1
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Datta A, Ritu, Kumar S, Chorol S, Mukhopadhyay P, Jain N. Oxidative Organic Transformations Photocatalyzed by NDI in Visible Light. Org Lett 2024; 26:7357-7362. [PMID: 39186013 DOI: 10.1021/acs.orglett.4c02558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
In this work, we report the synthesis and photocatalytic properties of N,N-bis(n-hexyl)-2-bromo-6-(n-hexylamino)-1,4,5,8-naphthalenetetracarboxylic diimide photocatalyst, NDI-PC, in visible light. In the presence of air or oxidant, NDI-PC efficiently enables multiple photooxygenations of isoquinolines, thiocyanation of phenylimidazopyridines, functionalization of quinolinones by allowing regioselective installation of an SCN, SeCN, SPh, SePh, Cl, Br, or I group at the C-3 position, and isomerization of alkenes. Mechanistic investigations suggest an oxidative photoredox process for oxygenation and C-H functionalization, while isomerization is believed to proceed through a photosensitization pathway.
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Affiliation(s)
- Anirban Datta
- Department of Chemistry, Indian Institution of Technology Delhi, Delhi-110016, India
| | - Ritu
- Department of Chemistry, Indian Institution of Technology Delhi, Delhi-110016, India
| | - Sharvan Kumar
- Department of Chemistry, Indian Institution of Technology Delhi, Delhi-110016, India
| | - Sonam Chorol
- School of Physical Sciences, Jawaharlal Nehru University, Delhi-110067, India
| | - Pritam Mukhopadhyay
- School of Physical Sciences, Jawaharlal Nehru University, Delhi-110067, India
| | - Nidhi Jain
- Department of Chemistry, Indian Institution of Technology Delhi, Delhi-110016, India
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2
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Shidara H, Shirai T, Ozaki-Noma R, Jitsuki S, Nagai T, Takemoto K. Optical inactivation of intracellular molecules by fast-maturating photosensitizing fluorescence protein, HyperNova. Commun Biol 2024; 7:945. [PMID: 39107369 PMCID: PMC11303530 DOI: 10.1038/s42003-024-06583-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 07/14/2024] [Indexed: 08/10/2024] Open
Abstract
Photosensitizing fluorescence protein is a promising tool for chromophore-assisted light inactivation (CALI) that enables specific oxidation and inactivation of intracellular molecules. However, a commonly used monomeric photosensitizing fluorescent protein, SuperNova, shows a low CALI efficiency due to its insufficient maturation at 37 °C, thereby limiting the application of CALI to various molecules, especially in mammalian cells. Here, we present a photosensitizing fluorescence protein, HyperNova, with markedly improved maturation at 37 °C, leading to greatly enhanced CALI efficiency. Exploiting this quality, HyperNova enables the application of CALI to variety of molecules such as a mitotic kinase and transcriptional factors that were highly challenging with conventional SuperNova. To further demonstrate the utility of HyperNova, we have also succeeded in developing novel CALI techniques for MAP kinases by HyperNova. Our findings suggest that HyperNova has the potential to expand the molecular toolbox for manipulating biological events in living cells, providing new avenues for investigating cellular signaling pathways.
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Affiliation(s)
- Hisashi Shidara
- Department of Biochemistry, Mie University Graduate School of Medicine, Mie, 514-8507, Japan
| | - Taku Shirai
- Department of Biochemistry, Mie University Graduate School of Medicine, Mie, 514-8507, Japan
| | | | - Susumu Jitsuki
- Department of Biochemistry, Mie University Graduate School of Medicine, Mie, 514-8507, Japan
| | - Takeharu Nagai
- SANKEN, Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Kiwamu Takemoto
- Department of Biochemistry, Mie University Graduate School of Medicine, Mie, 514-8507, Japan.
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3
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Zhou L, Na J, Liu X, Wu P. Chromophore-Assisted Light Inactivation for Protein Degradation and Its Application in Biomedicine. Bioengineering (Basel) 2024; 11:651. [PMID: 39061733 PMCID: PMC11273424 DOI: 10.3390/bioengineering11070651] [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: 04/25/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
The functional investigation of proteins holds immense significance in unraveling physiological and pathological mechanisms of organisms as well as advancing the development of novel pharmaceuticals in biomedicine. However, the study of cellular protein function using conventional genetic manipulation methods may yield unpredictable outcomes and erroneous conclusions. Therefore, precise modulation of protein activity within cells holds immense significance in the realm of biomedical research. Chromophore-assisted light inactivation (CALI) is a technique that labels photosensitizers onto target proteins and induces the production of reactive oxygen species through light control to achieve precise inactivation of target proteins. Based on the type and characteristics of photosensitizers, different excitation light sources and labeling methods are selected. For instance, KillerRed forms a fusion protein with the target protein through genetic engineering for labeling and inactivates the target protein via light activation. CALI is presently predominantly employed in diverse biomedical domains encompassing investigations into protein functionality and interaction, intercellular signal transduction research, as well as cancer exploration and therapy. With the continuous advancement of CALI technology, it is anticipated to emerge as a formidable instrument in the realm of life sciences, yielding more captivating outcomes for fundamental life sciences and precise disease diagnosis and treatment.
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Affiliation(s)
- Lvjia Zhou
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China; (L.Z.); (J.N.)
| | - Jintong Na
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China; (L.Z.); (J.N.)
| | - Xiyu Liu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China; (L.Z.); (J.N.)
| | - Pan Wu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China; (L.Z.); (J.N.)
- School of Pharmacy, Guangxi Medical University, Nanning 530021, China
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4
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Shidara H, Jitsuki S, Takemoto K. Chromophore-assisted light inactivation of target proteins for singularity biology. Biophys Physicobiol 2024; 21:e211009. [PMID: 39175862 PMCID: PMC11338683 DOI: 10.2142/biophysico.bppb-v21.s009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 02/13/2024] [Indexed: 08/24/2024] Open
Abstract
Singularity phenomena are rare events that occur only with a probability of one in tens of thousands and yet play an important role in the fate of the entire system. Recently, an ultra-wide-field microscopy imaging systems, AMATERAS, have been developed to reliably capture singularity phenomena. However, to determine whether a rare phenomenon captured by microscopy is a true singularity phenomenon-one with a significant impact on the entire system-, causal analysis is required. In this section, we introduce the CALI method, which uses light to inactivate molecules as one of the techniques enabling causal analysis. In addition, we discuss the technical innovations of the CALI method that are required to contribute to the future development of singularity biology.
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Affiliation(s)
- Hisashi Shidara
- Department of Biochemistry, Mie University Graduate School of Medicine, Mie 514-8507, Japan
| | - Susumu Jitsuki
- Department of Biochemistry, Mie University Graduate School of Medicine, Mie 514-8507, Japan
| | - Kiwamu Takemoto
- Department of Biochemistry, Mie University Graduate School of Medicine, Mie 514-8507, Japan
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5
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A multifunctional peroxidase-based reaction for imaging, sensing and networking of spatial biology. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119428. [PMID: 36610614 DOI: 10.1016/j.bbamcr.2022.119428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023]
Abstract
Peroxidase is a heme-containing enzyme that reduces hydrogen peroxide to water by extracting electron(s) from aromatic compounds via a sequential turnover reaction. This reaction can generate various aromatic radicals in the form of short-lived "spray" molecules. These can be either covalently attached to proximal proteins or polymerized via radical-radical coupling. Recent studies have shown that these peroxidase-generated radicals can be utilized as effective tools for spatial research in biological systems, including imaging studies aimed at the spatial localization of proteins using electron microscopy, spatial proteome mapping, and spatial sensing of metabolites (e.g., heme and hydrogen peroxide). This review may facilitate the wider utilization of these peroxidase-based methods for spatial discovery in cellular biology.
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6
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Chen Z, Zhao Y, Liu Y. Advanced Strategies in Enzyme Activity Regulation for Biomedical Applications. Chembiochem 2022; 23:e202200358. [PMID: 35896516 DOI: 10.1002/cbic.202200358] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/25/2022] [Indexed: 11/06/2022]
Abstract
Enzymes are important macromolecular biocatalysts that accelerate chemical and biochemical reactions in living organisms. Most human diseases are related to alterations in enzyme activity. Moreover, enzymes are potential therapeutic tools for treating different diseases, such as cancer, infections, and cardiovascular and cerebrovascular diseases. Precise remote enzyme activity regulation provides new opportunities to combat diseases. This review summarizes recent advances in the field of enzyme activity regulation, including reversible and irreversible regulation. It also discusses the mechanisms and approaches for on-demand control of these activities. Furthermore, a range of stimulus-responsive inhibitors, polymers, and nanoparticles for regulating enzyme activity and their prospective biomedical applications are summarized. Finally, the current challenges and future perspectives on enzyme activity regulation are discussed.
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Affiliation(s)
- Zihan Chen
- Nankai University, College of Chemistry, Tianjin, CHINA
| | - Yu Zhao
- Nankai University, College of Chemistry, Tianjin, CHINA
| | - Yang Liu
- Nankai University, College of Chemistry, 94 Weijin Rd., Mengminwei Bldg 412, 300071, Tianjin, CHINA
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7
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Aerssens D, Cadoni E, Tack L, Madder A. A Photosensitized Singlet Oxygen ( 1O 2) Toolbox for Bio-Organic Applications: Tailoring 1O 2 Generation for DNA and Protein Labelling, Targeting and Biosensing. Molecules 2022; 27:778. [PMID: 35164045 PMCID: PMC8838016 DOI: 10.3390/molecules27030778] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/17/2022] Open
Abstract
Singlet oxygen (1O2) is the excited state of ground, triplet state, molecular oxygen (O2). Photosensitized 1O2 has been extensively studied as one of the reactive oxygen species (ROS), responsible for damage of cellular components (protein, DNA, lipids). On the other hand, its generation has been exploited in organic synthesis, as well as in photodynamic therapy for the treatment of various forms of cancer. The aim of this review is to highlight the versatility of 1O2, discussing the main bioorganic applications reported over the past decades, which rely on its production. After a brief introduction on the photosensitized production of 1O2, we will describe the main aspects involving the biologically relevant damage that can accompany an uncontrolled, aspecific generation of this ROS. We then discuss in more detail a series of biological applications featuring 1O2 generation, including protein and DNA labelling, cross-linking and biosensing. Finally, we will highlight the methodologies available to tailor 1O2 generation, in order to accomplish the proposed bioorganic transformations while avoiding, at the same time, collateral damage related to an untamed production of this reactive species.
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Affiliation(s)
| | | | | | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium; (D.A.); (E.C.); (L.T.)
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8
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Hao L, Wang J, Pan ZY, Mao ZW, Tan CP. Photodegradation of carbonic anhydrase IX via a binding-enhanced ruthenium-based photosensitizer. Chem Commun (Camb) 2022; 58:8069-8072. [DOI: 10.1039/d2cc02337g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A binding-enhanced ruthenium-based photosensitizer is reported for photodegradation of carbonic anhydrase IX.
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Affiliation(s)
- Liang Hao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Jie Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Zheng-Yin Pan
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Cai-Ping Tan
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
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9
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Takemoto K. [Optical inactivation of molecular functions in vivo by chromophore-assisted light inactivation]. Nihon Yakurigaku Zasshi 2022; 157:238-243. [PMID: 35781452 DOI: 10.1254/fpj.22009] [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: 06/15/2023]
Abstract
Many biological phenomena have spatio-temporal characteristics, such as the expression of molecular activity locally or at a limited time. Such phenomena have been observed in various organisms from slime mold to mammals, and are considered to be one of the basic patterns in biological reactions. Live imaging studies using the fluorescent protein GFP and fluorescence microscopy have become a standard technique in the life sciences to reveal the dynamics of these characteristic biological phenomena. On the other hand, the characteristic behaviors of molecules and cells captured by microscopy only correlate with life phenomena, and the causal relationship of whether they really matter is unknown. It is unclear whether they are really important or not. Therefore, to elucidate their physiological significance, it is important to introduce spatiotemporal manipulation techniques to manipulate molecules and cells locally and at arbitrary timing, and to perform causal analysis in vivo. The chromophore-assisted light inactivation (CALI) method, which uses light to inactivate molecular functions, is an optical technology that enables such spatiotemporal manipulation, and has recently been used in vivo in various model organisms, attracting widespread attention. In this section, we will review the principle of the CALI method, actual research examples, in particular, its in vivo application, and future prospects.
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Affiliation(s)
- Kiwamu Takemoto
- Department of Biochemistry, Mie University, Graduate School of Medicine
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10
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Courtney TM, Hankinson CP, Horst TJ, Deiters A. Targeted protein oxidation using a chromophore-modified rapamycin analog. Chem Sci 2021; 12:13425-13433. [PMID: 34777761 PMCID: PMC8528027 DOI: 10.1039/d1sc04464h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 08/30/2021] [Indexed: 01/23/2023] Open
Abstract
Chemically induced dimerization of FKBP and FRB using rapamycin and rapamycin analogs has been utilized in a variety of biological applications. Formation of the FKBP-rapamycin-FRB ternary complex is typically used to activate a biological process and this interaction has proven to be essentially irreversible. In many cases, it would be beneficial to also have temporal control over deactivating a biological process once it has been initiated. Thus, we developed the first reactive oxygen species-generating rapamycin analog toward this goal. The BODIPY-rapamycin analog BORap is capable of dimerizing FKBP and FRB to form a ternary complex, and upon irradiation with 530 nm light, generates singlet oxygen to oxidize and inactivate proteins of interest fused to FKBP/FRB.
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Affiliation(s)
- Taylor M Courtney
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
| | | | - Trevor J Horst
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
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11
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Wavreil FDM, Poon J, Wessel GM, Yajima M. Light-induced, spatiotemporal control of protein in the developing embryo of the sea urchin. Dev Biol 2021; 478:13-24. [PMID: 34147471 DOI: 10.1016/j.ydbio.2021.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/10/2021] [Accepted: 06/12/2021] [Indexed: 11/18/2022]
Abstract
Differential protein regulation is a critical biological process that regulates cellular activity and controls cell fate determination. It is especially important during early embryogenesis when post-transcriptional events predominate differential fate specification in many organisms. Light-induced approaches have been a powerful technology to interrogate protein functions with temporal and spatial precision, even at subcellular levels within a cell by controlling laser irradiation on the confocal microscope. However, application and efficacy of these tools need to be tested for each model system or for the cell type of interest because of the complex nature of each system. Here, we introduce two types of light-induced approaches to track and control proteins at a subcellular level in the developing embryo of the sea urchin. We found that the photoconvertible fluorescent protein Kaede is highly efficient to distinguish pre-existing and newly synthesized proteins with no apparent phototoxicity, even when interrogating proteins associated with the mitotic spindle. Further, chromophore-assisted light inactivation (CALI) using miniSOG successfully inactivated target proteins of interest in the vegetal cortex and selectively delayed or inhibited asymmetric cell division. Overall, these light-induced manipulations serve as important molecular tools to identify protein function for for subcellular interrogations in developing embryos.
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Affiliation(s)
- Florence D M Wavreil
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI, 02912, USA
| | - Jessica Poon
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI, 02912, USA
| | - Gary M Wessel
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI, 02912, USA
| | - Mamiko Yajima
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI, 02912, USA.
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12
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TAKEMOTO K. Optical manipulation of molecular function by chromophore-assisted light inactivation. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2021; 97:197-209. [PMID: 33840676 PMCID: PMC8062263 DOI: 10.2183/pjab.97.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
In addition to simple on/off switches for molecular activity, spatiotemporal dynamics are also thought to be important for the regulation of cellular function. However, their physiological significance and in vivo importance remain largely unknown. Fluorescence imaging technology is a powerful technique that can reveal the spatiotemporal dynamics of molecular activity. In addition, because imaging detects the correlations between molecular activity and biological phenomena, the technique of molecular manipulation is also important to analyze causal relationships. Recent advances in optical manipulation techniques that artificially perturb molecules and cells via light can address this issue to elucidate the causality between manipulated target and its physiological function. The use of light enables the manipulation of molecular activity in microspaces, such as organelles and nerve spines. In this review, we describe the chromophore-assisted light inactivation method, which is an optical manipulation technique that has been attracting attention in recent years.
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Affiliation(s)
- Kiwamu TAKEMOTO
- Department of Biochemistry, Mie University, Graduate School of Medicine, Tsu-City, Mie, Japan
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13
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Genetically Encoded Photosensitizer for Destruction of Protein or Cell Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:265-279. [PMID: 33398819 DOI: 10.1007/978-981-15-8763-4_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There are several paths when excited molecules return to the ground state. In the case of fluorescent molecules, the dominant path is fluorescence emission that is greatly contributing to bioimaging. Meanwhile, photosensitizers transfer electron or energy from chromophore to the surrounding molecules, including molecular oxygen. Generated reactive oxygen species has potency to attack other molecules by oxidation. In this chapter, we introduce the chromophore-assisted light inactivation (CALI) method using a photosensitizer to inactivate proteins in a spatiotemporal manner and development of CALI tools, which is useful for investigation of protein functions and dynamics, by inactivation of the target molecules. Moreover, photosensitizers with high efficiency make it possible optogenetic control of cell ablation in living organisms and photodynamic therapy. Further development of photosensitizers with different excitation wavelengths will contribute to the investigation of multiple proteins or cell functions through inactivation in the different positions and timings.
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14
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Macias‐Contreras M, Zhu L. The Collective Power of Genetically Encoded Protein/Peptide Tags and Bioorthogonal Chemistry in Biological Fluorescence Imaging. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Miguel Macias‐Contreras
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
| | - Lei Zhu
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
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15
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Binns TC, Ayala AX, Grimm JB, Tkachuk AN, Castillon GA, Phan S, Zhang L, Brown TA, Liu Z, Adams SR, Ellisman MH, Koyama M, Lavis LD. Rational Design of Bioavailable Photosensitizers for Manipulation and Imaging of Biological Systems. Cell Chem Biol 2020; 27:1063-1072.e7. [PMID: 32698018 PMCID: PMC7483975 DOI: 10.1016/j.chembiol.2020.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/04/2020] [Accepted: 06/29/2020] [Indexed: 01/14/2023]
Abstract
Light-mediated chemical reactions are powerful methods for manipulating and interrogating biological systems. Photosensitizers, compounds that generate reactive oxygen species upon excitation with light, can be utilized for numerous biological experiments, but the repertoire of bioavailable photosensitizers is limited. Here, we describe the synthesis, characterization, and utility of two photosensitizers based upon the widely used rhodamine scaffold and demonstrate their efficacy for chromophore-assisted light inactivation, cell ablation in culture and in vivo, and photopolymerization of diaminobenzidine for electron microscopy. These chemical tools will facilitate a broad range of applications spanning from targeted destruction of proteins to high-resolution imaging.
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Affiliation(s)
- Thomas C Binns
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Graduate School, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Anthony X Ayala
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ariana N Tkachuk
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Guillaume A Castillon
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Sebastien Phan
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Lixia Zhang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Timothy A Brown
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Stephen R Adams
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - Mark H Ellisman
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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16
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Chiba M, Kamiya M, Tsuda-Sakurai K, Fujisawa Y, Kosakamoto H, Kojima R, Miura M, Urano Y. Activatable Photosensitizer for Targeted Ablation of lacZ-Positive Cells with Single-Cell Resolution. ACS CENTRAL SCIENCE 2019; 5:1676-1681. [PMID: 31660435 PMCID: PMC6813548 DOI: 10.1021/acscentsci.9b00678] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Indexed: 05/08/2023]
Abstract
To achieve highly selective ablation of lacZ-positive cells in a biological milieu in vivo, we developed an activatable photosensitizer, SPiDER-killer-βGal, targeted to β-galactosidase encoded by the lacZ reporter gene. Hydrolysis of SPiDER-killer-βGal by β-galactosidase simultaneously activates both its photosensitizing ability and its reactivity to nucleophiles, so that the phototoxic products generated by light irradiation are trapped inside the lacZ-positive cells. The combination of SPiDER-killer-βGal and light irradiation specifically killed lacZ-positive cells in coculture with cells without lacZ expression. Furthermore, β-galactosidase-expressing cells in the posterior region of cultured Drosophila wing discs and in pupal notum of live Drosophila pupae were selectively killed with single-cell resolution. This photosensitizer should be useful for specific ablation of targeted cells in living organisms, for example, to investigate cellular functions in complex networks.
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Affiliation(s)
- Mayumi Chiba
- Graduate
School of Medicine and Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mako Kamiya
- Graduate
School of Medicine and Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- PRESTO,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- E-mail:
| | - Kayoko Tsuda-Sakurai
- Graduate
School of Medicine and Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuya Fujisawa
- Graduate
School of Medicine and Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hina Kosakamoto
- Graduate
School of Medicine and Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryosuke Kojima
- Graduate
School of Medicine and Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- PRESTO,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Masayuki Miura
- Graduate
School of Medicine and Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasuteru Urano
- Graduate
School of Medicine and Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- CREST,
Japan Agency for Medical Research and Development (AMED), 1-7-1 Otemachi,
Chiyoda-ku, Tokyo 100-0004, Japan
- E-mail:
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17
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Trauner D, Morstein J. Fixing a Photosensitizer Unlocks and Localizes Its Lethality. ACS CENTRAL SCIENCE 2019; 5:1636-1638. [PMID: 31660430 PMCID: PMC6813549 DOI: 10.1021/acscentsci.9b00887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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18
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Claaßen C, Gerlach T, Rother D. Stimulus-Responsive Regulation of Enzyme Activity for One-Step and Multi-Step Syntheses. Adv Synth Catal 2019; 361:2387-2401. [PMID: 31244574 PMCID: PMC6582597 DOI: 10.1002/adsc.201900169] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/25/2019] [Indexed: 01/20/2023]
Abstract
Multi-step biocatalytic reactions have gained increasing importance in recent years because the combination of different enzymes enables the synthesis of a broad variety of industrially relevant products. However, the more enzymes combined, the more crucial it is to avoid cross-reactivity in these cascade reactions and thus achieve high product yields and high purities. The selective control of enzyme activity, i.e., remote on-/off-switching of enzymes, might be a suitable tool to avoid the formation of unwanted by-products in multi-enzyme reactions. This review compiles a range of methods that are known to modulate enzyme activity in a stimulus-responsive manner. It focuses predominantly on in vitro systems and is subdivided into reversible and irreversible enzyme activity control. Furthermore, a discussion section provides indications as to which factors should be considered when designing and choosing activity control systems for biocatalysis. Finally, an outlook is given regarding the future prospects of the field.
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Affiliation(s)
- Christiane Claaßen
- Institute of Bio- and Geosciences – Biotechnology (IBG-1)Forschungszentrum Jülich GmbH52425JülichGermany
| | - Tim Gerlach
- Institute of Bio- and Geosciences – Biotechnology (IBG-1)Forschungszentrum Jülich GmbH52425JülichGermany
- Aachen Biology and Biotechnology (ABBt)RWTH Aachen University52074AachenGermany
| | - Dörte Rother
- Institute of Bio- and Geosciences – Biotechnology (IBG-1)Forschungszentrum Jülich GmbH52425JülichGermany
- Aachen Biology and Biotechnology (ABBt)RWTH Aachen University52074AachenGermany
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19
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Xiong Y, Tian X, Ai HW. Molecular Tools to Generate Reactive Oxygen Species in Biological Systems. Bioconjug Chem 2019; 30:1297-1303. [PMID: 30986044 DOI: 10.1021/acs.bioconjchem.9b00191] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Reactive oxygen species (ROS) not only are byproducts of aerobic respiration, but also play vital roles in metabolism regulation and signal transductions. It is important to understand the functions of ROS in biological systems. In addition, scientists have made use of ROS to kill bacteria and tumors through a process known as photodynamic therapy (PDT). This paper provides a concise review of current molecular tools that can generate ROS in biological systems via either nongenetic or genetically encoded way. Challenges and perspectives are further discussed with the hope of broadening the applications of ROS generators in research and clinical settings.
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Affiliation(s)
- Ying Xiong
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, Department of Chemistry, and the UVA Cancer Center , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , Virginia 22908 , United States
| | - Xiaodong Tian
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, Department of Chemistry, and the UVA Cancer Center , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , Virginia 22908 , United States
| | - Hui-Wang Ai
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, Department of Chemistry, and the UVA Cancer Center , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , Virginia 22908 , United States
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20
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Riani YD, Matsuda T, Takemoto K, Nagai T. Green monomeric photosensitizing fluorescent protein for photo-inducible protein inactivation and cell ablation. BMC Biol 2018; 16:50. [PMID: 29712573 PMCID: PMC5928576 DOI: 10.1186/s12915-018-0514-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/06/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Photosensitizing fluorescent proteins, which generate reactive oxygen species (ROS) upon light irradiation, are useful for spatiotemporal protein inactivation and cell ablation. They give us clues about protein function, intracellular signaling pathways and intercellular interactions. Since ROS generation of a photosensitizer is specifically controlled by certain excitation wavelengths, utilizing colour variants of photosensitizing protein would allow multi-spatiotemporal control of inactivation. To expand the colour palette of photosensitizing protein, here we developed SuperNova Green from its red predecessor, SuperNova. RESULTS SuperNova Green is able to produce ROS spatiotemporally upon blue light irradiation. Based on protein characterization, SuperNova Green produces insignificant amounts of singlet oxygen and predominantly produces superoxide and its derivatives. We utilized SuperNova Green to specifically inactivate the pleckstrin homology domain of phospholipase C-δ1 and to ablate cancer cells in vitro. As a proof of concept for multi-spatiotemporal control of inactivation, we demonstrate that SuperNova Green can be used with its red variant, SuperNova, to perform independent protein inactivation or cell ablation studies in a spatiotemporal manner by selective light irradiation. CONCLUSION Development of SuperNova Green has expanded the photosensitizing protein toolbox to optogenetically control protein inactivation and cell ablation.
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Affiliation(s)
- Yemima Dani Riani
- Graduate School of Engineering, Osaka University, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Tomoki Matsuda
- Graduate School of Engineering, Osaka University, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan.,The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Osaka, Ibaraki, 567-0047, Japan
| | - Kiwamu Takemoto
- Graduate School of Medicine, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, 236-0027, Japan
| | - Takeharu Nagai
- Graduate School of Engineering, Osaka University, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan. .,The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Osaka, Ibaraki, 567-0047, Japan.
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21
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Bourke AM, Bowen AB, Kennedy MJ. New approaches for solving old problems in neuronal protein trafficking. Mol Cell Neurosci 2018; 91:48-66. [PMID: 29649542 DOI: 10.1016/j.mcn.2018.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 11/16/2022] Open
Abstract
Fundamental cellular properties are determined by the repertoire and abundance of proteins displayed on the cell surface. As such, the trafficking mechanisms for establishing and maintaining the surface proteome must be tightly regulated for cells to respond appropriately to extracellular cues, yet plastic enough to adapt to ever-changing environments. Not only are the identity and abundance of surface proteins critical, but in many cases, their regulated spatial positioning within surface nanodomains can greatly impact their function. In the context of neuronal cell biology, surface levels and positioning of ion channels and neurotransmitter receptors play essential roles in establishing important properties, including cellular excitability and synaptic strength. Here we review our current understanding of the trafficking pathways that control the abundance and localization of proteins important for synaptic function and plasticity, as well as recent technological advances that are allowing the field to investigate protein trafficking with increasing spatiotemporal precision.
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Affiliation(s)
- Ashley M Bourke
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Aaron B Bowen
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Matthew J Kennedy
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, United States.
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22
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemical Control of Biological Processes in Cells and Animals. Angew Chem Int Ed Engl 2018; 57:2768-2798. [PMID: 28521066 PMCID: PMC6026863 DOI: 10.1002/anie.201700171] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/06/2017] [Indexed: 12/13/2022]
Abstract
Biological processes are naturally regulated with high spatial and temporal control, as is perhaps most evident in metazoan embryogenesis. Chemical tools have been extensively utilized in cell and developmental biology to investigate cellular processes, and conditional control methods have expanded applications of these technologies toward resolving complex biological questions. Light represents an excellent external trigger since it can be controlled with very high spatial and temporal precision. To this end, several optically regulated tools have been developed and applied to living systems. In this review we discuss recent developments of optochemical tools, including small molecules, peptides, proteins, and nucleic acids that can be irreversibly or reversibly controlled through light irradiation, with a focus on applications in cells and animals.
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Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Taylor Courtney
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Yuta Naro
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
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23
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemische Steuerung biologischer Vorgänge in Zellen und Tieren. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201700171] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Taylor Courtney
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Yuta Naro
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Alexander Deiters
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
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24
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Jung HS, Han J, Shi H, Koo S, Singh H, Kim HJ, Sessler JL, Lee JY, Kim JH, Kim JS. Overcoming the Limits of Hypoxia in Photodynamic Therapy: A Carbonic Anhydrase IX-Targeted Approach. J Am Chem Soc 2017; 139:7595-7602. [PMID: 28459562 DOI: 10.1021/jacs.7b02396] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A major challenge in photodynamic cancer therapy (PDT) is avoiding PDT-induced hypoxia, which can lead to cancer recurrence and progression through activation of various angiogenic factors and significantly reduce treatment outcomes. Reported here is an acetazolamide (AZ)-conjugated BODIPY photosensitizer (AZ-BPS) designed to mitigate the effects of PDT-based hypoxia by combining the benefits of anti-angiogenesis therapy with PDT. AZ-BPS showed specific affinity to aggressive cancer cells (MDA-MB-231 cells) that overexpress carbonic anhydrase IX (CAIX). It displayed enhanced photocytotoxicity compared to a reference compound, BPS, which is an analogous PDT agent that lacks an acetazolamide unit. AZ-BPS also displayed an enhanced in vivo efficacy in a xenograft mouse tumor regrowth model relative to BPS, an effect attributed to inhibition of tumor angiogenesis by both PDT-induced ROS generation and CAIX knockdown. AZ-BPS was evaluated successfully in clinical samples collected from breast cancer patients. We thus believe that the combined approach described here represents an attractive therapeutic approach to targeting CAIX-overexpressing tumors.
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Affiliation(s)
- Hyo Sung Jung
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712-1224, United States
| | - Jiyou Han
- Department of Biological Sciences, Laboratory of Stem Cell Research and Biotechnology, Hyupsung University , Hwasung-si 18330, Korea
| | - Hu Shi
- Department of Chemistry, Sungkyunkwan University , Suwon 440-746, Korea
| | | | | | | | - Jonathan L Sessler
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712-1224, United States
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University , Suwon 440-746, Korea
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25
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Long MJC, Poganik JR, Ghosh S, Aye Y. Subcellular Redox Targeting: Bridging in Vitro and in Vivo Chemical Biology. ACS Chem Biol 2017; 12:586-600. [PMID: 28068059 DOI: 10.1021/acschembio.6b01148] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Networks of redox sensor proteins within discrete microdomains regulate the flow of redox signaling. Yet, the inherent reactivity of redox signals complicates the study of specific redox events and pathways by traditional methods. Herein, we review designer chemistries capable of measuring flux and/or mimicking subcellular redox signaling at the cellular and organismal level. Such efforts have begun to decipher the logic underlying organelle-, site-, and target-specific redox signaling in vitro and in vivo. These data highlight chemical biology as a perfect gateway to interrogate how nature choreographs subcellular redox chemistry to drive precision redox biology.
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Affiliation(s)
- Marcus J. C. Long
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Jesse R. Poganik
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Souradyuti Ghosh
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Yimon Aye
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, United States
- Department
of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
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26
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Souslova EA, Mironova KE, Deyev SM. Applications of genetically encoded photosensitizer miniSOG: from correlative light electron microscopy to immunophotosensitizing. JOURNAL OF BIOPHOTONICS 2017; 10:338-352. [PMID: 27435584 DOI: 10.1002/jbio.201600120] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 06/06/2023]
Abstract
Genetically encoded photosensitizers (PSs), e.g. ROS generating proteins, correspond to a novel class of PSs that are highly desirable for biological and medical applications since they can be used in combination with a variety of genetic engineering manipulations allowing for precise spatio-temporal control of ROS production within living cells and organisms. In contrast to the commonly used chemical PSs, they can be modified using genetic engineering approaches and targeted to particular cellular compartments and cell types. Mini Singlet Oxygen Generator (miniSOG), a small flavoprotein capable of singlet oxygen production upon blue light irradiation, was initially reported as a high contrast probe for correlative light electron microscopy (CLEM) without the need of exogenous ligands, probes or destructive permeabilizing detergents. Further miniSOG was successfully applied for chromophore-assisted light inactivation (CALI) of proteins, as well as for photo-induced cell ablation in tissue cultures and in Caenorhabditis elegans. Finally, a novel approach of immunophotosensitizing has been developed, exploiting the specificity of mini-antibodies or selective scaffold proteins and photo-induced cytotoxicity of miniSOG, which is particularly promising for selective non-invasive photodynamic therapy of cancer (PDT) due to the spatial selectivity and locality of destructive action compared to other methods of oncotherapy.
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Affiliation(s)
- Ekaterina A Souslova
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences (IBCH RAS), Miklukho-Maklaya str. 16/10, Moscow, 117997, Russia
| | - Kristina E Mironova
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences (IBCH RAS), Miklukho-Maklaya str. 16/10, Moscow, 117997, Russia
| | - Sergey M Deyev
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences (IBCH RAS), Miklukho-Maklaya str. 16/10, Moscow, 117997, Russia
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27
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Optical inactivation of synaptic AMPA receptors erases fear memory. Nat Biotechnol 2016; 35:38-47. [DOI: 10.1038/nbt.3710] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/26/2016] [Indexed: 12/14/2022]
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28
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Zhao L, Zhang J, Xu H, Geng H, Cheng Y. Conjugated Polymers/DNA Hybrid Materials for Protein Inactivation. ACS APPLIED MATERIALS & INTERFACES 2016; 8:22923-22929. [PMID: 27533365 DOI: 10.1021/acsami.6b07803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Chromophore-assisted light inactivation (CALI) is a powerful tool for analyzing protein functions due to the high degree of spatial and temporal resolution. In this work, we demonstrate a CALI approach based on conjugated polymers (CPs)/DNA hybrid material for protein inactivation. The target protein is conjugated with single-stranded DNA in advance. Single-stranded DNA can form CPs/DNA hybrid material with cationic CPs via electrostatic and hydrophobic interactions. Through the formation of CPs/DNA hybrid material, the target protein that is conjugated with DNA is brought into close proximity to CPs. Under irradiation, CPs harvest light and generate reactive oxygen species (ROS), resulting in the inactivation of the adjacent target protein. This approach can efficiently inactivate any target protein which is conjugated with DNA and has good specificity and universality, providing a new strategy for studies of protein function and adjustment of protein activity.
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Affiliation(s)
- Likun Zhao
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Hebei University , Baoding 071002, Hebei, P. R. China
| | - Jiangyan Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Hebei University , Baoding 071002, Hebei, P. R. China
| | - Huiming Xu
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Hebei University , Baoding 071002, Hebei, P. R. China
| | - Hao Geng
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Hebei University , Baoding 071002, Hebei, P. R. China
| | - Yongqiang Cheng
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Hebei University , Baoding 071002, Hebei, P. R. China
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29
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Lee H, Oh WC, Seong J, Kim J. Advanced Fluorescence Protein-Based Synapse-Detectors. Front Synaptic Neurosci 2016; 8:16. [PMID: 27445785 PMCID: PMC4927625 DOI: 10.3389/fnsyn.2016.00016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/13/2016] [Indexed: 11/13/2022] Open
Abstract
The complex information-processing capabilities of the central nervous system emerge from intricate patterns of synaptic input-output relationships among various neuronal circuit components. Understanding these capabilities thus requires a precise description of the individual synapses that comprise neural networks. Recent advances in fluorescent protein engineering, along with developments in light-favoring tissue clearing and optical imaging techniques, have rendered light microscopy (LM) a potent candidate for large-scale analyses of synapses, their properties, and their connectivity. Optically imaging newly engineered fluorescent proteins (FPs) tagged to synaptic proteins or microstructures enables the efficient, fine-resolution illumination of synaptic anatomy and function in large neural circuits. Here we review the latest progress in fluorescent protein-based molecular tools for imaging individual synapses and synaptic connectivity. We also identify associated technologies in gene delivery, tissue processing, and computational image analysis that will play a crucial role in bridging the gap between synapse- and system-level neuroscience.
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Affiliation(s)
- Hojin Lee
- Center for Functional Connectomics, Korea Institute of Science and TechnologySeoul, South Korea; Neuroscience Program, Korea University of Science and TechnologyDaejeon, South Korea
| | - Won Chan Oh
- Center for Functional Connectomics, Korea Institute of Science and Technology Seoul, South Korea
| | - Jihye Seong
- Neuroscience Program, Korea University of Science and TechnologyDaejeon, South Korea; Center for Diagnosis Treatment Care of Dementia, Korea Institute of Science and TechnologySeoul, South Korea
| | - Jinhyun Kim
- Center for Functional Connectomics, Korea Institute of Science and TechnologySeoul, South Korea; Neuroscience Program, Korea University of Science and TechnologyDaejeon, South Korea
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30
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Murrey HE, Judkins JC, Am Ende CW, Ballard TE, Fang Y, Riccardi K, Di L, Guilmette ER, Schwartz JW, Fox JM, Johnson DS. Systematic Evaluation of Bioorthogonal Reactions in Live Cells with Clickable HaloTag Ligands: Implications for Intracellular Imaging. J Am Chem Soc 2015; 137:11461-75. [PMID: 26270632 PMCID: PMC4572613 DOI: 10.1021/jacs.5b06847] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Bioorthogonal
reactions, including the strain-promoted azide–alkyne
cycloaddition (SPAAC) and inverse electron demand Diels–Alder
(iEDDA) reactions, have become increasingly popular for live-cell
imaging applications. However, the stability and reactivity of reagents
has never been systematically explored in the context of a living
cell. Here we report a universal, organelle-targetable system based
on HaloTag protein technology for directly comparing bioorthogonal
reagent reactivity, specificity, and stability using clickable HaloTag
ligands in various subcellular compartments. This system enabled a
detailed comparison of the bioorthogonal reactions in live cells and
informed the selection of optimal reagents and conditions for live-cell
imaging studies. We found that the reaction of sTCO with monosubstituted
tetrazines is the fastest reaction in cells; however, both reagents
have stability issues. To address this, we introduced a new variant
of sTCO, Ag-sTCO, which has much improved stability and can be used
directly in cells for rapid bioorthogonal reactions with tetrazines.
Utilization of Ag complexes of conformationally strained trans-cyclooctenes should greatly expand their usefulness especially when
paired with less reactive, more stable tetrazines.
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Affiliation(s)
- Heather E Murrey
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Joshua C Judkins
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Christopher W Am Ende
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - T Eric Ballard
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States.,Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development , Groton, Connecticut 06340, United States
| | - Yinzhi Fang
- Brown Laboratories, Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
| | - Keith Riccardi
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development , Groton, Connecticut 06340, United States
| | - Li Di
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development , Groton, Connecticut 06340, United States
| | - Edward R Guilmette
- Neuroscience and Pain Research Unit, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Joel W Schwartz
- Neuroscience and Pain Research Unit, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Joseph M Fox
- Brown Laboratories, Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
| | - Douglas S Johnson
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
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31
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Abstract
![]()
Exploration of protein function and
interaction is critical for
discovering links among genomics, proteomics, and disease state; yet,
the immense complexity of proteomics found in biological systems currently
limits our investigational capacity. Although affinity and autofluorescent
tags are widely employed for protein analysis, these methods have
been met with limited success because they lack specificity and require
multiple fusion tags and genetic constructs. As an alternative approach,
the innovative HaloTag protein fusion platform allows protein function
and interaction to be comprehensively analyzed using a single genetic
construct with multiple capabilities. This is accomplished using a
simplified process, in which a variable HaloTag ligand binds rapidly
to the HaloTag protein (usually linked to the protein of interest)
with high affinity and specificity. In this review, we examine all
current applications of the HaloTag technology platform for biomedical
applications, such as the study of protein isolation and purification,
protein function, protein–protein and protein–DNA interactions,
biological assays, in vitro cellular imaging, and in vivo molecular imaging. In addition, novel uses of the
HaloTag platform are briefly discussed along with potential future
applications.
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Affiliation(s)
- Christopher G England
- †Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Haiming Luo
- ‡Department of Radiology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Weibo Cai
- †Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,‡Department of Radiology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,§University of Wisconsin Carbone Cancer Center, Madison, Wisconsin 53705, United States
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32
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Sano Y, Watanabe W, Matsunaga S. Chromophore-assisted laser inactivation--towards a spatiotemporal-functional analysis of proteins, and the ablation of chromatin, organelle and cell function. J Cell Sci 2014; 127:1621-9. [PMID: 24737873 DOI: 10.1242/jcs.144527] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chromophore-assisted laser or light inactivation (CALI) has been employed as a promising technique to achieve spatiotemporal knockdown or loss-of-function of target molecules in situ. CALI is performed using photosensitizers as generators of reactive oxygen species (ROS). There are two CALI approaches that use either transgenic tags with chemical photosensitizers, or genetically encoded fluorescent protein fusions. Using spatially restricted microscopy illumination, CALI can address questions regarding, for example, protein isoforms, subcellular localization or phase-specific analyses of multifunctional proteins that other knockdown approaches, such as RNA interference or treatment with chemicals, cannot. Furthermore, rescue experiments can clarify the phenotypic capabilities of CALI after the depletion of endogenous targets. CALI can also provide information about individual events that are involved in the function of a target protein and highlight them in multifactorial events. Beyond functional analysis of proteins, CALI of nuclear proteins can be performed to induce cell cycle arrest, chromatin- or locus-specific DNA damage. Even at organelle level - such as in mitochondria, the plasma membrane or lysosomes - CALI can trigger cell death. Moreover, CALI has emerged as an optogenetic tool to switch off signaling pathways, including the optical depletion of individual neurons. In this Commentary, we review recent applications of CALI and discuss the utility and effective use of CALI to address open questions in cell biology.
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Affiliation(s)
- Yukimi Sano
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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Takemoto K, Matsuda T, Sakai N, Fu D, Noda M, Uchiyama S, Kotera I, Arai Y, Horiuchi M, Fukui K, Ayabe T, Inagaki F, Suzuki H, Nagai T. SuperNova, a monomeric photosensitizing fluorescent protein for chromophore-assisted light inactivation. Sci Rep 2014; 3:2629. [PMID: 24043132 PMCID: PMC3775092 DOI: 10.1038/srep02629] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 08/22/2013] [Indexed: 11/20/2022] Open
Abstract
Chromophore-assisted light inactivation (CALI) is a powerful technique for acute perturbation of biomolecules in a spatio-temporally defined manner in living specimen with reactive oxygen species (ROS). Whereas a chemical photosensitizer including fluorescein must be added to specimens exogenously and cannot be restricted to particular cells or sub-cellular compartments, a genetically-encoded photosensitizer, KillerRed, can be controlled in its expression by tissue specific promoters or subcellular localization tags. Despite of this superiority, KillerRed hasn't yet become a versatile tool because its dimerization tendency prevents fusion with proteins of interest. Here, we report the development of monomeric variant of KillerRed (SuperNova) by direct evolution using random mutagenesis. In contrast to KillerRed, SuperNova in fusion with target proteins shows proper localization. Furthermore, unlike KillerRed, SuperNova expression alone doesn't perturb mitotic cell division. Supernova retains the ability to generate ROS, and hence promote CALI-based functional analysis of target proteins overcoming the major drawbacks of KillerRed.
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Affiliation(s)
- Kiwamu Takemoto
- 1] Research Institute for Electronic Sciences, Hokkaido University, Kita-20 Nishi-10 Kita-ku, Sapporo, Hokkaido 001-0020, Japan [2] [3]
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Ichikawa Y, Kamiya M, Obata F, Miura M, Terai T, Komatsu T, Ueno T, Hanaoka K, Nagano T, Urano Y. Selective Ablation of β-Galactosidase-Expressing Cells with a Rationally Designed Activatable Photosensitizer. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403221] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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35
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Ichikawa Y, Kamiya M, Obata F, Miura M, Terai T, Komatsu T, Ueno T, Hanaoka K, Nagano T, Urano Y. Selective Ablation of β-Galactosidase-Expressing Cells with a Rationally Designed Activatable Photosensitizer. Angew Chem Int Ed Engl 2014; 53:6772-5. [DOI: 10.1002/anie.201403221] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Indexed: 11/09/2022]
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Lin JY, Sann SB, Zhou K, Nabavi S, Proulx CD, Malinow R, Jin Y, Tsien RY. Optogenetic inhibition of synaptic release with chromophore-assisted light inactivation (CALI). Neuron 2013; 79:241-53. [PMID: 23889931 DOI: 10.1016/j.neuron.2013.05.022] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2013] [Indexed: 12/18/2022]
Abstract
Optogenetic techniques provide effective ways of manipulating the functions of selected neurons with light. In the current study, we engineered an optogenetic technique that directly inhibits neurotransmitter release. We used a genetically encoded singlet oxygen generator, miniSOG, to conduct chromophore assisted light inactivation (CALI) of synaptic proteins. Fusions of miniSOG to VAMP2 and synaptophysin enabled disruption of presynaptic vesicular release upon illumination with blue light. In cultured neurons and hippocampal organotypic slices, synaptic release was reduced up to 100%. Such inhibition lasted >1 hr and had minimal effects on membrane electrical properties. When miniSOG-VAMP2 was expressed panneuronally in Caenorhabditis elegans, movement of the worms was reduced after illumination, and paralysis was often observed. The movement of the worms recovered overnight. We name this technique Inhibition of Synapses with CALI (InSynC). InSynC is a powerful way to silence genetically specified synapses with light in a spatially and temporally precise manner.
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Affiliation(s)
- John Y Lin
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0647, USA.
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37
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Popa I, Berkovich R, Alegre-Cebollada J, Badilla CL, Rivas-Pardo JA, Taniguchi Y, Kawakami M, Fernandez JM. Nanomechanics of HaloTag tethers. J Am Chem Soc 2013; 135:12762-71. [PMID: 23909704 PMCID: PMC3874216 DOI: 10.1021/ja4056382] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The active site of the Haloalkane Dehydrogenase (HaloTag) enzyme can be covalently attached to a chloroalkane ligand providing a mechanically strong tether, resistant to large pulling forces. Here we demonstrate the covalent tethering of protein L and I27 polyproteins between an atomic force microscopy (AFM) cantilever and a glass surface using HaloTag anchoring at one end and thiol chemistry at the other end. Covalent tethering is unambiguously confirmed by the observation of full length polyprotein unfolding, combined with high detachment forces that range up to ∼2000 pN. We use these covalently anchored polyproteins to study the remarkable mechanical properties of HaloTag proteins. We show that the force that triggers unfolding of the HaloTag protein exhibits a 4-fold increase, from 131 to 491 pN, when the direction of the applied force is changed from the C-terminus to the N-terminus. Force-clamp experiments reveal that unfolding of the HaloTag protein is twice as sensitive to pulling force compared to protein L and refolds at a slower rate. We show how these properties allow for the long-term observation of protein folding-unfolding cycles at high forces, without interference from the HaloTag tether.
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Affiliation(s)
- Ionel Popa
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, New York 10027, USA.
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38
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Zhou LS, Yang KW, Feng L, Xiao JM, Liu CC, Zhang YL, Crowder MW. Novel fluorescent risedronates: Synthesis, photodynamic inactivation and imaging of Bacillus subtilis. Bioorg Med Chem Lett 2013; 23:949-54. [DOI: 10.1016/j.bmcl.2012.12.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/14/2012] [Accepted: 12/17/2012] [Indexed: 12/11/2022]
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Mok SA, Lund K, Lapointe P, Campenot RB. A HaloTag® method for assessing the retrograde axonal transport of the p75 neurotrophin receptor and other proteins in compartmented cultures of rat sympathetic neurons. J Neurosci Methods 2013; 214:91-104. [PMID: 23348044 DOI: 10.1016/j.jneumeth.2013.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 10/19/2012] [Accepted: 01/08/2013] [Indexed: 11/30/2022]
Abstract
We have adapted HaloTag® (HT) technology for use in compartmented cultures of rat sympathetic neurons in order to provide a technique that can be broadly applied to studies of the retrograde transport of molecules that play roles in neurotrophin signaling. Transfected neurons expressing HT protein alone, HT protein fused to the p75 neurotrophin receptor (p75NTR) or HT protein fused to tubulin α-1B were maintained in compartmented cultures in which cell bodies and proximal axons of rat sympathetic neurons reside in proximal compartments and their distal axons extend into distal compartments. HT ligand containing a fluorescent tetramethylrhodamine (TMR) label was applied either in the distal compartments or the proximal compartments, and the transport of labeled proteins was assayed by gel fluorescence imaging and TMR immunoblot. HT protein expressed alone displayed little or no retrograde transport. HT protein fused to either the intracellular C-terminus or the extracellular N-terminus of p75NTR was retrogradely transported. The retrograde transport of p75NTR was augmented when the distal axons were provided with nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF) or antibodies to BDNF. The anterograde transport of HT protein fused to the N-terminus of tubulin α-1B was also demonstrated. We conclude that retrograde transport of HT fusion proteins provides a powerful and novel approach in studies of axonal transport.
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Affiliation(s)
- Sue-Ann Mok
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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40
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Hossion AML, Bio M, Nkepang G, Awuah SG, You Y. Visible Light Controlled Release of Anticancer Drug through Double Activation of Prodrug. ACS Med Chem Lett 2013; 4:124-7. [PMID: 24900573 DOI: 10.1021/ml3003617] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 11/21/2012] [Indexed: 12/28/2022] Open
Abstract
We designed and synthesized a novel double activatable prodrug system (drug-linker-deactivated photosensitizer), containing a photocleavable aminoacrylate-linker and a deactivated photosensitizer, to achieve the spatiotemporally controlled release of parent drugs using visible light. Three prodrugs of CA-4, SN-38, and coumarin were prepared to demonstrate the activation of deactivated photosensitizer by cellular esterase and the release of parent drugs by visible light (540 nm) via photounclick chemistry. Among these prodrugs, nontoxic coumarin prodrug was used to quantify the release of parent drug in live cells. About 99% coumarin was released from the coumarin prodrug after 24 h of incubation with MCF-7 cells followed by irradiation with low intensity visible light (8 mW/cm(2)) for 30 min. Less toxic prodrugs of CA-4 and SN-38 killed cancer cells as effectively as free drugs after the double activation.
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Affiliation(s)
- Abugafar M. L. Hossion
- Department of Pharmaceutical
Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Moses Bio
- Department of Pharmaceutical
Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
- Department of Chemistry and
Biochemistry, University of Oklahoma, Norman,
Oklahoma 73019, United States
| | - Gregory Nkepang
- Department of Pharmaceutical
Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
- Department of Chemistry and
Biochemistry, University of Oklahoma, Norman,
Oklahoma 73019, United States
| | - Samuel G. Awuah
- Department of Pharmaceutical
Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
- Department of Chemistry and
Biochemistry, University of Oklahoma, Norman,
Oklahoma 73019, United States
| | - Youngjae You
- Department of Pharmaceutical
Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
- Department of Chemistry and
Biochemistry, University of Oklahoma, Norman,
Oklahoma 73019, United States
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41
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Abstract
Chromophore-assisted laser inactivation (CALI) is a technique that uses photochemically-generated reactive oxygen species to acutely inactivate target proteins in living cells. Neural development includes highly dynamic cellular processes such as asymmetric cell division, migration, axon and dendrite outgrowth and synaptogenesis. Although many key molecules of neural development have been identified since the past decades, their spatiotemporal contributions to these cellular events are not well understood. CALI provides an appealing tool for elucidating the precise functions of these molecules during neural development. In this review, we summarize the principles of CALI, a recent microscopic setup to perform CALI experiments, and the application of CALI to the study of growth-cone motility and neuroblast asymmetric division.
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Affiliation(s)
- Wei Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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42
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Urh M, Rosenberg M. HaloTag, a Platform Technology for Protein Analysis. CURRENT CHEMICAL GENOMICS 2012; 6:72-8. [PMID: 23213345 PMCID: PMC3480824 DOI: 10.2174/1875397301206010072] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 08/03/2012] [Accepted: 08/05/2012] [Indexed: 01/01/2023]
Abstract
Understanding protein function and interaction is central to the elucidation of biological processes. Systematic analysis of protein interactions have shown that the eukaryotic proteome is highly interconnected and that biological function frequently depends on the orchestrated action of many proteins. Perturbation of these functions or interactions can lead to various disease states and pharmacologic intervention can result in corrective therapies. The fact that proteins rarely act in isolation, but rather comprise complex machines that stably and/or transiently interact with many different partners at different times, demands the need for robust tools that allow comprehensive global analyses of these events. Here we describe a powerful protein fusion technology, the HaloTag platform, and how it enables the study of many facets of protein biology by offering a broad choice of applications. We review the development of the key aspects of the technology and it's performance in both in vitro and in vivo applications. In particular, we focus on HaloTag's multifunctional utility in protein imaging, protein isolation and display, and in the study of protein complexes and interactions. We demonstrate it's potential to help elucidate important facets of proteomic biology across complex biological systems at the biochemical, cell-based and whole animal level.
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43
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Takei K. Chromophore/fluorophore-assisted light inactivation method. Nihon Yakurigaku Zasshi 2012; 140:226-30. [PMID: 23138321 DOI: 10.1254/fpj.140.226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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44
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Encell LP, Friedman Ohana R, Zimmerman K, Otto P, Vidugiris G, Wood MG, Los GV, McDougall MG, Zimprich C, Karassina N, Learish RD, Hurst R, Hartnett J, Wheeler S, Stecha P, English J, Zhao K, Mendez J, Benink HA, Murphy N, Daniels DL, Slater MR, Urh M, Darzins A, Klaubert DH, Bulleit RF, Wood KV. Development of a dehalogenase-based protein fusion tag capable of rapid, selective and covalent attachment to customizable ligands. CURRENT CHEMICAL GENOMICS 2012; 6:55-71. [PMID: 23248739 PMCID: PMC3520037 DOI: 10.2174/1875397301206010055] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 04/04/2012] [Accepted: 04/16/2012] [Indexed: 11/22/2022]
Abstract
Our fundamental understanding of proteins and their biological significance has been enhanced by genetic fusion tags, as they provide a convenient method for introducing unique properties to proteins so that they can be examinedin isolation. Commonly used tags satisfy many of the requirements for applications relating to the detection and isolation of proteins from complex samples. However, their utility at low concentration becomes compromised if the binding affinity for a detection or capture reagent is not adequate to produce a stable interaction. Here, we describe HaloTag® (HT7), a genetic fusion tag based on a modified haloalkane dehalogenase designed and engineered to overcome the limitation of affinity tags by forming a high affinity, covalent attachment to a binding ligand. HT7 and its ligand have additional desirable features. The tag is relatively small, monomeric, and structurally compatible with fusion partners, while the ligand is specific, chemically simple, and amenable to modular synthetic design. Taken together, the design features and molecular evolution of HT7 have resulted in a superior alternative to common tags for the overexpression, detection, and isolation of target proteins.
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45
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Liu X, Dix M, Speers AE, Bachovchin DA, Zuhl AM, Cravatt BF, Kodadek TJ. Rapid development of a potent photo-triggered inhibitor of the serine hydrolase RBBP9. Chembiochem 2012; 13:2082-93. [PMID: 22907802 DOI: 10.1002/cbic.201200445] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Indexed: 11/09/2022]
Abstract
The serine hydrolases constitute a large class of enzymes that play important roles in physiology. There is great interest in the development of potent and selective pharmacological inhibitors of these proteins. Traditional active-site inhibitors often have limited selectivity within this superfamily and are tedious and expensive to discover. Using the serine hydrolase RBBP9 as a model target, we designed a rapid and relatively inexpensive route to highly selective peptoid-based inhibitors that can be activated by visible light. This technology provides rapid access to photo-activated tool compounds capable of selectively blocking the function of particular serine hydrolases.
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Affiliation(s)
- Xiaodan Liu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
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46
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Gayoso MJ. MRT letter: A fast and easy method for general fluorescent staining of cultured cells on transparent or opaque supports. Microsc Res Tech 2012; 75:849-51. [DOI: 10.1002/jemt.22068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 04/09/2012] [Indexed: 01/07/2023]
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47
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Gao HZ, Yang KW, Wu XL, Liu JY, Feng L, Xiao JM, Zhou LS, Jia C, Shi Z. Novel Conjugation of Norvancomycin–Fluorescein for Photodynamic Inactivation of Bacillus subtilis. Bioconjug Chem 2011; 22:2217-21. [DOI: 10.1021/bc200382d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Hui-Zhou Gao
- Key Laboratory of Synthetic
and Natural Functional Molecule Chemistry of Ministry of Education;
College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic
and Natural Functional Molecule Chemistry of Ministry of Education;
College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Xiang-Long Wu
- Key Laboratory of Synthetic
and Natural Functional Molecule Chemistry of Ministry of Education;
College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Jia-Yun Liu
- Clinical Laboratory, Xijing Hospital, The Fourth Military Medical University
of Chinese PLA, Xi’an 710032, P. R. China
| | - Lei Feng
- Key Laboratory of Synthetic
and Natural Functional Molecule Chemistry of Ministry of Education;
College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Jian-Min Xiao
- Key Laboratory of Synthetic
and Natural Functional Molecule Chemistry of Ministry of Education;
College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Li-Sheng Zhou
- Key Laboratory of Synthetic
and Natural Functional Molecule Chemistry of Ministry of Education;
College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Chao Jia
- Key Laboratory of Synthetic
and Natural Functional Molecule Chemistry of Ministry of Education;
College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Zhen Shi
- Key Laboratory of Synthetic
and Natural Functional Molecule Chemistry of Ministry of Education;
College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
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48
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Affiliation(s)
- Doug Auld
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
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49
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Wombacher R, Cornish VW. Chemical tags: applications in live cell fluorescence imaging. JOURNAL OF BIOPHOTONICS 2011; 4:391-402. [PMID: 21567974 DOI: 10.1002/jbio.201100018] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 04/08/2011] [Accepted: 04/09/2011] [Indexed: 05/30/2023]
Abstract
Technologies to visualize cellular structures and dynamics enable cell biologists to gain insight into complex biological processes. Currently, fluorescent proteins are used routinely to investigate the behavior of proteins in live cells. Chemical biology techniques for selective labeling of proteins with fluorescent labels have become an attractive alternative to fluorescent protein labeling. In the last ten years the progress in the development of chemical tagging methods have been substantial offering a broad palette of applications for live cell fluorescent microscopy. Several methods for protein labeling have been established, using protein tags, peptide tags and enzyme mediated tagging. This review focuses on the different strategies to achieve the attachment of fluorophores to proteins in live cells and cast light on the advantages and disadvantages of each individual method. Selected experiments in which chemical tags have been successfully applied to live cell imaging will be discussed and evaluated.
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