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Hayashi G, Naito T, Miura S, Iwamoto N, Usui Y, Bando-Shimizu M, Suzuki S, Higashi K, Nonaka M, Oishi S, Murakami H. Generating a mirror-image monobody targeting MCP-1 via TRAP display and chemical protein synthesis. Nat Commun 2024; 15:10723. [PMID: 39715753 PMCID: PMC11666718 DOI: 10.1038/s41467-024-54902-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 11/20/2024] [Indexed: 12/25/2024] Open
Abstract
Biologically produced protein drugs are generally susceptible to degradation by proteases and often exhibit immunogenicity. To address this issue, mirror-image peptide/protein binders consisting of D-amino acids have been developed so far through the mirror-image phage display technique. Here, we develop a mirror-image protein binder derived from a monobody, one of the promising protein scaffolds, utilizing two notable technologies: chemical protein synthesis and TRAP display, an improved version of mRNA display. A sequential workflow of initial screening followed by affinity maturation, facilitated by TRAP display, generates an L-monobody with high affinity (KD = 1.3 nM) against monocyte chemoattractant protein-1 (MCP-1) D-enantiomer. The chemically synthesized D-monobody demonstrates strong and specific binding to L-MCP-1 and exhibits pharmaceutically favorable properties such as proteolytic resistance, minimal immune response, and a potent inhibitory effect on MCP-1-induced cell migration. This study elevates the value of mirror-image peptide/protein binders as an alternative modality in drug discovery.
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Affiliation(s)
- Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.
| | - Toshinori Naito
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Sayaka Miura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Naoya Iwamoto
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yusuke Usui
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Mika Bando-Shimizu
- Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sae Suzuki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Katsuaki Higashi
- Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Motohiro Nonaka
- Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University, Kyoto, Japan.
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan.
- Research Institute for Quantum and Chemical Innovation, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan.
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Ajiki M, Yoshikawa M, Miyazaki T, Kawasaki A, Aoki K, Nakatsu F, Tsukiji S. ORP9-PH domain-based fluorescent reporters for visualizing phosphatidylinositol 4-phosphate dynamics in living cells. RSC Chem Biol 2024; 5:544-555. [PMID: 38846081 PMCID: PMC11151866 DOI: 10.1039/d3cb00232b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/15/2024] [Indexed: 06/09/2024] Open
Abstract
Fluorescent reporters that visualize phosphatidylinositol 4-phosphate (PI4P) in living cells are indispensable to elucidate the roles of this fundamental lipid in cell physiology. However, currently available PI4P reporters have limitations, such as Golgi-biased localization and low detection sensitivity. Here, we present a series of fluorescent PI4P reporters based on the pleckstrin homology (PH) domain of oxysterol-binding protein-related protein 9 (ORP9). We show that the green fluorescent protein AcGFP1-tagged ORP9-PH domain can be used as a fluorescent PI4P reporter to detect cellular PI4P across its wide distribution at multiple cellular locations, including the plasma membrane (PM), Golgi, endosomes, and lysosomes with high specificity and contrast. We also developed blue, red, and near-infrared fluorescent PI4P reporters suitable for multicolor fluorescence imaging experiments. Finally, we demonstrate the utility of the ORP9-PH domain-based reporter to visualize dynamic changes in the PI4P distribution and level in living cells upon synthetic ER-PM membrane contact manipulation and GPCR stimulation. This work offers a new set of genetically encoded fluorescent PI4P reporters that are practically useful for the study of PI4P biology.
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Affiliation(s)
- Moeka Ajiki
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology Gokiso-cho, Showa-ku Nagoya 466-8555 Japan
| | - Masaru Yoshikawa
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology Gokiso-cho, Showa-ku Nagoya 466-8555 Japan
| | - Tomoki Miyazaki
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology Gokiso-cho, Showa-ku Nagoya 466-8555 Japan
| | - Asami Kawasaki
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University 1-757 Asahimachi, Chuo-ku Niigata 951-8510 Japan
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences 5-1 Higashiyama, Myodaiji-cho Okazaki Aichi 444-8787 Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences 5-1 Higashiyama, Myodaiji-cho Okazaki Aichi 444-8787 Japan
- Department of Basic Biology, Faculty of Life Science, SOKENDAI (The Graduate University for Advanced Studies) 5-1 Higashiyama, Myodaiji-cho Okazaki Aichi 444-8787 Japan
| | - Fubito Nakatsu
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University 1-757 Asahimachi, Chuo-ku Niigata 951-8510 Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology Gokiso-cho, Showa-ku Nagoya 466-8555 Japan
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology Gokiso-cho, Showa-ku Nagoya 466-8555 Japan
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Campbell E, Luxton T, Kohl D, Goodchild SA, Walti C, Jeuken LJC. Chimeric Protein Switch Biosensors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:1-35. [PMID: 38273207 DOI: 10.1007/10_2023_241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Rapid detection of protein and small-molecule analytes is a valuable technique across multiple disciplines, but most in vitro testing of biological or environmental samples requires long, laborious processes and trained personnel in laboratory settings, leading to long wait times for results and high expenses. Fusion of recognition with reporter elements has been introduced to detection methods such as enzyme-linked immunoassays (ELISA), with enzyme-conjugated secondary antibodies removing one of the many incubation and wash steps. Chimeric protein switch biosensors go further and provide a platform for homogenous mix-and-read assays where long wash and incubation steps are eradicated from the process. Chimeric protein switch biosensors consist of an enzyme switch (the reporter) coupled to a recognition element, where binding of the analyte results in switching the activity of the reporter enzyme on or off. Several chimeric protein switch biosensors have successfully been developed for analytes ranging from small molecule drugs to large protein biomarkers. There are two main formats of chimeric protein switch biosensor developed, one-component and multi-component, and these formats exhibit unique advantages and disadvantages. Genetically fusing a recognition protein to the enzyme switch has many advantages in the production and performance of the biosensor. A range of immune and synthetic binding proteins have been developed as alternatives to antibodies, including antibody mimetics or antibody fragments. These are mainly small, easily manipulated proteins and can be genetically fused to a reporter for recombinant expression or manipulated to allow chemical fusion. Here, aspects of chimeric protein switch biosensors will be reviewed with a comparison of different classes of recognition elements and switching mechanisms.
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Affiliation(s)
- Emma Campbell
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Timothy Luxton
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Declan Kohl
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | | | - Christoph Walti
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
| | - Lars J C Jeuken
- School of Biomedical Sciences, University of Leeds, Leeds, UK.
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
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Dormeshkin D, Shapira M, Dubovik S, Kavaleuski A, Katsin M, Migas A, Meleshko A, Semyonov S. Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. Front Immunol 2022; 13:965446. [PMID: 36189235 PMCID: PMC9524272 DOI: 10.3389/fimmu.2022.965446] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
The COVID−19 pandemic not only resulted in a global crisis, but also accelerated vaccine development and antibody discovery. Herein we report a synthetic humanized VHH library development pipeline for nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) isolation. Trinucleotide-based randomization of CDRs by Kunkel mutagenesis with the subsequent rolling-cycle amplification resulted in more than 1011 diverse phage display library in a manageable for a single person number of electroporation reactions. We identified a number of nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) by screening a novel synthetic humanized antibody library. In order to explore the most robust and fast method for affinity improvement, we performed affinity maturation by CDR1 and CDR2 shuffling and avidity engineering by multivalent trimeric VHH fusion protein construction. As a result, H7-Fc and G12x3-Fc binders were developed with the affinities in nM and pM range respectively. Importantly, these affinities are weakly influenced by most of SARS-CoV-2 VoC mutations and they retain moderate binding to BA.4\5. The plaque reduction neutralization test (PRNT) resulted in IC50 = 100 ng\ml and 9.6 ng\ml for H7-Fc and G12x3-Fc antibodies, respectively, for the emerging Omicron BA.1 variant. Therefore, these VHH could expand the present landscape of SARS-CoV-2 neutralization binders with the therapeutic potential for present and future SARS-CoV-2 variants.
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Affiliation(s)
- Dmitri Dormeshkin
- Laboratory of Molecular Diagnostics and Biotechnology, Institute of Bioorganic Chemistry of the National academy of Sciences of Belarus, Minsk, Belarus
- *Correspondence: Dmitri Dormeshkin,
| | - Michail Shapira
- Laboratory of Molecular Diagnostics and Biotechnology, Institute of Bioorganic Chemistry of the National academy of Sciences of Belarus, Minsk, Belarus
| | - Simon Dubovik
- Department of Biology, Belarusian State University, Minsk, Belarus
| | - Anton Kavaleuski
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Mikalai Katsin
- Imunovakcina, UAB, Vilnius, Lithuania
- Immunofusion, LLC, Minsk, Belarus
| | - Alexandr Migas
- Imunovakcina, UAB, Vilnius, Lithuania
- Immunofusion, LLC, Minsk, Belarus
| | | | - Sergei Semyonov
- Laboratory of Biosafety With Pathogens Collection, Republican Research and Practical Center for Epidemiology & Microbiology, Minsk, Belarus
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