1
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Turnbull JL, Miller EW. An open and shut case? Chemistry to control xanthene dyes. TRENDS IN CHEMISTRY 2024; 6:164-172. [PMID: 39036609 PMCID: PMC11257214 DOI: 10.1016/j.trechm.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Fluorescent dyes are an indispensable part of the scientific enterprise. Xanthene-based fluorophores, like fluorescein and rhodamine, have been in continual use across numerous fields since their invention in the late 19th century. Modern methods to synthesize and expand the scope of xanthene dye chemistry have enabled new colors, enhanced stability, and improved brightness. Modifications to the 3-position of xanthene dyes have been, until recently, less well-explored. Here, we discuss how small changes to the identity of the substituent at the 3-position of fluoresceins and rhodamines can profoundly alter the properties of xanthene dyes, with the potential to unlock new applications at the interface of chemistry and biology.
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Affiliation(s)
- Joshua L. Turnbull
- Department of Chemistry, University of California, Berkeley, CA 94720, United States of America
| | - Evan W. Miller
- Department of Chemistry, University of California, Berkeley, CA 94720, United States of America
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, United States of America
- Helen Wills Neuroscience Institute University of California, Berkeley, CA 94720, United States of America
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2
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He H, Yin J, Li M, Dessai CVP, Yi M, Teng X, Zhang M, Li Y, Du Z, Xu B, Cheng JX. Mapping enzyme activity in living systems by real-time mid-infrared photothermal imaging of nitrile chameleons. Nat Methods 2024; 21:342-352. [PMID: 38191931 PMCID: PMC11165695 DOI: 10.1038/s41592-023-02137-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 11/17/2023] [Indexed: 01/10/2024]
Abstract
Simultaneous spatial mapping of the activity of multiple enzymes in a living system can elucidate their functions in health and disease. However, methods based on monitoring fluorescent substrates are limited. Here, we report the development of nitrile (C≡N)-tagged enzyme activity reporters, named nitrile chameleons, for the peak shift between substrate and product. To image these reporters in real time, we developed a laser-scanning mid-infrared photothermal imaging system capable of imaging the enzymatic substrates and products at a resolution of 300 nm. We show that when combined, these tools can map the activity distribution of different enzymes and measure their relative catalytic efficiency in living systems such as cancer cells, Caenorhabditis elegans, and brain tissues, and can be used to directly visualize caspase-phosphatase interactions during apoptosis. Our method is generally applicable to a broad category of enzymes and will enable new analyses of enzymes in their native context.
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Affiliation(s)
- Hongjian He
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
- Photonics Center, Boston University, Boston, MA, USA
| | - Jiaze Yin
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
- Photonics Center, Boston University, Boston, MA, USA
| | - Mingsheng Li
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
- Photonics Center, Boston University, Boston, MA, USA
| | - Chinmayee Vallabh Prabhu Dessai
- Photonics Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Meihui Yi
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Xinyan Teng
- Photonics Center, Boston University, Boston, MA, USA
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Meng Zhang
- Photonics Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Yueming Li
- Photonics Center, Boston University, Boston, MA, USA
- Department of Mechanical Engineering, Boston University, Boston, MA, USA
| | - Zhiyi Du
- Photonics Center, Boston University, Boston, MA, USA
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Ji-Xin Cheng
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA.
- Photonics Center, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Department of Chemistry, Boston University, Boston, MA, USA.
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3
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Gil-Rivas A, de Pascual-Teresa B, Ortín I, Ramos A. New Advances in the Exploration of Esterases with PET and Fluorescent Probes. Molecules 2023; 28:6265. [PMID: 37687094 PMCID: PMC10488407 DOI: 10.3390/molecules28176265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023] Open
Abstract
Esterases are hydrolases that catalyze the hydrolysis of esters into the corresponding acids and alcohols. The development of fluorescent probes for detecting esterases is of great importance due to their wide spectrum of biological and industrial applications. These probes can provide a rapid and sensitive method for detecting the presence and activity of esterases in various samples, including biological fluids, food products, and environmental samples. Fluorescent probes can also be used for monitoring the effects of drugs and environmental toxins on esterase activity, as well as to study the functions and mechanisms of these enzymes in several biological systems. Additionally, fluorescent probes can be designed to selectively target specific types of esterases, such as those found in pathogenic bacteria or cancer cells. In this review, we summarize the recent fluorescent probes described for the visualization of cell viability and some applications for in vivo imaging. On the other hand, positron emission tomography (PET) is a nuclear-based molecular imaging modality of great value for studying the activity of enzymes in vivo. We provide some examples of PET probes for imaging acetylcholinesterases and butyrylcholinesterases in the brain, which are valuable tools for diagnosing dementia and monitoring the effects of anticholinergic drugs on the central nervous system.
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Affiliation(s)
- Alba Gil-Rivas
- Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28668 Boadilla del Monte, Spain
| | - Beatriz de Pascual-Teresa
- Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28668 Boadilla del Monte, Spain
| | - Irene Ortín
- Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28668 Boadilla del Monte, Spain
| | - Ana Ramos
- Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28668 Boadilla del Monte, Spain
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4
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Kim MJ, Li Y, Junge JA, Kim NK, Fraser SE, Zhang C. Development of Highly Fluorogenic Styrene Probes for Visualizing RNA in Live Cells. ACS Chem Biol 2023; 18:1523-1533. [PMID: 37200527 PMCID: PMC10367048 DOI: 10.1021/acschembio.3c00141] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/05/2023] [Indexed: 05/20/2023]
Abstract
Styrene dyes are useful imaging probes and fluorescent sensors due to their strong fluorogenic responses to environmental changes or binding macromolecules. Previously, indole-containing styrene dyes have been reported to selectively bind RNA in the nucleolus and cytoplasm. However, the application of these indole-based dyes in cell imaging is limited by their moderate fluorescence enhancement and quantum yields, as well as relatively high background associated with these green-emitting dyes. In this work, we have investigated the positional and electronic effects of the electron donor by generating regioisomeric and isosteric analogues of the indole ring. Select probes exhibited large Stokes shifts, enhanced molar extinction coefficients, and bathochromic shifts in their absorption and fluorescence wavelengths. In particular, the indolizine analogues displayed high membrane permeability, strong fluorogenic responses upon binding RNA, compatibility with fluorescence lifetime imaging microscopy (FLIM), low cytotoxicity, and excellent photostability. These indolizine dyes not only give rise to rapid, sensitive, and intense staining of nucleoli in live cells but can also resolve subnucleolar structures enabling highly detailed studies of nucleolar morphology. Furthermore, our dyes can partition into RNA coacervates and resolve the formation of multiphase complex coacervate droplets. These indolizine-containing styrene probes offer the highest fluorescence enhancement among the RNA-selective dyes reported in the literature; thus, these new dyes are excellent alternatives to the commercially available RNA dye, SYTO RNASelect, for visualizing RNA in live cells and in vitro.
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Affiliation(s)
- Moon Jung Kim
- Department
of Chemistry & Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| | - Yida Li
- Department
of Chemistry & Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| | - Jason A. Junge
- Department
of Biological Sciences, Division of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
- Translational
Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, United States
| | - Nathan K. Kim
- Department
of Chemistry & Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| | - Scott E. Fraser
- Department
of Biological Sciences, Division of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
- Translational
Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, United States
| | - Chao Zhang
- Department
of Chemistry & Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
- Department
of Biological Sciences, Division of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
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5
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Scheuplein NJ, Lohr T, Vivoli Vega M, Ankrett D, Seufert F, Kirchner L, Harmer NJ, Holzgrabe U. Fluorescent probe for the identification of potent inhibitors of the macrophage infectivity potentiator (Mip) protein of Burkholderia pseudomallei. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:211-222. [PMID: 37001588 DOI: 10.1016/j.slasd.2023.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/02/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023]
Abstract
The macrophage infectivity potentiator (Mip) protein belongs to the immunophilin superfamily. This class of enzymes catalyzes the interconversion between the cis and trans configuration of proline-containing peptide bonds. Mip has been shown to be important for the virulence of a wide range of pathogenic microorganisms, including the Gram-negative bacterium Burkholderia pseudomallei. Small molecules derived from the natural product rapamycin, lacking its immunosuppression-inducing moiety, inhibit Mip's peptidyl-prolyl cis-trans isomerase (PPIase) activity and lead to a reduction in pathogen load in vitro. Here, a fluorescence polarization assay (FPA) to enable the screening and effective development of BpMip inhibitors was established. A fluorescent probe was prepared, derived from previous pipecolic scaffold Mip inhibitors labeled with fluorescein. This probe showed moderate affinity for BpMip and enabled a highly robust FPA suitable for screening large compound libraries with medium- to high-throughput (Z factor ∼ 0.89) to identify potent new inhibitors. The FPA results are consistent with data from the protease-coupled PPIase assay. Analysis of the temperature dependence of the probe's binding highlighted that BpMip's ligand binding is driven by enthalpic rather than entropic effects. This has considerable consequences for the use of low-temperature kinetic assays.
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Affiliation(s)
- Nicolas Julian Scheuplein
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Theresa Lohr
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | | | - Dyan Ankrett
- Living Systems Institute, Stocker Road, Exeter EX4 4QD, UK
| | - Florian Seufert
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Lukas Kirchner
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | | | - Ulrike Holzgrabe
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, Würzburg 97074, Germany.
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6
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Usama SM, Marker SC, Li DH, Caldwell DR, Stroet M, Patel NL, Tebo AG, Hernot S, Kalen JD, Schnermann M. Method To Diversify Cyanine Chromophore Functionality Enables Improved Biomolecule Tracking and Intracellular Imaging. J Am Chem Soc 2023. [PMID: 37367935 DOI: 10.1021/jacs.3c01765] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Heptamethine indocyanines are invaluable probes for near-infrared (NIR) imaging. Despite broad use, there are only a few synthetic methods to assemble these molecules, and each has significant limitations. Here, we report the use of pyridinium benzoxazole (PyBox) salts as heptamethine indocyanine precursors. This method is high yielding, simple to implement, and provides access to previously unknown chromophore functionality. We applied this method to create molecules to address two outstanding objectives in NIR fluorescence imaging. First, we used an iterative approach to develop molecules for protein-targeted tumor imaging. When compared to common NIR fluorophores, the optimized probe increases the tumor specificity of monoclonal antibody (mAb) and nanobody conjugates. Second, we developed cyclizing heptamethine indocyanines with the goal of improving cellular uptake and fluorogenic properties. By modifying both the electrophilic and nucleophilic components, we demonstrate that the solvent sensitivity of the ring-open/ring-closed equilibrium can be modified over a wide range. We then show that a chloroalkane derivative of a compound with tuned cyclization properties undergoes particularly efficient no-wash live cell imaging using organelle-targeted HaloTag self-labeling proteins. Overall, the chemistry reported here broadens the scope of accessible chromophore functionality, and, in turn, enables the discovery of NIR probes with promising properties for advanced imaging applications.
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Affiliation(s)
- Syed Muhammad Usama
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Sierra C Marker
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Dong-Hao Li
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Donald R Caldwell
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Marcus Stroet
- Laboratory for in Vivo Cellular and Molecular Imaging, ICMI-BEFY/MIMA, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Nimit L Patel
- Small Animal Imaging Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland 21702, United States
| | - Alison G Tebo
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, United States
| | - Sophie Hernot
- Laboratory for in Vivo Cellular and Molecular Imaging, ICMI-BEFY/MIMA, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Joseph D Kalen
- Small Animal Imaging Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland 21702, United States
| | - Martin Schnermann
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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7
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Tacke E, Hoang MD, Tatoueix K, Keromnes B, Van Eslande E, Durand P, Pieters G, Chevalier A. Unprecedented perspectives on the application of CinNapht fluorophores provided by a "late-stage" functionalization strategy. Chem Sci 2023; 14:6000-6010. [PMID: 37293654 PMCID: PMC10246687 DOI: 10.1039/d3sc01365k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/02/2023] [Indexed: 06/10/2023] Open
Abstract
A simple and easy-to-implement process based on a nucleophilic aromatic substitution reaction with a wide variety of nucleophiles on a fluorinated CinNapht is described. This process has the key advantage of introducing multiple functionalities at a very late stage, thus providing access to new applications including the synthesis of photostable and bioconjugatable large Stokes shift red emitting dyes and selective organelle imaging agents, as well as AIEE-based wash-free lipid droplet imaging in live cells with high signal-to-noise ratio. The synthesis of bench-stable CinNapht-F has been optimized and can be reproduced on a large scale, making it an easy-to-store starting material that can be used at will to prepare new molecular imaging tools.
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Affiliation(s)
- Eléonore Tacke
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301 91198 Gif-sur-Yvette France
| | - Minh-Duc Hoang
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301 91198 Gif-sur-Yvette France
| | - Kevin Tatoueix
- Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris-Saclay, CEA, INRAE 91191 Gif-sur-Yvette France
| | - Benoît Keromnes
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301 91198 Gif-sur-Yvette France
| | - Elsa Van Eslande
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301 91198 Gif-sur-Yvette France
| | - Philippe Durand
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301 91198 Gif-sur-Yvette France
| | - Gregory Pieters
- Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris-Saclay, CEA, INRAE 91191 Gif-sur-Yvette France
| | - Arnaud Chevalier
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301 91198 Gif-sur-Yvette France
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8
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Behring L, Ruiz-Gómez G, Trapp C, Morales M, Wodtke R, Köckerling M, Kopka K, Pisabarro MT, Pietzsch J, Löser R. Dipeptide-Derived Alkynes as Potent and Selective Irreversible Inhibitors of Cysteine Cathepsins. J Med Chem 2023; 66:3818-3851. [PMID: 36867428 PMCID: PMC10041539 DOI: 10.1021/acs.jmedchem.2c01360] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The potential of designing irreversible alkyne-based inhibitors of cysteine cathepsins by isoelectronic replacement in reversibly acting potent peptide nitriles was explored. The synthesis of the dipeptide alkynes was developed with special emphasis on stereochemically homogeneous products obtained in the Gilbert-Seyferth homologation for C≡C bond formation. Twenty-three dipeptide alkynes and 12 analogous nitriles were synthesized and investigated for their inhibition of cathepsins B, L, S, and K. Numerous combinations of residues at positions P1 and P2 as well as terminal acyl groups allowed for the derivation of extensive structure-activity relationships, which were rationalized by computational covalent docking for selected examples. The determined inactivation constants of the alkynes at the target enzymes span a range of >3 orders of magnitude (3-10 133 M-1 s-1). Notably, the selectivity profiles of alkynes do not necessarily reflect those of the nitriles. Inhibitory activity at the cellular level was demonstrated for selected compounds.
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Affiliation(s)
- Lydia Behring
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden, Germany
- Technische Universität Dresden, School of Science, Faculty of Chemistry and Food Chemistry, Mommsenstraße 4, 01069 Dresden, Germany
| | - Gloria Ruiz-Gómez
- BIOTEC, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Christian Trapp
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Maryann Morales
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Robert Wodtke
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Martin Köckerling
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany
| | - Klaus Kopka
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden, Germany
- Technische Universität Dresden, School of Science, Faculty of Chemistry and Food Chemistry, Mommsenstraße 4, 01069 Dresden, Germany
| | - M Teresa Pisabarro
- BIOTEC, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Jens Pietzsch
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden, Germany
- Technische Universität Dresden, School of Science, Faculty of Chemistry and Food Chemistry, Mommsenstraße 4, 01069 Dresden, Germany
| | - Reik Löser
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden, Germany
- Technische Universität Dresden, School of Science, Faculty of Chemistry and Food Chemistry, Mommsenstraße 4, 01069 Dresden, Germany
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9
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Liu K, Xu Z, Zhao Z, Chen Y, Chai Y, Ma L, Li S. A Dual Fluorescence Assay Enables High-Throughput Screening for Poly(ethylene terephthalate) Hydrolases. CHEMSUSCHEM 2023; 16:e202202019. [PMID: 36511949 DOI: 10.1002/cssc.202202019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/03/2022] [Indexed: 06/17/2023]
Abstract
The drastically increasing consumption of petroleum-derived plastics hasserious environmental impacts and raises public concerns. Poly(ethylene terephthalate) (PET) is amongst the most extensively produced synthetic polymers. Enzymatic hydrolysis of PET recently emerged as an enticing path for plastic degradation and recycling. In-lab directed evolution has revealed the great potential of PET hydrolases (PETases). However, the time-consuming and laborious PETase assays hinder the identification of effective variants in large mutant libraries. Herein, we devise and validate a dual fluorescence-based high-throughput screening (HTS) assay for a representative IsPETase. The two-round HTS of a pilot library consisting of 2850 IsPETase variants yields six mutant IsPETases with 1.3-4.9 folds improved activities. Compared to the currently used structure- or computational redesign-based PETase engineering, this HTS approach provides a new strategy for discovery of new beneficial mutation patterns of PETases.
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Affiliation(s)
- Kun Liu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Ziping Xu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Zhiyi Zhao
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Yuexing Chen
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Yating Chai
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Li Ma
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, No. 168 Wenhai Middle Rd, Qingdao, Shandong, 266237, P. R. China
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10
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Dziuba D. Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications. Methods Appl Fluoresc 2022; 10. [PMID: 35738250 DOI: 10.1088/2050-6120/ac7bd8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden, Grand Est, 67401, FRANCE
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11
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In Vitro Biocompatibility of a Novel Semi-Rigid Shell Barrier System: As a New Application for Guided Bone Regeneration. Polymers (Basel) 2022; 14:polym14122451. [PMID: 35746025 PMCID: PMC9231217 DOI: 10.3390/polym14122451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 02/01/2023] Open
Abstract
This study evaluated the in vitro biocompatibility of a novel, semi-rigid shell barrier system for guided bone regeneration (GBR) based on polycaprolactone and biphasic calcium phosphate membranes and consisting of a semi-rigid shell (SR) and two semi-resorbable barrier membranes, i.e., a buffered (BF) and an airdried (AD) membrane. In vitro biocompatibility, cell cytotoxicity, cell proliferation and differentiation were evaluated with osteoblast (MC3T3-E1) and fibroblast (L929) cells compared to the d-PTFE membrane (Cytoplast®, CP). The osteoblasts and fibroblasts were well attached and proliferated on all materials from days 1, 3, and 7 without cell cytotoxicity. All groups showed that osteoblast and fibroblast cell proliferation increased from day 1 to day 14–17 and decreased on day 21. On day 21, the CP membrane presented significantly higher osteoblast cell numbers than the BF membrane and the SR shell (p = 0.000). The CP membrane presented a significantly higher amount of fibroblast cells than the other groups (p = 0.000). The SR shell and the BF membrane demonstrated higher osteoblast cell differentiation markers including ALP activity, osteocalcin, and mineral secretion than the CP and the AD membrane. The semi-rigid shell barrier system demonstrated good in vitro biocompatibility and supported osteogenic cell proliferation and differentiation better than the d-PTFE membrane.
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12
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Lam KY, Lee CS, Pichika MR, Cheng SF, Hang Tan RY. Light-responsive polyurethanes: classification of light-responsive moieties, light-responsive reactions, and their applications. RSC Adv 2022; 12:15261-15283. [PMID: 35693222 PMCID: PMC9118056 DOI: 10.1039/d2ra01506d] [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] [Received: 03/07/2022] [Accepted: 05/01/2022] [Indexed: 11/24/2022] Open
Abstract
Stimuli responsiveness has been an attractive feature of smart material design, wherein the chemical and physical properties of the material can be varied in response to small environmental change. Polyurethane (PU), a widely used synthetic polymer can be upgraded into a light-responsive smart polymer by introducing a light-sensitive moiety into the polymer matrix. For instance, azobenzene, spiropyran, and coumarin result in reversible light-induced reactions, while o-nitrobenzyl can result in irreversible light-induced reactions. These variations of light-stimulus properties endow PU with wide ranges of physical, mechanical, and chemical changes upon exposure to different wavelengths of light. PU responsiveness has rarely been reviewed even though it is known to be one of the most versatile polymers with diverse ranges of applications in household, automotive, electronic, construction, medical, and biomedical industries. This review focuses on the classes of light-responsive moieties used in PU systems, their synthesis, and the response mechanism of light-responsive PU-based materials, which also include dual- or multi-responsive light-responsive PU systems. The advantages and limitations of light-responsive PU are reviewed and challenges in the development of light-responsive PU are discussed.
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Affiliation(s)
- Ki Yan Lam
- School of Postgraduate, International Medical University No. 126, Jalan Jalil Perkasa 19, Bukit Jalil 57000 Kuala Lumpur Malaysia
| | - Choy Sin Lee
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University No. 126, Jalan Jalil Perkasa 19, Bukit Jalil 57000 Kuala Lumpur Malaysia
| | - Mallikarjuna Rao Pichika
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University No. 126, Jalan Jalil Perkasa 19, Bukit Jalil 57000 Kuala Lumpur Malaysia
- Centre for Bioactive Molecules and Drug Delivery, Institute for Research, Development and Innovation No. 126, Jalan Jalil Perkasa 19, Bukit Jalil 57000 Kuala Lumpur Malaysia
| | - Sit Foon Cheng
- Unit of Research on Lipids (URL), Department of Chemistry, Faculty of Science, University of Malaya Kuala Lumpur 50603 Malaysia
| | - Rachel Yie Hang Tan
- School of Postgraduate, International Medical University No. 126, Jalan Jalil Perkasa 19, Bukit Jalil 57000 Kuala Lumpur Malaysia
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14
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Sun X, Tamura R, Sumita M, Mori K, Terayama K, Tsuda K. Integrating Incompatible Assay Data Sets with Deep Preference Learning. ACS Med Chem Lett 2022; 13:70-75. [PMID: 35047110 PMCID: PMC8762726 DOI: 10.1021/acsmedchemlett.1c00439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 12/27/2021] [Indexed: 11/30/2022] Open
Abstract
A large amount of bioactivity assay data is already accumulated in public databases, but the integration of these data sets for quantitative structure-activity relationship (QSAR) studies is not straightforward due to differences in experimental methods and settings. We present an efficient deep-learning-based approach called Deep Preference Data Integration (DPDI). For integrating outcome variables of different assay types, a surrogate variable is introduced, and a neural network is trained such that the total order induced by the surrogate variable is maximally consistent with given data sets. In a task of predicting efficacy of factor Xa inhibitors, DPDI successfully integrated 2959 molecules distributed in 129 assay data sets. In most of our experiments, data integration improved prediction accuracy strongly in interpolation and extrapolation tasks, indicating that DPDI is an effective tool for QSAR studies.
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Affiliation(s)
- Xiaolin Sun
- Graduate
School of Frontier Sciences, The University
of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Ryo Tamura
- Graduate
School of Frontier Sciences, The University
of Tokyo, Kashiwa, Chiba 277-8561, Japan
- Research
and Services Division of Materials Data and Integrated System, National Institute for Materials Science, Tsukuba, Ibaraki 305-0047, Japan
- International
Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, Tsukuba, Ibaraki 305-0047, Japan
- RIKEN
Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
| | - Masato Sumita
- International
Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, Tsukuba, Ibaraki 305-0047, Japan
- RIKEN
Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
| | - Kenichi Mori
- Astellas
Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan
| | - Kei Terayama
- RIKEN
Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, Yokohama 230-0045, Japan
| | - Koji Tsuda
- Graduate
School of Frontier Sciences, The University
of Tokyo, Kashiwa, Chiba 277-8561, Japan
- Research
and Services Division of Materials Data and Integrated System, National Institute for Materials Science, Tsukuba, Ibaraki 305-0047, Japan
- RIKEN
Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
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15
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Bozhanova NG, Harp JM, Bender BJ, Gavrikov AS, Gorbachev DA, Baranov MS, Mercado CB, Zhang X, Lukyanov KA, Mishin AS, Meiler J. Computational redesign of a fluorogen activating protein with Rosetta. PLoS Comput Biol 2021; 17:e1009555. [PMID: 34748541 PMCID: PMC8601599 DOI: 10.1371/journal.pcbi.1009555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 11/18/2021] [Accepted: 10/11/2021] [Indexed: 11/24/2022] Open
Abstract
The use of unnatural fluorogenic molecules widely expands the pallet of available genetically encoded fluorescent imaging tools through the design of fluorogen activating proteins (FAPs). While there is already a handful of such probes available, each of them went through laborious cycles of in vitro screening and selection. Computational modeling approaches are evolving incredibly fast right now and are demonstrating great results in many applications, including de novo protein design. It suggests that the easier task of fine-tuning the fluorogen-binding properties of an already functional protein in silico should be readily achievable. To test this hypothesis, we used Rosetta for computational ligand docking followed by protein binding pocket redesign to further improve the previously described FAP DiB1 that is capable of binding to a BODIPY-like dye M739. Despite an inaccurate initial docking of the chromophore, the incorporated mutations nevertheless improved multiple photophysical parameters as well as the overall performance of the tag. The designed protein, DiB-RM, shows higher brightness, localization precision, and apparent photostability in protein-PAINT super-resolution imaging compared to its parental variant DiB1. Moreover, DiB-RM can be cleaved to obtain an efficient split system with enhanced performance compared to a parental DiB-split system. The possible reasons for the inaccurate ligand binding pose prediction and its consequence on the outcome of the design experiment are further discussed. Computational approaches have recently made significant progress in the protein engineering field evolving from a tool for helping experimentalists to prioritize or short-list mutations for testing to being capable of making fully reliable predictions. However, not all the fields of protein modeling are evolving at a similar pace. That is why evaluating the capabilities of computational tools on different tasks is important to provide other scientists with up-to-date information on the state of the field. Here we tested the performance of Rosetta (one of the leading macromolecule modeling tools) in improving small molecule-binding proteins. We successfully redesigned a fluorogen binding protein DiB1 –a protein that binds a non-fluorescent molecule and enforces its fluorescence in the obtained complex–for improved brightness and better performance in super-resolution imaging. Our results suggest that such tasks can be already achieved without laborious library screenings. However, the flexibility of the proteins might still be underestimated during standard modeling protocols and should be closely evaluated.
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Affiliation(s)
- Nina G. Bozhanova
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Joel M. Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Brian J. Bender
- Department of Pharmacology and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Alexey S. Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A. Gorbachev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail S. Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Christina B. Mercado
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Xuan Zhang
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | | | - Alexander S. Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Jens Meiler
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Drug Discovery, Leipzig University, Leipzig, Germany
- * E-mail:
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16
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Hoang MD, Bodin JB, Savina F, Steinmetz V, Bignon J, Durand P, Clavier G, Méallet-Renault R, Chevalier A. "CinNapht" dyes: a new cinnoline/naphthalimide fused hybrid fluorophore. Synthesis, photo-physical study and use for bio-imaging. RSC Adv 2021; 11:30088-30092. [PMID: 35493990 PMCID: PMC9041350 DOI: 10.1039/d1ra05110e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/31/2021] [Indexed: 12/17/2022] Open
Abstract
Six-membered-diaza ring of cinnoline has been fused on naphthalimide dye to give a donor-acceptor system called CinNapht. This red shifted fluorophore, that can be synthesised in gram scale, exhibits a large Stoke shift and a fluorescence quantum yield up to 0.33. It is also characterized by a strong solvatochromic effect from green to red emission as well and can be used for bio-imaging.
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Affiliation(s)
- Minh-Duc Hoang
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles UPR 2301 91198 Gif-sur-Yvette France
| | - Jean-Baptiste Bodin
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay Orsay 91405 France
| | - Farah Savina
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay Orsay 91405 France
| | - Vincent Steinmetz
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles UPR 2301 91198 Gif-sur-Yvette France
| | - Jérôme Bignon
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles UPR 2301 91198 Gif-sur-Yvette France
| | - Philippe Durand
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles UPR 2301 91198 Gif-sur-Yvette France
| | - Gilles Clavier
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, PPSM 91190 Gif-sur-Yvette France
| | - Rachel Méallet-Renault
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay Orsay 91405 France
| | - Arnaud Chevalier
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles UPR 2301 91198 Gif-sur-Yvette France
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17
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Usama SM, Inagaki F, Kobayashi H, Schnermann MJ. Norcyanine-Carbamates Are Versatile Near-Infrared Fluorogenic Probes. J Am Chem Soc 2021; 143:5674-5679. [PMID: 33844539 DOI: 10.1021/jacs.1c02112] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Fluorogenic probes in the near-infrared (NIR) region have the potential to provide stimuli-dependent information in living organisms. Here, we describe a new class of fluorogenic probes based on the heptamethine cyanine scaffold, the most broadly used NIR chromophore. These compounds result from modification of heptamethine norcyanines with stimuli-responsive carbamate linkers. The resulting cyanine carbamates (CyBams) exhibit exceptional turn-ON ratios (∼170×) due to dual requirements for NIR emission: carbamate cleavage through 1,6-elimination and chromophore protonation. Illustrating their utility in complex in vivo settings, a γ-glutamate substituted CyBam was applied to imaging γ-glutamyl transpeptidase (GGT) activity in a metastatic model of ovarian cancer. Overall, CyBams have significant potential to extend the reach of fluorogenic strategies to intact tissue and live animal imaging applications.
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Affiliation(s)
- Syed Muhammad Usama
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Fuyuki Inagaki
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Hisataka Kobayashi
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Martin J Schnermann
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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18
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Kamimura A, Umemoto H, Kawamoto T, Honda T. Development of Water Solubility of 2-Phenylsulfanylhydroquinone Dimer Dye. ACS OMEGA 2021; 6:9254-9262. [PMID: 33842794 PMCID: PMC8028172 DOI: 10.1021/acsomega.1c00703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
With the aim of developing a new fluorescence dye with enhanced photophysical properties, this study describes the modification of the 2-phenylsulfanylhydroquinone dimer to realize a new bioimaging molecule. The characteristics of the dimer were advanced by introducing tetraethylene glycol side chains to provide sufficient water solubility and a tether consisting of an N-hydroxysuccinimide-terminated C6-carbon chain to attach bioactive molecules. Two derivatives containing two or three tetraethylene glycol side chains were designed and prepared, and the latter showed sufficient water solubility for biochemical applications. Both compounds exhibited similar photophysical properties and blue fluorescence under UV light irradiation. The dye containing three tetraethylene glycol units reacted with bovine serum albumin in water to give fluorescent derivatives.
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Affiliation(s)
- Akio Kamimura
- Department
of Applied Chemistry, Yamaguchi University, Ube 755-8611, Japan
| | - Haruka Umemoto
- Department
of Applied Chemistry, Yamaguchi University, Ube 755-8611, Japan
| | - Takuji Kawamoto
- Department
of Applied Chemistry, Yamaguchi University, Ube 755-8611, Japan
| | - Takeshi Honda
- Department
of Pharmacology, School of Medicine, Yamaguchi
University, Ube 755-8505, Japan
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19
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Turnbull JL, Benlian BR, Golden RP, Miller EW. Phosphonofluoresceins: Synthesis, Spectroscopy, and Applications. J Am Chem Soc 2021; 143:6194-6201. [PMID: 33797899 DOI: 10.1021/jacs.1c01139] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Xanthene fluorophores, like fluorescein, have been versatile molecules across diverse fields of chemistry and life sciences. Despite the ubiquity of 3-carboxy and 3-sulfonofluorescein for the last 150 years, to date, no reports of 3-phosphonofluorescein exist. Here, we report the synthesis, spectroscopic characterization, and applications of 3-phosphonofluoresceins. The absorption and emission of 3-phosphonofluoresceins remain relatively unaltered from the parent 3-carboxyfluorescein. 3-Phosphonofluoresceins show enhanced water solubility compared to 3-carboxyfluorescein and persist in an open, visible light-absorbing state even at low pH and in low dielectric media while 3-carboxyfluoresceins tend to lactonize. In contrast, the spirocyclization tendency of 3-phosphonofluoresceins can be modulated by esterification of the phosphonic acid. The bis-acetoxymethyl ester of 3-phosphonofluorescein readily enters living cells, showing excellent accumulation (>6x) and retention (>11x), resulting in a nearly 70-fold improvement in cellular brightness compared to 3-carboxyfluorescein. In a complementary fashion, the free acid form of 3-phosphonofluorescein does not cross cellular membranes, making it ideally suited for incorporation into a voltage-sensing scaffold. We develop a new synthetic route to functionalized 3-phosphonofluoresceins to enable the synthesis of phosphono-voltage sensitive fluorophores, or phosVF2.1.Cl. Phosphono-VF2.1.Cl shows excellent membrane localization, cellular brightness, and voltage sensitivity (26% ΔF/F per 100 mV), rivaling that of sulfono-based VF dyes. In summary, we develop the first synthesis of 3-phosphonofluoresceins, characterize the spectroscopic properties of this new class of xanthene dyes, and utilize these insights to show the utility of 3-phosphonofluoresceins in intracellular imaging and membrane potential sensing.
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20
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Jenni S, Ponsot F, Baroux P, Collard L, Ikeno T, Hanaoka K, Quesneau V, Renault K, Romieu A. Design, synthesis and evaluation of enzyme-responsive fluorogenic probes based on pyridine-flanked diketopyrrolopyrrole dyes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 248:119179. [PMID: 33248891 DOI: 10.1016/j.saa.2020.119179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/30/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
The ever-growing demand for fluorogenic dyes usable in the rapid construction of analyte-responsive fluorescent probes, has recently contributed to a revival of interest in the chemistry of diketopyrrolopyrrole (DPP) pigments. In this context, we have explored the potential of symmetrical and unsymmetrical DPP derivatives bearing two or one 4-pyridyl substituents acting as optically tunable group(s). The unique fluorogenic behavior of these molecules, closely linked to N-substitution/charge state of their pyridine unit (i.e., neutral pyridine or cationic pyridinium), has been used to design DPP-based fluorescent probes for detection of hypoxia-related redox enzymes and penicillin G acylase (PGA). In this paper, we describe synthesis, spectral characterization and bioanalytical validations of these probes. Dramatic differences in terms of aqueous stability and enzymatic fluorescence activation were observed. This systematic study enables to delineate the scope of application of pyridine-flanked DPP fluorophores in the field of enzyme biosensing.
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Affiliation(s)
- Sébastien Jenni
- Institut de Chimie Moléculaire de l'Université de Bourgogne, UMR 6302, CNRS, Univ. Bourgogne Franche-Comté, 9, Avenue Alain Savary, 21000 Dijon, France.
| | - Flavien Ponsot
- Institut de Chimie Moléculaire de l'Université de Bourgogne, UMR 6302, CNRS, Univ. Bourgogne Franche-Comté, 9, Avenue Alain Savary, 21000 Dijon, France
| | - Pierre Baroux
- Institut de Chimie Moléculaire de l'Université de Bourgogne, UMR 6302, CNRS, Univ. Bourgogne Franche-Comté, 9, Avenue Alain Savary, 21000 Dijon, France
| | - Lucile Collard
- Institut de Chimie Moléculaire de l'Université de Bourgogne, UMR 6302, CNRS, Univ. Bourgogne Franche-Comté, 9, Avenue Alain Savary, 21000 Dijon, France
| | - Takayuki Ikeno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Valentin Quesneau
- Institut de Chimie Moléculaire de l'Université de Bourgogne, UMR 6302, CNRS, Univ. Bourgogne Franche-Comté, 9, Avenue Alain Savary, 21000 Dijon, France
| | - Kévin Renault
- Institut de Chimie Moléculaire de l'Université de Bourgogne, UMR 6302, CNRS, Univ. Bourgogne Franche-Comté, 9, Avenue Alain Savary, 21000 Dijon, France
| | - Anthony Romieu
- Institut de Chimie Moléculaire de l'Université de Bourgogne, UMR 6302, CNRS, Univ. Bourgogne Franche-Comté, 9, Avenue Alain Savary, 21000 Dijon, France.
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21
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Amoah C, Obuah C, Ainooson MK, Muller A. Synthesis, characterization and fluorescent properties of ferrocenyl pyrazole and triazole ligands and their palladium complexes. J Organomet Chem 2021. [DOI: 10.1016/j.jorganchem.2020.121664] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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22
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Vialykh EA, McKay G, Rosario-Ortiz FL. Computational Assessment of the Three-Dimensional Configuration of Dissolved Organic Matter Chromophores and Influence on Absorption Spectra. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15904-15913. [PMID: 33269593 DOI: 10.1021/acs.est.0c05860] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The three-dimensional configuration of dissolved organic matter (DOM) is an important factor in determining the role of DOM in natural and engineered systems, yet there is still considerable uncertainty regarding the formation and potential stability of molecular aggregates within DOM. In this paper, we describe a computational assessment of the three-dimensional configuration of DOM. Specifically, we were interested in evaluating the hypothesis that DOM forms thermodynamically stable molecular aggregates that as a result were potentially shielded from water solvent molecules. Molecular dynamics simulations of DOM model compounds carefully selected based on ultrahigh-resolution mass spectrometry data revealed that, while DOM does indeed form molecular aggregates, the large majority of molecules (especially, O-atom bearing molecules) are solvent accessible. Additionally, these computations revealed that molecular aggregates are weak and dissociate when placed in organic solvents (tetrahydrofuran, methyl tert-butyl ether). Time-dependent density functional theory calculations demonstrated long-wavelength absorbance for both model DOM chromophores and their molecular aggregates. This study has important implications for determining the origin of DOM optical properties and for enhancing our collective understanding of DOM three-dimensional structures.
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Affiliation(s)
- Elena A Vialykh
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Garrett McKay
- Zachry Department of Civil & Environmental Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Fernando L Rosario-Ortiz
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Environmental Engineering Program, University of Colorado Boulder, Boulder, Colorado 80309, United States
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23
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Deepika, Singh A, Chaudhari AK, Das S, Dubey NK. Zingiber zerumbet L. essential oil-based chitosan nanoemulsion as an efficient green preservative against fungi and aflatoxin B 1 contamination. J Food Sci 2020; 86:149-160. [PMID: 33314161 DOI: 10.1111/1750-3841.15545] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/26/2020] [Accepted: 11/06/2020] [Indexed: 02/03/2023]
Abstract
The present study envisages the potential application of chitosan-coated Zingiber zerumbet essential oil nanoemulsion (ZEO-CsNE) as green antimicrobial preservative against Aspergillus flavus, aflatoxin B1 (AFB1 ), and lipid peroxidation of stored functional foods. GC-MS analysis of ZEO exhibited the abundance of cis-geraniol (15.53%) as the major component. ZEO-CsNE showed biphasic release profile during in vitro release study conducted for 10 days. The ZEO-CsNE inhibited the growth of A. flavus (strain AF-LHP-SH1) and AFB1 production at 1.0 and 0.8 µL/mL, respectively. Interestingly, considerable reduction in ergosterol biosynthesis followed by enhanced leakage of vital cellular contents and methylglyoxal inhibition represents novel antifungal and antiaflatoxigenic mechanism of action, respectively. Further, ZEO-CsNE inhibited lipid peroxidation and AFB1 production in postharvest Salvia hispanica seeds during in situ trial and presented favorable safety profile (median lethal dose [LD50 ] = 29,114 µL/kg) for male mice. Based on overall observations, ZEO-CsNE could be recommended as a green antimicrobial substitute of synthetic preservatives for in vitro and in situ protection of functional food samples. PRACTICAL APPLICATION: Food industries are facing enormous amount of burden coming from fungal and aflatoxin contamination that can cause severe adverse effects to humans. Essential oils (EOs) are well known for their food preservative efficacy; however, some limitations such as oxidative instability in open system may limit their application directly into food system. The encapsulation of the EOs into polymeric matrix could provide a barrier that will protect the EOs from degradation. This research could provide a basis for utilization of EO after encapsulation into chitosan nanoemulsion for industrial-scale application for preservation of stored functional foods from fungal and aflatoxin contamination.
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Affiliation(s)
- Deepika
- Laboratory of Herbal Pesticides, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Akanksha Singh
- Laboratory of Herbal Pesticides, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Anand Kumar Chaudhari
- Laboratory of Herbal Pesticides, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Somenath Das
- Laboratory of Herbal Pesticides, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Nawal Kishore Dubey
- Laboratory of Herbal Pesticides, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
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24
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Tang J, Yu C, Loredo A, Chen Y, Xiao H. Site-Specific Incorporation of a Photoactivatable Fluorescent Amino Acid. Chembiochem 2020; 22:501-504. [PMID: 32961013 DOI: 10.1002/cbic.202000602] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/21/2020] [Indexed: 12/11/2022]
Abstract
Photoactivatable fluorophores are emerging optical probes for biological applications. Most photoactivatable fluorophores are relatively large in size and need to be activated by ultraviolet light; this dramatically limits their applications. To introduce photoactivatable fluorophores into proteins, recent investigations have explored several protein-labeling technologies, including fluorescein arsenical hairpin (FlAsH) Tag, HaloTag labeling, SNAPTag labeling, and other bioorthogonal chemistry-based methods. However, these technologies require a multistep labeling process. Here, by using genetic code expansion and a single sulfur-for-oxygen atom replacement within an existing fluorescent amino acid, we have site-specifically incorporated the photoactivatable fluorescent amino acid thioacridonylalanine (SAcd) into proteins in a single step. Moreover, upon exposure to visible light, SAcd can be efficiently desulfurized to its oxo derivatives, thus restoring the strong fluorescence of labeled proteins.
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Affiliation(s)
- Juan Tang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Chenfei Yu
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Axel Loredo
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Yuda Chen
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Han Xiao
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA
- Department of Biosciences, Rice University, 6100 Main Street, Houston, TX, 77005, USA
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA
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25
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Jun JV, Chenoweth DM, Petersson EJ. Rational design of small molecule fluorescent probes for biological applications. Org Biomol Chem 2020; 18:5747-5763. [PMID: 32691820 PMCID: PMC7453994 DOI: 10.1039/d0ob01131b] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fluorescent small molecules are powerful tools for visualizing biological events, embodying an essential facet of chemical biology. Since the discovery of the first organic fluorophore, quinine, in 1845, both synthetic and theoretical efforts have endeavored to "modulate" fluorescent compounds. An advantage of synthetic dyes is the ability to employ modern organic chemistry strategies to tailor chemical structures and thereby rationally tune photophysical properties and functionality of the fluorophore. This review explores general factors affecting fluorophore excitation and emission spectra, molar absorption, Stokes shift, and quantum efficiency; and provides guidelines for chemist to create novel probes. Structure-property relationships concerning the substituents are discussed in detail with examples for several dye families. We also present a survey of functional probes based on PeT, FRET, and environmental or photo-sensitivity, focusing on representative recent work in each category. We believe that a full understanding of dyes with diverse chemical moieties enables the rational design of probes for the precise interrogation of biochemical and biological phenomena.
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Affiliation(s)
- Joomyung V Jun
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA. and Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - David M Chenoweth
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA. and Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104, USA
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26
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Nonappa. Luminescent gold nanoclusters for bioimaging applications. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2020; 11:533-546. [PMID: 32280577 PMCID: PMC7136552 DOI: 10.3762/bjnano.11.42] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/18/2020] [Indexed: 05/27/2023]
Abstract
Luminescent nanomaterials have emerged as attractive candidates for sensing, catalysis and bioimaging applications in recent years. For practical use in bioimaging, nanomaterials with high photoluminescence, quantum yield, photostability and large Stokes shifts are needed. While offering high photoluminescence and quantum yield, semiconductor quantum dots suffer from toxicity and are susceptible to oxidation. In this context, atomically precise gold nanoclusters protected by thiol monolayers have emerged as a new class of luminescent nanomaterials. Low toxicity, bioavailability, photostability as well as tunable size, composition, and optoelectronic properties make them suitable for bioimaging and biosensing applications. In this review, an overview of the sensing of pathogens, and of in vitro and in vivo bioimaging using luminescent gold nanoclusters along with the limitations with selected examples are discussed.
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Affiliation(s)
- Nonappa
- Department of Applied Physics, Aalto University School of Science, Puumiehenkuja 2, FI-02150, Espoo, Finland
- Bioproducts and Biosystems, Aalto University School of Chemical Engineering, Kemistintie 1, FI-02150, Espoo, Finland
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27
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Miller MA, Day RA, Estabrook DA, Sletten EM. A Reduction-Sensitive Fluorous Fluorogenic Coumarin. Synlett 2020; 31:450-454. [PMID: 34349356 DOI: 10.1055/s-0039-1690770] [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] [Indexed: 10/25/2022]
Abstract
Fluorophores that are sensitive to their environment are useful tools for sensing chemical changes and probing biological systems. Here, we extend responsive fluorophores to the fluorous phase with the synthesis of a reduction-sensitive fluorous-soluble fluorogenic coumarin. We demonstrate that this fluorophore responds to various reducing agents, most notably glutathione, a key biological reductant. The fluorous solubility of this probe allows for its encapsulation into two different fluorous nanomaterials: perfluorocarbon nanoemulsions and fluorous core-shell micelles. The fluorogenic coumarin allows us to study how efficiently these vehicles protect the contents of their interior from the external environment. In the presence of glutathione, we observe different degrees of release for micelles and emulsions. This understanding will help guide future applications of fluorous nanomaterials as drug delivery vehicles.
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Affiliation(s)
- Margeaux A Miller
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, CA 90095, USA
| | - Rachael A Day
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, CA 90095, USA
| | - Daniel A Estabrook
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, CA 90095, USA
| | - Ellen M Sletten
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, CA 90095, USA
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28
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Gabr MT, Pigge FC. Expanding the Toolbox for Label-Free Enzyme Assays: A Dinuclear Platinum(II) Complex/DNA Ensemble with Switchable Near-IR Emission. Molecules 2019; 24:E4390. [PMID: 31805648 PMCID: PMC6930566 DOI: 10.3390/molecules24234390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/13/2022] Open
Abstract
Switchable luminescent bioprobes whose emission can be turned on as a function of specific enzymatic activity are emerging as important tools in chemical biology. We report a promising platform for the development of label-free and continuous enzymatic assays in high-throughput mode based on the reversible solvent-induced self-assembly of a neutral dinuclear Pt(II) complex. To demonstrate the utility of this strategy, the switchable luminescence of a dinuclear Pt(II) complex was utilized in developing an experimentally simple, fast (10 min), low cost, and label-free turn-on luminescence assay for the endonuclease enzyme DNAse I. The complex displays a near-IR (NIR) aggregation-induced emission at 785 nm in aqueous solution that is completely quenched upon binding to G-quadruplex DNA from the human c-myc oncogene. Luminescence is restored upon DNA degradation elicited by exposure to DNAse I. Correlation between near-IR luminescence intensity and DNAse I concentration in human serum samples allows for fast and label-free detection of DNAse I down to 0.002 U/mL. The Pt(II) complex/DNA assembly is also effective for identification of DNAse I inhibitors, and assays can be performed in multiwell plates compatible with high-throughput screening. The combination of sensitivity, speed, convenience, and cost render this method superior to all other reported luminescence-based DNAse I assays. The versatile response of the Pt(II) complex to DNA structures promises broad potential applications in developing real-time and label-free assays for other nucleases as well as enzymes that regulate DNA topology.
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29
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Kamimura A, Sakamoto S, Umemoto H, Kawamoto T, Sumimoto M. 2-Sulfanylhydroquinone Dimer as a Switchable Fluorescent Dye. Chemistry 2019; 25:14081-14088. [PMID: 31418938 DOI: 10.1002/chem.201903436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Indexed: 02/05/2023]
Abstract
A new dye was developed, the photoluminescence properties of which are controlled by a chemical reaction. The fluorescence properties of 2-sulfanylhydroquinone dimers depend on the number of hydroxyl groups that are acylated. Unprotected or monoacylated 2-sulfanylhydroquinone dimers displayed good fluorescence properties, whereas diacylated and tetraacylated 2-sulfanylhydroquinone dimers showed dramatically decreased fluorescence. A monomesylated derivative was devised, which shows good fluorescence characteristics as a switching fluorescence dye through a chemical reaction.
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Affiliation(s)
- Akio Kamimura
- Department Applied Chemistry, Yamaguchi University, Ube, 755-8611, Japan
| | - Sanshiro Sakamoto
- Department Applied Chemistry, Yamaguchi University, Ube, 755-8611, Japan
| | - Haruka Umemoto
- Department Applied Chemistry, Yamaguchi University, Ube, 755-8611, Japan
| | - Takuji Kawamoto
- Department Applied Chemistry, Yamaguchi University, Ube, 755-8611, Japan
| | - Michinori Sumimoto
- Department of Environmental Chemistry, Yamaguchi University, Ube, 755-8611, Japan
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30
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Renault K, Debieu S, Richard JA, Romieu A. Deeper insight into protease-sensitive "covalent-assembly" fluorescent probes for practical biosensing applications. Org Biomol Chem 2019; 17:8918-8932. [PMID: 31560014 DOI: 10.1039/c9ob01773a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We report a rational and systematic study devoted to the structural optimisation of a novel class of protease-sensitive fluorescent probes that we recently reported (S. Debieu and A. Romieu, Org. Biomol. Chem., 2017, 15, 2575-2584), based on the "covalent-assembly" strategy and using the targeted enzyme penicillin G acylase as a model protease to build a fluorescent pyronin dye by triggering a biocompatible domino cyclisation-aromatisation reaction. The aim is to identify ad hoc probe candidate(s) that might combine fast/reliable fluorogenic "turn-on" response, full stability in complex biological media and ability to release a second molecule of interest (drug or second fluorescent reporter), for applications in disease diagnosis and therapy. We base our strategy on screening a set of active methylene compounds (C-nucleophiles) to convert the parent probe to various pyronin caged precursors bearing Michael acceptor moieties of differing reactivities. In vitro stability and fluorescent enzymatic assays combined with HPLC-fluorescence analyses provide data useful for defining the most appropriate structural features for these fluorogenic scaffolds depending on the specifications inherent to biological application (from biosensing to theranostics) for which they will be used.
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Affiliation(s)
- Kévin Renault
- ICMUB, UMR 6302, CNRS, Univ. Bourgogne Franche-Comté, 9, Avenue Alain Savary, 21000 Dijon, France.
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31
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Zheng Q, Ayala AX, Chung I, Weigel AV, Ranjan A, Falco N, Grimm JB, Tkachuk AN, Wu C, Lippincott-Schwartz J, Singer RH, Lavis LD. Rational Design of Fluorogenic and Spontaneously Blinking Labels for Super-Resolution Imaging. ACS CENTRAL SCIENCE 2019; 5:1602-1613. [PMID: 31572787 PMCID: PMC6764213 DOI: 10.1021/acscentsci.9b00676] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Indexed: 05/24/2023]
Abstract
Rhodamine dyes exist in equilibrium between a fluorescent zwitterion and a nonfluorescent lactone. Tuning this equilibrium toward the nonfluorescent lactone form can improve cell-permeability and allow creation of "fluorogenic" compounds-ligands that shift to the fluorescent zwitterion upon binding a biomolecular target. An archetype fluorogenic dye is the far-red tetramethyl-Si-rhodamine (SiR), which has been used to create exceptionally useful labels for advanced microscopy. Here, we develop a quantitative framework for the development of new fluorogenic dyes, determining that the lactone-zwitterion equilibrium constant (K L-Z) is sufficient to predict fluorogenicity. This rubric emerged from our analysis of known fluorophores and yielded new fluorescent and fluorogenic labels with improved performance in cellular imaging experiments. We then designed a novel fluorophore-Janelia Fluor 526 (JF526)-with SiR-like properties but shorter fluorescence excitation and emission wavelengths. JF526 is a versatile scaffold for fluorogenic probes including ligands for self-labeling tags, stains for endogenous structures, and spontaneously blinking labels for super-resolution immunofluorescence. JF526 constitutes a new label for advanced microscopy experiments, and our quantitative framework will enable the rational design of other fluorogenic probes for bioimaging.
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Affiliation(s)
- Qinsi Zheng
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Anthony X. Ayala
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Inhee Chung
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Aubrey V. Weigel
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Anand Ranjan
- Department of Biology and Department of Molecular
Biology and Genetics, Johns Hopkins University, Baltimore,
Maryland 21218, United States
| | - Natalie Falco
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Ariana N. Tkachuk
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Carl Wu
- Department of Biology and Department of Molecular
Biology and Genetics, Johns Hopkins University, Baltimore,
Maryland 21218, United States
| | | | - Robert H. Singer
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
- Department of Anatomy and Structural Biology,
Albert Einstein College of Medicine, Bronx, New York 10461,
United States
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
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32
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Tang J, Robichaux MA, Wu KL, Pei J, Nguyen NT, Zhou Y, Wensel TG, Xiao H. Single-Atom Fluorescence Switch: A General Approach toward Visible-Light-Activated Dyes for Biological Imaging. J Am Chem Soc 2019; 141:14699-14706. [PMID: 31450884 DOI: 10.1021/jacs.9b06237] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photoactivatable fluorophores afford powerful molecular tools to improve the spatial and temporal resolution of subcellular structures and dynamics. By performing a single sulfur-for-oxygen atom replacement within common fluorophores, we have developed a facile and general strategy to obtain photoactivatable fluorogenic dyes across a broad spectral range. Thiocarbonyl substitution within fluorophores results in significant loss of fluorescence via a photoinduced electron transfer-quenching mechanism as suggested by theoretical calculations. Significantly, upon exposure to air and visible light residing in their absorption regime (365-630 nm), thio-caged fluorophores can be efficiently desulfurized to their oxo derivatives, thus restoring strong emission of the fluorophores. The effective photoactivation makes thio-caged fluorophores promising candidates for super-resolution imaging, which was realized by photoactivated localization microscopy (PALM) with low-power activation light under physiological conditions in the absence of cytotoxic additives (e.g., thiols, oxygen scavengers), a feature superior to traditional PALM probes. The versatility of this thio-caging strategy was further demonstrated by multicolor super-resolution imaging of lipid droplets and proteins of interest.
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Affiliation(s)
| | - Michael A Robichaux
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | | | | | - Nhung T Nguyen
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine , Texas A&M University , Houston , Texas 77030 , United States
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine , Texas A&M University , Houston , Texas 77030 , United States
| | - Theodore G Wensel
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology , Baylor College of Medicine , Houston , Texas 77030 , United States
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33
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Chen H, Zhou Y, Zheng K, Zhang N, Tan X, Chen W. A Light‐Up Fluorescent Probe for Detection of Formaldehyde in Serum and Gaseous Based on
d
‐PeT Process. ChemistrySelect 2019. [DOI: 10.1002/slct.201902120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Hui Chen
- College of Materials and Chemical EngineeringKey laboratory of inorganic nonmetallic crystalline and energy conversion materialsChina Three Gorges University Yichang 443002 P. R. China
| | - Yang Zhou
- College of Materials and Chemical EngineeringKey laboratory of inorganic nonmetallic crystalline and energy conversion materialsChina Three Gorges University Yichang 443002 P. R. China
| | - Kaibo Zheng
- College of Materials and Chemical EngineeringKey laboratory of inorganic nonmetallic crystalline and energy conversion materialsChina Three Gorges University Yichang 443002 P. R. China
- Guangxi Key laboratory of Chemistry and Engineering of forest ProductsGuangxi University for Nationalities Nanning 530006 P. R. China
| | - Nuonuo Zhang
- College of Materials and Chemical EngineeringKey laboratory of inorganic nonmetallic crystalline and energy conversion materialsChina Three Gorges University Yichang 443002 P. R. China
| | - Xuecai Tan
- Guangxi Key laboratory of Chemistry and Engineering of forest ProductsGuangxi University for Nationalities Nanning 530006 P. R. China
| | - Weifeng Chen
- College of Materials and Chemical EngineeringKey laboratory of inorganic nonmetallic crystalline and energy conversion materialsChina Three Gorges University Yichang 443002 P. R. China
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34
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Thiel Z, Rivera‐Fuentes P. Single‐Molecule Imaging of Active Mitochondrial Nitroreductases Using a Photo‐Crosslinking Fluorescent Sensor. Angew Chem Int Ed Engl 2019; 58:11474-11478. [DOI: 10.1002/anie.201904700] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/20/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Zacharias Thiel
- Laboratorium für Organische ChemieETH Zürich, HCI G329 Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Pablo Rivera‐Fuentes
- Laboratorium für Organische ChemieETH Zürich, HCI G329 Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
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35
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Thiel Z, Rivera‐Fuentes P. Einzelmolekülfluoreszenzmikroskopie aktiver mitochondrialer Nitroreduktasen unter Verwendung einer vernetzbaren fluoreszierenden Sonde. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zacharias Thiel
- Laboratorium für Organische ChemieETH Zürich, HCI G329 Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
| | - Pablo Rivera‐Fuentes
- Laboratorium für Organische ChemieETH Zürich, HCI G329 Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
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36
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Miceli M, Casati S, Ottria R, Di Leo S, Eberini I, Palazzolo L, Parravicini C, Ciuffreda P. Set-Up and Validation of a High Throughput Screening Method for Human Monoacylglycerol Lipase (MAGL) Based on a New Red Fluorescent Probe. Molecules 2019; 24:molecules24122241. [PMID: 31208066 PMCID: PMC6631453 DOI: 10.3390/molecules24122241] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/06/2019] [Accepted: 06/14/2019] [Indexed: 12/15/2022] Open
Abstract
Monoacylglycerol lipase (MAGL) is a serine hydrolase that has a key regulatory role in controlling the levels of 2-arachidonoylglycerol (2-AG), the main signaling molecule in the endocannabinoid system. Identification of selective modulators of MAGL enables both to provide new tools for investigating pathophysiological roles of 2-AG, and to discover new lead compounds for drug design. The development of sensitive and reliable methods is crucial to evaluate this modulatory activity. In the current study, we report readily synthesized long-wavelength putative fluorogenic substrates with different acylic side chains to find a new probe for MAGL activity. 7-Hydroxyresorufinyl octanoate proved to be the best substrate thanks to the highest rate of hydrolysis and the best Km and Vmax values. In addition, in silico evaluation of substrates interaction with the active site of MAGL confirms octanoate resorufine derivative as the molecule of choice. The well-known MAGL inhibitors URB602 and methyl arachidonylfluorophosphonate (MAFP) were used for the assay validation. The assay was highly reproducible with an overall average Z′ value of 0.86. The fast, sensitive and accurate method described in this study is suitable for low-cost high-throughput screening (HTS) of MAGL modulators and is a powerful new tool for studying MAGL activity.
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Affiliation(s)
- Matteo Miceli
- Dipartimento di Scienze Biomediche e Cliniche "Luigi Sacco", Università degli Studi di Milano, Via G.B. Grassi 74, 20157 Milano, Italy.
| | - Silvana Casati
- Dipartimento di Scienze Biomediche e Cliniche "Luigi Sacco", Università degli Studi di Milano, Via G.B. Grassi 74, 20157 Milano, Italy.
| | - Roberta Ottria
- Dipartimento di Scienze Biomediche e Cliniche "Luigi Sacco", Università degli Studi di Milano, Via G.B. Grassi 74, 20157 Milano, Italy.
| | - Simone Di Leo
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli Cervi 93, 20090 Segrate (MI), Italy.
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Chiara Parravicini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Pierangela Ciuffreda
- Dipartimento di Scienze Biomediche e Cliniche "Luigi Sacco", Università degli Studi di Milano, Via G.B. Grassi 74, 20157 Milano, Italy.
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37
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Mu R, Kong C, Yu W, Wang H, Ma Y, Li X, Wu J, Somersan-Karakaya S, Li H, Sun Z, Liu G. Nitrooxidoreductase Rv2466c-Dependent Fluorescent Probe for Mycobacterium tuberculosis Diagnosis and Drug Susceptibility Testing. ACS Infect Dis 2019; 5:949-961. [PMID: 30916931 DOI: 10.1021/acsinfecdis.9b00006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Firstly, this study demonstrated that natural product-inspired coumarin-based nitrofuranyl calanolides (NFCs) can form the Rv2466c-mycothiol (MSH)-NFC (RvMN) ternary complex via NFC binding to W21, N51, and Y61 of Rv2466c and be specifically reduced by Rv2466c, which is accompanied by the generation of a high level of fluorescence. Additionally, the results unveiled that the acetylated cysteine-glucosamine (AcCys-GlcN) motif of MSH is sufficient to interact with Rv2466c and adopt the active conformation that is essential for fully reducing NFCs. Further clinical translational investigation in this Article indicated that the novel fluorescent NFC probe can serve as a much needed high-throughput and low-cost detection method for detection of living Mycobacterium tuberculosis ( Mtb) and can precisely determine MIC values for a full range of available drugs. This method can greatly facilitate the development of phenotypic drug-susceptibility testing (pDST) that will allow the point-of-care treatment of tuberculosis (TB) within a week after diagnosis.
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Affiliation(s)
- Ran Mu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Chengcheng Kong
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P. R. China
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, P. R. China
| | - Wenjun Yu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Hongyao Wang
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Yao Ma
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Xueyuan Li
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Jie Wu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Selin Somersan-Karakaya
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Haitao Li
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Zhaogang Sun
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P. R. China
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, P. R. China
| | - Gang Liu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian District, Beijing 100084, P. R. China
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38
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Rapid Discovery of Illuminating Peptides for Instant Detection of Opioids in Blood and Body Fluids. Molecules 2019; 24:molecules24091813. [PMID: 31083395 PMCID: PMC6539258 DOI: 10.3390/molecules24091813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/03/2019] [Accepted: 05/05/2019] [Indexed: 01/03/2023] Open
Abstract
The United States is currently experiencing an opioid crisis, with more than 47,000 deaths in 2017 due to opioid overdoses. Current approaches for opioid identification and quantification in body fluids include immunoassays and chromatographic methods (e.g., LC-MS, GC-MS), which require expensive instrumentation and extensive sample preparation. Our aim was to develop a portable point-of-care device that can be used for the instant detection of opioids in body fluids. Here, we reported the development of a morphine-sensitive fluorescence-based sensor chip to sensitively detect morphine in the blood using a homogeneous immunoassay without any washing steps. Morphine-sensitive illuminating peptides were identified using a high throughput one-bead one-compound (OBOC) combinatorial peptide library approach. The OBOC libraries contain a large number of random peptides with a molecular rotor dye, malachite green (MG), that are coupled to the amino group on the side chain of lysine at different positions of the peptides. The OBOC libraries were then screened for fluorescent activation under a confocal microscope, using an anti-morphine monoclonal antibody as the screening probe, in the presence and absence of free morphine. Using this novel three-step fluorescent screening assay, we were able to identify the peptide-beads that fluoresce in the presence of an anti-morphine antibody, but lost fluorescence when the free morphine was present. After the positive beads were decoded using automatic Edman microsequencing, the morphine-sensitive illuminating peptides were then synthesized in soluble form, functionalized with an azido group, and immobilized onto microfabricated PEG-array spots on a glass slide. The sensor chip was then evaluated for the detection of morphine in plasma. We demonstrated that this proof-of-concept platform can be used to develop fluorescence-based sensors against morphine. More importantly, this technology can also be applied to the discovery of other novel illuminating peptidic sensors for the detection of illicit drugs and cancer biomarkers in body fluids.
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39
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Romieu A, Dejouy G, Valverde IE. Quest for novel fluorogenic xanthene dyes: Synthesis, spectral properties and stability of 3-imino-3H-xanthen-6-amine (pyronin) and its silicon analog. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.11.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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40
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Abstract
Photoacoustic imaging (PAI) is a powerful imaging modality capable of mapping the absorption of light in biological tissue via the PA effect. When chromophores are optically excited, subsequent energy loss in the form of heat generates local thermoelastic expansion. Repeated excitation from a pulsed laser induces pressure fluctuations that propagate through tissue and can be detected as ultrasound waves. By combining ultrasonic detection with optical excitation, PAI enables high-resolution image acquisition at centimeter depths. PAI is also relatively inexpensive and relies on safe, nonionizing excitation light in the near-infrared window, making it an attractive alternative to other common biomedical imaging modalities. Research in our group is aimed at developing small-molecule activatable probes that can be used for analyte detection in deep tissue via PAI. These probes contain reactive triggers that undergo a selective chemical reaction in the presence of specific stimuli to produce a spectral change that can be observed via PAI. Chemically tuning the absorbance profile of the probe and the reacted product such that they are both within the PA imaging window enables ratiometric imaging when each species is irradiated at a specific wavelength. Ratiometric imaging is an important design feature of these probes as it minimizes error associated with tissue-dependent signal fluctuations and instrumental variation. In this Account, we discuss key properties for designing small-molecule PA probes that can be applied for in vivo studies and the challenges associated with this area of probe development. We also highlight examples from our group including probes capable of detecting metal ions (Cu(II)), reactive nitrogen species (NO), and oxygen tension (hypoxia). Each of these targets can be sensed using a modular design strategy based on influencing the electronic and spectral properties of a NIR-absorbing dye platform. We demonstrate that ideal small-molecule PA probes have high molar absorptivity, low fluorescence quantum yields, and selective triggers that can reliably report on a single analyte in a complex biological setting. Probes must also be highly chemo- and photostable to enable long-term imaging studies. We show that these PA probes react rapidly and selectively and can be utilized for deep-tissue imaging in mouse models of various diseases. Overall, these examples represent a new class of biomedical imaging tools that seek to enable high-resolution molecular imaging capable of improving diagnostic methods and elucidating new biological discoveries. We anticipate that the combination of small-molecule PA probes with new PAI technology will enable noninvasive detection of analytes relevant to disease progression and mapping of tissue microenvironments.
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Affiliation(s)
- Hailey J. Knox
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
| | - Jefferson Chan
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
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Mahajan PG, Dige NC, Vanjare BD, Raza H, Hassan M, Seo SY, Hong SK, Lee KH. Synthesis and Studies of Fluorescein Based Derivatives for their Optical Properties, Urease Inhibition and Molecular Docking. J Fluoresc 2018; 28:1305-1315. [PMID: 30220013 DOI: 10.1007/s10895-018-2291-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
Abstract
Herein, we design and synthesized new fluorescein based derivatives by insitu formation of fluorescein ester and further treated with corresponding hydrazide and amine to yield respective compounds i.e. FB1, FB2, FB3 and FB4. The spectral purity and characterization was done by using IR, NMR and Mass spectroscopies. The synthesized derivatives were examined for their photophysical properties by using variety of organic solvents and results were discussed in details. The structural diversity of synthesized compounds motivate us to evaluate these compounds for urease inhibition. The compound FB3 (IC50 = 0.0456 μM) shows 100 fold more active against Jack bean urease than standard drug thiourea (IC50 = 4.7455 μM). Other synthesized compounds showed potent activity. Free radical percentage scavenging assay further supported the capacity of compounds to urease inhibition. While, molecular docking simulations helps to examine the molecular interactions of active compounds FB1, FB2, FB3 and FB4 within the binding site of urease enzyme.
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Affiliation(s)
- Prasad G Mahajan
- Department of Chemistry, Kongju National University, Gongju, Chungnam, 32588, Republic of Korea
| | - Nilam C Dige
- Department of Chemistry, Shivaji University, Kolhapur, Maharashtra, 416004, India
| | - Balasaheb D Vanjare
- Department of Chemistry, Kongju National University, Gongju, Chungnam, 32588, Republic of Korea
| | - Hussain Raza
- Department of Biological Sciences, Kongju National University, Gongju, Chungnam, 32588, Republic of Korea
| | - Mubashir Hassan
- Department of Biological Sciences, Kongju National University, Gongju, Chungnam, 32588, Republic of Korea
| | - Sung-Yum Seo
- Department of Biological Sciences, Kongju National University, Gongju, Chungnam, 32588, Republic of Korea
| | - Seong-Karp Hong
- Division of Bio and Health Sciences, Mokwon University, Seo-gu, Daejeon, 35349, Republic of Korea
| | - Ki Hwan Lee
- Department of Chemistry, Kongju National University, Gongju, Chungnam, 32588, Republic of Korea.
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Jiang X, Wang L, Carroll SL, Chen J, Wang MC, Wang J. Challenges and Opportunities for Small-Molecule Fluorescent Probes in Redox Biology Applications. Antioxid Redox Signal 2018; 29:518-540. [PMID: 29320869 PMCID: PMC6056262 DOI: 10.1089/ars.2017.7491] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 01/07/2018] [Indexed: 12/21/2022]
Abstract
SIGNIFICANCE The concentrations of reactive oxygen/nitrogen species (ROS/RNS) are critical to various biochemical processes. Small-molecule fluorescent probes have been widely used to detect and/or quantify ROS/RNS in many redox biology studies and serve as an important complementary to protein-based sensors with unique applications. Recent Advances: New sensing reactions have emerged in probe development, allowing more selective and quantitative detection of ROS/RNS, especially in live cells. Improvements have been made in sensing reactions, fluorophores, and bioavailability of probe molecules. CRITICAL ISSUES In this review, we will not only summarize redox-related small-molecule fluorescent probes but also lay out the challenges of designing probes to help redox biologists independently evaluate the quality of reported small-molecule fluorescent probes, especially in the chemistry literature. We specifically highlight the advantages of reversibility in sensing reactions and its applications in ratiometric probe design for quantitative measurements in living cells. In addition, we compare the advantages and disadvantages of small-molecule probes and protein-based probes. FUTURE DIRECTIONS The low physiological relevant concentrations of most ROS/RNS call for new sensing reactions with better selectivity, kinetics, and reversibility; fluorophores with high quantum yield, wide wavelength coverage, and Stokes shifts; and structural design with good aqueous solubility, membrane permeability, low protein interference, and organelle specificity. Antioxid. Redox Signal. 29, 518-540.
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Affiliation(s)
- Xiqian Jiang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas
| | - Lingfei Wang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas
| | - Shaina L. Carroll
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas
| | - Jianwei Chen
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas
| | - Meng C. Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
| | - Jin Wang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Center for Drug Discovery, Baylor College of Medicine, Houston, Texas
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43
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Chyan W, Raines RT. Enzyme-Activated Fluorogenic Probes for Live-Cell and in Vivo Imaging. ACS Chem Biol 2018; 13:1810-1823. [PMID: 29924581 DOI: 10.1021/acschembio.8b00371] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fluorogenic probes, small-molecule sensors that unmask brilliant fluorescence upon exposure to specific stimuli, are powerful tools for chemical biology. Those probes that respond to enzymatic catalysis illuminate the complex dynamics of biological processes at a level of spatiotemporal detail and sensitivity unmatched by other techniques. Here, we review recent advances in enzyme-activated fluorogenic probes for biological imaging. We organize our survey by enzyme classification, with emphasis on fluorophore masking strategies, modes of enzymatic activation, and the breadth of current and future applications. Key challenges such as probe selectivity and spectroscopic requirements are described alongside therapeutic, diagnostic, and theranostic opportunities.
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Affiliation(s)
- Wen Chyan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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45
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Cho U, Riordan DP, Ciepla P, Kocherlakota KS, Chen JK, Harbury PB. Ultrasensitive optical imaging with lanthanide lumiphores. Nat Chem Biol 2018; 14:15-21. [PMID: 29106397 PMCID: PMC5726931 DOI: 10.1038/nchembio.2513] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 10/02/2017] [Indexed: 11/12/2022]
Abstract
In principle, the millisecond emission lifetimes of lanthanide chelates should enable their ultrasensitive detection in biological systems by time-resolved optical microscopy. In practice, however, lanthanide imaging techniques have provided no better sensitivity than conventional fluorescence microscopy. Here, we identified three fundamental problems that have impeded lanthanide microscopy: low photon flux, inefficient excitation, and optics-derived background luminescence. We overcame these limitations with a new lanthanide imaging modality, transreflected illumination with luminescence resonance energy transfer (trLRET), which increases the time-integrated signal intensities of lanthanide lumiphores by 170-fold and the signal-to-background ratios by 75-fold. We demonstrate that trLRET provides at least an order-of-magnitude increase in detection sensitivity over that of conventional epifluorescence microscopy when used to visualize endogenous protein expression in zebrafish embryos. We also show that trLRET can be used to optically detect molecular interactions in vivo. trLRET promises to unlock the full potential of lanthanide lumiphores for ultrasensitive, autofluorescence-free biological imaging.
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Affiliation(s)
- Ukrae Cho
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Daniel P. Riordan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Paulina Ciepla
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Kiranmai S. Kocherlakota
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - James K. Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Pehr B. Harbury
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
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Gutiérrez-Arzaluz L, López-Arteaga R, Cortés-Guzmán F, Peon J. Nitrated Fluorophore Formation upon Two-Photon Excitation of an Azide with Extended Conjugation. J Phys Chem B 2017; 121:9910-9919. [PMID: 28981286 DOI: 10.1021/acs.jpcb.7b09446] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The transformation of an aromatic azide into a highly fluorescent species through a nonlinear optical process was studied. The azide system was designed to undergo N2 release and nitrene to nitro conversion upon two-photon electronic excitation. The formation of the nitro form of the compound through reactions with O2 and its high radiative quantum yield implies that the azide can be used as a biphotonic activatable fluorogen. The electronic state in which the azide to nitrene transformation takes place can be accessed nonlinearly with near-infrared light which allows for photoactivation with commonly available lasers. Furthermore, the system was built with a sulfonate functionality which allows for the molecule to be adsorbed at surfaces like that of cadmium sulfide nanocrystals which further improves the nonlinear optical absorption properties in the composite, through an energy transfer mechanism. The yield of the process as a function of the excitation photon energy together with computational studies indicate that the N2 release in this azide is due to a reactive channel in the second singlet excited state of the molecule. This feature implies that the system is intrinsically photostable for excitation below and above a certain wavelength and that the system can be phototriggered selectively by the nonlinear optical process.
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Affiliation(s)
- Luis Gutiérrez-Arzaluz
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria, México, 04510, México
| | - Rafael López-Arteaga
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria, México, 04510, México
| | - Fernando Cortés-Guzmán
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria, México, 04510, México
| | - Jorge Peon
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria, México, 04510, México
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Grimm J, Brown TA, Tkachuk AN, Lavis LD. General Synthetic Method for Si-Fluoresceins and Si-Rhodamines. ACS CENTRAL SCIENCE 2017; 3:975-985. [PMID: 28979939 PMCID: PMC5620978 DOI: 10.1021/acscentsci.7b00247] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Indexed: 05/24/2023]
Abstract
The century-old fluoresceins and rhodamines persist as flexible scaffolds for fluorescent and fluorogenic compounds. Extensive exploration of these xanthene dyes has yielded general structure-activity relationships where the development of new probes is limited only by imagination and organic chemistry. In particular, replacement of the xanthene oxygen with silicon has resulted in new red-shifted Si-fluoresceins and Si-rhodamines, whose high brightness and photostability enable advanced imaging experiments. Nevertheless, efforts to tune the chemical and spectral properties of these dyes have been hindered by difficult synthetic routes. Here, we report a general strategy for the efficient preparation of Si-fluoresceins and Si-rhodamines from readily synthesized bis(2-bromophenyl)silane intermediates. These dibromides undergo metal/bromide exchange to give bis-aryllithium or bis(aryl Grignard) intermediates, which can then add to anhydride or ester electrophiles to afford a variety of Si-xanthenes. This strategy enabled efficient (3-5 step) syntheses of known and novel Si-fluoresceins, Si-rhodamines, and related dye structures. In particular, we discovered that previously inaccessible tetrafluorination of the bottom aryl ring of the Si-rhodamines resulted in dyes with improved visible absorbance in solution, and a convenient derivatization through fluoride-thiol substitution. This modular, divergent synthetic method will expand the palette of accessible xanthenoid dyes across the visible spectrum, thereby pushing further the frontiers of biological imaging.
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48
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Kim JM, Seong BL. Highly chromophoric Cy5-methionine for N-terminal fluorescent tagging of proteins in eukaryotic translation systems. Sci Rep 2017; 7:11642. [PMID: 28912467 PMCID: PMC5599622 DOI: 10.1038/s41598-017-12028-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 09/01/2017] [Indexed: 12/16/2022] Open
Abstract
Despite significant advances on fluorescent labeling of target proteins to study their structural dynamics and function, there has been need for labeling with high quantum yield ensuring high sensitivity and selectivity without sacrificing the biological function of the protein. Here as a technical advancement over non-canonical amino acid incorporation, we provided a conceptual design of the N-terminal fluorescent tagging of proteins. Cy5-labeled methionine (Cy5-Met) was chemically synthesized, and then the purified Cy5-Met was coupled with synthetic human initiator tRNA by methionine tRNA synthetase. Cy5-Met-initiator tRNA (Cy5-Met-tRNAi) was purified and transfected into HeLa cells with HIV-Tat plasmid, resulting in an efficient production of Cy5-labeled HIV-Tat protein. Based on the universal requirement in translational initiation, the approach provides co-translational incorporation of N-terminal probe to a repertoire of proteins in the eukaryote system. This methodology has potential utility in the single molecule analysis of human proteins in vitro and in vivo for addressing to their complex biological structural and functional dynamics.
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Affiliation(s)
- Jung Min Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, South Korea
| | - Baik Lin Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, South Korea. .,Vaccine Translational Research Center, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, South Korea.
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49
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Chevalier A, Renard PY, Romieu A. Azo-Based Fluorogenic Probes for Biosensing and Bioimaging: Recent Advances and Upcoming Challenges. Chem Asian J 2017; 12:2008-2028. [DOI: 10.1002/asia.201700682] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Arnaud Chevalier
- Normandie Université, CNRS, UNIROUEN, INSA Rouen; COBRA (UMR 6014), IRCOF; rue Tesnières 76000 Rouen France
| | - Pierre-Yves Renard
- Normandie Université, CNRS, UNIROUEN, INSA Rouen; COBRA (UMR 6014), IRCOF; rue Tesnières 76000 Rouen France
| | - Anthony Romieu
- ICMUB, UMR 6302, CNRS; University Bourgogne Franche-Comté; 9, Avenue Alain Savary 21078 Dijon cedex France
- Institut Universitaire de France; 103, Boulevard Saint-Michel 75005 Paris France
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50
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Lavis LD. Teaching Old Dyes New Tricks: Biological Probes Built from Fluoresceins and Rhodamines. Annu Rev Biochem 2017; 86:825-843. [DOI: 10.1146/annurev-biochem-061516-044839] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
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