1
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Vasco A, Taylor RJ, Méndez Y, Bernardes GJL. On-Demand Thio-Succinimide Hydrolysis for the Assembly of Stable Protein-Protein Conjugates. J Am Chem Soc 2024; 146:20709-20719. [PMID: 39012647 PMCID: PMC11295205 DOI: 10.1021/jacs.4c03721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/17/2024]
Abstract
Chemical post-translational protein-protein conjugation is an important technique with growing applications in biotechnology and pharmaceutical research. Maleimides represent one of the most widely employed bioconjugation reagents. However, challenges associated with the instability of first- and second-generation maleimide technologies are yet to be fully addressed. We report the development of a novel class of maleimide reagents that can undergo on-demand ring-opening hydrolysis of the resulting thio-succinimide. This strategy enables rapid post-translational assembly of protein-protein conjugates. Thio-succinimide hydrolysis, triggered upon application of chemical, photochemical, or enzymatic stimuli, allowed homobifunctional bis-maleimide reagents to be applied in the production of stable protein-protein conjugates, with complete temporal control. Bivalent and bispecific protein-protein dimers constructed from small binders targeting antigens of oncological importance, PD-L1 and HER2, were generated with high purity, stability, and improved functionality compared to monomeric building blocks. The modularity of the approach was demonstrated through elaboration of the linker moiety through a bioorthogonal propargyl handle to produce protein-protein-fluorophore conjugates. Furthermore, extending the functionality of the homobifunctional reagents by temporarily masking reactive thiols included in the linker allowed the assembly of higher order trimeric and tetrameric single-domain antibody conjugates. The potential for the approach to be extended to proteins of greater biochemical complexity was demonstrated in the production of immunoglobulin single-domain antibody conjugates. On-demand control of thio-succinimide hydrolysis combined with the facile assembly of chemically defined homo- and heterodimers constitutes an important expansion of the chemical methods available for generating stable protein-protein conjugates.
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Affiliation(s)
| | | | - Yanira Méndez
- Yusuf Hamied Department of
Chemistry, University of Cambridge, CB2 1EW Cambridge, U.K.
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2
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Hartmann P, Bohdan K, Hommrich M, Juliá F, Vogelsang L, Eirich J, Zangl R, Farès C, Jacobs JB, Mukhopadhyay D, Mengeler JM, Vetere A, Sterling MS, Hinrichs H, Becker S, Morgner N, Schrader W, Finkemeier I, Dietz KJ, Griesinger C, Ritter T. Chemoselective umpolung of thiols to episulfoniums for cysteine bioconjugation. Nat Chem 2024; 16:380-388. [PMID: 38123842 PMCID: PMC10914617 DOI: 10.1038/s41557-023-01388-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 10/27/2023] [Indexed: 12/23/2023]
Abstract
Cysteine conjugation is an important tool in protein research and relies on fast, mild and chemoselective reactions. Cysteinyl thiols can either be modified with prefunctionalized electrophiles, or converted into electrophiles themselves for functionalization with selected nucleophiles in an independent step. Here we report a bioconjugation strategy that uses a vinyl thianthrenium salt to transform cysteine into a highly reactive electrophilic episulfonium intermediate in situ, to enable conjugation with a diverse set of bioorthogonal nucleophiles in a single step. The reactivity profile can connect several nucleophiles to biomolecules through a short and stable ethylene linker, ideal for introduction of infrared labels, post-translational modifications or NMR probes. In the absence of reactive exogenous nucleophiles, nucleophilic amino acids can react with the episulfonium intermediate for native peptide stapling and protein-protein ligation. Ready synthetic access to isotopologues of vinyl thianthrenium salts enables applications in quantitative proteomics. Such diverse applications demonstrate the utility of vinyl-thianthrenium-based bioconjugation as a fast, selective and broadly applicable tool for chemical biology.
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Affiliation(s)
- Philipp Hartmann
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Kostiantyn Bohdan
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Moritz Hommrich
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Fabio Juliá
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Lara Vogelsang
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Jürgen Eirich
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Rene Zangl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Frankfurt/Main, Germany
| | - Christophe Farès
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | | | | | | | - Alessandro Vetere
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | | | - Heike Hinrichs
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Stefan Becker
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Frankfurt/Main, Germany
| | - Wolfgang Schrader
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Iris Finkemeier
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | | | - Tobias Ritter
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany.
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3
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Zeng Y, Shi W, Liu Z, Xu H, Liu L, Hang J, Wang Y, Lu M, Zhou W, Huang W, Tang F. C-terminal modification and functionalization of proteins via a self-cleavage tag triggered by a small molecule. Nat Commun 2023; 14:7169. [PMID: 37935692 PMCID: PMC10630284 DOI: 10.1038/s41467-023-42977-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023] Open
Abstract
The precise modification or functionalization of the protein C-terminus is essential but full of challenges. Herein, a chemical approach to modify the C-terminus is developed by fusing a cysteine protease domain on the C-terminus of the protein of interest, which could achieve the non-enzymatic C-terminal functionalization by InsP6-triggered cysteine protease domain self-cleavage. This method demonstrates a highly efficient way to achieve protein C-terminal functionalization and is compatible with a wide range of amine-containing molecules and proteins. Additionally, a reversible C-terminal de-functionalization is found by incubating the C-terminal modified proteins with cysteine protease domain and InsP6, providing a tool for protein functionalization and de-functionalization. Last, various applications of protein C-terminal functionalization are provided in this work, as demonstrated by the site-specific assembly of nanobody drug conjugates, the construction of a bifunctional antibody, the C-terminal fluorescent labeling, and the C-terminal transpeptidation and glycosylation.
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Affiliation(s)
- Yue Zeng
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Wei Shi
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
| | - Zhi Liu
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, No. 138 Xianlin Rd, Nanjing, 210023, China
| | - Hao Xu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, No. 138 Xianlin Rd, Nanjing, 210023, China
| | - Liya Liu
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
| | - Jiaying Hang
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
| | - Yongqin Wang
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
| | - Mengru Lu
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
| | - Wei Zhou
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
| | - Wei Huang
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, No. 138 Xianlin Rd, Nanjing, 210023, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
| | - Feng Tang
- State Key Laboratory of Drug Research, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China.
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4
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Teng S, Zhang Z, Li B, Li L, Tan MCL, Jia Z, Loh TP. Thiol-Specific Silicon-Containing Conjugating Reagent: β-Silyl Alkynyl Carbonyl Compounds. Angew Chem Int Ed Engl 2023; 62:e202311906. [PMID: 37721855 DOI: 10.1002/anie.202311906] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 09/20/2023]
Abstract
Site-specific modification of thiol-containing biomolecules has been recognized as a versatile and powerful strategy for probing our biological systems and discovering novel therapeutics. The addition of lipophilic silicon moiety opens up new avenues for multi-disciplinary research with broad applications in both the medicinal and material sciences. However, adhering to the strict biocompatibility requirements, and achieving the introduction of labile silicon handle and high chemo-selectivity have been formidable. In this paper, we report silicon-based conjugating reagents including β-trialkylsilyl and silyl ether-tethered alkynones that selectively react with thiols under physiological conditions. The pH-neutral, metal-free and additive-free reaction yields stable products with broad substrate compatibility and full retention of silicon handles in most cases. Besides simple aliphatic and aromatic thiols, this approach is applicable in the labeling of thiols present in proteins, sugars and payloads, thereby expanding the toolbox of thiol conjugation.
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Affiliation(s)
- Shenghan Teng
- Strait Laboratory of Flexible Electronics (SLoFE), Strait Institute of Flexible Electronics (SIFE, Future Technologies), Fujian Normal University, Fuzhou, China
- Division of Chemistry and Biological Chemistry, School of Chemistry Chemical Engineering & Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
| | - Zhenguo Zhang
- Division of Chemistry and Biological Chemistry, School of Chemistry Chemical Engineering & Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
| | - Bohan Li
- Division of Chemistry and Biological Chemistry, School of Chemistry Chemical Engineering & Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
| | - Lanyang Li
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Melinda Chor Li Tan
- Division of Chemistry and Biological Chemistry, School of Chemistry Chemical Engineering & Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
| | - Zhenhua Jia
- Henan University of Technology, 100 Lianhua Street, Zhongyuan District, Zhengzhou, 450001, China
| | - Teck-Peng Loh
- Henan University of Technology, 100 Lianhua Street, Zhongyuan District, Zhengzhou, 450001, China
- Division of Chemistry and Biological Chemistry, School of Chemistry Chemical Engineering & Biotechnology, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
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5
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Fischer NH, Oliveira MT, Diness F. Chemical modification of proteins - challenges and trends at the start of the 2020s. Biomater Sci 2023; 11:719-748. [PMID: 36519403 DOI: 10.1039/d2bm01237e] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribosomally expressed proteins perform multiple, versatile, and specialized tasks throughout Nature. In modern times, chemically modified proteins, including improved hormones, enzymes, and antibody-drug-conjugates have become available and have found advanced industrial and pharmaceutical applications. Chemical modification of proteins is used to introduce new functionalities, improve stability or drugability. Undertaking chemical reactions with proteins without compromising their native function is still a core challenge as proteins are large conformation dependent multifunctional molecules. Methods for functionalization ideally should be chemo-selective, site-selective, and undertaken under biocompatible conditions in aqueous buffer to prevent denaturation of the protein. Here the present challenges in the field are discussed and methods for modification of the 20 encoded amino acids as well as the N-/C-termini and protein backbone are presented. For each amino acid, common and traditional modification methods are presented first, followed by more recent ones.
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Affiliation(s)
- Niklas Henrik Fischer
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Maria Teresa Oliveira
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Frederik Diness
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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6
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Wan C, Hou Z, Yang D, Zhou Z, Xu H, Wang Y, Dai C, Liang M, Meng J, Chen J, Yin F, Wang R, Li Z. The thiol-sulfoxonium ylide photo-click reaction for bioconjugation. Chem Sci 2023; 14:604-612. [PMID: 36741507 PMCID: PMC9847666 DOI: 10.1039/d2sc05650j] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/01/2022] [Indexed: 12/04/2022] Open
Abstract
Visible-light-mediated methods were heavily studied as a useful tool for cysteine-selective bio-conjugation; however, many current methods suffer from bio-incompatible reaction conditions and slow kinetics. To address these challenges, herein, we report a transition metal-free thiol-sulfoxonium ylide photo-click reaction that enables bioconjugation under bio-compatible conditions. The reaction is highly cysteine-selective and generally finished within minutes with naturally occurring riboflavin derivatives as organic photocatalysts. The catalysts and substrates are readily accessible and bench stable and have satisfactory water solubility. As a proof-of-concept study, the reaction was smoothly applied in chemo-proteomic analysis, which provides efficient tools to explore the druggable content of the human proteome.
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Affiliation(s)
- Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhen518055P. R. China
| | - Zhanfeng Hou
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhen518055P. R. China
| | - Dongyan Yang
- College of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and EngineeringGuangzhou510225P. R. China
| | - Ziyuan Zhou
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhen518116P. R. China
| | - Hongkun Xu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhen518055P. R. China
| | - Yuena Wang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhen518055P. R. China
| | - Chuan Dai
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhen518055P. R. China
| | - Mingchan Liang
- Pingshan Translational Medicine Center, Shenzhen Bay LaboratoryShenzhen518118P. R. China
| | - Jun Meng
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhen518116P. R. China
| | - Jiean Chen
- Pingshan Translational Medicine Center, Shenzhen Bay LaboratoryShenzhen518118P. R. China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay LaboratoryShenzhen518118P. R. China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay LaboratoryShenzhen518118P. R. China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhen518055P. R. China,Pingshan Translational Medicine Center, Shenzhen Bay LaboratoryShenzhen518118P. R. China
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7
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Stieger CE, Park Y, de Geus MAR, Kim D, Huhn C, Slenczka JS, Ochtrop P, Müchler JM, Süssmuth RD, Broichhagen J, Baik M, Hackenberger CPR. DFT-Guided Discovery of Ethynyl-Triazolyl-Phosphinates as Modular Electrophiles for Chemoselective Cysteine Bioconjugation and Profiling. Angew Chem Int Ed Engl 2022; 61:e202205348. [PMID: 35792701 PMCID: PMC9804898 DOI: 10.1002/anie.202205348] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Indexed: 01/09/2023]
Abstract
We report the density functional theory (DFT) guided discovery of ethynyl-triazolyl-phosphinates (ETPs) as a new class of electrophilic warheads for cysteine selective bioconjugation. By using CuI -catalysed azide alkyne cycloaddition (CuAAC) in aqueous buffer, we were able to access a variety of functional electrophilic building blocks, including proteins, from diethynyl-phosphinate. ETP-reagents were used to obtain fluorescent peptide-conjugates for receptor labelling on live cells and a stable and a biologically active antibody-drug-conjugate. Moreover, we were able to incorporate ETP-electrophiles into an azide-containing ubiquitin under native conditions and demonstrate their potential in protein-protein conjugation. Finally, we showcase the excellent cysteine-selectivity of this new class of electrophile in mass spectrometry based, proteome-wide cysteine profiling, underscoring the applicability in homogeneous bioconjugation strategies to connect two complex biomolecules.
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Affiliation(s)
- Christian E. Stieger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany,Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Yerin Park
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea,Center for Catalytic Hydrocarbon FunctionalizationsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
| | - Mark A. R. de Geus
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
| | - Dongju Kim
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea,Center for Catalytic Hydrocarbon FunctionalizationsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
| | - Christiane Huhn
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany,Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - J. Sophia Slenczka
- Institut für ChemieTechnische Universität BerlinStrasse des 17. Juni 12410623BerlinGermany
| | - Philipp Ochtrop
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany,Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Judith M. Müchler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany,Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Roderich D. Süssmuth
- Institut für ChemieTechnische Universität BerlinStrasse des 17. Juni 12410623BerlinGermany
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
| | - Mu‐Hyun Baik
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea,Center for Catalytic Hydrocarbon FunctionalizationsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany,Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
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8
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Keijzer JF, Zuilhof H, Albada B. Calibrating Catalytic DNA Nanostructures for Site‐Selective Protein Modification**. Chemistry 2022; 28:e202200895. [PMID: 35726668 PMCID: PMC9546015 DOI: 10.1002/chem.202200895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Indexed: 12/04/2022]
Abstract
Many biomedical fields rely on proteins that are selectively modified. These can be attached using reactive or catalytic moieties, but the position where these moieties are attached is often poorly controlled. We assessed how catalyst position affects the efficiency and selectivity of protein modification. For this, we anchored a template DNA strand to three different proteins, which were subsequently hybridized to DNA strands that contained catalysts at different positions. We found a strong correlation between the catalyst‐to‐protein distance and the efficiency of protein modification for acyl transfer catalysts, which operate via a covalently bound reactant intermediate. Additionally, we found that the catalyst's distance and orientation with respect to the protein surface, also influences its site‐selectivity. A catalyst operating with unbound reactant intermediates showed only enhanced efficiency. Our results are rationalized using computational simulations, showing that one‐point anchoring of the DNA construct leads to notable differences in the site of modification.
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Affiliation(s)
- Jordi F. Keijzer
- Laboratory of Organic Chemistry Wageningen University & Research Stippeneng 4 6708 WE Wageningen The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry Wageningen University & Research Stippeneng 4 6708 WE Wageningen The Netherlands
- School of Pharmaceutical Science & Technology Tianjin University 92 Weijin Road, Nankai District Tianjin 300072 P. R. China
- Department of Chemical and Materials Engineering Faculty of Engineering King Abdulaziz University 21589 Jeddah Saudi Arabia
| | - Bauke Albada
- Laboratory of Organic Chemistry Wageningen University & Research Stippeneng 4 6708 WE Wageningen The Netherlands
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9
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Taylor RJ, Geeson MB, Journeaux T, Bernardes GJL. Chemical and Enzymatic Methods for Post-Translational Protein-Protein Conjugation. J Am Chem Soc 2022; 144:14404-14419. [PMID: 35912579 PMCID: PMC9389620 DOI: 10.1021/jacs.2c00129] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fusion proteins play an essential role in the biosciences but suffer from several key limitations, including the requirement for N-to-C terminal ligation, incompatibility of constituent domains, incorrect folding, and loss of biological activity. This perspective focuses on chemical and enzymatic approaches for the post-translational generation of well-defined protein-protein conjugates, which overcome some of the limitations faced by traditional fusion techniques. Methods discussed range from chemical modification of nucleophilic canonical amino acid residues to incorporation of unnatural amino acid residues and a range of enzymatic methods, including sortase-mediated ligation. Through summarizing the progress in this rapidly growing field, the key successes and challenges associated with using chemical and enzymatic approaches are highlighted and areas requiring further development are discussed.
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Affiliation(s)
- Ross J Taylor
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Michael B Geeson
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Toby Journeaux
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
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10
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Taylor RJ, Aguilar Rangel M, Geeson MB, Sormanni P, Vendruscolo M, Bernardes GJL. π-Clamp-Mediated Homo- and Heterodimerization of Single-Domain Antibodies via Site-Specific Homobifunctional Conjugation. J Am Chem Soc 2022; 144:13026-13031. [PMID: 35834748 PMCID: PMC9335888 DOI: 10.1021/jacs.2c04747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Post-translational protein–protein conjugation
produces
bioconjugates that are unavailable via genetic fusion approaches.
A method for preparing protein–protein conjugates using π-clamp-mediated
cysteine arylation with pentafluorophenyl sulfonamide functional groups
is described. Two computationally designed antibodies targeting the
SARS-CoV-2 receptor binding domain were produced (KD = 146, 581 nM) with a π-clamp sequence near the
C-terminus and dimerized using this method to provide a 10–60-fold
increase in binding (KD = 8–15
nM). When two solvent-exposed cysteine residues were present on the
second protein domain, the π-clamp cysteine residue was selectively
modified over an Asp-Cys-Glu cysteine residue, allowing for subsequent
small-molecule conjugation. With this strategy, we build molecule–protein–protein
conjugates with complete chemical control over the sites of modification.
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Affiliation(s)
- Ross J Taylor
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Mauricio Aguilar Rangel
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Michael B Geeson
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Gonçalo J L Bernardes
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
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11
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Stieger CE, Park Y, de Geus MAR, Kim D, Huhn C, Slenczka JS, Ochtrop P, Müchler JM, Süssmuth R, Broichhagen J, Baik MH, Hackenberger C. DFT‐Guided Discovery of Ethynyl‐Triazolyl‐Phosphinates as Modular Electrophiles for Chemoselective Cysteine Bioconjugation and Profiling. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Christian Ewald Stieger
- Leibniz Institute for Molecular Pharmacology: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chemical Biology GERMANY
| | - Yerin Park
- KAIST: Korea Advanced Institute of Science and Technology Department of Chemistry KOREA, REPUBLIC OF
| | - Mark A. R. de Geus
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin eV: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chemical Biology GERMANY
| | - Dongju Kim
- KAIST: Korea Advanced Institute of Science and Technology Department of Chemistry KOREA, REPUBLIC OF
| | - Christiane Huhn
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin eV: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chem Bio Probes GERMANY
| | - Julie Sophia Slenczka
- Technische Universität Berlin: Technische Universitat Berlin Institut für Chemie GERMANY
| | - Philipp Ochtrop
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin eV: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chemical Biology GERMANY
| | - Judith Maria Müchler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin eV: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chemical Biology GERMANY
| | - Roderich Süssmuth
- Technische Universität Berlin: Technische Universitat Berlin Institut für Chemie GERMANY
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin eV: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chem Bio Probes GERMANY
| | - Mu-Hyun Baik
- KAIST: Korea Advanced Institute of Science and Technology Department of Chemistry KOREA, REPUBLIC OF
| | - Christian Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Deptm. of Chemical Biology Robert-Roessle Str. 10 13125 Berlin GERMANY
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12
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Wang C, Zhao Y, Zhao J. Recent Advances in Chemical Protein Modification via Cysteine. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202203008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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13
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Shen MH, Wang YJ, Wang Y, Zhou Y, Gu J, Liu XQ, Guo J, Ouyang M, Deng L, Xu HD. α-Vinyl azide–cysteine click coupling reaction enabled bioorthogonal peptide/protein modification. Org Chem Front 2022. [DOI: 10.1039/d2qo00736c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
α-Alkyl and α-aryl vinyl azides were found to be able to couple with cysteine-derived alkyl thiols chemoselectively under mild conditions, providing the corresponding β-ketosulfides with simultaneous extrusion of N2 and ammonia.
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Affiliation(s)
- Mei-Hua Shen
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Yu-Jiao Wang
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Yong Wang
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Ying Zhou
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Jie Gu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Xiao-Qian Liu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Jia Guo
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Mingxing Ouyang
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Linhong Deng
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Hua-Dong Xu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
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14
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Keijzer JF, Albada B. DNA-assisted site-selective protein modification. Biopolymers 2021; 113:e23483. [PMID: 34878181 PMCID: PMC9285461 DOI: 10.1002/bip.23483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/09/2022]
Abstract
Protein modification is important for various types of biomedical research, including proteomics and therapeutics. Many methodologies for protein modification exist, but not all possess the required level of efficiency and site selectivity. This review focuses on the use of DNA to achieve the desired conversions and levels of accuracy in protein modification by using DNA (i) as a template to help concentrate dilute reactants, (ii) as a guidance system to achieve selectivity by binding specific proteins, and (iii) even as catalytic entity or construct to enhance protein modification reactions.
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Affiliation(s)
- Jordi F Keijzer
- Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, The Netherlands
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, The Netherlands
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