1
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Gangemi CMA, Monforte M, Arrigo A, Bonaccorsi PM, Conoci S, Iaconis A, Puntoriero F, Franco D, Barattucci A. Synthesis of Bodipy-Tagged Galactoconjugates and Evaluation of Their Antibacterial Properties. Molecules 2024; 29:2299. [PMID: 38792159 PMCID: PMC11124175 DOI: 10.3390/molecules29102299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
As a development of our research on biocompatible glycoconjugate probes and specifically multi-chromophoric systems, herein, we report the synthesis and early bactericidal tests of two luminescent glycoconjugates whose basic structure is characterized by two boron dipyrromethene difluoride (BODIPY) moieties and three galactoside rings mounted on an oligophenylene ethynylene (OPE) skeleton. BODIPY fluorophores have found widespread application in many branches of biology in the last few decades. In particular, molecular platforms showing two different BODIPY groups have unique photophysical behavior useful in fluorescence imaging. Construction of the complex architecture of the new probes is accomplished through a convergent route that exploits a series of copper-free Heck-Cassar-Sonogashira cross-couplings. The great emergency due to the proliferation of bacterial infections, in conjunction with growing antibiotic resistance, requires the production of new multifunctional drugs and efficient methods for their targeted delivery to control bacteria-associated diseases. Preliminary studies of the glycoconjugate properties as antibacterial agents against representatives of Gram-negative (P. aeruginosa) and Gram-positive (S. aureus) pathogens, which are associated with chronic infections, indicated significant bactericidal activity ascribable to their structural features.
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Affiliation(s)
- Chiara Maria Antonietta Gangemi
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, V.le F. Stagno D’Alcontres 31, 98166 Messina, Italy; (C.M.A.G.); (M.M.); (A.A.); (P.M.B.); (S.C.); (A.I.); (F.P.)
| | - Maura Monforte
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, V.le F. Stagno D’Alcontres 31, 98166 Messina, Italy; (C.M.A.G.); (M.M.); (A.A.); (P.M.B.); (S.C.); (A.I.); (F.P.)
| | - Antonino Arrigo
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, V.le F. Stagno D’Alcontres 31, 98166 Messina, Italy; (C.M.A.G.); (M.M.); (A.A.); (P.M.B.); (S.C.); (A.I.); (F.P.)
| | - Paola Maria Bonaccorsi
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, V.le F. Stagno D’Alcontres 31, 98166 Messina, Italy; (C.M.A.G.); (M.M.); (A.A.); (P.M.B.); (S.C.); (A.I.); (F.P.)
| | - Sabrina Conoci
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, V.le F. Stagno D’Alcontres 31, 98166 Messina, Italy; (C.M.A.G.); (M.M.); (A.A.); (P.M.B.); (S.C.); (A.I.); (F.P.)
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via Francesco Selmi, 2, 40126 Bologna, Italy
- LAB Sense Beyond Nano—URT Department of Sciences Physics and Technologies of Matter (DSFTM) CNR, 98166 Messina, Italy
| | - Antonella Iaconis
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, V.le F. Stagno D’Alcontres 31, 98166 Messina, Italy; (C.M.A.G.); (M.M.); (A.A.); (P.M.B.); (S.C.); (A.I.); (F.P.)
| | - Fausto Puntoriero
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, V.le F. Stagno D’Alcontres 31, 98166 Messina, Italy; (C.M.A.G.); (M.M.); (A.A.); (P.M.B.); (S.C.); (A.I.); (F.P.)
| | - Domenico Franco
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, V.le F. Stagno D’Alcontres 31, 98166 Messina, Italy; (C.M.A.G.); (M.M.); (A.A.); (P.M.B.); (S.C.); (A.I.); (F.P.)
| | - Anna Barattucci
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, V.le F. Stagno D’Alcontres 31, 98166 Messina, Italy; (C.M.A.G.); (M.M.); (A.A.); (P.M.B.); (S.C.); (A.I.); (F.P.)
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2
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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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3
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Detwiler R, McPartlon TJ, Coffey CS, Kramer JR. Clickable Polyprolines from Azido-proline N-Carboxyanhydride. ACS POLYMERS AU 2023; 3:383-393. [PMID: 37841952 PMCID: PMC10571246 DOI: 10.1021/acspolymersau.3c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 10/17/2023]
Abstract
Polyproline is a material of great interest in biomedicine due to its helical scaffold of structural importance in collagen and mucins and its ability to gel and to change conformations in response to temperature. Appending of function-modulating chemical groups to such a material is desirable to diversify potential applications. Here, we describe the synthesis of high-molecular-weight homo, block, and statistical polymers of azide-functionalized proline. The azide groups served as moieties for highly efficient click-grafting, as stabilizers of the polyproline PPII helix, and as modulators of thermoresponsiveness. Saccharides and ethylene glycol were utilized to explore small-molecule grafting, and glutamate polymers were utilized to form polyelectrolyte bottlebrush architectures. Secondary structure effects of both the azide and click modifications, as well as lower critical solution temperature behavior, were characterized. The polyazidoprolines and click products were well tolerated by live human cells and are expected to find use in diverse biomedical applications.
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Affiliation(s)
- Rachel
E. Detwiler
- Department
of Biomedical Engineering, University of
Utah, Salt Lake
City, Utah 84112, United States
| | - Thomas J. McPartlon
- Department
of Molecular Pharmaceutics, University of
Utah, Salt Lake City, Utah 84112, United States
| | - Clara S. Coffey
- Department
of Biomedical Engineering, University of
Utah, Salt Lake
City, Utah 84112, United States
| | - Jessica R. Kramer
- Department
of Biomedical Engineering, University of
Utah, Salt Lake
City, Utah 84112, United States
- Department
of Molecular Pharmaceutics, University of
Utah, Salt Lake City, Utah 84112, United States
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4
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Molyneux S, Goss RJM. Fully Aqueous and Air-Compatible Cross-Coupling of Primary Alkyl Halides with Aryl Boronic Species: A Possible and Facile Method. ACS Catal 2023; 13:6365-6374. [PMID: 37180963 PMCID: PMC10167655 DOI: 10.1021/acscatal.3c00252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/04/2023] [Indexed: 05/16/2023]
Abstract
Aqueous transformations confer many advantages, including decreased environmental impact and increased opportunity for biomolecule modulation. Although several studies have been conducted to enable the cross-coupling of aryl halides in aqueous conditions, until now a process for the cross-coupling of primary alkyl halides in aqueous conditions was missing from the catalytic toolbox and considered impossible. Alkyl halide coupling in water suffers from severe problems. The reasons for this include the strong propensity for β-hydride elimination, the need for highly air- and water-sensitive catalysts and reagents, and the intolerance of many hydrophilic groups to cross-coupling conditions. Here, we report a broadly applicable and readily accessible process for the cross-coupling of water-soluble alkyl halides in water and air by using simple and commercially available bench-stable reagents. The trisulfonated aryl phosphine TXPTS in combination with a water-soluble palladium salt Na2PdCl4 allowed for the Suzuki-Miyaura coupling of water-soluble alkyl halides with aryl boronic acids, boronic esters, and borofluorate salts in mild, fully aqueous conditions. Multiple challenging functionalities, including unprotected amino acids, an unnatural halogenated amino acid within a peptide, and herbicides can be diversified in water. Structurally complex natural products were used as testbeds to showcase the late-stage tagging methodology of marine natural products to enable liquid chromatography-mass spectrometry (LC-MS) detection. This enabling methodology therefore provides a general method for the environmentally friendly and biocompatible derivatization of sp3 alkyl halide bonds.
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Affiliation(s)
- Samuel Molyneux
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K.
| | - Rebecca J. M. Goss
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K.
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5
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Decorated bacteria and the application in drug delivery. Adv Drug Deliv Rev 2022; 188:114443. [PMID: 35817214 DOI: 10.1016/j.addr.2022.114443] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/13/2022] [Accepted: 07/06/2022] [Indexed: 02/08/2023]
Abstract
The use of living bacteria either as therapeutic agents or drug carriers has shown great potential in treating a multitude of intractable diseases. However, cells are often fragile to unfriendly environmental stressors and limited by inadequately therapeutic responses, leading to unwanted cell death and a decline in treatment efficacy. Surface decoration of bacteria has emerged as a simple yet useful strategy that not only confers bacteria with extra capacity to resist environmental threats but also endows them with exogenous characteristics that are neither inherent nor naturally achievable. In this review, we systematically introduce the advancements of physicochemical and biological technologies for surface modification of bacteria, especially the single-cell surface decoration strategies of individual bacteria. We highlight the recent progress on surface decoration that aims to improve the bioavailability and efficacy of therapeutic bacterial agents and also to achieve enhanced and targeted delivery of conventional drugs. The promises along with challenges of surface-decorated bacteria as drug delivery systems for applications in cancer therapy, intestinal disease treatment, bioimaging, and diagnosis are further discussed with respect to future clinical translation. This review offers an overview of the advances of decorated bacteria for drug delivery applications and would contribute to the development of the next generation of advanced bacterial-based therapies.
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6
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Liu Y, Lai KL, Vong K. Transition Metal Scaffolds Used To Bring New‐to‐Nature Reactions into Biological Systems. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202200215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yifei Liu
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
| | - Ka Lun Lai
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
| | - Kenward Vong
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
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7
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Wei X, Du W, Duca M, Yu G, de Vries E, de Haan CAM, Pieters RJ. Preventing Influenza A Virus Infection by Mixed Inhibition of Neuraminidase and Hemagglutinin by Divalent Inhibitors. J Med Chem 2022; 65:7312-7323. [PMID: 35549211 PMCID: PMC9150099 DOI: 10.1021/acs.jmedchem.2c00319] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Divalent inhibitors
of the neuraminidase enzyme (NA) of the Influenza
A virus were synthesized with vastly different spacers. The spacers
varied from 14 to 56 atoms and were relatively rigid by way of the
building blocks and their connection by CuAAC. As the ligand for these
constructs, a Δ4-β-d-glucoronide was
used, which can be prepared form N-acetyl glucosamine.
This ligand showed good NA inhibitory potency but with room for improvement
by multivalency enhancement. The synthesized compounds showed modest
potency enhancement in NA activity assays but a sizeable potency increase
in a 4-day cytopathic effect assay. The demonstration that the compounds
can also inhibit hemagglutinin in addition to NA may be the cause
of the enhancement.
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Affiliation(s)
- Xuan Wei
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, Utrecht NL-3508 TB, The Netherlands
| | - Wenjuan Du
- Section Virology, Division Infectious Diseases and Immunology, Faculty Veterinary Medicine, Utrecht University, Utrecht NL-3508 TB, The Netherlands
| | - Margherita Duca
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, Utrecht NL-3508 TB, The Netherlands
| | - Guangyun Yu
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, Utrecht NL-3508 TB, The Netherlands
| | - Erik de Vries
- Section Virology, Division Infectious Diseases and Immunology, Faculty Veterinary Medicine, Utrecht University, Utrecht NL-3508 TB, The Netherlands
| | - Cornelis A M de Haan
- Section Virology, Division Infectious Diseases and Immunology, Faculty Veterinary Medicine, Utrecht University, Utrecht NL-3508 TB, The Netherlands
| | - Roland J Pieters
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, Utrecht NL-3508 TB, The Netherlands
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8
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Krabicová I, Dolenský B, Řezanka M. Selectivity of 1- O-Propargyl-d-Mannose Preparations. Molecules 2022; 27:1483. [PMID: 35268584 PMCID: PMC8911549 DOI: 10.3390/molecules27051483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 11/16/2022] Open
Abstract
Thanks to their ability to bind to specific biological receptors, mannosylated structures are examined in biomedical applications. One of the most common ways of linking a functional moiety to a structure is to use an azide-alkyne click reaction. Therefore, it is necessary to prepare and isolate a propargylated mannose derivative of high purity to maintain its bioactivity. Three known preparations of propargyl-α-mannopyranoside were revisited, and products were analysed by NMR spectroscopy. The preparations were shown to yield by-products that have not been described in the literature yet. Our experiments showed that one-step procedures could not provide pure propargyl-α-mannopyranoside, while a three-step procedure yielded the desired compound of high purity.
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Affiliation(s)
- Ilona Krabicová
- Department of Chemistry, Faculty of Science, Humanities and Education, Technical University of Liberec, Studentská 1402/2, 46117 Liberec, Czech Republic;
| | - Bohumil Dolenský
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology Prague, Technická 5, 16628 Prague, Czech Republic;
| | - Michal Řezanka
- Department of Nanochemistry, Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 1402/2, 46117 Liberec, Czech Republic
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9
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Geier SJ, Vogels CM, Melanson JA, Westcott SA. The transition metal-catalysed hydroboration reaction. Chem Soc Rev 2022; 51:8877-8922. [DOI: 10.1039/d2cs00344a] [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
This review covers the development of the transition metal-catalysed hydroboration reaction, from its beginnings in the 1980s to more recent developments including earth-abundant catalysts and an ever-expanding array of substrates.
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Affiliation(s)
- Stephen J. Geier
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB E4L 1G8, Canada
| | - Christopher M. Vogels
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB E4L 1G8, Canada
| | - Jennifer A. Melanson
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB E4L 1G8, Canada
| | - Stephen A. Westcott
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB E4L 1G8, Canada
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10
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Sornay C, Vaur V, Wagner A, Chaubet G. An overview of chemo- and site-selectivity aspects in the chemical conjugation of proteins. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211563. [PMID: 35116160 PMCID: PMC8790347 DOI: 10.1098/rsos.211563] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/20/2021] [Indexed: 05/03/2023]
Abstract
The bioconjugation of proteins-that is, the creation of a covalent link between a protein and any other molecule-has been studied for decades, partly because of the numerous applications of protein conjugates, but also due to the technical challenge it represents. Indeed, proteins possess inner physico-chemical properties-they are sensitive and polynucleophilic macromolecules-that make them complex substrates in conjugation reactions. This complexity arises from the mild conditions imposed by their sensitivity but also from selectivity issues, viz the precise control of the conjugation site on the protein. After decades of research, strategies and reagents have been developed to address two aspects of this selectivity: chemoselectivity-harnessing the reacting chemical functionality-and site-selectivity-controlling the reacting amino acid residue-most notably thanks to the participation of synthetic chemistry in this effort. This review offers an overview of these chemical bioconjugation strategies, insisting on those employing native proteins as substrates, and shows that the field is active and exciting, especially for synthetic chemists seeking new challenges.
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Affiliation(s)
- Charlotte Sornay
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Valentine Vaur
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
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11
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Thangarasu AK, Yadhukrishnan VO, Krishnakumar KA, Varma SS, Lankalapalli RS. Cu(I)-azidopyrrolo[3,2- d]pyrimidine Catalyzed Glaser-Hay Reaction under Mild Conditions. ACS ORGANIC & INORGANIC AU 2021; 2:3-7. [PMID: 36855403 PMCID: PMC9954286 DOI: 10.1021/acsorginorgau.1c00015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The limitation of the CuAAC "click" reaction with a 2-azidopyridine substrate, owing to its equilibrium with a tetrazole isomer, is exploited herein for its utility in the Glaser-Hay reaction. A catalytic combination of a 2-azidopyridine analogue, 4-azido-5H-pyrrolo[3,2-d]pyrimidine, and CuI afforded homocoupled products of terminal alkynes, without any trace of triazole product, under mild conditions with a broad substrate scope. Emphasis on carbohydrate-based substrates appended to a propargylic group led to 1,3-diynes in good to excellent yields.
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Affiliation(s)
- Arun K. Thangarasu
- Chemical
Sciences and Technology Division, CSIR-National
Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India,Academy
of Scientific & Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Velickakathu O. Yadhukrishnan
- Chemical
Sciences and Technology Division, CSIR-National
Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
| | - K. A. Krishnakumar
- Chemical
Sciences and Technology Division, CSIR-National
Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India,Academy
of Scientific & Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Sanjay Suresh Varma
- Chemical
Sciences and Technology Division, CSIR-National
Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
| | - Ravi S. Lankalapalli
- Chemical
Sciences and Technology Division, CSIR-National
Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India,Academy
of Scientific & Innovative Research (AcSIR), Ghaziabad-201002, India,
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12
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Oerlemans RAJF, Timmermans SBPE, van Hest JCM. Artificial Organelles: Towards Adding or Restoring Intracellular Activity. Chembiochem 2021; 22:2051-2078. [PMID: 33450141 PMCID: PMC8252369 DOI: 10.1002/cbic.202000850] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/15/2021] [Indexed: 12/15/2022]
Abstract
Compartmentalization is one of the main characteristics that define living systems. Creating a physically separated microenvironment allows nature a better control over biological processes, as is clearly specified by the role of organelles in living cells. Inspired by this phenomenon, researchers have developed a range of different approaches to create artificial organelles: compartments with catalytic activity that add new function to living cells. In this review we will discuss three complementary lines of investigation. First, orthogonal chemistry approaches are discussed, which are based on the incorporation of catalytically active transition metal-containing nanoparticles in living cells. The second approach involves the use of premade hybrid nanoreactors, which show transient function when taken up by living cells. The third approach utilizes mostly genetic engineering methods to create bio-based structures that can be ultimately integrated with the cell's genome to make them constitutively active. The current state of the art and the scope and limitations of the field will be highlighted with selected examples from the three approaches.
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Affiliation(s)
- Roy A. J. F. Oerlemans
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| | - Suzanne B. P. E. Timmermans
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| | - Jan C. M. van Hest
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
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13
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Cao J, Boatner LM, Desai HS, Burton NR, Armenta E, Chan NJ, Castellón JO, Backus KM. Multiplexed CuAAC Suzuki–Miyaura Labeling for Tandem Activity-Based Chemoproteomic Profiling. Anal Chem 2021; 93:2610-2618. [DOI: 10.1021/acs.analchem.0c04726] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Jian Cao
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
| | - Lisa M. Boatner
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Heta S. Desai
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
| | - Nikolas R. Burton
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Ernest Armenta
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Neil J. Chan
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - José O. Castellón
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
| | - Keriann M. Backus
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
- DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California 90095, United States
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14
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Zhao Q, Guo G, Zhu W, Zhu L, Da Y, Han Y, Xu H, Wu S, Cheng Y, Zhou Y, Cai X, Jiang X. Suzuki Cross-Coupling Reaction with Genetically Encoded Fluorosulfates for Fluorogenic Protein Labeling. Chemistry 2020; 26:15938-15943. [PMID: 32776653 DOI: 10.1002/chem.202002037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/24/2020] [Indexed: 11/09/2022]
Abstract
A palladium-catalyzed cross-coupling reaction with aryl halide functionalities has recently emerged as a valuable tool for protein modification. Herein, a new fluorogenic modification methodology for proteins, with genetically encoded fluorosulfate-l-tyrosine, which exhibits high efficiency and biocompatibility in bacterial cells as well as in aqueous medium, is described. Furthermore, the cross-coupling of 4-cyanophenylboronic acid on green fluorescent protein was shown to possess a unique fluorogenic property, which could open up the possibility of a responsive "off/on" switch with great potential to enable spectroscopic imaging of proteins with minimal background noise. Taken together, a convenient and efficient catalytic system has been developed that may provide broad utilities in protein visualization and live-cell imaging.
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Affiliation(s)
- Qian Zhao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Guoying Guo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Weiwei Zhu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Liping Zhu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P.R. China
| | - Yifan Da
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Ying Han
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Hongjiao Xu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Shuohan Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Yaping Cheng
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Yani Zhou
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, P.R. China
| | - Xiaoqing Cai
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Xianxing Jiang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
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15
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Li J, Zhang Y, Soubias O, Khago D, Chao FA, Li Y, Shaw K, Byrd RA. Optimization of sortase A ligation for flexible engineering of complex protein systems. J Biol Chem 2020; 295:2664-2675. [PMID: 31974162 DOI: 10.1074/jbc.ra119.012039] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/22/2020] [Indexed: 01/06/2023] Open
Abstract
Engineering and bioconjugation of proteins is a critically valuable tool that can facilitate a wide range of biophysical and structural studies. The ability to orthogonally tag or label a domain within a multidomain protein may be complicated by undesirable side reactions to noninvolved domains. Furthermore, the advantages of segmental (or domain-specific) isotopic labeling for NMR, or deuteration for neutron scattering or diffraction, can be realized by an efficient ligation procedure. Common methods-expressed protein ligation, protein trans-splicing, and native chemical ligation-each have specific limitations. Here, we evaluated the use of different variants of Staphylococcus aureus sortase A for a range of ligation reactions and demonstrate that conditions can readily be optimized to yield high efficiency (i.e. completeness of ligation), ease of purification, and functionality in detergents. These properties may enable joining of single domains into multidomain proteins, lipidation to mimic posttranslational modifications, and formation of cyclic proteins to aid in the development of nanodisc membrane mimetics. We anticipate that the method for ligating separate domains into a single functional multidomain protein reported here may enable many applications in structural biology.
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Affiliation(s)
- Jess Li
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702-1201
| | - Yue Zhang
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702-1201
| | - Olivier Soubias
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702-1201
| | - Domarin Khago
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702-1201
| | - Fa-An Chao
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702-1201
| | - Yifei Li
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702-1201
| | - Katherine Shaw
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702-1201
| | - R Andrew Byrd
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702-1201.
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16
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Panduwawala TD, Iqbal S, Thompson AL, Genov M, Pretsch A, Pretsch D, Liu S, Ebright RH, Howells A, Maxwell A, Moloney MG. Functionalised bicyclic tetramates derived from cysteine as antibacterial agents. Org Biomol Chem 2019; 17:5615-5632. [PMID: 31120090 PMCID: PMC6686852 DOI: 10.1039/c9ob01076a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Routes to bicyclic tetramates derived from cysteine permitting ready incorporation of functionality at two different points around the periphery of a heterocyclic skeleton are reported. This has enabled the identification of systems active against Gram-positive bacteria, some of which show gyrase and RNA polymerase inhibitory activity. In particular, tetramates substituted with glycosyl side chains, chosen to impart polarity and aqueous solubility, show high antibacterial activity coupled with modest gyrase/polymerase activity in two cases. An analysis of physicochemical properties indicates that the antibacterially active tetramates generally occupy physicochemical space with MW of 300-600, clog D7.4 of -2.5 to 4 and rel. PSA of 11-22%. This work demonstrates that biologically active 3D libraries are readily available by manipulation of a tetramate skeleton.
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Affiliation(s)
- Tharindi D Panduwawala
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, UK.
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17
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Abstract
![]()
The manipulation
and modulation of biomolecules has the potential
to herald new modes of Biology and Medicine through chemical “editing”.
Key to the success of such processes will be the selectivities, reactivities
and efficiencies that may be brought to bear in bond-formation and
bond-cleavage in a benign manner. In this Perspective, we use select
examples, primarily from our own research, to examine the current
opportunities, limitations and the particular potential of metal-mediated
processes as exemplars of possible alternative catalytic modes and
manifolds to those already found in nature.
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Affiliation(s)
- Patrick G Isenegger
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Benjamin G Davis
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Mansfield Road , Oxford OX1 3TA , United Kingdom
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18
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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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19
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Soldevila-Barreda JJ, Metzler-Nolte N. Intracellular Catalysis with Selected Metal Complexes and Metallic Nanoparticles: Advances toward the Development of Catalytic Metallodrugs. Chem Rev 2019; 119:829-869. [PMID: 30618246 DOI: 10.1021/acs.chemrev.8b00493] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Platinum-containing drugs (e.g., cisplatin) are among the most frequently used chemotherapeutic agents. Their tremendous success has spurred research and development of other metal-based drugs, with notable achievements. Generally, the vast majority of metal-based drug candidates in clinical and developmental stages are stoichiometric agents, i.e., each metal complex reacts only once with their biological target. Additionally, many of these metal complexes are involved in side reactions, which not only reduce the effective amount of the drug but may also cause toxicity. On a separate note, transition metal complexes and nanoparticles have a well-established history of being potent catalysts for selective molecular transformations, with examples such as the Mo- and Ru-based catalysts for metathesis reactions (Nobel Prize in 2005) or palladium catalysts for C-C bond forming reactions such as Heck, Negishi, or Suzuki reactions (Nobel Prize in 2010). Also, notably, no direct biological equivalent of these transformations exists in a biological environment such as bacteria or mammalian cells. It is, therefore, only logical that recent interest has focused on developing transition-metal based catalytic systems that are capable of performing transformations inside cells, with the aim of inducing medicinally relevant cellular changes. Because unlike in stoichiometric reactions, a catalytically active compound may turn over many substrate molecules, only very small amounts of such a catalytic metallodrug are required to achieve a desired pharmacologic effect, and therefore, toxicity and side reactions are reduced. Furthermore, performing catalytic reactions in biological systems also opens the door for new methodologies to study the behavior of biomolecules in their natural state, e.g., via in situ labeling or by increasing/depleting their concentration at will. There is, of course, an art to the choice of catalysts and reactions which have to be compatible with biological conditions, namely an aqueous, oxygen-containing environment. In this review, we aim to describe new developments that bring together the far-distant worlds of transition-metal based catalysis and metal-based drugs, in what is termed "catalytic metallodrugs". Here we will focus on transformations that have been performed on small biomolecules (such as shifting equilibria like in the NAD+/NADH or GSH/GSSG couples), on non-natural molecules such as dyes for imaging purposes, or on biomacromolecules such as proteins. Neither reactions involving release (e.g., CO) or transformation of small molecules (e.g., 1O2 production), degradation of biomolecules such as proteins, RNA or DNA nor light-induced medicinal chemistry (e.g., photodynamic therapy) are covered, even if metal complexes are centrally involved in those. In each section, we describe the (inorganic) chemistry involved, as well as selected examples of biological applications in the hope that this snapshot of a new but quickly developing field will indeed inspire novel research and unprecedented interactions across disciplinary boundaries.
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Affiliation(s)
- Joan Josep Soldevila-Barreda
- Inorganic Chemistry I-Bioinorganic Chemistry , Ruhr University Bochum , Universitätsstrasse 150 , 44780-D Bochum , Germany
| | - Nils Metzler-Nolte
- Inorganic Chemistry I-Bioinorganic Chemistry , Ruhr University Bochum , Universitätsstrasse 150 , 44780-D Bochum , Germany
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20
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Yan N, He Y, Wen H, Lai F, Yin D, Cui H. A Suzuki-Miyaura method for labelling proliferating cells containing incorporated BrdU. Analyst 2019; 143:1224-1233. [PMID: 29431786 DOI: 10.1039/c7an01934c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The 5-bromo-2'-deoxyuridine (BrdU) incorporation cell proliferation assay is the most commonly used method for assessing DNA replication. The current detection of BrdU in cells relies on antibody immunostaining, but has various limitations including low antibody specificity and poor tissue penetration. In this study, we utilised a Suzuki-Miyaura reaction to develop a chemical method to label cellular BrdU with fluorescent boronic acid probes. The coupling conditions were optimised for complex cellular environments, and the key observation was the need to use oxygen scavengers and zerovalent palladium to prevent side reactions and increase the rate of coupling. The reliability and specificity of the BrdU Suzuki-Miyaura labelling method were verified under various biological conditions. The applicability of the BrdU Suzuki-Miyaura labelling methodology was also investigated, and we show that labelling cellular BrdU is highly sensitive and reliable, which is comparable to the ideal performance of BrdU immunostaining. Moreover, the Suzuki-Miyaura reaction protocol provides high BrdU recognition specificity. Taken together, the BrdU Suzuki-Miyaura labelling protocol provides an attractive alternative to the more traditional cell proliferation assay.
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Affiliation(s)
- Ning Yan
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, China.
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21
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Alali U, Vallin A, Bil A, Khanchouche T, Mathiron D, Przybylski C, Beaulieu R, Kovensky J, Benazza M, Bonnet V. The uncommon strong inhibition of α-glucosidase by multivalent glycoclusters based on cyclodextrin scaffolds. Org Biomol Chem 2019; 17:7228-7237. [DOI: 10.1039/c9ob01344j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
New inhibitors of α-glucosidase based on perglycosylated cyclodextrins were synthesized via click-chemistry and compared to acarbose.
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22
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Bilyard MK, Bailey HJ, Raich L, Gafitescu MA, Machida T, Iglésias-Fernández J, Lee SS, Spicer CD, Rovira C, Yue WW, Davis BG. Palladium-mediated enzyme activation suggests multiphase initiation of glycogenesis. Nature 2018; 563:235-240. [PMID: 30356213 DOI: 10.1038/s41586-018-0644-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 08/31/2018] [Indexed: 11/09/2022]
Abstract
Biosynthesis of glycogen, the essential glucose (and hence energy) storage molecule in humans, animals and fungi1, is initiated by the glycosyltransferase enzyme, glycogenin (GYG). Deficiencies in glycogen formation cause neurodegenerative and metabolic disease2-4, and mouse knockout5 and inherited human mutations6 of GYG impair glycogen synthesis. GYG acts as a 'seed core' for the formation of the glycogen particle by catalysing its own stepwise autoglucosylation to form a covalently bound gluco-oligosaccharide chain at initiation site Tyr 195. Precise mechanistic studies have so far been prevented by an inability to access homogeneous glycoforms of this protein, which unusually acts as both catalyst and substrate. Here we show that unprecedented direct access to different, homogeneously glucosylated states of GYG can be accomplished through a palladium-mediated enzyme activation 'shunt' process using on-protein C-C bond formation. Careful mimicry of GYG intermediates recapitulates catalytic activity at distinct stages, which in turn allows discovery of triphasic kinetics and substrate plasticity in GYG's use of sugar substrates. This reveals a tolerant but 'proof-read' mechanism that underlies the precision of this metabolic process. The present demonstration of direct, chemically controlled access to intermediate states of active enzymes suggests that such ligation-dependent activation could be a powerful tool in the study of mechanism.
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Affiliation(s)
| | - Henry J Bailey
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Lluís Raich
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTC), Universitat de Barcelona, Barcelona, Spain
| | | | - Takuya Machida
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Javier Iglésias-Fernández
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTC), Universitat de Barcelona, Barcelona, Spain.,Institut de Química Computacional i Catalisi and Departament de Química, Universitat de Girona, Girona, Spain
| | - Seung Seo Lee
- Department of Chemistry, University of Oxford, Oxford, UK.,School of Chemistry, University of Southampton, Southampton, UK
| | | | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTC), Universitat de Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Wyatt W Yue
- Structural Genomics Consortium, University of Oxford, Oxford, UK.
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23
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Akgun B, Hall DG. Boronic Acids as Bioorthogonal Probes for Site‐Selective Labeling of Proteins. Angew Chem Int Ed Engl 2018; 57:13028-13044. [DOI: 10.1002/anie.201712611] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/23/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Burcin Akgun
- Department of Chemistry—CCIS 4–010University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Dennis G. Hall
- Department of Chemistry—CCIS 4–010University of Alberta Edmonton Alberta T6G 2G2 Canada
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24
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Akgun B, Hall DG. Boronsäuren als bioorthogonale Sonden für zentrenselektives Protein‐Labeling. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712611] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Burcin Akgun
- Department of Chemistry – CCIS 4-010University of Alberta Edmonton Alberta T6G 2G2 Kanada
| | - Dennis G. Hall
- Department of Chemistry – CCIS 4-010University of Alberta Edmonton Alberta T6G 2G2 Kanada
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25
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Abstract
Our understanding of the complex molecular processes of living organisms at the molecular level is growing exponentially. This knowledge, together with a powerful arsenal of tools for manipulating the structures of macromolecules, is allowing chemists to to harness and reprogram the cellular machinery in ways previously unimaged. Here we review one example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins with unprecedented precision.
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Affiliation(s)
- Douglas D. Young
- Department of Chemistry, College of William & Mary,
P.O. Box 8795, Williamsburg, VA 23187 (USA)
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute,
La Jolla, CA 92037 (USA),
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26
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Curtin BH, Manoni F, Park J, Sisto LJ, Lam YH, Gravel M, Roulston A, Harran PG. Assembly of Complex Macrocycles by Incrementally Amalgamating Unprotected Peptides with a Designed Four-Armed Insert. J Org Chem 2018; 83:3090-3108. [DOI: 10.1021/acs.joc.7b02958] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Brice H. Curtin
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Francesco Manoni
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Jiyong Park
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Luke J. Sisto
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Yu-hong Lam
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Michel Gravel
- Laboratory for Therapeutic Development, Rosalind and Morris Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Anne Roulston
- Laboratory for Therapeutic Development, Rosalind and Morris Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Patrick G. Harran
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
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27
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Miguel-Ávila J, Tomás-Gamasa M, Olmos A, Pérez PJ, Mascareñas JL. Discrete Cu(i) complexes for azide-alkyne annulations of small molecules inside mammalian cells. Chem Sci 2018; 9:1947-1952. [PMID: 29675241 PMCID: PMC5892125 DOI: 10.1039/c7sc04643j] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/15/2018] [Indexed: 12/31/2022] Open
Abstract
The archetype reaction of "click" chemistry, namely, the copper-promoted azide-alkyne cycloaddition (CuAAC), has found an impressive number of applications in biological chemistry. However, methods for promoting intermolecular annulations of exogenous, small azides and alkynes in the complex interior of mammalian cells, are essentially unknown. Herein we demonstrate that isolated, well-defined copper(i)-tris(triazolyl) complexes featuring designed ligands can readily enter mammalian cells and promote intracellular CuAAC annulations of small, freely diffusible molecules. In addition to simplifying protocols and avoiding the addition of "non-innocent" reductants, the use of these premade copper complexes leads to more efficient processes than with the alternative, in situ made copper species prepared from Cu(ii) sources, tris(triazole) ligands and sodium ascorbate. Under the reaction conditions, the well-defined copper complexes exhibit very good cell penetration properties, and do not present significant toxicities.
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Affiliation(s)
- Joan Miguel-Ávila
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
| | - María Tomás-Gamasa
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
| | - Andrea Olmos
- Laboratorio de Catálisis Homogénea , Unidad Asociada al CSIC , CIQSO-Centro de Investigación en Química Sostenible , Departamento de Química , Universidad de Huelva , Campus de El Carmen s/n , 21007 Huelva , Spain .
| | - Pedro J Pérez
- Laboratorio de Catálisis Homogénea , Unidad Asociada al CSIC , CIQSO-Centro de Investigación en Química Sostenible , Departamento de Química , Universidad de Huelva , Campus de El Carmen s/n , 21007 Huelva , Spain .
| | - José L Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
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28
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Baier M, Giesler M, Hartmann L. Split-and-Combine Approach Towards Branched Precision Glycomacromolecules and Their Lectin Binding Behavior. Chemistry 2018; 24:1619-1630. [DOI: 10.1002/chem.201704179] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Mischa Baier
- Institute of Organic and Macromolecular Chemistry; Heinrich-Heine-University Duesseldorf; Universitaetsstraße 1 40225 Duesseldorf Germany
| | - Markus Giesler
- Institute of Organic and Macromolecular Chemistry; Heinrich-Heine-University Duesseldorf; Universitaetsstraße 1 40225 Duesseldorf Germany
| | - Laura Hartmann
- Institute of Organic and Macromolecular Chemistry; Heinrich-Heine-University Duesseldorf; Universitaetsstraße 1 40225 Duesseldorf Germany
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29
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Vinogradova EV. Organometallic chemical biology: an organometallic approach to bioconjugation. PURE APPL CHEM 2017. [DOI: 10.1515/pac-2017-0207] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
AbstractThis review summarizes the history and recent developments of the field of organometallic chemical biology with a particular emphasis on the development of novel bioconjugation approaches. Over the years, numerous transformations have emerged for biomolecule modification with the use of organometallic reagents; these include [3+2] cycloadditions, C–C, C–S, C–N, and C–O bond forming processes, as well as metal-mediated deprotection (“decaging”) reactions. These conceptually new additions to the chemical biology toolkit highlight the potential of organometallic chemistry to make a significant impact in the field of chemical biology by providing further opportunities for the development of chemoselective, site-specific and spatially resolved methods for biomolecule structure and function manipulation. Examples of these transformations, as well as existing challenges and future prospects of this rapidly developing field are highlighted in this review.
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30
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Tamura T, Song Z, Amaike K, Lee S, Yin S, Kiyonaka S, Hamachi I. Affinity-Guided Oxime Chemistry for Selective Protein Acylation in Live Tissue Systems. J Am Chem Soc 2017; 139:14181-14191. [DOI: 10.1021/jacs.7b07339] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tomonori Tamura
- Department of Synthetic
Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Zhining Song
- Department of Synthetic
Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kazuma Amaike
- Department of Synthetic
Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shin Lee
- Department of Synthetic
Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Sifei Yin
- Magdalene College, University of Cambridge, Cambridge CB3 0AG, United Kingdom
| | - Shigeki Kiyonaka
- Department of Synthetic
Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic
Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Sanbancho, Chiyodaku, Tokyo 102-0075, Japan
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31
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Probst N, Grelier G, Ghermani N, Gandon V, Alami M, Messaoudi S. Intramolecular Pd-Catalyzed Anomeric C(sp3)–H Activation of Glycosyl Carboxamides. Org Lett 2017; 19:5038-5041. [DOI: 10.1021/acs.orglett.7b02170] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicolas Probst
- BioCIS, Univ Paris-Sud, CNRS, University Paris-Saclay, Châtenay-Malabry, France
| | - Gwendal Grelier
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Univ Paris-Sud, Université Paris-Saclay, 1, av de la Terrasse, 91198 Gif-sur-Yvette, France
| | - NourEddine Ghermani
- Institut
Galien, Univ-Sud, CNRS, University Paris-Saclay, Châtenay-Malabry 92296, France
| | - Vincent Gandon
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Univ Paris-Sud, Université Paris-Saclay, 1, av de la Terrasse, 91198 Gif-sur-Yvette, France
- Institut
de Chimie Moléculaire et des Matériaux d’Orsay, CNRS UMR 8182, Univ Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Mouâd Alami
- BioCIS, Univ Paris-Sud, CNRS, University Paris-Saclay, Châtenay-Malabry, France
| | - Samir Messaoudi
- BioCIS, Univ Paris-Sud, CNRS, University Paris-Saclay, Châtenay-Malabry, France
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32
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Sharma SV, Tong X, Pubill-Ulldemolins C, Cartmell C, Bogosyan EJA, Rackham EJ, Marelli E, Hamed RB, Goss RJM. Living GenoChemetics by hyphenating synthetic biology and synthetic chemistry in vivo. Nat Commun 2017; 8:229. [PMID: 28794415 PMCID: PMC5550429 DOI: 10.1038/s41467-017-00194-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/07/2017] [Indexed: 01/21/2023] Open
Abstract
Marrying synthetic biology with synthetic chemistry provides a powerful approach toward natural product diversification, combining the best of both worlds: expediency and synthetic capability of biogenic pathways and chemical diversity enabled by organic synthesis. Biosynthetic pathway engineering can be employed to insert a chemically orthogonal tag into a complex natural scaffold affording the possibility of site-selective modification without employing protecting group strategies. Here we show that, by installing a sufficiently reactive handle (e.g., a C–Br bond) and developing compatible mild aqueous chemistries, synchronous biosynthesis of the tagged metabolite and its subsequent chemical modification in living culture can be achieved. This approach can potentially enable many new applications: for example, assay of directed evolution of enzymes catalyzing halo-metabolite biosynthesis in living cells or generating and following the fate of tagged metabolites and biomolecules in living systems. We report synthetic biological access to new-to-nature bromo-metabolites and the concomitant biorthogonal cross-coupling of halo-metabolites in living cultures. Coupling synthetic biology and chemical reactions in cells is a challenging task. The authors engineer bacteria capable of generating bromo-metabolites, develop a mild Suzuki-Miyaura cross-coupling reaction compatible with cell growth and carry out the cross-coupling chemistry in live cell cultures.
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Affiliation(s)
- Sunil V Sharma
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Xiaoxue Tong
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Cristina Pubill-Ulldemolins
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Christopher Cartmell
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Emma J A Bogosyan
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,Analytical Development, GSK, Cobden Street, Montrose, Angus, DD10 8EA, UK
| | - Emma J Rackham
- School of Chemistry, University of East, Norwich, NR4 7TJ, UK.,School of Medicine, University of East Anglia, Bob Champion Research and Education Building, James Watson Road, Norwich, NR4 7UQ, UK
| | - Enrico Marelli
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Refaat B Hamed
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Rebecca J M Goss
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK. .,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.
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33
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Jbara M, Maity SK, Brik A. Palladium in der chemischen Synthese und Modifizierung von Proteinen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702370] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemie; Technion - Israel Institute of Technology; Haifa 3200008 Israel
| | - Suman Kumar Maity
- Schulich Faculty of Chemie; Technion - Israel Institute of Technology; Haifa 3200008 Israel
| | - Ashraf Brik
- Schulich Faculty of Chemie; Technion - Israel Institute of Technology; Haifa 3200008 Israel
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34
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Jbara M, Maity SK, Brik A. Palladium in the Chemical Synthesis and Modification of Proteins. Angew Chem Int Ed Engl 2017; 56:10644-10655. [DOI: 10.1002/anie.201702370] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Suman Kumar Maity
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
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35
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Indrigo E, Clavadetscher J, Chankeshwara SV, Megia-Fernandez A, Lilienkampf A, Bradley M. Intracellular delivery of a catalytic organometallic complex. Chem Commun (Camb) 2017; 53:6712-6715. [DOI: 10.1039/c7cc02988h] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We show the intracellular delivery of a homogeneous palladium–peptide catalyst able to bioorthogonally activate a profluorophore inside living prostate cancer cells.
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Affiliation(s)
- Eugenio Indrigo
- EaStCHEM
- School of Chemistry
- University of Edinburgh
- EH9 3FJ Edinburgh
- UK
| | | | | | | | | | - Mark Bradley
- EaStCHEM
- School of Chemistry
- University of Edinburgh
- EH9 3FJ Edinburgh
- UK
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36
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Chatterjee A, Ward TR. Recent Advances in the Palladium Catalyzed Suzuki–Miyaura Cross-Coupling Reaction in Water. Catal Letters 2016. [DOI: 10.1007/s10562-016-1707-8] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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37
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Indrigo E, Clavadetscher J, Chankeshwara SV, Lilienkampf A, Bradley M. Palladium-mediated in situ synthesis of an anticancer agent. Chem Commun (Camb) 2016; 52:14212-14214. [DOI: 10.1039/c6cc08666g] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Biocompatible heterogeneous Pd(0) catalysts were used in a Suzuki–Miyaura cross-coupling reaction to synthesise an anticancer agent in situ, leading to apoptosis of prostate cancer cells.
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Affiliation(s)
- Eugenio Indrigo
- EaStCHEM School of Chemistry
- University of Edinburgh
- EH9 3FJ Edinburgh
- UK
| | | | | | | | - Mark Bradley
- EaStCHEM School of Chemistry
- University of Edinburgh
- EH9 3FJ Edinburgh
- UK
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38
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Brooks AD, Yeung K, Lewis GG, Phillips ST. A Strategy for Minimizing Background Signal in Autoinductive Signal Amplification Reactions for Point-of-Need Assays. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2015; 7:7186-7192. [PMID: 26604988 PMCID: PMC4654960 DOI: 10.1039/c5ay00508f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Rapid point-of-need assays are used to detect abundant biomarkers. The development of in situ signal amplification reactions could extend these assays to screening and triaging of patients for trace levels of biomarkers, even in resource-limited settings. We, and others, have developed small molecule-based in situ signal amplification reactions that eventually may be useful in this context. Herein we describe a design strategy for minimizing background signal that may occur in the absence of the target analyte, thus moving this in situ signal amplification approach one step closer to practical applications. Specifically, we describe allylic ethers as privileged connectors for linking detection and propagating functionality in a small molecule signal amplification reagent. Allylic ethers minimize background reactions while still enabling controlled release of a propagating signal in order to continue the signal amplification reaction. This paper characterizes the ability of allylic ethers to provide an amplified response, and offers insight into additional design considerations that are needed before in situ small molecule-based signal amplification becomes a viable strategy for point-of-need diagnostics.
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39
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Cheng G, Lim RKV, Ramil CP, Lin Q. Storable N-phenylcarbamate palladacycles for rapid functionalization of an alkyne-encoded protein. Chem Commun (Camb) 2015; 50:11679-82. [PMID: 25140915 DOI: 10.1039/c4cc02969k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we report the synthesis of storable N-phenylcarbamate palladacycles that showed robust reactivity in the cross-coupling reaction with an alkyne-encoded protein with a second-order rate constant approaching 19 770 ± 930 M(-1) s(-1).
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Affiliation(s)
- Gang Cheng
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA.
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40
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Yang M, Li J, Chen PR. Transition metal-mediated bioorthogonal protein chemistry in living cells. Chem Soc Rev 2015; 43:6511-26. [PMID: 24867400 DOI: 10.1039/c4cs00117f] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Considerable attention has been focused on improving the biocompatibility of Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC), a hallmark of bioorthogonal reaction, in living cells. Besides creating copper-free versions of click chemistry such as strain promoted azide-alkyne cycloaddition (SPAAC), a central effort has also been made to develop various Cu(I) ligands that can prevent the cytotoxicity of Cu(I) ions while accelerating the CuAAC reaction. Meanwhile, additional transition metals such as palladium have been explored as alternative sources to promote a bioorthogonal conjugation reaction on cell surface, as well as within an intracellular environment. Furthermore, transition metal mediated chemical conversions beyond conjugation have also been utilized to manipulate protein activity within living systems. We highlight these emerging examples that significantly enriched our protein chemistry toolkit, which will likely expand our view on the definition and applications of bioorthogonal chemistry.
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Affiliation(s)
- Maiyun Yang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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41
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Weiss JT, Carragher NO, Unciti-Broceta A. Palladium-mediated dealkylation of N-propargyl-floxuridine as a bioorthogonal oxygen-independent prodrug strategy. Sci Rep 2015; 5:9329. [PMID: 25788464 PMCID: PMC4365405 DOI: 10.1038/srep09329] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 02/26/2015] [Indexed: 12/21/2022] Open
Abstract
Herein we report the development and biological screening of a bioorthogonal palladium-labile prodrug of the nucleoside analogue floxuridine, a potent antineoplastic drug used in the clinic to treat advanced cancers. N-propargylation of the N3 position of its uracil ring resulted in a vast reduction of its biological activity (~6,250-fold). Cytotoxic properties were bioorthogonally rescued in cancer cell culture by heterogeneous palladium chemistry both in normoxia and hypoxia. Within the same environment, the reported chemo-reversible prodrug exhibited up to 1,450-fold difference of cytotoxicity whether it was in the absence or presence of the extracellular palladium source, underlining the precise modulation of bioactivity enabled by this bioorthogonally-activated prodrug strategy.
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Affiliation(s)
- Jason T Weiss
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Neil O Carragher
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Asier Unciti-Broceta
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, UK
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42
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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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43
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Affiliation(s)
- Omar Boutureira
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili , C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
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44
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Ramawat KG, Mérillon JM. Major Advances in the Development of Synthetic Oligosaccharide-Based Vaccines. POLYSACCHARIDES 2015. [PMCID: PMC7123674 DOI: 10.1007/978-3-319-16298-0_65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Because of their involvement in a variety of different biological processes and their occurrence onto pathogens and malignant cell surface, carbohydrates have been identified as ideal candidates for vaccine formulation. However, as free oligosaccharides are poorly immunogenic and do not induce immunological memory in the most at risk population (infants and young children, elderly and immunocompromised patients), glycoconjugate vaccines containing the same carbohydrate antigen covalently linked to an immunogenic carrier protein have gained a prominent role. Accordingly, a number of glycoconjugate vaccines mostly directed against infections caused by bacterial pathogens have been licensed and are currently available on the market. However, also glycoconjugate vaccines suffer from significant drawbacks. The challenging procedures required for the isolation and purification of the carbohydrate antigen from its natural source often lead to poor homogeneity and presence of biological contaminants, resulting in batch-to-batch variability. Moreover, in some cases, the overwhelming immunogenicity of the carrier protein may induce the carbohydrate epitope suppression, causing hyporesponsiveness. The development of synthetic oligosaccharide-based vaccine candidates, characterized by the presence of pure and well-defined synthetic oligosaccharide structures, is expected to meet the requirement of homogeneous and highly reproducible preparations. In the present chapter, we report on the major advances in the development of synthetic carbohydrate-based vaccines. First of all, we describe different strategies developed during the last years to circumvent the inherent difficulties of classical oligosaccharide synthesis, such as the one-pot glycosylation and the solid-phase synthesis, and their application to the preparation of carbohydrate antigens apt to conjugation with protein carriers. Next, we discuss the most representative methodologies employed for the chemical ligation of oligosaccharide structures to proteins. Finally, in the last section, we report significant examples of fully synthetic vaccines exploiting the multivalency effect. These constructs are based on the concept that the conjugation of multiple copies of synthetic oligosaccharide antigens to multivalent scaffolds, such as dendrimers, (cyclo)peptides, gold nanoparticles, and calixarenes, raises cooperative interactions between carbohydrates and immune receptors, leading to strong enhancement of the saccharide antigen immunogenicity.
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Affiliation(s)
| | - Jean-Michel Mérillon
- Groupe d’Etude des Substances Végétales à Activité Biologique, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, Villenave d'Ornon, France
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45
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Spicer CD, Davis BG. Selective chemical protein modification. Nat Commun 2014; 5:4740. [PMID: 25190082 DOI: 10.1038/ncomms5740] [Citation(s) in RCA: 716] [Impact Index Per Article: 71.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 07/21/2014] [Indexed: 02/06/2023] Open
Abstract
Chemical modification of proteins is an important tool for probing natural systems, creating therapeutic conjugates and generating novel protein constructs. Site-selective reactions require exquisite control over both chemo- and regioselectivity, under ambient, aqueous conditions. There are now various methods for achieving selective modification of both natural and unnatural amino acids--each with merits and limitations--providing a 'toolkit' that until 20 years ago was largely limited to reactions at nucleophilic cysteine and lysine residues. If applied in a biologically benign manner, this chemistry could form the basis of true Synthetic Biology.
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Affiliation(s)
- Christopher D Spicer
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Benjamin G Davis
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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46
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Hauke S, Best M, Schmidt TT, Baalmann M, Krause A, Wombacher R. Two-step protein labeling utilizing lipoic acid ligase and Sonogashira cross-coupling. Bioconjug Chem 2014; 25:1632-7. [PMID: 25152073 DOI: 10.1021/bc500349h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Labeling proteins in their natural settings with fluorescent proteins or protein tags often leads to problems. Despite the high specificity, these methods influence the natural functions due to the rather large size of the proteins used. Here we present a two-step labeling procedure for the attachment of various fluorescent probes to a small peptide sequence (13 amino acids) using enzyme-mediated peptide labeling in combination with palladium-catalyzed Sonogashira cross-coupling. We identified p-iodophenyl derivatives from a small library that can be covalently attached to a lysine residue within a specific 13-amino-acid peptide sequence by Escherichia coli lipoic acid ligase A (LplA). The derivatization with p-iodophenyl subsequently served as a reactive handle for bioorthogonal transition metal-catalyzed Sonogashira cross-coupling with alkyne-functionalized fluorophores on both the peptide as well as on the protein level. Our two-step labeling strategy combines high selectivity of enzyme-mediated labeling with the chemoselectivity of palladium-catalyzed Sonogashira cross-coupling.
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Affiliation(s)
- Sebastian Hauke
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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47
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Chankeshwara SV, Indrigo E, Bradley M. Palladium-mediated chemistry in living cells. Curr Opin Chem Biol 2014; 21:128-35. [DOI: 10.1016/j.cbpa.2014.07.007] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 11/29/2022]
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48
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Weiss JT, Fraser C, Rubio-Ruiz B, Myers SH, Crispin R, Dawson JC, Brunton VG, Patton EE, Carragher NO, Unciti-Broceta A. N-alkynyl derivatives of 5-fluorouracil: susceptibility to palladium-mediated dealkylation and toxigenicity in cancer cell culture. Front Chem 2014; 2:56. [PMID: 25121087 PMCID: PMC4114543 DOI: 10.3389/fchem.2014.00056] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 07/10/2014] [Indexed: 01/23/2023] Open
Abstract
Palladium-activated prodrug therapy is an experimental therapeutic approach that relies on the unique chemical properties and biocompatibility of heterogeneous palladium catalysis to enable the spatially-controlled in vivo conversion of a biochemically-stable prodrug into its active form. This strategy, which would allow inducing local activation of systemically administered drug precursors by mediation of an implantable activating device made of Pd0, has been proposed by our group as a way to reach therapeutic levels of the active drug in the affected tissue/organ while reducing its systemic toxicity. In the seminal study of such an approach, we reported that propargylation of the N1 position of 5-fluorouracil suppressed the drug's cytotoxic properties, showed high stability in cell culture and facilitated the bioorthogonal restoration of the drug's pharmacological activity in the presence of extracellular Pd0-functionalized resins. To provide additional insight on the properties of this system, we have investigated different N1-alkynyl derivatives of 5-fluorouracil and shown that the presence of substituents near the triple bond influence negatively on its sensitivity to palladium catalysis under biocompatible conditions. Comparative studies of the N1- vs. the N3-propargyl derivatives of 5-fluorouracil revealed that masking each or both positions equally led to inactive derivatives (>200-fold reduction of cytotoxicity relative to the unmodified drug), whereas the depropargylation process occurred faster at the N1 position than at the N3, thus resulting in greater toxigenic properties in cancer cell culture.
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Affiliation(s)
- Jason T Weiss
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh, UK
| | - Craig Fraser
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh, UK
| | - Belén Rubio-Ruiz
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh, UK
| | - Samuel H Myers
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh, UK
| | - Richard Crispin
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh, UK ; MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh, UK
| | - John C Dawson
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh, UK
| | - Valerie G Brunton
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh, UK
| | - E Elizabeth Patton
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh, UK ; MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh, UK
| | - Neil O Carragher
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh, UK
| | - Asier Unciti-Broceta
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh, UK
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49
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Weiss JT, Dawson JC, Fraser C, Rybski W, Torres-Sánchez C, Bradley M, Patton EE, Carragher NO, Unciti-Broceta A. Development and bioorthogonal activation of palladium-labile prodrugs of gemcitabine. J Med Chem 2014; 57:5395-404. [PMID: 24867590 PMCID: PMC4078945 DOI: 10.1021/jm500531z] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Bioorthogonal
chemistry has become one of the main driving forces
in current chemical biology, inspiring the search for novel biocompatible
chemospecific reactions for the past decade. Alongside the well-established
labeling strategies that originated the bioorthogonal paradigm, we
have recently proposed the use of heterogeneous palladium chemistry
and bioorthogonal Pd0-labile prodrugs to develop spatially
targeted therapies. Herein, we report the generation of biologically
inert precursors of cytotoxic gemcitabine by introducing Pd0-cleavable groups in positions that are mechanistically relevant
for gemcitabine’s pharmacological activity. Cell viability
studies in pancreatic cancer cells showed that carbamate functionalization
of the 4-amino group of gemcitabine significantly reduced (>23-fold)
the prodrugs’ cytotoxicity. The N-propargyloxycarbonyl
(N-Poc) promoiety displayed the highest sensitivity
to heterogeneous palladium catalysis under biocompatible conditions,
with a reaction half-life of less than 6 h. Zebrafish studies with
allyl, propargyl, and benzyl carbamate-protected rhodamines confirmed N-Poc as the most suitable masking group for implementing in vivo bioorthogonal organometallic chemistry.
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Affiliation(s)
- Jason T Weiss
- Edinburgh Cancer Research UK Centre, and ‡MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh , Crewe Road South, Edinburgh EH4 2XR, U.K
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50
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King M, Wagner A. Developments in the Field of Bioorthogonal Bond Forming Reactions—Past and Present Trends. Bioconjug Chem 2014; 25:825-39. [DOI: 10.1021/bc500028d] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mathias King
- Laboratory of Functional
Chemo-Systems (UMR 7199), Labex Medalis, University of Strasbourg - CNRS, 74 Route du Rhin, BP 60024, 67401 Illkirch-Graffenstaden, France
| | - Alain Wagner
- Laboratory of Functional
Chemo-Systems (UMR 7199), Labex Medalis, University of Strasbourg - CNRS, 74 Route du Rhin, BP 60024, 67401 Illkirch-Graffenstaden, France
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