1
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Jankech T, Gerhardtova I, Majerova P, Piestansky J, Jampilek J, Kovac A. Derivatization of carboxylic groups prior to their LC analysis - A review. Anal Chim Acta 2024; 1300:342435. [PMID: 38521569 DOI: 10.1016/j.aca.2024.342435] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
Carboxylic acids (CAs) represent a large group of important molecules participating in various biologically significant processes. Analytical study of these compounds is typically performed by liquid chromatography (LC) combined with various types of detection. However, their analysis is often accompanied by a wide variety of problems depending on used separation system or detection method. The dominant ones are: i) poor chromatographic behavior of the CAs in reversed-phase LC; ii) absence of a chromophore (or fluorophore); iii) weak ionization in mass spectrometry (MS). To overcome these problems, targeted chemical modification, and derivatization, come into play. Therefore, derivatization still plays an important and, in many cases, irreplaceable role in sample preparation, and new derivatization methods of CAs are constantly being developed. The most commonly used type of reaction for CAs derivatization is amidation. In recent years, an increased interest in the isotopic labeling derivatization method has been observed. In this review, we comprehensively summarize the possibilities and actual trends in the derivatization of CAs that have been published over the past decade.
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Affiliation(s)
- Timotej Jankech
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovak Republic; Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovak Republic
| | - Ivana Gerhardtova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovak Republic; Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovak Republic
| | - Petra Majerova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovak Republic
| | - Juraj Piestansky
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovak Republic; Department of Galenic Pharmacy, Faculty of Pharmacy, Comenius University Bratislava, Odbojarov 10, 832 32 Bratislava, Slovak Republic
| | - Josef Jampilek
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovak Republic; Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovak Republic
| | - Andrej Kovac
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovak Republic.
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2
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Zhao T, Sachon E, Micouin L, Piccardi R. α-Silylated Diazoalkynes: New Tools for Bioconjugation of Proteins. Chemistry 2024; 30:e202302807. [PMID: 38305813 DOI: 10.1002/chem.202302807] [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: 08/28/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/03/2024]
Abstract
α-Silylated diazoalkynes are stabilized diazo compounds that can selectively react with carboxylic residues in buffered aqueous media. In-situ fluoride induced desilylation increases this reactivity, leading to a very fast reaction. Application to the selective functionalization of RNase A, followed by post-functionalization using click chemistry, is described. These new reagents expand the toolbox for native protein modification at carboxylic residues.
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Affiliation(s)
- Tuan Zhao
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS, F-75006, Paris, France
| | - Emmanuelle Sachon
- Laboratoire des Biomolécules, LBM, Sorbonne Université, École normale supérieure, PSL University, CNRS, Paris, France
| | - Laurent Micouin
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS, F-75006, Paris, France
| | - Riccardo Piccardi
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS, F-75006, Paris, France
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3
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Lin W, Gerullat L, Braadland PR, Fournier A, Hov JR, Globisch D. Rapid and Bifunctional Chemoselective Metabolome Analysis of Liver Disease Plasma Using the Reagent 4-Nitrophenyl-2H-azirine. Angew Chem Int Ed Engl 2024; 63:e202318579. [PMID: 38235602 DOI: 10.1002/anie.202318579] [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: 12/04/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/19/2024]
Abstract
Primary sclerosing cholangitis (PSC) is a chronic inflammatory disease of the bile ducts that has been associated with diverse metabolic carboxylic acids. Mass spectrometric techniques are the method of choice for their analysis. However, the broad investigation of this metabolite class remains challenging. Derivatization of carboxylic acids represents a strategy to overcome these limitations but available methods suffer from diverse analytical challenges. Herein, we have designed a novel strategy introducing 4-nitrophenyl-2H-azirine as a new chemoselective moiety for the first time for carboxylic acid metabolites. This moiety was selected as it rapidly forms a stable amide bond and also generates a new ketone, which can be analyzed by our recently developed quant-SCHEMA method specific for carbonyl metabolites. Optimization of this new method revealed a high reproducibility and robustness, which was utilized to validate 102 metabolic carboxylic acids using authentic synthetic standard conjugates in human plasma samples including nine metabolites that were newly detected. Using this sequential analysis of the carbonyl- and carboxylic acid-metabolomes revealed alterations of the ketogenesis pathway, which demonstrates the vast benefit of our unique methodology. We anticipate that the developed azirine moiety with rapid functional group transformation will find broad application in diverse chemical biology research fields.
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Affiliation(s)
- Weifeng Lin
- Department of Chemistry-, BMC, Science for Life Laboratory, Uppsala University, Box 576, SE-75123, Uppsala, Sweden
| | - Lars Gerullat
- Department of Chemistry-, BMC, Science for Life Laboratory, Uppsala University, Box 576, SE-75123, Uppsala, Sweden
| | - Peder R Braadland
- Norwegian PSC Research Center at Department of Transplantation Medicine, Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424, Oslo, Norway
| | - Anaïs Fournier
- Department of Chemistry-, BMC, Science for Life Laboratory, Uppsala University, Box 576, SE-75123, Uppsala, Sweden
| | - Johannes R Hov
- Norwegian PSC Research Center at Department of Transplantation Medicine, Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424, Oslo, Norway
| | - Daniel Globisch
- Department of Chemistry-, BMC, Science for Life Laboratory, Uppsala University, Box 576, SE-75123, Uppsala, Sweden
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4
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Tanimoto H, Adachi R, Tanisawa K, Tomohiro T. Amphos-Mediated Conversion of Alkyl Azides to Diazo Compounds and One-Pot Azide-Site Selective Transient Protection, Click Conjugation, and Deprotective Transformation. Org Lett 2024. [PMID: 38502004 DOI: 10.1021/acs.orglett.4c00566] [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: 03/20/2024]
Abstract
A one-pot conversion of alkyl azides to diazo compounds is outlined. After the reaction of α-azidocarbonyl compounds with Amphos, treatment of the resulting phosphazides with silica gel in a wet solvent afforded α-diazo carbonyl products. Through the azido group protection property of Amphos, inter- and intramolecular azide-site selective reactions of azido group protection, click functionalization, and deprotection of the diazo group have been demonstrated in one pot.
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Affiliation(s)
- Hiroki Tanimoto
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Ryo Adachi
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Kodai Tanisawa
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Takenori Tomohiro
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
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5
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Zheng Q, Zhang Z, Guiley KZ, Shokat KM. Strain-release alkylation of Asp12 enables mutant selective targeting of K-Ras-G12D. Nat Chem Biol 2024:10.1038/s41589-024-01565-w. [PMID: 38443470 DOI: 10.1038/s41589-024-01565-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/30/2024] [Indexed: 03/07/2024]
Abstract
K-Ras is the most commonly mutated oncogene in human cancer. The recently approved non-small cell lung cancer drugs sotorasib and adagrasib covalently capture an acquired cysteine in K-Ras-G12C mutation and lock it in a signaling-incompetent state. However, covalent inhibition of G12D, the most frequent K-Ras mutation particularly prevalent in pancreatic ductal adenocarcinoma, has remained elusive due to the lack of aspartate-targeting chemistry. Here we present a set of malolactone-based electrophiles that exploit ring strain to crosslink K-Ras-G12D at the mutant aspartate to form stable covalent complexes. Structural insights from X-ray crystallography and exploitation of the stereoelectronic requirements for attack of the electrophile allowed development of a substituted malolactone that resisted attack by aqueous buffer but rapidly crosslinked with the aspartate-12 of K-Ras in both GDP and GTP state. The GTP-state targeting allowed effective suppression of downstream signaling, and selective inhibition of K-Ras-G12D-driven cancer cell proliferation in vitro and xenograft growth in mice.
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Affiliation(s)
- Qinheng Zheng
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Ziyang Zhang
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
| | - Keelan Z Guiley
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
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6
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Xuan W, Ma JA. Pinpointing Acidic Residues in Proteins. ChemMedChem 2024; 19:e202300623. [PMID: 38303683 DOI: 10.1002/cmdc.202300623] [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: 11/08/2023] [Revised: 12/18/2023] [Indexed: 02/03/2024]
Abstract
It is of great importance to pinpoint specific residues or sites of a protein in biological contexts to enable desired mechanism of action for small molecules or to precisely control protein function. In this regard, acidic residues including aspartic acid (Asp) and glutamic acid (Glu) hold great potential due to their great prevalence and unique function. To unlock the largely untapped potential, great efforts have been made recently by synthetic chemists, chemical biologists and pharmacologists. Herein, we would like to highlight the remarkable progress and particularly introduce the electrophiles that exhibit reactivity to carboxylic acids, the light-induced reactivities to carboxylic acids and the genetically encoded noncanonical amino acids that allow protein manipulations at acidic residues. We also comment on certain unresolved challenges, hoping to draw more attention to this rapidly developing area.
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Affiliation(s)
- Weimin Xuan
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Jun-An Ma
- Department of Chemistry, Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, P. R. China
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7
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Cabanero DC, Kariofillis SK, Johns AC, Kim J, Ni J, Park S, Parker DL, Ramil CP, Roy X, Shah NH, Rovis T. Photocatalytic Activation of Aryl(trifluoromethyl) Diazos to Carbenes for High-Resolution Protein Labeling with Red Light. J Am Chem Soc 2024; 146:1337-1345. [PMID: 38165744 DOI: 10.1021/jacs.3c09545] [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: 01/04/2024]
Abstract
State-of-the-art methods in photoproximity labeling center on the targeted generation and capture of short-lived reactive intermediates to provide a snapshot of local protein environments. Diazirines are the current gold standard for high-resolution proximity labeling, generating short-lived aryl(trifluoromethyl) carbenes. Here, we present a method to access aryl(trifluoromethyl) carbenes from a stable diazo source via tissue-penetrable, deep red to near-infrared light (600-800 nm). The operative mechanism of this activation involves Dexter energy transfer from photoexcited osmium(II) photocatalysts to the diazo, thus revealing an aryl(trifluoromethyl) carbene. The labeling preferences of the diazo probe with amino acids are studied, showing high reactivity toward heteroatom-H bonds. Upon the synthesis of a biotinylated diazo probe, labeling studies are conducted on native proteins as well as proteins conjugated to the Os photocatalyst. Finally, we demonstrate that the conjugation of a protein inhibitor to the photocatalyst also enables selective protein labeling in the presence of spectator proteins and achieves specific labeling of a membrane protein on the surface of mammalian cells via a two-antibody photocatalytic system.
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Affiliation(s)
- David C Cabanero
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Stavros K Kariofillis
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Andrew C Johns
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Jinwoo Kim
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Jizhi Ni
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Sangho Park
- Discovery Biology, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Dann L Parker
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Carlo P Ramil
- Discovery Chemistry, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Xavier Roy
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Neel H Shah
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Tomislav Rovis
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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8
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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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9
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Pan S, Ding A, Li Y, Sun Y, Zhan Y, Ye Z, Song N, Peng B, Li L, Huang W, Shao H. Small-molecule probes from bench to bedside: advancing molecular analysis of drug-target interactions toward precision medicine. Chem Soc Rev 2023; 52:5706-5743. [PMID: 37525607 DOI: 10.1039/d3cs00056g] [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: 08/02/2023]
Abstract
Over the past decade, remarkable advances have been witnessed in the development of small-molecule probes. These molecular tools have been widely applied for interrogating proteins, pathways and drug-target interactions in preclinical research. While novel structures and designs are commonly explored in probe development, the clinical translation of small-molecule probes remains limited, primarily due to safety and regulatory considerations. Recent synergistic developments - interfacing novel chemical probes with complementary analytical technologies - have introduced and expedited diverse biomedical opportunities to molecularly characterize targeted drug interactions directly in the human body or through accessible clinical specimens (e.g., blood and ascites fluid). These integrated developments thus offer unprecedented opportunities for drug development, disease diagnostics and treatment monitoring. In this review, we discuss recent advances in the structure and design of small-molecule probes with novel functionalities and the integrated development with imaging, proteomics and other emerging technologies. We further highlight recent applications of integrated small-molecule technologies for the molecular analysis of drug-target interactions, including translational applications and emerging opportunities for whole-body imaging, tissue-based measurement and blood-based analysis.
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Affiliation(s)
- Sijun Pan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Aixiang Ding
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yisi Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yaxin Sun
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yueqin Zhan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Zhenkun Ye
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Ning Song
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Wei Huang
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Huilin Shao
- Institute for Health Innovation & Technology, National University of Singapore, Singapore 117599, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore 117583, Singapore
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10
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Chauhan P, V. R, Kumar M, Molla R, V. B. U, Rai V. Dis integrate (DIN) Theory Enabling Precision Engineering of Proteins. ACS Cent Sci 2023; 9:137-150. [PMID: 36844488 PMCID: PMC9951294 DOI: 10.1021/acscentsci.2c01455] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Indexed: 06/18/2023]
Abstract
The chemical toolbox for the selective modification of proteins has witnessed immense interest in the past few years. The rapid growth of biologics and the need for precision therapeutics have fuelled this growth further. However, the broad spectrum of selectivity parameters creates a roadblock to the field's growth. Additionally, bond formation and dissociation are significantly redefined during the translation from small molecules to proteins. Understanding these principles and developing theories to deconvolute the multidimensional attributes could accelerate the area. This outlook presents a disintegrate (DIN) theory for systematically disintegrating the selectivity challenges through reversible chemical reactions. An irreversible step concludes the reaction sequence to render an integrated solution for precise protein bioconjugation. In this perspective, we highlight the key advancements, unsolved challenges, and potential opportunities.
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11
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Jin F, Zhao L. Fluorescence Probe Based on Pyrimidine Applied for Rapid Identification of Different Amino Acids. Russ J Bioorg Chem 2023. [DOI: 10.1134/s1068162023020085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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12
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Thomas RP, Grant EK, Dickinson ER, Zappacosta F, Edwards LJ, Hann MM, House D, Tomkinson NCO, Bush JT. Reactive fragments targeting carboxylate residues employing direct to biology, high-throughput chemistry. RSC Med Chem 2023; 14:671-679. [PMID: 37122547 PMCID: PMC10131605 DOI: 10.1039/d2md00453d] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
We present a carboxylate-targeting reactive fragment screening platform using 2-aryl-5-carboxytetrazole (ACT) as the photoreactive functionality. This work will provide a simple accessible method to rapidly discover tool molecules to interrogate important biological targets.
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Affiliation(s)
- Ross P. Thomas
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Emma K. Grant
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | | | | | - Lee J. Edwards
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Michael M. Hann
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - David House
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Nicholas C. O. Tomkinson
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Jacob T. Bush
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
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13
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Zeng LY, Liu Y, Han J, Chen J, Liu S, Xi B. O-Methylation of carboxylic acids with streptozotocin. Org Biomol Chem 2022; 20:5230-5233. [PMID: 35621003 DOI: 10.1039/d2ob00578f] [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: 11/21/2022]
Abstract
The clinically used DNA-alkylating drug streptozotocin (STZ) was investigated using a simple work-up as an O-methylating agent to transform various carboxylic acids, sulfonic acids and phosphorous acids into corresponding methyl esters, and did so with yields of up to 97% in 4 h at room temperature. Good substrate tolerance was observed, and benefited from the mild conditions and compatibility of the reaction with water.
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Affiliation(s)
- Li-Yan Zeng
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharma-ceutical Sciences, Southern Medical University, Guangzhou, 510515, China.,College of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Yang Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharma-ceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Jiakun Han
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharma-ceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Jinhong Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharma-ceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Shuwen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharma-ceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Baomin Xi
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharma-ceutical Sciences, Southern Medical University, Guangzhou, 510515, China
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14
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Abstract
Photochemistry has recently attracted the interest of synthetic chemists to conduct photolysis reactions of diazoalkanes. In this feature article, we provide a concise overview on this field, starting with discoveries...
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15
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Chandrasekharan SP, Dhami A, Kumar S, Mohanan K. Recent advances in pyrazole synthesis employing diazo compounds and synthetic analogues. Org Biomol Chem 2022; 20:8787-8817. [DOI: 10.1039/d2ob01918c] [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: 11/06/2022]
Abstract
This review summarizes the recent developments in the construction of pyrazoles using diazo compounds, nitrile imines and their synthetic equivalents.
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Affiliation(s)
- Sanoop P. Chandrasekharan
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Anamika Dhami
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Sandeep Kumar
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Kishor Mohanan
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research, Ghaziabad-201002, India
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16
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Pessatti T, Terenzi H, Bertoldo J. Protein Modifications: From Chemoselective Probes to Novel Biocatalysts. Catalysts 2021; 11:1466. [DOI: 10.3390/catal11121466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Chemical reactions can be performed to covalently modify specific residues in proteins. When applied to native enzymes, these chemical modifications can greatly expand the available set of building blocks for the development of biocatalysts. Nucleophilic canonical amino acid sidechains are the most readily accessible targets for such endeavors. A rich history of attempts to design enhanced or novel enzymes, from various protein scaffolds, has paved the way for a rapidly developing field with growing scientific, industrial, and biomedical applications. A major challenge is to devise reactions that are compatible with native proteins and can selectively modify specific residues. Cysteine, lysine, N-terminus, and carboxylate residues comprise the most widespread naturally occurring targets for enzyme modifications. In this review, chemical methods for selective modification of enzymes will be discussed, alongside with examples of reported applications. We aim to highlight the potential of such strategies to enhance enzyme function and create novel semisynthetic biocatalysts, as well as provide a perspective in a fast-evolving topic.
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17
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Abstract
Nearly all FDA approved drugs and bioactive small molecules exert their effects by binding to and modulating proteins. Consequently, understanding how small molecules interact with proteins at an molecular level is a central challenge of modern chemical biology and drug development. Complementary to structure-guided approaches, chemoproteomics has emerged as a method capable of high-throughput identification of proteins covalently bound by small molecules. To profile noncovalent interactions, established chemoproteomic workflows typically incorporate photoreactive moieties into small molecule probes, which enable trapping of small molecule-protein interactions (SMPIs). This strategy, termed photoaffinity labelling (PAL), has been utilized to profile an array of small molecule interactions, including for drugs, lipids, metabolites, and cofactors. Herein we describe the discovery of photocrosslinking chemistries, including a comparison of the strengths and limitations of implementation of each chemotype in chemoproteomic workflows. In addition, we highlight key examples where photoaffinity labelling has enabled target deconvolution and interaction site mapping.
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Affiliation(s)
- Nikolas R Burton
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA.
| | - Phillip Kim
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Keriann M Backus
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
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18
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Stevens CA, Kaur K, Klok HA. Self-assembly of protein-polymer conjugates for drug delivery. Adv Drug Deliv Rev 2021; 174:447-460. [PMID: 33984408 DOI: 10.1016/j.addr.2021.05.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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: 10/30/2020] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 01/07/2023]
Abstract
Protein-polymer conjugates are a class of molecules that combine the stability of polymers with the diversity, specificity, and functionality of biomolecules. These bioconjugates can result in hybrid materials that display properties not found in their individual components and can be particularly relevant for drug delivery applications. Engineering amphiphilicity into these bioconjugate materials can lead to phase separation and the assembly of high-order structures. The assembly, termed self-assembly, of these hierarchical structures entails multiple levels of organization: at each level, new properties emerge, which are, in turn, influenced by lower levels. Here, we provide a critical review of protein-polymer conjugate self-assembly and how these materials can be used for therapeutic applications and drug delivery. In addition, we discuss central bioconjugate design questions and propose future perspectives for the field of protein-polymer conjugate self-assembly.
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Affiliation(s)
- Corey A Stevens
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland.
| | - Kuljeet Kaur
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
| | - Harm-Anton Klok
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
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19
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20
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Lu GH, Huang TC, Hsueh HC, Yang SC, Cho TW, Chou HH. Novel N-transfer reagent for converting α-amino acid derivatives to α-diazo compounds. Chem Commun (Camb) 2021; 57:4839-4842. [PMID: 33870368 DOI: 10.1039/d1cc01285a] [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: 12/27/2022]
Abstract
A novel universal N-transfer reagent for direct and effective transformation of α-amino ketones, acetamides, and esters to the corresponding α-diazo products under mild basic conditions has been developed. This one-step synthetic approach not only allows for generation of α-substituted-α-diazo carbonyl compounds from α-amino acid derivatives but also permits preparation of α-diazo dipeptides from N-terminal dipeptides (32 examples, up to 91%).
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Affiliation(s)
- Guan-Han Lu
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan.
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21
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Liu J, Xu J, Pajkert R, Mei H, Röschenthaler GV, Han J. Esterification of Carboxylic Acids with (β-Diazo-α,α-difluoroethyl)phosphonates under Photochemical Conditions. Acta Chimica Sinica 2021. [DOI: 10.6023/a21030096] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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22
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Affiliation(s)
- Yanan Zhou
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, P. R. China
| | - Chengjun Wu
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, P. R. China
| | - Hongzhi Ma
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, P. R. China
| | - Jianchao Chen
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, P. R. China
| | - Tiemin Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, P. R. China
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23
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O'Brien JGK, Jemas A, Asare-Okai PN, Am Ende CW, Fox JM. Probing the Mechanism of Photoaffinity Labeling by Dialkyldiazirines through Bioorthogonal Capture of Diazoalkanes. Org Lett 2020; 22:9415-9420. [PMID: 33259213 DOI: 10.1021/acs.orglett.0c02714] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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
Dialkyldiazirines have emerged as reagents of choice for biological photoaffinity labeling studies. The mechanism of crosslinking has dramatic consequences for biological applications where instantaneous labeling is desirable, as carbene insertions display different chemoselectivity and are much faster than competing mechanisms involving diazo or ylide intermediates. Here, deuterium labeling and diazo compound trapping experiments are employed to demonstrate that both carbene and diazo mechanisms operate in the reactions of a dialkyldiazirine motif that is commonly utilized for biological applications. For the fraction of intermolecular labeling that does involve a carbene mechanism, direct insertion is not necessarily involved, as products derived from a carbonyl ylide are also observed. We demonstrate that a strained cycloalkyne can intercept diazo compound intermediates and serve as a bioorthogonal probe for studying the contribution of the diazonium mechanism of photoaffinity labeling on a model protein under aqueous conditions.
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Affiliation(s)
- Jessica G K O'Brien
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Andrew Jemas
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Papa Nii Asare-Okai
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Christopher W Am Ende
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Joseph M Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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24
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Abstract
Chemical modification of proteins in living cells permits valuable glimpses into the molecular interactions that underpin dynamic cellular events. While genetic engineering methods are often preferred, selective labeling of endogenous proteins in a complex intracellular milieu with chemical approaches represents a significant challenge. In this study, we report novel diazocoumarin compounds that can be photoactivated by visible (430-490 nm) and near-infrared light (800 nm) irradiation to photo-uncage reactive carbene intermediates, which could subsequently undergo an insertion reaction with concomitant fluorescence "turned on". With these new molecules in hand, we have developed a new approach for rapid, selective, and fluorogenic labeling of endogenous protein in living cells. By using CA-II and eDHFR as model proteins, we demonstrated that subcellular localization of proteins can be precisely visualized by live-cell imaging and protein levels can be reliably quantified in multiple cell types using flow cytometry. Dynamic protein regulations such as hypoxia-induced CA-IX accumulation can also be detected. In addition, by two-photon excitation with an 800 nm laser, cell-selective labeling can also be achieved with spatially controlled irradiation. Our method circumvents the cytotoxicity of UV light and obviates the need for introducing external reporters with "click chemistries". We believe that this approach of fluorescence labeling of endogenous protein by bioorthogonal photoirradiation opens up exciting opportunities for discoveries and mechanistic interrogation in chemical biology.
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Affiliation(s)
- Sheng-Yao Dai
- Morningside Laboratory for Chemical Biology, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dan Yang
- Morningside Laboratory for Chemical Biology, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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25
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Tobiesen HN, Leth LA, Iversen MV, Næsborg L, Bertelsen S, Jørgensen KA. Stereoselective Oxidative Bioconjugation of Amino Acids and Oligopeptides to Aldehydes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008513] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Henriette N. Tobiesen
- Department of Chemistry Aarhus University 8000 Aarhus C Denmark
- Research Chemistry, Global Research Technologies Novo Nordisk A/S 2760 Maaloev Denmark
| | - Lars A. Leth
- Department of Chemistry Aarhus University 8000 Aarhus C Denmark
| | - Marc V. Iversen
- Department of Chemistry Aarhus University 8000 Aarhus C Denmark
| | - Line Næsborg
- Department of Chemistry Aarhus University 8000 Aarhus C Denmark
| | - Søren Bertelsen
- Research Chemistry, Global Research Technologies Novo Nordisk A/S 2760 Maaloev Denmark
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26
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Tobiesen HN, Leth LA, Iversen MV, Næsborg L, Bertelsen S, Jørgensen KA. Stereoselective Oxidative Bioconjugation of Amino Acids and Oligopeptides to Aldehydes. Angew Chem Int Ed Engl 2020; 59:18490-18494. [DOI: 10.1002/anie.202008513] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Indexed: 01/09/2023]
Affiliation(s)
- Henriette N. Tobiesen
- Department of Chemistry Aarhus University 8000 Aarhus C Denmark
- Research Chemistry, Global Research Technologies Novo Nordisk A/S 2760 Maaloev Denmark
| | - Lars A. Leth
- Department of Chemistry Aarhus University 8000 Aarhus C Denmark
| | - Marc V. Iversen
- Department of Chemistry Aarhus University 8000 Aarhus C Denmark
| | - Line Næsborg
- Department of Chemistry Aarhus University 8000 Aarhus C Denmark
| | - Søren Bertelsen
- Research Chemistry, Global Research Technologies Novo Nordisk A/S 2760 Maaloev Denmark
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27
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Bernardim B, Dunsmore L, Li H, Hocking B, Nuñez-Franco R, Navo CD, Jiménez-Osés G, Burtoloso ACB, Bernardes GJL. Precise Installation of Diazo-Tagged Side-Chains on Proteins to Enable In Vitro and In-Cell Site-Specific Labeling. Bioconjug Chem 2020; 31:1604-1610. [DOI: 10.1021/acs.bioconjchem.0c00232] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Barbara Bernardim
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Lavinia Dunsmore
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - He Li
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Brad Hocking
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Reyes Nuñez-Franco
- Computational Chemistry Lab, CIC bioGUNE-BRTA, Derio, Bizkaia, 48160, Spain
| | - Claudio D. Navo
- Computational Chemistry Lab, CIC bioGUNE-BRTA, Derio, Bizkaia, 48160, Spain
| | | | - Antonio C. B. Burtoloso
- Instituto de Química de São Carlos, Universidade de São Paulo, Avenida Joao Dagnone, 1100, CEP 13563-120, São Carlos, São Paolo, Brazil
| | - Gonçalo J. L. Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
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28
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Ma N, Hu J, Zhang ZM, Liu W, Huang M, Fan Y, Yin X, Wang J, Ding K, Ye W, Li Z. 2 H-Azirine-Based Reagents for Chemoselective Bioconjugation at Carboxyl Residues Inside Live Cells. J Am Chem Soc 2020; 142:6051-6059. [PMID: 32159959 DOI: 10.1021/jacs.9b12116] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein modification by chemical reagents has played an essential role in the treatment of human diseases. However, the reagents currently used are limited to the covalent modification of cysteine and lysine residues. It is thus desirable to develop novel methods that can covalently modify other residues. Despite the fact that the carboxyl residues are crucial for maintaining the protein function, few selective labeling reactions are currently available. Here, we describe a novel reactive probe, 3-phenyl-2H-azirine, that enables chemoselective modification of carboxyl groups in proteins under both in vitro and in situ conditions with excellent efficiency. Furthermore, proteome-wide profiling of reactive carboxyl residues was performed with a quantitative chemoproteomic platform.
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Affiliation(s)
- Nan Ma
- School of Pharmacy, Jinan University, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Jun Hu
- School of Pharmacy, Jinan University, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Wenyan Liu
- School of Pharmacy, Jinan University, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Minhao Huang
- School of Pharmacy, Jinan University, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Youlong Fan
- School of Pharmacy, Jinan University, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xingfeng Yin
- Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangdong 510632, China
| | - Jigang Wang
- The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China.,Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ke Ding
- School of Pharmacy, Jinan University, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Wencai Ye
- School of Pharmacy, Jinan University, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, 601 Huangpu Avenue West, Guangzhou 510632, China
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29
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Abstract
The field of protein bioconjugation draws attention from stakeholders in chemistry, biology, and medicine. This review provides an overview of the present status, challenges, and opportunities for organic chemists.
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Affiliation(s)
- Neelesh C. Reddy
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
| | - Mohan Kumar
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
| | - Rajib Molla
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
| | - Vishal Rai
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
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30
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Müller A, Langó T, Turiák L, Ács A, Várady G, Kucsma N, Drahos L, Tusnády GE. Covalently modified carboxyl side chains on cell surface leads to a novel method toward topology analysis of transmembrane proteins. Sci Rep 2019; 9:15729. [PMID: 31673029 PMCID: PMC6823493 DOI: 10.1038/s41598-019-52188-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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] [Received: 07/31/2019] [Accepted: 10/05/2019] [Indexed: 12/13/2022] Open
Abstract
The research on transmembrane proteins (TMPs) is quite widespread due to their biological importance. Unfortunately, only a little amount of structural data is available of TMPs. Since technical difficulties arise during their high-resolution structure determination, bioinformatics and other experimental approaches are widely used to characterize their low-resolution structure, namely topology. Experimental and computational methods alone are still limited to determine TMP topology, but their combination becomes significant for the production of reliable structural data. By applying amino acid specific membrane-impermeable labelling agents, it is possible to identify the accessible surface of TMPs. Depending on the residue-specific modifications, new extracellular topology data is gathered, allowing the identification of more extracellular segments for TMPs. A new method has been developed for the experimental analysis of TMPs: covalent modification of the carboxyl groups on the accessible cell surface, followed by the isolation and digestion of these proteins. The labelled peptide fragments and their exact modification sites are identified by nanoLC-MS/MS. The determined peptides are mapped to the primary sequences of TMPs and the labelled sites are utilised as extracellular constraints in topology predictions that contribute to the refined low-resolution structure data of these proteins.
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Affiliation(s)
- Anna Müller
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117, Hungary
| | - Tamás Langó
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117, Hungary
| | - Lilla Turiák
- Institute of Organic Chemistry, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117, Hungary
| | - András Ács
- Institute of Organic Chemistry, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117, Hungary
| | - György Várady
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117, Hungary
| | - Nóra Kucsma
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117, Hungary
| | - László Drahos
- Institute of Organic Chemistry, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117, Hungary
| | - Gábor E Tusnády
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117, Hungary.
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31
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Baumann AL, Hackenberger CPR. Tag and release: strategies for the intracellular cleavage of protein conjugates. Curr Opin Chem Biol 2019; 52:39-46. [DOI: 10.1016/j.cbpa.2019.04.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 01/12/2023]
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32
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Rawale DG, Thakur K, Adusumalli SR, Rai V. Chemical Methods for Selective Labeling of Proteins: Chemical Methods for Selective Labeling of Proteins. European J Org Chem 2019; 2019:6749-63. [DOI: 10.1002/ejoc.201900801] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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33
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Xiong H, Wu X, Wang H, Sun S, Yu J, Cheng J. The Reaction of
o
‐Aminoacetophenone
N
‐Tosylhydrazone and CO
2
toward 1,4‐Dihydro‐2
H
‐3,1‐benzoxazin‐2‐ones. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900341] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hao Xiong
- School of Petrochemical Engineering, Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, Jiangsu Province Key Laboratory of Fine Petrochemical EngineeringChangzhou University Changzhou 213164 People's Republic of China
| | - Xiaopeng Wu
- School of Petrochemical Engineering, Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, Jiangsu Province Key Laboratory of Fine Petrochemical EngineeringChangzhou University Changzhou 213164 People's Republic of China
| | - Hepan Wang
- School of Petrochemical Engineering, Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, Jiangsu Province Key Laboratory of Fine Petrochemical EngineeringChangzhou University Changzhou 213164 People's Republic of China
| | - Song Sun
- School of Petrochemical Engineering, Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, Jiangsu Province Key Laboratory of Fine Petrochemical EngineeringChangzhou University Changzhou 213164 People's Republic of China
| | - Jin‐Tao Yu
- School of Petrochemical Engineering, Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, Jiangsu Province Key Laboratory of Fine Petrochemical EngineeringChangzhou University Changzhou 213164 People's Republic of China
| | - Jiang Cheng
- School of Petrochemical Engineering, Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, Jiangsu Province Key Laboratory of Fine Petrochemical EngineeringChangzhou University Changzhou 213164 People's Republic of China
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34
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Shemsi AM, Khanday FA, Qurashi A, Khalil A, Guerriero G, Siddiqui KS. Site-directed chemically-modified magnetic enzymes: fabrication, improvements, biotechnological applications and future prospects. Biotechnol Adv 2019; 37:357-381. [DOI: 10.1016/j.biotechadv.2019.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/13/2019] [Accepted: 02/08/2019] [Indexed: 02/08/2023]
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35
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Abstract
Site-selective bioconjugation to native protein residues is a powerful tool for protein functionalization, with cysteine and lysine side chains being the most common points for attachment owing to their high nucleophilicity. We now report a strategy for histidine modification using thiophosphorodichloridate reagents that mimic post-translational histidine phosphorylation, enabling fast and selective labeling of protein histidines under mild conditions where various payloads can be introduced via copper-assisted alkyne-azide cycloaddition (CuAAC) chemistry. We establish that these reagents are particularly effective at covalent modification of His-tags, which are common motifs to facilitate protein purification, as illustrated by selective attachment of polyarginine cargoes to enhance the uptake of proteins into living cells. This work provides a starting point for probing and enhancing protein function using histidine-directed chemistry.
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Affiliation(s)
- Shang Jia
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Dan He
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Christopher J Chang
- Department of Chemistry , University of California , Berkeley , California 94720 , United States.,Department of Molecular and Cell Biology , University of California , Berkeley , California 94720 , United States.,Howard Hughes Medical Institute , University of California , Berkeley , California 94720 , United States
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36
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Aydillo C, Mazo N, Navo CD, Jiménez‐Osés G. Elusive Dehydroalanine Derivatives with Enhanced Reactivity. Chembiochem 2019; 20:1246-1250. [DOI: 10.1002/cbic.201800758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Indexed: 02/04/2023]
Affiliation(s)
- Carlos Aydillo
- Departamento de QuímicaUniversidad de La Rioja Madre de Dios, 53 26006 Logroño Spain
- Department of Pharmaceutical Technology and ChemistryFaculty of Pharmacy and NutritionUniversity of Navarra Irunlarrea 3 31008 Pamplona Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA) Irunlarrea 3 31008 Pamplona Spain
| | - Nuria Mazo
- Departamento de QuímicaUniversidad de La Rioja Madre de Dios, 53 26006 Logroño Spain
| | - Claudio D. Navo
- Departamento de QuímicaUniversidad de La Rioja Madre de Dios, 53 26006 Logroño Spain
- CIC bioGUNEBizkaia Technology Park Building 801A 48170 Derio Spain
| | - Gonzalo Jiménez‐Osés
- Departamento de QuímicaUniversidad de La Rioja Madre de Dios, 53 26006 Logroño Spain
- CIC bioGUNEBizkaia Technology Park Building 801A 48170 Derio Spain
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37
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Affiliation(s)
- Htet Htet San
- School of Chemistry and Chemical Engineering and Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, People’s Republic of China
| | - Chun-Ying Wang
- School of Chemistry and Chemical Engineering and Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, People’s Republic of China
| | - Hai-Peng Zeng
- School of Chemistry and Chemical Engineering and Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, People’s Republic of China
| | - Shi-Tao Fu
- School of Chemistry and Chemical Engineering and Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, People’s Republic of China
| | - Min Jiang
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry (SIOC), Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Xiang-Ying Tang
- School of Chemistry and Chemical Engineering and Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, People’s Republic of China
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38
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Ohata J, Martin SC, Ball ZT. Metallvermittelte Funktionalisierung natürlicher Peptide und Proteine: Biokonjugation mit Übergangsmetallen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201807536] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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)
- Jun Ohata
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
| | - Samuel C. Martin
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
| | - Zachary T. Ball
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
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39
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Ohata J, Martin SC, Ball ZT. Metal‐Mediated Functionalization of Natural Peptides and Proteins: Panning for Bioconjugation Gold. Angew Chem Int Ed Engl 2019; 58:6176-6199. [DOI: 10.1002/anie.201807536] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Jun Ohata
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
| | - Samuel C. Martin
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
| | - Zachary T. Ball
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
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40
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41
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Procacci B, Roy SS, Norcott P, Turner N, Duckett SB. Unlocking a Diazirine Long-Lived Nuclear Singlet State via Photochemistry: NMR Detection and Lifetime of an Unstabilized Diazo-Compound. J Am Chem Soc 2018; 140:16855-16864. [PMID: 30407809 PMCID: PMC6300312 DOI: 10.1021/jacs.8b10923] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 11/30/2022]
Abstract
![]()
Diazirines
are important for photoaffinity labeling, and their
photoisomerization is relatively well-known. This work shows how hyperpolarized
NMR spectroscopy can be used to characterize an unstable diazo-compound
formed via photoisomerization of a 15N2-labeled
silyl-ether-substituted diazirine. This diazirine is prepared in a
nuclear spin singlet state via catalytic transfer of spin order from para-hydrogen. The active hyperpolarization catalyst is
characterized to provide insight into the mechanism. The photochemical
isomerization of the diazirine into the diazo-analogue allows the
NMR invisible nuclear singlet state of the parent compound to be probed.
The identity of the diazo-species is confirmed by trapping with N-phenyl maleimide via a cycloaddition reaction to afford
bicyclic pyrazolines that also show singlet state character. The presence
of singlet states in the diazirine and the diazo-compound is validated
by comparison of experimental nutation behavior with theoretical simulation.
The magnetic state lifetime of the diazo-compound is determined as
12 ± 1 s in CD3OD solution at room temperature, whereas
its chemical lifetime is measured as 100 ± 5 s by related hyperpolarized
NMR studies. Indirect evidence for the generation of the photoproduct para-N2 is presented.
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Affiliation(s)
- Barbara Procacci
- Centre for Hyperpolarisation in Magnetic Resonance, Department of Chemistry, York Science Park , University of York , York YO10 5NY , United Kingdom
| | - Soumya S Roy
- Centre for Hyperpolarisation in Magnetic Resonance, Department of Chemistry, York Science Park , University of York , York YO10 5NY , United Kingdom
| | - Philip Norcott
- Centre for Hyperpolarisation in Magnetic Resonance, Department of Chemistry, York Science Park , University of York , York YO10 5NY , United Kingdom
| | - Norman Turner
- Accelerator Research Group, University of Huddersfield , Queensgate, Huddersfield HD1 3DH , United Kingdom
| | - Simon B Duckett
- Centre for Hyperpolarisation in Magnetic Resonance, Department of Chemistry, York Science Park , University of York , York YO10 5NY , United Kingdom
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42
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Affiliation(s)
- Shubo Du
- Department of Chemistry, National University of Singapore, 117543, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 117456, Singapore
| | - Si Si Liew
- Department of Chemistry, National University of Singapore, 117543, Singapore
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, P.R. China
| | - Shao Q. Yao
- Department of Chemistry, National University of Singapore, 117543, Singapore
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43
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Mukherjee H, Grimster NP. Beyond cysteine: recent developments in the area of targeted covalent inhibition. Curr Opin Chem Biol 2018; 44:30-38. [DOI: 10.1016/j.cbpa.2018.05.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/09/2018] [Indexed: 12/28/2022]
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44
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Abstract
Aryldiazoacetates can undergo photolysis under blue light irradiation (460–490 nm) at room temperature and under air in the presence of numerous trapping agents, such as styrene, carboxylic acids, amines, alkanes and arenes, thus providing a straighforward and general platform for their mild functionalization.
Aryldiazoacetates can undergo photolysis under blue light irradiation (460–490 nm) at room temperature and under air in the presence of numerous trapping agents, such as styrene, carboxylic acids, amines, alkanes and arenes, thus providing a straighforward and general platform for their mild functionalization.
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Affiliation(s)
- Igor D Jurberg
- Department of Chemistry , Emory University , 1515 Dickey Drive , Atlanta , Georgia 30322 , USA.,Institute of Chemistry , State University of Campinas , Rua Monteiro Lobato 270 , Campinas , São Paulo 13083-970 , Brazil .
| | - Huw M L Davies
- Department of Chemistry , Emory University , 1515 Dickey Drive , Atlanta , Georgia 30322 , USA
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45
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Iacobucci C, Götze M, Piotrowski C, Arlt C, Rehkamp A, Ihling C, Hage C, Sinz A. Carboxyl-Photo-Reactive MS-Cleavable Cross-Linkers: Unveiling a Hidden Aspect of Diazirine-Based Reagents. Anal Chem 2018; 90:2805-2809. [DOI: 10.1021/acs.analchem.7b04915] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Claudio Iacobucci
- Department of Pharmaceutical Chemistry
and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, Halle/Saale D-06120, Germany
| | - Michael Götze
- Department of Pharmaceutical Chemistry
and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, Halle/Saale D-06120, Germany
| | - Christine Piotrowski
- Department of Pharmaceutical Chemistry
and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, Halle/Saale D-06120, Germany
| | - Christian Arlt
- Department of Pharmaceutical Chemistry
and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, Halle/Saale D-06120, Germany
| | - Anne Rehkamp
- Department of Pharmaceutical Chemistry
and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, Halle/Saale D-06120, Germany
| | - Christian Ihling
- Department of Pharmaceutical Chemistry
and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, Halle/Saale D-06120, Germany
| | - Christoph Hage
- Department of Pharmaceutical Chemistry
and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, Halle/Saale D-06120, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry
and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, Halle/Saale D-06120, Germany
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46
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Zhang X, Wang JH, Tan D, Li Q, Li M, Gong Z, Tang C, Liu Z, Dong MQ, Lei X. Carboxylate-Selective Chemical Cross-Linkers for Mass Spectrometric Analysis of Protein Structures. Anal Chem 2018; 90:1195-1201. [DOI: 10.1021/acs.analchem.7b03789] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Xiaoyun Zhang
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
Synthetic and Functional Biomolecules Center, and Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jian-Hua Wang
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
| | - Dan Tan
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
| | - Qiang Li
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
Synthetic and Functional Biomolecules Center, and Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| | - Maodong Li
- Center
for Quantitative Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhou Gong
- CAS
Key Laboratory of Magnetic Resonance in Biological Systems, State
Key Laboratory of Magnetic Resonance and Atomic Molecular Physics,
National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Chun Tang
- CAS
Key Laboratory of Magnetic Resonance in Biological Systems, State
Key Laboratory of Magnetic Resonance and Atomic Molecular Physics,
National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Zhirong Liu
- Center
for Quantitative Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meng-Qiu Dong
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
| | - Xiaoguang Lei
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
Synthetic and Functional Biomolecules Center, and Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
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47
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Bloom S, Liu C, Kölmel DK, Qiao JX, Zhang Y, Poss MA, Ewing WR, MacMillan DWC. Decarboxylative alkylation for site-selective bioconjugation of native proteins via oxidation potentials. Nat Chem 2017; 10:205-211. [PMID: 29359756 DOI: 10.1038/nchem.2888] [Citation(s) in RCA: 240] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/04/2017] [Indexed: 02/07/2023]
Abstract
The advent of antibody-drug conjugates as pharmaceuticals has fuelled a need for reliable methods of site-selective protein modification that furnish homogeneous adducts. Although bioorthogonal methods that use engineered amino acids often provide an elegant solution to the question of selective functionalization, achieving homogeneity using native amino acids remains a challenge. Here, we explore visible-light-mediated single-electron transfer as a mechanism towards enabling site- and chemoselective bioconjugation. Specifically, we demonstrate the use of photoredox catalysis as a platform to selectivity wherein the discrepancy in oxidation potentials between internal versus C-terminal carboxylates can be exploited towards obtaining C-terminal functionalization exclusively. This oxidation potential-gated technology is amenable to endogenous peptides and has been successfully demonstrated on the protein insulin. As a fundamentally new approach to bioconjugation this methodology provides a blueprint toward the development of photoredox catalysis as a generic platform to target other redox-active side chains for native conjugation.
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Affiliation(s)
- Steven Bloom
- Merck Center for Catalysis at Princeton University, Washington Road, Princeton, New Jersey 08544, USA
| | - Chun Liu
- Merck Center for Catalysis at Princeton University, Washington Road, Princeton, New Jersey 08544, USA
| | - Dominik K Kölmel
- Merck Center for Catalysis at Princeton University, Washington Road, Princeton, New Jersey 08544, USA
| | - Jennifer X Qiao
- Merck Center for Catalysis at Princeton University, Washington Road, Princeton, New Jersey 08544, USA.,Bristol-Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, USA
| | - Yong Zhang
- Merck Center for Catalysis at Princeton University, Washington Road, Princeton, New Jersey 08544, USA.,Bristol-Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, USA
| | - Michael A Poss
- Merck Center for Catalysis at Princeton University, Washington Road, Princeton, New Jersey 08544, USA.,Bristol-Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, USA
| | - William R Ewing
- Merck Center for Catalysis at Princeton University, Washington Road, Princeton, New Jersey 08544, USA.,Bristol-Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, USA
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Washington Road, Princeton, New Jersey 08544, USA
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48
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Kubyshkin V, Budisa N. Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models. Beilstein J Org Chem 2017; 13:2442-2457. [PMID: 29234471 PMCID: PMC5704756 DOI: 10.3762/bjoc.13.241] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 08/04/2017] [Accepted: 10/19/2017] [Indexed: 12/17/2022] Open
Abstract
Fluorinated moieties are highly valuable to chemists due to the sensitive NMR detectability of the 19F nucleus. Fluorination of molecular scaffolds can also selectively influence a molecule's polarity, conformational preferences and chemical reactivity, properties that can be exploited for various chemical applications. A powerful route for incorporating fluorine atoms in biomolecules is last-stage fluorination of peptide scaffolds. One of these methods involves esterification of the C-terminus of peptides using a diazomethane species. Here, we provide an investigation of the physicochemical consequences of peptide esterification with partially fluorinated ethyl groups. Derivatives of N-acetylproline are used to model the effects of fluorination on the lipophilicity, hydrolytic stability and on conformational properties. The conformational impact of the 2,2-difluoromethyl ester on several neutral and charged oligopeptides was also investigated. Our results demonstrate that partially fluorinated esters undergo variable hydrolysis in biologically relevant buffers. The hydrolytic stability can be tailored over a broad pH range by varying the number of fluorine atoms in the ester moiety or by introducing adjacent charges in the peptide sequence.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis group, Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin 10623, Germany
| | - Nediljko Budisa
- Biocatalysis group, Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin 10623, Germany
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49
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Abstract
Cloaking its carboxyl groups with a hydrophobic moiety is shown to enable a protein to enter the cytosol of a mammalian cell. Diazo compounds derived from (p-methylphenyl)glycine were screened for the ability to esterify the green fluorescent protein (GFP) in an aqueous environment. Esterification of GFP with 2-diazo-2-(p-methylphenyl)-N,N-dimethylacetamide was efficient. The esterified protein entered the cytosol by traversing the plasma membrane directly, like a small-molecule prodrug. As with prodrugs, the nascent esters are substrates for endogenous esterases, which regenerate native protein. Thus, esterification could provide a general means to deliver native proteins to the cytosol.
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Affiliation(s)
- Kalie A. Mix
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jo E. Lomax
- Program in Cellular and Molecular Biology, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Ronald T. Raines
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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50
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Peng SQ, Zhang XW, Zhang L, Hu XG. Esterification of Carboxylic Acids with Difluoromethyl Diazomethane and Interrupted Esterification with Trifluoromethyl Diazomethane: A Fluorine Effect. Org Lett 2017; 19:5689-5692. [DOI: 10.1021/acs.orglett.7b02866] [Citation(s) in RCA: 26] [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: 12/14/2022]
Affiliation(s)
- Shan-Qing Peng
- National
Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang, 330022, China
| | - Xiao-Wei Zhang
- National
Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang, 330022, China
| | - Long Zhang
- Key
Laboratory for Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xiang-Guo Hu
- National
Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang, 330022, China
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