1
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Lins J, Miloslavina YA, Carrara SC, Rösler L, Hofmann S, Herr K, Theiß F, Wienands L, Avrutina O, Kolmar H, Buntkowsky G. Parahydrogen-induced polarization allows 2000-fold signal enhancement in biologically active derivatives of the peptide-based drug octreotide. Sci Rep 2023; 13:6388. [PMID: 37076553 PMCID: PMC10115808 DOI: 10.1038/s41598-023-33577-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/14/2023] [Indexed: 04/21/2023] Open
Abstract
Octreotide, a somatostatin analogue, has shown its efficacy for the diagnostics and treatment of various types of cancer, i.e., in octreotide scan, as radio-marker after labelling with a radiopharmaceutical. To avoid toxicity of radio-labeling, octreotide-based assays can be implemented into magnetic resonance techniques, such as MRI and NMR. Here we used a Parahydrogen-Induced Polarization (PHIP) approach as a cheap, fast and straightforward method. Introduction of L-propargyl tyrosine as a PHIP marker at different positions of octreotide by manual Solid-Phase Peptide Synthesis (SPPS) led to up to 2000-fold proton signal enhancement (SE). Cell binding studies confirmed that all octreotide variants retained strong binding affinity to the surface of human-derived cancer cells expressing somatostatin receptor 2. The hydrogenation reactions were successfully performed in methanol and under physiologically compatible mixtures of water with methanol or ethanol. The presented results open up new application areas of biochemical and pharmacological studies with octreotide.
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Affiliation(s)
- Jonas Lins
- Eduard-Zintl-Institute for Inorganic and Physical Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Yuliya A Miloslavina
- Eduard-Zintl-Institute for Inorganic and Physical Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Stefania C Carrara
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Lorenz Rösler
- Eduard-Zintl-Institute for Inorganic and Physical Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Sarah Hofmann
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Kevin Herr
- Eduard-Zintl-Institute for Inorganic and Physical Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Franziska Theiß
- Eduard-Zintl-Institute for Inorganic and Physical Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Laura Wienands
- Eduard-Zintl-Institute for Inorganic and Physical Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Olga Avrutina
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Harald Kolmar
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany.
| | - Gerd Buntkowsky
- Eduard-Zintl-Institute for Inorganic and Physical Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany.
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2
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G. Keller S, Kamiya M, Urano Y. Recent Progress in Small Spirocyclic, Xanthene-Based Fluorescent Probes. Molecules 2020; 25:E5964. [PMID: 33339370 PMCID: PMC7766215 DOI: 10.3390/molecules25245964] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022] Open
Abstract
The use of fluorescent probes in a multitude of applications is still an expanding field. This review covers the recent progress made in small molecular, spirocyclic xanthene-based probes containing different heteroatoms (e.g., oxygen, silicon, carbon) in position 10'. After a short introduction, we will focus on applications like the interaction of probes with enzymes and targeted labeling of organelles and proteins, detection of small molecules, as well as their use in therapeutics or diagnostics and super-resolution microscopy. Furthermore, the last part will summarize recent advances in the synthesis and understanding of their structure-behavior relationship including novel computational approaches.
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Affiliation(s)
- Sascha G. Keller
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (S.G.K.); (M.K.)
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (S.G.K.); (M.K.)
| | - Yasuteru Urano
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (S.G.K.); (M.K.)
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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3
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Bucevičius J, Keller-Findeisen J, Gilat T, Hell SW, Lukinavičius G. Rhodamine-Hoechst positional isomers for highly efficient staining of heterochromatin. Chem Sci 2019; 10:1962-1970. [PMID: 30881625 PMCID: PMC6385482 DOI: 10.1039/c8sc05082a] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/11/2018] [Indexed: 12/13/2022] Open
Abstract
Hoechst conjugates to fluorescent dyes are popular DNA stains for live-cell imaging, but the relationship between their structure and performance remains elusive. This study of carboxyrhodamine-Hoechst 33258 conjugates reveals that a minimal change in the attachment point of the dye has dramatic effects on the properties of the final probe. All tested 6'-carboxyl dye-containing probes exhibited dual-mode binding to DNA and formed a dimmer complex at high DNA concentrations. The 5'-carboxyl dye-containing probes exhibited single-mode binding to DNA which translated into increased brightness and lower cytotoxicity. Up to 10-fold brighter nuclear staining by the newly developed probes allowed acquisition of stimulated emission depletion (STED) nanoscopy images of outstanding quality in living and fixed cells. Therefore we were able to estimate a diameter of ∼155 nm of the heterochromatin exclusion zones in the nuclear pore region in living cells and intact chicken erythrocytes and to localize telomeres relative to heterochromatin in living U-2 OS cells. Employing the highly efficient probes for two-color STED allowed visualization of DNA and tubulin structures in intact nucleated erythrocytes - a system where imaging is greatly hampered by high haemoglobin absorbance.
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Affiliation(s)
- Jonas Bucevičius
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
| | - Jan Keller-Findeisen
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
| | - Tanja Gilat
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
| | - Stefan W Hell
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
| | - Gražvydas Lukinavičius
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
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4
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Shah S, Leon L. Structural transitions and encapsulation selectivity of thermoresponsive polyelectrolyte complex micelles. J Mater Chem B 2019; 7:6438-6448. [DOI: 10.1039/c9tb01194c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Polyelectrolyte complex micelles containing thermoresponsive coronas can exhibit varying morphologies and encapsulate multivalently charged therapeutics for drug delivery applications.
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Affiliation(s)
- Sachit Shah
- Department of Materials Science and Engineering
- University of Central Florida
- Orlando
- USA
| | - Lorraine Leon
- Department of Materials Science and Engineering
- University of Central Florida
- Orlando
- USA
- NanoScience Technology Center
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5
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Abstract
Deubiquitinating enzymes (DUBs) are of interest as potential new targets for pharmacological intervention. Active-site-directed probes can be used for the accurate profiling of DUB activity as well as the identification of DUBs and DUB inhibitor selectivity. Previously, active-site directed DUB probes have been obtained using intein-based methods that have inherent limitations. Total chemical synthesis of ubiquitin allows for easy incorporation of different tags, such as fluorescent reporters, affinity tags, and cleavable linkers. Here, we describe the total chemical synthesis of a fluorescent active-site directed DUB probe, which facilitates fast, in-gel detection of active DUBs and circumvents the use of Western blot analysis. In addition, an in-gel activity-based DUB profiling assay is described in detail, in which the fluorescent DUB probe is used to visualize active DUBs in cell lysates. Finally, an inhibition assay is described in which the fluorescent probe is used to determine the specificity and potency of a small molecule DUB inhibitor.
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6
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Tatulchenkov MY, Prokhorenko IA, Kvach MV, Navakouski ME, Stepanova IA, Pilchenko NV, Gontarev SV, Sharko OL, Korshun VA, Shmanai VV. Phosphoramidite reagents and solid-phase supports based on hydroxyprolinol for the synthesis of modified oligonucleotides. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017040148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Astakhova K, Golovin AV, Prokhorenko IA, Ustinov AV, Stepanova IA, Zatsepin TS, Korshun VA. Design of 2′-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.04.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Haack RA, Gayda S, Himmelsbach RJ, Tetin SY. Unexpected reactivity of the 2′-carboxyl functionality in rhodamine dyes. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.03.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Abstract
A one-step, operationally simple protocol for the synthesis of isomerically pure rhodamine dyes from phthalaldehydic acids is reported. Using a mixture of 2,2,2-trifluoroethanol and water as reaction media allows for clean and efficient formation of various rhodamines as a single isomer. This method was successfully applied to the synthesis of several isomerically pure rhodamines, including 6-carboxytetramethylrhodamine and 6-carboxy-X-rhodamine (6-CXR) on gram scale. A simple, one-step, Pd-catalyzed hydroxycarbonylation approach to phthalaldehydic acids from appropriately substituted dihalobenzadehydes is also described.
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Affiliation(s)
- Stephen J Dwight
- Promega Biosciences LLC, 277 Granada Drive, San Luis Obispo, California 93401, United States
| | - Sergiy Levin
- Promega Biosciences LLC, 277 Granada Drive, San Luis Obispo, California 93401, United States
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10
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Mudd G, Pi IP, Fethers N, Dodd PG, Barbeau OR, Auer M. A general synthetic route to isomerically pure functionalized rhodamine dyes. Methods Appl Fluoresc 2015; 3:045002. [DOI: 10.1088/2050-6120/3/4/045002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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11
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Skoblov AY, Vichuzhanin MV, Farzan VM, Veselova OA, Konovalova TA, Podkolzin AT, Shipulin GA, Zatsepin TS. Solid- and solution-phase synthesis and application of R6G dual-labeled oligonucleotide probes. Bioorg Med Chem 2015; 23:6749-56. [DOI: 10.1016/j.bmc.2015.08.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/17/2015] [Accepted: 08/28/2015] [Indexed: 12/25/2022]
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12
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Loas A, Radford RJ, Deliz Liang A, Lippard SJ. Solid-phase synthesis provides a modular, lysine-based platform for fluorescent discrimination of nitroxyl and biological thiols. Chem Sci 2015; 6:4131-4140. [PMID: 28717469 PMCID: PMC5497726 DOI: 10.1039/c5sc00880h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/05/2015] [Indexed: 11/24/2022] Open
Abstract
A synthetically facile solid-phase approach yields fluorescent Cu(ii)-based lysine conjugates which selectively detect nitroxyl and thiols in live cells.
We describe a modular, synthetically facile solid-phase approach aimed at separating the fluorescent reporter and binding unit of small-molecule metal-based sensors. The first representatives contain a lysine backbone functionalized with a tetramethylrhodamine fluorophore, and they operate by modulating the oxidation state of a copper ion ligated to an [N4] (cyclam) or an [N2O] (quinoline-phenolate) moiety. We demonstrate the selectivity of their Cu(ii) complexes for sensing nitroxyl (HNO) and thiols (RSH), respectively, and investigate the mechanism responsible for the observed reactivity in each case. The two lysine conjugates are cell permeable in the active, Cu(ii)-bound forms and retain their analyte selectivity intracellularly, even in the presence of interfering species such as nitric oxide, nitrosothiols, and hydrogen sulfide. Moreover, we apply the new probes to discriminate between distinct levels of intracellular HNO and RSH generated upon stimulation of live HeLa cells with ascorbate and hydrogen sulfide, respectively. The successful implementation of the lysine-based sensors to gain insight into biosynthetic pathways validates the method as a versatile tool for producing libraries of analogues with minimal synthetic effort.
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Affiliation(s)
- Andrei Loas
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , MA 02139 , USA . ; ; Tel: +1-617-253-1892
| | - Robert J Radford
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , MA 02139 , USA . ; ; Tel: +1-617-253-1892
| | - Alexandria Deliz Liang
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , MA 02139 , USA . ; ; Tel: +1-617-253-1892
| | - Stephen J Lippard
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , MA 02139 , USA . ; ; Tel: +1-617-253-1892
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13
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Moriguchi H, Kawai T, Tanaka Y. Simple bilayer on-chip valves using reversible sealability of PDMS. RSC Adv 2015. [DOI: 10.1039/c4ra10300a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Simple bilayer on-chip valves exploiting the reversible sealability of PDMS were realized by patterning the non-covalent area between two parallel microchannels.
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Affiliation(s)
| | - Takayuki Kawai
- Quantitative Biology Center (QBiC)
- RIKEN
- Kobe
- Japan
- Japan Science and Technology Agency
| | - Yo Tanaka
- Quantitative Biology Center (QBiC)
- RIKEN
- Kobe
- Japan
- Graduate School of Frontier Biosciences
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14
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Jack T, Simonin J, Ruepp MD, Thompson AJ, Gertsch J, Lochner M. Characterizing new fluorescent tools for studying 5-HT₃ receptor pharmacology. Neuropharmacology 2014; 90:63-73. [PMID: 25460187 DOI: 10.1016/j.neuropharm.2014.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 10/30/2014] [Accepted: 11/16/2014] [Indexed: 11/12/2022]
Abstract
The pharmacological characterization of ligands depends upon the ability to accurately measure their binding properties. Fluorescence provides an alternative to more traditional approaches such as radioligand binding. Here we describe the binding and spectroscopic properties of eight fluorescent 5-HT3 receptor ligands. These were tested on purified receptors, expressed receptors on live cells, or in vivo. All compounds had nanomolar affinities with fluorescent properties extending from blue to near infra-red emission. A fluorescein-derivative had the highest affinity as measured by fluorescence polarization (FP; 1.14 nM), flow cytometry (FC; 3.23 nM) and radioligand binding (RB; 1.90 nM). Competition binding with unlabeled 5-HT3 receptor agonists (5-HT, mCPBG, quipazine) and antagonists (granisetron, palonosetron, tropisetron) yielded similar affinities in all three assays. When cysteine substitutions were introduced into the 5-HT3 receptor binding site the same changes in binding affinity were seen for both granisetron and the fluorescein-derivative, suggesting that they both adopt orientations that are consistent with co-crystal structures of granisetron with a homologous protein (5HTBP). As expected, in vivo live imaging in anaesthetized mice revealed staining in the abdominal cavity in intestines, but also in salivary glands. The unexpected presence of 5-HT3 receptors in mouse salivary glands was confirmed by Western blots. Overall, these results demonstrate the wide utility of our new high-affinity fluorescently-labeled 5-HT3 receptor probes, ranging from in vitro receptor pharmacology, including FC and FP ligand competition, to live imaging of 5-HT3 expressing tissues.
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Affiliation(s)
- Thomas Jack
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | - Jonathan Simonin
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | - Andrew J Thompson
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | - Jürg Gertsch
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
| | - Martin Lochner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
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15
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Desvergne A, Cheng Y, Grosay-Gaudrel S, Maréchal X, Reboud-Ravaux M, Genin E, Vidal J. Noncovalent Fluorescent Probes of Human Immuno- and Constitutive Proteasomes. J Med Chem 2014; 57:9211-7. [DOI: 10.1021/jm5011429] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Audrey Desvergne
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8256, Biological Adaptation and Ageing (B2A), Integrated Cellular Ageing and Inflammation, 7 Quai St Bernard, 75005 Paris, France
- CNRS, UMR 8256, Biological Adaptation and Ageing (B2A), 75005 Paris, France
| | - Yan Cheng
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8256, Biological Adaptation and Ageing (B2A), Integrated Cellular Ageing and Inflammation, 7 Quai St Bernard, 75005 Paris, France
- CNRS, UMR 8256, Biological Adaptation and Ageing (B2A), 75005 Paris, France
| | - Sophie Grosay-Gaudrel
- Université de Rennes 1, CPM, Bâtiment 10A, Campus de Beaulieu, 35042 Rennes Cedex, France
- CNRS, UMR 6510, Chimie et Photonique Moléculaires, 35042 Rennes, France
| | - Xavier Maréchal
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8256, Biological Adaptation and Ageing (B2A), Integrated Cellular Ageing and Inflammation, 7 Quai St Bernard, 75005 Paris, France
- CNRS, UMR 8256, Biological Adaptation and Ageing (B2A), 75005 Paris, France
| | - Michèle Reboud-Ravaux
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8256, Biological Adaptation and Ageing (B2A), Integrated Cellular Ageing and Inflammation, 7 Quai St Bernard, 75005 Paris, France
- CNRS, UMR 8256, Biological Adaptation and Ageing (B2A), 75005 Paris, France
| | - Emilie Genin
- Université de Rennes 1, CPM, Bâtiment 10A, Campus de Beaulieu, 35042 Rennes Cedex, France
- CNRS, UMR 6510, Chimie et Photonique Moléculaires, 35042 Rennes, France
| | - Joëlle Vidal
- Université de Rennes 1, CPM, Bâtiment 10A, Campus de Beaulieu, 35042 Rennes Cedex, France
- CNRS, UMR 6510, Chimie et Photonique Moléculaires, 35042 Rennes, France
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16
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Fomich MA, Kvach MV, Navakouski MJ, Weise C, Baranovsky AV, Korshun VA, Shmanai VV. Azide phosphoramidite in direct synthesis of azide-modified oligonucleotides. Org Lett 2014; 16:4590-3. [PMID: 25156193 DOI: 10.1021/ol502155g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Azide and phosphoramidite functions were found to be compatible within one molecule and stable for months in solution kept frozen at -20 °C. An azide-carrying phosphoramidite was used for direct introduction of multiple azide modifications into synthetic oligonucleotides. A series of azide-containing oligonucleotides were modified further using click reactions with alkynes.
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Affiliation(s)
- Maksim A Fomich
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, 220072 Minsk, Belarus
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17
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Portal CF, Seifert JM, Buehler C, Meisner-Kober NC, Auer M. Novel 1:1 Labeling and Purification Process for C-Terminal Thioester and Single Cysteine Recombinant Proteins Using Generic Peptidic Toolbox Reagents. Bioconjug Chem 2014; 25:1213-22. [DOI: 10.1021/bc5000059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Christophe F. Portal
- School
of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, The King’s Buildings, CH Waddington Building
3.07, Mayfield Road, Edinburgh EH9 3JD, United Kingdom
| | - Jan-Marcus Seifert
- Innovative
Screening Technologies Unit, Novartis Institutes for BioMedical Research, Brunnerstrasse 59, A-1235 Vienna, Austria
- Marinomed Biotechnologie GmbH, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Christof Buehler
- Innovative
Screening Technologies Unit, Novartis Institutes for BioMedical Research, Brunnerstrasse 59, A-1235 Vienna, Austria
- Supercomputing Systems AG, Technoparkstrasse
1, 8005 Zürich, Switzerland
| | - Nicole-Claudia Meisner-Kober
- Innovative
Screening Technologies Unit, Novartis Institutes for BioMedical Research, Brunnerstrasse 59, A-1235 Vienna, Austria
- Novartis Institutes for BioMedical Research, Novartis Campus Forum 1, 4056 Basel, Switzerland
| | - Manfred Auer
- School
of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, The King’s Buildings, CH Waddington Building
3.07, Mayfield Road, Edinburgh EH9 3JD, United Kingdom
- Innovative
Screening Technologies Unit, Novartis Institutes for BioMedical Research, Brunnerstrasse 59, A-1235 Vienna, Austria
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18
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Evaluation of intrinsic spectroscopic properties of chromophore assemblies by shielding with cyclohexyl base pairs within a DNA duplex. Bioorg Med Chem 2013; 21:6191-7. [DOI: 10.1016/j.bmc.2013.04.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 03/28/2013] [Accepted: 04/05/2013] [Indexed: 11/21/2022]
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19
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Kvach MV, Tsybulsky DA, Shmanai VV, Prokhorenko IA, Stepanova IA, Korshun VA. Non-nucleoside phosphoramidites of xanthene dyes (FAM, JOE, and TAMRA) for oligonucleotide labeling. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2013; Chapter 4:4.55.1-4.55.33. [PMID: 23512693 DOI: 10.1002/0471142700.nc0455s52] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This unit describes the preparation of 5- and 6-carboxy derivatives of the xanthene fluorescent dyes fluorescein (FAM), 4',5'-dichloro-2',7'-dimethoxy-fluorescein (JOE), and tetramethylrhodamine (TAMRA) as individual isomers, and their conversion to non-nucleoside phosphoramidite reagents suitable for oligonucleotide labeling. The use of a cyclohexylcarbonyl (Chc) protecting group for blocking of phenolic hydroxyls facilitates the chromatographic separation of isomers of carboxy-FAM and carboxy-JOE as pentafluorophenyl esters. Acylation of 3-dimethylaminophenol with 1,2,4-benzenetricarboxylic anhydride gave a mixture of 4-dimethylamino-2-hydroxy-2',4'(5')-dicarboxybenzophenones, easily separable into individual compounds upon fractional crystallization. Individual isomeric benzophenones are precursors of 5- or 6-carboxytetramethylrhodamines. The dyes were converted into 6-aminohexanol- (JOE), 4-trans-aminocyclohexanol- (FAM and JOE), and hydroxyprolinol-based (TAMRA) phosphoramidite reagents.
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Affiliation(s)
| | | | | | | | - Irina A Stepanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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20
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Vollrath A, Schubert S, Schubert US. Fluorescence imaging of cancer tissue based on metal-free polymeric nanoparticles – a review. J Mater Chem B 2013; 1:1994-2007. [DOI: 10.1039/c3tb20089b] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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21
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de Jong A, Merkx R, Berlin I, Rodenko B, Wijdeven RHM, El Atmioui D, Yalçin Z, Robson CN, Neefjes JJ, Ovaa H. Ubiquitin-based probes prepared by total synthesis to profile the activity of deubiquitinating enzymes. Chembiochem 2012; 13:2251-8. [PMID: 23011887 PMCID: PMC3487179 DOI: 10.1002/cbic.201200497] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Indexed: 11/08/2022]
Abstract
Epitope-tagged active-site-directed probes are widely used to visualize the activity of deubiquitinases (DUBs) in cell extracts, to investigate the specificity and potency of small-molecule DUB inhibitors, and to isolate and identify DUBs by mass spectrometry. With DUBs arising as novel potential drug targets, probes are required that can be produced in sufficient amounts and to meet the specific needs of a given experiment. The established method for the generation of DUB probes makes use of labor-intensive intein-based methods that have inherent limitations concerning the incorporation of unnatural amino acids and the amount of material that can be obtained. Here, we describe the total chemical synthesis of active-site-directed probes and their application to activity-based profiling and identification of functional DUBs. This synthetic methodology allowed the easy incorporation of desired tags for specific applications, for example, fluorescent reporters, handles for immunoprecipitation or affinity pull-down, and cleavable linkers. Additionally, the synthetic method can be scaled up to provide significant amounts of probe. Fluorescent ubiquitin probes allowed faster, in-gel detection of active DUBs, as compared to (immuno)blotting procedures. A biotinylated probe holding a photocleavable linker enabled the affinity pull-down and subsequent mild, photorelease of DUBs. Also, DUB activity levels were monitored in response to overexpression or knockdown, and to inhibition by small molecules. Furthermore, fluorescent probes revealed differential DUB activity profiles in a panel of lung and prostate cancer cells.
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Affiliation(s)
- Annemieke de Jong
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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Yu H, Xiao Y, Guo H. From Spirolactam Mixtures to Regioisomerically Pure 5- and 6-Rhodamines: A Chemodosimeter-Inspired Strategy. Org Lett 2012; 14:2014-7. [DOI: 10.1021/ol300523m] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Haibo Yu
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China
| | - Yi Xiao
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China
| | - Haiying Guo
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China
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Tsybulsky DA, Kvach MV, Stepanova IA, Korshun VA, Shmanai VV. 4',5'-Dichloro-2',7'-dimethoxy-5(6)-carboxyfluorescein (JOE): synthesis and spectral properties of oligonucleotide conjugates. J Org Chem 2011; 77:977-84. [PMID: 22148236 DOI: 10.1021/jo202229t] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A convenient procedure for the preparation of the fluorescent dye 4',5'-dichloro-2',7'-dimethoxy-5(6)-carboxyfluorescein (JOE) is reported; the overall yield achieved starting from isovanillin is 10 times higher (40% vs 4%) compared to the known procedure. Isomers (5- and 6-) are easily chromatographically separable as pentafluorophenyl esters of 3',6'-O-bis(cyclohexylcarbonyl) derivatives. Four non-nucleoside JOE phosphoramidites based on 5- and 6-isomers and flexible 6-aminohexanol (AH) or rigid 4-trans-aminocyclohexanol (ACH) linkers have been prepared and used for oligonucleotide labeling. Spectral and photophysical properties of 5'-JOE-modified oligonucleotides have been studied. Fluorescence quantum yield of the dye correlates with the nature of the linker (rigid vs flexible) and with the presence of dG nucleosides in close proximity to a JOE residue.
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Affiliation(s)
- Dmitry A Tsybulsky
- Institute of Physical Organic Chemistry, Surganova 13, 220072 Minsk, Belarus
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Heterocyclic Dyes: Preparation, Properties, and Applications. PROGRESS IN HETEROCYCLIC CHEMISTRY 2011. [DOI: 10.1016/s0959-6380(11)22002-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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