1
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Pezacki AT, Gonciarz RL, Okamura T, Matier CD, Torrente L, Cheng K, Miller SG, Ralle M, Ward NP, DeNicola GM, Renslo AR, Chang CJ. A tandem activity-based sensing and labeling strategy reveals antioxidant response element regulation of labile iron pools. Proc Natl Acad Sci U S A 2024; 121:e2401579121. [PMID: 38968123 DOI: 10.1073/pnas.2401579121] [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: 01/23/2024] [Accepted: 05/29/2024] [Indexed: 07/07/2024] Open
Abstract
Iron is an essential element for life owing to its ability to participate in a diverse array of oxidation-reduction reactions. However, misregulation of iron-dependent redox cycling can also produce oxidative stress, contributing to cell growth, proliferation, and death pathways underlying aging, cancer, neurodegeneration, and metabolic diseases. Fluorescent probes that selectively monitor loosely bound Fe(II) ions, termed the labile iron pool, are potentially powerful tools for studies of this metal nutrient; however, the dynamic spatiotemporal nature and potent fluorescence quenching capacity of these bioavailable metal stores pose challenges for their detection. Here, we report a tandem activity-based sensing and labeling strategy that enables imaging of labile iron pools in live cells through enhancement in cellular retention. Iron green-1 fluoromethyl (IG1-FM) reacts selectively with Fe(II) using an endoperoxide trigger to release a quinone methide dye for subsequent attachment to proximal biological nucleophiles, providing a permanent fluorescent stain at sites of elevated labile iron. IG1-FM imaging reveals that degradation of the major iron storage protein ferritin through ferritinophagy expands the labile iron pool, while activation of nuclear factor-erythroid 2-related factor 2 (NRF2) antioxidant response elements (AREs) depletes it. We further show that lung cancer cells with heightened NRF2 activation, and thus lower basal labile iron, have reduced viability when treated with an iron chelator. By connecting labile iron pools and NRF2-ARE activity to a druggable metal-dependent vulnerability in cancer, this work provides a starting point for broader investigations into the roles of transition metal and antioxidant signaling pathways in health and disease.
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Affiliation(s)
- Aidan T Pezacki
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Ryan L Gonciarz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Toshitaka Okamura
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Carson D Matier
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Laura Torrente
- Department of Metabolism and Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Ke Cheng
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Sophia G Miller
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239
| | - Martina Ralle
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239
| | - Nathan P Ward
- Department of Metabolism and Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Gina M DeNicola
- Department of Metabolism and Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158
| | - Christopher J Chang
- Department of Chemistry, University of California, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720
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2
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Zhang S, Tang Q, Zhang X, Chen X. Proximitomics by Reactive Species. ACS CENTRAL SCIENCE 2024; 10:1135-1147. [PMID: 38947200 PMCID: PMC11212136 DOI: 10.1021/acscentsci.4c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 07/02/2024]
Abstract
The proximitome is defined as the entire collection of biomolecules spatially in the proximity of a biomolecule of interest. More broadly, the concept of the proximitome can be extended to the totality of cells proximal to a specific cell type. Since the spatial organization of biomolecules and cells is essential for almost all biological processes, proximitomics has recently emerged as an active area of scientific research. One of the growing strategies for proximitomics leverages reactive species-which are generated in situ and spatially confined, to chemically tag and capture proximal biomolecules and cells for systematic analysis. In this Outlook, we summarize different types of reactive species that have been exploited for proximitomics and discuss their pros and cons for specific applications. In addition, we discuss the current challenges and future directions of this exciting field.
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Affiliation(s)
- Shaoran Zhang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Qi Tang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People’s
Republic of China
| | - Xu Zhang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Xing Chen
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
- Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People’s
Republic of China
- Synthetic
and Functional Biomolecules Center, Peking
University, Beijing 100871, People’s
Republic of China
- Key
Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry
of Education, Peking University, Beijing 100871, People’s Republic of China
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3
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Kamp M, Surmacki J, Segarra Mondejar M, Young T, Chrabaszcz K, Joud F, Zecchini V, Speed A, Frezza C, Bohndiek SE. Raman micro-spectroscopy reveals the spatial distribution of fumarate in cells and tissues. Nat Commun 2024; 15:5386. [PMID: 38918386 PMCID: PMC11199670 DOI: 10.1038/s41467-024-49403-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 06/04/2024] [Indexed: 06/27/2024] Open
Abstract
Aberrantly accumulated metabolites elicit intra- and inter-cellular pro-oncogenic cascades, yet current measurement methods require sample perturbation/disruption and lack spatio-temporal resolution, limiting our ability to fully characterize their function and distribution. Here, we show that Raman spectroscopy (RS) can directly detect fumarate in living cells in vivo and animal tissues ex vivo, and that RS can distinguish between Fumarate hydratase (Fh1)-deficient and Fh1-proficient cells based on fumarate concentration. Moreover, RS reveals the spatial compartmentalization of fumarate within cellular organelles in Fh1-deficient cells: consistent with disruptive methods, we observe the highest fumarate concentration (37 ± 19 mM) in mitochondria, where the TCA cycle operates, followed by the cytoplasm (24 ± 13 mM) and then the nucleus (9 ± 6 mM). Finally, we apply RS to tissues from an inducible mouse model of FH loss in the kidney, demonstrating RS can classify FH status. These results suggest RS could be adopted as a valuable tool for small molecule metabolic imaging, enabling in situ non-destructive evaluation of fumarate compartmentalization.
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Affiliation(s)
- Marlous Kamp
- Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Chemistry, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Jakub Surmacki
- Lodz University of Technology, Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular Spectroscopy, Wroblewskiego 15, 93-590, Lodz, Poland
| | - Marc Segarra Mondejar
- Hutchison/MRC Cancer Unit, University of Cambridge, Biomedical Campus, Cambridge, CB2 0XZ, UK
- CECAD, Joseph-Stelzmann-Straße 26, 50931, Cologne, Germany
| | - Tim Young
- Hutchison/MRC Cancer Unit, University of Cambridge, Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Karolina Chrabaszcz
- Institute of Nuclear Physics, Polish Academy of Sciences, Department of Experimental Physics of Complex Systems, Radzikowskiego 152, 31-342, Krakow, Poland
| | - Fadwa Joud
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Vincent Zecchini
- Hutchison/MRC Cancer Unit, University of Cambridge, Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Alyson Speed
- Hutchison/MRC Cancer Unit, University of Cambridge, Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Christian Frezza
- Hutchison/MRC Cancer Unit, University of Cambridge, Biomedical Campus, Cambridge, CB2 0XZ, UK.
- CECAD, Joseph-Stelzmann-Straße 26, 50931, Cologne, Germany.
| | - Sarah E Bohndiek
- Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK.
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.
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4
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Cheng R, Nishikawa Y, Wagatsuma T, Kambe T, Tanaka YK, Ogra Y, Tamura T, Hamachi I. Protein-Labeling Reagents Selectively Activated by Copper(I). ACS Chem Biol 2024; 19:1222-1228. [PMID: 38747299 DOI: 10.1021/acschembio.4c00011] [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: 06/22/2024]
Abstract
Copper is an essential trace element that participates in many biological processes through its unique redox cycling between cuprous (Cu+) and cupric (Cu2+) oxidation states. To elucidate the biological functions of copper, chemical biology tools that enable selective visualization and detection of copper ions and proteins in copper-rich environments are required. Herein, we describe the design of Cu+-responsive reagents based on a conditional protein labeling strategy. Upon binding Cu+, the probes generated quinone methide via oxidative bond cleavage, which allowed covalent labeling of surrounding proteins with high Cu+ selectivity. Using gel- and imaging-based analyses, the best-performing probe successfully detected changes in the concentration of labile Cu+ in living cells. Moreover, conditional proteomics analysis suggested intramitochondrial Cu+ accumulation in cells undergoing cuproptosis. Our results highlight the power of Cu+-responsive protein labeling in providing insights into the molecular mechanisms of Cu+ metabolism and homeostasis.
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Affiliation(s)
- Rong Cheng
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuki Nishikawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takumi Wagatsuma
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Taiho Kambe
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yu-Ki Tanaka
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8675, Japan
| | - Yasumitsu Ogra
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8675, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO (Exploratory Research for Advanced Technology, JST), Sanbancho, Chiyodaku, Tokyo 102-0075, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO (Exploratory Research for Advanced Technology, JST), Sanbancho, Chiyodaku, Tokyo 102-0075, Japan
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5
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Mino T, Nonaka H, Hamachi I. Molecular anchoring and fluorescent labeling in animals compatible with tissue clearing for 3D imaging. Curr Opin Chem Biol 2024; 81:102474. [PMID: 38838505 DOI: 10.1016/j.cbpa.2024.102474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 06/07/2024]
Abstract
Analyzing the quantity and distribution of molecules throughout intact biological tissue is crucial for understanding various biological phenomena. Traditional methods involving destructive extraction result in the loss of spatial information. Conversely, tissue-clearing techniques combined with fluorescence imaging have recently emerged as a powerful tool for deep tissue imaging without sacrificing spatial coverage. Key to this approach is the anchoring and labeling of targets in intact tissue. In this review, methods for anchoring and labeling proteins, lipids, carbohydrates, and small molecules are presented. Future directions include the development of activity-based probes that work in vivo and mark transient events with spatial information to enable a deeper understanding of biological phenomena.
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Affiliation(s)
- Takeharu Mino
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hiroshi Nonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan.
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6
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Yi M, Ashton-Rickardt G, Tan W, Liu Z, He H, Hsieh JT, Xu B. Accelerating Cellular Uptake with Unnatural Amino Acid for Inhibiting Immunosuppressive Cancer Cells. Chemistry 2024; 30:e202400691. [PMID: 38527252 PMCID: PMC11132931 DOI: 10.1002/chem.202400691] [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: 02/20/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
Targeting immunosuppressive metastatic cancer cells is a key challenge in therapy. We recently have shown that a rigid-rod aromatic, pBP-NBD, that responds to enzymes and kill immunosuppressive metastatic osteosarcoma (mOS) and castration resistant prostate cancer (CRPC) cells in mimetic bone microenvironment. However, pBP-NBD demonstrated moderate efficacy against CRPC cells. To enhance activity, we incorporated the unnatural amino acid L- or D-4,4'-biphenylalanine (L- or D-BiP) into pBP-NBD, drastically increasing cellular uptake and CRPC inhibition. Specifically, we inserted BiP into pBP-NBD to target mOS (Saos2 and SJSA1) and CRPC (VCaP and PC3) cells with overexpressed phosphatases. Our results show that the D-peptide backbone with an aspartate methyl diester at the C-terminal offers the highest activity against these immunosuppressive mOS and CRPC cells. Importantly, imaging shows that the peptide assemblies almost instantly enter the cells and accumulate primarily within the endoplasmic reticulum of Saos2, SJSA1, and PC3 cells and at the lysosomes of VCaP cells. By using BiP to boost cellular uptake and self-assembly within cancer cells, this work illustrates an unnatural hydrophobic amino acid as a versatile and effective residue to boost endocytosis of synthetic peptides for intracellular self-assembly.
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Affiliation(s)
- Meihui Yi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | | | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Zhiyu Liu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Jer-Tsong Hsieh
- Department of Urology, Southwestern Medical Center, University of Texas, Dallas, TX 75235, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
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7
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Huo W, Takayama K, Miki K, Nogita K, Shao S, Suzuki A, Morimoto T, Mu H, Ohe K. AIE-ESIPT Photoluminescent Probe Based on 3-(3-Hydroxypyridin-2-yl)isoquinolin-4-ol for the Detection of Intracellular Hydrogen Peroxide. Chemistry 2024:e202401451. [PMID: 38803241 DOI: 10.1002/chem.202401451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 05/29/2024]
Abstract
Excited-state intramolecular proton transfer (ESIPT) molecules, which feature large Stokes shifts to avoid self-absorption, play an essential role in photoluminescent bioimaging probes. Herein, we report the development of an ESIPT molecule 3-(3-hydroxypyridin-2-yl)isoquinolin-4-ol (PiQ). PiQ not only undergoes a distinct ESIPT process unlike the symmetrical 2,2'-bipyridyl-3,3'-diol but also exhibits aggregation-induced emission (AIE) characteristics. PiQ self-assembles into aggregates with an average size of 241.0±51.9 nm in aqueous solutions, leading to significantly enhanced photoluminescence. On the basis of the ESIPT and AIE characteristics of PiQ, the latter is functionalized with a hydrogen peroxide-responsive 4-pinacoratoborylbenzyl group (B) and a carboxylesterase-responsive acetyl group (A) to produce a photoluminescent probe B-PiQ-A. The potential of PiQ for applications in bioimaging and chemical sensing is underscored by its efficient detection of both endogenous and exogenous hydrogen peroxide in living cells.
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Affiliation(s)
- Wenting Huo
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Kohei Takayama
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Koji Miki
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Kohei Nogita
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Shuai Shao
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Ayako Suzuki
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Takashi Morimoto
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Huiying Mu
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Kouichi Ohe
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
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8
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Li Y, Pan K, Gao Y, Li J, Zang Y, Li X. Deconvoluting nitric oxide-protein interactions with spatially resolved multiplex imaging. Chem Sci 2024; 15:6562-6571. [PMID: 38699271 PMCID: PMC11062118 DOI: 10.1039/d4sc00767k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/28/2024] [Indexed: 05/05/2024] Open
Abstract
Simultaneous imaging of nitric oxide (NO) and its proximal proteins should facilitate the deconvolution of NO-protein interactions. While immunostaining is a primary assay to localize proteins in non-genetically manipulated samples, NO imaging probes with immunostaining-compatible signals remain unexplored. Herein, probe NOP-1 was developed with an NO-triggered proximal protein labeling capacity and fluorogenic signals. The trick is to fuse the native chemical ligation of acyl benzotriazole with the protein-conjugation-induced fluorogenic response of Si-rhodamine fluorophore. NOP-1 predominantly existed in the non-fluorescent spirocyclic form. Yet, its acyl o-phenylenediamine moiety was readily activated by NO into acyl benzotriazole to conjugate proximal proteins, providing a fluorogenic response and translating the transient cellular NO signal into a permanent stain compatible with immunostaining. NOP-1 was utilized to investigate NO signaling in hypoglycemia-induced neurological injury, providing direct evidence of NO-induced apoptosis during hypoglycemia. Mechanistically, multiplex imaging revealed the overlap of cellular NOP-1 fluorescence with immunofluorescence for α-tubulin and NO2-Tyr. Importantly, α-tubulin was resolved from NOP-1 labeled proteins. These results suggest that NO played a role in hypoglycemia-induced apoptosis, at least in part, through nitrating α-tubulin. This study fills a crucial gap in current imaging probes, providing a valuable tool for unraveling the complexities of NO signaling in biological processes.
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Affiliation(s)
- Yi Li
- College of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University 866 Yuhangtang Street Hangzhou 310058 China
| | - Kaijun Pan
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University Nanjing 210009 China
| | - Yanan Gao
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University Nanjing 210009 China
| | - Jia Li
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University Nanjing 210009 China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medical, Chinese Academy of Sciences Shanghai 201203 China
| | - Yi Zang
- Lingang Laboratory Shanghai 201203 China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medical, Chinese Academy of Sciences Shanghai 201203 China
| | - Xin Li
- College of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University 866 Yuhangtang Street Hangzhou 310058 China
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University Jiashan 314100 China
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9
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Sakamoto DM, Tamura I, Yi B, Hasegawa S, Saito Y, Yamada N, Takakusagi Y, Kubota SI, Kobayashi M, Harada H, Hanaoka K, Taki M, Nangaku M, Tainaka K, Sando S. Whole-Body and Whole-Organ 3D Imaging of Hypoxia Using an Activatable Covalent Fluorescent Probe Compatible with Tissue Clearing. ACS NANO 2024; 18:5167-5179. [PMID: 38301048 DOI: 10.1021/acsnano.3c12716] [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: 02/03/2024]
Abstract
Elucidation of biological phenomena requires imaging of microenvironments in vivo. Although the seamless visualization of in vivo hypoxia from the level of whole-body to single-cell has great potential to discover unknown phenomena in biological and medical fields, no methodology for achieving it has been established thus far. Here, we report the whole-body and whole-organ imaging of hypoxia, an important microenvironment, at single-cell resolution using activatable covalent fluorescent probes compatible with tissue clearing. We initially focused on overcoming the incompatibility of fluorescent dyes and refractive index matching solutions (RIMSs), which has greatly hindered the development of fluorescent molecular probes in the field of tissue clearing. The fluorescent dyes compatible with RIMS were then incorporated into the development of activatable covalent fluorescent probes for hypoxia. We combined the probes with tissue clearing, achieving comprehensive single-cell-resolution imaging of hypoxia in a whole mouse body and whole organs.
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Affiliation(s)
- Daichi M Sakamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Iori Tamura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Bo Yi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Sho Hasegawa
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Yutaro Saito
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Naoki Yamada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yoichi Takakusagi
- Quantum Hyperpolarized MRI Team, Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba-city 263-8555, Japan
- Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba-city 263-8555, Japan
| | - Shimpei I Kubota
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Kita-15, Nishi-7, Kita-ku, Sapporo, Hokkaido 060-0815, Japan
| | - Minoru Kobayashi
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Genome Dynamics, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroshi Harada
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Genome Dynamics, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kenjiro Hanaoka
- Division of Analytical Chemistry for Drug Discovery, Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Masayasu Taki
- Institute of Transformative Bio-Molecules, Nagoya University, Furo, Chikusa, Nagoya 464-8601, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Kazuki Tainaka
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata 951-8585, Japan
- Gftd DeSci, Gftd DAO, Nishikawa Building, 20 Kikuicho, Shinjuku-ku, Tokyo 162-0044, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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10
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Punzalan C, Wang L, Bajrami B, Yao X. Measurement and utilization of the proteomic reactivity by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:166-192. [PMID: 36924435 DOI: 10.1002/mas.21837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Chemical proteomics, which involves studying the covalent modifications of proteins by small molecules, has significantly contributed to our understanding of protein function and has become an essential tool in drug discovery. Mass spectrometry (MS) is the primary method for identifying and quantifying protein-small molecule adducts. In this review, we discuss various methods for measuring proteomic reactivity using MS and covalent proteomics probes that engage through reactivity-driven and proximity-driven mechanisms. We highlight the applications of these methods and probes in live-cell measurements, drug target identification and validation, and characterizing protein-small molecule interactions. We conclude the review with current developments and future opportunities in the field, providing our perspectives on analytical considerations for MS-based analysis of the proteomic reactivity landscape.
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Affiliation(s)
- Clodette Punzalan
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- AD Bio US, Takeda, Lexington, Massachusetts, 02421, USA
| | - Bekim Bajrami
- Chemical Biology & Proteomics, Biogen, Cambridge, Massachusetts, USA
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Biology, University of Connecticut, Storrs, Connecticut, USA
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11
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Wang G, Li Q, Guo Y, Chen L, Yao Y, Zhong Y, Sun J, Yan X, Wang H, Wang X, Ding L, Ju H. Interception Proximity Labeling for Interrogating Cell Efflux Microenvironment. Anal Chem 2023; 95:17798-17807. [PMID: 37976298 DOI: 10.1021/acs.analchem.3c03879] [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: 11/19/2023]
Abstract
The difficulty in elucidating the microenvironment of extracellular H2O2 efflux has led to the lack of a critical extracellular link in studies of the mechanisms of redox signaling pathways. Herein, we mounted horseradish peroxidase (HRP) to glycans expressed globally on the living cell surface and constructed an interception proximity labeling (IPL) platform for H2O2 efflux. The release of endogenous H2O2 is used as a "physiological switch" for HRP to enable proximity labeling. Using this platform, we visualize the oxidative stress state of tumor cells under the condition of nutrient withdrawal, as well as that of macrophages exposed to nonparticulate stimuli. Furthermore, in combination with a proteomics technique, we identify candidate proteins at the invasion interface between fungal mimics (zymosan) and macrophages by interception labeling of locally accumulated H2O2 and confirm that Toll-like receptor 2 binds zymosan in a glycan-dependent manner. The IPL platform has great potential to elucidate the mechanisms underlying biological processes involving redox pathways.
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Affiliation(s)
- Guyu Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qiang Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yuna Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Liusheng Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yunyan Yao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yihong Zhong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jiahui Sun
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiaomin Yan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hongwei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Xiaojian Wang
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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12
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Li S, Zhao J, Han G, Zhang X, Li N, Zhang Z. Silicon dioxide-induced endoplasmic reticulum stress of alveolar macrophages and its role on the formation of silicosis fibrosis: a review article. Toxicol Res (Camb) 2023; 12:1024-1033. [PMID: 38145097 PMCID: PMC10734631 DOI: 10.1093/toxres/tfad099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 09/01/2023] [Accepted: 10/07/2023] [Indexed: 12/26/2023] Open
Abstract
Silicosis is a chronic lung inflammatory disease induced by long-term inhalation of high concentrations of silicon dioxide (SiO2), characterized by pulmonary fibrosis. Inhalation of silica invades alveolar macrophages (AMs) and changes the micro-environment of the cell, resulting in abnormal morphology and dysfunction of the endoplasmic reticulum (ER). Once beyond the range of cell regulation, the endoplasmic reticulum stress (ERS) will occur, which will lead to cell damage, necrosis, and apoptosis, eventually causing silicosis fibrosis through various mechanisms. This is a complex and delicate process accompanied by various macrophage-derived cytokines. Unfortunately, the details have not been systematically summarized yet. In this review, we systematically introduce the basic two processes: the process of inducing ERS by inhaling SiO2 and the process of inducing pulmonary fibrosis by ERS. Moreover, the underlying mechanism of the above two sequential events is also be discussed. We conclude that the ERS of alveolar macrophages caused by silica dust are involved deeply in the pathogenesis of silicosis. Therefore, changing the states of SiO2-induced ERS of macrophage may be an attractive therapeutic target for silicosis fibrosis.
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Affiliation(s)
- Shuang Li
- Department of Public Health and Management, Binzhou Medical University, Guanhai Road 346, Yantai 264003, Shandong Province, China
- Department of Public Health, Jining Medical University, Jianshe South Road 45, Jining 272067, Shandong Province, China
| | - Jiahui Zhao
- Department of Public Health, Jining Medical University, Jianshe South Road 45, Jining 272067, Shandong Province, China
- Department of Public Health, Weifang Medical University, Baotong west Street 7166, Weifang 261053, Shandong Province, China
| | - Guizhi Han
- Department of Public Health, Jining Medical University, Jianshe South Road 45, Jining 272067, Shandong Province, China
| | - Xin Zhang
- Department of Public Health and Management, Binzhou Medical University, Guanhai Road 346, Yantai 264003, Shandong Province, China
| | - Ning Li
- Department of Public Health and Management, Binzhou Medical University, Guanhai Road 346, Yantai 264003, Shandong Province, China
| | - Zhaoqiang Zhang
- Department of Public Health and Management, Binzhou Medical University, Guanhai Road 346, Yantai 264003, Shandong Province, China
- Department of Public Health, Jining Medical University, Jianshe South Road 45, Jining 272067, Shandong Province, China
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13
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He C, Ke Z, Liu K, Peng J, Yang Q, Wang L, Feng G, Fang J. Nanozyme-based dual-signal sensing system for colorimetric and photothermal detection of AChE activity in the blood of liver-injured mice. Anal Bioanal Chem 2023; 415:2655-2664. [PMID: 36995409 DOI: 10.1007/s00216-023-04663-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 03/31/2023]
Abstract
Acetylcholinesterase (AChE), a crucial enzyme related to liver function, is involved in numerous physiological processes such as neurotransmission and muscular contraction. The currently reported techniques for detecting AChE mainly rely on a single signal output, limiting their high-accuracy quantification. The few reported dual-signal assays are challenging to implement in dual-signal point-of-care testing (POCT) because of the need for large instruments, costly modifications, and trained operators. Herein, we report a colorimetric and photothermal dual-signal POCT sensing platform based on CeO2-TMB (3,3',5,5'-tetramethylbenzidine) for the visualization of AChE activity in liver-injured mice. The method compensates for the false positives of a single signal and realizes the rapid, low-cost portable detection of AChE. More importantly, the CeO2-TMB sensing platform enables the diagnosis of liver injury and provides an effective tool for studying liver disease in basic medicine and clinical applications. Rapid colorimetric and photothermal biosensor for sensitive detection of acetylcholinesterase (I) and acetylcholinesterase levels in mouse serum (II).
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Affiliation(s)
- Chang He
- School of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Zhenyi Ke
- School of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Kai Liu
- School of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Jiasheng Peng
- School of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Qinghui Yang
- School of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Lixiang Wang
- School of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Guangfu Feng
- School of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
| | - Jun Fang
- School of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
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14
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Sakamoto S, Hamachi I. Ligand‐Directed Chemistry for Protein Labeling for Affinity‐Based Protein Analysis. Isr J Chem 2023. [DOI: 10.1002/ijch.202200077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo-ku 615-8510 Kyoto Japan
- JST-ERATO Hamachi Innovative Molecular Technology for Neuroscience 615-8530 Kyoto Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo-ku 615-8510 Kyoto Japan
- JST-ERATO Hamachi Innovative Molecular Technology for Neuroscience 615-8530 Kyoto Japan
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15
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Oxidative Stress in Age-Related Neurodegenerative Diseases: An Overview of Recent Tools and Findings. Antioxidants (Basel) 2023; 12:antiox12010131. [PMID: 36670993 PMCID: PMC9854433 DOI: 10.3390/antiox12010131] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
Reactive oxygen species (ROS) have been described to induce a broad range of redox-dependent signaling reactions in physiological conditions. Nevertheless, an excessive accumulation of ROS leads to oxidative stress, which was traditionally considered as detrimental for cells and organisms, due to the oxidative damage they cause to biomolecules. During ageing, elevated ROS levels result in the accumulation of damaged proteins, which may exhibit altered enzymatic function or physical properties (e.g., aggregation propensity). Emerging evidence also highlights the relationship between oxidative stress and age-related pathologies, such as protein misfolding-based neurodegenerative diseases (e.g., Parkinson's (PD), Alzheimer's (AD) and Huntington's (HD) diseases). In this review we aim to introduce the role of oxidative stress in physiology and pathology and then focus on the state-of-the-art techniques available to detect and quantify ROS and oxidized proteins in live cells and in vivo, providing a guide to those aiming to characterize the role of oxidative stress in ageing and neurodegenerative diseases. Lastly, we discuss recently published data on the role of oxidative stress in neurological disorders.
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16
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Messina MS, Quargnali G, Chang CJ. Activity-Based Sensing for Chemistry-Enabled Biology: Illuminating Principles, Probes, and Prospects for Boronate Reagents for Studying Hydrogen Peroxide. ACS BIO & MED CHEM AU 2022; 2:548-564. [PMID: 36573097 PMCID: PMC9782337 DOI: 10.1021/acsbiomedchemau.2c00052] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022]
Abstract
Activity-based sensing (ABS) offers a general approach that exploits chemical reactivity as a method for selective detection and manipulation of biological analytes. Here, we illustrate the value of this chemical platform to enable new biological discovery through a case study in the design and application of ABS reagents for studying hydrogen peroxide (H2O2), a major type of reactive oxygen species (ROS) that regulates a diverse array of vital cellular signaling processes to sustain life. Specifically, we summarize advances in the use of activity-based boronate probes for the detection of H2O2 featuring high molecular selectivity over other ROS, with an emphasis on tailoring designs in chemical structure to promote new biological principles of redox signaling.
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Affiliation(s)
- Marco S. Messina
- Department
of Chemistry and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Gianluca Quargnali
- Department
of Chemistry and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Christopher J. Chang
- Department
of Chemistry and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
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17
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A fluorogenic probe for predicting treatment response in non-small cell lung cancer with EGFR-activating mutations. Nat Commun 2022; 13:6944. [PMID: 36376325 PMCID: PMC9663578 DOI: 10.1038/s41467-022-34627-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
Therapeutic responses of non-small cell lung cancer (NSCLC) to epidermal growth factor receptor (EGFR) - tyrosine kinase inhibitors (TKIs) are known to be associated with EGFR mutations. However, a proportion of NSCLCs carrying EGFR mutations still progress on EGFR-TKI underlining the imperfect correlation. Structure-function-based approaches have recently been reported to perform better in retrospectively predicting patient outcomes following EGFR-TKI treatment than exon-based method. Here, we develop a multicolor fluorescence-activated cell sorting (FACS) with an EGFR-TKI-based fluorogenic probe (HX103) to profile active-EGFR in tumors. HX103-based FACS shows an overall agreement with gene mutations of 82.6%, sensitivity of 81.8% and specificity of 83.3% for discriminating EGFR-activating mutations from wild-type in surgical specimens from NSCLC patients. We then translate HX103 to the clinical studies for prediction of EGFR-TKI sensitivity. When integrating computed tomography imaging with HX103-based FACS, we find a high correlation between EGFR-TKI therapy response and probe labeling. These studies demonstrate HX103-based FACS provides a high predictive performance for response to EGFR-TKI, suggesting the potential utility of an EGFR-TKI-based probe in precision medicine trials to stratify NSCLC patients for EGFR-TKI treatment.
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18
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Wang H, Wang Z, Gao H, Liu J, Qiao Z, Zhao B, Liang Z, Jiang B, Zhang L, Zhang Y. A photo-oxidation driven proximity labeling strategy enables profiling of mitochondrial proteome dynamics in living cells. Chem Sci 2022; 13:11943-11950. [PMID: 36320915 PMCID: PMC9580500 DOI: 10.1039/d2sc04087e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/27/2022] [Indexed: 07/21/2023] Open
Abstract
Mapping the proteomic landscape of mitochondria with spatiotemporal precision plays a pivotal role in elucidating the delicate biological functions and complex relationship with other organelles in a variety of dynamic physiological processes which necessitates efficient and controllable chemical tools. We herein report a photo-oxidation driven proximity labeling strategy to profile the mitochondrial proteome by light dependence in living cells with high spatiotemporal resolution. Taking advantage of organelle-localizable organic photoactivated probes generating reactive species and nucleophilic substrates for proximal protein oxidation and trapping, mitochondrial proteins were selectively labeled by spatially limited reactions in their native environment. Integration of photo-oxidation driven proximity labeling and quantitative proteomics facilitated the plotting of the mitochondrial proteome in which up to 310 mitochondrial proteins were identified with a specificity of 64% in HeLa cells. Furthermore, mitochondrial proteome dynamics was deciphered in drug resistant Huh7 and LPS stimulated HMC3 cells which were hard-to-transfect. A number of differential proteins were quantified which were intimately linked to critical processes and provided insights into the related molecular mechanisms of drug resistance and neuroinflammation in the perspective of mitochondria. The photo-oxidation driven proximity labeling strategy offers solid technical support to a highly precise proteomic platform in time and finer space for more knowledge of subcellular biology.
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Affiliation(s)
- He Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhiting Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Hang Gao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jianhui Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Zichun Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Bo Jiang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
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19
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Wang S, Tan W, Lang W, Qian H, Guo S, Zhu L, Ge J. Fluorogenic and Mitochondria-Localizable Probe Enables Selective Labeling and Imaging of Nitroreductase. Anal Chem 2022; 94:7272-7277. [PMID: 35549110 DOI: 10.1021/acs.analchem.2c00512] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nitroreductase (NTR), one of the flavin-dependent enzymes and an upregulated enzyme under tumor hypoxia, has been studied for decades. Many fluorescent probes were developed to detect NTR activity; however, these probes tend to diffuse away from their reaction site (NTR) inevitably, leading to inappropriate sample fixation, lower accuracy of NTR localization, and weaker signal-to-noise ratio. Herein, we present the design, synthesis, in vitro evaluation, and biological applications of an NTR-activatable fluorogenic and labeling probe FY. By integrating with quinone methide (QM) proximity-based protein labeling, the additional fluoromethyl group on FY serves as a potential origin of QM. Compared with conventional fluorescent probes, this new NTR probe not only offers mitochondrial localizable and fluorogenic response but also achieves permanent retention on the site of activation with an enhanced spatial resolution to improve the detection sensitivity even after cell fixation. We believe our work could offer an expandable synthetic approach to develop these permanent labeling and imaging fluorescence probes for deciphering complex biological events.
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Affiliation(s)
- Shuyi Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Tan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wenjie Lang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huijuan Qian
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shuhong Guo
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Liquan Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
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20
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Zhang N, Song Z, Sun H, Shi Z, Li C, Guo C. Imidazole-induced manganese oxide nanocrystals on carbon nanofiber hybridized with gold nanoparticles as bifunctional biomimetic enzyme in live-cell assays. J Colloid Interface Sci 2022; 614:288-297. [DOI: 10.1016/j.jcis.2022.01.097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/31/2021] [Accepted: 01/16/2022] [Indexed: 10/19/2022]
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21
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Guo S, Yuan C, Lang W, Hong D, Liu J, Huang J, Dong J, Ge J. Photocontrollable Probes for Mitochondrial Protein Profiling. Chembiochem 2022; 23:e202200066. [PMID: 35344259 DOI: 10.1002/cbic.202200066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/21/2022] [Indexed: 11/10/2022]
Abstract
Mitochondrion is the core site of cell signaling, energy metabolism and biosynthesis. Here, taking advantage of activitybased probes, we synthesized two photocontrollable probes ( YGH-1 and YGH-2 ), composed of a mitochondrial localization moiety "triphenylphosphonium", a photo triggered group to achieve spatial and temporal controlled protein capture and an alkyne group to enrich the labeled protein. Proteomic validation was further carried out to facilitate identifications of mitochondrial proteomes in HeLa cells. The results showed that half of identified protein hits (~300) labeled by probes YGH-1 and YGH-2 belong to mitochondria, mostly localizing in mitochondrial matrix and inner mitochondrial membrane. Our research results provide a new tool for spatial and temporal analysis of subcellular proteome.
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Affiliation(s)
- Shuhong Guo
- Zhejiang University of Technology Chaohui Campus: Zhejiang University of Technology, College of Biotechnology and Bioengineering, CHINA
| | - Chaonan Yuan
- Zhejiang University of Technology, College of Biotechnology and Bioengineering, CHINA
| | - Wenjie Lang
- Zhejiang University of Technology Chaohui Campus: Zhejiang University of Technology, College of Biotechnology and Bioengineering, CHINA
| | - Danqi Hong
- Zhejiang University of Technology Chaohui Campus: Zhejiang University of Technology, College of Biotechnology and Bioengineering, CHINA
| | - Jian Liu
- Zhejiang University of Technology Chaohui Campus: Zhejiang University of Technology, College of Biotechnology and Bioengineering, CHINA
| | - Jintao Huang
- Zhejiang University of Technology Chaohui Campus: Zhejiang University of Technology, College of Biotechnology and Bioengineering, CHINA
| | - Jia Dong
- Zhejiang University of Technology Chaohui Campus: Zhejiang University of Technology, College of Biotechnology and Bioengineering, CHINA
| | - Jingyan Ge
- Zhejiang University of Technology, College of Biotechnology and Bioengineering, Chaowang Road 18, Hangzhou, China, 310014, Hangzhou, CHINA
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22
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Liang T, Zhang D, Hu W, Tian C, Zeng L, Wu T, Lei D, Qiang T, Yang X, Sun X. A dual lock-and-key two photon fluorescence probe in response to hydrogen peroxide and viscosity: Application in cellular imaging and inflammation therapy. Talanta 2021; 235:122719. [PMID: 34517587 DOI: 10.1016/j.talanta.2021.122719] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 02/08/2023]
Abstract
Here, a dual lock-and-key fluorescence probe was developed for visualizing the inflammatory process in myocardial H9C2 cells. The probe possessed two-photon properties, viscosity sensitivity, and hydrogen peroxide (H2O2) responsiveness. A thiocarbamate spacer between fluorophore and H2O2 responsive unit enabled the release of carbonyl sulfide (COS). This rapidly converts to the anti-inflammatory hydrogen sulfide (H2S) by the ubiquitous enzyme carbon anhydrase. The probe displayed a dual response towards hydrogen peroxide and viscosity in vitro. No obvious fluorescence changes were observed towards either hydrogen peroxide or viscosity alone. In cellular experiments, the probe demonstrated good biocompatibility, low toxicity, and was shown responses towards exogenous and endogenous hydrogen peroxide under viscosity conditions. LPS induced cell inflammation showed it was able to effectively alleviate the inflammation-caused damage by releasing H2S and eliminating H2O2. The new protocol demonstrates its promising to achieve diagnosis and treatment of cellular inflammatory process.
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Affiliation(s)
- Tianyu Liang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; College of Bioresources and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Dongliang Zhang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, The Fourth Military Medical University, Xi 'an, 710032, China
| | - Wei Hu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; College of Bioresources and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China.
| | - Chenyang Tian
- Department of Burns and Cutaneous Surgery, Xijing Hospital, The Fourth Military Medical University, Xi 'an, 710032, China
| | - Lingyu Zeng
- Department of Chemistry, The University of Texas at Austin, Texas, 78712, United States
| | - Tianhong Wu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Dongqing Lei
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Taotao Qiang
- College of Bioresources and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Xuekang Yang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, The Fourth Military Medical University, Xi 'an, 710032, China.
| | - Xiaolong Sun
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China.
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23
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Long MJC, Huang KT, Aye Y. The not so identical twins: (dis)similarities between reactive electrophile and oxidant sensing and signaling. Chem Soc Rev 2021; 50:12269-12291. [PMID: 34779447 DOI: 10.1039/d1cs00467k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In this tutorial review, we compare and contrast the chemical mechanisms of electrophile/oxidant sensing, and the molecular mechanisms of signal propagation. We critically analyze biological systems in which these different pathways are believed to be manifest and what the data really mean. Finally, we discuss applications of this knowledge to disease treatment and drug development.
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Affiliation(s)
| | - Kuan-Ting Huang
- Swiss Federal Institute of Technology in Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Yimon Aye
- Swiss Federal Institute of Technology in Lausanne (EPFL), 1015 Lausanne, Switzerland.
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24
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Kumar M, Reddy NC, Rai V. Chemical technologies for precise protein bioconjugation interfacing biology and medicine. Chem Commun (Camb) 2021; 57:7083-7095. [PMID: 34180471 DOI: 10.1039/d1cc02268g] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Proteins provide an excellent means to monitor and regulate biological processes. Hence, a precise chemical toolbox for their modification becomes indispensable. In this perspective, this feature article outlines our efforts to establish the core principles of chemoselectivity, site-selectivity, site-specificity, site-modularity, residue-modularity, and protein-specificity. With the knowledge to systematically regulate these parameters, the field has access to technological platforms that can address multiple challenges at the interface of chemistry, biology, and medicine.
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Affiliation(s)
- Mohan Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
| | - Neelesh C Reddy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
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25
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A tandem activity-based sensing and labeling strategy enables imaging of transcellular hydrogen peroxide signaling. Proc Natl Acad Sci U S A 2021; 118:2018513118. [PMID: 33622793 DOI: 10.1073/pnas.2018513118] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Reactive oxygen species (ROS) like hydrogen peroxide (H2O2) are transient species that have broad actions in signaling and stress, but spatioanatomical understanding of their biology remains insufficient. Here, we report a tandem activity-based sensing and labeling strategy for H2O2 imaging that enables capture and permanent recording of localized H2O2 fluxes. Peroxy Green-1 Fluoromethyl (PG1-FM) is a diffusible small-molecule probe that senses H2O2 by a boronate oxidation reaction to trigger dual release and covalent labeling of a fluorescent product, thus preserving spatial information on local H2O2 changes. This unique reagent enables visualization of transcellular redox signaling in a microglia-neuron coculture cell model, where selective activation of microglia for ROS production increases H2O2 in nearby neurons. In addition to identifying ROS-mediated cell-to-cell communication, this work provides a starting point for the design of chemical probes that can achieve high spatial fidelity by combining activity-based sensing and labeling strategies.
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26
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Wang H, Zhang Y, Zeng K, Qiang J, Cao Y, Li Y, Fang Y, Zhang Y, Chen Y. Selective Mitochondrial Protein Labeling Enabled by Biocompatible Photocatalytic Reactions inside Live Cells. JACS AU 2021; 1:1066-1075. [PMID: 34467350 PMCID: PMC8395695 DOI: 10.1021/jacsau.1c00172] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Indexed: 06/01/2023]
Abstract
Biocompatible reactions are powerful tools to probe protein functions in their native environment. Due to the difficulty of penetrating the live-cell membrane and the complex intracellular environment, the biocompatible reactions inside live cells are challenging, especially at the subcellular level with spatial resolution. Here we report the first biocompatible photocatalytic azide conjugation reaction inside live cells to achieve the mitochondria-selective proteins labeling. The organic dyes acridine orange, fluorescein, and rhodamine 123 were developed as the biocompatible photocatalysts for the proteins labeling with aryl azides, which yielded benzazirines and ketenimines from triplet nitrenes for the protein nucleophilic residue trapping. The photocatalytic azide conjugation reaction with rhodamine 123 selectively labeled the mitochondrial proteins via the organic dye's mitochondrial localization. In response to the mitochondrial stress induced by rotenone, this photocatalytic azide-promoted labeling method mapped the dynamic mitochondrial proteome changes with high temporal-spatial precision and identified several potential mitochondrial stress-response proteins for the first time. The high temporal-spatial precision of this photocatalytic azide-promoted labeling method holds excellent potential for intracellular protein network investigations.
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Affiliation(s)
- Haoyan Wang
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Center
for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, University of Chinese Academy
of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yixin Zhang
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Center
for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, University of Chinese Academy
of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Kaixing Zeng
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Center
for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, University of Chinese Academy
of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- School
of Physical Science and Technology, ShanghaiTech
University, 100 Haike
Road, Shanghai 201210, China
| | - Jiali Qiang
- Interdisciplinary
Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 26 Qiuyue Rd., Pudong, Shanghai 201210, China
| | - Ye Cao
- Interdisciplinary
Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 26 Qiuyue Rd., Pudong, Shanghai 201210, China
| | - Yunxia Li
- Interdisciplinary
Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 26 Qiuyue Rd., Pudong, Shanghai 201210, China
| | - Yanshan Fang
- Interdisciplinary
Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., Pudong, Shanghai 201203, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaoyang Zhang
- Interdisciplinary
Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 26 Qiuyue Rd., Pudong, Shanghai 201210, China
| | - Yiyun Chen
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Center
for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, University of Chinese Academy
of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- School
of Physical Science and Technology, ShanghaiTech
University, 100 Haike
Road, Shanghai 201210, China
- School
of
Chemistry and Material Sciences, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China
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27
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Tabish TA, Abbas A, Narayan RJ. Graphene nanocomposites for transdermal biosensing. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 13:e1699. [PMID: 33480118 DOI: 10.1002/wnan.1699] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/23/2020] [Accepted: 12/26/2020] [Indexed: 12/12/2022]
Abstract
Transdermal biosensors for the real-time and continuous detection and monitoring of target molecules represent an intriguing pathway for enhancing health outcomes in a cost-effective and non-invasive fashion. Many transdermal biosensor devices contain microneedles and other miniaturized components. There remains an unmet clinical need for microneedle transdermal biosensors to obtain a more accurate, rapid, and reliable insight into the real-time monitoring of disease. The ability to monitor biomarkers at an intradermal molecular level in a non-invasive manner remains the next technological gap to solve real-world clinical problems. The emergence of the two-dimensional material graphene with unique material properties and the ability to quantify analytes and physiological status can enable the detection of critical biomarkers indicative of human disease. The development of a user-friendly, affordable, and non-invasive transdermal biosensing device for continuous and personalized monitoring of target molecules could be beneficial for many patients. This focus article considers the use of graphene-based transdermal biosensors for health monitoring, evaluation of these sensors for glucose and hydrogen peroxide detection via in vitro, in vivo, and ex vivo studies, recent technological innovations, and potential challenges. This article is categorized under: Diagnostic Tools > Biosensing.
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Affiliation(s)
| | - Aumber Abbas
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
| | - Roger J Narayan
- Joint Department of Biomedical Engineering, University of North Carolina and North Carolina State University, Raleigh, North Carolina, USA
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28
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Mino T, Sakamoto S, Hamachi I. Recent applications of N-acyl imidazole chemistry in chemical biology. Biosci Biotechnol Biochem 2021; 85:53-60. [PMID: 33577657 DOI: 10.1093/bbb/zbaa026] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 12/26/2022]
Abstract
N-Acyl imidazoles are unique electrophiles that exhibit moderate reactivity, relatively long-half life, and high solubility in water. Thanks to their tunable reactivity and chemical selectivity, the application of N-acyl imidazole derivatives has launched to a number of chemical biology researches, which include chemical synthesis of peptide/protein, chemical labeling of native proteins of interest (POIs), and structural analysis and functional manipulation of RNAs. Since proteins and RNAs play pivotal roles in numerous biological events in all living organisms, the methods that enable the chemical modification of endogenously existing POIs and RNAs in live cells may offer a variety of opportunities not only for fundamental scientific study but also for biotechnology and drug development. In this review, we discuss the recent progress of N-acyl imidazole chemistry that contributes to the chemical labeling and functional control of endogenous proteins and RNAs under multimolecularly crowded biological conditions of live cells.
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Affiliation(s)
- Takeharu Mino
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan
| | - Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan.,ERATO, Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
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