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Ukegawa T, Komatsu T, Minoda M, Matsumoto T, Iwasaka T, Mizuno T, Tachibana R, Sakamoto S, Hanaoka K, Kusuhara H, Honda K, Watanabe R, Urano Y. Thioester-Based Coupled Fluorogenic Assays in Microdevice for the Detection of Single-Molecule Enzyme Activities of Esterases with Specified Substrate Recognition. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306559. [PMID: 38140707 PMCID: PMC10933651 DOI: 10.1002/advs.202306559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/06/2023] [Indexed: 12/24/2023]
Abstract
Single-molecule enzyme activity assay is a platform that enables the analysis of enzyme activities at single proteoform level. The limitation of the targetable enzymes is the major drawback of the assay, but the general assay platform is reported to study single-molecule enzyme activities of esterases based on the coupled assay using thioesters as substrate analogues. The coupled assay is realized by developing highly water-soluble thiol-reacting probes based on phosphonate-substituted boron dipyrromethene (BODIPY). The system enables the detection of cholinesterase activities in blood samples at single-molecule level, and it is shown that the dissecting alterations of single-molecule esterase activities can serve as an informative platform for activity-based diagnosis.
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Affiliation(s)
- Tatsuya Ukegawa
- Graduate School of Pharmaceutical SciencesThe University of Tokyo7‐3‐1 Hongo, Bunkyo‐kuTokyo113‐0033Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical SciencesThe University of Tokyo7‐3‐1 Hongo, Bunkyo‐kuTokyo113‐0033Japan
| | - Mayano Minoda
- Graduate School of Pharmaceutical SciencesThe University of Tokyo7‐3‐1 Hongo, Bunkyo‐kuTokyo113‐0033Japan
| | - Takuya Matsumoto
- Graduate School of Pharmaceutical SciencesThe University of Tokyo7‐3‐1 Hongo, Bunkyo‐kuTokyo113‐0033Japan
| | - Takumi Iwasaka
- Graduate School of Pharmaceutical SciencesThe University of Tokyo7‐3‐1 Hongo, Bunkyo‐kuTokyo113‐0033Japan
| | - Tadahaya Mizuno
- Graduate School of Pharmaceutical SciencesThe University of Tokyo7‐3‐1 Hongo, Bunkyo‐kuTokyo113‐0033Japan
| | - Ryo Tachibana
- Graduate School of Pharmaceutical SciencesThe University of Tokyo7‐3‐1 Hongo, Bunkyo‐kuTokyo113‐0033Japan
| | - Shingo Sakamoto
- Graduate School of Pharmaceutical SciencesThe University of Tokyo7‐3‐1 Hongo, Bunkyo‐kuTokyo113‐0033Japan
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical SciencesKeio University1‐5‐30, Shibakoen, Minato‐kuTokyo105–8512Japan
| | - Hiroyuki Kusuhara
- Graduate School of Pharmaceutical SciencesThe University of Tokyo7‐3‐1 Hongo, Bunkyo‐kuTokyo113‐0033Japan
| | - Kazufumi Honda
- Graduate School of MedicineNippon Medical School1‐1‐5 Sendagi, Bunkyo‐kuTokyo113–8602Japan
- Institute for Advanced Medical ScienceNippon Medical School1‐1‐5 Sendagi, Bunkyo‐kuTokyo113–8602Japan
| | - Rikiya Watanabe
- Cluster for Pioneering ResearchRiken, 2‐1 Hirosawa, WakoSaitama351‐0198Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical SciencesThe University of Tokyo7‐3‐1 Hongo, Bunkyo‐kuTokyo113‐0033Japan
- Graduate School of MedicineThe University of Tokyo7‐3‐1 Hongo, Bunkyo‐kuTokyo113‐0033Japan
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Zhang L, Zhang R, Cong X, He M, Zhao X, Fan J, Peng X, Cui J, Sun W. Near-Infrared Fluorescence Probe for Monoamine Oxidase A with a Large Stokes Shift for Intraoperative Navigation. ACS APPLIED BIO MATERIALS 2024; 7:1115-1124. [PMID: 38194480 DOI: 10.1021/acsabm.3c01038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Monoamine oxidase A (MAO-A) is a dimeric flavoprotein that is found in the mitochondrial membrane. Currently, there is a lack of near-infrared fluorescent probes (NIR-FPs) with good specificity and high sensitivity for detecting MAO-A, making it difficult to accurately recognize and image cells in vitro and in vivo. In this study, the NIR-FP DDM-NH2 was designed and synthesized in order to detect MAO-A specifically in live biological systems. The probe comprised two functional components: dicyanoisophosphone as an NIR dye precursor and alanine as a recognition moiety. After identifying MAO-A, the probe exhibited an NIR emission peak at 770 nm with a significant Stokes shift (180 nm), 11-fold response factor, low detection limit of 99.7 nM, and considerably higher affinity toward MAO-A than that toward MAO-B, indicating high sensitivity. In addition, DDM-NH2 was effective when applied to the image-based assessment of MAO-A activity in HeLa cells, zebrafish, and tumor-bearing mice, demonstrating great potential for visualization-based research and MAO-A application in vivo.
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Affiliation(s)
- Linhao Zhang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Rong Zhang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Xinyue Cong
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Maomao He
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Xin Zhao
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Jiangli Fan
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
- Ningbo Institute of Dalian University of Technology, Ningbo 315016, China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Jingnan Cui
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Wen Sun
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
- Ningbo Institute of Dalian University of Technology, Ningbo 315016, China
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Sakamoto S, Hiraide H, Minoda M, Iwakura N, Suzuki M, Ando J, Takahashi C, Takahashi I, Murai K, Kagami Y, Mizuno T, Koike T, Nara S, Morizane C, Hijioka S, Kashiro A, Honda K, Watanabe R, Urano Y, Komatsu T. Identification of activity-based biomarkers for early-stage pancreatic tumors in blood using single-molecule enzyme activity screening. CELL REPORTS METHODS 2024; 4:100688. [PMID: 38218189 PMCID: PMC10831938 DOI: 10.1016/j.crmeth.2023.100688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/30/2023] [Accepted: 12/15/2023] [Indexed: 01/15/2024]
Abstract
Single-molecule enzyme activity-based enzyme profiling (SEAP) is a methodology to globally analyze protein functions in living samples at the single-molecule level. It has been previously applied to detect functional alterations in phosphatases and glycosidases. Here, we expand the potential for activity-based biomarker discovery by developing a semi-automated synthesis platform for fluorogenic probes that can detect various peptidases and protease activities at the single-molecule level. The peptidase/protease probes were prepared on the basis of a 7-amino-4-methylcoumarin fluorophore. The introduction of a phosphonic acid to the core scaffold made the probe suitable for use in a microdevice-based assay, while phosphonic acid served as the handle for the affinity separation of the probe using Phos-tag. Using this semi-automated scheme, 48 fluorogenic probes for the single-molecule peptidase/protease activity analysis were prepared. Activity-based screening using blood samples revealed altered single-molecule activity profiles of CD13 and DPP4 in blood samples of patients with early-stage pancreatic tumors. The study shows the power of single-molecule enzyme activity screening to discover biomarkers on the basis of the functional alterations of proteins.
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Affiliation(s)
- Shingo Sakamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hideto Hiraide
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mayano Minoda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Nozomi Iwakura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Misa Suzuki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jun Ando
- Cluster for Pioneering Research, Riken, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Chiharu Takahashi
- Cluster for Pioneering Research, Riken, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ikuko Takahashi
- Cluster for Pioneering Research, Riken, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kazue Murai
- Cluster for Pioneering Research, Riken, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yu Kagami
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tadahaya Mizuno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tohru Koike
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Satoshi Nara
- Department of Hepatobiliary and Pancreatic Surgery, National Cancer Center Hospital, 5-1-1, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Chigusa Morizane
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, 5-1-1, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Susumu Hijioka
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, 5-1-1, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Ayumi Kashiro
- Institute for Advanced Medical Science, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan; Graduate School of Medicine, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan
| | - Kazufumi Honda
- Institute for Advanced Medical Science, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan; Graduate School of Medicine, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan
| | - Rikiya Watanabe
- Cluster for Pioneering Research, Riken, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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Nagano N, Ichihashi Y, Komatsu T, Matsuzaki H, Hata K, Watanabe T, Misawa Y, Suzuki M, Sakamoto S, Kagami Y, Kashiro A, Takeuchi K, Kanemitsu Y, Ochiai H, Watanabe R, Honda K, Urano Y. Development of fluorogenic substrates for colorectal tumor-related neuropeptidases for activity-based diagnosis. Chem Sci 2023; 14:4495-4499. [PMID: 37152255 PMCID: PMC10155908 DOI: 10.1039/d2sc07029d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/29/2023] [Indexed: 05/09/2023] Open
Abstract
The M3 metalloproteases, neurolysin and THOP1, are neuropeptidases that are expressed in various tissues and metabolize neuropeptides, such as neurotensin. The biological roles of these enzymes are not well characterized, partially because the chemical tools to analyse their activities are not well developed. Here, we developed a fluorogenic substrate probe for neurolysin and thimet oligopeptidase 1 (THOP1), which enabled the analysis of enzymatic activity changes in tissue and plasma samples. In particular, the probe was useful for studying enzyme activities in a single-molecule enzyme assay platform, which can detect enzyme activity with high sensitivity. We detected the activity of neurolysin in plasma samples and revealed higher enzyme activity in the blood samples of patients with colorectal tumor. The result indicated that single-molecule neurolysin activity is a promising candidate for a blood biomarker for colorectal cancer diagnosis.
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Affiliation(s)
- Norimichi Nagano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yuki Ichihashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Hiroyuki Matsuzaki
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Keisuke Hata
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Toshiaki Watanabe
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yoshihiro Misawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Misa Suzuki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Shingo Sakamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yu Kagami
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Ayumi Kashiro
- Institute for Advanced Medical Sciences, Nippon Medical School 1-1-5 Sendagi Bunkyo-ku Tokyo 113-0033 Japan
| | - Keiko Takeuchi
- Institute for Advanced Medical Sciences, Nippon Medical School 1-1-5 Sendagi Bunkyo-ku Tokyo 113-0033 Japan
| | - Yukihide Kanemitsu
- National Cancer Center Hospital 5-1-1 Tsukiji Chuo-ku Tokyo 104-0045 Japan
| | - Hiroki Ochiai
- National Cancer Center Hospital 5-1-1 Tsukiji Chuo-ku Tokyo 104-0045 Japan
| | - Rikiya Watanabe
- Cluster for Pioneering Research, RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Kazufumi Honda
- Institute for Advanced Medical Sciences, Nippon Medical School 1-1-5 Sendagi Bunkyo-ku Tokyo 113-0033 Japan
- Graduate School of Medicine, Nippon Medical School 1-1-5 Sendagi Bunkyo-ku Tokyo 113-8602 Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Graduate School of Medicine, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
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5
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Huang Y, Feng W, Zhang GQ, Qiu Y, Li L, Pan L, Cao N. An enzyme-activatable dual-readout probe for sensitive β-galactosidase sensing and Escherichia coli analysis. Front Bioeng Biotechnol 2022; 10:1052801. [PMID: 36394024 PMCID: PMC9659582 DOI: 10.3389/fbioe.2022.1052801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 10/17/2022] [Indexed: 11/28/2022] Open
Abstract
Rapid and accurate sensing of β-galactosidase (β-gal) activity is particularly critical for the early detection of many diseases and has become a topic of interest in recent years. However, most traditional probes for β-gal sensing often suffer from the disadvantages of narrow dynamic range, low reaction efficiency and are only employed with either colorimetric or fluorescence sensing. Furthermore, β-galactosidase sensing based assay for efficient detection and antibiotic resistance analysis of Escherichia coli (E.coli) is not available. Here, an enzyme-induced probe assay was reported for dual sensitive fluorescence and colorimetric measurement of β-gal activity, and was further employed for detection of Escherichia coli and their antibiotic resistance analysis. The DCM-βgal probe was virtually non-emissive in aqueous solution, while it could be activated by β-gal to produce bright emission. Under optimized conditions, DCM-βgal displayed high sensitivity, selectivity and rapid response to β-gal with a low detection limit of 1.5 × 10−3 U ml−1. Importantly, this assay was successfully applied to sensitive detection of E. coli cells with a fast detection process within 5 h and a low detection concentration of 1 × 103 CFU ml−1. Furthermore, the enzyme-activatable assay was also successfully applied for high throughput E. coli antibiotic resistance analysis. The DCM-βgal strategy is applied for the first time on the detection of E. coli cells and their antibiotic resistance analysis. It is provided with the advantages of high selectively, a simple operation, low cost and rapid detection. The detection platform can also be extended to analyze the level of β-gal in other types of cells or biological samples. Overall, the simple, effective and dual-readout assay holds promise for efficient sensing of β-gal activity and provides a potential tool for E. coli detection and their antibiotic resistance analysis.
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Affiliation(s)
- Yifang Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, China
- *Correspondence: Yifang Huang, ; Nannan Cao,
| | - Weiwei Feng
- Department of Gastroenterology, Meizhou People’s Hospital, Meizhou, China
- Department of Laboratory Medicine and Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Guo-Qiang Zhang
- Key Laboratory of Bioactive Materials, State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Ministry of Education, and College of Life Sciences, Nankai University, Tianjin, China
| | - Yuling Qiu
- Guangxi Key Laboratory of Thalassemia Research, Guangxi Medical University, Nanning, China
| | - Linlin Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, China
| | - Liqiu Pan
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, China
| | - Nannan Cao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Yifang Huang, ; Nannan Cao,
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Deng X, Wu Y, Xu H, Yan J, Liu H, Zhang B. Recent research progress in galactose-based fluorescent probes for detection of biomarkers of liver diseases. Chem Commun (Camb) 2022; 58:12518-12527. [DOI: 10.1039/d2cc04180d] [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
This highlight illustrates the challenges and latest progress in galactose-based fluorescent probes for early diagnosis of liver diseases.
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Affiliation(s)
- Xiaojing Deng
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China
| | - Yingxu Wu
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China
| | - Hu Xu
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian 16044, China
| | - Jiawei Yan
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China
| | - Huanying Liu
- School of Mechanical and Power Engineering, Dalian Ocean University, Dalian 116023, China
| | - Boyu Zhang
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China
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Anttila MM, Vickerman BM, Wang Q, Lawrence DS, Allbritton NL. Photoactivatable Reporter to Perform Multiplexed and Temporally Controlled Measurements of Kinase and Protease Activity in Single Cells. Anal Chem 2021; 93:16664-16672. [PMID: 34865468 PMCID: PMC8753264 DOI: 10.1021/acs.analchem.1c04225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Peptide bioreporters were developed to perform multiplexed measurements of the activation of epidermal growth factor receptor kinase (EGFR), Akt kinase (Akt/protein kinase B), and proteases/peptidases in single cells. The performance characteristics of the three reporters were assessed by measuring the reporter's proteolytic stability, kinetic constants for EGFR and Akt, and dephosphorylation rate. The reporter displaying optimal performance was composed of 6-carboxyfluorescein (6-FAM) on the peptide N-terminus, an Akt substrate sequence employing a threonine phosphorylation site for Akt, followed by a tri-D arginine linker, and finally an EGFR substrate sequence bearing a phosphatase-resistant 7-(S)-hydroxy-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (L-htc) residue as the EGFR phosphorylation site. Importantly, use of a single electrophoretic condition separated the mono- and diphosphorylated products as well as proteolytic forms permitting the quantitation of multiple enzyme activities simultaneously using a single reporter. Because the Akt and EGFR substrates were linked, a known ratio (EGFR/Akt) of the reporter was loaded into cells. A photoactivatable version of the reporter was synthesized by adding two 4,5-dimethoxy-2-nitrobenzyl (DMNB) moieties to mask the EGFR and Akt phosphorylation sites. The DMNB moieties were readily photocleaved following exposure to 360 nm light, unmasking the phosphorylation sites on the reporter. The new photoactivatable reporter permitted multiplexed measurements of kinase signaling and proteolytic degradation in single cells in a temporally controlled manner. This work will facilitate the development of a new generation of multiplexed activity-based reporters capable of light-initiated measurement of enzymatic activity in single cells.
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Affiliation(s)
- Matthew M. Anttila
- Department of Chemistry, Chapel Hill, North Carolina 27599
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
- Department of Bioengineering, University of Washington, Seattle, Washington, 98125
| | - Brianna M. Vickerman
- Department of Chemistry, Chapel Hill, North Carolina 27599
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Qunzhao Wang
- Division of Chemical Biology and Medicinal Chemistry UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - David S. Lawrence
- Department of Chemistry, Chapel Hill, North Carolina 27599
- Division of Chemical Biology and Medicinal Chemistry UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599
- Department of Pharmacology, School of Medicine, Chapel Hill, North Carolina 27599
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Nancy L. Allbritton
- Department of Bioengineering, University of Washington, Seattle, Washington, 98125
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Singh A, Gao M, Beck MW. Human carboxylesterases and fluorescent probes to image their activity in live cells. RSC Med Chem 2021; 12:1142-1153. [PMID: 34355180 PMCID: PMC8292992 DOI: 10.1039/d1md00073j] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 04/26/2021] [Indexed: 12/12/2022] Open
Abstract
Human carboxylesterases (CESs) are serine hydrolases that are responsible for the phase I metabolism of an assortment of ester, amide, thioester, carbonate, and carbamate containing drugs. CES activity is known to be influenced by a variety of factors including single nucleotide polymorphisms, alternative splicing, and drug-drug interactions. These different factors contribute to interindividual variability of CES activity which has been demonstrated to influence clinical outcomes among people treated with CES-substrate therapeutics. Detailed exploration of the factors that influence CES activity is emerging as an important area of research. The use of fluorescent probes with live cell imaging techniques can selectively visualize the real-time activity of CESs and have the potential to be useful tools to help reveal the impacts of CES activity variations on human health. This review summarizes the properties of the five known human CESs including factors reported to or that could potentially influence their activity before discussing the design aspects and use considerations of CES fluorescent probes in general in addition to highlighting several well-characterized probes.
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Affiliation(s)
- Anchal Singh
- Department of Chemistry and Biochemistry, Eastern Illinois University Charleston IL 61920 USA +1 217 581 6227
| | - Mingze Gao
- Department of Biological Sciences, Eastern Illinois University Charleston IL 61920 USA
| | - Michael W Beck
- Department of Chemistry and Biochemistry, Eastern Illinois University Charleston IL 61920 USA +1 217 581 6227
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Establishment of live-cell-based coupled assay system for identification of compounds to modulate metabolic activities of cells. Cell Rep 2021; 36:109311. [PMID: 34233188 DOI: 10.1016/j.celrep.2021.109311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 03/29/2021] [Accepted: 06/04/2021] [Indexed: 12/29/2022] Open
Abstract
In this study, we present a live-cell-based fluorometric coupled assay system to identify the compounds that can regulate the targeted metabolic pathways in live cells. The assay is established through targeting specific metabolic pathways and using "input" and "output" metabolite pairs. The changes in the extracellular output that are generated and released into the extracellular media from the input are assessed as the activity of the pathway. The screening for the glycolytic pathway and amino acid metabolism reveals the activities of the present drugs, 6-BIO and regorafenib, that regulate the metabolic fate of tumor cells.
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11
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Xie Y, Yang L, Chen Q, Zhang J, Feng L, Chen JL, Hao Q, Zhang L, Sun H. Single-step fluorescent probes to detect decrotonylation activity of HDACs through intramolecular reactions. Eur J Med Chem 2020; 212:113120. [PMID: 33422982 DOI: 10.1016/j.ejmech.2020.113120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 02/07/2023]
Abstract
Lysine crotonylation plays vital roles in gene transcription and cellular metabolism. Nevertheless, methods for dissecting the molecular mechanisms of decrotonyaltion remains limited. So far, there is no single-step fluorescent method developed for enzymatic decrotonylation activity detection. The major difficulty is that the aliphatic crotonylated lysine doesn't allow π-conjugation to a fluorophore and decrotonylation can not modulate the electronic state directly. Herein, we have designed and synthesized two activity-based single-step fluorogenic probes KTcr-I and KTcr-II for detecting enzymatic decrotonylation activity. These two probes can be recognized by histone deacetylases and undergo intramolecular nucleophilic exchange reaction to generate fluorescence signal. Notably, peptide sequence-dependent effect was observed. KTcr-I can be recognized by Sirt2 more effectively, while KTcr-II with LGKcr peptide sequence preferentially reacted with HDAC3. Compared to other methods of studying enzymatic decrotonylation activity, our single-step fluorescent method has a number of advantages, such as facileness, high sensitivity, cheap facility and little material consumed. We envision that the probes developed in this study will provide useful tools to screen inhibitors which suppress the decrotonylation activity of HDACs. Such probes will be useful for further delineating the roles of decrotonylation enzyme and aid in biomarker identification and drug discovery.
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Affiliation(s)
- Yusheng Xie
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Liu Yang
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Qingxin Chen
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Jie Zhang
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Ling Feng
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Jian Lin Chen
- School of Science and Technology, The Open University of Hong Kong, Hong Kong Special Administrative Region
| | - Quan Hao
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Liang Zhang
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China; Department of Biomedical Science, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Hongyan Sun
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China.
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12
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Soga N, Ota A, Nakajima K, Watanabe R, Ueno H, Noji H. Monodisperse Liposomes with Femtoliter Volume Enable Quantitative Digital Bioassays of Membrane Transporters and Cell-Free Gene Expression. ACS NANO 2020; 14:11700-11711. [PMID: 32864949 DOI: 10.1021/acsnano.0c04354] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Digital bioassays have emerged as a new category of bioanalysis. However, digital bioassays for membrane transporter proteins have not been well established yet despite high demands in molecular physiology and molecular pharmacology due to the lack of biologically functional monodisperse liposomes with femtoliter volumes. Here, we established a simple and robust method to produce femtoliter-sized liposomes (femto-liposomes). We prepared 106 monodispersed water-in-oil droplets stabilized by a lipid monolayer using a polyethylene glycol-coated femtoliter reactor array device. Droplets were subjected to the optimized emulsion transfer process for femto-liposome production. Liposomes were monodispersed (coefficient of variation = 5-15%) and had suitable diameter (0.6-5.3 μm) and uniform volumes of subfemtoliter or a few femtoliters; thus, they were termed uniform femto-liposomes. The unilamellarity of uniform femto-liposomes allowed quantitative single-molecule analysis of passive and active transporter proteins: α-hemolysin and FoF1-ATPase. Digital gene expression in uniform femto-liposomes (cell-free transcription and translation from single DNA molecules) was also demonstrated, showing the versatility of digital assays for membrane transporter proteins and cell-free synthetic biology.
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Affiliation(s)
- Naoki Soga
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akira Ota
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kota Nakajima
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Rikiya Watanabe
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- PRIME, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Hiroshi Ueno
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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13
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Sakamoto S, Komatsu T, Watanabe R, Zhang Y, Inoue T, Kawaguchi M, Nakagawa H, Ueno T, Okusaka T, Honda K, Noji H, Urano Y. Multiplexed single-molecule enzyme activity analysis for counting disease-related proteins in biological samples. SCIENCE ADVANCES 2020; 6:eaay0888. [PMID: 32195342 PMCID: PMC7065886 DOI: 10.1126/sciadv.aay0888] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 12/11/2019] [Indexed: 05/24/2023]
Abstract
We established an ultrasensitive method for identifying multiple enzymes in biological samples by using a multiplexed microdevice-based single-molecule enzymatic assay. We used a paradigm in which we "count" the number of enzyme molecules by profiling their single enzyme activity characteristics toward multiple substrates. In this proof-of-concept study of the single enzyme activity-based protein profiling (SEAP), we were able to detect the activities of various phosphoric ester-hydrolyzing enzymes such as alkaline phosphatases, tyrosine phosphatases, and ectonucleotide pyrophosphatases in blood samples at the single-molecule level and in a subtype-discriminating manner, demonstrating its potential usefulness for the diagnosis of diseases based on ultrasensitive detection of enzymes.
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Affiliation(s)
- Shingo Sakamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Rikiya Watanabe
- Molecular Physiology Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yi Zhang
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Taiki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mitsuyasu Kawaguchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1, Tanabedori, Mizuho-ku, Nagoya-shi, Aichi 467-8603, Japan
| | - Hidehiko Nakagawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1, Tanabedori, Mizuho-ku, Nagoya-shi, Aichi 467-8603, Japan
| | - Takaaki Ueno
- Department of Oral and Maxillofacial Surgery, Osaka Medical College, 2-7 Daigakumachi, Takatsuki-shi, Osaka 569-8686, Japan
| | - Takuji Okusaka
- Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, 5-1-1, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Kazufumi Honda
- Department of Biomarkers for Early Detection of Cancer, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Hiroyuki Noji
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Core Research for Evolutional Science and Technology (CREST) Investigator, Japan Agency for Medical Research and Development (AMED), 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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14
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Komatsu T, Urano Y. Chemical toolbox for 'live' biochemistry to understand enzymatic functions in living systems. J Biochem 2020; 167:139-149. [PMID: 31553443 DOI: 10.1093/jb/mvz074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 08/30/2019] [Indexed: 11/12/2022] Open
Abstract
In this review, we present an overview of the recent advances in chemical toolboxes that are used to provide insights into 'live' protein functions in living systems. Protein functions are mediated by various factors inside of cells, such as protein-protein interactions, posttranslational modifications, and they are also subject to environmental factors such as pH, redox states and crowding conditions. Obtaining a true understanding of protein functions in living systems is therefore a considerably difficult task. Recent advances in research tools have allowed us to consider 'live' biochemistry as a valid approach to precisely understand how proteins function in a live cell context.
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Affiliation(s)
- Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Core Research for Evolutional Science and Technology (CREST) Investigator, Japan Agency for Medical Research and Development (AMED), 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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15
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A near-infrared fluorescent probe for the ratiometric detection and living cell imaging of β-galactosidase. Anal Bioanal Chem 2019; 411:7957-7966. [PMID: 31732786 DOI: 10.1007/s00216-019-02181-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/23/2019] [Accepted: 09/30/2019] [Indexed: 02/03/2023]
Abstract
β-Galactosidase (β-gal) has captured the attention of biologists, chemists, and medical researchers as an important biomarker for cell senescence and primary ovarian cancer. Therefore, many fluorescent probes with visible light emission have been developed for the detection and imaging of β-gal in living cells. However, near-infrared (NIR) ratiometric probes are more suitable for bioimaging because near-infrared light can effectively avoid the interference of autofluorescence and the ratiometric approach can improve sensitivity and accuracy of the detection. In this work, we designed an NIR ratiometric probe (TMG) for the highly sensitive detection of β-gal. Using a spontaneous degradation mechanism based on the ICT effect, the change in ratio (F650/F580) exhibited a prominent β-gal-dependent performance and proved a strong linear response to the activity of β-gal at an enzyme concentration between 0 and 200 U L-1, with a limit of detection as low as 0.86 U L-1, and the response speed is much faster than the same type of probes previously reported. The probe also revealed an excellent biocompatibility and a large Stokes shift. Moreover, fluorescence microscopy imaging experiments confirmed that this probe could be successfully used for the detection of endogenous β-gal in living cells. Graphical abstract.
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16
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Xie Y, Chen L, Wang R, Wang J, Li J, Xu W, Li Y, Yao SQ, Zhang L, Hao Q, Sun H. Chemical Probes Reveal Sirt2's New Function as a Robust "Eraser" of Lysine Lipoylation. J Am Chem Soc 2019; 141:18428-18436. [PMID: 31644285 DOI: 10.1021/jacs.9b06913] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Lysine lipoylation, a highly conserved lysine post-translational modification, plays a critical role in regulating cell metabolism. The catalytic activity of a number of vital metabolic proteins, such as pyruvate dehydrogenase (PDH), depends on lysine lipoylation. Despite its important roles, the detailed biological regulatory mechanism of lysine lipoylation remains largely unexplored. Herein we designed a powerful affinity-based probe, KPlip, to interrogate the interactions of lipoylated peptide/proteins under native cellular environment. Large-scale chemical proteomics analysis revealed a number of binding proteins of KPlip, including sirtuin 2 (Sirt2), an NAD+-dependent protein deacylase. To explore the potential activity of Sirt2 toward lysine lipoylation, we designed a single-step fluorogenic probe, KTlip, which reports delipoylation activity in a continuous manner. The results showed that Sirt2 led to significant delipoylation of KTlip, displaying up to a 60-fold fluorescence increase in the assay. Further kinetic experiments with different peptide substrates revealed that Sirt2 can catalyze the delipoylation of peptide (DLAT-PDH, K259) with a remarkable catalytic efficiency (kcat/Km) of 3.26 × 103 s-1 M-1. The activity is about 400-fold higher than that of Sirt4, the only mammalian enzyme with known delipoylation activity. Furthermore, overexpression and silencing experiments demonstrated that Sirt2 regulates the lipoylation level and the activity of endogenous PDH, thus unequivocally confirming that PDH is a genuine physiological substrate of Sirt2. Using our chemical probes, we have successfully established the relationship between Sirt2 and lysine lipoylation in living cells for the first time. We envision that such chemical probes will serve as useful tools for delineating the roles of lysine lipoylation in biology and diseases.
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Affiliation(s)
- Yusheng Xie
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films) , City University of Hong Kong , 83 Tat Chee Avenue , Kowloon , Hong Kong , China.,Key Laboratory of Biochip Technology, Biotech and Health Centre , Shenzhen Research Institute of City University of Hong Kong , Shenzhen 518057 , China
| | - Lanfang Chen
- School of Biomedical Sciences , University of Hong Kong , Hong Kong , China
| | - Rui Wang
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences , City University of Hong Kong , 83 Tat Chee Avenue , Kowloon , Hong Kong , China
| | - Jigang Wang
- Department of Pharmacology , National University of Singapore , Singapore 119077 , Singapore
| | - Jingyu Li
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences , City University of Hong Kong , 83 Tat Chee Avenue , Kowloon , Hong Kong , China
| | - Wei Xu
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences , City University of Hong Kong , 83 Tat Chee Avenue , Kowloon , Hong Kong , China
| | - Yingxue Li
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences , City University of Hong Kong , 83 Tat Chee Avenue , Kowloon , Hong Kong , China
| | - Shao Q Yao
- Department of Chemistry , National University of Singapore , Singapore 119077 , Singapore
| | - Liang Zhang
- Key Laboratory of Biochip Technology, Biotech and Health Centre , Shenzhen Research Institute of City University of Hong Kong , Shenzhen 518057 , China.,Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences , City University of Hong Kong , 83 Tat Chee Avenue , Kowloon , Hong Kong , China
| | - Quan Hao
- School of Biomedical Sciences , University of Hong Kong , Hong Kong , China
| | - Hongyan Sun
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films) , City University of Hong Kong , 83 Tat Chee Avenue , Kowloon , Hong Kong , China.,Key Laboratory of Biochip Technology, Biotech and Health Centre , Shenzhen Research Institute of City University of Hong Kong , Shenzhen 518057 , China
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17
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Feng L, Ning J, Tian X, Wang C, Zhang L, Ma X, James TD. Fluorescent probes for bioactive detection and imaging of phase II metabolic enzymes. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.213026] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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18
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Hananya N, Press O, Das A, Scomparin A, Satchi‐Fainaro R, Sagi I, Shabat D. Persistent Chemiluminescent Glow of Phenoxy‐dioxetane Luminophore Enables Unique CRET‐Based Detection of Proteases. Chemistry 2019; 25:14679-14687. [DOI: 10.1002/chem.201903489] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Nir Hananya
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences Tel Aviv University Tel Aviv 6997801 Israel
| | - Ofir Press
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences Tel Aviv University Tel Aviv 6997801 Israel
| | - Alakesh Das
- Department of Biological Regulation Weizmann Institute of Science Rehovot 7610001 Israel
| | - Anna Scomparin
- Department of Physiology and Pharmacology Sackler Faculty of Medicine Tel Aviv University Tel Aviv 6997801 Israel
- Department of Drug Science and Technology University of Turin Via P. Giuria 9 10125 Turin Italy
| | - Ronit Satchi‐Fainaro
- Department of Physiology and Pharmacology Sackler Faculty of Medicine Tel Aviv University Tel Aviv 6997801 Israel
| | - Irit Sagi
- Department of Biological Regulation Weizmann Institute of Science Rehovot 7610001 Israel
| | - Doron Shabat
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences Tel Aviv University Tel Aviv 6997801 Israel
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19
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State-of-the-art: functional fluorescent probes for bioimaging and pharmacological research. Acta Pharmacol Sin 2019; 40:717-723. [PMID: 30487651 DOI: 10.1038/s41401-018-0190-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/19/2018] [Indexed: 12/14/2022] Open
Abstract
Cardiovascular diseases, neuropsychiatric disorders, and cancers seriously endanger human health. Mechanistic and pharmacological mechanisms of candidate drugs are central to the translational paradigm. Since many signal transduction and molecular events are implicated in these diseases, a novel method to interrogate the key pharmacological mechanisms is required to accelerate innovative drug discovery. Much attention now focuses on the real-time visualization of molecular disease events to yield new insights to the pathogenesis of the diseases. This review focuses on recent advances in the development of chemical probes for imaging pathological events to facilitate the study of the underlying pharmacodynamics and toxicity involved. As reviewed here, optical imaging is now frequently viewed as an indispensable technique in the field of biological research. Promoting interdisciplinary collaboration among chemistry, biology and medicine, is necessary to further refine functional fluorescent probes for diagnostic and therapeutic applications.
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20
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Halloran MW, Lumb JP. Recent Applications of Diazirines in Chemical Proteomics. Chemistry 2019; 25:4885-4898. [PMID: 30444029 DOI: 10.1002/chem.201805004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/12/2018] [Indexed: 02/06/2023]
Abstract
The elucidation of substrate-protein interactions is an important component of the drug development process. Due to the complexity of native cellular environments, elucidating these fundamental biochemical interactions remains challenging. Photoaffinity labeling (PAL) is a versatile technique that can provide insight into ligand-target interactions. By judicious modification of substrates with a photoreactive group, PAL creates a covalent crosslink between a substrate and its biological target following UV-irradiation. Among the commonly employed photoreactive groups, diazirines have emerged as the gold standard. In this Minireview, recent developments in the field of diazirine-based photoaffinity labeling will be discussed, with emphasis being placed on their applications in chemical proteomic studies.
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Affiliation(s)
- Matthew W Halloran
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Jean-Philip Lumb
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
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21
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Novel fluorescent probe for rapid and ratiometric detection of β-galactosidase and live cell imaging. Talanta 2018; 192:308-313. [PMID: 30348394 DOI: 10.1016/j.talanta.2018.09.061] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/10/2018] [Accepted: 09/18/2018] [Indexed: 01/29/2023]
Abstract
β-Galactosidase (β-gal) is an important biomarker for primary ovarian cancers and cell senescence; however, a fast response fluorescent probe for ratiometric monitoring is still rare. A novel, ratiometric water-soluble fluorescent probe (FLM) for β-gal was developed. The emission ratio F550/F450 reached the maxima at about 5 min and can be used for real-time detection of β-gal; the ratio gained an ultimate enhancement of about 260-fold. The ratio (F550/F450) displayed brilliant β-gal-dependent performance and responded linearly with β-gal activity. The probe showed wonderful biocompatibility and was successfully used for the bioimaging of endogenous β-gal in the human ovarian cancer cell line OVCAR-3.
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22
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Yan Z, Wang J, Zhang Y, Zhang S, Qiao J, Zhang X. An iridium complex-based probe for photoluminescence lifetime imaging of human carboxylesterase 2 in living cells. Chem Commun (Camb) 2018; 54:9027-9030. [PMID: 30047956 DOI: 10.1039/c8cc04481c] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A novel photoluminescence lifetime probe (Ir-TB) has been developed for the detection and imaging of hCE2 in living cells. A large lifetime increase by around 300 ns after the enzymatic reaction makes it an ideal tool to distinguish hCE2-hydrolyzed probes from those non-hydrolyzed ones via PLIM for the first time.
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Affiliation(s)
- Zihe Yan
- Department of Chemistry, Beijing Key laboratory of Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
| | - Jinyu Wang
- Department of Chemistry, Beijing Key laboratory of Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
| | - Yanxin Zhang
- Department of Chemistry, Key Lab of Organic Optoelectronics and Molecular Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China.
| | - Sichun Zhang
- Department of Chemistry, Beijing Key laboratory of Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
| | - Juan Qiao
- Department of Chemistry, Key Lab of Organic Optoelectronics and Molecular Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China.
| | - Xinrong Zhang
- Department of Chemistry, Beijing Key laboratory of Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
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23
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White A, Koelper A, Russell A, Larsen EM, Kim C, Lavis LD, Hoops GC, Johnson RJ. Fluorogenic structure activity library pinpoints molecular variations in substrate specificity of structurally homologous esterases. J Biol Chem 2018; 293:13851-13862. [PMID: 30006352 DOI: 10.1074/jbc.ra118.003972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/11/2018] [Indexed: 01/08/2023] Open
Abstract
Cellular esterases catalyze many essential biological functions by performing hydrolysis reactions on diverse substrates. The promiscuity of esterases complicates assignment of their substrate preferences and biological functions. To identify universal factors controlling esterase substrate recognition, we designed a 32-member structure-activity relationship (SAR) library of fluorogenic ester substrates and used this library to systematically interrogate esterase preference for chain length, branching patterns, and polarity to differentiate common classes of esterase substrates. Two structurally homologous bacterial esterases were screened against this library, refining their previously broad overlapping substrate specificity. Vibrio cholerae esterase ybfF displayed a preference for γ-position thioethers and ethers, whereas Rv0045c from Mycobacterium tuberculosis displayed a preference for branched substrates with and without thioethers. We determined that this substrate differentiation was partially controlled by individual substrate selectivity residues Tyr-119 in ybfF and His-187 in Rv0045c; reciprocal substitution of these residues shifted each esterase's substrate preference. This work demonstrates that the selectivity of esterases is tuned based on transition state stabilization, identifies thioethers as an underutilized functional group for esterase substrates, and provides a rapid method for differentiating structural isozymes. This SAR library could have multifaceted future applications, including in vivo imaging, biocatalyst screening, molecular fingerprinting, and inhibitor design.
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Affiliation(s)
- Alex White
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - Andrew Koelper
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - Arielle Russell
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - Erik M Larsen
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - Charles Kim
- the Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147-2439
| | - Luke D Lavis
- the Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147-2439
| | - Geoffrey C Hoops
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - R Jeremy Johnson
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
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24
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Development and validation of an improved diced electrophoresis gel assay cutter-plate system for enzymomics studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:82-87. [PMID: 29928991 DOI: 10.1016/j.bbapap.2018.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/08/2018] [Accepted: 06/10/2018] [Indexed: 11/22/2022]
Abstract
Diced electrophoresis gel (DEG) assay is a methodology to identify enzymes with a specified activity in complex cell or tissue lysates by means of two-dimensional separation using isoelectric focusing and native PAGE, followed by dicing of the gel into small pieces that are assayed separately, and digestion and peptide fingerprinting to identify the protein(s) of interest in positive wells. The existing hand-made system has some disadvantages, and here we describe the development and validation of an improved cutter-plate system that enables simple, reliable and reproducible DEG assay in a 384-well plate-based format with signal readout using fluorometric or LC-MS-based reaction monitoring. To illustrate the usefulness of this system, we describe its application to profile esterase activities in ovarian adenocarcinoma SKOV3 cell lysate and mouse liver lysate that activate a fluorogenic substrate, fluorescein dibutyrate (FDBu), as well as esterase activities in mouse liver lysate that activate S-bromobenzylglutathione dicyclopentyl ester (BBGDC), a prodrug of anti-tumor agent S-bromobenzylglutathione. The activity spot patterns detected for FDBu and BBGDC were completely different, indicating that different metabolic systems are involved in hydrolysis of these substrates. The major detected spot in each case was identified. The developed system provides a highly reproducible general assay platform that should be useful for characterizing novel protein functions in complex bio-samples, as well as enzymomics studies.
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25
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Zhang Q, Zhang J, Gavathiotis E. ICBS 2017 in Shanghai-Illuminating Life with Chemical Innovation. ACS Chem Biol 2018; 13:1111-1122. [PMID: 29677443 PMCID: PMC6855916 DOI: 10.1021/acschembio.8b00220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Qi Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Jingyu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Evripidis Gavathiotis
- Department of Biochemistry, Department of Medicine, Albert Einstein College of Medicine, New York 10461, United States
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26
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Kuriki Y, Kamiya M, Kubo H, Komatsu T, Ueno T, Tachibana R, Hayashi K, Hanaoka K, Yamashita S, Ishizawa T, Kokudo N, Urano Y. Establishment of Molecular Design Strategy To Obtain Activatable Fluorescent Probes for Carboxypeptidases. J Am Chem Soc 2018; 140:1767-1773. [DOI: 10.1021/jacs.7b11014] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Mako Kamiya
- PRESTO (Japan)
Science
and Technology Agency (JST), 4-1-8
Honcho Kawaguchi-shi, Saitama 332-0012, Japan
| | - Hidemasa Kubo
- Division
of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | | | | | | | | | | | | | - Takeaki Ishizawa
- Department
of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Norihiro Kokudo
- Department
of Surgery, National Center for Global Health and Medicine, 1-21-1
Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Yasuteru Urano
- CREST (Japan)
Agency for Medical Research and Development (AMED), 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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27
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Komatsu T. Potential of Enzymomics Methodologies to Characterize Disease-Related Protein Functions. Chem Pharm Bull (Tokyo) 2017; 65:605-610. [PMID: 28674330 DOI: 10.1248/cpb.c17-00144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Enzymatic functions are often altered during disease onset and progression, and therefore chemical-biological studies, which utilize chemical knowledge to discover novel protein functions, are often employed to find proteins with functions closely related to disease phenotypes. Such studies are known as forward chemical-biological approaches and form part of the emerging field of enzymomics (omics of enzymes). This review provides an overview of methodologies available for discovering and characterizing disease-related alterations of enzymatic functions and prospects for the future.
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Affiliation(s)
- Toru Komatsu
- The University of Tokyo Graduate School of Pharmaceutical Sciences.,Precursory Research for Embryonic Science and Technology (PRESTO) Investigator
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28
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Sakamoto S, Komatsu T, Ueno T, Hanaoka K, Urano Y. Fluorescence detection of serum albumin with a turnover-based sensor utilizing Kemp elimination reaction. Bioorg Med Chem Lett 2017; 27:3464-3467. [PMID: 28587820 DOI: 10.1016/j.bmcl.2017.05.076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/23/2017] [Accepted: 05/25/2017] [Indexed: 11/28/2022]
Abstract
The Kemp elimination reaction is a well-known chemical reaction that is facilitated on a protein surface microenvironment, and in particular is highly accelerated in a unique binding pocket of serum albumin. We have designed and synthesized a fluorescently activatable coumarin derivative with a benzisoxazole scaffold to enable monitoring of the Kemp elimination reaction in terms of fluorescence change for the first time. We show that this fluorescent sensor can sensitively and selectively quantitate serum albumin in blood samples. It also works in a dry-chemistry format.
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Affiliation(s)
- Shingo Sakamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Tasuku Ueno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Core Research for Evolutional Science and Technology (CREST) Investigator, Japan Agency for Medical Research and Development (AMED), 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan.
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29
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Zhang J, Li C, Dutta C, Fang M, Zhang S, Tiwari A, Werner T, Luo FT, Liu H. A novel near-infrared fluorescent probe for sensitive detection of β-galactosidase in living cells. Anal Chim Acta 2017; 968:97-104. [PMID: 28395779 DOI: 10.1016/j.aca.2017.02.039] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 02/16/2017] [Accepted: 02/27/2017] [Indexed: 12/28/2022]
Abstract
A novel near-infrared fluorescent probe for β-galactosidase has been developed based on a hemicyanine skeleton, which is conjugated with a d-galactose residue via a glycosidic bond. The probe serves as a substrate of β-galactosidase and displays rapid and sensitive turn-on fluorescent responses to β-galactosidase in aqueous solution. A 12.8-fold enhancement of fluorescence intensity at 703 nm was observed after incubation of 10 nM of β-galactosidase with 5 μM probe for 10 min. The probe can sensitively detect as little as 0.1 nM of β-galactosidase and shows linear responses to the enzyme concentration below 1.4 nM. The kinetic study showed that the probe has high binding affinity to β-galactosidase with Km = 3.6 μM. The probe was used to detect β-galactosidase in living cells by employing the premature cell senescence model. The probe exhibited strong fluorescent signals in senescent cells but not in normal cells, which demonstrates that the probe is able to detect the endogenous senescence-associated β-galactosidase in living cells.
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Affiliation(s)
- Jingtuo Zhang
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Cong Li
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Colina Dutta
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Mingxi Fang
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Shuwei Zhang
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Ashutosh Tiwari
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA.
| | - Thomas Werner
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA.
| | - Fen-Tair Luo
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan, Republic of China.
| | - Haiying Liu
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA.
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30
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Onagi J, Komatsu T, Ichihashi Y, Kuriki Y, Kamiya M, Terai T, Ueno T, Hanaoka K, Matsuzaki H, Hata K, Watanabe T, Nagano T, Urano Y. Discovery of Cell-Type-Specific and Disease-Related Enzymatic Activity Changes via Global Evaluation of Peptide Metabolism. J Am Chem Soc 2017; 139:3465-3472. [PMID: 28191944 DOI: 10.1021/jacs.6b11376] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Cellular homeostasis is maintained by a complex network of reactions catalyzed by enormous numbers of enzymatic activities (the enzymome), which serve to determine the phenotypes of cells. Here, we focused on the enzymomics of proteases and peptidases because these enzymes are an important class of disease-related proteins. We describe a system that (A) simultaneously evaluates metabolic activities of peptides using a series of exogenous peptide substrates and (B) identifies the enzymes that metabolize the specified peptide substrate with high throughput. We confirmed that the developed system was able to discover cell-type-specific and disease-related exo- and endopeptidase activities and identify the responsible enzymes. For example, we found that the activity of the endopeptidase neurolysin is highly elevated in human colorectal tumor tissue samples. This simple but powerful enzymomics platform should be widely applicable to uncover cell-type-specific reactions and altered enzymatic functions with potential value as biomarkers or drug targets in various disease states and to investigate the mechanisms of the underlying pathologies.
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Affiliation(s)
| | - Toru Komatsu
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | | | | | - Mako Kamiya
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | | | | | | | | | | | | | | | - Yasuteru Urano
- Core Research for Evolutional Science and Technology (CREST) Investigator, Japan Agency for Medical Research and Development (AMED) , 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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31
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Kimura Y, Komatsu T, Yanagi K, Hanaoka K, Ueno T, Terai T, Kojima H, Okabe T, Nagano T, Urano Y. Development of Chemical Tools to Monitor and Control Isoaspartyl Peptide Methyltransferase Activity. Angew Chem Int Ed Engl 2016; 56:153-157. [DOI: 10.1002/anie.201608677] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 11/07/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Yusuke Kimura
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Precursory Research for Embryonic Science and Technology, PRESTO, Japan, Science and Technology Agency, JST; 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1, Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kouichi Yanagi
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Tasuku Ueno
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takuya Terai
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Hirotatsu Kojima
- Discovery Initiative (DDI); The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takayoshi Okabe
- Discovery Initiative (DDI); The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Tetsuo Nagano
- Discovery Initiative (DDI); The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Graduate School of Medicine; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Core Research for Evolutional Science and Technology, CREST, Investigator, Japan, Agency for Medical Research and Development, AMED; 1-7-1 Otemachi Chiyoda-ku Tokyo 100-0004 Japan
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1, Hongo Bunkyo-ku Tokyo 113-0033 Japan
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32
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Kimura Y, Komatsu T, Yanagi K, Hanaoka K, Ueno T, Terai T, Kojima H, Okabe T, Nagano T, Urano Y. Development of Chemical Tools to Monitor and Control Isoaspartyl Peptide Methyltransferase Activity. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yusuke Kimura
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Precursory Research for Embryonic Science and Technology, PRESTO, Japan, Science and Technology Agency, JST 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1, Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kouichi Yanagi
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Tasuku Ueno
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takuya Terai
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Hirotatsu Kojima
- Discovery Initiative (DDI) The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takayoshi Okabe
- Discovery Initiative (DDI) The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Tetsuo Nagano
- Discovery Initiative (DDI) The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Graduate School of Medicine The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Core Research for Evolutional Science and Technology, CREST, Investigator, Japan, Agency for Medical Research and Development, AMED 1-7-1 Otemachi Chiyoda-ku Tokyo 100-0004 Japan
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1, Hongo Bunkyo-ku Tokyo 113-0033 Japan
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33
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Xie Y, Ge J, Lei H, Peng B, Zhang H, Wang D, Pan S, Chen G, Chen L, Wang Y, Hao Q, Yao SQ, Sun H. Fluorescent Probes for Single-Step Detection and Proteomic Profiling of Histone Deacetylases. J Am Chem Soc 2016; 138:15596-15604. [DOI: 10.1021/jacs.6b07334] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yusheng Xie
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Jingyan Ge
- College
of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People’s Republic of China
| | - Haipeng Lei
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Bo Peng
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Huatang Zhang
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Danyang Wang
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Sijun Pan
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Ganchao Chen
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Lanfang Chen
- Department
of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong, People’s Republic of China
| | - Yi Wang
- Department
of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong, People’s Republic of China
| | - Quan Hao
- Department
of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong, People’s Republic of China
| | - Shao Q. Yao
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Hongyan Sun
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
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34
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Abstract
Enzymes are essential for life, especially in the development of disease and on drug effects, but as we cannot yet directly observe the inside interactions and only partially observe biochemical outcomes, tools "translating" these processes into readable information are essential for better understanding of enzymes as well as for developing effective tools to fight against diseases. Therefore, sensitive small molecule probes suitable for direct in vivo monitoring of enzyme activities are ultimately desirable. For fulfilling this desire, two-photon small molecule enzymatic probes (TSMEPs) producing amplified fluorescent signals based on enzymatic conversion with better photophysical properties and deeper penetration in intact tissues and whole animals have been developed and demonstrated to be powerful in addressing the issues described above. Nonetheless, currently available TSMEPs only cover a small portion of enzymes despite the distinct advantages of two-photon fluorescence microscopy. In this Account, we would like to share design principles for TSMEPs as potential indicators of certain pathology-related biomarkers together with their applications in disease models to inspire more elegant work to be done in this area. Highlights will be addressed on how to equip two-photon fluorescent probes with features amenable for direct assessment of enzyme activities in complex pathological environments. We give three recent examples from our laboratory and collaborations in which TSMEPs are applied to visualize the distribution and activity of enzymes at cellular and organism levels. The first example shows that we could distinguish endogenous phosphatase activity in different organelles; the second illustrates that TSMEP is suitable for specific and sensitive detection of a potential Parkinson's disease marker (monoamine oxidase B) in a variety of biological systems from cells to patient samples, and the third identifies that TSMEPs can be applied to other enzyme families (proteases). Indeed, TSMEPs have helped to uncover new biological roles and functions of a series of enzymes; therefore, we hope to encourage more TSMEPs to be developed for diverse enzymes. Meanwhile, improvements in the TSMEP properties (such as new two-photon fluorophores with longer excitation and emission wavelengths and strategies allowing high specificity) are also indispensable for producing high-fidelity information inside biological systems. We are enthusiastic however that, with these efforts and wider applications of TSMEPs in both research studies and further clinical diagnoses, comprehensive knowledge of enzyme contributions to various physiologies will be obtained.
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Affiliation(s)
- Linghui Qian
- Department
of Chemistry, National University of Singapore 117543, Singapore
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), Nanjing 211816, P. R. China
| | - Shao Q. Yao
- Department
of Chemistry, National University of Singapore 117543, Singapore
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35
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Komatsu T, Yoshioka K, Hanaoka K, Terai T, Ueno T, Nagano T, Urano Y. Identification of Lung Inflammation-Related Elevation of Acylamino Acid Releasing Enzyme (APEH) Activity Using an Enzymomics Approach. Chem Pharm Bull (Tokyo) 2016; 64:1533-1538. [DOI: 10.1248/cpb.c16-00540] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
- Precursory Research for Embryonic Science and Technology (PRESTO) Investigator, Japan Science and Technology Agency (JST)
| | - Kentaro Yoshioka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | - Takuya Terai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | - Tasuku Ueno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | | | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
- Graduate School of Medicine, The University of Tokyo
- Core Research for Evolutional Science and Technology (CREST) Investigator, Japan Agency for Medical Research and Development (AMED)
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36
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Yoshioka K, Komatsu T, Nakada A, Onagi J, Kuriki Y, Kawaguchi M, Terai T, Ueno T, Hanaoka K, Nagano T, Urano Y. Identification of Tissue-Restricted Bioreaction Suitable for in Vivo Targeting by Fluorescent Substrate Library-Based Enzyme Discovery. J Am Chem Soc 2015; 137:12187-90. [DOI: 10.1021/jacs.5b05884] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Toru Komatsu
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | | | | | | | | | | | | | | | | | - Yasuteru Urano
- CREST, Japan Agency for Medical Research and Development (AMED), Chiyoda-ku, Tokyo 100-0004, Japan
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