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van Rooden EJ, Kohsiek M, Kreekel R, van Esbroeck ACM, van den Nieuwendijk AMCH, Janssen APA, van den Berg RJBHN, Overkleeft HS, van der Stelt M. Design and Synthesis of Quenched Activity-based Probes for Diacylglycerol Lipase and α,β-Hydrolase Domain Containing Protein 6. Chem Asian J 2018; 13:3491-3500. [PMID: 29901868 DOI: 10.1002/asia.201800452] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/16/2018] [Indexed: 11/08/2022]
Abstract
Diacylglycerol lipases (DAGL) are responsible for the biosynthesis of the endocannabinoid 2-arachidonoylglycerol. The fluorescent activity-based probes DH379 and HT-01 have been previously shown to label DAGLs and to cross-react with the serine hydrolase ABHD6. Here, we report the synthesis and characterization of two new quenched activity-based probes 1 and 2, the design of which was based on the structures of DH379 and HT-01, respectively. Probe 1 contains a BODIPY-FL and a 2,4-dinitroaniline moiety as a fluorophore-quencher pair, whereas probe 2 employs a Cy5-fluorophore and a cAB40-quencher. The fluorescence of both probes was quenched with relative quantum yields of 0.34 and 0.0081, respectively. The probes showed target inhibition as characterized in activity-based protein profiling assays using human cell- and mouse brain lysates, but were unfortunately not active in living cells, presumably due to limited cell permeability.
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Affiliation(s)
- E J van Rooden
- Molecular Physiology, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - M Kohsiek
- Molecular Physiology, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - R Kreekel
- Molecular Physiology, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - A C M van Esbroeck
- Molecular Physiology, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | | | - A P A Janssen
- Molecular Physiology, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - R J B H N van den Berg
- Bio-organic Synthesis, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - H S Overkleeft
- Bio-organic Synthesis, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - M van der Stelt
- Molecular Physiology, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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Targetable fluorescent sensors for advanced cell function analysis. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2017. [DOI: 10.1016/j.jphotochemrev.2017.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Kamikawa Y, Hori Y, Yamashita K, Jin L, Hirayama S, Standley DM, Kikuchi K. Design of a protein tag and fluorogenic probe with modular structure for live-cell imaging of intracellular proteins. Chem Sci 2015; 7:308-314. [PMID: 29861984 PMCID: PMC5952543 DOI: 10.1039/c5sc02351c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/28/2015] [Indexed: 01/17/2023] Open
Abstract
Conditional fluorescence imaging is a powerful technique for precise spatiotemporal analysis of proteins in live cells upon administration of a synthetic probe. To be applicable to various biological phenomena, probes must be membrane-permeable, have a high signal-to-noise ratio, and work quickly. To date, few probes meet all of these requirements. Here, we designed a fluorogenic probe (AcFCANB) that could label intracellular proteins fused to the photoactive yellow protein (PYP) tag in live cells within 30 min and used it to image heterochromatin protein 1 localization in nuclei. AcFCANB is based on a modular platform consisting of fluorophore, ligand and quencher. We accelerated the labeling reaction by strategic mutations of charged residues on the surface of PYP. A simple model based on molecular dynamics simulations quantitatively reproduced the cooperative effect of multiple mutations on labeling rate.
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Affiliation(s)
| | - Yuichiro Hori
- Graduate School of Engineering , Osaka University , Osaka 565-0871 , Japan . .,IFReC , Osaka University , Osaka 565-0871 , Japan.,JST , PRESTO , Osaka 565-0871 , Japan
| | | | - Lin Jin
- IFReC , Osaka University , Osaka 565-0871 , Japan
| | - Shinya Hirayama
- Graduate School of Engineering , Osaka University , Osaka 565-0871 , Japan .
| | | | - Kazuya Kikuchi
- Graduate School of Engineering , Osaka University , Osaka 565-0871 , Japan . .,IFReC , Osaka University , Osaka 565-0871 , Japan
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Yoshimura A, Mizukami S, Mori Y, Yoshioka Y, Kikuchi K. 1H MRI Detection of Gene Expression in Living Cells by Using Protein Tag and Biotinylation Probe. CHEM LETT 2014. [DOI: 10.1246/cl.130942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Shin Mizukami
- Graduate School of Engineering, Osaka University
- Immunology Frontier Research Center (IFReC), Osaka University
| | - Yuki Mori
- Immunology Frontier Research Center (IFReC), Osaka University
- High Performance Bioimaging Research Facility, Graduate School of Frontier Biosciences, Osaka University
| | - Yoshichika Yoshioka
- Immunology Frontier Research Center (IFReC), Osaka University
- High Performance Bioimaging Research Facility, Graduate School of Frontier Biosciences, Osaka University
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University
- Immunology Frontier Research Center (IFReC), Osaka University
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Mizukami S, Hori Y, Kikuchi K. Small-molecule-based protein-labeling technology in live cell studies: probe-design concepts and applications. Acc Chem Res 2014; 47:247-56. [PMID: 23927788 DOI: 10.1021/ar400135f] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of genetic engineering techniques allows researchers to combine functional proteins with fluorescent proteins (FPs) to produce fusion proteins that can be visualized in living cells, tissues, and animals. However, several limitations of FPs, such as slow maturation kinetics or issues with photostability under laser illumination, have led researchers to examine new technologies beyond FP-based imaging. Recently, new protein-labeling technologies using protein/peptide tags and tag-specific probes have attracted increasing attention. Although several protein-labeling systems are com mercially available, researchers continue to work on addressing some of the limitations of this technology. To reduce the level of background fluorescence from unlabeled probes, researchers have pursued fluorogenic labeling, in which the labeling probes do not fluoresce until the target proteins are labeled. In this Account, we review two different fluorogenic protein-labeling systems that we have recently developed. First we give a brief history of protein labeling technologies and describe the challenges involved in protein labeling. In the second section, we discuss a fluorogenic labeling system based on a noncatalytic mutant of β-lactamase, which forms specific covalent bonds with β-lactam antibiotics such as ampicillin or cephalosporin. Based on fluorescence (or Förster) resonance energy transfer and other physicochemical principles, we have developed several types of fluorogenic labeling probes. To extend the utility of this labeling system, we took advantage of a hydrophobic β-lactam prodrug structure to achieve intracellular protein labeling. We also describe a small protein tag, photoactive yellow protein (PYP)-tag, and its probes. By utilizing a quenching mechanism based on close intramolecular contact, we incorporated a turn-on switch into the probes for fluorogenic protein labeling. One of these probes allowed us to rapidly image a protein while avoiding washout. In the future, we expect that protein-labeling systems with finely designed probes will lead to novel methodologies that allow researchers to image biomolecules and to perturb protein functions.
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Affiliation(s)
- Shin Mizukami
- Graduate School of Engineering and Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuichiro Hori
- Graduate School of Engineering and Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
- PRESTO, JST, Suita, Osaka 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering and Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
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Protein labeling with fluorogenic probes for no-wash live-cell imaging of proteins. Curr Opin Chem Biol 2013; 17:644-50. [DOI: 10.1016/j.cbpa.2013.05.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/14/2013] [Accepted: 05/14/2013] [Indexed: 12/11/2022]
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Mizukami S. Development of molecular imaging tools to investigate protein functions by chemical probe design. Chem Pharm Bull (Tokyo) 2012; 59:1435-46. [PMID: 22130363 DOI: 10.1248/cpb.59.1435] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular imaging technologies, which enable the visualization of the behaviors or functions of biomolecules in living systems, have received considerable attention from life scientists. Novel imaging technologies that overcome the limitations of current imaging techniques are desired. In this review, two independent technologies that were recently developed by the authors are described. The first technology is for smart (19)F magnetic resonance imaging (MRI) probes that were developed for in vivo applications. These probes were developed by exploiting paramagnetic relaxation enhancement in order to detect hydrolase activity. With respect to cellular applications, gene expression in cells was visualized using one of the (19)F MRI probes. It was confirmed that this probe design principle is effective for various hydrolases, and broad applications are expected. The second technology is for practical protein labeling. This labeling method is based on a mutant β-lactamase and its specific labeling probes. Since the probe is fluorescence resonance energy transfer (FRET)-based, this labeling method achieves both specific and fluorogenic labeling of target proteins. In addition, derivatization of the probe enabled the labeling of intracellular proteins and the modification of various functional molecules.
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Affiliation(s)
- Shin Mizukami
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan.
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Sadhu KK, Mizukami S, Lanam CR, Kikuchi K. Fluorogenic Protein Labeling through Photoinduced Electron Transfer-Based BL-Tag Technology. Chem Asian J 2011; 7:272-6. [DOI: 10.1002/asia.201100647] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Indexed: 11/09/2022]
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Sadhu KK, Mizukami S, Hori Y, Kikuchi K. Switching Modulation for Protein Labeling with Activatable Fluorescent Probes. Chembiochem 2011; 12:1299-308. [DOI: 10.1002/cbic.201100137] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Indexed: 12/14/2022]
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