment. Heavy chain-only antibodies, discovered in camelids, have been truncated to yield single-domain antibody fragments (VHHs or nanobodies) that overcome many of these shortcomings. Whereas they are known as crystallization chaperones for membrane proteins or as simple alternatives to conventional antibodies, nanobodies have been applied in settings where the use of standard antibodies or their derivatives would be impractical or impossible. We review recent examples in which the unique properties of nanobodies have been combined with complementary methods, such as chemical functionalization, to provide tools with unique and useful properties.
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Affiliation(s)
- Ross W Cheloha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Charlotte Wijne
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA.
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50
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Li G, Li Y, Chu Y, Zhang A, Pan J, Wang H, Xu G. [Construction of camelidae natural nanobody phage dispaly library and screening, production and identification of anti-CD19 nanobody]. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 2020; 36:1036-1043. [PMID: 33210599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Objective To construct and verify camelidae natural nanobody phage display library for selection of nanobodies against various antigens, and to obtain and identify the nanobody targeting CD19. Methods The total RNA of spleen of Bactrian camel was reverse transcribed and the variable region gene fragment of its heavy chain was obtained by nested PCR. It was constructed into the pCANTAB5e phagemid vector and electrotransformed into TG1 E. coli to develop the natural nanobody phage display library. After rescued by the KM13 helper phage, its capacity and diversity were analyzed and identified. Nanobody against CD19 was screened using biotinylated antigen combined with streptavidin magnetic beads, followed by ELISA, sequencing, exogenous expression and verification. Results The constructed natural phage nanobody display library had great diversity, and its fragment insertion rate was about 100%. The amino acid homology of 20 randomly selected clones was 65.85%, and the titer of the display library rescued by the helper phage was 9.0×1013 CFU/mL. After panning with CD19 as the antigen, the positive clones were sequenced and analyzed, and finally anti-CD19 nanobody sequences were obtained. The exogenously expressed anti-CD19 nanobody based on the sequences was verified having the ability to bind to CD19. Conclusion A camelidae natural nanobody phage display library with high titer and great diversity has been successfully constructed. Three anti-CD19 nanobody sequences have been obtained by panning with CD19. In addition, this study provides technical support for researching and developing diagnostic kits and antibody drugs targeting CD19, and it is a novel direction to improve CAR-T cells targeting CD19.
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Affiliation(s)
- Guangqi Li
- Department of Laboratory Medicine, Clinical Medical College, Ningxia Medical University, Yinchuan 750004, China
| | - Yanning Li
- Department of Laboratory Medicine, Clinical Medical College, Ningxia Medical University, Yinchuan 750004, China
| | - Yuankui Chu
- Department of Laboratory Medicine, Clinical Medical College, Ningxia Medical University, Yinchuan 750004, China
| | - Aijun Zhang
- Department of Laboratory Medicine, Clinical Medical College, Ningxia Medical University, Yinchuan 750004, China
| | - Junfei Pan
- Department of Laboratory Medicine, Clinical Medical College, Ningxia Medical University, Yinchuan 750004, China
| | - Hongxia Wang
- Department of Laboratory Medicine, Clinical Medical College, Ningxia Medical University, Yinchuan 750004, China
| | - Guangxian Xu
- Department of Laboratory Medicine, Clinical Medical College, Ningxia Medical University, Yinchuan 750004, China. *Corresponding author, E-mail:
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