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Fujita K, Urano Y. Activity-Based Fluorescence Diagnostics for Cancer. Chem Rev 2024; 124:4021-4078. [PMID: 38518254 DOI: 10.1021/acs.chemrev.3c00612] [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: 03/24/2024]
Abstract
Fluorescence imaging is one of the most promising approaches to achieve intraoperative assessment of the tumor/normal tissue margins during cancer surgery. This is critical to improve the patients' prognosis, and therefore various molecular fluorescence imaging probes have been developed for the identification of cancer lesions during surgery. Among them, "activatable" fluorescence probes that react with cancer-specific biomarker enzymes to generate fluorescence signals have great potential for high-contrast cancer imaging due to their low background fluorescence and high signal amplification by enzymatic turnover. Over the past two decades, activatable fluorescence probes employing various fluorescence control mechanisms have been developed worldwide for this purpose. Furthermore, new biomarker enzymatic activities for specific types of cancers have been identified, enabling visualization of various types of cancers with high sensitivity and specificity. This Review focuses on recent advances in the design, function and characteristics of activatable fluorescence probes that target cancer-specific enzymatic activities for cancer imaging and also discusses future prospects in the field of activity-based diagnostics for cancer.
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Shimizu T, Tanaka S, Kitagawa Y, Sakaguchi Y, Kamiya M, Takayanagi S, Takami H, Urano Y, Saito N. Advancement of fluorescent aminopeptidase probes for rapid cancer detection-current uses and neurosurgical applications. Front Surg 2024; 11:1298709. [PMID: 38516394 PMCID: PMC10954885 DOI: 10.3389/fsurg.2024.1298709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024] Open
Abstract
Surgical resection is considered for most brain tumors to obtain tissue diagnosis and to eradicate or debulk the tumor. Glioma, the most common primary malignant brain tumor, generally has a poor prognosis despite the multidisciplinary treatments with radical resection and chemoradiotherapy. Surgical resection of glioma is often complicated by the obscure border between the tumor and the adjacent brain tissues and by the tumor's infiltration into the eloquent brain. 5-aminolevulinic acid is frequently used for tumor visualization, as it exhibits high fluorescence in high-grade glioma. Here, we provide an overview of the fluorescent probes currently used for brain tumors, as well as those under development for other cancers, including HMRG-based probes, 2MeSiR-based probes, and other aminopeptidase probes. We describe our recently developed HMRG-based probes in brain tumors, such as PR-HMRG, combined with the existing diagnosis approach. These probes are remarkably effective for cancer cell recognition. Thus, they can be potentially integrated into surgical treatment for intraoperative detection of cancers.
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Affiliation(s)
- Takenori Shimizu
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shota Tanaka
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Kitagawa
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Yusuke Sakaguchi
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mako Kamiya
- Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Shunsaku Takayanagi
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hirokazu Takami
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuteru Urano
- Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory of Chemistry and Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Nobuhito Saito
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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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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Takahashi R, Ishizawa T, Inagaki Y, Tanaka M, Ogasawara A, Kuriki Y, Fujita K, Kamiya M, Ushiku T, Urano Y, Hasegawa K. Real-Time Fluorescence Imaging to Identify Cholangiocarcinoma in the Extrahepatic Biliary Tree Using an Enzyme-Activatable Probe. Liver Cancer 2023; 12:590-602. [PMID: 38058421 PMCID: PMC10697719 DOI: 10.1159/000530645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/03/2023] [Indexed: 12/08/2023] Open
Abstract
Introduction Complete resection is the only possible treatment for cholangiocarcinoma in the extrahepatic biliary tree (eCCA), although current imaging modalities are limited in their ability to accurately diagnose longitudinal spread. We aimed to develop fluorescence imaging techniques for real-time identification of eCCA using an enzyme-activatable probe, which emits fluorescence immediately after activation by a cancer-specific enzyme. Methods Using lysates and small tissue fragments collected from surgically resected specimens, we selected the most specific probe for eCCA from among 800 enzyme-activatable probes. The selected probe was directly sprayed onto resected specimens and fluorescence images were acquired; these images were evaluated for diagnostic accuracy. We also comprehensively searched for enzymes that could activate the probe, then compared their expression levels in cancer and non-cancer tissues. Results Analyses of 19 samples (four cancer lysates, seven non-cancer lysates, and eight bile samples) and 54 tissue fragments (13 cancer tissues and 41 non-cancer tissues) revealed that PM-2MeSiR was the most specific fluorophore for eCCA. Fluorescence images of 7 patients were obtained; these images enabled rapid identification of cancerous regions, which closely matched histopathology findings in 4 patients. Puromycin-sensitive aminopeptidase was identified as the enzyme that might activate the probe, and its expression was upregulated in eCCA. Conclusion Fluorescence imaging with PM-2MeSiR, which may be activated by puromycin-sensitive aminopeptidase, yielded generally high accuracy. This technique may be useful for real-time identification of the spread of eCCA during surgery and endoscopic examinations.
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Affiliation(s)
- Ryugen Takahashi
- Hepato-Biliary-Pancreatic Surgery Division, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku Tokyo, Japan
| | - Takeaki Ishizawa
- Hepato-Biliary-Pancreatic Surgery Division, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku Tokyo, Japan
- Department of Hepatobiliary-Pancreatic Surgery, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yoshinori Inagaki
- Hepato-Biliary-Pancreatic Surgery Division, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku Tokyo, Japan
| | - Mariko Tanaka
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akira Ogasawara
- Laboratory of Chemistry and Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yugo Kuriki
- Laboratory of Chemistry and Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kyohhei Fujita
- Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mako Kamiya
- Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuteru Urano
- Laboratory of Chemistry and Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Hasegawa
- Hepato-Biliary-Pancreatic Surgery Division, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku Tokyo, Japan
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Kawashima S, Yoshida D, Yoshioka T, Ogasawara A, Fujita K, Yanagiya M, Nagano M, Konoeda C, Hino H, Kitano K, Sato M, Hino R, Kojima R, Komatsu T, Kamiya M, Urano Y, Nakajima J. Rapid imaging of lung cancer using a red fluorescent probe to detect dipeptidyl peptidase 4 and puromycin-sensitive aminopeptidase activities. Sci Rep 2022; 12:9100. [PMID: 35650221 PMCID: PMC9160295 DOI: 10.1038/s41598-022-12665-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/11/2022] [Indexed: 11/09/2022] Open
Abstract
Rapid identification of lung-cancer micro-lesions is becoming increasingly important to improve the outcome of surgery by accurately defining the tumor/normal tissue margins and detecting tiny tumors, especially for patients with low lung function and early-stage cancer. The purpose of this study is to select and validate the best red fluorescent probe for rapid diagnosis of lung cancer by screening a library of 400 red fluorescent probes based on 2-methyl silicon rhodamine (2MeSiR) as the fluorescent scaffold, as well as to identify the target enzymes that activate the selected probe, and to confirm their expression in cancer cells. The selected probe, glutamine-alanine-2-methyl silicon rhodamine (QA-2MeSiR), showed 96.3% sensitivity and 85.2% specificity for visualization of lung cancer in surgically resected specimens within 10 min. In order to further reduce the background fluorescence while retaining the same side-chain structure, we modified QA-2MeSiR to obtain glutamine-alanine-2-methoxy silicon rhodamine (QA-2OMeSiR). This probe rapidly visualized even borderline lesions. Dipeptidyl peptidase 4 and puromycin-sensitive aminopeptidase were identified as enzymes mediating the cleavage and consequent fluorescence activation of QA-2OMeSiR, and it was confirmed that both enzymes are expressed in lung cancer. QA-2OMeSiR is a promising candidate for clinical application.
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Affiliation(s)
- Shun Kawashima
- Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Yoshida
- Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takafusa Yoshioka
- Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akira Ogasawara
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kyohhei Fujita
- Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masahiro Yanagiya
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masaaki Nagano
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Chihiro Konoeda
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Haruaki Hino
- Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kentaro Kitano
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masaaki Sato
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Rumi Hino
- Department of Sports and Health Science, Daito Bunka University, Saitama, Japan
| | - Ryosuke Kojima
- Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Mako Kamiya
- Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuteru Urano
- Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. .,Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
| | - Jun Nakajima
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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6
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Takahashi R, Ishizawa T, Sato M, Inagaki Y, Takanka M, Kuriki Y, Kamiya M, Ushiku T, Urano Y, Hasegawa K. Fluorescence Imaging Using Enzyme-Activatable Probes for Real-Time Identification of Pancreatic Cancer. Front Oncol 2021; 11:714527. [PMID: 34490111 PMCID: PMC8417470 DOI: 10.3389/fonc.2021.714527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/04/2021] [Indexed: 01/11/2023] Open
Abstract
Introduction Radical resection is the only curative treatment for pancreatic cancer, which is a life-threatening disease. However, it is often not easy to accurately identify the extent of the tumor before and during surgery. Here we describe the development of a novel method to detect pancreatic tumors using a tumor-specific enzyme-activatable fluorescence probe. Methods Tumor and non-tumor lysate or small specimen collected from the resected specimen were selected to serve as the most appropriate fluorescence probe to distinguish cancer tissues from noncancerous tissues. The selected probe was sprayed onto the cut surface of the resected specimen of cancer tissue to acquire a fluorescence image. Next, we evaluated the ability of the probe to detect the tumor and calculated the tumor-to-background ratio (TBR) by comparing the fluorescence image with the pathological extent of the tumor. Finally, we searched for a tumor-specific enzyme that optimally activates the selected probe. Results Using a library comprising 309 unique fluorescence probes, we selected GP-HMRG as the most appropriate activatable fluorescence probe. We obtained eight fluorescence images of resected specimens, among which four approximated the pathological findings of the tumor, which achieved the highest TBR. Finally, dipeptidyl-peptidase IV (DPP-IV) or a DPP-IV-like enzyme was identified as the target enzyme. Conclusion This novel method may enable rapid and real-time visualization of pancreatic cancer through the enzymatic activities of cancer tissues.
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Affiliation(s)
- Ryugen Takahashi
- Hepato-Biliary-Pancreatic Surgery Division, Department of Surgery, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Takeaki Ishizawa
- Hepato-Biliary-Pancreatic Surgery Division, Department of Surgery, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Masumitsu Sato
- Hepato-Biliary-Pancreatic Surgery Division, Department of Surgery, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Yoshinori Inagaki
- Hepato-Biliary-Pancreatic Surgery Division, Department of Surgery, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Mariko Takanka
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yugo Kuriki
- Laboratory of Chemistry and Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Mako Kamiya
- Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuteru Urano
- Laboratory of Chemistry and Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.,Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Hasegawa
- Hepato-Biliary-Pancreatic Surgery Division, Department of Surgery, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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Kitagawa Y, Tanaka S, Kamiya M, Kuriki Y, Yamamoto K, Shimizu T, Nejo T, Hana T, Matsuura R, Koike T, Yamazawa E, Kushihara Y, Takahashi S, Nomura M, Takami H, Takayanagi S, Mukasa A, Urano Y, Saito N. A Novel Topical Fluorescent Probe for Detection of Glioblastoma. Clin Cancer Res 2021; 27:3936-3947. [PMID: 34031057 DOI: 10.1158/1078-0432.ccr-20-4518] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/12/2021] [Accepted: 05/17/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Five-aminolevulinic acid (5-ALA) is widely used as an intraoperative fluorescent probe for radical resection of high-grade glioma, and thus aids in extending progression-free survival of patients. However, there exist some cases where 5-ALA fails to fluoresce. In some other cases, it may undergo fluorescence quenching but cannot be orally readministered during surgery. This study aimed to develop a novel hydroxymethyl rhodamine green (HMRG)-based fluorescence labeling system that can be repeatedly administered as a topical spray during surgery for the detection of glioblastoma. EXPERIMENTAL DESIGN We performed a three-stage probe screening using tumor lysates and fresh tumor tissues with our probe library consisting of a variety of HMRG probes with different dipeptides. We then performed proteome and transcript expression analyses to detect candidate enzymes responsible for cleaving the probe. Moreover, in vitro and ex vivo studies using U87 glioblastoma cell line were conducted to validate the findings. RESULTS The probe screening identified proline-arginine-HMRG (PR-HMRG) as the optimal probe that distinguished tumors from peritumoral tissues. Proteome analysis identified calpain-1 (CAPN1) to be responsible for cleaving the probe. CAPN1 was highly expressed in tumor tissues which reacted to the PR-HMRG probe. Knockdown of this enzyme suppressed fluorescence intensity in U87 glioblastoma cells. In situ assay using a mouse U87 xenograft model demonstrated marked contrast of fluorescence with the probe between the tumor and peritumoral tissues. CONCLUSIONS The novel fluorescent probe PR-HMRG is effective in detecting glioblastoma when applied topically. Further investigations are warranted to assess the efficacy and safety of its clinical use.
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Affiliation(s)
- Yosuke Kitagawa
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shota Tanaka
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Mako Kamiya
- Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yugo Kuriki
- Laboratory of Chemistry and Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kyoko Yamamoto
- Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takenori Shimizu
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takahide Nejo
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Taijun Hana
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Reiko Matsuura
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tsukasa Koike
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Erika Yamazawa
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Kushihara
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satoshi Takahashi
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masashi Nomura
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hirokazu Takami
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shunsaku Takayanagi
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akitake Mukasa
- Department of Neurosurgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yasuteru Urano
- Laboratory of Chemical Biology and Molecular Imaging, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. .,Laboratory of Chemistry and Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Nobuhito Saito
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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8
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Fujita K, Kamiya M, Urano Y. Rapid and Sensitive Detection of Cancer Cells with Activatable Fluorescent Probes for Enzyme Activity. Methods Mol Biol 2021; 2274:193-206. [PMID: 34050473 DOI: 10.1007/978-1-0716-1258-3_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fluorescence (FL)-guided detection of cancer is one of the most promising approaches to achieve intraoperative assessment of surgical margins. Enzymes, such as aminopeptidase, carboxypeptidase, and glycosidase, whose activities are increased in cancer, have attracted great interest as imaging targets for rapid and sensitive visualization of cancerous tissues with fluorescent probes. Activatable probes, which are initially nonfluorescent but become strongly fluorescent upon rapid one-step cleavage of their substrate moiety by the target enzyme, are especially promising for practical clinical application during surgical or endoscopic procedures due to the highly amplified FL change generated by enzyme-catalyzed turnover at lesion sites. Here, we describe robust protocols for using activatable fluorescent probes targeting cancer-associated enzyme activities to visualize cultured cancer cells, metastatic cancer in a mouse model, and cancerous lesions in surgical specimens from patients.
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Affiliation(s)
- Kyohhei Fujita
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Yasuteru Urano
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
- CREST, Japan Agency for Medical Research and Development, Tokyo, Japan.
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Fujita K, Kamiya M, Yoshioka T, Ogasawara A, Hino R, Kojima R, Ueo H, Urano Y. Rapid and Accurate Visualization of Breast Tumors with a Fluorescent Probe Targeting α-Mannosidase 2C1. ACS CENTRAL SCIENCE 2020; 6:2217-2227. [PMID: 33376783 PMCID: PMC7760471 DOI: 10.1021/acscentsci.0c01189] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Indexed: 05/21/2023]
Abstract
Accurate detection of breast tumors and discrimination of tumor from normal tissues during breast-conserving surgery are essential to reduce the risk of misdiagnosis or recurrence. However, existing probes show substantial background signals in normal breast tissues. In this study, we focus on glycosidase activities in breast tumors. We synthesized a series of 12 fluorescent probes and performed imaging-based evaluation on surgically resected human breast specimens. Among them, the α-mannosidase-reactive fluorescent probe HMRef-αMan detected breast cancer with 90% sensitivity and 100% specificity. We identified α-mannosidase 2C1 as the target enzyme and confirmed its overexpression in various breast tumors. We found that fibroadenoma, the most common benign breast lesion in young woman, tends to have higher α-mannosidase 2C1 activity than malignant cancer. Combined application of green-emitting HMRef-αMan and a red-emitting γ-glutamyltranspeptidase probe enabled efficient dual-color, dual-target optical discrimination of malignant and benign tumors.
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Affiliation(s)
- Kyohhei Fujita
- Graduate School of Medicine and Graduate School
of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo, 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, Tokyo 113-0033, Japan
- PRESTO,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Takafusa Yoshioka
- Graduate School of Medicine and Graduate School
of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Akira Ogasawara
- Graduate School of Medicine and Graduate School
of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Rumi Hino
- Daito
Bunka University, Department of Sports and
Health Science, 560 Iwadono, Higashimatsuyama, Saitama 355-8501, Japan
| | - Ryosuke Kojima
- Graduate School of Medicine and Graduate School
of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
- PRESTO,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hiroaki Ueo
- Ueo
Breast Cancer Hospital, 1-3-5 Futamatacho, Oita, Oita 870-0887, Japan
| | - Yasuteru Urano
- Graduate School of Medicine and Graduate School
of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
- CREST,
Japan
Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda,
Tokyo 100-0004, Japan
- E-mail
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10
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Parasar B, Chang PV. Finding the Sweet Spot for Breast Cancer Detection. ACS CENTRAL SCIENCE 2020; 6:2123-2125. [PMID: 33376773 PMCID: PMC7760063 DOI: 10.1021/acscentsci.0c01439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- Bibudha Parasar
- Department
of Chemistry and Chemical Biology, Department of Microbiology and
Immunology, Cornell Center for Immunology, and Cornell Institute of Host-Microbe Interactions
& Disease, Cornell University, Ithaca, New York 14853, United States
| | - Pamela V. Chang
- Department
of Chemistry and Chemical Biology, Department of Microbiology and
Immunology, Cornell Center for Immunology, and Cornell Institute of Host-Microbe Interactions
& Disease, Cornell University, Ithaca, New York 14853, United States
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11
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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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12
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Ichihashi Y, Komatsu T, Kyo E, Matsuzaki H, Hata K, Watanabe T, Ueno T, Hanaoka K, Urano Y. Separation-Based Enzymomics Assay for the Discovery of Altered Peptide-Metabolizing Enzymatic Activities in Biosamples. Anal Chem 2019; 91:11497-11501. [PMID: 31424921 DOI: 10.1021/acs.analchem.9b03016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We have developed a novel method to globally monitor the enzymatic activities of biological samples based on performing the global activity analysis on a proteome separated by native electrophoresis. The study of the alteration in peptide-metabolizing enzymatic activity in colorectal tumor specimens led us to the discovery of elevated thimet oligopeptidase activity, which contributed to the faster consumption of immune-stimulating peptide neurotensin.
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Affiliation(s)
- 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
| | - Etsu Kyo
- 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
| | - 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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13
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Gel-based proteomics in disease research: Is it still valuable? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:9-16. [PMID: 30392562 DOI: 10.1016/j.bbapap.2018.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/30/2018] [Accepted: 08/09/2018] [Indexed: 12/17/2022]
Abstract
Gel electrophoresis had been the primary method in proteomics. In the early era of proteomics, gel electrophoresis was a dominant technique of sample preparation for mass spectrometry analysis. Particularly, two-dimensional electrophoresis provided high-resolution proteome separation, and was regarded as the standard methodology for the separation of wide-range proteomes. However, gel electrophoresis turned downwards due to the progress of other separations including liquid chromatography and ionization techniques, resulting gel-free proteomics finally becoming dominant players at present. There are numerous advantages in gel-free approach in aspects of current trends of disease research. Interestingly, gel-free approaches are still advanced, it seems that gel electrophoresis will not be disappeared. The unique features of gel electrophoresis can be complementary for gel-free and it is suitable for the new wave of top-down functional proteomics.
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14
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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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15
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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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16
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Bassett B, Waibel B, White A, Hansen H, Stephens D, Koelper A, Larsen EM, Kim C, Glanzer A, Lavis LD, Hoops GC, Johnson RJ. Measuring the Global Substrate Specificity of Mycobacterial Serine Hydrolases Using a Library of Fluorogenic Ester Substrates. ACS Infect Dis 2018; 4:904-911. [PMID: 29648787 PMCID: PMC5993602 DOI: 10.1021/acsinfecdis.7b00263] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Among the proteins required for lipid metabolism in Mycobacterium tuberculosis are a significant number of uncharacterized serine hydrolases, especially lipases and esterases. Using a streamlined synthetic method, a library of immolative fluorogenic ester substrates was expanded to better represent the natural lipidomic diversity of Mycobacterium. This expanded fluorogenic library was then used to rapidly characterize the global structure activity relationship (SAR) of mycobacterial serine hydrolases in M. smegmatis under different growth conditions. Confirmation of fluorogenic substrate activation by mycobacterial serine hydrolases was performed using nonspecific serine hydrolase inhibitors and reinforced the biological significance of the SAR. The hydrolases responsible for the global SAR were then assigned using gel-resolved activity measurements, and these assignments were used to rapidly identify the relative substrate specificity of previously uncharacterized mycobacterial hydrolases. These measurements provide a global SAR of mycobacterial hydrolase activity, a picture of cycling hydrolase activity, and a detailed substrate specificity profile for previously uncharacterized hydrolases.
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Affiliation(s)
- Braden Bassett
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Brent Waibel
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Alex White
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Heather Hansen
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Dominique Stephens
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Andrew Koelper
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Erik M. Larsen
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Charles Kim
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Dr., Ashburn, VA 20147-2439 (USA)
| | - Adam Glanzer
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - Luke D. Lavis
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Dr., Ashburn, VA 20147-2439 (USA)
| | - Geoffrey C. Hoops
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
| | - R. Jeremy Johnson
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208-3443 (USA)
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17
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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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18
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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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19
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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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20
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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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21
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Yoshioka K, Komatsu T, Hanaoka K, Ueno T, Terai T, Nagano T, Urano Y. Discovery of a pyruvylated peptide-metabolizing enzyme using a fluorescent substrate-based protein discovery technique. Chem Commun (Camb) 2016; 52:4377-80. [PMID: 26925595 DOI: 10.1039/c6cc00829a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We employed a fluorescent substrate-based target discovery approach to screen the enzymome for metabolic activity towards pyruvyl-amidated peptides, and identified an acylamino acid-releasing enzyme (APEH). Cells overexpressing APEH exhibited higher metabolic activity towards the probe, N-pyruvyl-leucyl-7-amido-4-methylcoumarin (Pyr-Leu-AMC), while the selective APEH inhibitor AA74-1 blocked the reaction. Metabolism of various pyruvylated peptides in liver lysate was almost completely blocked by AA74-1. Pyruvyl peptides are synthesized in response to oxidative stress, but their biological role is poorly understood; identification of a key contributor to their metabolism should stimulate research on pathways leading from oxidative stress to protein modification and biological output.
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Affiliation(s)
- Kentaro Yoshioka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan and Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Tasuku Ueno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Takuya Terai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Tetsuo Nagano
- Drug Discovery Initiative, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan.
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan and Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan and 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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22
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Komatsu T, Urano Y. Evaluation of enzymatic activities in living systems with small-molecular fluorescent substrate probes. ANAL SCI 2016; 31:257-65. [PMID: 25864668 DOI: 10.2116/analsci.31.257] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this review, we aim to present an overview of how small-molecular fluorescent substrate probes for studying enzymatic functions are developed and how they are used in biological applications, under the following four headings: (1) History of Visual Detection of Enzymatic Activities, (2) Strategies to Design Fluorescent Substrate Probes to Measure Enzymatic Activities, (3) Development of Fluorescent Substrate Probes Suitable for Biological Studies, and (4) Biological Applications of Fluorescent Substrate Probes for Studying Enzymes.
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Affiliation(s)
- Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, 2) JST PRESTO, 4-1-9-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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23
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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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24
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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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25
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Niu G, Liu W, Wu J, Zhou B, Chen J, Zhang H, Ge J, Wang Y, Xu H, Wang P. Aminobenzofuran-Fused Rhodamine Dyes with Deep-Red to Near-Infrared Emission for Biological Applications. J Org Chem 2015; 80:3170-5. [DOI: 10.1021/acs.joc.5b00077] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Guangle Niu
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials
and CityU-CAS Joint Laboratory of Functional Materials and Devices,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weimin Liu
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials
and CityU-CAS Joint Laboratory of Functional Materials and Devices,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jiasheng Wu
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials
and CityU-CAS Joint Laboratory of Functional Materials and Devices,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Bingjiang Zhou
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials
and CityU-CAS Joint Laboratory of Functional Materials and Devices,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhong Chen
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials
and CityU-CAS Joint Laboratory of Functional Materials and Devices,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyan Zhang
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials
and CityU-CAS Joint Laboratory of Functional Materials and Devices,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jiechao Ge
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials
and CityU-CAS Joint Laboratory of Functional Materials and Devices,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ying Wang
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials
and CityU-CAS Joint Laboratory of Functional Materials and Devices,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Haitao Xu
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials
and CityU-CAS Joint Laboratory of Functional Materials and Devices,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Pengfei Wang
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials
and CityU-CAS Joint Laboratory of Functional Materials and Devices,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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26
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Tallman KR, Beatty KE. Far-red fluorogenic probes for esterase and lipase detection. Chembiochem 2014; 16:70-5. [PMID: 25469918 DOI: 10.1002/cbic.201402548] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 11/05/2022]
Abstract
Fluorogenic enzyme probes go from a dark to a bright state following hydrolysis and can provide a sensitive, real-time readout of enzyme activity. They are useful for examining enzymatic activity in bacteria, including the human pathogen Mycobacterium tuberculosis. Herein, we describe two fluorogenic esterase probes derived from the far-red fluorophore 7-hydroxy-9H-(1,3-dichloro-9,9-dimethylacridin-2-one) (DDAO). These probes offer enhanced optical properties compared to existing esterase probes because the hydrolysis product, DDAO, excites above 600 nm while retaining a good quantum yield (ϕ=0.40). We validated both probes with a panel of commercially available enzymes alongside known resorufin- and fluorescein-derived esterase substrates. Furthermore, we used these probes to reveal esterase activity in protein gel-resolved mycobacterial lysates. These probes represent new tools for esterase detection and characterization and should find use in a variety of applications.
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Affiliation(s)
- Katie R Tallman
- Department of Physiology and Pharmacology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 SW Moody Avenue, CL3B, Portland, OR 97201 (USA)
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