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Zhang R, Yan H, Liu Z, Liu X, Yan G, Liu X, Chen Y. [Preparation and characterization of a fluorogenic ddRFP-M biosensor as a specific SARS-CoV-2 main protease substrate]. Sheng Wu Gong Cheng Xue Bao 2024; 40:496-506. [PMID: 38369836 DOI: 10.13345/j.cjb.230502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The conventional peptide substrates of SARS-CoV-2 main protease (Mpro) are frequently associated with high cost, unstable kinetics, and multistep synthesis. Hence, there is an urgent need to design affordable and stable Mpro substrates for pharmacological research. Herein, we designed a functional Mpro substrate based on a dimerization-dependent red fluorescent protein (ddRFP) for the evaluation of Mpro inhibitors in vitro. The codon-optimized DNA fragment encoding RFP-A1 domain, a polypeptide linker containing Mpro cleavage sequence (AVLQS), and the RFP-B1 domain was subcloned into the pET-28a vector. After transformation into Escherichia coli Rosetta(DE3) cells, the kanamycin resistant transformants were selected. Using a low temperature induction strategy, most of the target proteins (ddRFP-M) presented in the supernatant fractions were collected and purified by a HisTrapTM chelating column. Subsequently, the inhibition of Mpro by ensitrelvir and baicalein was assessed using ddRFP-M assay, and the biochemical properties of ddRFP-M substrate were analyzed. Our results showed that the fluorogenic substrate ddRFP-M was successfully prepared from E. coli cells, and this biosensor exhibited the expected specificity, sensitivity, and reliability. In conclusion, the production of the fluorogenic substrate ddRFP-M provides an expedient avenue for the assessment of Mpro inhibitors in vitro.
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Affiliation(s)
- Rui Zhang
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Haohao Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Zhicheng Liu
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Xiaoli Liu
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Gangan Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Xiaoping Liu
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Yunyu Chen
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu 241002, Anhui, China
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2
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Wang DW, Yu SY, Pang ZL, Ma DJ, Liang L, Wang X, Wei T, Yang HZ, Ma YQ, Xi Z. Discovery of a Broad-Spectrum Fluorogenic Agonist for Strigolactone Receptors through a Computational Approach. J Agric Food Chem 2021; 69:10486-10495. [PMID: 34478295 DOI: 10.1021/acs.jafc.1c03471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Strigolactones (SLs) are plant hormones that play various roles in plant physiology, including provoking the germination of parasitic weeds Orobanche and Striga. A family of α/β-hydrolases have been proposed to be the SL receptor proteins. Effective assays for measuring the activity of SL receptors could promote the development of SL-related biology and chemistry. In this study, we developed a new approach called pharmacophore-linked probe virtual screening (PPVS). Its application yielded an effective "off-on" probe named Xilatone Red (XLR). This probe showed a broad spectrum and excellent sensitivity toward SL receptors, including ShD14 (Striga D14), for which the detection limit was determined to be in the micromolar range, outperforming that of the commercial fluorogenic agonist Yoshimulactone Green (YLG). Upon hydrolysis by SL receptors, XLR provided fluorogenic and colorimetric signaling responses. Furthermore, XLR could induce germination of Phelipanche aegyptiaca seeds and prevent Arabidopsis max4-1 branching defects at micromolar concentrations. Our molecular simulations revealed the essential factors in the molecular perception of XLR. We anticipate that this study can prompt the discovery of high-performance SL agonists/antagonists to combat parasitic weeds.
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Affiliation(s)
- Da-Wei Wang
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, National Pesticide Engineering Research Center, and Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Shu-Yi Yu
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, National Pesticide Engineering Research Center, and Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Zhi-Li Pang
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, National Pesticide Engineering Research Center, and Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - De-Jun Ma
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, National Pesticide Engineering Research Center, and Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Lu Liang
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, National Pesticide Engineering Research Center, and Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Xia Wang
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, National Pesticide Engineering Research Center, and Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Tao Wei
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, National Pesticide Engineering Research Center, and Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Huang-Ze Yang
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, National Pesticide Engineering Research Center, and Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Yong-Qing Ma
- The State Key Laboratory of Soil Erosion and Dryland Farming, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, National Pesticide Engineering Research Center, and Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
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Hira J, Uddin MJ, Haugland MM, Lentz CS. From Differential Stains to Next Generation Physiology: Chemical Probes to Visualize Bacterial Cell Structure and Physiology. Molecules 2020; 25:E4949. [PMID: 33114655 PMCID: PMC7663024 DOI: 10.3390/molecules25214949] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/16/2022] Open
Abstract
Chemical probes have been instrumental in microbiology since its birth as a discipline in the 19th century when chemical dyes were used to visualize structural features of bacterial cells for the first time. In this review article we will illustrate the evolving design of chemical probes in modern chemical biology and their diverse applications in bacterial imaging and phenotypic analysis. We will introduce and discuss a variety of different probe types including fluorogenic substrates and activity-based probes that visualize metabolic and specific enzyme activities, metabolic labeling strategies to visualize structural features of bacterial cells, antibiotic-based probes as well as fluorescent conjugates to probe biomolecular uptake pathways.
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Affiliation(s)
- Jonathan Hira
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
| | - Md. Jalal Uddin
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
| | - Marius M. Haugland
- Department of Chemistry and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway;
| | - Christian S. Lentz
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
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Miura K, Aoyama Y, Natsu Y, Koyama R, Hirano T, Nishio T, Hakamata W. Development of Specific Fluorogenic Substrates for Human β-N-Acetyl-D-hexosaminidase A for Cell-Based Assays. Chem Pharm Bull (Tokyo) 2020; 68:526-533. [PMID: 32475856 DOI: 10.1248/cpb.c20-00069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Inhibitors of human β-N-acetyl-D-hexosaminidase (hHEX) A and human O-GlcNAcase (hOGA) reportedly play roles in multiple diseases, suggesting their potential for pharmacological chaperone (PC) therapy of Sandhoff disease (SD) and Tay-Sachs disease (TSD), as lysosomal storage diseases, and Alzheimer's disease and progressive supranuclear palsy, respectively. In particular, hHEXA inhibitors as PCs have been shown to successfully enhance hHEXA levels, leading to the chronic form of SD and TSD. In the diagnosis of enzyme deficiencies in SD and TSD, artificial hHEXA substrates based on 4-methylumbelliferone as a fluorophore are available and generally used; however, they do not have sufficient performance to screen for potential inhibitors for a PC therapy from compound libraries. Further, there are currently few fluorogenic substrates for hHEXA suitable for such requirements and there are no substrates ideal for cell-based inhibitor screening. Here, we clarified the difference in enzyme active site structure between hHEXA and hOGA from their tertiary structures. To develop lysosome-localized hHEXA-specific fluorogenic substrates based on the difference in their active site structures, our developed quinone methide cleavage substrate design platform was applied for the molecular design of substrates. Thereafter, we synthesized via the shortest route and evaluated novel three-color fluorogenic substrates for hHEXA that exhibited excellent specificity and sensitivity in three human cell lines. The designed substrates represent the first-in-a class of new substrates that can be utilized to screen hHEXA inhibitors in adherent human cultured cells.
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Affiliation(s)
- Kazuki Miura
- Department of Chemistry and Life Science, College of Bioresource Sciences, Nihon University
| | - Yuka Aoyama
- Department of Chemistry and Life Science, College of Bioresource Sciences, Nihon University
| | - Yurika Natsu
- Department of Chemistry and Life Science, College of Bioresource Sciences, Nihon University
| | - Ryosuke Koyama
- Department of Chemistry and Life Science, College of Bioresource Sciences, Nihon University
| | - Takako Hirano
- Department of Chemistry and Life Science, College of Bioresource Sciences, Nihon University
| | - Toshiyuki Nishio
- Department of Chemistry and Life Science, College of Bioresource Sciences, Nihon University
| | - Wataru Hakamata
- Department of Chemistry and Life Science, College of Bioresource Sciences, Nihon University
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5
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Gruba N, Bielecka E, Wysocka M, Wojtysiak A, Brzezińska-Bodal M, Sychowska K, Kalińska M, Magoch M, Pęcak A, Falkowski K, Wiśniewska M, Sąsiadek L, Płaza K, Kroll E, Pejkovska A, Rehders M, Brix K, Dubin G, Kantyka T, Potempa J, Lesner A. Development of Chemical Tools to Monitor Human Kallikrein 13 (KLK13) Activity. Int J Mol Sci 2019; 20:E1557. [PMID: 30925705 DOI: 10.3390/ijms20071557] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/14/2019] [Accepted: 03/25/2019] [Indexed: 12/17/2022] Open
Abstract
Kallikrein 13 (KLK13) was first identified as an enzyme that is downregulated in a subset of breast tumors. This serine protease has since been implicated in a number of pathological processes including ovarian, lung and gastric cancers. Here we report the design, synthesis and deconvolution of libraries of internally quenched fluorogenic peptide substrates to determine the specificity of substrate binding subsites of KLK13 in prime and non-prime regions (according to the Schechter and Berger convention). The substrate with the consensus sequential motive ABZ-Val-Arg-Phe-Arg-ANB-NH2 demonstrated selectivity towards KLK13 and was successfully converted into an activity-based probe by the incorporation of a chloromethylketone warhead and biotin bait. The compounds described may serve as suitable tools to detect KLK13 activity in diverse biological samples, as exemplified by overexpression experiments and targeted labeling of KLK13 in cell lysates and saliva. In addition, we describe the development of selective activity-based probes targeting KLK13, to our knowledge the first tool to analyze the presence of the active enzyme in biological samples.
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Ogawa F, Takeda M, Miyanaga K, Tani K, Yamazawa R, Ito K, Tarui A, Sato K, Omote M. Development of a fluorogenic small substrate for dipeptidyl peptidase-4. Beilstein J Org Chem 2017; 13:2690-2697. [PMID: 29564006 PMCID: PMC5753067 DOI: 10.3762/bjoc.13.267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/29/2017] [Indexed: 11/23/2022] Open
Abstract
A series of aniline and m-phenylenediamine derivatives with electron-withdrawing 3,3,3-trifluoropropenyl substituents were synthesized as small and chemically stable fluorescent organic compounds. Their fluorescence performances were evaluated by converting 2,4-disubstituted aniline 1 to the non-fluorescent dipeptide analogue H-Gly-Pro-1 for the use as a fluorogenic substrate for dipeptidyl peptidase-4 (DPP-4). The progress of the enzymatic hydrolysis of H-Gly-Pro-1 with DPP-4 was monitored by fluorometric determination of 1 released into the reaction medium. The results suggest that 1 could be used as fluorophore in OFF–ON-type fluorogenic probes.
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Affiliation(s)
- Futa Ogawa
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Masanori Takeda
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Kanae Miyanaga
- Division of Natural Sciences, Osaka Kyoiku University, Asahigaoka, Kashiwara, Osaka 582-8582, Japan
| | - Keita Tani
- Division of Natural Sciences, Osaka Kyoiku University, Asahigaoka, Kashiwara, Osaka 582-8582, Japan
| | - Ryuji Yamazawa
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Kiyoshi Ito
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Atsushi Tarui
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Kazuyuki Sato
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Masaaki Omote
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
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7
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Pal N, Wu M, Lu HP. Probing conformational dynamics of an enzymatic active site by an in situ single fluorogenic probe under piconewton force manipulation. Proc Natl Acad Sci U S A 2016; 113:15006-11. [PMID: 27940917 DOI: 10.1073/pnas.1613404114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unraveling the conformational details of an enzyme during the essential steps of a catalytic reaction (i.e., enzyme-substrate interaction, enzyme-substrate active complex formation, nascent product formation, and product release) is challenging due to the transient nature of intermediate conformational states, conformational fluctuations, and the associated complex dynamics. Here we report our study on the conformational dynamics of horseradish peroxidase using single-molecule multiparameter photon time-stamping spectroscopy with mechanical force manipulation, a newly developed single-molecule fluorescence imaging magnetic tweezers nanoscopic approach. A nascent-formed fluorogenic product molecule serves as a probe, perfectly fitting in the enzymatic reaction active site for probing the enzymatic conformational dynamics. Interestingly, the product releasing dynamics shows the complex conformational behavior with multiple product releasing pathways. However, under magnetic force manipulation, the complex nature of the multiple product releasing pathways disappears and more simplistic conformations of the active site are populated.
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8
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Lentz CS, Ordonez AA, Kasperkiewicz P, La Greca F, O’Donoghue AJ, Schulze CJ, Powers JC, Craik CS, Drag M, Jain SK, Bogyo M. Design of Selective Substrates and Activity-Based Probes for Hydrolase Important for Pathogenesis 1 (HIP1) from Mycobacterium tuberculosis. ACS Infect Dis 2016; 2:807-815. [PMID: 27739665 PMCID: PMC5109297 DOI: 10.1021/acsinfecdis.6b00092] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Although serine proteases are important mediators of Mycobacterium tuberculosis (Mtb) virulence, there are currently no tools to selectively block or visualize members of this family of enzymes. Selective reporter substrates or activity-based probes (ABPs) could provide a means to monitor infection and response to therapy using imaging methods. Here, we use a combination of substrate selectivity profiling and focused screening to identify optimized reporter substrates and ABPs for the Mtb "Hydrolase important for pathogenesis 1" (Hip1) serine protease. Hip1 is a cell-envelope-associated enzyme with minimal homology to host proteases, making it an ideal target for probe development. We identified substituted 7-amino-4-chloro-3-(2-bromoethoxy)isocoumarins as irreversible inhibitor scaffolds. Furthermore, we used specificity data to generate selective reporter substrates and to further optimize a selective chloroisocoumarin inhibitor. These new reagents are potentially useful in delineating the roles of Hip1 during pathogenesis or as diagnostic imaging tools for specifically monitoring Mtb infections.
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Affiliation(s)
| | | | - Paulina Kasperkiewicz
- Division
of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego
27, 50-370 Wroclaw, Poland
| | - Florencia La Greca
- Department of Pharmaceutical Chemistry, University of California—San Francisco, San Francisco, United States
| | - Anthony J. O’Donoghue
- Department of Pharmaceutical Chemistry, University of California—San Francisco, San Francisco, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California—San Diego, La Jolla, California 92093 United States
| | | | - James C. Powers
- Department of
Chemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California—San Francisco, San Francisco, United States
| | - Marcin Drag
- Division
of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego
27, 50-370 Wroclaw, Poland
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Jia Y, Li P, Song W, Zhao G, Zheng D, Li D, Wang Y, Wang J, Li C, Han K. Rational Design of a Profluorescent Substrate for S-adenosylhomocysteine Hydrolase and its Applications in Bioimaging and Inhibitor Screening. ACS Appl Mater Interfaces 2016; 8:25818-25824. [PMID: 27626909 DOI: 10.1021/acsami.6b09190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
S-Adenosylhomocysteine hydrolase (SAHase) is a cellular enzyme that plays a key role in the methylation process, and a potential drug target in the discovery of antiviral and anticancer agents. There is increasing interest in determining its activity in the biological and clinical fields with chemosensors but with limited success so far. Herein, we designed and developed for the first time an off/on-type of fluorogenic substrate (NADE) that is directly responsive to SAHase activity. NADE used 1,8-naphthalimide as the signal reporter and adenosine (Ade) as the reaction center; removal of the Ade moiety enhanced the fluorescence by >10-fold. Kinetic study showed that NADE followed a non-Michaelis-Menten pattern that corresponded to the allosteric behavior of SAHase. NADE showed excellent selectivity and functioned efficiently in cells, allowing the microscopic imaging of SAHase activity. NADE can also be used to identify and measure the effectiveness of inhibitors in a markedly superior way. In a word, NADE would be broadly useful in clinical applications and academic studies.
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Affiliation(s)
- Yan Jia
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences (CAS) , 457 Zhongshan Road, Dalian 116023, P. R. China
- Graduate School of the Chinese Academy of Sciences , Beijing, P. R. China
| | - Peng Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences (CAS) , 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Wei Song
- The First Affiliated Hospital of Dalian Medical University , Dalian 116023, P. R. China
| | - Guangjiu Zhao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences (CAS) , 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Daoyuan Zheng
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences (CAS) , 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Dongmei Li
- College of Pharmacy, Nankai University , Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China
| | - Yanni Wang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences (CAS) , 457 Zhongshan Road, Dalian 116023, P. R. China
- Graduate School of the Chinese Academy of Sciences , Beijing, P. R. China
| | - Jiayue Wang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences (CAS) , 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Chunyan Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences (CAS) , 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences (CAS) , 457 Zhongshan Road, Dalian 116023, P. R. China
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Abstract
Fluorogenic substrates for cathepsin D; A-Tyr-Phe(NO2)-Leu-Leu (A; Ala-Arg-Pro-Lys-Pro-Leu-Leu-, Arg-Pro-Lys-Pro-Leu-Leu-, Pro-Lys-Pro-Leu-Leu-, Lys-Pro-Leu-Leu-, Pro-Leu-Leu-) and B-Phe(NO2)-Tyr-Leu-Leu (B; Arg-Pro-Lys-Pro-Leu-Leu-, Pro-Lys-Pro-Leu-Leu-, Lys-Pro-Leu-Leu-, Pro-Leu-Leu-) (Phe(NO2), p-nitrophenylalanine) were synthesized and digested by cathepsin D and pepsin. The fluorescence at 303 nm (excitation at 260 nm) was increased with the hydrolysis of the substrates. The minimum detectable cathepsin D concentrations for these substrates were 0.5-4 nM and pepsin concentrations were 0.1-0.8 nM except Pro-Leu-Leu-Tyr-Phe(NO2)-Leu-Leu under the following conditions: substrate concentration, 20 μM; measuring time, 3 min. The hydrolysis rate constants (kcat/Km) of B-Phe(NO2)-Tyr-Leu-Leu for cathepsin D were same or 2-3 times greater than A-Tyr-Phe(NO2)-Leu-Leu. On the other hand, those of B-Phe(NO2)-Tyr-Leu-Leu for pepsin were the same or 4-20 times greater than A-Tyr-Phe(NO2)-Leu-Leu. The hydrolysis rates of the substrates by both enzymes tend to increase with the increase of the peptide chain length. The best substrate for cathepsin D was Arg-Pro-Lys-Pro-Leu-Leu-Phe(NO2)-Tyr-Leu-Leu and its kcat/Km was 1.3 μM(-1) s(-1).
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Kim S, Kim H, Choi Y, Kim Y. A New Strategy for Fluorogenic Esterase Probes Displaying Low Levels of Non-specific Hydrolysis. Chemistry 2015; 21:9645-9. [PMID: 26033618 DOI: 10.1002/chem.201501127] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Indexed: 11/06/2022]
Abstract
A new design for fluorescence probes of esterase activity that features a carboxylate-side pro-fluorophore is demonstrated with boron dipyrromethene (BODIPY)-based probes 1 a and 1 b. Because the design relies on the enzyme-catalyzed hydrolysis of an ester group that is not electronically activated, these probes exhibit a stability to background hydrolysis that is far superior to classical alcohol-side profluorophore-based probes, large signal-to-noise ratios, reduced sensitivity to pH variations, and high enzymatic reactivity. The utility of probe 1 a was established with a real-time fluorescence imaging experiment of endogenous esterase activity that does not require washing of the extracellular medium.
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Affiliation(s)
- Sungwoo Kim
- Department of Chemistry, Institute of Nanosensor and Biotechnology, Dankook University, 152 Jukjeon-ro, Suji-gu, Yongin-si, Gyeonggi-do, 448-701 (Korea), Fax: (+82) 31-8005-3148
| | - Hyunjin Kim
- Molecular Imaging & Therapy Branch, National Cancer Center, 323 Ilsan-ro, Goyang-si, Gyeonggi-do, 410-769 (Korea)
| | - Yongdoo Choi
- Molecular Imaging & Therapy Branch, National Cancer Center, 323 Ilsan-ro, Goyang-si, Gyeonggi-do, 410-769 (Korea).
| | - Youngmi Kim
- Department of Chemistry, Institute of Nanosensor and Biotechnology, Dankook University, 152 Jukjeon-ro, Suji-gu, Yongin-si, Gyeonggi-do, 448-701 (Korea), Fax: (+82) 31-8005-3148.
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Coleman DJ, Kuntz DA, Venkatesan M, Cook GM, Williamson SP, Rose DR, Naleway JJ. A long-wavelength fluorescent substrate for continuous fluorometric determination of alpha-mannosidase activity: resorufin alpha-D-mannopyranoside. Anal Biochem 2010; 399:7-12. [PMID: 20026005 DOI: 10.1016/j.ab.2009.11.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 11/05/2009] [Accepted: 11/13/2009] [Indexed: 11/21/2022]
Abstract
A simple and reliable continuous assay for measurement of alpha-mannosidase activity is described and demonstrated for analysis with two recombinant human enzymes using the new substrate resorufin alpha-d-mannopyranoside (Res-Man). The product of enzyme reaction, resorufin, exhibits fluorescence emission at 585 nm with excitation at 571 nm and has a pK(a) of 5.8, allowing continuous measurement of fluorescence turnover at or near physiological pH values for human lysosomal and Drosophila Golgi alpha-mannosidases. The assay performed using recombinant Drosophila Golgi alpha-mannosidase (dGMII) has been shown to give the kinetic parameters K(m) of 200 microM and V(max) of 11 nmol/min per nmol dGMII. Methods for performing the assay using several concentrations of the known alpha-mannosidase inhibitor swainsonine are also presented, demonstrating a potential for use of the assay as a simple method for high-throughput screening of inhibitors potentially useful in cancer treatment.
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Yatzeck MM, Lavis LD, Chao TY, Chandran SS, Raines RT. A highly sensitive fluorogenic probe for cytochrome P450 activity in live cells. Bioorg Med Chem Lett 2008; 18:5864-6. [PMID: 18595692 PMCID: PMC2586036 DOI: 10.1016/j.bmcl.2008.06.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 06/03/2008] [Accepted: 06/04/2008] [Indexed: 11/30/2022]
Abstract
A derivative of rhodamine 110 has been designed and assessed as a probe for cytochrome P450 activity. This probe is the first to utilize a 'trimethyl lock' that is triggered by cleavage of an ether bond. In vitro, fluorescence was manifested by the CYP1A1 isozyme with k(cat)/K(M)=8.8x10(3)M(-1)s(-1) and K(M)=0.09microM. In cellulo, the probe revealed the induction of cytochrome P450 activity by the carcinogen 2,3,7,8-tetrachlorodibenzo-p-dioxin, and its repression by the chemoprotectant resveratrol.
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Affiliation(s)
- Melissa M Yatzeck
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1322, USA
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Kuo CJ, Shie JJ, Fang JM, Yen GR, Hsu JTA, Liu HG, Tseng SN, Chang SC, Lee CY, Shih SR, Liang PH. Design, synthesis, and evaluation of 3C protease inhibitors as anti-enterovirus 71 agents. Bioorg Med Chem 2008; 16:7388-98. [PMID: 18583140 PMCID: PMC7125518 DOI: 10.1016/j.bmc.2008.06.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 06/07/2008] [Accepted: 06/10/2008] [Indexed: 10/31/2022]
Abstract
Human enterovirus (EV) belongs to the picornavirus family, which consists of over 200 medically relevant viruses. A peptidomimetic inhibitor AG7088 was developed to inhibit the 3C protease of rhinovirus (a member of the family), a chymotrypsin-like protease required for viral replication, by forming a covalent bond with the active site Cys residue. In this study, we have prepared the recombinant 3C protease from EV71 (TW/2231/98), a particular strain which causes severe outbreaks in Asia, and developed inhibitors against the protease and the viral replication. For inhibitor design, the P3 group of AG7088, which is not interacting with the rhinovirus protease, was replaced with a series of cinnamoyl derivatives directly linked to P2 group through an amide bond to simplify the synthesis. While the replacement caused decreased potency, the activity can be largely improved by substituting the alpha,beta-unsaturated ester with an aldehyde at the P1' position. The best inhibitor 10b showed EC(50) of 18 nM without apparent toxicity (CC(50)>25 microM). Our study provides potent inhibitors of the EV71 3C protease as anti-EV71 agents and facilitates the combinatorial synthesis of derivatives for further improving the inhibitory activity.
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Key Words
- ev, enterovirus
- rv, rhinovirus
- sars-cov, severe acute respiratory syndrome-coronavirus
- ninta, nickel nitrilo-tri-acetic acid
- dabcyl, 4-(4-dimethylaminophenylazo)benzoic acid
- edans, 5-[(2-aminoethyl)amino]naphthalene-1-sulfonic acid
- boc, tert-butyloxycarbonyl
- cbz, benzyloxycarbonyl
- mes, 2-n-morpholono-ethanesulfonic acid
- dmem, dulbecco’s modified eagle’s medium
- fbs, fetal bovine serum
- protease
- picornaviridae
- inhibitor
- enterovirus
- computer modeling
- fluorogenic substrate
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Affiliation(s)
- Chih-Jung Kuo
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Taipei 11529, Taiwan
- Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
| | - Jiun-Jie Shie
- The Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jim-Min Fang
- The Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Guei-Rung Yen
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Chu-Nan, Taiwan
| | - John T.-A. Hsu
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Chu-Nan, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Hun-Ge Liu
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Taipei 11529, Taiwan
| | - Sung-Nain Tseng
- Department of Medical Biotechnology & Laboratory Science, Chang Gung University, Tao-Yuan, Taiwan
| | - Shih-Cheng Chang
- Department of Medical Biotechnology & Laboratory Science, Chang Gung University, Tao-Yuan, Taiwan
- Clinical Virology Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan, Taiwan
| | - Ching-Yin Lee
- Department of Medical Biotechnology & Laboratory Science, Chang Gung University, Tao-Yuan, Taiwan
- Clinical Virology Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan, Taiwan
| | - Shin-Ru Shih
- Department of Medical Biotechnology & Laboratory Science, Chang Gung University, Tao-Yuan, Taiwan
- Clinical Virology Laboratory, Department of Clinical Pathology, Chang Gung Memorial Hospital, Tao-Yuan, Taiwan
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Taipei 11529, Taiwan
- Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- The Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
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15
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Lauer-Fields JL, Nagase H, Fields GB. Development of a solid-phase assay for analysis of matrix metalloproteinase activity. J Biomol Tech 2004; 15:305-16. [PMID: 15585827 PMCID: PMC2291699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Proteases play fundamentally important roles in normal physiology and disease pathology. Methods for detection of active proteolysis may greatly aid in the diagnosis of disease progression, and suggest modes of therapeutic intervention. Most assays for proteolytic potential are limited by a lack of specificity and/or quantification. We have developed a solid-phase activity assay for members of the matrix metalloproteinase (MMP) family that is specific and can be used to quantify active enzyme concentration. The assay has two principal components: a capture antibody that immobilizes the MMP without perturbing the enzyme active site, and a fluorescence resonance energy transfer substrate for monitoring proteolysis at low enzyme concentrations. The assay was standardized for MMP-1, MMP-3, MMP-13, and MMP-14. The efficiency of the assay was found to be critically dependent upon the quality of the antibodies, the use of substrates exhibiting high specific activities for the enzymes, and enzyme samples that are fresh. The assay was applied to studies of constitutive and induced MMP activity in human melanoma cells. Analysis of several melanoma cell lines, and comparison with prior studies, correlated higher constitutive MMP-13 activity with higher levels of the cell surface receptor CD44. Ligands to two different melanoma cell surface receptors (the alpha2beta1 integrin or CD44) were found to induce different proteolytic profiles, suggesting that the extracellular matrix can modulate melanoma invasion. Overall, the solid-phase MMP activity assay was found to be valuable for analysis of protease activity in cellular environments. The solid-phase assay is suitably flexible to allow studies of virtually any proteolytic enzyme for which appropriate substrates and antibodies are available.
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Affiliation(s)
- Janelle L Lauer-Fields
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431-0991, USA
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Abstract
A continuous assay method, such as one that utilizes an increase in fluorescence upon hydrolysis, allows for rapid and convenient kinetic evaluation of proteases. To better understand MMP behaviors and to aid in the design of MMP inhibitors, a variety of sequence specificity, phage display, and combinatorial chemistry studies have been performed. Results of these studies have been valuable for defining the differences in MMPs and for creating quenched fluorescent substrates that utilize fluorescence resonance energy transfer (FRET)/intramolecular fluorescence energy transfer (IFET). FRET triple-helical substrates have been constructed to examine the collagenolytic activity of MMP family members. The present chapter provides an overview of MMP and related FRET substrates and describes how to construct and utilize these substrates.
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Affiliation(s)
- Gregg B. Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431 U.S.A. Phone 561-297-2093, Fax 561-297-2759
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