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Ma J, Sun R, Xia K, Xia Q, Liu Y, Zhang X. Design and Application of Fluorescent Probes to Detect Cellular Physical Microenvironments. Chem Rev 2024; 124:1738-1861. [PMID: 38354333 DOI: 10.1021/acs.chemrev.3c00573] [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: 02/16/2024]
Abstract
The microenvironment is indispensable for functionality of various biomacromolecules, subcellular compartments, living cells, and organisms. In particular, physical properties within the biological microenvironment could exert profound effects on both the cellular physiology and pathology, with parameters including the polarity, viscosity, pH, and other relevant factors. There is a significant demand to directly visualize and quantitatively measure the fluctuation in the cellular microenvironment with spatiotemporal resolution. To satisfy this need, analytical methods based on fluorescence probes offer great opportunities due to the facile, sensitive, and dynamic detection that these molecules could enable in varying biological settings from in vitro samples to live animal models. Herein, we focus on various types of small molecule fluorescent probes for the detection and measurement of physical parameters of the microenvironment, including pH, polarity, viscosity, mechanical force, temperature, and electron potential. For each parameter, we primarily describe the chemical mechanisms underlying how physical properties are correlated with changes of various fluorescent signals. This review provides both an overview and a perspective for the development of small molecule fluorescent probes to visualize the dynamic changes in the cellular environment, to expand the knowledge for biological process, and to enrich diagnostic tools for human diseases.
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Affiliation(s)
- Junbao Ma
- Department of Chemistry and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310030, Zhejiang Province, China
| | - Rui Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Kaifu Xia
- Department of Chemistry and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310030, Zhejiang Province, China
| | - Qiuxuan Xia
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, Chinese Academy of Sciences Dalian Liaoning 116023, China
| | - Xin Zhang
- Department of Chemistry and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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Brown T, Nguyen T, Zhou B, Zheng YG. Chemical probes and methods for the study of protein arginine methylation. RSC Chem Biol 2023; 4:647-669. [PMID: 37654509 PMCID: PMC10467615 DOI: 10.1039/d3cb00018d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 07/28/2023] [Indexed: 09/02/2023] Open
Abstract
Protein arginine methylation is a widespread post-translational modification (PTM) in eukaryotic cells. This chemical modification in proteins functionally modulates diverse cellular processes from signal transduction, gene expression, and DNA damage repair to RNA splicing. The chemistry of arginine methylation entails the transfer of the methyl group from S-adenosyl-l-methionine (AdoMet, SAM) onto a guanidino nitrogen atom of an arginine residue of a target protein. This reaction is catalyzed by about 10 members of protein arginine methyltransferases (PRMTs). With impacts on a variety of cellular processes, aberrant expression and activity of PRMTs have been shown in many disease conditions. Particularly in oncology, PRMTs are commonly overexpressed in many cancerous tissues and positively correlated with tumor initiation, development and progression. As such, targeting PRMTs is increasingly recognized as an appealing therapeutic strategy for new drug discovery. In the past decade, a great deal of research efforts has been invested in illuminating PRMT functions in diseases and developing chemical probes for the mechanistic study of PRMTs in biological systems. In this review, we provide a brief developmental history of arginine methylation along with some key updates in arginine methylation research, with a particular emphasis on the chemical aspects of arginine methylation. We highlight the research endeavors for the development and application of chemical approaches and chemical tools for the study of functions of PRMTs and arginine methylation in regulating biology and disease.
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Affiliation(s)
- Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Terry Nguyen
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Bo Zhou
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
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Qin X, Yang X, Du L, Li M. Polarity-based fluorescence probes: properties and applications. RSC Med Chem 2021; 12:1826-1838. [PMID: 34825183 PMCID: PMC8597426 DOI: 10.1039/d1md00170a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/07/2021] [Indexed: 11/21/2022] Open
Abstract
Local polarity can affect the physical or chemical behaviors of surrounding molecules, especially in organisms. Cell polarity is the ultimate feedback of cellular status and regulation mechanisms. Hence, the abnormal alteration of polarity in organisms is closely linked with functional disorders and many diseases. It is incredibly significant to monitor and detect local polarity to explain the biological processes and diagnoses of some diseases. Because of their in vivo safe and real-time monitoring, several polarity-sensitive fluorophores and fluorescent probes have gradually emerged and been used in modern research. This review summarizes the fluorescence properties and applications of several representative polarity-sensitive fluorescent probes.
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Affiliation(s)
- Xiaojun Qin
- School of Pharmacy, Guangxi Medical University Nanning Guangxi 530021 China
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Cheeloo College of Medicine, Shandong University Jinan Shandong 250012 China
| | - Xingye Yang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Cheeloo College of Medicine, Shandong University Jinan Shandong 250012 China
| | - Lupei Du
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Cheeloo College of Medicine, Shandong University Jinan Shandong 250012 China
| | - Minyong Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Cheeloo College of Medicine, Shandong University Jinan Shandong 250012 China
- State Key Laboratory of Microbial Technology, Shandong University Jinan Shandong 250100 China
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Li X, Li X, Ma H. A near-infrared fluorescent probe reveals decreased mitochondrial polarity during mitophagy. Chem Sci 2019; 11:1617-1622. [PMID: 34084390 PMCID: PMC8148031 DOI: 10.1039/c9sc05505c] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mitophagy is a selective form of autophagy by which dysfunctional and damaged mitochondria are degraded in autolysosomes. Since defective mitophagy is closely related to various pathological processes, investigation on the detailed mitophagy process is of great importance. In this respect, disclosing the alterations of mitochondrial microenvironments is expected to be a promising way. However, an appropriate method for monitoring the fluctuations of mitochondrial polarity during mitophagy is still lacking. Here, we report a near-infrared hydroxyl-hemicyanine fluorescent probe that responds to polarity exclusively. Both the shift of emission maxima and the fluorescence intensity ratios at two different wavelengths of the probe can be applied to quantifying the polarity accurately. With ratiometric fluorescence imaging, the polarity differences of normal and cancer cells are clearly discriminated. Most importantly, the mitochondrial polarity variations during starvation and drug-induced mitophagy are determined for the first time. The observed decrease of mitochondrial polarity during mitophagy, together with the rationally designed probe, may facilitate the study on the vital role of mitophagy in physiological and pathological bioprocesses.
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Affiliation(s)
- Xiaoyi Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China .,University of Chinese Academy of Sciences Beijing 100049 China
| | - Xiaohua Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
| | - Huimin Ma
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China .,University of Chinese Academy of Sciences Beijing 100049 China
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Gong Y, Andina D, Nahar S, Leroux JC, Gauthier MA. Releasable and traceless PEGylation of arginine-rich antimicrobial peptides. Chem Sci 2017; 8:4082-4086. [PMID: 30155213 PMCID: PMC6094173 DOI: 10.1039/c7sc00770a] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/21/2017] [Indexed: 02/01/2023] Open
Abstract
This study reports a strategy to temporarily mask arginine residues within antimicrobial peptides (AMPs) with methoxy poly(ethylene glycol) (mPEG). PEGylation protects AMPs from serum proteases, and can be released at a pharmaceutically-relevant rate. Fully active and unmodified (i.e., native) AMPs are released with time.
Arginine-rich antimicrobial peptides (AMPs) are emerging therapeutics of interest. However, their applicability is limited by their short circulation half-life, caused in part by their small size and digestion by blood proteases. This study reports a strategy to temporarily mask arginine residues within AMPs with methoxy poly(ethylene glycol). Based on the reagent used, release of AMPs occurred in hours to days in a completely traceless fashion. In vitro, conjugates were insensitive to serum proteases, and released native AMP with full in vitro bioactivity. This strategy is thus highly relevant and should be adaptable to the entire family of arginine-rich AMPs. It may potentially be used to improve AMP-therapies by providing a more steady concentration of AMP in the blood after a single injection, avoiding toxic effects at high AMP doses, and reducing the number of doses required over the treatment duration.
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Affiliation(s)
- Y Gong
- Institute of Pharmaceutical Sciences , Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology Zurich (ETHZ) , Zurich 8093 , Switzerland
| | - D Andina
- Institute of Pharmaceutical Sciences , Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology Zurich (ETHZ) , Zurich 8093 , Switzerland
| | - S Nahar
- EMT Research Center , Institut National de la Recherche Scientifique (INRS) , Varennes J3X 1S2 , Canada .
| | - J-C Leroux
- Institute of Pharmaceutical Sciences , Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology Zurich (ETHZ) , Zurich 8093 , Switzerland
| | - M A Gauthier
- EMT Research Center , Institut National de la Recherche Scientifique (INRS) , Varennes J3X 1S2 , Canada .
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Thompson DA, Ng R, Dawson PE. Arginine selective reagents for ligation to peptides and proteins. J Pept Sci 2016; 22:311-9. [DOI: 10.1002/psc.2867] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Darren A. Thompson
- Department of Chemistry; The Scripps Research Institute; 10550 N. Torrey Pines Rd. San Diego CA 92037 USA
| | - Raymond Ng
- University of California, San Diego; 9500 Gilman Dr San Diego CA 92093 USA
| | - Philip E. Dawson
- Department of Chemistry; The Scripps Research Institute; 10550 N. Torrey Pines Rd. San Diego CA 92037 USA
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Gauthier MA, Klok HA. Arginine-Specific Modification of Proteins with Polyethylene Glycol. Biomacromolecules 2010; 12:482-93. [DOI: 10.1021/bm101272g] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Marc A. Gauthier
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
| | - Harm-Anton Klok
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
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Link M, Li X, Kleim J, Wolfbeis OS. Click Chemistry Based Method for the Preparation of Maleinimide-Type Thiol-Reactive Labels. European J Org Chem 2010. [DOI: 10.1002/ejoc.201001085] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Zhang TL, Han BH. The visualized polarity-sensitive magnetic nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:8893-8900. [PMID: 20143867 DOI: 10.1021/la9046512] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Three polarity-sensitive organic molecules (DIAA, DIUA, and DISA) were designed and synthesized for functionalizing high-quality superparamagnetic Fe(3)O(4) nanoparticles (NPs) via the ligand exchange strategy to prepare polarity-sensitive Fe(3)O(4) NPs. The functional group is chosen to be the carboxyl group (one for DIAA and DIUA, two for DISA) that is a universal coordinating site for iron oxide NPs. The method for binding these functional molecules onto the surface of the NPs is simple and straightforward. Among the three molecules, the DISA molecules passivate the NPs' surface most efficiently owing to their particular structure with two carboxyl groups and a general good solubility. The DISA-functionalized Fe(3)O(4) NPs (DISA-Fe(3)O(4) NPs) display distinctly different fluorescence emissions in various solvents of different polarities with the magnetism well preserving. The prepared polarity-sensitive Fe(3)O(4) NPs that are dual functional can be used as a visualized polarity sensor and perform NPs' superparamagnetic properties simultaneously. It also provides a conceptual design for preparing the polarity-sensitive nanomaterials with multifunction.
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Affiliation(s)
- Tian-Long Zhang
- National Center for Nanoscience and Technology, Beijing 100190, China
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Jia J, Chen W, Ma H, Wang K, Zhao C. Use of a rhodamine-based bifunctional probe in N-terminal specific labeling of Thermomyces lanuginosus xylanase. MOLECULAR BIOSYSTEMS 2010; 6:1829-33. [DOI: 10.1039/c005223j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Wang S, Chen S, Ma H. Analysis of local structure of Arg10 domain in apo-α-lactalbumin with a polarity-sensitive arginine-specific fluorescent probe. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s11426-009-0027-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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