1
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Burger N, Chouchani ET. A new era of cysteine proteomics - Technological advances in thiol biology. Curr Opin Chem Biol 2024; 79:102435. [PMID: 38382148 DOI: 10.1016/j.cbpa.2024.102435] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024]
Abstract
Cysteines are amenable to a diverse set of modifications that exhibit critical regulatory functions over the proteome and thereby control a wide range of cellular processes. Proteomic technologies have emerged as a powerful strategy to interrogate cysteine modifications across the proteome. Recent advancements in enrichment strategies, multiplexing capabilities and increased analytical sensitivity have enabled deeper quantitative cysteine profiling, capturing a substantial proportion of the cysteine proteome. This is complemented by a rapidly growing repertoire of analytical strategies illuminating the diverse landscape of cysteine modifications. Cysteine chemoproteomics technologies have evolved into a powerful strategy to facilitate the development of covalent drugs, opening unprecedented opportunities to target the extensive undrugged proteome. Herein we review recent technological and scientific advances that shape the cysteine proteomics field.
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Affiliation(s)
- Nils Burger
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
| | - Edward T Chouchani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
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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] [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: 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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Chauhan P, V R, Kumar M, Molla R, Mishra SD, Basa S, Rai V. Chemical technology principles for selective bioconjugation of proteins and antibodies. Chem Soc Rev 2024; 53:380-449. [PMID: 38095227 DOI: 10.1039/d3cs00715d] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Proteins are multifunctional large organic compounds that constitute an essential component of a living system. Hence, control over their bioconjugation impacts science at the chemistry-biology-medicine interface. A chemical toolbox for their precision engineering can boost healthcare and open a gateway for directed or precision therapeutics. Such a chemical toolbox remained elusive for a long time due to the complexity presented by the large pool of functional groups. The precise single-site modification of a protein requires a method to address a combination of selectivity attributes. This review focuses on guiding principles that can segregate them to simplify the task for a chemical method. Such a disintegration systematically employs a multi-step chemical transformation to deconvolute the selectivity challenges. It constitutes a disintegrate (DIN) theory that offers additional control parameters for tuning precision in protein bioconjugation. This review outlines the selectivity hurdles faced by chemical methods. It elaborates on the developments in the perspective of DIN theory to demonstrate simultaneous regulation of reactivity, chemoselectivity, site-selectivity, modularity, residue specificity, and protein specificity. It discusses the progress of such methods to construct protein and antibody conjugates for biologics, including antibody-fluorophore and antibody-drug conjugates (AFCs and ADCs). It also briefs how this knowledge can assist in developing small molecule-based covalent inhibitors. In the process, it highlights an opportunity for hypothesis-driven routes to accelerate discoveries of selective methods and establish new targetome in the precision engineering of proteins and antibodies.
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Affiliation(s)
- Preeti Chauhan
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Ragendu V
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Mohan Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Rajib Molla
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Surya Dev Mishra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Sneha Basa
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
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4
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Burton NR, Polasky DA, Shikwana F, Ofori S, Yan T, Geiszler DJ, Veiga Leprevost FD, Nesvizhskii AI, Backus KM. Solid-Phase Compatible Silane-Based Cleavable Linker Enables Custom Isobaric Quantitative Chemoproteomics. J Am Chem Soc 2023; 145:21303-21318. [PMID: 37738129 DOI: 10.1021/jacs.3c05797] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Mass spectrometry-based chemoproteomics has emerged as an enabling technology for functional biology and drug discovery. To address limitations of established chemoproteomics workflows, including cumbersome reagent synthesis and low throughput sample preparation, here, we established the silane-based cleavable isotopically labeled proteomics (sCIP) method. The sCIP method is enabled by a high yielding and scalable route to dialkoxydiphenylsilane fluorenylmethyloxycarbonyl (DADPS-Fmoc)-protected amino acid building blocks, which enable the facile synthesis of customizable, isotopically labeled, and chemically cleavable biotin capture reagents. sCIP is compatible with both MS1- and MS2-based quantitation, and the sCIP-MS2 method is distinguished by its click-assembled isobaric tags in which the reporter group is encoded in the sCIP capture reagent and balancer in the pan cysteine-reactive probe. The sCIP-MS2 workflow streamlines sample preparation with early stage isobaric labeling and sample pooling, allowing for high coverage and increased sample throughput via customized low cost six-plex sample multiplexing. When paired with a custom FragPipe data analysis workflow and applied to cysteine-reactive fragment screens, sCIP proteomics revealed established and unprecedented cysteine-ligand pairs, including the discovery that mitochondrial uncoupling agent FCCP acts as a covalent-reversible cysteine-reactive electrophile.
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Affiliation(s)
- Nikolas R Burton
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Flowreen Shikwana
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Samuel Ofori
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Tianyang Yan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Daniel J Geiszler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Keriann M Backus
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California 90095, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California 90095, United States
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5
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Liu XY, Ji X, Heinis C, Waser J. Peptide-Hypervalent Iodine Reagent Chimeras: Enabling Peptide Functionalization and Macrocyclization. Angew Chem Int Ed Engl 2023; 62:e202306036. [PMID: 37311172 DOI: 10.1002/anie.202306036] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 04/29/2023] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 06/15/2023]
Abstract
Herein, we report a novel strategy for the modification of peptides based on the introduction of highly reactive hypervalent iodine reagents-ethynylbenziodoxolones (EBXs)-onto peptides. These peptide-EBXs can be readily accessed, by both solution- and solid-phase peptide synthesis (SPPS). They can be used to couple the peptide to other peptides or a protein through reaction with Cys, leading to thioalkynes in organic solvents and hypervalent iodine adducts in water buffer. Furthermore, a photocatalytic decarboxylative coupling to the C-terminus of peptides was developed using an organic dye and was also successful in an intramolecular fashion, leading to macrocyclic peptides with unprecedented crosslinking. A rigid linear aryl alkyne linker was essential to achieve high affinity for Keap1 at the Nrf2 binding site with potential protein-protein interaction inhibition.
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Affiliation(s)
- Xing-Yu Liu
- Laboratory of Catalysis and Organic Synthesis, Ecole Polytechnique Fédérale de Lausanne, EPFL, 1015, Lausanne, Switzerland
| | - Xinjian Ji
- Laboratory of Therapeutic Proteins and Peptides, Ecole Polytechnique Fédérale de Lausanne, EPFL, 1015, Lausanne, Switzerland
| | - Christian Heinis
- Laboratory of Therapeutic Proteins and Peptides, Ecole Polytechnique Fédérale de Lausanne, EPFL, 1015, Lausanne, Switzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic Synthesis, Ecole Polytechnique Fédérale de Lausanne, EPFL, 1015, Lausanne, Switzerland
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6
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Abstract
The amidated peptides are an important class of biologically active compounds due to their unique biological properties and wide applications as potential peptide drugs and biomarkers. Despite the abundance of free amide motifs (Asn, Gln, and C-terminal amide) in native peptides, late-stage modification of the amide unit in naturally occurring peptides remains very rare because of the intrinsically weak nucleophilicity of amides and the interference of multiple competing nucleophilic residues, which generally lead to undesired side reactions. Herein, chemoselective arylation of amides in unprotected polypeptides has been developed under an air atmosphere to afford the N-aryl amide peptides bearing various functional motifs. Its success relies on the combination of gold catalysis and silver salt to differentiate the relative inert amide among a collection of reactive nucleophilic amino acid residues (e.g., -NH2, -OH, and -COOH), favoring the C-N bond coupling toward amides over other more nucleophilic groups. Experimental and DFT studies reveal a crucial role of the silver cation, which serves as a transient coordination mask of the more reactive reaction sites, overcoming the inherently low reactivity of amides. The excellent biocompatibility of this strategy has been applied to functionalize a wide range of peptide drugs and complex peptides. The application could be further extended to peptide labeling and peptide stapling.
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Affiliation(s)
- Weipeng Li
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yu Chen
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yinghan Chen
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Siyu Xia
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wenju Chang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Chengjian Zhu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Green Catalysis Center, College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jin Xie
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- State Key Laboratory of Chemistry and Utilization of Carbon-Based Energy Resources, College of Chemistry, Xinjiang University, Urumqi 830017, China
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7
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Abstract
The high selectivity and affinity of antibodies toward their antigens have made them a highly valuable tool in disease therapy, diagnosis, and basic research. A plethora of chemical and genetic approaches have been devised to make antibodies accessible to more "undruggable" targets and equipped with new functions of illustrating or regulating biological processes more precisely. In this Review, in addition to introducing how naked antibodies and various antibody conjugates (such as antibody-drug conjugates, antibody-oligonucleotide conjugates, antibody-enzyme conjugates, etc.) work in therapeutic applications, special attention has been paid to how chemistry tools have helped to optimize the therapeutic outcome (i.e., with enhanced efficacy and reduced side effects) or facilitate the multifunctionalization of antibodies, with a focus on emerging fields such as targeted protein degradation, real-time live-cell imaging, catalytic labeling or decaging with spatiotemporal control as well as the engagement of antibodies inside cells. With advances in modern chemistry and biotechnology, well-designed antibodies and their derivatives via size miniaturization or multifunctionalization together with efficient delivery systems have emerged, which have gradually improved our understanding of important biological processes and paved the way to pursue novel targets for potential treatments of various diseases.
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Affiliation(s)
- Linghui Qian
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xuefen Lin
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xue Gao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Rizwan Ullah Khan
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jia-Yu Liao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shubo Du
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544
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Abstract
Although alkynes are one of the smallest functional groups, they are among the most versatile building blocks for organic chemistry, with applications ranging from biochemistry to material sciences. Alkynylation reactions have traditionally relied on the use of acetylenes as nucleophiles. The discovery and development of ethynyl hypervalent iodine reagents have allowed to greatly expand the transfer of alkynes as electrophilic synthons. In this feature article the progress in the field since 2018 will be presented. After a short introduction on alkynylation reactions and hypervalent iodine reagents, the developments in the synthesis of alkynyl hypervalent iodine reagents will be discussed. Their recent use in base-mediated and transition-metal catalyzed alkynylations will be described. Progress in radical-based alkynylations and atom-economical transformations will then be presented.
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Affiliation(s)
- Eliott Le Du
- Laboratory of Catalysis and Organic Synthesis, Institute of Chemical Sciences and Engineering École Polytechnique Fédérale de Lausanne EPFL, SB ISIC, LCSO, BCH 4306, 1015, Lausanne, Switzerland.
| | - Jérôme Waser
- Laboratory of Catalysis and Organic Synthesis, Institute of Chemical Sciences and Engineering École Polytechnique Fédérale de Lausanne EPFL, SB ISIC, LCSO, BCH 4306, 1015, Lausanne, Switzerland.
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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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: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Abstract
Cysteine bioconjugation serves as a powerful tool in biological research and has been widely used for chemical modification of proteins, constructing antibody-drug conjugates, and enabling cell imaging studies. Cysteine conjugation reactions with fast kinetics and exquisite selectivity have been under heavy pursuit as they would allow clean protein modification with just stoichiometric amounts of reagents, which minimizes side reactions, simplifies purification and broadens functional group tolerance. In this concept, we summarize the recent advances in fast cysteine bioconjugation, and discuss the mechanism and chemical principles that underlie the high efficiencies of the newly developed cysteine reactive reagents.
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Affiliation(s)
- Fa-Jie Chen
- Department of Chemistry, Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Jianmin Gao
- Department of Chemistry, Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
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12
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Dowman LJ, Kulkarni SS, Alegre-Requena JV, Giltrap AM, Norman AR, Sharma A, Gallegos LC, Mackay AS, Welegedara AP, Watson EE, van Raad D, Niederacher G, Huhmann S, Proschogo N, Patel K, Larance M, Becker CFW, Mackay JP, Lakhwani G, Huber T, Paton RS, Payne RJ. Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine. Nat Commun 2022; 13:6885. [PMID: 36371402 PMCID: PMC9653470 DOI: 10.1038/s41467-022-34530-z] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/27/2022] [Indexed: 11/15/2022] Open
Abstract
The importance of modified peptides and proteins for applications in drug discovery, and for illuminating biological processes at the molecular level, is fueling a demand for efficient methods that facilitate the precise modification of these biomolecules. Herein, we describe the development of a photocatalytic method for the rapid and efficient dimerization and site-specific functionalization of peptide and protein diselenides. This methodology, dubbed the photocatalytic diselenide contraction, involves irradiation at 450 nm in the presence of an iridium photocatalyst and a phosphine and results in rapid and clean conversion of diselenides to reductively stable selenoethers. A mechanism for this photocatalytic transformation is proposed, which is supported by photoluminescence spectroscopy and density functional theory calculations. The utility of the photocatalytic diselenide contraction transformation is highlighted through the dimerization of selenopeptides, and by the generation of two families of protein conjugates via the site-selective modification of calmodulin containing the 21st amino acid selenocysteine, and the C-terminal modification of a ubiquitin diselenide.
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Affiliation(s)
- Luke J. Dowman
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Sameer S. Kulkarni
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Juan V. Alegre-Requena
- grid.47894.360000 0004 1936 8083Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872 USA
| | - Andrew M. Giltrap
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Alexander R. Norman
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Ashish Sharma
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence in Exciton Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Liliana C. Gallegos
- grid.47894.360000 0004 1936 8083Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872 USA
| | - Angus S. Mackay
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Adarshi P. Welegedara
- grid.1001.00000 0001 2180 7477Research School of Chemistry, Australian National University, Canberra, ACT 2601 Australia
| | - Emma E. Watson
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Damian van Raad
- grid.1001.00000 0001 2180 7477Research School of Chemistry, Australian National University, Canberra, ACT 2601 Australia
| | - Gerhard Niederacher
- grid.10420.370000 0001 2286 1424Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Susanne Huhmann
- grid.10420.370000 0001 2286 1424Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Nicholas Proschogo
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia
| | - Karishma Patel
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006 Australia
| | - Mark Larance
- grid.1013.30000 0004 1936 834XCharles Perkins Centre and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006 Australia
| | - Christian F. W. Becker
- grid.10420.370000 0001 2286 1424Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Joel P. Mackay
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006 Australia
| | - Girish Lakhwani
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence in Exciton Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Thomas Huber
- grid.1001.00000 0001 2180 7477Research School of Chemistry, Australian National University, Canberra, ACT 2601 Australia
| | - Robert S. Paton
- grid.47894.360000 0004 1936 8083Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872 USA
| | - Richard J. Payne
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
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13
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Declas N, Maynard JRJ, Menin L, Gasilova N, Götze S, Sprague JL, Stallforth P, Matile S, Waser J. Tyrosine bioconjugation with hypervalent iodine. Chem Sci 2022; 13:12808-12817. [PMID: 36519034 PMCID: PMC9645396 DOI: 10.1039/d2sc04558c] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/03/2022] [Indexed: 01/24/2023] Open
Abstract
Hypervalent iodine reagents have recently emerged as powerful tools for late-stage peptide and protein functionalization. Herein we report a tyrosine bioconjugation methodology for the introduction of hypervalent iodine onto biomolecules under physiological conditions. Tyrosine residues were engaged in a selective addition onto the alkynyl bond of ethynylbenziodoxolones (EBX), resulting in stable vinylbenziodoxolones (VBX) bioconjugates. The methodology was successfully applied to peptides and proteins and tolerated all other nucleophilic residues, with the exception of cysteine. The generated VBX were further functionalized by palladium-catalyzed cross-coupling and azide-alkyne cycloaddition reactions. The method could be successfully used to modify bioactive natural products and native streptavidin to enable thiol-mediated cellular uptake.
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Affiliation(s)
- Nina Declas
- Laboratory of Catalysis and Organic Synthesis, Institut des Sciences et Ingénierie Chimique, Ecole Polytechnique Fédérale de LausanneCH-1015LausanneSwitzerland
| | - John R. J. Maynard
- Department of Organic Chemistry, University of Geneva1211 GenevaSwitzerland
| | - Laure Menin
- Institut des Sciences et Ingénierie Chimique, Ecole Polytechnique Fédérale de Lausanne, EPFL1015 LausanneSwitzerland
| | - Natalia Gasilova
- Institut des Sciences et Ingénierie Chimique, Ecole Polytechnique Fédérale de Lausanne, EPFL1015 LausanneSwitzerland
| | - Sebastian Götze
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI)07745 JenaGermany
| | - Jakob L. Sprague
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI)07745 JenaGermany
| | - Pierre Stallforth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI)07745 JenaGermany
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva1211 GenevaSwitzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic Synthesis, Institut des Sciences et Ingénierie Chimique, Ecole Polytechnique Fédérale de LausanneCH-1015LausanneSwitzerland
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14
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Li J, Zhou C, Liang H, Guo XQ, Chen LM, Kang TR. Direct One‐Pot Construction of Diaryl Thioethers and 1,3‐Diynes through a Copper(I)‐Catalyzed Reaction of λ3‐Iodanes with Thiophenols. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jun Li
- Chengdu University School of Pharmacy CHINA
| | - Chuang Zhou
- Chengdu University School of Food and Biological Engineering CHINA
| | - Hong Liang
- Chengdu University School of Pharmacy CHINA
| | | | - Lian-Mei Chen
- Chengdu University School of Food and Biological Engineering CHINA
| | - Tai-Ran Kang
- Chengdu University School of Food and Biological Engineering No 1, SHIDA ROAD 610106 Chengdu CHINA
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15
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He SD, Guo XQ, Li J, Zhang YC, Chen LM, Kang TR. Base‐Promoted Reaction of Phenols with Spirocylic λ3‐iodanes: Access to both 2‐Iodovinyl Aryl Ethers and Diaryl Ethers. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Shun-Dong He
- Chengdu University Sichuan Industrial Institute of Antibiotics, School of Pharmacy Chengdu CHINA
| | - Xiao-Qiang Guo
- Chengdu University Sichuan Industrial Institute of Antibiotics, School of Pharmacy CHINA
| | - Jun Li
- Chengdu University Sichuan Industrial Institute of Antibiotics, School of Pharmacy CHINA
| | - Yu-Cheng Zhang
- Chengdu University Sichuan Industrial Institute of Antibiotics, School of Pharmacy CHINA
| | - Lian-Mei Chen
- Chengdu University School of Food and Biological Engineering CHINA
| | - Tai-Ran Kang
- Chengdu University School of Food and Biological Engineering No 1, SHIDA ROAD 610106 Chengdu CHINA
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16
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Abstract
Tools that facilitate the chemical modification of peptides and proteins are gaining an increasing amount of interest across many avenues of chemical biology as they enable a plethora of therapeutic, imaging and diagnostic applications. Cysteine residues and disulfide bonds have been highlighted as appealing targets for modification due to the highly homogenous nature of the products that can be formed through their site-selective modification. Amongst the reagents available for the site-selective modification of cysteine(s)/disulfide(s), pyridazinediones (PDs) have played a particularly important and enabling role. In this review, we outline the unique chemical features that make PDs especially well-suited to cysteine/disulfide modification on a wide variety of proteins and peptides, as well as provide context as to the problems solved (and applications enabled) by this technology.
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Affiliation(s)
- Calise Bahou
- UCL Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, UK.
| | - Vijay Chudasama
- UCL Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, UK.
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17
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Allouche EMD, Grinhagena E, Waser J. Hypervalent Iodine‐Mediated Late‐Stage Peptide and Protein Functionalization. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Emmanuelle M. D. Allouche
- Laboratory of Catalysis and Organic Synthesis Institute of Chemical Sciences and Engineering Ecole Polytechnique Fédérale de Lausanne, EPFL, SB ISIC, LCSO, BCH 1402 1015 Lausanne Switzerland
| | - Elija Grinhagena
- Laboratory of Catalysis and Organic Synthesis Institute of Chemical Sciences and Engineering Ecole Polytechnique Fédérale de Lausanne, EPFL, SB ISIC, LCSO, BCH 1402 1015 Lausanne Switzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic Synthesis Institute of Chemical Sciences and Engineering Ecole Polytechnique Fédérale de Lausanne, EPFL, SB ISIC, LCSO, BCH 1402 1015 Lausanne Switzerland
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18
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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19
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Sornay C, Vaur V, Wagner A, Chaubet G. An overview of chemo- and site-selectivity aspects in the chemical conjugation of proteins. R Soc Open Sci 2022; 9:211563. [PMID: 35116160 PMCID: PMC8790347 DOI: 10.1098/rsos.211563] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/20/2021] [Indexed: 05/03/2023]
Abstract
The bioconjugation of proteins-that is, the creation of a covalent link between a protein and any other molecule-has been studied for decades, partly because of the numerous applications of protein conjugates, but also due to the technical challenge it represents. Indeed, proteins possess inner physico-chemical properties-they are sensitive and polynucleophilic macromolecules-that make them complex substrates in conjugation reactions. This complexity arises from the mild conditions imposed by their sensitivity but also from selectivity issues, viz the precise control of the conjugation site on the protein. After decades of research, strategies and reagents have been developed to address two aspects of this selectivity: chemoselectivity-harnessing the reacting chemical functionality-and site-selectivity-controlling the reacting amino acid residue-most notably thanks to the participation of synthetic chemistry in this effort. This review offers an overview of these chemical bioconjugation strategies, insisting on those employing native proteins as substrates, and shows that the field is active and exciting, especially for synthetic chemists seeking new challenges.
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Affiliation(s)
- Charlotte Sornay
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Valentine Vaur
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
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20
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Abegg D, Tomanik M, Qiu N, Pechalrieu D, Shuster A, Commare B, Togni A, Herzon SB, Adibekian A. Chemoproteomic Profiling by Cysteine Fluoroalkylation Reveals Myrocin G as an Inhibitor of the Nonhomologous End Joining DNA Repair Pathway. J Am Chem Soc 2021; 143:20332-20342. [PMID: 34817176 DOI: 10.1021/jacs.1c09724] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chemoproteomic profiling of cysteines has emerged as a powerful method for screening the proteome-wide targets of cysteine-reactive fragments, drugs, and natural products. Herein, we report the development and an in-depth evaluation of a tetrafluoroalkyl benziodoxole (TFBX) as a cysteine-selective chemoproteomic probe. We show that this probe features numerous key improvements compared to the traditionally used cysteine-reactive probes, including a superior target occupancy, faster labeling kinetics, and broader proteomic coverage, thus enabling profiling of cysteines directly in live cells. In addition, the fluorine "signature" of probe 7 constitutes an additional advantage resulting in a more confident adduct-amino acid site assignment in mass-spectrometry-based identification workflows. We demonstrate the utility of our new probe for proteome-wide target profiling by identifying the cellular targets of (-)-myrocin G, an antiproliferative fungal natural product with a to-date unknown mechanism of action. We show that this natural product and a simplified analogue target the X-ray repair cross-complementing protein 5 (XRCC5), an ATP-dependent DNA helicase that primes DNA repair machinery for nonhomologous end joining (NHEJ) upon DNA double-strand breaks, making them the first reported inhibitors of this biomedically highly important protein. We further demonstrate that myrocins disrupt the interaction of XRCC5 with DNA leading to sensitization of cancer cells to the chemotherapeutic agent etoposide as well as UV-light-induced DNA damage. Altogether, our next-generation cysteine-reactive probe enables broader and deeper profiling of the cysteinome, rendering it a highly attractive tool for elucidation of targets of electrophilic small molecules.
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Affiliation(s)
- Daniel Abegg
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Martin Tomanik
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Nan Qiu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Dany Pechalrieu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Anton Shuster
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Bruno Commare
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Antonio Togni
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States.,Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - Alexander Adibekian
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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21
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Byrne SA, Bedding MJ, Corcilius L, Ford DJ, Zhong Y, Franck C, Larance M, Mackay JP, Payne RJ. Late-stage modification of peptides and proteins at cysteine with diaryliodonium salts. Chem Sci 2021; 12:14159-14166. [PMID: 34760200 PMCID: PMC8565360 DOI: 10.1039/d1sc03127a] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/21/2021] [Indexed: 01/03/2023] Open
Abstract
The modification of peptides and proteins has emerged as a powerful means to efficiently prepare high value bioconjugates for a range of applications in chemical biology and for the development of next-generation therapeutics. Herein, we report a novel method for the chemoselective late-stage modification of peptides and proteins at cysteine in aqueous buffer with suitably functionalised diaryliodonium salts, furnishing stable thioether-linked synthetic conjugates. The power of this new platform is showcased through the late-stage modification of the affibody zEGFR and the histone protein H2A.
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Affiliation(s)
- Stephen A Byrne
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
| | - Max J Bedding
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
| | - Leo Corcilius
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
| | - Daniel J Ford
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
| | - Yichen Zhong
- School of Life and Environmental Sciences, The University of Sydney Sydney NSW 2006 Australia
| | - Charlotte Franck
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
- School of Life and Environmental Sciences, The University of Sydney Sydney NSW 2006 Australia
| | - Mark Larance
- School of Life and Environmental Sciences, The University of Sydney Sydney NSW 2006 Australia
- Charles Perkins Centre, The University of Sydney NSW 2006 Australia
| | - Joel P Mackay
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
- School of Life and Environmental Sciences, The University of Sydney Sydney NSW 2006 Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
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22
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Kang MS, Kong TWS, Khoo JYX, Loh TP. Recent developments in chemical conjugation strategies targeting native amino acids in proteins and their applications in antibody-drug conjugates. Chem Sci 2021; 12:13613-13647. [PMID: 34760149 PMCID: PMC8549674 DOI: 10.1039/d1sc02973h] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
Many fields in chemical biology and synthetic biology require effective bioconjugation methods to achieve their desired functions and activities. Among such biomolecule conjugates, antibody-drug conjugates (ADCs) need a linker that provides a stable linkage between cytotoxic drugs and antibodies, whilst conjugating in a biologically benign, fast and selective fashion. This review focuses on how the development of novel organic synthesis can solve the problems of traditional linker technology. The review shall introduce and analyse the current developments in the modification of native amino acids on peptides or proteins and their applicability to ADC linker. Thereafter, the review shall discuss in detail each endogenous amino acid's intrinsic reactivity and selectivity aspects, and address the research effort to construct an ADC using each conjugation method.
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Affiliation(s)
- Min Sun Kang
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Theresa Wai See Kong
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Joycelyn Yi Xin Khoo
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Teck-Peng Loh
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University 21 Nanyang Link 637371 Singapore
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23
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Abstract
Hypervalent iodine compounds are powerful reagents for the development of novel transformations. As they exhibit low toxicity, high functional group tolerance, and stability in biocompatible media, they have been used for the functionalization of biomolecules. Herein, we report recent advances up to June 2021 in peptide and protein modification using hypervalent iodine reagents. Their use as group transfer or oxidizing reagents is discussed in this Minireview, including methods targeting polar, aromatic, or aliphatic amino acids and peptide termini.
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Affiliation(s)
- Emmanuelle M D Allouche
- Laboratory of Catalysis and Organic Synthesis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, EPFL, SB ISIC, LCSO, BCH 1402, 1015, Lausanne, Switzerland
| | - Elija Grinhagena
- Laboratory of Catalysis and Organic Synthesis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, EPFL, SB ISIC, LCSO, BCH 1402, 1015, Lausanne, Switzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic Synthesis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, EPFL, SB ISIC, LCSO, BCH 1402, 1015, Lausanne, Switzerland
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24
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Wan LQ, Zhang X, Zou Y, Shi R, Cao JG, Xu SY, Deng LF, Zhou L, Gong Y, Shu X, Lee GY, Ren H, Dai L, Qi S, Houk KN, Niu D. Nonenzymatic Stereoselective S-Glycosylation of Polypeptides and Proteins. J Am Chem Soc 2021; 143:11919-11926. [PMID: 34323481 DOI: 10.1021/jacs.1c05156] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Here we report a nonenzymatic glycosylation reaction that builds axial S-glycosidic bonds under biorelevant conditions. This strategy is enabled by the design and use of allyl glycosyl sulfones as precursors to glycosyl radicals and exploits the exceptional functional group tolerance of radical processes. Our method introduces a variety of unprotected glycosyl units to the cysteine residues of peptides in a highly selective fashion. Through developing the second-generation protocol, we applied our method in the direct glycosylation of complex polypeptides and proteins. Computational studies were performed to elucidate the reaction mechanism.
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Affiliation(s)
- Li-Qiang Wan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China.,Department of Chemical Engineering, Sichuan University, Chengdu 610024, China
| | - Xia Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China.,Department of Chemical Engineering, Sichuan University, Chengdu 610024, China
| | - Yike Zou
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Rong Shi
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China.,Department of Chemical Engineering, Sichuan University, Chengdu 610024, China
| | - Jin-Ge Cao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China.,Department of Chemical Engineering, Sichuan University, Chengdu 610024, China
| | - Shi-Yang Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China.,Department of Chemical Engineering, Sichuan University, Chengdu 610024, China
| | - Li-Fan Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China.,Department of Chemical Engineering, Sichuan University, Chengdu 610024, China
| | - Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yanqiu Gong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaoling Shu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ga Young Lee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Haiyan Ren
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lunzhi Dai
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Shiqian Qi
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Dawen Niu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China.,Department of Chemical Engineering, Sichuan University, Chengdu 610024, China
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25
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Abstract
We report the functionalization of cysteine residues with lipophilic alkynes bearing a silyl group or an alkyl chain using amphiphilic ethynylbenziodoxolone reagents (EBXs). The reactions were carried out in buffer (pH 6 to 9), without organic co-solvent or removal of oxygen, either at 37 °C or room temperature. The transformation led to a significant increase of peptide lipophilicity and worked for aromatic thiols, homocysteine, cysteine, and peptides containing 4 to 18 amino acids. His6 -Cys-Ubiquitin was also alkynylated under physiological conditions. Under acidic conditions, the thioalkynes were converted into thioesters, which could be cleaved in the presence of hydroxylamine.
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Affiliation(s)
- Abhaya Kumar Mishra
- Laboratory of Catalysis and Organic SynthesisEcole Polytechnique Fédérale de LausanneEPFL SB ISIC LCSO, BCH 43061015LausanneSwitzerland
| | - Romain Tessier
- Laboratory of Catalysis and Organic SynthesisEcole Polytechnique Fédérale de LausanneEPFL SB ISIC LCSO, BCH 43061015LausanneSwitzerland
- Present address: Department of Chemical BiologyMax Planck Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Durga Prasad Hari
- Laboratory of Catalysis and Organic SynthesisEcole Polytechnique Fédérale de LausanneEPFL SB ISIC LCSO, BCH 43061015LausanneSwitzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic SynthesisEcole Polytechnique Fédérale de LausanneEPFL SB ISIC LCSO, BCH 43061015LausanneSwitzerland
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26
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Affiliation(s)
- Abhaya Kumar Mishra
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 4306 1015 Lausanne Switzerland
| | - Romain Tessier
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 4306 1015 Lausanne Switzerland
- Present address: Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Durga Prasad Hari
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 4306 1015 Lausanne Switzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 4306 1015 Lausanne Switzerland
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27
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Laserna V, Istrate A, Kafuta K, Hakala TA, Knowles TPJ, Alcarazo M, Bernardes GJL. Protein Conjugation by Electrophilic Alkynylation Using 5-(Alkynyl)dibenzothiophenium Triflates. Bioconjug Chem 2021; 32:1570-1575. [PMID: 34232618 DOI: 10.1021/acs.bioconjchem.1c00317] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
5-(Alkynyl)dibenzothiophenium triflates are introduced as new reagents to prepare different protein conjugates through site-selective cysteine alkynylation. The protocol developed allows a highly efficient label of free cysteine-containing proteins with relevant biological roles, such as ubiquitin, the C2A domain of Synaptotagmin-I, or HER2 targeting nanobodies. An electrophilic bis-alkynylating reagent was also designed. The second alkynylating handle thus introduced in the desired protein enables access to protein-thiol, protein-peptide, and protein-protein conjugates, and even diubiquitin dimers can be prepared through this approach. The low excess of reagent needed, mild reaction conditions used, short reaction times, and stability of the S-C(alkyne) bonds at physiological conditions make this approach an interesting addition to the toolbox of classical, site-selective cysteine-conjugation methods.
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Affiliation(s)
- Victor Laserna
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Alena Istrate
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Kevin Kafuta
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstr. 2, 37077-Göttingen, Germany
| | - Tuuli A Hakala
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom.,Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Manuel Alcarazo
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstr. 2, 37077-Göttingen, Germany
| | - Gonçalo J L Bernardes
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom.,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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28
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Lim B, Cheng Y, Kato T, Pham A, Le Du E, Mishra AK, Grinhagena E, Moreau D, Sakai N, Waser J, Matile S. Inhibition of Thiol‐Mediated Uptake with Irreversible Covalent Inhibitors. Helv Chim Acta 2021. [DOI: 10.1002/hlca.202100085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Bumhee Lim
- Department of Organic Chemistry University of Geneva Quai Ernest Ansermet 30 CH-1211 Geneva 4 Switzerland
- National Centre of Competence in Research (NCCR) Chemical Biology Quai Ernest Ansermet 30 CH-1211 Geneva 4 Switzerland
| | - Yangyang Cheng
- Department of Organic Chemistry University of Geneva Quai Ernest Ansermet 30 CH-1211 Geneva 4 Switzerland
- National Centre of Competence in Research (NCCR) Chemical Biology Quai Ernest Ansermet 30 CH-1211 Geneva 4 Switzerland
| | - Takehiro Kato
- Department of Organic Chemistry University of Geneva Quai Ernest Ansermet 30 CH-1211 Geneva 4 Switzerland
- National Centre of Competence in Research (NCCR) Chemical Biology Quai Ernest Ansermet 30 CH-1211 Geneva 4 Switzerland
| | - Anh‐Tuan Pham
- Department of Organic Chemistry University of Geneva Quai Ernest Ansermet 30 CH-1211 Geneva 4 Switzerland
- National Centre of Competence in Research (NCCR) Chemical Biology Quai Ernest Ansermet 30 CH-1211 Geneva 4 Switzerland
| | - Eliott Le Du
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO BCH 4306 1015 Lausanne Switzerland
| | - Abhaya Kumar Mishra
- National Centre of Competence in Research (NCCR) Chemical Biology Quai Ernest Ansermet 30 CH-1211 Geneva 4 Switzerland
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO BCH 4306 1015 Lausanne Switzerland
| | - Elija Grinhagena
- National Centre of Competence in Research (NCCR) Chemical Biology Quai Ernest Ansermet 30 CH-1211 Geneva 4 Switzerland
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO BCH 4306 1015 Lausanne Switzerland
| | - Dimitri Moreau
- National Centre of Competence in Research (NCCR) Chemical Biology Quai Ernest Ansermet 30 CH-1211 Geneva 4 Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry University of Geneva Quai Ernest Ansermet 30 CH-1211 Geneva 4 Switzerland
- National Centre of Competence in Research (NCCR) Chemical Biology Quai Ernest Ansermet 30 CH-1211 Geneva 4 Switzerland
| | - Jerome Waser
- National Centre of Competence in Research (NCCR) Chemical Biology Quai Ernest Ansermet 30 CH-1211 Geneva 4 Switzerland
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO BCH 4306 1015 Lausanne Switzerland
| | - Stefan Matile
- Department of Organic Chemistry University of Geneva Quai Ernest Ansermet 30 CH-1211 Geneva 4 Switzerland
- National Centre of Competence in Research (NCCR) Chemical Biology Quai Ernest Ansermet 30 CH-1211 Geneva 4 Switzerland
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29
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Willems P, Van Breusegem F, Huang J. Contemporary proteomic strategies for cysteine redoxome profiling. Plant Physiol 2021; 186:110-124. [PMID: 33793888 PMCID: PMC8154054 DOI: 10.1093/plphys/kiaa074] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/24/2020] [Indexed: 05/08/2023]
Abstract
Protein cysteine residues are susceptible to oxidative modifications that can affect protein functions. Proteomic techniques that comprehensively profile the cysteine redoxome, the repertoire of oxidized cysteine residues, are pivotal towards a better understanding of the protein redox signaling. Recent technical advances in chemical tools and redox proteomic strategies have greatly improved selectivity, in vivo applicability, and quantification of the cysteine redoxome. Despite this substantial progress, still many challenges remain. Here, we provide an update on the recent advances in proteomic strategies for cysteine redoxome profiling, compare the advantages and disadvantages of current methods and discuss the outstanding challenges and future perspectives for plant redoxome research.
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Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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30
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Park Y, Baumann AL, Moon H, Byrne S, Kasper MA, Hwang S, Sun H, Baik MH, Hackenberger CPR. The mechanism behind enhanced reactivity of unsaturated phosphorus(v) electrophiles towards thiols. Chem Sci 2021; 12:8141-8148. [PMID: 34194704 PMCID: PMC8208129 DOI: 10.1039/d1sc01730f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Vinyl- and ethynyl phosphorus(v) electrophiles are a versatile class of thiol-reactive reagents suitable for cysteine-selective peptide and protein modifications, especially for the generation of antibody conjugates. Herein we investigated the reactivity of various P(v) reagents towards thiol addition. Complementing previous studies, we observed that the heteroatoms X (X = S, O, NH) as well as the vinyl- vs. ethynyl-substituent bound to phosphorus greatly influence the overall reactivity. These experimentally observed trends, as well as the high Z-selectivity for thiol additions to ethynyl derivatives, were further elucidated using DFT calculations. Hyperconjugation was a key means of stabilizing the intermediate generated upon the thiol addition, thus determining both the reactivity and stereoselectivity of unsaturated P(v) electrophiles. Specifically, the energetically low-lying σ antibonding orbital of the P–S bond more readily stabilizes the electron density from the lone pair (LP) of the generated carbanion, rendering the phosphonothiolates more reactive compared to the derivatives bearing oxygen and nitrogen. Our studies provide a detailed mechanistic picture for designing P(v)-based electrophiles with fine-tuned reactivity profiles. Computational analysis of different unsaturated phosphorus(v) electrophiles revealed a mechanistic picture to rationalize their selectivity and reactivity in cysteine-selective peptide and protein modifications.![]()
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Affiliation(s)
- Yerin Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea .,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Alice L Baumann
- Chemical Biology Department, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany .,Department of Chemistry, Humboldt Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Hyejin Moon
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea .,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Stephen Byrne
- Chemical Biology Department, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany .,Department of Chemistry, Humboldt Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Marc-André Kasper
- Chemical Biology Department, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany .,Department of Chemistry, Humboldt Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Songhwan Hwang
- Chemical Biology Department, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
| | - Han Sun
- Chemical Biology Department, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
| | - Mu-Hyun Baik
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
| | - Christian P R Hackenberger
- Chemical Biology Department, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany .,Department of Chemistry, Humboldt Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
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31
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Ceballos J, Grinhagena E, Sangouard G, Heinis C, Waser J. Cys-Cys and Cys-Lys Stapling of Unprotected Peptides Enabled by Hypervalent Iodine Reagents. Angew Chem Int Ed Engl 2021; 60:9022-9031. [PMID: 33450121 PMCID: PMC8048981 DOI: 10.1002/anie.202014511] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 10/29/2020] [Revised: 12/22/2020] [Indexed: 12/31/2022]
Abstract
Easy access to a wide range of structurally diverse stapled peptides is crucial for the development of inhibitors of protein-protein interactions. Herein, we report bis-functional hypervalent iodine reagents for two-component cysteine-cysteine and cysteine-lysine stapling yielding structurally diverse thioalkyne linkers. This stapling method works with unprotected natural amino acid residues and does not require pre-functionalization or metal catalysis. The products are stable to purification and isolation. Post-stapling modification can be accessed via amidation of an activated ester, or via cycloaddition onto the formed thioalkyne group. Increased helicity and binding affinity to MDM2 was obtained for a i,i+7 stapled peptide.
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Affiliation(s)
- Javier Ceballos
- Laboratory of Catalysis and Organic SynthesisEcole Polytechnique Fédérale de LausanneEPFL SB ISIC LCSO, BCH 14021015LausanneSwitzerland
| | - Elija Grinhagena
- Laboratory of Catalysis and Organic SynthesisEcole Polytechnique Fédérale de LausanneEPFL SB ISIC LCSO, BCH 14021015LausanneSwitzerland
| | - Gontran Sangouard
- Laboratory of Therapeutic Proteins and PeptidesEcole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LPPT, BCH 53051015LausanneSwitzerland
| | - Christian Heinis
- Laboratory of Therapeutic Proteins and PeptidesEcole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LPPT, BCH 53051015LausanneSwitzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic SynthesisEcole Polytechnique Fédérale de LausanneEPFL SB ISIC LCSO, BCH 14021015LausanneSwitzerland
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32
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Shimbo D, Maruyama T, Tada N, Itoh A. N-Alkenylation of hydroxamic acid derivatives with ethynyl benziodoxolone to synthesize cis-enamides through vinyl benziodoxolones. Org Biomol Chem 2021; 19:2442-2447. [PMID: 33666207 DOI: 10.1039/d1ob00055a] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The stereoselective synthesis of cis-β-N-alkoxyamidevinyl benziodoxolones (cis-β-N-RO-amide-VBXs) from O-alkyl hydroxamic acids in the presence of an ethynyl benziodoxolone-acetonitrile complex (EBX-MeCN) is reported herein. The reaction was performed under mild conditions including an aqueous solvent, a mild base, and room temperature. The reaction tolerated various O-alkyl hydroxamic acids derived from carboxylic acids, such as amino acids, pharmaceuticals, and natural products. Vinyl dideuterated cis-β-N-MeO-amide-VBXs were also synthesized using deuterium oxide as the deuterium source. Valine-derived cis-β-N-MeO-amide-VBX was stereospecifically derivatized to hydroxamic acid-derived cis-enamides without the loss of stereoselectivity or reduction in the deuterium/hydrogen ratio.
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Affiliation(s)
- Daisuke Shimbo
- Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu 501-1196, Japan.
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33
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Ceballos J, Grinhagena E, Sangouard G, Heinis C, Waser J. Cys–Cys and Cys–Lys Stapling of Unprotected Peptides Enabled by Hypervalent Iodine Reagents. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014511] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Javier Ceballos
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 1402 1015 Lausanne Switzerland
| | - Elija Grinhagena
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 1402 1015 Lausanne Switzerland
| | - Gontran Sangouard
- Laboratory of Therapeutic Proteins and Peptides Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LPPT, BCH 5305 1015 Lausanne Switzerland
| | - Christian Heinis
- Laboratory of Therapeutic Proteins and Peptides Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LPPT, BCH 5305 1015 Lausanne Switzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic Synthesis Ecole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 1402 1015 Lausanne Switzerland
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34
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Li J, Deng JJ, Yin Z, Hu QL, Ge Y, Song Z, Zhang Y, Chan ASC, Li H, Xiong XF. Cleavable and tunable cysteine-specific arylation modification with aryl thioethers. Chem Sci 2021; 12:5209-5215. [PMID: 34168774 PMCID: PMC8179606 DOI: 10.1039/d0sc06576e] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/10/2021] [Indexed: 12/29/2022] Open
Abstract
Cysteine represents an attractive target for peptide/protein modification due to the intrinsic high nucleophilicity of the thiol group and low natural abundance. Herein, a cleavable and tunable covalent modification approach for cysteine containing peptides/proteins with our newly designed aryl thioethers via a S N Ar approach was developed. Highly efficient and selective bioconjugation reactions can be carried out under mild and biocompatible conditions. A series of aryl groups bearing different bioconjugation handles, affinity or fluorescent tags are well tolerated. By adjusting the skeleton and steric hindrance of aryl thioethers slightly, the modified products showed a tunable profile for the regeneration of the native peptides.
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Affiliation(s)
- Jian Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Jun-Jie Deng
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Zhibin Yin
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Qi-Long Hu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Yang Ge
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Zhendong Song
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Ying Zhang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Albert S C Chan
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Huilin Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Xiao-Feng Xiong
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
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35
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Walsh SJ, Bargh JD, Dannheim FM, Hanby AR, Seki H, Counsell AJ, Ou X, Fowler E, Ashman N, Takada Y, Isidro-Llobet A, Parker JS, Carroll JS, Spring DR. Site-selective modification strategies in antibody-drug conjugates. Chem Soc Rev 2021; 50:1305-1353. [PMID: 33290462 DOI: 10.1039/d0cs00310g] [Citation(s) in RCA: 184] [Impact Index Per Article: 61.3] [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] [Indexed: 12/13/2022]
Abstract
Antibody-drug conjugates (ADCs) harness the highly specific targeting capabilities of an antibody to deliver a cytotoxic payload to specific cell types. They have garnered widespread interest in drug discovery, particularly in oncology, as discrimination between healthy and malignant tissues or cells can be achieved. Nine ADCs have received approval from the US Food and Drug Administration and more than 80 others are currently undergoing clinical investigations for a range of solid tumours and haematological malignancies. Extensive research over the past decade has highlighted the critical nature of the linkage strategy adopted to attach the payload to the antibody. Whilst early generation ADCs were primarily synthesised as heterogeneous mixtures, these were found to have sub-optimal pharmacokinetics, stability, tolerability and/or efficacy. Efforts have now shifted towards generating homogeneous constructs with precise drug loading and predetermined, controlled sites of attachment. Homogeneous ADCs have repeatedly demonstrated superior overall pharmacological profiles compared to their heterogeneous counterparts. A wide range of methods have been developed in the pursuit of homogeneity, comprising chemical or enzymatic methods or a combination thereof to afford precise modification of specific amino acid or sugar residues. In this review, we discuss advances in chemical and enzymatic methods for site-specific antibody modification that result in the generation of homogeneous ADCs.
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Affiliation(s)
- Stephen J Walsh
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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36
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Das B, Gupta P. Luminescent terpyridine appended geminal bisazide and bistriazoles: multinuclear Pt(II) complexes and AIPE-based DNA detection with the naked eye. Dalton Trans 2021; 50:10225-10236. [PMID: 34236066 DOI: 10.1039/d1dt01108a] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report square planar Pt(ii) complexes as luminescent biosensors for DNA detection in solution. The sensing is attributed to the aggregation induced bright red photoluminescence (AIPE) of the complexes in the presence of DNA that can be seen with the naked eye using only a 360 nm light source. Terpyridine appended luminescent geminal bistriazoles (L1-L4, from geminal bisazide A through azide-alkyne 'click' cycloaddition) with versatile chelating sites were explored for metal coordination and reaction with Pt(dmso)2Cl2 yielding tetranuclear and dinuclear complexes of Pt(ii) with different N∩N ligand environments. Thermally stable gem-bisazide and bistriazoles are hardly reported in the literature and this is the first report of terpyridine appended geminal bisazide and bistriazoles.
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Affiliation(s)
- Bishnu Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India.
| | - Parna Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India.
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37
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Abstract
Ellman's reagent has caused substantial confusion and concern as a probe for thiol-mediated uptake because it is the only established inhibitor available but works neither efficiently nor reliably. Here we use fluorescent cyclic oligochalcogenides that enter cells by thiol-mediated uptake to systematically screen for more potent inhibitors, including epidithiodiketopiperazines, benzopolysulfanes, disulfide-bridged γ-turned peptides, heteroaromatic sulfones and cyclic thiosulfonates, thiosulfinates and disulfides. With nanomolar activity, the best inhibitors identified are more than 5000 times better than Ellman's reagent. Different activities found with different reporters reveal thiol-mediated uptake as a complex multitarget process. Preliminary results on the inhibition of the cellular uptake of pseudo-lentivectors expressing SARS-CoV-2 spike protein do not exclude potential of efficient inhibitors of thiol-mediated uptake for the development of new antivirals. Thiol-reactive inhibitors for the cellular entry of cyclic oligochalcogenide (COC) transporters and SARS-CoV-2 spike pseudo-lentivirus are reported.![]()
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Affiliation(s)
- Yangyang Cheng
- Department of Organic Chemistry, University of Geneva Geneva Switzerland http://www.unige.ch/sciences/chiorg/matile/ +41 22 379 6523
| | - Anh-Tuan Pham
- Department of Organic Chemistry, University of Geneva Geneva Switzerland http://www.unige.ch/sciences/chiorg/matile/ +41 22 379 6523
| | - Takehiro Kato
- Department of Organic Chemistry, University of Geneva Geneva Switzerland http://www.unige.ch/sciences/chiorg/matile/ +41 22 379 6523
| | - Bumhee Lim
- Department of Organic Chemistry, University of Geneva Geneva Switzerland http://www.unige.ch/sciences/chiorg/matile/ +41 22 379 6523
| | - Dimitri Moreau
- Department of Organic Chemistry, University of Geneva Geneva Switzerland http://www.unige.ch/sciences/chiorg/matile/ +41 22 379 6523
| | - Javier López-Andarias
- Department of Organic Chemistry, University of Geneva Geneva Switzerland http://www.unige.ch/sciences/chiorg/matile/ +41 22 379 6523
| | - Lili Zong
- Department of Organic Chemistry, University of Geneva Geneva Switzerland http://www.unige.ch/sciences/chiorg/matile/ +41 22 379 6523
| | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva Geneva Switzerland http://www.unige.ch/sciences/chiorg/matile/ +41 22 379 6523
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva Geneva Switzerland http://www.unige.ch/sciences/chiorg/matile/ +41 22 379 6523
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38
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Abstract
Copper-catalyzed cross-coupling of thiols and bromoalkynes affords a mild, rapid, and selective Csp-S coupling with broad scope, enabling the use of aryl-, alkyl-, and silyl-substituted alkynyl coupling partners (38 total examples, 50-99% yields). Importantly, the method enables the preparation of difficult-to-access bis-heteroatom-functionalized (S,S-, S,P-, and S,N-) alkynes.
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Affiliation(s)
- Éric Godin
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, Complexe des Sciences, 1375 Avenue Thérèse-Lavoie-Roux, Montréal, Québec H2V 0B3, Canada
| | - Jeffrey Santandrea
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, Complexe des Sciences, 1375 Avenue Thérèse-Lavoie-Roux, Montréal, Québec H2V 0B3, Canada
| | - Antoine Caron
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, Complexe des Sciences, 1375 Avenue Thérèse-Lavoie-Roux, Montréal, Québec H2V 0B3, Canada
| | - Shawn K Collins
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, Complexe des Sciences, 1375 Avenue Thérèse-Lavoie-Roux, Montréal, Québec H2V 0B3, Canada
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39
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Abstract
The site-selective modification of biomolecules has grown spectacularly in recent years. The presence of a large number of functional groups in a biomolecule makes its chemo- and regioselective modification a challenging goal. In this context, transition-metal-mediated reactions are emerging as a powerful tool owing to their unique reactivity and good functional group compatibility, allowing highly efficient and selective bioconjugation reactions that operate under mild conditions. This Minireview focuses on the current state of organometallic chemistry for bioconjugation, highlighting the potential of transition metals for the development of chemoselective and site-specific methods for functionalization of peptides, proteins and nucleic acids. The importance of the selection of ligands attached to the transition metal for conferring the desired chemoselectivity will be highlighted.
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Affiliation(s)
- Jessica Rodríguez
- Laboratoire Hétérochimie Fondamentale et Appliquée, Université Paul Sabatier/CNRS UMR 5069, 118 Route de Narbonne, 31062, Toulouse Cedex 09, France
| | - Miguel Martínez-Calvo
- Centro de Investigaciones Científicas Avanzadas (CICA), AE CICA-INIBIC, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, Campus de Elviña, 15071 A, Coruña, Galicia, Spain
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