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Imai M, Colas K, Suga H. Protein Grafting Techniques: From Peptide Epitopes to Lasso-Grafted Neobiologics. Chempluschem 2024:e202400152. [PMID: 38693599 DOI: 10.1002/cplu.202400152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/03/2024]
Abstract
Protein engineering techniques have vastly expanded their domain of impact, notably following the success of antibodies. Likewise, smaller peptide therapeutics have carved an increasingly significant niche for themselves in the pharmaceutical landscape. The concept of grafting such peptides onto larger protein scaffolds, thus harvesting the advantages of both, has given rise to a variety of protein engineering strategies that are reviewed herein. We also describe our own "Lasso-Grafting" approach, which combines traditional grafting concepts with mRNA display to streamline the production of multiple grafted drug candidates for virtually any target.
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Affiliation(s)
- Mikio Imai
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kilian Colas
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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Kawakami N, Sato H, Terasaka N, Matsumoto K, Suga H. MET-Activating Ubiquitin Multimers. Angew Chem Int Ed Engl 2023; 62:e202307157. [PMID: 37450419 DOI: 10.1002/anie.202307157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Receptor tyrosine kinases (RTKs) are generally activated through their dimerization and/or oligomerization induced by their cognate ligands, and one such RTK hepatocyte growth factor (HGF) receptor, known as MET, plays an important role in tissue regeneration. Here we show the development of ubiquitin (Ub)-based protein ligand multimers, referred to as U-bodies, which act as surrogate agonists for MET and are derived from MET-binding macrocyclic peptides. Monomeric Ub constructs (U-body) were first generated by genetic implantation of a macrocyclic peptide pharmacophore into a structural loop of Ub (lasso-grafting) and subsequent optimization of its flanking spacer sequences via mRNA display. Such U-body constructs exhibit potent binding affinity to MET, thermal stability, and proteolytic stability. The U-body constructs also partially/fully inhibited or enhanced HGF-induced MET-phosphorylation. Their multimerization to dimeric, tetrameric, and octameric U-bodies linked by an appropriate peptide linker yielded potent MET activation activity and downstream cell proliferation-promoting activity. This work suggests that lasso-grafting of macrocycles to Ub is an effective approach to devising protein-based artificial RTK agonists and it can be useful in the development of a new class of biologics for various therapeutic applications.
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Affiliation(s)
- Naoya Kawakami
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroki Sato
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University Kakuma-machi, Kanazawa City, Ishikawa, 920-1192, Japan
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University Kakuma-machi, Kanazawa City, Ishikawa, 920-1192, Japan
| | - Naohiro Terasaka
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Kunio Matsumoto
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University Kakuma-machi, Kanazawa City, Ishikawa, 920-1192, Japan
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University Kakuma-machi, Kanazawa City, Ishikawa, 920-1192, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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Cowan R, Trokter M, Oleksy A, Fedorova M, Sawmynaden K, Worzfeld T, Offermanns S, Matthews D, Carr MD, Hall G. Nanobody inhibitors of Plexin-B1 identify allostery in plexin-semaphorin interactions and signalling. J Biol Chem 2023; 299:104740. [PMID: 37088134 DOI: 10.1016/j.jbc.2023.104740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/29/2023] [Accepted: 04/18/2023] [Indexed: 04/25/2023] Open
Abstract
Plexin-B1 is a receptor for the cell surface semaphorin, Sema4D. This signalling system has been implicated in a variety of human diseases, including cancer, multiple sclerosis and osteoporosis. Whilst inhibitors of the Plexin-B1:Sema4D interaction have been previously reported, understanding their mechanism has been hindered by an incomplete structural view of Plexin-B1. In this study, we have raised and characterised a pair of nanobodies that are specific for mouse Plexin-B1, and which inhibit the binding of Sema4D to mouse Plexin-B1 and its biological activity. Structural studies of these nanobodies reveal that they inhibit the binding of Sema4D in an allosteric manner, binding to epitopes not previously reported. In addition, we report the first unbound structure of human Plexin-B1, which reveals that Plexin-B1 undergoes a conformational change on Sema4D binding. These changes mirror those seen upon binding of allosteric peptide modulators, which suggests a new model for understanding Plexin-B1 signalling, and provides a potential innovative route for therapeutic modulation of Plexin-B1.
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Affiliation(s)
- Richard Cowan
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Martina Trokter
- LifeArc, Centre for Therapeutics Discovery, Open Innovation Campus, Stevenage, UK
| | - Arkadiusz Oleksy
- LifeArc, Centre for Therapeutics Discovery, Open Innovation Campus, Stevenage, UK
| | - Marina Fedorova
- LifeArc, Centre for Therapeutics Discovery, Open Innovation Campus, Stevenage, UK
| | - Kovilen Sawmynaden
- LifeArc, Centre for Therapeutics Discovery, Open Innovation Campus, Stevenage, UK
| | - Thomas Worzfeld
- Institute of Pharmacology, University of Marburg, Karl-von-Frisch-Str. 2 35043, Germany; Max-Planck Institute for Heart and Lung Research, Ludwigstr. 43, 61231, Bad Nauheim, Germany
| | - Stefan Offermanns
- Max-Planck Institute for Heart and Lung Research, Ludwigstr. 43, 61231, Bad Nauheim, Germany
| | - David Matthews
- LifeArc, Centre for Therapeutics Discovery, Open Innovation Campus, Stevenage, UK
| | - Mark D Carr
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Gareth Hall
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
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Sakai K, Sugano-Nakamura N, Mihara E, Rojas-Chaverra NM, Watanabe S, Sato H, Imamura R, Voon DCC, Sakai I, Yamasaki C, Tateno C, Shibata M, Suga H, Takagi J, Matsumoto K. Designing receptor agonists with enhanced pharmacokinetics by grafting macrocyclic peptides into fragment crystallizable regions. Nat Biomed Eng 2023; 7:164-176. [PMID: 36344661 PMCID: PMC9991925 DOI: 10.1038/s41551-022-00955-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 09/26/2022] [Indexed: 11/09/2022]
Abstract
Short half-lives in circulation and poor transport across the blood-brain barrier limit the utility of cytokines and growth factors acting as receptor agonists. Here we show that surrogate receptor agonists with longer half-lives in circulation and enhanced transport rates across the blood-brain barrier can be generated by genetically inserting macrocyclic peptide pharmacophores into the structural loops of the fragment crystallizable (Fc) region of a human immunoglobulin. We used such 'lasso-grafting' approach, which preserves the expression levels of the Fc region and its affinity for the neonatal Fc receptor, to generate Fc-based protein scaffolds with macrocyclic peptides binding to the receptor tyrosine protein kinase Met. The Met agonists dimerized Met, inducing biological responses that were similar to those induced by its natural ligand. Moreover, lasso-grafting of the Fc region of the mouse anti-transferrin-receptor antibody with Met-binding macrocyclic peptides enhanced the accumulation of the resulting Met agonists in brain parenchyma in mice. Lasso-grafting may allow for designer protein therapeutics with enhanced stability and pharmacokinetics.
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Affiliation(s)
- Katsuya Sakai
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan. .,WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan.
| | - Nozomi Sugano-Nakamura
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Japan
| | - Emiko Mihara
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Japan
| | | | - Sayako Watanabe
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Japan
| | - Hiroki Sato
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan.,Tumor Microenvironment Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Ryu Imamura
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan.,WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Dominic Chih-Cheng Voon
- Inflammation and Epithelial Plasticity Unit, Cancer Research Institute, Kanazawa University, Kanazawa, Japan.,Cancer Model Research Innovative Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Itsuki Sakai
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Chihiro Yamasaki
- Research and Development Department, PhoenixBio Co. Ltd, Higashihiroshima, Japan
| | - Chise Tateno
- Research and Development Department, PhoenixBio Co. Ltd, Higashihiroshima, Japan
| | - Mikihiro Shibata
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan.,High-speed AFM for Biological Application Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Japan.
| | - Kunio Matsumoto
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan. .,WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan. .,Tumor Microenvironment Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan.
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