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Grover K, Koblova A, Pezacki AT, Chang CJ, New EJ. Small-Molecule Fluorescent Probes for Binding- and Activity-Based Sensing of Redox-Active Biological Metals. Chem Rev 2024; 124:5846-5929. [PMID: 38657175 DOI: 10.1021/acs.chemrev.3c00819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Although transition metals constitute less than 0.1% of the total mass within a human body, they have a substantial impact on fundamental biological processes across all kingdoms of life. Indeed, these nutrients play crucial roles in the physiological functions of enzymes, with the redox properties of many of these metals being essential to their activity. At the same time, imbalances in transition metal pools can be detrimental to health. Modern analytical techniques are helping to illuminate the workings of metal homeostasis at a molecular and atomic level, their spatial localization in real time, and the implications of metal dysregulation in disease pathogenesis. Fluorescence microscopy has proven to be one of the most promising non-invasive methods for studying metal pools in biological samples. The accuracy and sensitivity of bioimaging experiments are predominantly determined by the fluorescent metal-responsive sensor, highlighting the importance of rational probe design for such measurements. This review covers activity- and binding-based fluorescent metal sensors that have been applied to cellular studies. We focus on the essential redox-active metals: iron, copper, manganese, cobalt, chromium, and nickel. We aim to encourage further targeted efforts in developing innovative approaches to understanding the biological chemistry of redox-active metals.
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Affiliation(s)
- Karandeep Grover
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alla Koblova
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Aidan T Pezacki
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Christopher J Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Elizabeth J New
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Nano Institute, The University of Sydney, Sydney, New South Wales 2006, Australia
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2
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Kumar S, Nabet B. A chemical magnet: Approaches to guide precise protein localization. Bioorg Med Chem 2024; 102:117672. [PMID: 38461554 PMCID: PMC11064470 DOI: 10.1016/j.bmc.2024.117672] [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: 01/20/2024] [Revised: 02/26/2024] [Accepted: 03/01/2024] [Indexed: 03/12/2024]
Abstract
Small molecules that chemically induce proximity between two proteins have been widely used to precisely modulate protein levels, stability, and activity. Recently, several studies developed novel strategies that employ heterobifunctional molecules that co-opt shuttling proteins to control the spatial localization of a target protein, unlocking new potential within this domain. Together, these studies lay the groundwork for novel targeted protein relocalization modalities that can rewire the protein circuitry and interactome to influence biological outcomes.
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Affiliation(s)
- Saurav Kumar
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.
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3
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Nakamura A, Goto Y, Sugiyama H, Tsukiji S, Aoki K. Chemogenetic Manipulation of Endogenous Proteins in Fission Yeast Using a Self-Localizing Ligand-Induced Protein Translocation System. ACS Chem Biol 2023; 18:2506-2515. [PMID: 37990966 DOI: 10.1021/acschembio.3c00478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Cells sense extracellular stimuli through membrane receptors and process information through an intracellular signaling network. Protein translocation triggers intracellular signaling, and techniques such as chemically induced dimerization (CID) have been used to manipulate signaling pathways by altering the subcellular localization of signaling molecules. However, in the fission yeast Schizosaccharomyces pombe, the commonly used FKBP-FRB system has technical limitations, and therefore, perturbation tools with low cytotoxicity and high temporal resolution are needed. We here applied our recently developed self-localizing ligand-induced protein translocation (SLIPT) system to S. pombe and successfully perturbed several cell cycle-related proteins. The SLIPT system utilizes self-localizing ligands to recruit binding partners to specific subcellular compartments such as the plasma membrane or nucleus. We optimized the self-localizing ligands to maintain the long-term recruitment of target molecules to the plasma membrane. By knocking in genes encoding the binding partners for self-localizing ligands, we observed changes in the localization of several endogenous molecules and found perturbations in the cell cycle and associated phenotypes. This study demonstrates the effectiveness of the SLIPT system as a chemogenetic tool for rapid perturbation of endogenous molecules in S. pombe, providing a valuable approach for studying intracellular signaling and cell cycle regulation with an improved temporal resolution.
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Affiliation(s)
- Akinobu Nakamura
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yuhei Goto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Hironori Sugiyama
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
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4
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Li B, Wang Y, Liu B. Transformable DNA Nanorobots Reversibly Regulating Cell Membrane Receptors for Modulation of Cellular Migrations. ACS NANO 2023; 17:22571-22579. [PMID: 37965838 DOI: 10.1021/acsnano.3c06305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Oligomerization of cellular membrane receptors plays crucial roles in activating intracellular downstream signaling cascades for controlling cellular behaviors in physiological and pathological processes. However, the reversible and controllable regulation of receptors in a user-defined manner remains challenging. Herein, we developed a versatile DNA nanorobot (nR) with installed aptamers and hairpin structures to reversibly and controllably regulate cell migration. This was achieved by dimerization and de-dimerization of mesenchymal-epithelial transition (Met) receptors through DNA strand displacement reactions. The functionalized DNA nR not only plays similar roles as hepatocyte growth factor (HGF) in inducing cell migration but also allows a downgrade to the original state of cell migration. The advanced DNA nanomachines can be flexibly designed to target other receptors for manipulating cellular behaviors and thus represent a powerful tool for the future of biological and medical engineering.
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Affiliation(s)
- Bin Li
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, People's Republic of China
| | - Yuning Wang
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, People's Republic of China
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Tsuruta A, Kanetani D, Shiiba Y, Inoki T, Yoshida Y, Matsunaga N, Koyanagi S, Ohdo S. Modulation of cell physiology by bispecific nanobodies enabling changes in the intracellular localization of organelle proteins. Biochem Pharmacol 2023; 215:115708. [PMID: 37506923 DOI: 10.1016/j.bcp.2023.115708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/08/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
Proteins localize to their respective organelles in cells. This localization is changed by activation or repression in response to signal transduction. Therefore, the appropriate intracellular localization of proteins is important for their functions to be exerted. However, difficulties are associated with controlling the localization of endogenous proteins. In the present study, we developed a conceptually new method of controlling the intracellular localization of endogenous proteins using bispecific nanobodies (BiNbs). BiNbs recognize proteins expressed in the inner membrane, cytoskeleton, nucleus, and peroxisomes, but not in mitochondria or endoplasmic reticulum. BiNbs designed to recognize β-CATENIN and the intrinsic cytosolic protein VIMENTIN (3 × Flag β-CAT-VIM BiNbs) decreased the β-CATENIN-mediated transactivation of target genes by preventing its nuclear localization. Furthermore, 3 × Flag β-CAT-VIM BiNbs suppressed the proliferation and invasion of the VIMENTIN-expressing breast cancer cell line MDA-MB-231, but not MDA-MB-468, in which the expression of VIMENTIN was defective. The present results revealed that changes in the intracellular localization of specific proteins by BiNbs modulated the physiology and functions of cells. The development of BiNbs to recognize proteins specifically expressed in target cells may be a useful approach for eliciting cell-selective effects.
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Affiliation(s)
- Akito Tsuruta
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; Department of Glocal Healthcare, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Daiki Kanetani
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuki Shiiba
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takuto Inoki
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuya Yoshida
- Department of Clinical Pharmacokinetics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Matsunaga
- Department of Clinical Pharmacokinetics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satoru Koyanagi
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; Department of Glocal Healthcare, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shigehiro Ohdo
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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Li A, Liu Y, Chen Z, Li S, Zhong R, Cheng D, Chen L, He L. Development of a Golgi-targeted fluorescent chemosensor for detecting ferrous ions overload under Golgi stress. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 294:122560. [PMID: 36881962 DOI: 10.1016/j.saa.2023.122560] [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: 01/12/2023] [Revised: 02/19/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Ferrous ion (Fe2+) is a crucial metal ion in the body and participates in the diseases related to oxidation and reduction. Golgi apparatus is the main subcellular organelle of Fe2+ transport in cells, and the stability of its structure is related to the Fe2+ at an appropriate concentration. In this work, a turn-on type Golgi-targeting fluorescent chemosensor Gol-Cou-Fe2+ was rationally designed for sensitive and selective detection of Fe2+. Gol-Cou-Fe2+ showed excellent capacity of detecting exogenous and endogenous Fe2+ in HUVEC and HepG2 cells. It was used to capture the up-regulated Fe2+ level during the hypoxia. Moreover, the fluorescence of sensor was enhanced over time under Golgi stress combining with the reduce of Golgi matrix protein GM130. However, elimination of Fe2+ or addition of nitric oxide (NO) would restore the fluorescence intensity of Gol-Cou-Fe2+ and the expression of GM130 in HUVEC. Thus, development of chemosensor Gol-Cou-Fe2+ provides a new window for tracking Golgi Fe2+ and elucidating Golgi stress-related diseases.
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Affiliation(s)
- Ao Li
- School of Pharmacy, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang 421001, PR China
| | - Yalan Liu
- School of Pharmacy, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang 421001, PR China
| | - Zhe Chen
- School of Pharmacy, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang 421001, PR China
| | - Songjiao Li
- School of Pharmacy, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang 421001, PR China
| | - Rongbin Zhong
- Cinical Research Institute, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang 421001, PR China
| | - Dan Cheng
- Cinical Research Institute, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang 421001, PR China
| | - Linxi Chen
- School of Pharmacy, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang 421001, PR China.
| | - Longwei He
- School of Pharmacy, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang 421001, PR China.
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7
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Sawada S, Yoshikawa M, Tsutsui K, Miyazaki T, Kano K, Mishiro-Sato E, Tsukiji S. Palmitoylation-Dependent Small-Molecule Fluorescent Probes for Live-Cell Golgi Imaging. ACS Chem Biol 2023; 18:1047-1053. [PMID: 37098188 DOI: 10.1021/acschembio.3c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Small-molecule fluorescent probes enabling visualization of the Golgi apparatus in living cells are essential tools for studying Golgi-associated biological processes and diseases. So far, several fluorescent Golgi stains have been developed by linking ceramide lipids to fluorophores. However, ceramide-based probes suffer from cumbersome staining procedures and low Golgi specificity. Here, we introduce fluorescent Golgi-staining probes based on the tri-N-methylated myristoyl-Gly-Cys (myrGC3Me) motif. The cell-permeable myrGC3Me motif localizes to the Golgi membrane upon S-palmitoylation. By modularly conjugating the myrGC3Me motif to fluorophores, we developed blue, green, and red fluorescent Golgi probes, all of which allowed simple and rapid staining of the Golgi in living cells with high specificity and no cytotoxicity. The probe was also applicable to the visualization of dynamic changes of the Golgi morphology induced by drug treatments and during cell division. The present work provides an entirely new series of live-cell Golgi probes useful for cell biological and diagnostic applications.
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Affiliation(s)
- Shunsuke Sawada
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Masaru Yoshikawa
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Keita Tsutsui
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Tomoki Miyazaki
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Keiko Kano
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya 464-8602, Japan
| | - Emi Mishiro-Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya 464-8602, Japan
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya 466-8555, Japan
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya 466-8555, Japan
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8
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Iglesias-Artola JM, Nadler A. The Road to Quantitative Lipid Biochemistry in Living Cells. Acc Chem Res 2023; 56:810-820. [PMID: 36943016 PMCID: PMC10077588 DOI: 10.1021/acs.accounts.2c00804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
ConspectusTraditional cell biological techniques are not readily suitable for studying lipid signaling events because genetic perturbations are much slower than the interconversion of lipids in complex metabolic networks. For this reason, novel chemical biological approaches have been developed. One approach is to chemically modify a lipid with a so-called "caging group" that renders it inactive, but this cage can be removed photochemically inside cells to release the bioactive molecule. These caged compounds offer unique advantages for studying the kinetics of cellular biochemistry and have been extensively used in the past. However, a limitation of conventional caged compounds is their ability to diffuse freely inside the cell, which does not permit localized activation below optical precision. This poses a challenge for studying lipid signaling as lipid function inside cells is tightly linked to their parent membrane. An ideal lipid probe should, therefore, be restricted to a single organelle membrane or preferentially to a single leaflet. We first demonstrated the plasma-membrane-specific photorelease of fatty acids by employing sulfonated caging groups. Using these caged fatty acid probes we demonstrated that lipid localization determines signaling outcome. Generalizing this approach, we designed a so-called "click cage" that can be coupled to lipids and offers the possibility to attach organelle targeting groups via click chemistry. Using this strategy, we have synthesized plasma membrane, lysosomal, mitochondria, and endoplasmic-reticulum-targeted lipids that can be used to dissect organelle-specific signaling events. To reduce the synthetic effort associated with generating caged compounds, we designed a coumarin triflate reagent that allows the direct functionalization of phosphate- or carboxylate-containing compounds. With this novel reagent, we synthesized a small library of photocaged G-protein-coupled receptor (GPCR) ligands to study the underlying lipid signaling dynamics. Most recently, we have focused on quantifying the kinetics of lipid signaling for different diacylglycerol (DAG) species using plasma-membrane-targeted caged DAGs. Using this approach, we quantitatively measured lipid-protein affinities and lipid transbilayer dynamics in living cells. After analyzing DAGs with different acyl chain length and saturation degree, we discovered that affinities can vary by up to an order of magnitude. This finding clearly shows that cells are able to distinguish between individual DAG species, thereby demonstrating that lipid diversity matters in cellular signal processing. Although the recent advances have yielded valuable tools to study lipid signaling, challenges remain on specifically targeting the different leaflets of organelle membranes. Furthermore, it is necessary to simplify the experimental approaches required for parametrizing and corroborating quantitative kinetic models of lipid signaling. In the future, we envision that the application of leaflet-specific caged lipids to model membrane systems will be of crucial importance for understanding lipid asymmetry.
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Affiliation(s)
- Juan M Iglesias-Artola
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
| | - André Nadler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
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Lu S, Dai Z, Cui Y, Kong DM. Recent Development of Advanced Fluorescent Molecular Probes for Organelle-Targeted Cell Imaging. BIOSENSORS 2023; 13:360. [PMID: 36979572 PMCID: PMC10046058 DOI: 10.3390/bios13030360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/10/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Fluorescent molecular probes are very powerful tools that have been generally applied in cell imaging in the research fields of biology, pathology, pharmacology, biochemistry, and medical science. In the last couple of decades, numerous molecular probes endowed with high specificity to particular organelles have been designed to illustrate intracellular images in more detail at the subcellular level. Nowadays, the development of cell biology has enabled the investigation process to go deeply into cells, even at the molecular level. Therefore, probes that can sketch a particular organelle's location while responding to certain parameters to evaluate intracellular bioprocesses are under urgent demand. It is significant to understand the basic ideas of organelle properties, as well as the vital substances related to each unique organelle, for the design of probes with high specificity and efficiency. In this review, we summarize representative multifunctional fluorescent molecular probes developed in the last decade. We focus on probes that can specially target nuclei, mitochondria, endoplasmic reticulums, and lysosomes. In each section, we first briefly introduce the significance and properties of different organelles. We then discuss how probes are designed to make them highly organelle-specific. Finally, we also consider how probes are constructed to endow them with additional functions to recognize particular physical/chemical signals of targeted organelles. Moreover, a perspective on the challenges in future applications of highly specific molecular probes in cell imaging is also proposed. We hope that this review can provide researchers with additional conceptual information about developing probes for cell imaging, assisting scientists interested in molecular biology, cell biology, and biochemistry to accelerate their scientific studies.
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Affiliation(s)
- Sha Lu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhiqi Dai
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yunxi Cui
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
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10
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Development of a Golgi-targeted superoxide anion fluorescent probe for elucidating protein GOLPH3 function in myocardial ischemia-reperfusion injury. Anal Chim Acta 2023; 1255:341100. [PMID: 37032049 DOI: 10.1016/j.aca.2023.341100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/28/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023]
Abstract
Superoxide anion (O2•-) is an important reactive oxygen species (ROS) and participates in various physiological and pathological processes in the organism. The O2•- burst induced by ischemia-reperfusion (I/R) is associated with cardiovascular disease and promotes the cell apoptosis. In this work, a turn-on type Golgi-targeting fluorescent probe Gol-Cou-O2•- was rationally designed for sensitive and selective detection of O2•-. The minimum detection limit concentration for O2•- was about 3.9 × 10-7 M in aqueous solution. Gol-Cou-O2•- showed excellent capacity of detecting exogenous and endogenous O2•- in living cells and zebrafish, and was also used to capture the up-regulated O2•- level during the duration of I/R process in cardiomyocytes. Golgi Phosphoprotein 3 (GOLPH3) is a potential Golgi stress marker protein and plays a key role in cells apoptosis during I/R. The fluorescence imaging and flow cytometry assay results indicated that silencing GOLPH3 through siRNA could give rise to the down-regulated O2•- level and alleviation of apoptosis in I/R myocardial cells. Thus, development of Gol-Cou-O2•- provides a diagnostic tool for myocardial oxidative stress injury and distinct insights on roles of GOLPH3 in myocardial I/R injury.
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11
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Suzuki S, Yoshikawa M, Sawada S, Devaraj NK, Tsukiji S. Miniaturized Synthetic Palmitoylation Motifs for Small-Molecule Localization in Living Cells. Bioconjug Chem 2023; 34:169-173. [PMID: 36534355 DOI: 10.1021/acs.bioconjchem.2c00517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Conjugating small-molecule ligands to synthetic motifs that can localize to specific organelles or membranes in living cells is a practical approach to develop compounds as chimeric tools or drugs that can manipulate biological processes in a subcellular site-specific manner. However, the number of available organelle-targeted synthetic motifs for small-molecule localization is limited. We have recently developed a synthetic myristoyl-DCys motif for small-molecule localization that undergoes S-palmitoylation via the cellular palmitoylation machinery and localizes to the Golgi surface. Herein, we show that the lipid acyl chain of the myristoyl (C14)-DCys motif can be as short as 10-carbons and still retain the palmitoylation-dependent Golgi localization property in cells. This discovery led to the identification of four new derivatives for small-molecule localization: tridecanoyl (C13)-, dodecanoyl (C12)-, undecanoyl (C11)-, and decanoyl (C10)-DCys motifs. We demonstrated that even the short decanoyl-DCys palmitoylation motif could be used to generate small-molecule ligand conjugates that functioned as chemical tools for controlling protein localization and cell signaling. The miniaturized synthetic palmitoylation motifs identified in this work may find applications in creating various Golgi-localizable chimeric molecules for use in chemical biology and drug development.
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Affiliation(s)
- Sachio Suzuki
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Masaru Yoshikawa
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Shunsuke Sawada
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan.,Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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12
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Li L, Li M, Wang M, Zhang L, Yu Y, Zhang J, Ma B, Wang W. A "Cell Space Station" for Spatiotemporal Molecular Manipulation of Immune Checkpoint. ACS NANO 2022; 16:16332-16342. [PMID: 36194211 DOI: 10.1021/acsnano.2c05483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Spatiotemporal manipulation of protein distributions, abundances, and functions based on molecular level remains a significant challenge in studying biological systems and developing therapeutics. Particularly, such a nanotherapeutic platform though both specific and internal way is extremely lacking. Herein, we put forward a click chemistry-driven protein sorting (PROCLISORT) strategy, which acted in a cell space station (CSS) to achieve the sequential regulation of specific protein along the entire PD-1 immune checkpoint axis. From the spatial dimension, CSS could achieve comprehensive recognition, anchoring and blocking PD-L1/PD-L2 as well as transport PD-L1 among organelles at the subcellular level. From the time dimension, through the booting control via click reaction, the occurrence of these biological regulatory events became controllable and sequential, thus resulting in rapid and durable down-regulation of PD-L1. Through these smart tasks, this CSS stimulated a satisfactory tumor-immune-therapy effect both in vitro and in vivo. With a rational design, this multistage booting nanoplatform holds promise for molecular manipulation along the disease-related pathway in various living systems.
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Affiliation(s)
- Lingyun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Mengzhen Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Minxuan Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Limin Zhang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Yao Yu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Jiatao Zhang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Bing Ma
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Weizhi Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
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13
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Morita K, Nishimura K, Yamamoto S, Shimizu N, Yashiro T, Kawabata R, Aoi T, Tamura A, Maruyama T. In Situ Synthesis of an Anticancer Peptide Amphiphile Using Tyrosine Kinase Overexpressed in Cancer Cells. JACS AU 2022; 2:2023-2028. [PMID: 36186562 PMCID: PMC9516706 DOI: 10.1021/jacsau.2c00301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 06/16/2023]
Abstract
Cell-selective killing using molecular self-assemblies is an emerging concept for cancer therapy. Reported molecular self-assemblies are triggered by hydrolysis of well-designed molecules inside or outside cancer cells. This hydrolysis can occur in cancer and normal cells because of the abundance of water in living systems. Here, we report the in situ synthesis of a self-assembling molecule using a tyrosine kinase overexpressed in cancer cells. We designed a tyrosine-containing peptide amphiphile (C16-E4Y) that is transformed into a phosphorylated peptide amphiphile (C16-E4pY) by the overexpressed tyrosine kinase. Phosphorylation of C16-E4Y promoted self-assembly to form nanofibers in cancer cells. C16-E4Y exhibited selective cytotoxicity toward cancer cells overexpressing the tyrosine kinase. Self-assembled C16-E4pY induced endoplasmic reticulum stress that caused apoptotic cell death. Animal experiments revealed that C16-E4Y has antitumor activity. These results show that an enzyme overexpressed in cancer cells is available for intracellular synthesis of an antitumor self-assembling drug that is cell-selective.
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Affiliation(s)
- Kenta Morita
- Department
of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Kanon Nishimura
- Department
of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Shota Yamamoto
- Department
of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Natsumi Shimizu
- Department
of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Tomoko Yashiro
- Department
of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Ryoko Kawabata
- Department
of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Takashi Aoi
- Graduate
School of Medicine, Kobe University, 7-5-2 Kusunoki-cho, Chuou-ku, Kobe 650-0017, Japan
| | - Atsuo Tamura
- Department
of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
| | - Tatsuo Maruyama
- Department
of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan
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14
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Mo J, Chen J, Shi Y, Sun J, Wu Y, Liu T, Zhang J, Zheng Y, Li Y, Chen Z. Third-Generation Covalent TMP-Tag for Fast Labeling and Multiplexed Imaging of Cellular Proteins. Angew Chem Int Ed Engl 2022; 61:e202207905. [PMID: 35816052 DOI: 10.1002/anie.202207905] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Indexed: 11/10/2022]
Abstract
Self-labeling protein tags can introduce advanced molecular motifs to specific cellular proteins. Here we introduce the third-generation covalent TMP-tag (TMP-tag3) and showcase its comparison with HaloTag and SNAP-tag. TMP-tag3 is based on a proximity-induced covalent Michael addition between an engineered Cys of E. coli dihydrofolate reductase (eDHFR) and optimized trimethoprim (TMP)-acrylamide conjugates with minimal linkers. Compared to previous versions, the TMP-tag3 features an enhanced permeability when conjugated to fluorogenic spirocyclic rhodamines. As a small protein, the 18-kD eDHFR is advantageous in tagging selected mitochondrial proteins which are less compatible with bulkier HaloTag fusions. The proximal N-C termini of eDHFR also enable facile insertion into various protein loops. TMP-tag3, HaloTag, and SNAP-tag are orthogonal to each other, collectively forming a toolbox for multiplexed live-cell imaging of cellular proteins under fluorescence nanoscopy.
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Affiliation(s)
- Jiaming Mo
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Jingting Chen
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Yabo Shi
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Jingfu Sun
- PKU-Nanjing Institute of Translational Medicine, Nanjing, 211800, Jiangsu, China
| | - Yunxiang Wu
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Tianyan Liu
- Peking-Tsinghua Center for Life Science, Peking University, Beijing, Yiheyuan Road No.5, Beijing, 100871, China
| | - Junwei Zhang
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Yu Zheng
- Peking-Tsinghua Center for Life Science, Peking University, Beijing, Yiheyuan Road No.5, Beijing, 100871, China.,State Key Laboratory of Membrane Biology, PKU-IDG/McGovern Institute for Brain Research, School of Life Science, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Yulong Li
- Peking-Tsinghua Center for Life Science, Peking University, Beijing, Yiheyuan Road No.5, Beijing, 100871, China.,State Key Laboratory of Membrane Biology, PKU-IDG/McGovern Institute for Brain Research, School of Life Science, Peking University, Yiheyuan Road No.5, Beijing, 100871, China.,Chinese Institute for Brain Research, Beijing, 102206, China
| | - Zhixing Chen
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China.,PKU-Nanjing Institute of Translational Medicine, Nanjing, 211800, Jiangsu, China.,Peking-Tsinghua Center for Life Science, Peking University, Beijing, Yiheyuan Road No.5, Beijing, 100871, China
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15
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Mo J, Chen J, Shi Y, Sun J, Wu Y, Liu T, Zhang J, Zheng Y, Li Y, Chen Z. Third‐Generation Covalent TMP‐Tag for Fast Labeling and Multiplexed Imaging of Cellular Proteins. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jiaming Mo
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Jingting Chen
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Yabo Shi
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Jingfu Sun
- PKU-Nanjing Institute of translational medicine n/a CHINA
| | - Yunxiang Wu
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Tianyan Liu
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Junwei Zhang
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Yu Zheng
- Peking University School of life science CHINA
| | - Yulong Li
- Peking University School of life science CHINA
| | - Zhixing Chen
- Peking University College of Future Technology 5 Yiheyuan Rd. 100871 Beijing CHINA
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16
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A chemogenetic platform for controlling plasma membrane signaling and synthetic signal oscillation. Cell Chem Biol 2022; 29:1446-1464.e10. [PMID: 35835118 DOI: 10.1016/j.chembiol.2022.06.005] [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: 03/22/2021] [Revised: 04/22/2022] [Accepted: 06/20/2022] [Indexed: 12/31/2022]
Abstract
Chemogenetic methods enabling the rapid translocation of specific proteins to the plasma membrane (PM) in a single protein-single ligand manner are useful tools in cell biology. We recently developed a technique, in which proteins fused to an Escherichia coli dihydrofolate reductase (eDHFR) variant carrying N-terminal hexalysine residues are recruited from the cytoplasm to the PM using the synthetic myristoyl-d-Cys-tethered trimethoprim (mDcTMP) ligand. However, this system achieved PM-specific translocation only when the eDHFR tag was fused to the N terminus of proteins, thereby limiting its application. In this report, we engineered a universal PM-targeting tag for mDcTMP-induced protein translocation by grafting the hexalysine motif into an intra-loop region of eDHFR. We demonstrate the broad applicability of the new loop-engineered eDHFR tag and mDcTMP pair for conditional PM recruitment and activation of various tag-fused signaling proteins with different fusion configurations and for reversibly and repeatedly controlling protein localization to generate synthetic signal oscillations.
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17
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Miura Y, Senoo A, Doura T, Kiyonaka S. Chemogenetics of cell surface receptors: beyond genetic and pharmacological approaches. RSC Chem Biol 2022; 3:269-287. [PMID: 35359495 PMCID: PMC8905536 DOI: 10.1039/d1cb00195g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/20/2022] [Indexed: 11/29/2022] Open
Abstract
Cell surface receptors transmit extracellular information into cells. Spatiotemporal regulation of receptor signaling is crucial for cellular functions, and dysregulation of signaling causes various diseases. Thus, it is highly desired to control receptor functions with high spatial and/or temporal resolution. Conventionally, genetic engineering or chemical ligands have been used to control receptor functions in cells. As the alternative, chemogenetics has been proposed, in which target proteins are genetically engineered to interact with a designed chemical partner with high selectivity. The engineered receptor dissects the function of one receptor member among a highly homologous receptor family in a cell-specific manner. Notably, some chemogenetic strategies have been used to reveal the receptor signaling of target cells in living animals. In this review, we summarize the developing chemogenetic methods of transmembrane receptors for cell-specific regulation of receptor signaling. We also discuss the prospects of chemogenetics for clinical applications.
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Affiliation(s)
- Yuta Miura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
| | - Akinobu Senoo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
| | - Tomohiro Doura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
| | - Shigeki Kiyonaka
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
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18
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Xu J, Sun X, Kim K, Brand RM, Hartman D, Ma H, Brand RE, Bai M, Liu Y. Ultrastructural visualization of chromatin in cancer pathogenesis using a simple small-molecule fluorescent probe. SCIENCE ADVANCES 2022; 8:eabm8293. [PMID: 35245126 PMCID: PMC8896800 DOI: 10.1126/sciadv.abm8293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Imaging chromatin organization at the molecular-scale resolution remains an important endeavor in basic and translational research. Stochastic optical reconstruction microscopy (STORM) is a powerful superresolution imaging technique to visualize nanoscale molecular organization down to the resolution of ~20 to 30 nm. Despite the substantial progress in imaging chromatin organization in cells and model systems, its routine application on assessing pathological tissue remains limited. It is, in part, hampered by the lack of simple labels that consistently generates high-quality STORM images on the highly processed clinical tissue. We developed a fast, simple, and robust small-molecule fluorescent probe-cyanine 5-conjugated Hoechst-for routine superresolution imaging of nanoscale nuclear architecture on clinical tissue. We demonstrated the biological and clinical significance of imaging superresolved chromatin structure in cancer development and its potential clinical utility for cancer risk stratification.
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Affiliation(s)
- Jianquan Xu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Xuejiao Sun
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Kwangho Kim
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Rhonda M. Brand
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Douglas Hartman
- Department of Pathology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Hongqiang Ma
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Randall E. Brand
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Mingfeng Bai
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, University of Pittsburgh, Pittsburgh, PA 15213, USA
- University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA 15232, USA
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19
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Doumane M, Caillaud MC, Jaillais Y. Experimental manipulation of phosphoinositide lipids: from cells to organisms. Trends Cell Biol 2022; 32:445-461. [DOI: 10.1016/j.tcb.2022.01.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/14/2022]
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20
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Lin J, Yang K, New EJ. Strategies for organelle targeting of fluorescent probes. Org Biomol Chem 2021; 19:9339-9357. [PMID: 34515288 DOI: 10.1039/d1ob01447a] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescent tools have emerged as an important tool for studying the distinct chemical microenvironments of organelles, due to their high specificity and ability to be used in non-destructive, live cellular studies. These tools fall largely in two categories: exogenous fluorescent dyes, or endogenous labels such as genetically encoded fluorescent proteins. In both cases, the probe must be targeted to the organelle of interest. To date, many organelle-targeted fluorescent tools have been reported and used to uncover new information about processes that underpin health and disease. However, the majority of these tools only apply a handful of targeting groups, and less-studied organelles have few robust targeting strategies. While the development of new, robust strategies is difficult, it is essential to develop such strategies to allow for the development of new tools and broadening the effective study of organelles. This review aims to provide a comprehensive overview of the major targeting strategies for both endogenous and exogenous fluorescent cargo, outlining the specific challenges for targeting each organelle type and as well as new developments in the field.
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Affiliation(s)
- Jiarun Lin
- School of Chemistry, The University of Sydney, NSW, 2006, Australia. .,The University of Sydney Nano Institute (Sydney Nano), The University of Sydney, NSW 2006, Australia
| | - Kylie Yang
- School of Chemistry, The University of Sydney, NSW, 2006, Australia.
| | - Elizabeth J New
- School of Chemistry, The University of Sydney, NSW, 2006, Australia. .,The University of Sydney Nano Institute (Sydney Nano), The University of Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, NSW 2006, Australia
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21
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Yoshii T, Oki C, Watahiki R, Nakamura A, Tahara K, Kuwata K, Furuta T, Tsukiji S. Chemo-optogenetic Protein Translocation System Using a Photoactivatable Self-Localizing Ligand. ACS Chem Biol 2021; 16:1557-1565. [PMID: 34339163 DOI: 10.1021/acschembio.1c00416] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Manipulating subcellular protein localization using light is a powerful approach for controlling signaling processes with high spatiotemporal precision. The most widely used strategy for this is based on light-induced protein heterodimerization. The use of small synthetic molecules that can control the localization of target proteins in response to light without the need for a second protein has several advantages. However, such methods have not been well established. Herein, we present a chemo-optogenetic approach for controlling protein localization using a photoactivatable self-localizing ligand (paSL). We developed a paSL that can recruit tag-fused proteins of interest from the cytoplasm to the plasma membrane within seconds upon light illumination. This paSL-induced protein translocation (paSLIPT) is reversible and enables the spatiotemporal control of signaling processes in living cells, even in a local region. paSLIPT can also be used to implement simultaneous optical stimulation and multiplexed imaging of molecular processes in a single cell, offering an attractive and novel chemo-optogenetic platform for interrogating and engineering dynamic cellular functions.
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Affiliation(s)
- Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Choji Oki
- Department of Nanopharmaceutical Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Rei Watahiki
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan
| | - Akinobu Nakamura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
| | - Kai Tahara
- Department of Nanopharmaceutical Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Toshiaki Furuta
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- Department of Nanopharmaceutical Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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22
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Inaba H, Matsuura K. Modulation of Microtubule Properties and Functions by Encapsulation of Nanomaterials Using a Tau-Derived Peptide. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210202] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-Minami, Tottori 680-8552, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-Minami, Tottori 680-8552, Japan
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23
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Farley S, Laguerre A, Schultz C. Caged lipids for subcellular manipulation. Curr Opin Chem Biol 2021; 65:42-48. [PMID: 34119744 DOI: 10.1016/j.cbpa.2021.04.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/20/2022]
Abstract
We present recently developed strategies to manipulate lipid levels in live cells by light. We focus on photoremovable protecting groups that lead to subcellular restricted localization and activation and discuss alternative techniques. We emphasize the development of organelle targeting of caged lipids and discuss recent advances in chromatic orthogonality of caging groups for future applications.
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Affiliation(s)
- Scotland Farley
- Dept. Chemical Physiology & Biochemistry, Oregon Health and Science University (OHSU), Portland, OR, USA
| | - Aurélien Laguerre
- Dept. Chemical Physiology & Biochemistry, Oregon Health and Science University (OHSU), Portland, OR, USA
| | - Carsten Schultz
- Dept. Chemical Physiology & Biochemistry, Oregon Health and Science University (OHSU), Portland, OR, USA.
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24
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Yamamoto S, Nishimura K, Morita K, Kanemitsu S, Nishida Y, Morimoto T, Aoi T, Tamura A, Maruyama T. Microenvironment pH-Induced Selective Cell Death for Potential Cancer Therapy Using Nanofibrous Self-Assembly of a Peptide Amphiphile. Biomacromolecules 2021; 22:2524-2531. [PMID: 33960189 DOI: 10.1021/acs.biomac.1c00267] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Self-assembly of synthetic molecules has been drawing broad attention as a novel emerging approach in drug discovery. Here, we report selective cell death induced by a novel peptide amphiphile that self-assembles to form entangled nanofibers (hydrogel) based on intracellular pH (pHi). We found that a palmitoylated hexapeptide (C16-VVAEEE) formed a hydrogel below pH 7. The formation of the nanofibrous self-assembly was responsive to a small pH change around pH 7. The cytotoxicity of C16-VVAEEE was correlated with pHi of cells. Microscope observation demonstrated the self-assembly of C16-VVAEEE inside HEK293 cells. In vivo experiments revealed that the transcutaneous administration of C16-VVAEEE showed remarkable anti-tumor activity. This study proposes that distinct microenvironment inside living cells can be used as a trigger for the intracellular self-assembly of a peptide amphiphile, which provide a new clue to drug discovery.
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Affiliation(s)
- Shota Yamamoto
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Kanon Nishimura
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Kenta Morita
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Sayuki Kanemitsu
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Yuki Nishida
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Tomoyuki Morimoto
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Takashi Aoi
- Division of Advanced Medical Science, Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
| | - Atsuo Tamura
- Graduate School of Science, Department of Chemistry, Kobe University, Nada, Kobe 657-8501, Japan
| | - Tatsuo Maruyama
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.,Research Center for Membrane and Film Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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25
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Yoshikawa M, Yoshii T, Ikuta M, Tsukiji S. Synthetic Protein Condensates That Inducibly Recruit and Release Protein Activity in Living Cells. J Am Chem Soc 2021; 143:6434-6446. [PMID: 33890764 DOI: 10.1021/jacs.0c12375] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Compartmentation of proteins into biomolecular condensates or membraneless organelles formed by phase separation is an emerging principle for the regulation of cellular processes. Creating synthetic condensates that accommodate specific intracellular proteins on demand would have various applications in chemical biology, cell engineering, and synthetic biology. Here, we report the construction of synthetic protein condensates capable of recruiting and/or releasing proteins of interest in living mammalian cells in response to a small molecule or light. By a modular combination of a tandem fusion of two oligomeric proteins, which forms phase-separated synthetic protein condensates in cells, with a chemically induced dimerization tool, we first created a chemogenetic protein condensate system that can rapidly recruit target proteins from the cytoplasm to the condensates by addition of a small-molecule dimerizer. We next coupled the protein-recruiting condensate system with an engineered proximity-dependent protease, which gave a second protein condensate system wherein target proteins previously expressed inside the condensates are released into the cytoplasm by small-molecule-triggered protease recruitment. Furthermore, an optogenetic condensate system that allows reversible release and sequestration of protein activity in a repeatable manner using light was constructed successfully. These condensate systems were applicable to control protein activity and cellular processes such as membrane ruffling and ERK signaling in a time scale of minutes. This proof-of-principle work provides a new platform for chemogenetic and optogenetic control of protein activity in mammalian cells and represents a step toward tailor-made engineering of synthetic protein condensate-based soft materials with various functionalities for biological and biomedical applications.
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Affiliation(s)
- Masaru Yoshikawa
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan.,PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Masahiro Ikuta
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan.,Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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26
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Chin MY, Espinosa JA, Pohan G, Markossian S, Arkin MR. Reimagining dots and dashes: Visualizing structure and function of organelles for high-content imaging analysis. Cell Chem Biol 2021; 28:320-337. [PMID: 33600764 PMCID: PMC7995685 DOI: 10.1016/j.chembiol.2021.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/18/2020] [Accepted: 01/20/2021] [Indexed: 12/16/2022]
Abstract
Organelles are responsible for biochemical and cellular processes that sustain life and their dysfunction causes diseases from cancer to neurodegeneration. While researchers are continuing to appreciate new roles of organelles in disease, the rapid development of specifically targeted fluorescent probes that report on the structure and function of organelles will be critical to accelerate drug discovery. Here, we highlight four organelles that collectively exemplify the progression of phenotypic discovery, starting with mitochondria, where many functional probes have been described, then continuing with lysosomes and Golgi and concluding with nascently described membraneless organelles. We introduce emerging probe designs to explore organelle-specific morphology and dynamics and highlight recent case studies using high-content analysis to stimulate further development of probes and approaches for organellar high-throughput screening.
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Affiliation(s)
- Marcus Y Chin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Jether Amos Espinosa
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Grace Pohan
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Sarine Markossian
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Michelle R Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA.
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27
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Suzuki S, Hatano Y, Yoshii T, Tsukiji S. Chemogenetic Control of Protein Localization and Mammalian Cell Signaling by SLIPT. Methods Mol Biol 2021; 2312:237-251. [PMID: 34228294 DOI: 10.1007/978-1-0716-1441-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Chemical control of protein localization is a powerful approach for manipulating mammalian cellular processes. Self-localizing ligand-induced protein translocation (SLIPT) is an emerging platform that enables control of protein localization in living mammalian cells using synthetic self-localizing ligands (SLs). We recently established a chemogenetic SLIPT system, in which any protein of interest fused to an engineered variant of Escherichia coli dihydrofolate reductase, DHFRiK6, can be rapidly and specifically translocated from the cytoplasm to the inner leaflet of the plasma membrane (PM) using a trimethoprim (TMP)-based PM-targeting SL, mDcTMP. The mDcTMP-mediated PM recruitment of DHFRiK6-fusion proteins can be efficiently returned to the cytoplasm by subsequent addition of free TMP, enabling temporal and reversible control over the protein localization. Here we describe the use of this mDcTMP/DHFRiK6-based SLIPT system for inducing (1) reversible protein translocation and (2) synthetic activation of the Raf/ERK pathway. This system provides a simple and versatile tool in mammalian synthetic biology for temporally manipulating various signaling molecules and pathways at the PM.
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Affiliation(s)
- Sachio Suzuki
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
| | - Yuka Hatano
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan.
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan.
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28
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Yoshii T, Tahara K, Suzuki S, Hatano Y, Kuwata K, Tsukiji S. An Improved Intracellular Synthetic Lipidation-Induced Plasma Membrane Anchoring System for SNAP-Tag Fusion Proteins. Biochemistry 2020; 59:3044-3050. [DOI: 10.1021/acs.biochem.0c00410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kai Tahara
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
| | - Sachio Suzuki
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
| | - Yuka Hatano
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
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29
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Nakamura A, Oki C, Sawada S, Yoshii T, Kuwata K, Rudd AK, Devaraj NK, Noma K, Tsukiji S. Designer Palmitoylation Motif-Based Self-Localizing Ligand for Sustained Control of Protein Localization in Living Cells and Caenorhabditis elegans. ACS Chem Biol 2020; 15:837-843. [PMID: 32182034 DOI: 10.1021/acschembio.0c00014] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Inducing protein translocation to the plasma membrane (PM) is an important approach for manipulating diverse signaling molecules/pathways in living cells. We previously devised a new chemogenetic system, in which a protein fused to Escherichia coli dihydrofolate reductase (eDHFR) can be rapidly translocated from the cytoplasm to the PM using a trimethoprim (TMP)-based self-localizing ligand (SL), mgcTMP. However, mgcTMP-induced protein translocation turned out to be transient and spontaneously reversed within 1 h, limiting its application. Here, we first demonstrated that the spontaneous reverse translocation was caused by cellular degradation of mgcTMP, presumably by proteases. To address this problem, we newly developed a proteolysis-resistant SL, mDcTMP. This mDcTMP now allows sustained PM localization of eDHFR-fusion proteins (over several hours to a day), and it was applicable to inducing prolonged signal activation and cell differentiation. mDcTMP also worked in live nematodes, making it an attractive new tool for probing and controlling living systems.
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Affiliation(s)
- Akinobu Nakamura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Choji Oki
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Shunsuke Sawada
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Andrew K. Rudd
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Neal K. Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Kentaro Noma
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Group of Nutritional Neuroscience, Neuroscience Institute, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- Frontier Research Institute for Materials Science (FRIMS), Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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30
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Nakamura A, Oki C, Kato K, Fujinuma S, Maryu G, Kuwata K, Yoshii T, Matsuda M, Aoki K, Tsukiji S. Engineering Orthogonal, Plasma Membrane-Specific SLIPT Systems for Multiplexed Chemical Control of Signaling Pathways in Living Single Cells. ACS Chem Biol 2020; 15:1004-1015. [PMID: 32162909 DOI: 10.1021/acschembio.0c00024] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Most cell behaviors are the outcome of processing information from multiple signals generated upon cell stimulation. Thus, a systematic understanding of cellular systems requires methods that allow the activation of more than one specific signaling molecule or pathway within a cell. However, the construction of tools suitable for such multiplexed signal control remains challenging. In this work, we aimed to develop a platform for chemically manipulating multiple signaling molecules/pathways in living mammalian cells based on self-localizing ligand-induced protein translocation (SLIPT). SLIPT is an emerging chemogenetic tool that controls protein localization and cell signaling using synthetic self-localizing ligands (SLs). Focusing on the inner leaflet of the plasma membrane (PM), where there is a hub of intracellular signaling networks, here we present the design and engineering of two new PM-specific SLIPT systems based on an orthogonal eDHFR and SNAP-tag pair. These systems rapidly induce translocation of eDHFR- and SNAP-tag-fusion proteins from the cytoplasm to the PM specifically in a time scale of minutes upon addition of the corresponding SL. We then show that the combined use of the two systems enables chemically inducible, individual translocation of two distinct proteins in the same cell. Finally, by integrating the orthogonal SLIPT systems with fluorescent reporters, we demonstrate simultaneous multiplexed activation and fluorescence imaging of endogenous ERK and Akt activities in a single cell. Collectively, orthogonal PM-specific SLIPT systems provide a powerful new platform for multiplexed chemical signal control in living single cells, offering new opportunities for dissecting cell signaling networks and synthetic cell manipulation.
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Affiliation(s)
- Akinobu Nakamura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Choji Oki
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Kenya Kato
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Satoko Fujinuma
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Gembu Maryu
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Michiyuki Matsuda
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhiro Aoki
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, Faculty of Life Science, SOKENDAI, The Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- Frontier Research Institute for Materials Science (FRIMS), Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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31
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Yu G, Feng N, Zhao D, Wang H, Jin Y, Liu D, Li Z, Yang X, Ge K, Zhang J. A highly selective and sensitive upconversion nanoprobe for monitoring hydroxyl radicals in living cells and the liver. SCIENCE CHINA-LIFE SCIENCES 2020; 64:434-442. [PMID: 32239367 DOI: 10.1007/s11427-019-1601-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 11/05/2019] [Indexed: 10/24/2022]
Abstract
Excessive reactive oxygen species (ROS) would attack living cells and cause a series of oxidative stress related diseases, such as liver damage. Hydroxyl radicals (·OH) are currently known as one of the most toxic and harmful free radicals to organisms. Therefore, studies involving hydroxyl radicals have become important research topics in the fields of biology, biochemistry, and biomedicine. In addition, imaging of analytes using upconversion nanoparticles (UCNPs) possesses significant advantages over that using general fluorescent dyes or nanoparticles due to its high spatial resolution, reduced photodamage, and deep tissue penetration properties. Herein, we designed a highly selective and sensitive hydroxyl radical nanoprobe based on the luminescence resonance energy transfer between upconversion nanoparticles and methylene blue (MB). The concentration of ·OH could be determined by the fluorescence recovery of the UCNPs due to the oxidative damage of MB. Using this nanoprobe, the ·OH in living cells or in liver tissues could be monitored with high sensitivity and selectivity.
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Affiliation(s)
- Guangshun Yu
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, 071002, China
| | - Na Feng
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, 071002, China
| | - Dan Zhao
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, 071002, China
| | - Hao Wang
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, 071002, China
| | - Yi Jin
- College of Medical Science, Hebei University, Baoding, 071002, China
| | - Dandan Liu
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, 071002, China
| | - Zhenhua Li
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, 071002, China
| | - Xinjian Yang
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, 071002, China.
| | - Kun Ge
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, 071002, China
| | - Jinchao Zhang
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, 071002, China.
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32
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Tamura T, Takato M, Shiono K, Hamachi I. Development of a Photoactivatable Proximity Labeling Method for the Identification of Nuclear Proteins. CHEM LETT 2020. [DOI: 10.1246/cl.190804] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Mikiko Takato
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Keiya Shiono
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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33
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Li J, Wang L, Tian J, Zhou Z, Li J, Yang H. Nongenetic engineering strategies for regulating receptor oligomerization in living cells. Chem Soc Rev 2020; 49:1545-1568. [DOI: 10.1039/c9cs00473d] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nongenetic strategies for regulating receptor oligomerization in living cells based on DNA, protein, small molecules and physical stimuli.
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Affiliation(s)
- Jingying Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
| | - Liping Wang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
| | - Jinmiao Tian
- Institute of Molecular Medicine
- Renji Hospital
- School of Medicine
- Shanghai Jiao Tong University
- Shanghai
| | - Zhilan Zhou
- Institute of Molecular Medicine
- Renji Hospital
- School of Medicine
- Shanghai Jiao Tong University
- Shanghai
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
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34
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Sawada S, Nakamura A, Yoshii T, Kuwata K, Nakatsu F, Tsukiji S. Protein-recruiting synthetic molecules targeting the Golgi surface. Chem Commun (Camb) 2020; 56:15422-15425. [DOI: 10.1039/d0cc06908f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthetic molecules consisting of a small-molecule ligand and a tri-N-methylated myristoyl-Gly-Cys lipopeptide serve as chemical tools to rapidly recruit their target proteins from the cytoplasm to the Golgi surface in living cells.
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Affiliation(s)
- Shunsuke Sawada
- Department of Nanopharmaceutical Sciences
- Graduate School of Engineering
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Akinobu Nakamura
- Department of Life Science and Applied Chemistry
- Graduate School of Engineering
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry
- Graduate School of Engineering
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM)
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Fubito Nakatsu
- Department of Neurochemistry and Molecular Cell Biology
- Graduate School of Medical and Dental Sciences
- Niigata University
- Niigata 951-8510
- Japan
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences
- Graduate School of Engineering
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
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35
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Suzuki S, Ikuta M, Yoshii T, Nakamura A, Kuwata K, Tsukiji S. Golgi recruitment assay for visualizing small-molecule ligand–target engagement in cells. Chem Commun (Camb) 2020; 56:7961-7964. [DOI: 10.1039/d0cc02020f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A Golgi recruitment (G-REC) assay is developed as a new method for visualizing small-molecule ligand–target engagement in living cells.
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Affiliation(s)
- Sachio Suzuki
- Department of Nanopharmaceutical Sciences
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Masahiro Ikuta
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- PRESTO, Japan Science and Technology Agency (JST)
| | - Akinobu Nakamura
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM)
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- Department of Life Science and Applied Chemistry
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36
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Nakamura A, Katahira R, Sawada S, Shinoda E, Kuwata K, Yoshii T, Tsukiji S. Chemogenetic Control of Protein Anchoring to Endomembranes in Living Cells with Lipid-Tethered Small Molecules. Biochemistry 2019; 59:205-211. [DOI: 10.1021/acs.biochem.9b00807] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Akinobu Nakamura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
| | - Rika Katahira
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Shunsuke Sawada
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
| | - Eri Shinoda
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho,
Showa-ku, Nagoya 466-8555, Japan
- Frontier Research Institute for Materials Science (FRIMS), Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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37
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Xiang Y, Chen L, Zhou R, Huang Y. Enhanced intracellular and intranuclear drug delivery mediated by biomimetic peptide SVS-1 for anticancer therapy. Int J Pharm 2019; 570:118668. [PMID: 31494237 DOI: 10.1016/j.ijpharm.2019.118668] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/20/2019] [Accepted: 09/04/2019] [Indexed: 12/17/2022]
Abstract
Tumor cell nucleus is the ultimate target of many first-line chemotherapeutics and therapeutic genes. However, nuclear drug delivery is always hampered by multiple intracellular obstacles especially low efficiency of cellular uptake and insufficient nuclear trafficking. It is urgent to establish novel nuclear drug delivery systems to simultaneously overcome barriers including cell membranes and nuclear envelope. Herein, an N-(2-hydroxypropyl) methacrylamide (HPMA) polymer-based drug delivery system was designed to achieve enhanced intracellular and intranuclear drug delivery. A biomimetic peptide (SVS-1), derived from antimicrobial peptides, which was reported to efficiently penetrate cell membranes and translocate rapidly into nucleus without decreasing cell viability, was conjugated to the HPMA copolymer backbone. The in vitro studies showed that SVS-1 could enhance the uptake and nuclei accumulation of HPMA copolymer by 4.1 and 7.0-fold on human cervical cancer cells (HeLa) separately compared with corresponding non-SVS-1 modified HPMA copolymers (P-DOX). This also transferred to greater DNA damage, more apoptosis and superior cytotoxicity (2.4-fold) of doxorubicin which was chosen as the model drug and attached to SVS-1 modified HPMA copolymer (SVS-1-P-DOX). Furthermore, the in vivo investigation revealed that compared with free doxorubicin, SVS-1-P-DOX not only showed prolonged blood circulation and preferential tumor accumulation, but also suppressed tumor growth more efficiently with tumor growth inhibition of 78.7% in HeLa tumor-bearing BALB/c nude mice without causing noticeable physiological change in major organs. These results demonstrated that the SVS-1 modification was a promising strategy for contemporaneously overcome cell membranes and nuclear envelope, which might provide new opportunities for constructing nucleus-targeted anticancer therapy.
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Affiliation(s)
- Yucheng Xiang
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministry of Education), West China School of Pharmacy, Sichuan University, No. 17, Block 3, South Renmin Road, Chengdu 610041, PR China
| | - Liqiang Chen
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministry of Education), West China School of Pharmacy, Sichuan University, No. 17, Block 3, South Renmin Road, Chengdu 610041, PR China
| | - Rui Zhou
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministry of Education), West China School of Pharmacy, Sichuan University, No. 17, Block 3, South Renmin Road, Chengdu 610041, PR China
| | - Yuan Huang
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministry of Education), West China School of Pharmacy, Sichuan University, No. 17, Block 3, South Renmin Road, Chengdu 610041, PR China.
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38
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Hatanaka W, Takeuchi H, Koga M, Ryujin TA, Kishimura A, Katayama Y, Tsukiji S, Mori T. Synthesis of Transmembrane Molecules by Click Chemistry. CHEM LETT 2019. [DOI: 10.1246/cl.190009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Wataru Hatanaka
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hiroki Takeuchi
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Minaho Koga
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Taka-aki Ryujin
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Akihiro Kishimura
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- International Research Center for Molecular Systems, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshiki Katayama
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- International Research Center for Molecular Systems, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Department of Biomedical Engineering, Chung Yuan Christian University, 200 Chung Pei Rd., Chung Li, 32023 ROC, Taiwan
| | - Shinya Tsukiji
- Frontier Research Institute for Materials Science (FRIMS), Department of Life Science and Applied Chemistry, Department of Nanopharmaceutical Sciences Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Takeshi Mori
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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39
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Zhu H, Tamura T, Hamachi I. Chemical proteomics for subcellular proteome analysis. Curr Opin Chem Biol 2019; 48:1-7. [DOI: 10.1016/j.cbpa.2018.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/02/2018] [Accepted: 08/03/2018] [Indexed: 11/17/2022]
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40
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Li L, Liang J, Luo H, Tam KM, Tse ECM, Li Y. A new chemical approach for proximity labelling of chromatin-associated RNAs and proteins with visible light irradiation. Chem Commun (Camb) 2019; 55:12340-12343. [DOI: 10.1039/c9cc06251c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new nucleus-localized singlet oxygen generator was designed and synthesized.
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Affiliation(s)
- Lan Li
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Jiying Liang
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Hao Luo
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - K. Ming Tam
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Edmund C. M. Tse
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Ying Li
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
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41
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Tamura T, Hamachi I. Chemistry for Covalent Modification of Endogenous/Native Proteins: From Test Tubes to Complex Biological Systems. J Am Chem Soc 2018; 141:2782-2799. [DOI: 10.1021/jacs.8b11747] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tomonori Tamura
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO, Japan Science and Technology Agency (JST), 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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42
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Hirayama T, Inden M, Tsuboi H, Niwa M, Uchida Y, Naka Y, Hozumi I, Nagasawa H. A Golgi-targeting fluorescent probe for labile Fe(ii) to reveal an abnormal cellular iron distribution induced by dysfunction of VPS35. Chem Sci 2018; 10:1514-1521. [PMID: 30809369 PMCID: PMC6357701 DOI: 10.1039/c8sc04386h] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/22/2018] [Indexed: 12/16/2022] Open
Abstract
Fluctuation of labile Fe(ii) at Golgi apparatus was specifically detected by a new fluorescent probe.
Iron is involved in numerous physiologically essential processes in our body. However, excessive iron is a pathogenic factor in neurodegenerative diseases, causing aberrant oxidative stress. Divalent metal transporter 1 (DMT1) acts as a primary transporter of Fe(ii) ions. The intracellular delivery of DMT1 toward the cellular membrane via the trans-Golgi network during the endocytotic process is partially regulated by a retromer-mediated protein-sorting system comprising vacuolar protein-sorting proteins (VPSs). Thus, together with DMT1, the Golgi-apparatus acts as a hub organelle in the delivery system for intracellular Fe(ii) ions. Dysfunction of the VPS-relevant protein sorting system can induce the abnormal delivery of DMT1 toward lysosomes concomitantly with Fe(ii) ions. To explore this issue, we developed a fluorescent probe, Gol-SiRhoNox, for the Golgi-specific detection of Fe(ii) ions by integrating our original N-oxide-based Fe(ii)-specific chemical switch, a new Golgi-localizable chemical motif, and polarity-sensitive fluorogenic scaffold. Our synchronous imaging study using Gol-SiRhoNox and LysoRhoNox, a previously developed fluorescent probe for lysosomal Fe(ii), revealed that the intracellular distribution balance of Fe(ii) ions between the Golgi apparatus and lysosomes is normally Golgi-dominant, whereas the lysosome-specific elevation of Fe(ii) ions was observed in cells with induced dysfunction of VPS35, a member of the retromer complex. Treatment of cells with dysfunctional VPS35 with R55, a molecular chaperone, resulted in the restoration of the subcellular distribution of Fe(ii) ions to the Golgi-dominant state. These results indicate that the impairment of the DMT1 traffic machinery affects subcellular iron homeostasis, promoting Fe(ii) leakage at the Golgi and lysosomal accumulation of Fe(ii) through missorting of DMT1.
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Affiliation(s)
- Tasuku Hirayama
- Laboratory of Pharmaceutical and Medicinal Chemistry , Gifu Pharmaceutical University , 1-25-4, Daigaku-Nishi , Gifu , 501-1196 , Japan .
| | - Masatoshi Inden
- Laboratory of Medical Therapeutics and Molecular Therapeutics , Gifu Pharmaceutical University , 1-25-4, Daigaku-Nishi , Gifu , 501-1196 , Japan .
| | - Hitomi Tsuboi
- Laboratory of Pharmaceutical and Medicinal Chemistry , Gifu Pharmaceutical University , 1-25-4, Daigaku-Nishi , Gifu , 501-1196 , Japan .
| | - Masato Niwa
- Laboratory of Pharmaceutical and Medicinal Chemistry , Gifu Pharmaceutical University , 1-25-4, Daigaku-Nishi , Gifu , 501-1196 , Japan .
| | - Yasuhiro Uchida
- Laboratory of Medical Therapeutics and Molecular Therapeutics , Gifu Pharmaceutical University , 1-25-4, Daigaku-Nishi , Gifu , 501-1196 , Japan .
| | - Yuki Naka
- Laboratory of Medical Therapeutics and Molecular Therapeutics , Gifu Pharmaceutical University , 1-25-4, Daigaku-Nishi , Gifu , 501-1196 , Japan .
| | - Isao Hozumi
- Laboratory of Medical Therapeutics and Molecular Therapeutics , Gifu Pharmaceutical University , 1-25-4, Daigaku-Nishi , Gifu , 501-1196 , Japan .
| | - Hideko Nagasawa
- Laboratory of Pharmaceutical and Medicinal Chemistry , Gifu Pharmaceutical University , 1-25-4, Daigaku-Nishi , Gifu , 501-1196 , Japan .
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43
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Hoechst-naphthalimide dyad with dual emissions as specific and ratiometric sensor for nucleus DNA damage. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2017.07.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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44
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Tang R, Wang M, Ray M, Jiang Y, Jiang Z, Xu Q, Rotello VM. Active Targeting of the Nucleus Using Nonpeptidic Boronate Tags. J Am Chem Soc 2017; 139:8547-8551. [PMID: 28598151 DOI: 10.1021/jacs.7b02801] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Active intracellular transport is a central mechanism in cell biology, directed by a limited set of naturally occurring signaling peptides. Here, we report the first nonpeptide moiety that recruits intracellular transport machinery for nuclear targeting. Proteins synthetically modified with a simple aromatic boronate motif are actively trafficked to the nucleus via the importin α/β pathway. Significantly, proteins too large to passively diffuse through nuclear pores were readily imported into the nucleus through this boronate-mediated pathway. The use of this simple motif to provide active intracellular targeting provides a promising strategy for directing subcellular localization for therapeutic and fundamental applications.
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Affiliation(s)
- Rui Tang
- Department of Chemistry, University of Massachusetts , 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Ming Wang
- Department of Biomedical Engineering, Tufts University , 4 Colby Street, Medford, Massachusetts 02115, United States
| | - Moumita Ray
- Department of Chemistry, University of Massachusetts , 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Ying Jiang
- Department of Chemistry, University of Massachusetts , 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Ziwen Jiang
- Department of Chemistry, University of Massachusetts , 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University , 4 Colby Street, Medford, Massachusetts 02115, United States
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts , 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
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45
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Design and synthesis of a second-generation ligand-tethered calcium indicator for plant cell biology based on the fundamental analyses of the structure and physical property. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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46
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Stiller C, Krüger DM, Brauckhoff N, Schmidt M, Janning P, Salamon H, Grossmann TN. Translocation of an Intracellular Protein via Peptide-Directed Ligation. ACS Chem Biol 2017; 12:504-509. [PMID: 28001046 DOI: 10.1021/acschembio.6b01013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ligand-directed reactions allow chemical transformations at very low reactant concentrations and can thus provide access to efficient approaches for the post-translational modification of proteins. The development of these proximity-induced reactions is hampered by the number of appropriate ligands and the lack of design principles. Addressing these limitations, we report a proximity-induced labeling system which applies a moderate affinity peptide ligand. The design process was structure-guided and supported by molecular dynamics simulations. We show that selective protein labeling can be performed inside living cells enabling the subcellular translocation of a protein via ligand-directed chemistry for the first time.
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Affiliation(s)
- Christiane Stiller
- Chemical Genomics
Centre of the Max Planck Society, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
- Technical University Dortmund, Department of Chemistry
and Chemical Biology, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Dennis M. Krüger
- Chemical Genomics
Centre of the Max Planck Society, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
- Technical University Dortmund, Department of Chemistry
and Chemical Biology, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Nicolas Brauckhoff
- Chemical Genomics
Centre of the Max Planck Society, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Marcel Schmidt
- Chemical Genomics
Centre of the Max Planck Society, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Petra Janning
- Max Planck Institute
of Molecular Physiology, Otto-Hahn-Str.
11, 44227 Dortmund, Germany
| | - Hazem Salamon
- Chemical Genomics
Centre of the Max Planck Society, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Tom N. Grossmann
- Chemical Genomics
Centre of the Max Planck Society, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
- Technical University Dortmund, Department of Chemistry
and Chemical Biology, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
- Max Planck Institute
of Molecular Physiology, Otto-Hahn-Str.
11, 44227 Dortmund, Germany
- VU University Amsterdam, Department of Chemistry
and Pharmaceutical Sciences, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
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47
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Tachibana R, Terai T, Boncompain G, Sugiyama S, Saito N, Perez F, Urano Y. Improving the Solubility of Artificial Ligands of Streptavidin to Enable More Practical Reversible Switching of Protein Localization in Cells. Chembiochem 2017; 18:358-362. [PMID: 27905160 DOI: 10.1002/cbic.201600640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Indexed: 12/21/2022]
Abstract
Chemical inducers that can control target-protein localization in living cells are powerful tools to investigate dynamic biological systems. We recently reported the retention using selective hook or "RUSH" system for reversible localization change of proteins of interest by addition/washout of small-molecule artificial ligands of streptavidin (ALiS). However, the utility of previously developed ALiS was restricted by limited solubility in water. Here, we overcame this problem by X-ray crystal structure-guided design of a more soluble ALiS derivative (ALiS-3), which retains sufficient streptavidin-binding affinity for use in the RUSH system. The ALiS-3-streptavidin interaction was characterized in detail. ALiS-3 is a convenient and effective tool for dynamic control of α-mannosidase II localization between ER and Golgi in living cells.
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Affiliation(s)
- Ryo Tachibana
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takuya Terai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Present address: Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Gaelle Boncompain
- Institut Curie, Centre de Recherche, PSL Research University, 26, rue d'Ulm, Paris, 75248, France.,CNRS, UMR144, PSL Research University, 26, rue d'Ulm, Paris, 75248, France
| | - Shigeru Sugiyama
- Graduate School of Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Nae Saito
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Franck Perez
- Institut Curie, Centre de Recherche, PSL Research University, 26, rue d'Ulm, Paris, 75248, France.,CNRS, UMR144, PSL Research University, 26, rue d'Ulm, Paris, 75248, France
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,CREST, JST, 7 Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan
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48
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Tsukiji S. [Small-molecule Ligands That Manipulate the Intracellular Location of Proteins]. YAKUGAKU ZASSHI 2016; 136:9-16. [PMID: 26725661 DOI: 10.1248/yakushi.15-00225-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Synthetic small-molecule ligands that control the intracellular location of proteins would be powerful tools for regulating cellular systems. However, the creation of such molecules has long remained unexplored because of the lack of a design methodology. Here, we introduce a new type of synthetic ligands, self-localizing ligands (SLLs), which spontaneously localize to specific subcellular regions in mammalian cells. We show that SLLs bind their target (exogenously expressed and endogenous) proteins and relocate them rapidly from the cytoplasm to their targeting sites. SLL-induced protein translocation is applicable to manipulate diverse synthetic/endogenous signaling pathways. These results validate the utility of SLLs in the spatial control of intracellular protein localization and signaling processes, opening a new direction in the design of small-molecule-based chemical tools or drugs for cell regulation.
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Affiliation(s)
- Shinya Tsukiji
- Department of Bioengineering, Nagaoka University of Technology
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49
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Wang H, Feng Z, Wang Y, Zhou R, Yang Z, Xu B. Integrating Enzymatic Self-Assembly and Mitochondria Targeting for Selectively Killing Cancer Cells without Acquired Drug Resistance. J Am Chem Soc 2016; 138:16046-16055. [PMID: 27960313 PMCID: PMC5291163 DOI: 10.1021/jacs.6b09783] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Targeting organelles by modulating the redox potential of mitochondria is a promising approach to kill cancer cells that minimizes acquired drug resistance. However, it lacks selectivity because mitochondria perform essential functions for (almost) all cells. We show that enzyme-instructed self-assembly (EISA), a bioinspired molecular process, selectively generates the assemblies of redox modulators (e.g., triphenyl phosphinium (TPP)) in the pericellular space of cancer cells for uptake, which allows selectively targeting the mitochondria of cancer cells. The attachment of TPP to a pair of enantiomeric, phosphorylated tetrapeptides produces the precursors (L-1P or D-1P) that form oligomers. Upon dephosphorylation catalyzed by ectophosphatases (e.g., alkaline phosphatase (ALP)) overexpressed on cancer cells (e.g., Saos2), the oligomers self-assemble to form nanoscale assemblies only on the surface of the cancer cells. The cancer cells thus uptake these assemblies of TPP via endocytosis, mainly via a caveolae/raft-dependent pathway. Inside the cells, the assemblies of TPP-peptide conjugates escape from the lysosome, induce dysfunction of mitochondria to release cytochrome c, and result in cell death, while the controls (i.e., omitting TPP motif, inhibiting ALP, or removing phosphate trigger) hardly kill the Saos2 cells. Most importantly, the repeated stimulation of the cancers by the precursors, unexpectedly, sensitizes the cancer cells to the precursors. As the first example of the integration of subcellular targeting with cell targeting, this study validates the spatial control of the assemblies of nonspecific cytotoxic agents by EISA as a promising molecular process for selectively killing cancer cells without inducing acquired drug resistance.
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Affiliation(s)
- Huaimin Wang
- Department of Chemistry, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States.,State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Collaborative Innovation Center of Chemical Science, Nankai University , Tianjin 300071, P.R. China
| | - Zhaoqianqi Feng
- Department of Chemistry, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
| | - Youzhi Wang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Collaborative Innovation Center of Chemical Science, Nankai University , Tianjin 300071, P.R. China
| | - Rong Zhou
- Department of Chemistry, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
| | - Zhimou Yang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Collaborative Innovation Center of Chemical Science, Nankai University , Tianjin 300071, P.R. China
| | - Bing Xu
- Department of Chemistry, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
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50
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Feng W, Qiao QL, Leng S, Miao L, Yin WT, Wang LQ, Xu ZC. A 1,8-naphthalimide-derived turn-on fluorescent probe for imaging lysosomal nitric oxide in living cells. CHINESE CHEM LETT 2016. [DOI: 10.1016/j.cclet.2016.06.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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