201
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Recent Advances in Selective and Irreversible Covalent Ligand Development and Validation. Cell Chem Biol 2019; 26:1486-1500. [PMID: 31631011 DOI: 10.1016/j.chembiol.2019.09.012] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/06/2019] [Accepted: 09/26/2019] [Indexed: 12/20/2022]
Abstract
Some of the most widely used drugs, such as aspirin and penicillin, are covalent drugs. Covalent binding can improve potency, selectivity, and duration of the effects, but the intrinsic reactivity represents a potential liability and may result in idiosyncratic toxicity. For decades, the cons were believed to outweigh the pros, and covalent targeting was deprioritized in drug discovery. Recently, several covalent inhibitors have been approved for cancer treatment, thus rebooting the field. In this review, we briefly reflect on the history of selective covalent targeting, and provide a comprehensive overview of emerging developments from a chemical biology stand-point. Our discussion will reflect on efforts to validate irreversible covalent ligands, expand the scope of targets, and discover new ligands and warheads. We conclude with a brief commentary of remaining limitations and emerging opportunities in selective covalent targeting.
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202
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Zang J, Chen Y, Zhu W, Lin S. Chemoselective Methionine Bioconjugation on a Polypeptide, Protein, and Proteome. Biochemistry 2019; 59:132-138. [PMID: 31592657 DOI: 10.1021/acs.biochem.9b00789] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Methionine is one of the most hydrophobic, redox-sensitive, and one of the only two sulfur-containing amino acids on protein. Because of these biochemical properties, the methionine residue plays a central role in a variety of biological processes, such as metal coordination, antioxidant stress, and aging. However, studies on the molecular functions of methionine are much less common than the other primary sulfur-containing amino acid, cysteine. The limited number of publications on methionine-related studies is partially due to the lack of tools for methionine modification. Methionine bioconjugation offers a new strategy to decipher the biological function of methionine and expands the toolbox for protein functionalization in the context of the application, such as synthesizing proteins with novel properties and producing new biomaterials. The purpose of this Perspective is to highlight the biochemical properties and functions of methionine, list recent progress in the development of methionine bioconjugation reagents, and briefly demonstrate the application of these reagents on polypeptides, proteins, and proteomes.
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Affiliation(s)
- Jia Zang
- Life Sciences Institute , Zhejiang University , Hangzhou 310058 , China
| | - Yulin Chen
- Life Sciences Institute , Zhejiang University , Hangzhou 310058 , China
| | - Wenxuan Zhu
- Life Sciences Institute , Zhejiang University , Hangzhou 310058 , China
| | - Shixian Lin
- Life Sciences Institute , Zhejiang University , Hangzhou 310058 , China
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203
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A mesophilic cysteine-less split intein for protein trans-splicing applications under oxidizing conditions. Proc Natl Acad Sci U S A 2019; 116:22164-22172. [PMID: 31611397 DOI: 10.1073/pnas.1909825116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Split intein-mediated protein trans-splicing has found extensive applications in chemical biology, protein chemistry, and biotechnology. However, an enduring limitation of all well-established split inteins has been the requirement to carry out the reaction in a reducing environment due to the presence of 1 or 2 catalytic cysteines that need to be in a reduced state for splicing to occur. The concomitant exposure of the fused proteins to reducing agents severely limits the scope of protein trans-splicing by excluding proteins sensitive to reducing conditions, such as those containing critical disulfide bonds. Here we report the discovery, characterization, and engineering of a completely cysteine-less split intein (CL intein) that is capable of efficient trans-splicing at ambient temperatures, without a denaturation step, and in the absence of reducing agents. We demonstrate its utility for the site-specific chemical modification of nanobodies and an antibody Fc fragment by N- and C-terminal trans-splicing with short peptide tags (CysTag) that consist of only a few amino acids and have been prelabeled on a single cysteine using classical cysteine bioconjugation. We also synthesized the short N-terminal fragment of the atypically split CL intein by solid-phase peptide synthesis. Furthermore, using the CL intein in combination with a nanobody-epitope pair as a high-affinity mediator, we showed chemical labeling of the extracellular domain of a cell surface receptor on living mammalian cells with a short CysTag containing a synthetic fluorophore. The CL intein thus greatly expands the scope of applications for protein trans-splicing.
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204
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Ueda T, Tamura T, Hamachi I. Development of a Cell-Based Ligand-Screening System for Identifying Hsp90 Inhibitors. Biochemistry 2019; 59:179-182. [DOI: 10.1021/acs.biochem.9b00781] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Tsuyoshi Ueda
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomonori Tamura
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO, Japan Science and Technology Agency (JST), 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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205
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Chang J, Cai W, Liang C, Tang Q, Chen X, Jiang Y, Mao L, Wang M. Enzyme-Instructed Activation of Pro-protein Therapeutics In Vivo. J Am Chem Soc 2019; 141:18136-18141. [DOI: 10.1021/jacs.9b08669] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jin Chang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiqi Cai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunjing Liang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiao Tang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianghan Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Jiang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Lanqun Mao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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206
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Arttamangkul S, Plazek A, Platt EJ, Jin H, Murray TF, Birdsong WT, Rice KC, Farrens DL, Williams JT. Visualizing endogenous opioid receptors in living neurons using ligand-directed chemistry. eLife 2019; 8:49319. [PMID: 31589142 PMCID: PMC6809603 DOI: 10.7554/elife.49319] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/06/2019] [Indexed: 12/11/2022] Open
Abstract
Identifying neurons that have functional opioid receptors is fundamental for the understanding of the cellular, synaptic and systems actions of opioids. Current techniques are limited to post hoc analyses of fixed tissues. Here we developed a fluorescent probe, naltrexamine-acylimidazole (NAI), to label opioid receptors based on a chemical approach termed ‘traceless affinity labeling’. In this approach, a high affinity antagonist naltrexamine is used as the guide molecule for a transferring reaction of acylimidazole at the receptor. This reaction generates a fluorescent dye covalently linked to the receptor while naltrexamine is liberated and leaves the binding site. The labeling induced by this reagent allowed visualization of opioid-sensitive neurons in rat and mouse brains without loss of function of the fluorescently labeled receptors. The ability to locate endogenous receptors in living tissues will aid considerably in establishing the distribution and physiological role of opioid receptors in the CNS of wild type animals.
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Affiliation(s)
- Seksiri Arttamangkul
- The Vollum Institute, Oregon Health & Science University, Portland, United States
| | - Andrew Plazek
- Medicinal Chemistry Core, Oregon Health & Science University, Portland, United States
| | - Emily J Platt
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, United States
| | - Haihong Jin
- Medicinal Chemistry Core, Oregon Health & Science University, Portland, United States
| | - Thomas F Murray
- Department of Pharmacology, School of Medicine, Creighton University, Omaha, United States
| | - William T Birdsong
- The Vollum Institute, Oregon Health & Science University, Portland, United States
| | - Kenner C Rice
- Drug Design and Synthesis Section, Intramural Research Program, NIDA and NIAAA, Bethesda, United States
| | - David L Farrens
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, United States
| | - John T Williams
- The Vollum Institute, Oregon Health & Science University, Portland, United States
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207
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208
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209
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Conway LP, Garg N, Lin W, Vujasinovic M, Löhr JM, Globisch D. Chemoselective probe for detailed analysis of ketones and aldehydes produced by gut microbiota in human samples. Chem Commun (Camb) 2019; 55:9080-9083. [PMID: 31287110 DOI: 10.1039/c9cc04605d] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
New strategies are required for the discovery of unknown bioactive molecules produced by gut microbiota in the human host. Herein, we utilize a chemoselective probe immobilized to magnetic beads for analysis of carbonyls in human fecal samples. We identified 112 metabolites due to femtomole analysis and an increased mass spectrometric sensitivity by up to six orders of magnitude.
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Affiliation(s)
- Louis P Conway
- Department of Medicinal Chemistry, Science for Life Laboratory, Uppsala University, Box 574, SE-75123 Uppsala, Sweden.
| | - Neeraj Garg
- Department of Medicinal Chemistry, Science for Life Laboratory, Uppsala University, Box 574, SE-75123 Uppsala, Sweden.
| | - Weifeng Lin
- Department of Medicinal Chemistry, Science for Life Laboratory, Uppsala University, Box 574, SE-75123 Uppsala, Sweden.
| | - Miroslav Vujasinovic
- Department for Digestive Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - J-Matthias Löhr
- Department for Digestive Diseases, Karolinska University Hospital, Stockholm, Sweden and Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institute, Stockholm, Sweden
| | - Daniel Globisch
- Department of Medicinal Chemistry, Science for Life Laboratory, Uppsala University, Box 574, SE-75123 Uppsala, Sweden.
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210
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Mortensen MR, Skovsgaard MB, Gothelf KV. Considerations on Probe Design for Affinity‐Guided Protein Conjugation. Chembiochem 2019; 20:2711-2728. [DOI: 10.1002/cbic.201900157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Michael R. Mortensen
- Center for Multifunctional Biomolecular Drug DesignInterdisciplinary Nanoscience CenterAarhus University Gustav Wieds Vej 14 8000 Aarhus C Denmark
- Department of ChemistryAarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Mikkel B. Skovsgaard
- Center for Multifunctional Biomolecular Drug DesignInterdisciplinary Nanoscience CenterAarhus University Gustav Wieds Vej 14 8000 Aarhus C Denmark
- Department of ChemistryAarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Kurt V. Gothelf
- Center for Multifunctional Biomolecular Drug DesignInterdisciplinary Nanoscience CenterAarhus University Gustav Wieds Vej 14 8000 Aarhus C Denmark
- Department of ChemistryAarhus University Langelandsgade 140 8000 Aarhus C Denmark
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211
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Dai Y, Weng J, George J, Chen H, Lin Q, Wang J, Royzen M, Zhang Q. Three-Component Protein Modification Using Mercaptobenzaldehyde Derivatives. Org Lett 2019; 21:3828-3833. [PMID: 31058515 DOI: 10.1021/acs.orglett.9b01294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A chemoselective primary amine modification strategy that enables the three-component, one-pot bioconjugation is described. The specifically designed, mercaptobenzaldehyde-based bifunctional linker achieves highly selective and robust amine labeling under biocompatible conditions. This linker demonstrates wide functional group tolerance and is simple to prepare, which allowed facile payload incorporation. Finally, our studies have shown that the introduction of linker does not impair the function of modified protein such as insulin.
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Affiliation(s)
- Yuanwei Dai
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Jiaping Weng
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Justin George
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Huan Chen
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Qishan Lin
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Jun Wang
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Maksim Royzen
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Qiang Zhang
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
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212
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Fredy JW, Cutolo G, Poret B, Nehmé R, Hubert-Roux M, Gandolfo P, Castel H, Schuler M, Tatibouët A, Sabot C, Renard PY. Diverted Natural Lossen-type Rearrangement for Bioconjugation through in Situ Myrosinase-Triggered Isothiocyanate Synthesis. Bioconjug Chem 2019; 30:1385-1394. [DOI: 10.1021/acs.bioconjchem.9b00153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Jean Wilfried Fredy
- Normandie Univ, CNRS, UNIROUEN, INSA Rouen, COBRA (UMR 6014), 76000 Rouen, France
| | - Giuliano Cutolo
- Institut de Chimie Organique et Analytique - ICOA UMR 7311 CNRS, Université d’Orléans, Rue de Chartres, BP6759, 45067 cedex 02 Orléans, France
| | - Benjamin Poret
- Normandie Univ, UNIROUEN, INSERM U1239, DC2N, Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France
| | - Reine Nehmé
- Institut de Chimie Organique et Analytique - ICOA UMR 7311 CNRS, Université d’Orléans, Rue de Chartres, BP6759, 45067 cedex 02 Orléans, France
| | - Marie Hubert-Roux
- Normandie Univ, CNRS, UNIROUEN, INSA Rouen, COBRA (UMR 6014), 76000 Rouen, France
| | - Pierrick Gandolfo
- Normandie Univ, UNIROUEN, INSERM U1239, DC2N, Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France
| | - Hélène Castel
- Normandie Univ, UNIROUEN, INSERM U1239, DC2N, Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France
| | - Marie Schuler
- Institut de Chimie Organique et Analytique - ICOA UMR 7311 CNRS, Université d’Orléans, Rue de Chartres, BP6759, 45067 cedex 02 Orléans, France
| | - Arnaud Tatibouët
- Institut de Chimie Organique et Analytique - ICOA UMR 7311 CNRS, Université d’Orléans, Rue de Chartres, BP6759, 45067 cedex 02 Orléans, France
| | - Cyrille Sabot
- Normandie Univ, CNRS, UNIROUEN, INSA Rouen, COBRA (UMR 6014), 76000 Rouen, France
| | - Pierre-Yves Renard
- Normandie Univ, CNRS, UNIROUEN, INSA Rouen, COBRA (UMR 6014), 76000 Rouen, France
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213
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António JPM, Russo R, Carvalho CP, Cal PMSD, Gois PMP. Boronic acids as building blocks for the construction of therapeutically useful bioconjugates. Chem Soc Rev 2019; 48:3513-3536. [DOI: 10.1039/c9cs00184k] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review summarizes boronic acid's contribution to the development of bioconjugates with a particular focus on the molecular mechanisms underlying its role in the construction and function of the bioconjugate, namely as a bioconjugation warhead, as a payload and as part of a bioconjugate linker.
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Affiliation(s)
- João P. M. António
- Research Institute for Medicines (iMed.ULisboa)
- Faculty of Pharmacy
- Universidade de Lisboa
- Lisbon
- Portugal
| | - Roberto Russo
- Research Institute for Medicines (iMed.ULisboa)
- Faculty of Pharmacy
- Universidade de Lisboa
- Lisbon
- Portugal
| | - Cátia Parente Carvalho
- Research Institute for Medicines (iMed.ULisboa)
- Faculty of Pharmacy
- Universidade de Lisboa
- Lisbon
- Portugal
| | - Pedro M. S. D. Cal
- Instituto de Medicina Molecular
- Faculty of Medicine
- Universidade de Lisboa
- Lisbon
- Portugal
| | - Pedro M. P. Gois
- Research Institute for Medicines (iMed.ULisboa)
- Faculty of Pharmacy
- Universidade de Lisboa
- Lisbon
- Portugal
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