1
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Giltrap A, Yuan Y, Davis BG. Late-Stage Functionalization of Living Organisms: Rethinking Selectivity in Biology. Chem Rev 2024; 124:889-928. [PMID: 38231473 PMCID: PMC10870719 DOI: 10.1021/acs.chemrev.3c00579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/18/2024]
Abstract
With unlimited selectivity, full post-translational chemical control of biology would circumvent the dogma of genetic control. The resulting direct manipulation of organisms would enable atomic-level precision in "editing" of function. We argue that a key aspect that is still missing in our ability to do this (at least with a high degree of control) is the selectivity of a given chemical reaction in a living organism. In this Review, we systematize existing illustrative examples of chemical selectivity, as well as identify needed chemical selectivities set in a hierarchy of anatomical complexity: organismo- (selectivity for a given organism over another), tissuo- (selectivity for a given tissue type in a living organism), cellulo- (selectivity for a given cell type in an organism or tissue), and organelloselectivity (selectivity for a given organelle or discrete body within a cell). Finally, we analyze more traditional concepts such as regio-, chemo-, and stereoselective reactions where additionally appropriate. This survey of late-stage biomolecule methods emphasizes, where possible, functional consequences (i.e., biological function). In this way, we explore a concept of late-stage functionalization of living organisms (where "late" is taken to mean at a given state of an organism in time) in which programmed and selective chemical reactions take place in life. By building on precisely analyzed notions (e.g., mechanism and selectivity) we believe that the logic of chemical methodology might ultimately be applied to increasingly complex molecular constructs in biology. This could allow principles developed at the simple, small-molecule level to progress hierarchically even to manipulation of physiology.
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Affiliation(s)
- Andrew
M. Giltrap
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Yizhi Yuan
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Benjamin G. Davis
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
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2
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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] [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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3
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Köckenberger J, Klemt I, Sauer C, Arkhypov A, Reshetnikov V, Mokhir A, Heinrich MR. Cyanine- and Rhodamine-Derived Alkynes for the Selective Targeting of Cancerous Mitochondria through Radical Thiol-Yne Coupling in Live Cells. Chemistry 2023; 29:e202301340. [PMID: 37171462 DOI: 10.1002/chem.202301340] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/13/2023]
Abstract
Despite their long history and their synthetic potential underlined by various recent advances, radical thiol-yne coupling reactions have so far only rarely been exploited for the functionalization of biomolecules, and no examples yet exist for their application in live cells - although natural thiols show widespread occurrence therein. By taking advantage of the particular cellular conditions of mitochondria in cancer cells, we have demonstrated that radical thiol-yne coupling represents a powerful reaction principle for the selective targeting of these organelles. Within our studies, fluorescently labeled reactive alkyne probes were investigated, for which the fluorescent moiety was chosen to enable both mitochondria accumulation as well as highly sensitive detection. After preliminary studies under cell-free conditions, the most promising alkyne-dye conjugates were evaluated in various cellular experiments comprising analysis by flow cytometry and microscopy. All in all, these results pave the way for improved future therapeutic strategies relying on live-cell compatibility and selectivity among cellular compartments.
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Affiliation(s)
- Johannes Köckenberger
- Department of Chemistry and Pharmacy Pharmaceutical Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Insa Klemt
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Caroline Sauer
- Department of Chemistry and Pharmacy Pharmaceutical Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Anton Arkhypov
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Viktor Reshetnikov
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Andriy Mokhir
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Markus R Heinrich
- Department of Chemistry and Pharmacy Pharmaceutical Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
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4
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Chen X, Josephson B, Davis BG. Carbon-Centered Radicals in Protein Manipulation. ACS CENTRAL SCIENCE 2023; 9:614-638. [PMID: 37122447 PMCID: PMC10141601 DOI: 10.1021/acscentsci.3c00051] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Indexed: 05/03/2023]
Abstract
Methods to directly post-translationally modify proteins are perhaps the most straightforward and operationally simple ways to create and study protein post-translational modifications (PTMs). However, precisely altering or constructing the C-C scaffolds pervasive throughout biology is difficult with common two-electron chemical approaches. Recently, there has been a surge of new methods that have utilized single electron/radical chemistry applied to site-specifically "edit" proteins that have started to create this potential-one that in principle could be near free-ranging. This review provides an overview of current methods that install such "edits", including those that generate function and/or PTMs, through radical C-C bond formation (as well as C-X bond formation via C• where illustrative). These exploit selectivity for either native residues, or preinstalled noncanonical protein side-chains with superior radical generating or accepting abilities. Particular focus will be on the radical generation approach (on-protein or off-protein, use of light and photocatalysts), judging the compatibility of conditions with proteins and cells, and novel chemical biology applications afforded by these methods. While there are still many technical hurdles, radical C-C bond formation on proteins is a promising and rapidly growing area in chemical biology with long-term potential for biological editing.
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Affiliation(s)
- Xuanxiao Chen
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
- The
Rosalind Franklin Institute, Oxfordshire, OX11 OFA, U.K.
| | - Brian Josephson
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
| | - Benjamin G. Davis
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
- The
Rosalind Franklin Institute, Oxfordshire, OX11 OFA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford, OX1 3QT, U.K.
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5
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Shen MH, Wang YJ, Wang Y, Zhou Y, Gu J, Liu XQ, Guo J, Ouyang M, Deng L, Xu HD. α-Vinyl azide–cysteine click coupling reaction enabled bioorthogonal peptide/protein modification. Org Chem Front 2022. [DOI: 10.1039/d2qo00736c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
α-Alkyl and α-aryl vinyl azides were found to be able to couple with cysteine-derived alkyl thiols chemoselectively under mild conditions, providing the corresponding β-ketosulfides with simultaneous extrusion of N2 and ammonia.
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Affiliation(s)
- Mei-Hua Shen
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Yu-Jiao Wang
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Yong Wang
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Ying Zhou
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Jie Gu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Xiao-Qian Liu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Jia Guo
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Mingxing Ouyang
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Linhong Deng
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Hua-Dong Xu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
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6
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McLean JT, Benny A, Nolan MD, Swinand G, Scanlan EM. Cysteinyl radicals in chemical synthesis and in nature. Chem Soc Rev 2021; 50:10857-10894. [PMID: 34397045 DOI: 10.1039/d1cs00254f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nature harnesses the unique properties of cysteinyl radical intermediates for a diverse range of essential biological transformations including DNA biosynthesis and repair, metabolism, and biological photochemistry. In parallel, the synthetic accessibility and redox chemistry of cysteinyl radicals renders them versatile reactive intermediates for use in a vast array of synthetic applications such as lipidation, glycosylation and fluorescent labelling of proteins, peptide macrocyclization and stapling, desulfurisation of peptides and proteins, and development of novel therapeutics. This review provides the reader with an overview of the role of cysteinyl radical intermediates in both chemical synthesis and biological systems, with a critical focus on mechanistic details. Direct insights from biological systems, where applied to chemical synthesis, are highlighted and potential avenues from nature which are yet to be explored synthetically are presented.
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Affiliation(s)
- Joshua T McLean
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Alby Benny
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Mark D Nolan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Glenna Swinand
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Eoin M Scanlan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
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7
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Fairbanks BD, Macdougall LJ, Mavila S, Sinha J, Kirkpatrick BE, Anseth KS, Bowman CN. Photoclick Chemistry: A Bright Idea. Chem Rev 2021; 121:6915-6990. [PMID: 33835796 PMCID: PMC9883840 DOI: 10.1021/acs.chemrev.0c01212] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
At its basic conceptualization, photoclick chemistry embodies a collection of click reactions that are performed via the application of light. The emergence of this concept has had diverse impact over a broad range of chemical and biological research due to the spatiotemporal control, high selectivity, and excellent product yields afforded by the combination of light and click chemistry. While the reactions designated as "photoclick" have many important features in common, each has its own particular combination of advantages and shortcomings. A more extensive realization of the potential of this chemistry requires a broader understanding of the physical and chemical characteristics of the specific reactions. This review discusses the features of the most frequently employed photoclick reactions reported in the literature: photomediated azide-alkyne cycloadditions, other 1,3-dipolarcycloadditions, Diels-Alder and inverse electron demand Diels-Alder additions, radical alternating addition chain transfer additions, and nucleophilic additions. Applications of these reactions in a variety of chemical syntheses, materials chemistry, and biological contexts are surveyed, with particular attention paid to the respective strengths and limitations of each reaction and how that reaction benefits from its combination with light. Finally, challenges to broader employment of these reactions are discussed, along with strategies and opportunities to mitigate such obstacles.
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Affiliation(s)
- Benjamin D Fairbanks
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Laura J Macdougall
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Sudheendran Mavila
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Jasmine Sinha
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Bruce E Kirkpatrick
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
- The BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
- Medical Scientist Training Program, School of Medicine, University of Colorado, Aurora, Coorado 80045, United States
| | - Kristi S Anseth
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
- The BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Christopher N Bowman
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
- Materials Science and Engineering Program, University of Colorado, Boulder, Colorado 80303, United States
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8
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Waddington MA, Zheng X, Stauber JM, Hakim Moully E, Montgomery HR, Saleh LMA, Král P, Spokoyny AM. An Organometallic Strategy for Cysteine Borylation. J Am Chem Soc 2021; 143:8661-8668. [PMID: 34060827 DOI: 10.1021/jacs.1c02206] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Synthetic bioconjugation at cysteine (Cys) residues in peptides and proteins has emerged as a powerful tool in chemistry. Soft nucleophilicity of the sulfur in Cys renders an exquisite chemoselectivity with which various functional groups can be placed onto this residue under benign conditions. While a variety of reactions have been successful at producing Cys-based bioconjugates, the majority of these feature sulfur-carbon bonds. We report Cys-borylation, wherein a benchtop stable Pt(II)-based organometallic reagent can be used to transfer a boron-rich cluster onto a sulfur moiety in unprotected peptides forging a boron-sulfur bond. Cys-borylation proceeds at room temperature and tolerates a variety of functional groups present in complex polypeptides. Further, the bioconjugation strategy can be applied to a model protein modification of Cys-containing DARPin (designed ankyrin repeat protein). The resultant bioconjugates show no additional toxicity compared to their Cys alkyl-based congeners. Finally, we demonstrate how the developed Cys-borylation can enhance the proteolytic stability of the resultant peptide bioconjugates while maintaining the binding affinity to a protein target.
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Affiliation(s)
- Mary A Waddington
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Xin Zheng
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Julia M Stauber
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Elamar Hakim Moully
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Hayden R Montgomery
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Liban M A Saleh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States.,Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Alexander M Spokoyny
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States.,California NanoSystems Institute (CNSI), University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, California 90095, United States
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9
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Zheng J, Mao Y, Feng S, Tian R. Combining Metabolic Alkyne Labeling and Click Chemistry for Secretome Analysis of
Serum‐Containing
Conditioned Medium
†. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202000752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jiangnan Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen Guangdong 518055 China
| | - Yuan Mao
- School of Life Science and Engineering, Southwest Jiaotong University Chengdu Sichuan 610031 China
| | - Shun Feng
- School of Life Science and Engineering, Southwest Jiaotong University Chengdu Sichuan 610031 China
| | - Ruijun Tian
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen Guangdong 518055 China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology 1088 Xueyuan Road Shenzhen Guangdong 518055 China
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10
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Naowarojna N, Cheng R, Lopez J, Wong C, Qiao L, Liu P. Chemical modifications of proteins and their applications in metalloenzyme studies. Synth Syst Biotechnol 2021; 6:32-49. [PMID: 33665390 PMCID: PMC7897936 DOI: 10.1016/j.synbio.2021.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/14/2020] [Accepted: 01/03/2021] [Indexed: 12/21/2022] Open
Abstract
Protein chemical modifications are important tools for elucidating chemical and biological functions of proteins. Several strategies have been developed to implement these modifications, including enzymatic tailoring reactions, unnatural amino acid incorporation using the expanded genetic codes, and recognition-driven transformations. These technologies have been applied in metalloenzyme studies, specifically in dissecting their mechanisms, improving their enzymatic activities, and creating artificial enzymes with non-natural activities. Herein, we summarize some of the recent efforts in these areas with an emphasis on a few metalloenzyme case studies.
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Affiliation(s)
| | | | - Juan Lopez
- Department of Chemistry, Boston University, Boston, MA, 02215, United States
| | - Christina Wong
- Department of Chemistry, Boston University, Boston, MA, 02215, United States
| | - Lu Qiao
- Department of Chemistry, Boston University, Boston, MA, 02215, United States
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA, 02215, United States
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11
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Li J, Deng JJ, Yin Z, Hu QL, Ge Y, Song Z, Zhang Y, Chan ASC, Li H, Xiong XF. Cleavable and tunable cysteine-specific arylation modification with aryl thioethers. Chem Sci 2021; 12:5209-5215. [PMID: 34168774 PMCID: PMC8179606 DOI: 10.1039/d0sc06576e] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/10/2021] [Indexed: 12/29/2022] Open
Abstract
Cysteine represents an attractive target for peptide/protein modification due to the intrinsic high nucleophilicity of the thiol group and low natural abundance. Herein, a cleavable and tunable covalent modification approach for cysteine containing peptides/proteins with our newly designed aryl thioethers via a S N Ar approach was developed. Highly efficient and selective bioconjugation reactions can be carried out under mild and biocompatible conditions. A series of aryl groups bearing different bioconjugation handles, affinity or fluorescent tags are well tolerated. By adjusting the skeleton and steric hindrance of aryl thioethers slightly, the modified products showed a tunable profile for the regeneration of the native peptides.
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Affiliation(s)
- Jian Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Jun-Jie Deng
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Zhibin Yin
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Qi-Long Hu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Yang Ge
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Zhendong Song
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Ying Zhang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Albert S C Chan
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Huilin Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
| | - Xiao-Feng Xiong
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University Guangzhou 510006 P. R. China
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12
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Guo AD, Wu KH, Chen XH. Light-induced efficient and residue-selective bioconjugation of native proteins via indazolone formation. RSC Adv 2021; 11:2235-2241. [PMID: 35424183 PMCID: PMC8693682 DOI: 10.1039/d0ra10154k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 12/15/2020] [Indexed: 12/03/2022] Open
Abstract
Chemical modification of proteins has emerged as a powerful tool to realize enormous applications, such as development of novel biologics and functional studies of individual protein. We report a light-induced lysine-selective native protein conjugation approach via indazolone formation, conferring reliable chemoselectivity, excellent efficiency, temporal control and biocompatibility under operationally simple and mild conditions, in vitro and in living systems. This straightforward protocol demonstrates the generality and accessibility for direct and rapid functionalization of diverse native proteins, which suggests a new avenue of great importance to bioconjugation, medicinal chemistry and chemical biology.
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Affiliation(s)
- An-Di Guo
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Ke-Huan Wu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Xiao-Hua Chen
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine Nanjing 210023 China
- University of Chinese Academy of Sciences Beijing 100049 China
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13
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Verhelst SHL, Bonger KM, Willems LI. Bioorthogonal Reactions in Activity-Based Protein Profiling. Molecules 2020; 25:E5994. [PMID: 33352858 PMCID: PMC7765892 DOI: 10.3390/molecules25245994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/27/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a powerful technique to label and detect active enzyme species within cell lysates, cells, or whole animals. In the last two decades, a wide variety of applications and experimental read-out techniques have been pursued in order to increase our understanding of physiological and pathological processes, to identify novel drug targets, to evaluate selectivity of drugs, and to image probe targets in cells. Bioorthogonal chemistry has substantially contributed to the field of ABPP, as it allows the introduction of tags, which may be bulky or have unfavorable physicochemical properties, at a late stage in the experiment. In this review, we give an overview of the bioorthogonal reactions that have been implemented in ABPP, provide examples of applications of bioorthogonal chemistry in ABPP, and share some thoughts on future directions.
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Affiliation(s)
- Steven H. L. Verhelst
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven, Herestr. 49, Box 802, 3000 Leuven, Belgium
- AG Chemical Proteomics, Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Kimberly M. Bonger
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Lianne I. Willems
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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14
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Nolan MD, Scanlan EM. Applications of Thiol-Ene Chemistry for Peptide Science. Front Chem 2020; 8:583272. [PMID: 33282831 PMCID: PMC7689097 DOI: 10.3389/fchem.2020.583272] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022] Open
Abstract
Radical thiol-ene chemistry has been demonstrated for a range of applications in peptide science, including macrocyclization, glycosylation and lipidation amongst a myriad of others. The thiol-ene reaction offers a number of advantages in this area, primarily those characteristic of "click" reactions. This provides a chemical approach to peptide modification that is compatible with aqueous conditions with high orthogonality and functional group tolerance. Additionally, the use of a chemical approach for peptide modification affords homogeneous peptides, compared to heterogeneous mixtures often obtained through biological methods. In addition to peptide modification, thiol-ene chemistry has been applied in novel approaches to biological studies through synthesis of mimetics and use in development of probes. This review will cover the range of applications of the radical-mediated thiol-ene reaction in peptide and protein science.
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Affiliation(s)
- Mark D Nolan
- School of Chemistry, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin, Ireland
| | - Eoin M Scanlan
- School of Chemistry, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin, Ireland
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15
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Recent advances of thiol-selective bioconjugation reactions. Curr Opin Chem Biol 2020; 58:28-36. [DOI: 10.1016/j.cbpa.2020.04.017] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 01/09/2023]
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16
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Borbás A. Photoinitiated Thiol-ene Reactions of Enoses: A Powerful Tool for Stereoselective Synthesis of Glycomimetics with Challenging Glycosidic Linkages. Chemistry 2020; 26:6090-6101. [PMID: 31910299 PMCID: PMC7317871 DOI: 10.1002/chem.201905408] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/03/2020] [Indexed: 12/21/2022]
Abstract
Thioglycosides and C-glycosides represent pharmacologically useful classes of glycomimetics that possess a high degree of biological stability. One emerging tool for the stereoselective synthesis of thioglycosides is the photoinitiated addition of thiols to unsaturated sugars. Moreover, thiyl radical-mediated reactions of exo-glycals and 1-substituted endo-glycals offer facile routes to β-C-glycosidic structures. This Concept article summarizes the thiol-ene coupling strategies developed recently by our group and Somsák's group for the synthesis of several kinds of glycomimetics which are difficult to synthesize by conventional methods. One unusual characteristic of the thiol-ene reactions of endo-glycals is that heating inhibits, whereas cooling promotes the reaction. This unique temperature dependence as well as the effects of the enose structures and thiol configurations on the efficacy and stereoselectivity of the reactions are also discussed.
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Affiliation(s)
- Anikó Borbás
- Department of Pharmaceutical ChemistryUniversity of DebrecenEgyetem tér 14032DebrecenHungary
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17
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Passos MLC, Sousa E, Saraiva MLMFS. Immobilized imidazolium-based ionic liquids in C18 for solid-phase extraction. Analyst 2020; 145:2701-2708. [PMID: 32072997 DOI: 10.1039/c9an02479d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, two solid-phases based on imidazolium-based ionic liquids were obtained and characterized for solid-phase extraction of fluoroquinolones. The process of immobilization was performed replacing a toxic reagent by UV-irradiation to get a harmless process. The obtained solid-phases were characterized by nuclear magnetic resonance spectroscopy and elemental analysis. Each solid-phase was packed in a cartridge and was used in solid-phase extraction processes for norfloxacin and ciprofloxacin, after the optimization of some parameters such as the elution solvent, the eluent volume and, the sample volume to be used during the loading step. The developed solid-phases with immobilized ionic liquids were successfully implemented for the studied compounds and indicate high probabilities to be useful in solid-phase extractions of other fluoroquinolones.
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Affiliation(s)
- Marieta L C Passos
- LAQV, REQUIMTE, Department of Chemical Sciences, Laboratory of Applied Chemistry, Faculty of Pharmacy, Porto University, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
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18
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Reddy NC, Kumar M, Molla R, Rai V. Chemical methods for modification of proteins. Org Biomol Chem 2020; 18:4669-4691. [DOI: 10.1039/d0ob00857e] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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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19
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Gupta K, Toombes GE, Swartz KJ. Exploring structural dynamics of a membrane protein by combining bioorthogonal chemistry and cysteine mutagenesis. eLife 2019; 8:50776. [PMID: 31714877 PMCID: PMC6850778 DOI: 10.7554/elife.50776] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022] Open
Abstract
The functional mechanisms of membrane proteins are extensively investigated with cysteine mutagenesis. To complement cysteine-based approaches, we engineered a membrane protein with thiol-independent crosslinkable groups using azidohomoalanine (AHA), a non-canonical methionine analogue containing an azide group that can selectively react with cycloalkynes through a strain-promoted azide-alkyne cycloaddition (SPAAC) reaction. We demonstrate that AHA can be readily incorporated into the Shaker Kv channel in place of methionine residues and modified with azide-reactive alkyne probes in Xenopus oocytes. Using voltage-clamp fluorometry, we show that AHA incorporation permits site-specific fluorescent labeling to track voltage-dependent conformational changes similar to cysteine-based methods. By combining AHA incorporation and cysteine mutagenesis in an orthogonal manner, we were able to site-specifically label the Shaker Kv channel with two different fluorophores simultaneously. Our results identify a facile and straightforward approach for chemical modification of membrane proteins with bioorthogonal chemistry to explore their structure-function relationships in live cells. Living cells can sense cues from their environment via molecules located at the interface between the inside and the outside of the cell. These molecules are mostly proteins and are made up of building blocks known as amino acids. To understand how these proteins work, fluorescent probes can be attached to amino acids within them – which can then tell when different parts of proteins move in response to a signal. Scientists often target fluorescent probes at the amino acid cysteine, because it has a chemically reactive side group and is rare enough so that unique positions can be labeled in the protein of interest. However, being able to target other amino acids would allow scientists to ask, and potentially solve, more precise questions about these proteins. Methionine is another amino acid that has a low abundance in most proteins. Previous research has shown that the cell’s normal protein-building machinery can incorporate synthetic versions of methionine into proteins. This suggested that the introduction of chemically reactive alternatives to methionine could offer a way to label membrane proteins with fluorescent probes and free up the cysteines to be targeted with other approaches. Gupta et al. set out to develop a straightforward method to achieve this and started with a well-studied membrane protein, called Shaker, and cells from female African clawed frogs, which are widely used to study membrane proteins. Gupta et al. found that the cells could readily take up a chemically reactive methionine alternative called azidohomoalanine (AHA) from their surrounding solution and incorporate it within the Shaker protein. The AHA took the place of the methionines that are normally found in Shaker, and just like in cysteine-based methods, fluorescent probes could be easily attached to the AHAs in this membrane protein. Shaker is a protein that allows potassium ions to flow across the cell membrane by changing shape in response to the membrane voltage. The fluorescence from those probes also changed with the membrane voltage in a way that was comparable to cysteine-mediated approaches. This indicated that the AHA modification could also be used to track structural changes in the Shaker protein. Finally, Gupta et al. showed that AHA- and cysteine-mediated labeling approaches could be combined to attach two different fluorescent probes onto the Shaker protein. This method will expand the toolbox for researchers studying the relationship between the structure and function of membrane proteins in live cells. In future, it could be applied more widely once the properties of the fluorescent probes for AHA-mediated labeling can be optimized.
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Affiliation(s)
- Kanchan Gupta
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, United States
| | - Gilman Es Toombes
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, United States
| | - Kenton J Swartz
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, United States
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20
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Scalabrini M, Hamon J, Linossier I, Ferrières V, Réhel K. Pseudomonas aeruginosa resistance of monosaccharide-functionalized glass surfaces. Colloids Surf B Biointerfaces 2019; 183:110383. [DOI: 10.1016/j.colsurfb.2019.110383] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/16/2019] [Accepted: 07/19/2019] [Indexed: 01/10/2023]
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21
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Kalhor HR, Rezaei M. Conversion of 3,6‐O‐Dimethylfluorescein to Fluorescein‐Based Xanthylium Derivative: Characterization and Covalent Attachment to Bovine Serum Albumin. ChemistrySelect 2019. [DOI: 10.1002/slct.201902296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Hamid Reza Kalhor
- Biochemistry Research LaboratoryChemistry Department, SharifUniversity of technology, Tehran Iran
| | - Mohsen Rezaei
- Biochemistry Research LaboratoryChemistry Department, SharifUniversity of technology, Tehran Iran
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22
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Affiliation(s)
- Seiji SAKAMOTO
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University
| | - Itaru HAMACHI
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University
- ERATO Innovative Molecular Technology for Neuroscience Project, Japan Science and Technology Agency (JST)
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23
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Zhang Y, Park KY, Suazo KF, Distefano MD. Recent progress in enzymatic protein labelling techniques and their applications. Chem Soc Rev 2018; 47:9106-9136. [PMID: 30259933 PMCID: PMC6289631 DOI: 10.1039/c8cs00537k] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein-based conjugates are valuable constructs for a variety of applications. Conjugation of proteins to fluorophores is commonly used to study their cellular localization and the protein-protein interactions. Modification of therapeutic proteins with either polymers or cytotoxic moieties greatly enhances their pharmacokinetics or potency. To label a protein of interest, conventional direct chemical reaction with the side-chains of native amino acids often yields heterogeneously modified products. This renders their characterization complicated, requires difficult separation steps and may impact protein function. Although modification can also be achieved via the insertion of unnatural amino acids bearing bioorthogonal functional groups, these methods can have lower protein expression yields, limiting large scale production. As a site-specific modification method, enzymatic protein labelling is highly efficient and robust under mild reaction conditions. Significant progress has been made over the last five years in modifying proteins using enzymatic methods for numerous applications, including the creation of clinically relevant conjugates with polymers, cytotoxins or imaging agents, fluorescent or affinity probes to study complex protein interaction networks, and protein-linked materials for biosensing. This review summarizes developments in enzymatic protein labelling over the last five years for a panel of ten enzymes, including sortase A, subtiligase, microbial transglutaminase, farnesyltransferase, N-myristoyltransferase, phosphopantetheinyl transferases, tubulin tyrosin ligase, lipoic acid ligase, biotin ligase and formylglycine generating enzyme.
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Affiliation(s)
- Yi Zhang
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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24
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Sun S, Oliveira BL, Jiménez‐Osés G, Bernardes GJL. Radical-Mediated Thiol-Ene Strategy: Photoactivation of Thiol-Containing Drugs in Cancer Cells. Angew Chem Int Ed Engl 2018; 57:15832-15835. [PMID: 30300959 PMCID: PMC6391964 DOI: 10.1002/anie.201811338] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Indexed: 12/28/2022]
Abstract
Photoactivated drugs provide an opportunity to improve efficacy alongside reducing side-effects in the treatment of severe diseases such as cancer. Described herein is a photoactivation decaging method of isobutylene-caged thiols through a UV-initiated thiol-ene reaction. The method was demonstrated with an isobutylene-caged cysteine, cyclic disulfide-peptide, and thiol-containing drug, all of which were rapidly and efficiently released under mild UV irradiation in the presence of thiol sources and a photoinitiator. Importantly, it is shown that the activity of histone deacetylase inhibitor largazole can be switched off when stapled, but selectively switched on within cancer cells when irradiated with non-phototoxic light.
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Affiliation(s)
- Shuang Sun
- Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
| | - Bruno L. Oliveira
- Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
| | - Gonzalo Jiménez‐Osés
- Departamento de Química.Centro de Investigación en Síntesis Química.Universidad de La Rioja26006LogroñoSpain
| | - Gonçalo J. L. Bernardes
- Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
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25
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Marra A, Dong J, Ma T, Giuntini S, Crescenzo E, Cerofolini L, Martinucci M, Luchinat C, Fragai M, Nativi C, Dondoni A. Protein Glycosylation through Sulfur Fluoride Exchange (SuFEx) Chemistry: The Key Role of a Fluorosulfate Thiolactoside. Chemistry 2018; 24:18981-18987. [PMID: 30252969 DOI: 10.1002/chem.201803912] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/23/2018] [Indexed: 11/09/2022]
Abstract
Protein glycosylation is the most complex post-translational modification process. More than 50 % of human cells proteins are glycosylated, whereas bacteria such as E. coli do not have this modification machinery. Indeed, the carbohydrate residues in natural proteins affect their folding, immunogenicity, and stability toward proteases, besides controlling biological properties and activities. It is therefore important to introduce such structural modification in bioengineered proteins lacking the presence of carbohydrate residues. This is not trivial as it requires reagents and conditions compatible with the protein's stability and reactivity. This work reports on the introduction of lactose moieties in two natural proteins, namely ubiquitin (Ub) and l-asparaginase II (ANSII). The synthetic route employed is based on the sulfur(VI) fluoride exchange (SuFEx) coupling of a lactose tethered arylfluorosulfate (Lact-Ar-OSO2 F) with the ϵ-NH2 group of lysine residues of the proteins. This metal-free click SuFEx reaction relies on the properties of the fluorosulfate employed, which is easily prepared in multigram scale from available precursors and reacts chemoselectively with the ϵ-NH2 group of lysine residues under mild conditions. Thus, iterative couplings of Lact-Ar-OSO2 F to Ub and ANSII, afforded multiple glycosylations of these proteins so that up to three and four Lact-Ar-OSO2 groups were introduced in Ub and ANSII, respectively, via the formation of a sulfamoyl (OSO2 -NH) linkage.
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Affiliation(s)
- Alberto Marra
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, Université de Montpellier, CNRS, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, 34296, Montpellier- cedex 5, France
| | - Jiajia Dong
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, P. R. China
| | - Tiancheng Ma
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, P. R. China
| | - Stefano Giuntini
- Department of Chemistry, University of Florence, via della Lastruccia, 3-13, Sesto F.no (FI), 50019, Italy.,CERM and CIRMMP, via Luigi Sacconi, 6, 50019, Sesto F.no (FI), Italy
| | - Elisa Crescenzo
- Department of Chemistry, University of Florence, via della Lastruccia, 3-13, Sesto F.no (FI), 50019, Italy.,CERM and CIRMMP, via Luigi Sacconi, 6, 50019, Sesto F.no (FI), Italy
| | - Linda Cerofolini
- Department of Chemistry, University of Florence, via della Lastruccia, 3-13, Sesto F.no (FI), 50019, Italy.,CERM and CIRMMP, via Luigi Sacconi, 6, 50019, Sesto F.no (FI), Italy
| | - Marco Martinucci
- Department of Chemistry, University of Florence, via della Lastruccia, 3-13, Sesto F.no (FI), 50019, Italy
| | - Claudio Luchinat
- Department of Chemistry, University of Florence, via della Lastruccia, 3-13, Sesto F.no (FI), 50019, Italy.,CERM and CIRMMP, via Luigi Sacconi, 6, 50019, Sesto F.no (FI), Italy
| | - Marco Fragai
- Department of Chemistry, University of Florence, via della Lastruccia, 3-13, Sesto F.no (FI), 50019, Italy.,CERM and CIRMMP, via Luigi Sacconi, 6, 50019, Sesto F.no (FI), Italy
| | - Cristina Nativi
- Department of Chemistry, University of Florence, via della Lastruccia, 3-13, Sesto F.no (FI), 50019, Italy
| | - Alessandro Dondoni
- Interdisciplinary Center for the Study of Inflammation, University of, Ferrara, Italy
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26
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Sun S, Oliveira BL, Jiménez-Osés G, Bernardes GJL. Radical-Mediated Thiol-Ene Strategy: Photoactivation of Thiol-Containing Drugs in Cancer Cells. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811338] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Shuang Sun
- Department of Chemistry; University of Cambridge; Lensfield Road CB2 1EW Cambridge UK
| | - Bruno L. Oliveira
- Department of Chemistry; University of Cambridge; Lensfield Road CB2 1EW Cambridge UK
| | - Gonzalo Jiménez-Osés
- Departamento de Química.; Centro de Investigación en Síntesis Química.; Universidad de La Rioja; 26006 Logroño Spain
| | - Gonçalo J. L. Bernardes
- Department of Chemistry; University of Cambridge; Lensfield Road CB2 1EW Cambridge UK
- Instituto de Medicina Molecular; Faculdade de Medicina; Universidade de Lisboa; Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
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27
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Yu J, Yang X, Sun Y, Yin Z. Highly Reactive and Tracelessly Cleavable Cysteine‐Specific Modification of Proteins via 4‐Substituted Cyclopentenone. Angew Chem Int Ed Engl 2018; 57:11598-11602. [DOI: 10.1002/anie.201804801] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/12/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Jian Yu
- Center of Basic Molecular Science (CBMS)Department of ChemistryTsinghua University Beijing 100084 China
| | - Xiaoyue Yang
- Center of Basic Molecular Science (CBMS)Department of ChemistryTsinghua University Beijing 100084 China
| | - Yang Sun
- Center of Basic Molecular Science (CBMS)Department of ChemistryTsinghua University Beijing 100084 China
| | - Zheng Yin
- Center of Basic Molecular Science (CBMS)Department of ChemistryTsinghua University Beijing 100084 China
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28
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Abstract
The conjugation of biomolecules can impart materials with the bioactivity necessary to modulate specific cell behaviors. While the biological roles of particular polypeptide, oligonucleotide, and glycan structures have been extensively reviewed, along with the influence of attachment on material structure and function, the key role played by the conjugation strategy in determining activity is often overlooked. In this review, we focus on the chemistry of biomolecule conjugation and provide a comprehensive overview of the key strategies for achieving controlled biomaterial functionalization. No universal method exists to provide optimal attachment, and here we will discuss both the relative advantages and disadvantages of each technique. In doing so, we highlight the importance of carefully considering the impact and suitability of a particular technique during biomaterial design.
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Affiliation(s)
- Christopher D. Spicer
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, Stockholm, Sweden
| | - E. Thomas Pashuck
- NJ
Centre for Biomaterials, Rutgers University, 145 Bevier Road, Piscataway, New Jersey United States
| | - Molly M. Stevens
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, Stockholm, Sweden
- Department
of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, Exhibition Road, London, United Kingdom
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29
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Yu J, Yang X, Sun Y, Yin Z. Highly Reactive and Tracelessly Cleavable Cysteine-Specific Modification of Proteins via 4-Substituted Cyclopentenone. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jian Yu
- Center of Basic Molecular Science (CBMS); Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Xiaoyue Yang
- Center of Basic Molecular Science (CBMS); Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Yang Sun
- Center of Basic Molecular Science (CBMS); Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Zheng Yin
- Center of Basic Molecular Science (CBMS); Department of Chemistry; Tsinghua University; Beijing 100084 China
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30
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Bakkum T, van Leeuwen T, Sarris AJC, van Elsland DM, Poulcharidis D, Overkleeft HS, van Kasteren SI. Quantification of Bioorthogonal Stability in Immune Phagocytes Using Flow Cytometry Reveals Rapid Degradation of Strained Alkynes. ACS Chem Biol 2018; 13:1173-1179. [PMID: 29693370 PMCID: PMC5962927 DOI: 10.1021/acschembio.8b00355] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
One of the areas
in which bioorthogonal chemistry—chemistry
performed inside a cell or organism—has become of pivotal importance
is in the study of host–pathogen interactions. The incorporation
of bioorthogonal groups into the cell wall or proteome of intracellular
pathogens has allowed study within the endolysosomal system. However,
for the approach to be successful, the incorporated bioorthogonal
groups must be stable to chemical conditions found within these organelles,
which are some of the harshest found in metazoans: the groups are
exposed to oxidizing species, acidic conditions, and reactive thiols.
Here we present an assay that allows the assessment of the stability
of bioorthogonal groups within host cell phagosomes. Using a flow
cytometry-based assay, we have quantified the relative label stability
inside dendritic cell phagosomes of strained and unstrained alkynes.
We show that groups that were shown to be stable in other systems
were degraded by as much as 79% after maturation of the phagosome.
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Affiliation(s)
- Thomas Bakkum
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Tyrza van Leeuwen
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Alexi J. C. Sarris
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Daphne M. van Elsland
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Dimitrios Poulcharidis
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Sander I. van Kasteren
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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31
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Zhang C, Dai P, Vinogradov AA, Gates ZP, Pentelute BL. Site-Selective Cysteine-Cyclooctyne Conjugation. Angew Chem Int Ed Engl 2018; 57:6459-6463. [PMID: 29575377 DOI: 10.1002/anie.201800860] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/07/2018] [Indexed: 11/06/2022]
Abstract
We report a site-selective cysteine-cyclooctyne conjugation reaction between a seven-residue peptide tag (DBCO-tag, Leu-Cys-Tyr-Pro-Trp-Val-Tyr) at the N or C terminus of a peptide or protein and various aza-dibenzocyclooctyne (DBCO) reagents. Compared to a cysteine peptide control, the DBCO-tag increases the rate of the thiol-yne reaction 220-fold, thereby enabling selective conjugation of DBCO-tag to DBCO-linked fluorescent probes, affinity tags, and cytotoxic drug molecules. Fusion of DBCO-tag with the protein of interest enables regioselective cysteine modification on proteins that contain multiple endogenous cysteines; these examples include green fluorescent protein and the antibody trastuzumab. This study demonstrates that short peptide tags can aid in accelerating bond-forming reactions that are often slow to non-existent in water.
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Affiliation(s)
- Chi Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Peng Dai
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Alexander A Vinogradov
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Zachary P Gates
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
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32
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Zhang C, Dai P, Vinogradov AA, Gates ZP, Pentelute BL. Site‐Selective Cysteine–Cyclooctyne Conjugation. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800860] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Chi Zhang
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Peng Dai
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Alexander A. Vinogradov
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Zachary P. Gates
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Bradley L. Pentelute
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
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33
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Watanabe K, Ohshima T. Bioconjugation with Thiols by Benzylic Substitution. Chemistry 2018; 24:3959-3964. [PMID: 29457301 DOI: 10.1002/chem.201706149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Indexed: 12/11/2022]
Abstract
A benzylic substitution of 3-indolyl(hydroxyl)acetate derivatives with thiols proceeded specifically in the presence of amino, carboxy, and phosphate groups in weakly acidic aqueous solutions under nearly physiological condition, while no reaction occurred at pH over 7. Kinetic studies revealed that the reaction followed second-order kinetics (first-order in the reactant and first-order in thiol) in contrast with the SN 1 mechanism of common benzylic substitution of alcohols. The utility of the present method for functionalization of biomacromolecules was demonstrated using several model proteins, such as lysozyme, insulin, trypsin, and serum albumin. The catalytic bioactivity of lysozyme in lysis of Micrococcus lysodeikticus cells was completely retained after the modification.
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Affiliation(s)
- Kenji Watanabe
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Takashi Ohshima
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
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34
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Thompson JW, Griffin ME, Hsieh-Wilson LC. Methods for the Detection, Study, and Dynamic Profiling of O-GlcNAc Glycosylation. Methods Enzymol 2017; 598:101-135. [PMID: 29306432 PMCID: PMC5886303 DOI: 10.1016/bs.mie.2017.06.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The addition of O-linked β-N-acetylglucosamine (O-GlcNAc) to serine/threonine residues of proteins is a ubiquitous posttranslational modification found in all multicellular organisms. Like phosphorylation, O-GlcNAc glycosylation (O-GlcNAcylation) is inducible and regulates a myriad of physiological and pathological processes. However, understanding the diverse functions of O-GlcNAcylation is often challenging due to the difficulty of detecting and quantifying the modification. Thus, robust methods to study O-GlcNAcylation are essential to elucidate its key roles in the regulation of individual proteins, complex cellular processes, and disease. In this chapter, we describe a set of chemoenzymatic labeling methods to (1) detect O-GlcNAcylation on proteins of interest, (2) monitor changes in both the total levels of O-GlcNAcylation and its stoichiometry on proteins of interest, and (3) enable mapping of O-GlcNAc to specific serine/threonine residues within proteins to facilitate functional studies. First, we outline a procedure for the expression and purification of a multiuse mutant galactosyltransferase enzyme (Y289L GalT). We then describe the use of Y289L GalT to modify O-GlcNAc residues with a functional handle, N-azidoacetylgalactosamine (GalNAz). Finally, we discuss several applications of the copper-catalyzed azide-alkyne cycloaddition "click" reaction to attach various alkyne-containing chemical probes to GalNAz and demonstrate how this functionalization of O-GlcNAc-modified proteins can be used to realize (1)-(3) above. Overall, these methods, which utilize commercially available reagents and standard protein analytical tools, will serve to advance our understanding of the diverse and important functions of O-GlcNAcylation.
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Affiliation(s)
- John W Thompson
- California Institute of Technology, Pasadena, CA, United States
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35
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Synthesis of Novel Saccharin Derivatives. Molecules 2017; 22:molecules22040516. [PMID: 28333118 PMCID: PMC6153755 DOI: 10.3390/molecules22040516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 03/20/2017] [Accepted: 03/20/2017] [Indexed: 11/16/2022] Open
Abstract
The synthesis of saccharin (1,2-benzisothiazol-3-one-1,1-dioxide) derivatives substituted on the benzene ring has seen limited development despite the longevity of this compound’s use as an artificial sweetener. This type of saccharin derivative would however present attractive properties for the development of new bioactive, drug-like small molecule compounds. Here we report the derivatisation of the benzene ring of saccharin using Cu(I)-catalyzed azide alkyne cycloaddition (CuAAC) to synthesise a diverse library of novel saccharin-1,2,3-triazole conjugates. All library compounds retain the capability for interactions with biomolecules via the unmodified sulfonamide and lactam groups of the parent saccharin core heterocycle. The compounds also encompass alternate orientations of the 1,2,3-triazole heterocycle, thus further adding diversity to the potential hydrogen bonding interactions of these compounds with biomolecules of therapeutic interest. Our findings demonstrate that specifically functionalized derivatives of saccharin may be prepared from either saccharin azide or saccharin alkyne building blocks in high yield using CuAAC.
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36
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Sangwan R, Mandal PK. Recent advances in photoinduced glycosylation: oligosaccharides, glycoconjugates and their synthetic applications. RSC Adv 2017. [DOI: 10.1039/c7ra01858d] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Carbohydrates have been demonstrated to perform imperative act in biological processes. This review highlights recent uses of photoinduced glycosylation in carbohydrate chemistry for the synthesis of oligosaccharides, thiosugars, glycoconjugates and glycoprotein.
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Affiliation(s)
- Rekha Sangwan
- Medicinal and Process Chemistry Division
- CSIR-Central Drug Research Institute
- Lucknow
- India
- Academy of Scientific and Innovative Research
| | - Pintu Kumar Mandal
- Medicinal and Process Chemistry Division
- CSIR-Central Drug Research Institute
- Lucknow
- India
- Academy of Scientific and Innovative Research
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37
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Laradji AM, McNitt CD, Yadavalli NS, Popik VV, Minko S. Robust, Solvent-Free, Catalyst-Free Click Chemistry for the Generation of Highly Stable Densely Grafted Poly(ethylene glycol) Polymer Brushes by the Grafting To Method and Their Properties. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b01573] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Amine M. Laradji
- Nanostructured Materials Lab and ‡Department of Chemistry, The University of Georgia, Athens, Georgia 30602, United States
| | - Christopher D. McNitt
- Nanostructured Materials Lab and ‡Department of Chemistry, The University of Georgia, Athens, Georgia 30602, United States
| | - Nataraja S. Yadavalli
- Nanostructured Materials Lab and ‡Department of Chemistry, The University of Georgia, Athens, Georgia 30602, United States
| | - Vladimir V. Popik
- Nanostructured Materials Lab and ‡Department of Chemistry, The University of Georgia, Athens, Georgia 30602, United States
| | - Sergiy Minko
- Nanostructured Materials Lab and ‡Department of Chemistry, The University of Georgia, Athens, Georgia 30602, United States
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38
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Thiol-ene-Enabled Detection of Thiophosphorylation as a Labeling Strategy for Phosphoproteins. Methods Mol Biol 2016; 1355:3-15. [PMID: 26584915 DOI: 10.1007/978-1-4939-3049-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The adenosine triphosphate (ATP) analogue adenosine 5'-O-(3-thiotriphosphate) (ATPγS) has been applied as a tool to study kinase-substrate phosphorylation. Not only does the transfer of a thiophosphate group represent a unique modification amid the phosphoproteome, but it can also be stable to phosphatase activity. However, detection of this species is complicated due to the similar chemical reactivity of thiophosphate and proteinaceous thiols. Here, we describe a novel method for detection of protein thiophosphorylation utilizing the thiol-ene reaction. By first chemoselectively capping protein thiols through radical chemistry, kinase-catalyzed thiophosphorylation can be visualized specifically.
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39
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Modem S, Kankala S, Balaboina R, Thirukovela NS, Jonnalagadda SB, Vadde R, Vasam CS. Decarbonylation of Salicylaldehyde Activated byp-Cymene Ruthenium(II) Dimer: Implication for Catalytic Alkyne Hydrothiolation. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600809] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Sarangapani Modem
- Department of Chemistry; Kakatiya University; 506009 Warangal Telangana State India
| | - Shravankumar Kankala
- Department of Chemistry; Kakatiya University; 506009 Warangal Telangana State India
- School of Chemistry and Physics; University of Kwazulu-Natal; Westville Compus, Chiltern Hills 4000 Durban South Africa
| | - Ramesh Balaboina
- Department of Chemistry; Kakatiya University; 506009 Warangal Telangana State India
| | | | - Sreekantha B. Jonnalagadda
- School of Chemistry and Physics; University of Kwazulu-Natal; Westville Compus, Chiltern Hills 4000 Durban South Africa
| | - Ravinder Vadde
- Department of Chemistry; Kakatiya University; 506009 Warangal Telangana State India
| | - Chandra Sekhar Vasam
- Department of Chemistry; Satavahana University; Karimnagar Telangana State India
- Department of Pharmaceutical Chemistry; Telangana University; Nizamabad Telangana State India
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40
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Long MC, Poganik JR, Aye Y. On-Demand Targeting: Investigating Biology with Proximity-Directed Chemistry. J Am Chem Soc 2016; 138:3610-22. [PMID: 26907082 PMCID: PMC4805449 DOI: 10.1021/jacs.5b12608] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Indexed: 11/28/2022]
Abstract
Proximity enhancement is a central chemical tenet underpinning an exciting suite of small-molecule toolsets that have allowed us to unravel many biological complexities. The leitmotif of this opus is "tethering"-a strategy in which a multifunctional small molecule serves as a template to bring proteins/biomolecules together. Scaffolding approaches have been powerfully applied to control diverse biological outcomes such as protein-protein association, protein stability, activity, and improve imaging capabilities. A new twist on this strategy has recently appeared, in which the small-molecule probe is engineered to unleash controlled amounts of reactive chemical signals within the microenvironment of a target protein. Modification of a specific target elicits a precisely timed and spatially controlled gain-of-function (or dominant loss-of-function) signaling response. Presented herein is a unique personal outlook conceptualizing the powerful proximity-enhanced chemical biology toolsets into two paradigms: "multifunctional scaffolding" versus "on-demand targeting". By addressing the latest advances and challenges in the established yet constantly evolving multifunctional scaffolding strategies as well as in the emerging on-demand precision targeting (and related) systems, this Perspective is aimed at choosing when it is best to employ each of the two strategies, with an emphasis toward further promoting novel applications and discoveries stemming from these innovative chemical biology platforms.
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Affiliation(s)
- Marcus
J. C. Long
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
| | - Jesse R. Poganik
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
| | - Yimon Aye
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
- Department
of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
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41
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Gu ZY, Cao JJ, Wang SY, Ji SJ. The involvement of the trisulfur radical anion in electron-catalyzed sulfur insertion reactions: facile synthesis of benzothiazine derivatives under transition metal-free conditions. Chem Sci 2016; 7:4067-4072. [PMID: 30155050 PMCID: PMC6013918 DOI: 10.1039/c6sc00240d] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/03/2016] [Indexed: 11/21/2022] Open
Abstract
An efficient and practical synthesis of benzothiazine by K2S initiated sulfur insertion reaction with enaminones via electron catalysis is developed. This protocol provides a new, environment-friendly and simple strategy to construct benzothiazine derivatives via formation of two C-S bonds under transition metal-free, additive-free and oxidant-free conditions. K2S not only provides the sulfur insertion source, but also ignites the reaction through the formation of a trisulfur radical anion and electrons in DMF.
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Affiliation(s)
- Zheng-Yang Gu
- Key Laboratory of Organic Synthesis of Jiangsu Province , College of Chemistry , Chemical Engineering and Materials Science & Collaborative Innovation Center of Suzhou Nano Science and Technology , Soochow University , Suzhou 215123 , China . ;
| | - Jia-Jia Cao
- Key Laboratory of Organic Synthesis of Jiangsu Province , College of Chemistry , Chemical Engineering and Materials Science & Collaborative Innovation Center of Suzhou Nano Science and Technology , Soochow University , Suzhou 215123 , China . ;
| | - Shun-Yi Wang
- Key Laboratory of Organic Synthesis of Jiangsu Province , College of Chemistry , Chemical Engineering and Materials Science & Collaborative Innovation Center of Suzhou Nano Science and Technology , Soochow University , Suzhou 215123 , China . ;
| | - Shun-Jun Ji
- Key Laboratory of Organic Synthesis of Jiangsu Province , College of Chemistry , Chemical Engineering and Materials Science & Collaborative Innovation Center of Suzhou Nano Science and Technology , Soochow University , Suzhou 215123 , China . ;
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42
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Gunnoo SB, Madder A. Chemical Protein Modification through Cysteine. Chembiochem 2016; 17:529-53. [DOI: 10.1002/cbic.201500667] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Smita B. Gunnoo
- Organic & Biomimetic Chemistry Research Group; Department of Organic and Macromolecular Chemistry; Ghent University; Krijgslaan 281 9000 Gent Belgium
| | - Annemieke Madder
- Organic & Biomimetic Chemistry Research Group; Department of Organic and Macromolecular Chemistry; Ghent University; Krijgslaan 281 9000 Gent Belgium
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43
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Healy J, Rasmussen T, Miller S, Booth IR, Conway SJ. The photochemical thiol-ene reaction as a versatile method for the synthesis of glutathione S-conjugates targeting the bacterial potassium efflux system Kef. Org Chem Front 2016; 3:439-446. [PMID: 27110363 PMCID: PMC4819703 DOI: 10.1039/c5qo00436e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/15/2016] [Indexed: 01/10/2023]
Abstract
The thiol-ene coupling reaction is emerging as an important conjugation reaction that is suitable for use in a biological setting. Here, we explore the utility of this reaction for the synthesis of glutathione-S-conjugates (GSX) and present a general, operationally simple, protocol with a wide substrate scope. The GSX afforded are an important class of compounds and provide invaluable molecular tools to study glutathione-binding proteins. In this study we apply the diverse library of GSX synthesised to further our understanding of the structural requirements for binding to the glutathione-binding protein, Kef, a bacterial K+ efflux system, found in many bacterial pathogens. This system is vital to the survival of bacteria upon exposure to electrophiles, and plays an essential role in the maintenance of intracellular pH and K+ homeostasis. Consequently, Kef is an appealing target for the development of novel antibacterial drugs.
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Affiliation(s)
- Jess Healy
- Department of Chemistry , Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK . ; ; Department of Pharmaceutical and Biological Chemistry , UCL School of Pharmacy , University College London , 29/39 Brunswick Square , WC1N, 1AX , UK
| | - Tim Rasmussen
- Institute of Medical Sciences , University of Aberdeen , Foresterhill , Aberdeen , AB25 2ZD , UK
| | - Samantha Miller
- Institute of Medical Sciences , University of Aberdeen , Foresterhill , Aberdeen , AB25 2ZD , UK
| | - Ian R Booth
- Institute of Medical Sciences , University of Aberdeen , Foresterhill , Aberdeen , AB25 2ZD , UK
| | - Stuart J Conway
- Department of Chemistry , Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK . ;
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44
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McSweeney L, Dénès F, Scanlan EM. Thiyl-Radical Reactions in Carbohydrate Chemistry: From Thiosugars to Glycoconjugate Synthesis. European J Org Chem 2016. [DOI: 10.1002/ejoc.201501543] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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45
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van Elsland DM, Bos E, de Boer W, Overkleeft HS, Koster AJ, van Kasteren SI. Detection of bioorthogonal groups by correlative light and electron microscopy allows imaging of degraded bacteria in phagocytes. Chem Sci 2016; 7:752-758. [PMID: 28791116 PMCID: PMC5529995 DOI: 10.1039/c5sc02905h] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/21/2015] [Indexed: 01/07/2023] Open
Abstract
The interaction between parasites and phagocytic immune cells is a key inter-species interaction in biology. Normally, phagocytosis results in the killing of invaders, but obligate intracellular parasites hijack the pathway to ensure their survival and replication. The in situ study of these parasites in the phagocytic pathway is very difficult, as genetic modification is often complicated and, if successful, only allows the tracking of pathogen phagocytosis up until the degradation of the engineered reporter constructs. Here we combine bioorthogonal chemistry with correlative light-electron microscopy (CLEM) to follow bacterial processing in the phagolysosomal system. Labelled bacteria are produced using bioorthogonal non-canonical amino tagging (BONCAT), precluding the need for any genetic modification. The bacterial proteome - even during degradation - was then visualised using a novel CLEM-based approach. This allowed us to obtain high resolution information about the subcellular location of the degrading bacteria, even after the proteolytic degradation of reporter constructs. To further explore the potential of CLEM-based imaging of bioorthogonal functionalities, azide-labelled glycans were imaged by this same approach, as well as active-subpopulations of enzymes using a 2-step activity-based protein profiling strategy.
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Affiliation(s)
- Daphne M van Elsland
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Institute for Chemical Immunology , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands
| | - Erik Bos
- Department of Molecular Cell Biology , Section Electron Microscopy , Leiden University Medical Center , Leiden , The Netherlands .
| | - Wouter de Boer
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Institute for Chemical Immunology , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands
| | - Herman S Overkleeft
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Institute for Chemical Immunology , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands
| | - Abraham J Koster
- Department of Molecular Cell Biology , Section Electron Microscopy , Leiden University Medical Center , Leiden , The Netherlands .
| | - Sander I van Kasteren
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Institute for Chemical Immunology , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands
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46
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Brewer TF, Garcia FJ, Onak CS, Carroll KS, Chang CJ. Chemical approaches to discovery and study of sources and targets of hydrogen peroxide redox signaling through NADPH oxidase proteins. Annu Rev Biochem 2015; 84:765-90. [PMID: 26034893 DOI: 10.1146/annurev-biochem-060614-034018] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hydrogen peroxide (H2O2) is a prime member of the reactive oxygen species (ROS) family of molecules produced during normal cell function and in response to various stimuli, but if left unchecked, it can inflict oxidative damage on all types of biological macromolecules and lead to cell death. In this context, a major source of H2O2 for redox signaling purposes is the NADPH oxidase (Nox) family of enzymes, which were classically studied for their roles in phagocytic immune response but have now been found to exist in virtually all mammalian cell types in various isoforms with distinct tissue and subcellular localizations. Downstream of this tightly regulated ROS generation, site-specific, reversible covalent modification of proteins, particularly oxidation of cysteine thiols to sulfenic acids, represents a prominent posttranslational modification akin to phosphorylation as an emerging molecular mechanism for transforming an oxidant signal into a dynamic biological response. We review two complementary types of chemical tools that enable (a) specific detection of H2O2 generated at its sources and (b) mapping of sulfenic acid posttranslational modification targets that mediate its signaling functions, which can be used to study this important chemical signal in biological systems.
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47
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Ema T, Inoue H. Chemical Modification of Lipase for Rational Enhancement of Enantioselectivity. CHEM LETT 2015. [DOI: 10.1246/cl.150667] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Tadashi Ema
- Division of Applied Chemistry, Graduate School of Natural Science and Technology, Okayama University
| | - Hiroki Inoue
- Division of Applied Chemistry, Graduate School of Natural Science and Technology, Okayama University
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48
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Stanley M, Han C, Knebel A, Murphy P, Shpiro N, Virdee S. Orthogonal thiol functionalization at a single atomic center for profiling transthiolation activity of E1 activating enzymes. ACS Chem Biol 2015; 10:1542-54. [PMID: 25845023 DOI: 10.1021/acschembio.5b00118] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Transthiolation is a fundamental biological reaction and is utilized by many enzymes involved in the conjugation of ubiquitin and ubiquitin-like proteins. However, tools that enable selective profiling of this activity are lacking. Transthiolation requires cysteine-cysteine juxtaposition; therefore a method that enables irreversible "stapling" of proximal thiols would facilitate the development of novel probes that could be used to profile this activity. Herein, we characterize biocompatible chemistry that enables sequential functionalization of cysteines within proteins at a single atomic center. We use our method to develop a new class of activity-based probe that profiles transthiolation activity of human E1 activating enzymes. We demonstrate use in vitro and in situ and compatibility with competitive activity-based protein profiling. We also use the probe to gain insight into the determinants of transthiolation between E2 and a RING-in-between-RING (RBR) E3 ligase. Furthermore, we anticipate that this method of thiol functionalization will have broad utility by enabling simple redox-stable cross-linking of proximal cysteines in general.
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Affiliation(s)
- Mathew Stanley
- MRC Protein
Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Cong Han
- MRC Protein
Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Axel Knebel
- MRC Protein
Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Paul Murphy
- MRC Protein
Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Natalia Shpiro
- MRC Protein
Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Satpal Virdee
- MRC Protein
Phosphorylation
and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
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49
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Koniev O, Wagner A. Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions for bioconjugation. Chem Soc Rev 2015; 44:5495-551. [PMID: 26000775 DOI: 10.1039/c5cs00048c] [Citation(s) in RCA: 397] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioconjugation methodologies have proven to play a central enabling role in the recent development of biotherapeutics and chemical biology approaches. Recent endeavours in these fields shed light on unprecedented chemical challenges to attain bioselectivity, biocompatibility, and biostability required by modern applications. In this review the current developments in various techniques of selective bond forming reactions of proteins and peptides were highlighted. The utility of each endogenous amino acid-selective conjugation methodology in the fields of biology and protein science has been surveyed with emphasis on the most relevant among reported transformations; selectivity and practical use have been discussed.
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Affiliation(s)
- Oleksandr Koniev
- Laboratory of Functional Chemo-Systems (UMR 7199), Labex Medalis, University of Strasbourg, 74 Route du Rhin, 67401 Illkirch-Graffenstaden, France.
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50
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De Munari S, Schiffner T, Davis BG. A Triply Divergent Reagent for Glycoprotein Synthesis. Isr J Chem 2015. [DOI: 10.1002/ijch.201400182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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