1
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Miao Y, Yu ZQ, Xu S, Yan M. Quinone Methide Based Self-Immobilizing Molecular Fluorescent Probes for In Situ Imaging of Enzymes. Chem Asian J 2024; 19:e202400189. [PMID: 38514393 DOI: 10.1002/asia.202400189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 03/23/2024]
Abstract
Enzymes play important roles not only in normal physiological processes but in the development of many diseases. In situ imaging of enzymes with high-resolution in living systems would helpful for clinical diagnosis and treatment. However, many molecular fluorescent probes suffer from the drawback of diffusing away from the reaction site of enzymes even out of the cells, losing the in situ information and resulting in poor imaging resolution. Quinone methide (QM) based self-immobilizing probes allow the fluorescent signal to be immobilized near the target for an extended period without deactivating the target enzymes, ensuring that it will provide amplified signals and in situ information of the target with high resolution. In this review, we summarized the recent progress of QM-based self-immobilizing probes including their design strategies, working mechanisms, classifications and applications in in situ enzyme imaging. This review calls for the development of more activatable QM-based probe with the advantages of high stability in the absence of the target but very high labeling efficiency after activation.
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Affiliation(s)
- Yeru Miao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
| | - Zhen-Qing Yu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
| | - Shuai Xu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
| | - Mei Yan
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China
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2
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Yamin D, Uskoković V, Wakil AM, Goni MD, Shamsuddin SH, Mustafa FH, Alfouzan WA, Alissa M, Alshengeti A, Almaghrabi RH, Fares MAA, Garout M, Al Kaabi NA, Alshehri AA, Ali HM, Rabaan AA, Aldubisi FA, Yean CY, Yusof NY. Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria. Diagnostics (Basel) 2023; 13:3246. [PMID: 37892067 PMCID: PMC10606640 DOI: 10.3390/diagnostics13203246] [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: 09/30/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
Antibiotic resistance is a global public health concern, posing a significant threat to the effectiveness of antibiotics in treating bacterial infections. The accurate and timely detection of antibiotic-resistant bacteria is crucial for implementing appropriate treatment strategies and preventing the spread of resistant strains. This manuscript provides an overview of the current and emerging technologies used for the detection of antibiotic-resistant bacteria. We discuss traditional culture-based methods, molecular techniques, and innovative approaches, highlighting their advantages, limitations, and potential future applications. By understanding the strengths and limitations of these technologies, researchers and healthcare professionals can make informed decisions in combating antibiotic resistance and improving patient outcomes.
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Affiliation(s)
- Dina Yamin
- Al-Karak Public Hospital, Karak 61210, Jordan;
- Institute for Research in Molecular Medicine, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia;
| | - Vuk Uskoković
- TardigradeNano LLC., Irvine, CA 92604, USA;
- Department of Mechanical Engineering, San Diego State University, San Diego, CA 92182, USA
| | - Abubakar Muhammad Wakil
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia;
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, University of Maiduguri, Maiduguri 600104, Borno, Nigeria
| | - Mohammed Dauda Goni
- Public Health and Zoonoses Research Group, Faculty of Veterinary Medicine, University Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia;
| | - Shazana Hilda Shamsuddin
- Department of Pathology, School of Medical Sciences, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia;
| | - Fatin Hamimi Mustafa
- Department of Electronic & Computer Engineering, Faculty of Electrical Engineering, University Teknologi Malaysia, Johor Bharu 81310, Johor, Malaysia;
| | - Wadha A. Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait;
- Microbiology Unit, Department of Laboratories, Farwania Hospital, Farwania 85000, Kuwait
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia;
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia;
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah 41491, Saudi Arabia
| | - Rana H. Almaghrabi
- Pediatric Department, Prince Sultan Medical Military City, Riyadh 12233, Saudi Arabia;
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
| | - Mona A. Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia;
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Nawal A. Al Kaabi
- College of Medicine and Health Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates;
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi 51900, United Arab Emirates
| | - Ahmad A. Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia;
| | - Hamza M. Ali
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah 41411, Saudi Arabia;
| | - Ali A. Rabaan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | | | - Chan Yean Yean
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, University Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
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3
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Ma Y, Liang Y, Guo M, Min D, Zheng L, Tang Y, Sun X. Strategic design of lysine-targeted irreversible covalent NDM-1 inhibitors. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.108072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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4
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Keil J, Rafn GR, Turan IM, Aljohani MA, Sahebjam-Atabaki R, Sun XL. Sialidase Inhibitors with Different Mechanisms. J Med Chem 2022; 65:13574-13593. [PMID: 36252951 PMCID: PMC9620260 DOI: 10.1021/acs.jmedchem.2c01258] [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] [Received: 08/02/2022] [Indexed: 11/28/2022]
Abstract
Sialidases, or neuraminidases, are enzymes that catalyze the hydrolysis of sialic acid (Sia)-containing molecules, mostly removal of the terminal Sia (desialylation). By desialylation, sialidase can modulate the functionality of the target compound and is thus often involved in biological pathways. Inhibition of sialidases with inhibitors is an important approach for understanding sialidase function and the underlying mechanisms and could serve as a therapeutic approach as well. Transition-state analogues, such as anti-influenza drugs oseltamivir and zanamivir, are major sialidase inhibitors. In addition, difluoro-sialic acids were developed as mechanism-based sialidase inhibitors. Further, fluorinated quinone methide-based suicide substrates were reported. Sialidase product analogue inhibitors were also explored. Finally, natural products have shown competitive inhibiton against viral, bacterial, and human sialidases. This Perspective describes sialidase inhibitors with different mechanisms and their activities and future potential, which include transition-state analogue inhibitors, mechanism-based inhibitors, suicide substrate inhibitors, product analogue inhibitors, and natural product inhibitors.
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Affiliation(s)
- Joseph
M. Keil
- Department of Chemistry, Chemical and
Biomedical Engineering and Center for Gene Regulation in Health and
Disease (GRHD), Cleveland State University, Cleveland, Ohio 44115, United States
| | - Garrett R. Rafn
- Department of Chemistry, Chemical and
Biomedical Engineering and Center for Gene Regulation in Health and
Disease (GRHD), Cleveland State University, Cleveland, Ohio 44115, United States
| | - Isaac M. Turan
- Department of Chemistry, Chemical and
Biomedical Engineering and Center for Gene Regulation in Health and
Disease (GRHD), Cleveland State University, Cleveland, Ohio 44115, United States
| | - Majdi A. Aljohani
- Department of Chemistry, Chemical and
Biomedical Engineering and Center for Gene Regulation in Health and
Disease (GRHD), Cleveland State University, Cleveland, Ohio 44115, United States
| | - Reza Sahebjam-Atabaki
- Department of Chemistry, Chemical and
Biomedical Engineering and Center for Gene Regulation in Health and
Disease (GRHD), Cleveland State University, Cleveland, Ohio 44115, United States
| | - Xue-Long Sun
- Department of Chemistry, Chemical and
Biomedical Engineering and Center for Gene Regulation in Health and
Disease (GRHD), Cleveland State University, Cleveland, Ohio 44115, United States
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5
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Detection of Bacterial α-l-Fucosidases with an Ortho-Quinone Methide-Based Probe and Mapping of the Probe-Protein Adducts. Molecules 2022; 27:molecules27051615. [PMID: 35268716 PMCID: PMC8911971 DOI: 10.3390/molecules27051615] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 11/24/2022] Open
Abstract
Fucosidases are associated with several pathological conditions and play an important role in the health of the human gut. For example, fucosidases have been shown to be indicators and/or involved in hepatocellular carcinoma, breast cancer, and helicobacter pylori infections. A prerequisite for the detection and profiling of fucosidases is the formation of a specific covalent linkage between the enzyme of interest and the activity-based probe (ABP). The most commonly used fucosidase ABPs are limited to only one of the classes of fucosidases, the retaining fucosidases. New approaches are needed that allow for the detection of the second class of fucosidases, the inverting type. Here, we report an ortho-quinone methide-based probe with an azide mini-tag that selectively labels both retaining and inverting bacterial α-l-fucosidases. Mass spectrometry-based intact protein and sequence analysis of a probe-labeled bacterial fucosidase revealed almost exclusive single labeling at two specific tryptophan residues outside of the active site. Furthermore, the probe could detect and image extracellular fucosidase activity on the surface of live bacteria.
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6
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Abe A, Kamiya M. A versatile toolbox for investigating biological processes based on quinone methide chemistry: From self-immolative linkers to self-immobilizing agents. Bioorg Med Chem 2021; 44:116281. [PMID: 34216983 DOI: 10.1016/j.bmc.2021.116281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/12/2021] [Indexed: 11/26/2022]
Abstract
Quinone methide (QM) species have been included in the design of various functional molecules. In this review, we present a comprehensive overview of bioanalytical tools based on QM chemistry. In the first part, we focus on self-immolative linkers that have been incorporated into functional molecules such as prodrugs and fluorescent probes. In the latter half, we outline how the highly electrophilic property of QMs, enabling them to react rapidly with neighboring nucleophiles, has been applied to develop inhibitors or labeling probes for enzymes, as well as self-immobilizing fluorogenic probes with high spatial resolution. This review systematically summarizes the versatile QM toolbox available for investigating biological processes.
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Affiliation(s)
- Atsuki Abe
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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7
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Luijkx YMCA, Jongkees S, Strijbis K, Wennekes T. Development of a 1,2-difluorofucoside activity-based probe for profiling GH29 fucosidases. Org Biomol Chem 2021; 19:2968-2977. [PMID: 33729259 DOI: 10.1039/d1ob00054c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
GH29 α-l-fucosidases catalyze hydrolysis of terminal α-l-fucosyl linkages with varying specificity and are expressed by prominent members of the human gut microbiota. Both homeostasis and dysbiosis at the human intestinal microbiota interface have been correlated with altered fucosidase activity. Herein we describe the development of a 2-deoxy-2-fluoro fucosyl fluoride derivative with an azide mini-tag as an activity-based probe (ABP) for selective in vitro labelling of GH29 α-l-fucosidases. Only catalytically active fucosidases are inactivated by this ABP, allowing their functionalization with a biotin reporter group via the CuAAC reaction and subsequent in-gel detection at nanogram levels. The ABP we present here is shown to be active against a GH29 α-l-fucosidase from Bacteroides fragilis and capable of labeling two other GH29 α-l-fucosidases with different linkage specificity, illustrating its broader utility. This novel ABP is a valuable addition to the toolbox of fucosidase probes by allowing identification and functional studies of the wide variety of GH29 fucosidases, including those in the gut microbiota.
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Affiliation(s)
- Yvette M C A Luijkx
- Department Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
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8
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Li Y, Xue C, Fang Z, Xu W, Xie H. In Vivo Visualization of γ-Glutamyl Transpeptidase Activity with an Activatable Self-Immobilizing Near-Infrared Probe. Anal Chem 2020; 92:15017-15024. [DOI: 10.1021/acs.analchem.0c02954] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yuyao Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Chenghong Xue
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhijun Fang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weipan Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Hexin Xie
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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9
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Noguchi K, Shimomura T, Ohuchi Y, Ishiyama M, Shiga M, Mori T, Katayama Y, Ueno Y. β-Galactosidase-Catalyzed Fluorescent Reporter Labeling of Living Cells for Sensitive Detection of Cell Surface Antigens. Bioconjug Chem 2020; 31:1740-1744. [PMID: 32538077 DOI: 10.1021/acs.bioconjchem.0c00180] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The ability to detect cell surface proteins using fluorescent-dye-labeled antibodies is crucial for the reliable identification of many cell types. However, the different types of cell surface proteins used to identify cells are currently limited in number because they need to be expressed at high levels to exceed background cellular autofluorescence, especially in the shorter-wavelength region. Herein we report on a new method, quinone methide-based catalyzed labeling for signal amplification (CLAMP), in which the fluorescence signal is amplified by an enzymatic reaction that strongly facilitates the detection of cell surface proteins on living cells. We used β-galactosidase as an amplification enzyme and designed a substrate for it, called MUGF, that contains a fluoromethyl group. Upon removal of the galactosyl group in MUGF by β-galactosidase labeling of the target cell surface proteins, the resulting product containing the quinone methide group was found to be both cell-membrane-permeable and reactive with intracellular nucleophiles, thereby providing fluorescent adducts. Using this method, we successfully detected several cell surface proteins, including programmed death ligand 1 protein, which is difficult to detect using conventional fluorescent-dye-labeled antibodies.
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Affiliation(s)
- Katsuya Noguchi
- Dojindo Laboratories, 2025-5 Tabaru, Mashiki-machi, Kumamoto 861-2202, Japan
| | - Takashi Shimomura
- Dojindo Laboratories, 2025-5 Tabaru, Mashiki-machi, Kumamoto 861-2202, Japan
| | - Yuya Ohuchi
- Dojindo Laboratories, 2025-5 Tabaru, Mashiki-machi, Kumamoto 861-2202, Japan
| | - Munetaka Ishiyama
- Dojindo Laboratories, 2025-5 Tabaru, Mashiki-machi, Kumamoto 861-2202, Japan
| | - Masanobu Shiga
- Dojindo Laboratories, 2025-5 Tabaru, Mashiki-machi, Kumamoto 861-2202, Japan
| | - Takeshi Mori
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshiki Katayama
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Department of Biomedical Engineering, Chung Yuan Christian University, Taoyuan 32023, Taiwan
| | - Yuichiro Ueno
- Dojindo Laboratories, 2025-5 Tabaru, Mashiki-machi, Kumamoto 861-2202, Japan
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10
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Johnson BM, Shu YZ, Zhuo X, Meanwell NA. Metabolic and Pharmaceutical Aspects of Fluorinated Compounds. J Med Chem 2020; 63:6315-6386. [PMID: 32182061 DOI: 10.1021/acs.jmedchem.9b01877] [Citation(s) in RCA: 310] [Impact Index Per Article: 77.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The applications of fluorine in drug design continue to expand, facilitated by an improved understanding of its effects on physicochemical properties and the development of synthetic methodologies that are providing access to new fluorinated motifs. In turn, studies of fluorinated molecules are providing deeper insights into the effects of fluorine on metabolic pathways, distribution, and disposition. Despite the high strength of the C-F bond, the departure of fluoride from metabolic intermediates can be facile. This reactivity has been leveraged in the design of mechanism-based enzyme inhibitors and has influenced the metabolic fate of fluorinated compounds. In this Perspective, we summarize the literature associated with the metabolism of fluorinated molecules, focusing on examples where the presence of fluorine influences the metabolic profile. These studies have revealed potentially problematic outcomes with some fluorinated motifs and are enhancing our understanding of how fluorine should be deployed.
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Affiliation(s)
- Benjamin M Johnson
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Yue-Zhong Shu
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb Company, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Xiaoliang Zhuo
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Nicholas A Meanwell
- Discovery Chemistry Platforms, Small Molecule Drug Discovery, Bristol Myers Squibb Company, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
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11
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Omote M, Karuo Y, Dousei S, Sakamoto M, Tarui A, Sato K, Kawai K. Construction of Quaternary Carbon Center by the Reaction of Aza-o-Quinone Methide Mediated Carbocation Intermediate. HETEROCYCLES 2020. [DOI: 10.3987/com-19-s(f)33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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12
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Abstract
Biomedical use cases for self-immolative polymers.
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Affiliation(s)
- Yue Xiao
- College of Chemistry
- Green Catalysis Center
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications
- Zhengzhou University
- Zhengzhou 450001
| | - Xuyu Tan
- Department of Chemistry and Chemical Biology
- Northeastern University
- Boston
- USA
| | - Zhaohui Li
- College of Chemistry
- Green Catalysis Center
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications
- Zhengzhou University
- Zhengzhou 450001
| | - Ke Zhang
- Department of Chemistry and Chemical Biology
- Northeastern University
- Boston
- USA
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13
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Song H, Li Y, Chen Y, Xue C, Xie H. Highly Efficient Multiple‐Labeling Probes for the Visualization of Enzyme Activities. Chemistry 2019; 25:13994-14002. [DOI: 10.1002/chem.201903458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/30/2019] [Indexed: 01/19/2023]
Affiliation(s)
- Heng Song
- State Key Laboratory of Bioreactor EngineeringShanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Yuyao Li
- State Key Laboratory of Bioreactor EngineeringShanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Yefeng Chen
- State Key Laboratory of Bioreactor EngineeringShanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Chenghong Xue
- State Key Laboratory of Bioreactor EngineeringShanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Hexin Xie
- State Key Laboratory of Bioreactor EngineeringShanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and Technology Shanghai 200237 P. R. China
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14
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Koide R, Nishimura S. Antiadhesive Nanosomes Facilitate Targeting of the Lysosomal GlcNAc Salvage Pathway through Derailed Cancer Endocytosis. Angew Chem Int Ed Engl 2019; 58:14513-14518. [DOI: 10.1002/anie.201907778] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/02/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Ryosuke Koide
- Graduate School of Life Science and Faculty of Advanced Life Science Hokkaido University N21, W11, kita-ku Sapporo 001-0021 Japan
| | - Shin‐Ichiro Nishimura
- Graduate School of Life Science and Faculty of Advanced Life Science Hokkaido University N21, W11, kita-ku Sapporo 001-0021 Japan
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15
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Koide R, Nishimura S. Antiadhesive Nanosomes Facilitate Targeting of the Lysosomal GlcNAc Salvage Pathway through Derailed Cancer Endocytosis. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ryosuke Koide
- Graduate School of Life Science and Faculty of Advanced Life Science Hokkaido University N21, W11, kita-ku Sapporo 001-0021 Japan
| | - Shin‐Ichiro Nishimura
- Graduate School of Life Science and Faculty of Advanced Life Science Hokkaido University N21, W11, kita-ku Sapporo 001-0021 Japan
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16
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Marques ARA, Willems LI, Herrera Moro D, Florea BI, Scheij S, Ottenhoff R, van Roomen CPAA, Verhoek M, Nelson JK, Kallemeijn WW, Biela-Banas A, Martin OR, Cachón-González MB, Kim NN, Cox TM, Boot RG, Overkleeft HS, Aerts JMFG. A Specific Activity-Based Probe to Monitor Family GH59 Galactosylceramidase, the Enzyme Deficient in Krabbe Disease. Chembiochem 2017; 18:402-412. [DOI: 10.1002/cbic.201600561] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Indexed: 11/07/2022]
Affiliation(s)
- André R. A. Marques
- Department of Biochemistry; Academic Medical Center; University of Amsterdam; Meibergdreef 15 1105 AZ Amsterdam The Netherlands
- Present address: Institute of Biochemistry; Christian-Albrechts-University of Kiel; Otto-Hahn-Platz 9 24098 Kiel Germany
| | - Lianne I. Willems
- Department of Bio-organic Synthesis; Leiden Institute of Chemistry; Leiden University; Einsteeinweg 55 2300 RA Leiden The Netherlands
- Present address: Department of Chemistry; Simon Fraser University; 8888 University Drive Burnaby V5A 1S6 BC Canada
| | - Daniela Herrera Moro
- Department of Biochemistry; Academic Medical Center; University of Amsterdam; Meibergdreef 15 1105 AZ Amsterdam The Netherlands
| | - Bogdan I. Florea
- Department of Bio-organic Synthesis; Leiden Institute of Chemistry; Leiden University; Einsteeinweg 55 2300 RA Leiden The Netherlands
| | - Saskia Scheij
- Department of Biochemistry; Academic Medical Center; University of Amsterdam; Meibergdreef 15 1105 AZ Amsterdam The Netherlands
| | - Roelof Ottenhoff
- Department of Biochemistry; Academic Medical Center; University of Amsterdam; Meibergdreef 15 1105 AZ Amsterdam The Netherlands
| | - Cindy P. A. A. van Roomen
- Department of Biochemistry; Academic Medical Center; University of Amsterdam; Meibergdreef 15 1105 AZ Amsterdam The Netherlands
| | - Marri Verhoek
- Department of Biochemistry; Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2300 RA Leiden The Netherlands
| | - Jessica K. Nelson
- Department of Biochemistry; Academic Medical Center; University of Amsterdam; Meibergdreef 15 1105 AZ Amsterdam The Netherlands
| | - Wouter W. Kallemeijn
- Department of Biochemistry; Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2300 RA Leiden The Netherlands
| | - Anna Biela-Banas
- Institute of Organic and Analytical Chemistry; Université D'Orléans; Rue de Chartres B. P. 6759 45100 Orléans France
| | - Olivier R. Martin
- Institute of Organic and Analytical Chemistry; Université D'Orléans; Rue de Chartres B. P. 6759 45100 Orléans France
| | - M. Begoña Cachón-González
- Department of Medicine; University of Cambridge; Addenbrooke's Hospital; Hills Road Cambridge CB2 2QQ UK
| | - Nee Na Kim
- Department of Medicine; University of Cambridge; Addenbrooke's Hospital; Hills Road Cambridge CB2 2QQ UK
| | - Timothy M. Cox
- Department of Medicine; University of Cambridge; Addenbrooke's Hospital; Hills Road Cambridge CB2 2QQ UK
| | - Rolf G. Boot
- Department of Biochemistry; Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2300 RA Leiden The Netherlands
| | - Herman S. Overkleeft
- Department of Bio-organic Synthesis; Leiden Institute of Chemistry; Leiden University; Einsteeinweg 55 2300 RA Leiden The Netherlands
| | - Johannes M. F. G. Aerts
- Department of Biochemistry; Academic Medical Center; University of Amsterdam; Meibergdreef 15 1105 AZ Amsterdam The Netherlands
- Department of Biochemistry; Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2300 RA Leiden The Netherlands
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17
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Lumba MA, Willis LM, Santra S, Rana R, Schito L, Rey S, Wouters BG, Nitz M. A β-galactosidase probe for the detection of cellular senescence by mass cytometry. Org Biomol Chem 2017; 15:6388-6392. [DOI: 10.1039/c7ob01227f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Enzyme substrates for mass cytometry applications enable new dimensions in multiparametric cellular assays.
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Affiliation(s)
- M. A. Lumba
- Department of Chemistry
- University of Toronto
- Toronto
- M5S 3H6 Canada
| | - L. M. Willis
- Department of Chemistry
- University of Toronto
- Toronto
- M5S 3H6 Canada
| | - S. Santra
- Department of Chemistry
- University of Toronto
- Toronto
- M5S 3H6 Canada
| | - R. Rana
- Department of Chemistry
- University of Toronto
- Toronto
- M5S 3H6 Canada
| | - L. Schito
- Princess Margaret Cancer Centre and The Campbell Family Institute for Cancer Research
- University Health Network
- Toronto
- Canada
| | - S. Rey
- Princess Margaret Cancer Centre and The Campbell Family Institute for Cancer Research
- University Health Network
- Toronto
- Canada
| | - B. G. Wouters
- Princess Margaret Cancer Centre and The Campbell Family Institute for Cancer Research
- University Health Network
- Toronto
- Canada
| | - M. Nitz
- Department of Chemistry
- University of Toronto
- Toronto
- M5S 3H6 Canada
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18
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Polaske NW, Kelly BD, Ashworth-Sharpe J, Bieniarz C. Quinone Methide Signal Amplification: Covalent Reporter Labeling of Cancer Epitopes using Alkaline Phosphatase Substrates. Bioconjug Chem 2016; 27:660-6. [DOI: 10.1021/acs.bioconjchem.5b00652] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nathan W. Polaske
- Ventana Medical Systems, Inc., 1910 East Innovation
Park Drive, Tucson, Arizona 85755, United States
| | - Brian D. Kelly
- Ventana Medical Systems, Inc., 1910 East Innovation
Park Drive, Tucson, Arizona 85755, United States
| | - Julia Ashworth-Sharpe
- Ventana Medical Systems, Inc., 1910 East Innovation
Park Drive, Tucson, Arizona 85755, United States
| | - Christopher Bieniarz
- Ventana Medical Systems, Inc., 1910 East Innovation
Park Drive, Tucson, Arizona 85755, United States
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19
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Willems LI, Jiang J, Li KY, Witte MD, Kallemeijn WW, Beenakker TJN, Schröder SP, Aerts JMFG, van der Marel GA, Codée JDC, Overkleeft HS. From Covalent Glycosidase Inhibitors to Activity-Based Glycosidase Probes. Chemistry 2014; 20:10864-72. [DOI: 10.1002/chem.201404014] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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20
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Stubbs KA. Activity-based proteomics probes for carbohydrate-processing enzymes: current trends and future outlook. Carbohydr Res 2014; 390:9-19. [DOI: 10.1016/j.carres.2014.02.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/21/2014] [Accepted: 02/22/2014] [Indexed: 11/27/2022]
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21
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Shao Q, Zheng Y, Dong X, Tang K, Yan X, Xing B. A Covalent Reporter of β-Lactamase Activity for Fluorescent Imaging and Rapid Screening of Antibiotic-Resistant Bacteria. Chemistry 2013; 19:10903-10. [DOI: 10.1002/chem.201301654] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Indexed: 01/16/2023]
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22
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Kai H, Hinou H, Naruchi K, Matsushita T, Nishimura SI. Macrocyclic Mechanism-Based Inhibitor for Neuraminidases. Chemistry 2012; 19:1364-72. [DOI: 10.1002/chem.201200859] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 10/24/2012] [Indexed: 01/13/2023]
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23
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Kai H, Hinou H, Nishimura SI. Aglycone-focused randomization of 2-difluoromethylphenyl-type sialoside suicide substrates for neuraminidases. Bioorg Med Chem 2012; 20:2739-46. [DOI: 10.1016/j.bmc.2012.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 01/31/2012] [Accepted: 02/01/2012] [Indexed: 11/29/2022]
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24
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Sen D, Sarkar A, Gosling A, Gras SL, Stevens GW, Kentish SE, Bhattacharya P, Barber AR, Bhattacharjee C. Feasibility study of enzyme immobilization on polymeric membrane: A case study with enzymatically galacto-oligosaccharides production from lactose. J Memb Sci 2011. [DOI: 10.1016/j.memsci.2011.05.032] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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Gandy MN, Debowski AW, Stubbs KA. A general method for affinity-based proteomic profiling of exo-α-glycosidases. Chem Commun (Camb) 2011; 47:5037-9. [PMID: 21431156 DOI: 10.1039/c1cc10308c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis of iminosugar-based affinity-based proteomics probes for use in probing exo-α-glycosidase activity.
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Affiliation(s)
- Michael N Gandy
- Chemistry M313, School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA Australia6009
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26
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Witte MD, van der Marel GA, Aerts JMFG, Overkleeft HS. Irreversible inhibitors and activity-based probes as research tools in chemical glycobiology. Org Biomol Chem 2011; 9:5908-26. [DOI: 10.1039/c1ob05531c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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27
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Kwan DH, Chen H, Ratananikom K, Hancock SM, Watanabe Y, Kongsaeree PT, Samuels AL, Withers SG. Self‐Immobilizing Fluorogenic Imaging Agents of Enzyme Activity. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201005705] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- David H. Kwan
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | - Hong‐Ming Chen
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | | | - Susan M. Hancock
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | - Yoichiro Watanabe
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | | | - A. Lacey Samuels
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | - Stephen G. Withers
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
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28
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Kwan DH, Chen H, Ratananikom K, Hancock SM, Watanabe Y, Kongsaeree PT, Samuels AL, Withers SG. Self‐Immobilizing Fluorogenic Imaging Agents of Enzyme Activity. Angew Chem Int Ed Engl 2010; 50:300-3. [DOI: 10.1002/anie.201005705] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- David H. Kwan
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | - Hong‐Ming Chen
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | | | - Susan M. Hancock
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | - Yoichiro Watanabe
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | | | - A. Lacey Samuels
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
| | - Stephen G. Withers
- Departments of Chemistry and Botany, University of British Columbia, Vancouver, B.C. V6T 1Z1 (Canada), Fax: (+1) 604‐822‐8869
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29
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Vuong TV, Wilson DB. Glycoside hydrolases: catalytic base/nucleophile diversity. Biotechnol Bioeng 2010; 107:195-205. [PMID: 20552664 DOI: 10.1002/bit.22838] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent studies have shown that a number of glycoside hydrolase families do not follow the classical catalytic mechanisms, as they lack a typical catalytic base/nucleophile. A variety of mechanisms are used to replace this function, including substrate-assisted catalysis, a network of several residues, and the use of non-carboxylate residues or exogenous nucleophiles. Removal of the catalytic base/nucleophile by mutation can have a profound impact on substrate specificity, producing enzymes with completely new functions.
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Affiliation(s)
- Thu V Vuong
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
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30
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Carvalho ST, Sola-Penna M, Oliveira IA, Pita S, Goncalves AS, Neves BC, Sousa FR, Freire-de-Lima L, Kurogochi M, Hinou H, Nishimura SI, Mendonca-Previato L, Previato JO, Todeschini AR. A new class of mechanism-based inhibitors for Trypanosoma cruzi trans-sialidase and their influence on parasite virulence. Glycobiology 2010; 20:1034-45. [DOI: 10.1093/glycob/cwq065] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Weinstain R, Baran PS, Shabat D. Activity-Linked Labeling of Enzymes by Self-Immolative Polymers. Bioconjug Chem 2009; 20:1783-91. [DOI: 10.1021/bc9002037] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Roy Weinstain
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 Israel, and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Phil S. Baran
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 Israel, and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Doron Shabat
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 Israel, and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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32
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Neunert G, Polewski P, Walejko P, Markiewicz M, Witkowski S, Polewski K. Glycosidic moiety changes the spectroscopic properties of dl-alpha-tocopherol in DMSO/water solution and in organic solvents. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2009; 73:301-308. [PMID: 19346158 DOI: 10.1016/j.saa.2009.02.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 02/13/2009] [Accepted: 02/19/2009] [Indexed: 05/27/2023]
Abstract
In this study we estimated how conjugation with a sugar moiety influences the spectral properties of tocopherol and relate the spectroscopic properties of glycosides to solvent properties such as viscosity and polarity. Spectroscopic properties (absorption, fluorescence, fluorescence anisotropy and fluorescence lifetime) of three dl-alpha-tocopheryl glycosides (dl-alpha-tocopheryl orthoacetate derivative and glycosides of dl-alpha-tocopherol model compounds: 2,2,5,7,8-pentamethyl-6-chromanol and Trolox) were studied in DMSO/water solution. In all investigated compounds dissolved in DMSO/water mixture the absorption and emission maxima were blue-shifted. The fluorescence lifetimes were longer compared with those obtained for the parent compounds, except for the Trolox glucoside, in which it was shorter. The observed effect is connected with an increase in the electronic energy in the ground state due to electron rearrangement in the chromanol system caused by interaction with the sugar moiety. The extent of the spectral shift is related to the sugar moiety substituted at the phenolic oxygen rather than to substitution at the 2a position in the chromanol ring. The fluorescent properties of dl-alpha-tocopheryl glucoside in organic solvents were measured. The Stokes shift was related to the orientational polarizability of the solvents. The study of viscosity suggested two different mechanisms explaining the results observed in a low- and high-viscosity environment. The results indicated the fundamental role of interactions between the chromophore and sugar moiety in a low-viscosity environment. The results obtained at high values of viscosity are discussed in terms of a frictional boundary solvent-solute interaction model.
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Affiliation(s)
- G Neunert
- Department of Physics, Poznan University of Life Sciences, 60-637 Poznan, ul. Wojska Polskiego 38/42, Poland
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33
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Ahmed V, Liu Y, Taylor SD. Multiple Pathways for the Irreversible Inhibition of Steroid Sulfatase with Quinone Methide-Generating Suicide Inhibitors. Chembiochem 2009; 10:1457-61. [DOI: 10.1002/cbic.200900143] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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34
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Bojarová P, Kren V. Glycosidases: a key to tailored carbohydrates. Trends Biotechnol 2009; 27:199-209. [PMID: 19250692 DOI: 10.1016/j.tibtech.2008.12.003] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Revised: 12/03/2008] [Accepted: 12/12/2008] [Indexed: 10/21/2022]
Abstract
In recent years, carbohydrate-processing enzymes have become the enzymes of choice in many applications thanks to their stereoselectivity and efficiency. This review presents recent developments in glycosidase-catalyzed synthesis via two complementary approaches: the use of wild-type enzymes with engineered substrates, and mutant glycosidases. Genetic engineering has recently produced glucuronyl synthases, an inverting xylosynthase and the first mutant endo-beta-N-acetylglucosaminidase. A thorough selection of enzyme strains and aptly modified substrates have resulted in rare glycostructures, such as N-acetyl-beta-galactosaminuronates, beta1,4-linked mannosides and alpha1,4-linked galactosides. The efficient selection of mutant enzymes is facilitated by high-throughput screening assays involving the co-expression of coupled enzymes or chemical complementation. Selective glycosidase inhibitors and highly specific glycosidases are finding attractive applications in biomedicine, biology and proteomics.
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Affiliation(s)
- Pavla Bojarová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Center of Biocatalysis and Biotransformation, Vídenská 1083, CZ-142 20, Praha 4, Czech Republic
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35
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Stubbs KA, Vocadlo DJ. Affinity-Based Proteomics Probes; Tools for Studying Carbohydrate-Processing Enzymes. Aust J Chem 2009. [DOI: 10.1071/ch09140] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
As more information becomes available through the efforts of high-throughput screens, there is increasing pressure on the three main ‘omic’ fields, genomics, proteomics, and metabolomics, to organize this material into useful libraries that enable further understanding of biological systems. Proteomics especially is faced with two highly challenging tasks. The first is assigning the activity of thousands of putative proteins, the existence of which has been suggested by genomics studies. The second is to serve as a link between genomics and metabolomics by demonstrating which enzymes play roles in specific metabolic pathways. Underscoring these challenges in one area are the thousands of putative carbohydrate-processing enzymes that have been bioinformatically identified, mostly in prokaryotes, but that have unknown or unverified activities. Using two brief examples, we illustrate how biochemical pathways within bacteria that involve carbohydrate-processing enzymes present interesting potential antimicrobial targets, offering a clear motivation for gaining a functional understanding of biological proteomes. One method for studying proteomes that has been developed recently is to use synthetic compounds termed activity-based proteomics probes. Activity-based proteomic profiling using such probes facilitates rapid identification of enzyme activities within proteomes and assignment of function to putative enzymes. Here we discuss the general design principles for these probes with particular reference to carbohydrate-processing enzymes and give an example of using such a probe for the profiling of a bacterial proteome.
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36
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Hekmat O, He S, Warren RAJ, Withers SG. A Mechanism-Based ICAT Strategy for Comparing Relative Expression and Activity Levels of Glycosidases in Biological Systems. J Proteome Res 2008; 7:3282-92. [DOI: 10.1021/pr7008302] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Omid Hekmat
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B.C., Canada, V6T 1Z1, and Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, B.C., Canada, V6T 1Z3
| | - Shouming He
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B.C., Canada, V6T 1Z1, and Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, B.C., Canada, V6T 1Z3
| | - R. Antony J. Warren
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B.C., Canada, V6T 1Z1, and Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, B.C., Canada, V6T 1Z3
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B.C., Canada, V6T 1Z1, and Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, B.C., Canada, V6T 1Z3
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37
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Rempel BP, Withers SG. Covalent inhibitors of glycosidases and their applications in biochemistry and biology. Glycobiology 2008; 18:570-86. [PMID: 18499865 DOI: 10.1093/glycob/cwn041] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Glycoside hydrolases are important enzymes in a number of essential biological processes. Irreversible inhibitors of this class of enzyme have attracted interest as probes of both structure and function. In this review we discuss some of the compounds used to covalently modify glycosidases, their use in residue identification, structural and mechanistic investigations, and finally their applications, both in vitro and in vivo, to complex biological systems.
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Affiliation(s)
- Brian P Rempel
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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38
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Park S, Lee MR, Shin I. Chemical tools for functional studies of glycans. Chem Soc Rev 2008; 37:1579-91. [DOI: 10.1039/b713011m] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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39
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Stubbs KA, Scaffidi A, Debowski AW, Mark BL, Stick RV, Vocadlo DJ. Synthesis and Use of Mechanism-Based Protein-Profiling Probes for Retaining β-d-Glucosaminidases Facilitate Identification ofPseudomonas aeruginosaNagZ. J Am Chem Soc 2008; 130:327-35. [DOI: 10.1021/ja0763605] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Lu CP, Ren CT, Wu SH, Chu CY, Lo LC. Development of an Activity-Based Probe for Steroid Sulfatases. Chembiochem 2007; 8:2187-90. [DOI: 10.1002/cbic.200700279] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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41
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Hekmat O, Florizone C, Kim YW, Eltis LD, Warren RAJ, Withers SG. Specificity Fingerprinting of Retaining β-1,4-Glycanases in theCellulomonas fimi Secretome Using Two Fluorescent Mechanism-Based Probes. Chembiochem 2007; 8:2125-32. [DOI: 10.1002/cbic.200700481] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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42
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Affiliation(s)
- Anca Dragulescu-Andrasi
- Molecular Imaging Program at Stanford, Department of Radiology and Bio-X Program, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA 94305-5484, USA
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43
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Komatsu T, Kikuchi K, Takakusa H, Hanaoka K, Ueno T, Kamiya M, Urano Y, Nagano T. Design and synthesis of an enzyme activity-based labeling molecule with fluorescence spectral change. J Am Chem Soc 2007; 128:15946-7. [PMID: 17165702 DOI: 10.1021/ja0657307] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methods of covalent labeling of a specific tag protein with small-molecular dyes play an important role in studying dynamic behaviors of proteins in living cells. On the basis of quinone methide chemistry, we designed and synthesized a beta-galactosidase labeling probe, CMFbeta-gal, which shows a fluorescence wavelength change accompanying the labeling reaction, owing to fluorescence resonance energy transfer (FRET). Since the FRET efficiency changes accompanying the labeling reaction, fluorescence of labeled protein can be observed separately from that of the unreacted probe, so immediate detection of the target protein is possible. This is the first report of a protein labeling probe which features a change of fluorescence wavelength upon reaction, allowing the labeled protein to be detected even in the presence of unreacted probe.
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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
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44
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Shie TH, Chiang YL, Lin JJ, Li YK, Lo LC. Facile synthesis toward the construction of an activity probe library for glycosidases. Carbohydr Res 2006; 341:443-56. [PMID: 16414035 DOI: 10.1016/j.carres.2005.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2005] [Revised: 11/29/2005] [Accepted: 12/14/2005] [Indexed: 11/29/2022]
Abstract
Chemical probes that selectively label the glycoside hydrolase (GH) subfamilies have proven to be a powerful tool in GH-related research. We have previously demonstrated the design and synthesis of an activity probe for beta-glucosidase adopting a cassette-like design in a model study. Herein we report an improved synthetic route using (4-hydroxyphenyl)acetic acid 2-cyanoethyl ester as the precursor for the latent trapping device. Parallel syntheses were performed for the preparation of a library based on the structure of a key intermediate. The recognition head of this library covers a series of six sugars, including alpha- and beta-d-Glc, alpha- and beta-d-Gal, alpha-d-Man, and alpha-l-Fuc. Each member in this versatile intermediate library could serve as the building block in constructing an activity probe for GHs. As demonstrated in this study, three probes that have the 1,2-cis configuration were thus prepared for the first time to target alpha-d-glucosidase, alpha-d-galactosidase, and alpha-l-fucosidase, respectively.
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Affiliation(s)
- Tong-Hong Shie
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
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45
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Williams SJ, Hekmat O, Withers SG. Synthesis and Testing of Mechanism-Based Protein-Profiling Probes for Retaining Endo-glycosidases. Chembiochem 2006; 7:116-24. [PMID: 16397879 DOI: 10.1002/cbic.200500279] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
New functional proteomics methods are required for targeting and identification of subsets of a proteome in an activity-based fashion. Glycosidases play critical roles in biology, yet a robust method for functional analysis of their activities and identities in biological proteomes is still lacking. An aryl 2-deoxy-2-fluoro xylobioside inactivator was conjugated through cleavable and noncleavable linker arms to a biotin tag, thereby yielding two new active-site-directed reagents for activity-based profiling of retaining beta-glycanases in complex proteomes. Crucially, these tagged reagents possess high specificity for their target enzymes with kinetic parameters similar to those of the untagged reagent. Western blotting showed that these reagents bind and covalently label active retaining beta-glycanases both in pure enzyme samples and in the secreted proteome of the soil bacterium Cellulomonas fimi. Such reagents therefore show great promise for future activity-based targeting of glycanases.
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Affiliation(s)
- Spencer J Williams
- Protein Engineering Network of Centres of Excellence of Canada, Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T 1Z1, Canada
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46
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Hinou H, Kurogochi M, Nishimura SI. Mechanism‐Based Inhibitors to Probe Transitional States of Glycoside Hydrolases. Methods Enzymol 2006; 415:202-12. [PMID: 17116476 DOI: 10.1016/s0076-6879(06)15013-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Recent structural and kinetic studies indicate that glycosidases (glycoside hydrolases) change the peripheral structure of their catalytic sites dynamically to trim glycan structures. Inhibitors that label specific amino acid residues in the active site of these enzymes based on its mechanism of action are powerful tools to probe such a hidden transitional state. This chapter describes methods of mechanism-based irreversible inhibitors having fluorescence tags, including synthesis, inhibitory assay, rapid separation of the peptides containing labeled residues using antibody column, and proteomic analysis of key amino acid residues using matrix-assisted laser desorption/ionization-time-of-flight (TOF)/TOF mass spectrometry.
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Affiliation(s)
- Hiroshi Hinou
- Hokkaido University, Graduate School of Advanced Life Science, Sapporo, Japan
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47
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Stubbs KA, Vocadlo DJ. Functional Proteomic Profiling of Glycan‐Processing Enzymes. Methods Enzymol 2006; 415:253-68. [PMID: 17116479 DOI: 10.1016/s0076-6879(06)15016-8] [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: 05/12/2023]
Abstract
Glycoconjugates play critical roles in regulating cellular and organismal functions. Consequently, defining the relative levels of these glycoconjugates under varied physiological conditions is important. Thus identifying and understanding the regulation of the enzymes that process these glycoconjugates are essential steps in understanding the role of this "glycocode" in development and disease. Activity-based affinity reagents are useful tools for probing these enzymes and should facilitate the unraveling of proteomes. One advantage of activity-based affinity probes is that they can simultaneously reveal multiple enzymes having similar activities. These probes can also be used to enrich proteomes of interest, thereby facilitating identification and cloning of new carbohydrate-processing enzymes. Here we review the current state of activity-based affinity probes for profiling carbohydrate-processing enzymes, focusing on successes and limitations, general design features, and a specific example describing profiling of exoglycosidases from cell lysates.
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Affiliation(s)
- Keith A Stubbs
- Department of Chemistry, Simon Frasier University, Burnaby, British Columbia, Canada
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48
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Bunik VI, Denton TT, Xu H, Thompson CM, Cooper AJL, Gibson GE. Phosphonate analogues of alpha-ketoglutarate inhibit the activity of the alpha-ketoglutarate dehydrogenase complex isolated from brain and in cultured cells. Biochemistry 2005; 44:10552-61. [PMID: 16060664 DOI: 10.1021/bi0503100] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The alpha-ketoglutarate dehydrogenase complex (KGDHC), a control point of the tricarboxylic acid cycle, is partially inactivated in brain in many neurodegenerative diseases. Potent and specific KGDHC inhibitors are needed to probe how the reduced KGDHC activity alters brain function. Previous studies showed that succinyl phosphonate (SP) effectively inhibits muscle and Escherichia coli KGDHC [Biryukov, A. I., Bunik, V. I., Zhukov, Yu. N., Khurs, E. N., and Khomutov, R. M. (1996) FEBS Lett. 382, 167-170]. To identify the phosphonates with the highest affinity toward brain KGDHC and with the greatest effect in living cells, we investigated the ability of SP and several of its ethyl esters to inhibit brain KGDHC, other alpha-keto acid-dependent enzymes, and KGDHC in intact cells. At a concentration of 0.01 mM, SP and its phosphonoethyl (PESP) and carboxyethyl (CESP) esters completely inhibited isolated brain KGDHC even in the presence of a 200-fold higher concentration of its substrate [alpha-ketoglutarate (KG)], while the diethyl (DESP) and triethyl (TESP) esters were ineffective. In cultured human fibroblasts, 0.01 mM SP, PESP, or CESP produced 70% inhibition of KGDHC. DESP and TESP were also inhibitory in the cell system, but only after preincubation, suggesting the release of their charged groups by cellular esterases. Thus, SP and its monoethyl esters target cellular KGDHC directly, while the di- and triethyl esters are activated in intact cells. When tested on other enzymes that bind KG or related alpha-keto acids, SP had minimal effects and its two esters (CESP and TESP) were ineffective even at a concentration (0.1 mM) 1 order of magnitude higher than that which inhibited cellular KGDHC activity. The high specificity in targeting KGDHC, penetration into cells, and minimal transformation by cellular enzymes indicate that SP and its esters should be useful in studying the effects of reduced KGDHC activity on neuronal and brain function.
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Affiliation(s)
- Victoria I Bunik
- School of Bioinformatics and Bioengineering and Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russian Federation.
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Mohal N, Bernet B, Vasella A. Synthesis of a Fusion-Isomeric Cellobionoimidazole and Its Evaluation against thesyn-Protonating Glycosidase Cel7A. Helv Chim Acta 2005. [DOI: 10.1002/hlca.200590260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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50
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Takaya K, Nagahori N, Kurogochi M, Furuike T, Miura N, Monde K, Lee YC, Nishimura SI. Rational design, synthesis, and characterization of novel inhibitors for human beta1,4-galactosyltransferase. J Med Chem 2005; 48:6054-65. [PMID: 16162007 DOI: 10.1021/jm0504297] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An affinity labeling reagent, uridine 5'-(6-amino-{2-[(7-bromomethyl-2-naphthyl)methoxycarbonylmethoxy]ethoxy}acetyl-6-deoxy-alpha-D-galactopyranosyl) diphosphate (1a), was designed on the basis of 3D docking simulation and synthesized to investigate the functional role of Trp310 residue located in the small loop near the active site of human recombinant galactosyltransferase (betaGalT-1). Mass spectrometric analysis revealed that the Trp310 residue of betaGalT1 can be selectively modified with the naphthylmethyl group of compound 1a at the C-3 position of the indole ring. This result motivated us to synthesize novel uridine-5'-diphosphogalactose (UDP-Gal) analogues as candidates for mechanism-based inhibitors for betaGalT-1. We found that uridine 5'-(6-O-[10-(2-naphthyl)-3,6,9-trioxadecanyl]-alpha-d-galactopyranosyl) diphosphate (2) is the strongest inhibitor (K(i) = 1.86 microM) against UDP-Gal (Km = 4.91 microM) among compounds reported previously. A cold spray ionization time-of-flight mass spectrometry study demonstrated that the complex of this inhibitor and betaGalT-1 cannot interact with an acceptor substrate in the presence of Mn2+.
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Affiliation(s)
- Kenji Takaya
- Division of Biological Sciences, Frontier Research Center for Post-Genome Science and Technology, Graduate School of Science, Hokkaido University, N-21, W-11, Sapporo 001-0021, Japan
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