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Journal articles on the topic 'Click-chemistry based activity probe'

Author: Grafiati

Published: 4 June 2021

Last updated: 10 February 2022

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1

Luijkx, Yvette M. C. A., Seino Jongkees, Karin Strijbis, and Tom Wennekes. "Development of a 1,2-difluorofucoside activity-based probe for profiling GH29 fucosidases." Organic & Biomolecular Chemistry 19, no. 13 (2021): 2968–77. http://dx.doi.org/10.1039/d1ob00054c.

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2

Bell, Jessica L., Andrew J. Haak, Susan M. Wade, Yihan Sun, Richard R. Neubig, and Scott D. Larsen. "Design and synthesis of tag-free photoprobes for the identification of the molecular target for CCG-1423, a novel inhibitor of the Rho/MKL1/SRF signaling pathway." Beilstein Journal of Organic Chemistry 9 (May 21, 2013): 966–73. http://dx.doi.org/10.3762/bjoc.9.111.

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CCG-1423 and related analogues represent a new class of inhibitors of Rho/MKL1/SRF-mediated gene transcription, a pathway that has been implicated in both cancer and fibrosis. The molecular target for these compounds is unknown. To facilitate its identification, a series of tag-free photoaffinity probes was designed and synthesized, each one containing a photoactivatable group and an acetylenic end group for subsequent attachment to a fluorescent tag using click chemistry. All were confirmed to maintain biological activity in a cell-based assay for inhibition of SRE-Luc expression. The functio

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3

Ismail, Hanafy M., Victoria Barton, Matthew Phanchana, et al. "Artemisinin activity-based probes identify multiple molecular targets within the asexual stage of the malaria parasites Plasmodium falciparum 3D7." Proceedings of the National Academy of Sciences 113, no. 8 (2016): 2080–85. http://dx.doi.org/10.1073/pnas.1600459113.

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The artemisinin (ART)-based antimalarials have contributed significantly to reducing global malaria deaths over the past decade, but we still do not know how they kill parasites. To gain greater insight into the potential mechanisms of ART drug action, we developed a suite of ART activity-based protein profiling probes to identify parasite protein drug targets in situ. Probes were designed to retain biological activity and alkylate the molecular target(s) of Plasmodium falciparum 3D7 parasites in situ. Proteins tagged with the ART probe can then be isolated using click chemistry before identif

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4

Chen, Guilin, Hui Feng, Wenbin Xi, Jing Xu, Saifei Pan, and Zhaosheng Qian. "Thiol–ene click reaction-induced fluorescence enhancement by altering the radiative rate for assaying butyrylcholinesterase activity." Analyst 144, no. 2 (2019): 559–66. http://dx.doi.org/10.1039/c8an01808a.

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5

Yan, Xiaowen, Yacui Luo, Zhubao Zhang, et al. "Europium-Labeled Activity-Based Probe through Click Chemistry: Absolute Serine Protease Quantification Using 153Eu Isotope Dilution ICP/MS." Angewandte Chemie 124, no. 14 (2012): 3414–19. http://dx.doi.org/10.1002/ange.201108277.

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6

Yan, Xiaowen, Yacui Luo, Zhubao Zhang, et al. "Europium-Labeled Activity-Based Probe through Click Chemistry: Absolute Serine Protease Quantification Using 153Eu Isotope Dilution ICP/MS." Angewandte Chemie International Edition 51, no. 14 (2012): 3358–63. http://dx.doi.org/10.1002/anie.201108277.

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7

Yao, Tingting, Xiaowei Xu, and Rong Huang. "Recent Advances about the Applications of Click Reaction in Chemical Proteomics." Molecules 26, no. 17 (2021): 5368. http://dx.doi.org/10.3390/molecules26175368.

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Despite significant advances in biological and analytical approaches, a comprehensive portrait of the proteome and its dynamic interactions and modifications remains a challenging goal. Chemical proteomics is a growing area of chemical biology that seeks to design small molecule probes to elucidate protein composition, distribution, and relevant physiological and pharmacological functions. Click chemistry focuses on the development of new combinatorial chemical methods for carbon heteroatom bond (C-X-C) synthesis, which have been utilized extensively in the field of chemical proteomics. Click

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8

Lin, Vivian S. "Interrogating Plant-Microbe Interactions with Chemical Tools: Click Chemistry Reagents for Metabolic Labeling and Activity-Based Probes." Molecules 26, no. 1 (2021): 243. http://dx.doi.org/10.3390/molecules26010243.

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Continued expansion of the chemical biology toolbox presents many new and diverse opportunities to interrogate the fundamental molecular mechanisms driving complex plant–microbe interactions. This review will examine metabolic labeling with click chemistry reagents and activity-based probes for investigating the impacts of plant-associated microbes on plant growth, metabolism, and immune responses. While the majority of the studies reviewed here used chemical biology approaches to examine the effects of pathogens on plants, chemical biology will also be invaluable in future efforts to investig

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9

Tyler, Dean S., Johanna Vappiani, Tatiana Cañeque, et al. "Click chemistry enables preclinical evaluation of targeted epigenetic therapies." Science 356, no. 6345 (2017): 1397–401. http://dx.doi.org/10.1126/science.aal2066.

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The success of new therapies hinges on our ability to understand their molecular and cellular mechanisms of action. We modified BET bromodomain inhibitors, an epigenetic-based therapy, to create functionally conserved compounds that are amenable to click chemistry and can be used as molecular probes in vitro and in vivo. We used click proteomics and click sequencing to explore the gene regulatory function of BRD4 (bromodomain containing protein 4) and the transcriptional changes induced by BET inhibitors. In our studies of mouse models of acute leukemia, we used high-resolution microscopy and

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10

Serim, Sevnur, Susanne V. Mayer, and Steven H. L. Verhelst. "Tuning activity-based probe selectivity for serine proteases by on-resin ‘click’ construction of peptide diphenyl phosphonates." Organic & Biomolecular Chemistry 11, no. 34 (2013): 5714. http://dx.doi.org/10.1039/c3ob40907d.

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11

Vaidya, Aditya S., Francis C. Peterson, James Eckhardt, et al. "Click-to-lead design of a picomolar ABA receptor antagonist with potent activity in vivo." Proceedings of the National Academy of Sciences 118, no. 38 (2021): e2108281118. http://dx.doi.org/10.1073/pnas.2108281118.

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Abscisic acid (ABA) is a key plant hormone that mediates both plant biotic and abiotic stress responses and many other developmental processes. ABA receptor antagonists are useful for dissecting and manipulating ABA’s physiological roles in vivo. We set out to design antagonists that block receptor–PP2C interactions by modifying the agonist opabactin (OP), a synthetically accessible, high-affinity scaffold. Click chemistry was used to create an ∼4,000-member library of C4-diversified opabactin derivatives that were screened for receptor antagonism in vitro. This revealed a peptidotriazole moti

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12

Verhelst, Steven H. L., Kimberly M. Bonger, and Lianne I. Willems. "Bioorthogonal Reactions in Activity-Based Protein Profiling." Molecules 25, no. 24 (2020): 5994. http://dx.doi.org/10.3390/molecules25245994.

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Activity-based protein profiling (ABPP) is a powerful technique to label and detect active enzyme species within cell lysates, cells, or whole animals. In the last two decades, a wide variety of applications and experimental read-out techniques have been pursued in order to increase our understanding of physiological and pathological processes, to identify novel drug targets, to evaluate selectivity of drugs, and to image probe targets in cells. Bioorthogonal chemistry has substantially contributed to the field of ABPP, as it allows the introduction of tags, which may be bulky or have unfavora

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13

Wang, Jun, Mahesh Uttamchandani, Junqi Li, Mingyu Hu, and Shao Q. Yao. "“Click” synthesis of small molecule probes for activity-based fingerprinting of matrix metalloproteases." Chem. Commun., no. 36 (2006): 3783–85. http://dx.doi.org/10.1039/b609446e.

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14

Cavett, Valerie, and Brian M. Paegel. "Multiplexed Enzyme Activity-Based Probe Display via Hybridization." ACS Combinatorial Science 22, no. 11 (2020): 579–85. http://dx.doi.org/10.1021/acscombsci.0c00116.

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15

Gao, Xinxin, and Jin Zhang. "FRET-Based Activity Biosensors to Probe Compartmentalized Signaling." ChemBioChem 11, no. 2 (2009): 147–51. http://dx.doi.org/10.1002/cbic.200900594.

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16

Cavalli, Silvia, Anna J. S. Houben, Harald M. H. G. Albers, et al. "Development of an Activity-Based Probe for Autotaxin." ChemBioChem 11, no. 16 (2010): 2311–17. http://dx.doi.org/10.1002/cbic.201000349.

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17

Kikuchi, Kazuya, Shigeki Hashimoto, Shin Mizukami, and Tetsuo Nagano. "Anion Sensor-Based Ratiometric Peptide Probe for Protein Kinase Activity." Organic Letters 11, no. 13 (2009): 2732–35. http://dx.doi.org/10.1021/ol9006508.

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18

Lu, Chun-Ping, Chien-Tai Ren, Shih-Hsiung Wu, Chi-Yuan Chu, and Lee-Chiang Lo. "Development of an Activity-Based Probe for Steroid Sulfatases." ChemBioChem 8, no. 18 (2007): 2187–90. http://dx.doi.org/10.1002/cbic.200700279.

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19

Schleifenbaum, Andreas, Gunter Stier, Alexander Gasch, Michael Sattler, and Carsten Schultz. "Genetically Encoded FRET Probe for PKC Activity Based on Pleckstrin." Journal of the American Chemical Society 126, no. 38 (2004): 11786–87. http://dx.doi.org/10.1021/ja0460155.

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20

Shaulov-Rotem, Yulia, Emmanuelle Merquiol, Tommy Weiss-Sadan, et al. "A novel quenched fluorescent activity-based probe reveals caspase-3 activity in the endoplasmic reticulum during apoptosis." Chemical Science 7, no. 2 (2016): 1322–37. http://dx.doi.org/10.1039/c5sc03207e.

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21

Hira, Jonathan, Md Jalal Uddin, Marius M. Haugland, and Christian S. Lentz. "From Differential Stains to Next Generation Physiology: Chemical Probes to Visualize Bacterial Cell Structure and Physiology." Molecules 25, no. 21 (2020): 4949. http://dx.doi.org/10.3390/molecules25214949.

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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 strateg

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22

Bennett, Kristen, Natalie C. Sadler, Aaron T. Wright, Chris Yeager, and Michael R. Hyman. "Activity-Based Protein Profiling of Ammonia Monooxygenase in Nitrosomonas europaea." Applied and Environmental Microbiology 82, no. 8 (2016): 2270–79. http://dx.doi.org/10.1128/aem.03556-15.

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ABSTRACTNitrosomonas europaeais an aerobic nitrifying bacterium that oxidizes ammonia (NH3) to nitrite (NO2−) through the sequential activities of ammonia monooxygenase (AMO) and hydroxylamine dehydrogenase (HAO). Many alkynes are mechanism-based inactivators of AMO, and here we describe an activity-based protein profiling method for this enzyme using 1,7-octadiyne (17OD) as a probe. Inactivation of NH4+-dependent O2uptake byN. europaeaby 17OD was time- and concentration-dependent. The effects of 17OD were specific for ammonia-oxidizing activity, andde novoprotein synthesis was required to ree

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23

Hong, Jong-Ah, Na-Eun Choi, Yeo-Kyoung La, Ho Yeon Nam, Jiwon Seo, and Jiyoun Lee. "Development of a smart activity-based probe to detect subcellular activity of asparaginyl endopeptidase in living cells." Organic & Biomolecular Chemistry 15, no. 38 (2017): 8018–22. http://dx.doi.org/10.1039/c7ob01467h.

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24

Gu, Xiaodong, Ying Huang, Bruce S. Levison, et al. "Identification of Critical Paraoxonase 1 Residues Involved in High Density Lipoprotein Interaction." Journal of Biological Chemistry 291, no. 4 (2015): 1890–904. http://dx.doi.org/10.1074/jbc.m115.678334.

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Paraoxonase 1 (PON1) is a high density lipoprotein (HDL)-associated protein with atherosclerosis-protective and systemic anti-oxidant functions. We recently showed that PON1, myeloperoxidase, and HDL bind to one another in vivo forming a functional ternary complex (Huang, Y., Wu, Z., Riwanto, M., Gao, S., Levison, B. S., Gu, X., Fu, X., Wagner, M. A., Besler, C., Gerstenecker, G., Zhang, R., Li, X. M., Didonato, A. J., Gogonea, V., Tang, W. H., et al. (2013) J. Clin. Invest. 123, 3815–3828). However, specific residues on PON1 involved in the HDL-PON1 interaction remain unclear. Unambiguous ide

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25

Tantama, Mathew, Wan-Chen Lin, and Stuart Licht. "An Activity-Based Protein Profiling Probe for the Nicotinic Acetylcholine Receptor." Journal of the American Chemical Society 130, no. 47 (2008): 15766–67. http://dx.doi.org/10.1021/ja805868x.

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26

Serdiuk, Illia E., Milena Reszka, Henryk Myszka, Karol Krzymiński, Beata Liberek та Alexander D. Roshal. "Flavonol-based fluorescent indicator for determination of β-glucosidase activity". RSC Advances 6, № 48 (2016): 42532–36. http://dx.doi.org/10.1039/c6ra06062e.

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27

Hu, Juan, Wen-can Li, Jian-Ge Qiu, BingHua Jiang, and Chun-yang Zhang. "A multifunctional DNA nanostructure based on multicolor FRET for nuclease activity assay." Analyst 145, no. 18 (2020): 6054–60. http://dx.doi.org/10.1039/d0an01212b.

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28

Jiang, Jie, Haifeng Sun, Yanlei Hu, Gang Lu, Jiwei Cui, and Jingcheng Hao. "AIE + ESIPT activity-based NIR Cu2+ sensor with dye participated binding strategy." Chemical Communications 57, no. 62 (2021): 7685–88. http://dx.doi.org/10.1039/d1cc02233d.

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An activity-based Cu<sup>2+</sup> fluorescent probe functions through chelation with Cu<sup>2+</sup>via dye-based multidentate binding, which in turn specifically triggers the probe to undergo hydrolysis to release a NIR emission with AIE + ESIPT properties.

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29

Ucar, Ahmet, Eva González-Fernández, Matteo Staderini, et al. "Miniaturisation of a peptide-based electrochemical protease activity sensor using platinum microelectrodes." Analyst 145, no. 3 (2020): 975–82. http://dx.doi.org/10.1039/c9an02321f.

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30

Poreba, Marcin, Wioletta Rut, Matej Vizovisek, et al. "Selective imaging of cathepsin L in breast cancer by fluorescent activity-based probes." Chemical Science 9, no. 8 (2018): 2113–29. http://dx.doi.org/10.1039/c7sc04303a.

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31

Howell, Amy, Santosh Keshipeddy, Yu Shi, Nathan Hnatiuk, Martha Morton, and Xudong Yao. "Design and Synthesis of an Activity-Based Probe Template for Protein Kinases." Synlett 2010, no. 04 (2009): 521–24. http://dx.doi.org/10.1055/s-0029-1218543.

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32

Howell, Amy, Santosh Keshipeddy, Yu Shi, Nathan Hnatiuk, Martha Morton, and Xudong Yao. "Design and Synthesis of an Activity-Based Probe Template for Protein Kinases." Synlett 2010, no. 07 (2010): 1142. http://dx.doi.org/10.1055/s-0029-1219805.

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33

Hirayama, Yuichiro, Yuta Tsunematsu, Yuko Yoshikawa, et al. "Activity-Based Probe for Screening of High-Colibactin Producers from Clinical Samples." Organic Letters 21, no. 12 (2019): 4490–94. http://dx.doi.org/10.1021/acs.orglett.9b01345.

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34

Xiao, Wei, Fang Liu, Gen-Ping Yan, et al. "Yttrium vanadates based ratiometric fluorescence probe for alkaline phosphatase activity sensing." Colloids and Surfaces B: Biointerfaces 185 (January 2020): 110618. http://dx.doi.org/10.1016/j.colsurfb.2019.110618.

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35

Schwaid, Adam G., Wanida Ruangsiriluk, Allan R. Reyes, et al. "Development of a selective activity-based probe for glycosylated LIPA." Bioorganic & Medicinal Chemistry Letters 26, no. 8 (2016): 1993–96. http://dx.doi.org/10.1016/j.bmcl.2016.02.089.

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36

Wangngae, Sirilak, Thitima Pewklang, Kantapat Chansaenpak, et al. "A chalcone-based fluorescent responsive probe for selective detection of nitroreductase activity in bacteria." New Journal of Chemistry 45, no. 26 (2021): 11566–73. http://dx.doi.org/10.1039/d1nj01794b.

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37

Xiao, Junpeng, Petr Broz, Aaron W. Puri, et al. "A Coupled Protein and Probe Engineering Approach for Selective Inhibition and Activity-Based Probe Labeling of the Caspases." Journal of the American Chemical Society 135, no. 24 (2013): 9130–38. http://dx.doi.org/10.1021/ja403521u.

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38

He, Yong, Junli Yu, Xiangzi Hu, et al. "An activity-based fluorescent probe and its application for differentiating alkaline phosphatase activity in different cell lines." Chemical Communications 56, no. 87 (2020): 13323–26. http://dx.doi.org/10.1039/d0cc06129h.

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39

Park, Sun Young, Eugeine Jung, Jong Seung Kim, Sung-Gil Chi, and Min Hee Lee. "Cancer-Specific hNQO1-Responsive Biocompatible Naphthalimides Providing a Rapid Fluorescent Turn-On with an Enhanced Enzyme Affinity." Sensors 20, no. 1 (2019): 53. http://dx.doi.org/10.3390/s20010053.

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Human NAD(P)H:quinone oxidoreductase 1 (hNQO1) is overexpressed in cancer cells and associated with the drug resistance factor of cancer. The objective of this work is the development of fluorescent probes for the efficient detection of hNQO1 activity in cancer cells, which can be employed for the cancer diagnosis and therapeutic agent development. Herein, we report naphthalimide-based fluorescent probes 1 and 2 that can detect hNQO1. For hNQO1 activity, the probes showed a significant fluorescence increase at 540 nm. In addition, probe 1, the naphthalimide containing a triphenylphosphonium sa

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40

Luo, Jiajie, Hongyi Zhang, Jialiang Guan, et al. "Detection of lipase activity in human serum based on a ratiometric fluorescent probe." New Journal of Chemistry 45, no. 21 (2021): 9561–68. http://dx.doi.org/10.1039/d1nj01155c.

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41

Gao, Congcong, Baoquan Che, and Hong Dai. "A new G-triplex-based strategy for sensitivity enhancement of the detection of endonuclease activity and inhibition." RSC Advances 11, no. 45 (2021): 28008–13. http://dx.doi.org/10.1039/d1ra04203c.

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A new G-triplex-based probe was developed for detecting EcoRI activity and inhibition. The probe showed good selectivity towards EcoRI. The assay was colorimetric and can be monitored by the naked eye.

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42

Das, Sayantan, Julian Ihssen, Lukas Wick, Urs Spitz, and Doron Shabat. "Chemiluminescent Carbapenem‐Based Molecular Probe for Detection of Carbapenemase Activity in Live Bacteria." Chemistry – A European Journal 26, no. 16 (2020): 3647–52. http://dx.doi.org/10.1002/chem.202000217.

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43

Jin, Qiang, Hongying Ma, Lei Feng, et al. "Sensing cytochrome P450 1A1 activity by a resorufin-based isoform-specific fluorescent probe." Chinese Chemical Letters 31, no. 11 (2020): 2945–49. http://dx.doi.org/10.1016/j.cclet.2020.05.038.

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44

Niu, Niu, Huipeng Zhou, Ning Liu, Hong Jiang, Zhenzhen Hu, and Cong Yu. "A perylene-based membrane intercalating conjugated oligoelectrolyte with efficient photodynamic antimicrobial activity." Chemical Communications 55, no. 30 (2019): 4395–98. http://dx.doi.org/10.1039/c9cc01357a.

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45

Xu, Hao, Hairat Sabit, Gordon L. Amidon, and H. D. Hollis Showalter. "An improved synthesis of a fluorophosphonate–polyethylene glycol–biotin probe and its use against competitive substrates." Beilstein Journal of Organic Chemistry 9 (January 15, 2013): 89–96. http://dx.doi.org/10.3762/bjoc.9.12.

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The fluorophosphonate (FP) moiety attached to a biotin tag is a prototype chemical probe used to quantitatively analyze and enrich active serine hydrolases in complex proteomes in an approach called activity-based protein profiling (ABPP). In this study we have designed a novel synthetic route to a known FP probe linked by polyethylene glycol to a biotin tag (FP–PEG–biotin). Our route markedly increases the efficiency of the probe synthesis and overcomes several problems of a prior synthesis. As a proof of principle, FP–PEG–biotin was evaluated against isolated protein mixtures and different r

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46

Shi, Fanping, Danyi Shang, and Zonghua Wang. "An rGQD/chitosan nanocomposite-based pH-sensitive probe: application to sensing in urease activity assays." New Journal of Chemistry 43, no. 34 (2019): 13398–407. http://dx.doi.org/10.1039/c9nj03268a.

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We used the intriguing pH-responsive protonation/deprotonation transitions of chitosan and the fluorescence properties of reduced graphene quantum dots to design a novel pH probe and realize the real-time monitoring of urease activity.

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47

Zhang, Bin, Lijing Xu, Yindi Zhou, Weijian Zhang, Yuanhong Wang, and Yu Zhu. "Synthesis and activity of a coumarin‐based fluorescent probe for hydroxyl radical detection." Luminescence 35, no. 2 (2019): 305–11. http://dx.doi.org/10.1002/bio.3728.

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48

Ohta, Yuhei, Hiroo Wakita, Mitsuyasu Kawaguchi, Naoya Ieda, Shigehiro Osada, and Hidehiko Nakagawa. "Ratiometric assay of CARM1 activity using a FRET-based fluorescent probe." Bioorganic & Medicinal Chemistry Letters 29, no. 22 (2019): 126728. http://dx.doi.org/10.1016/j.bmcl.2019.126728.

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49

Zhan, Ruoyu, Angela Jun Hiong Tan, and Bin Liu. "Conjugated polyelectrolyte as signal amplifier for fluorogenic probe based enzyme activity study." Polym. Chem. 2, no. 2 (2011): 417–21. http://dx.doi.org/10.1039/c0py00265h.

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50

Koenders, Sebastiaan T. A., Eva J. Rooden, Hans Elst, Bogdan I. Florea, Herman S. Overkleeft, and Mario Stelt. "STA‐55, an Easily Accessible, Broad‐Spectrum, Activity‐Based Aldehyde Dehydrogenase Probe." ChemBioChem 21, no. 13 (2020): 1911–17. http://dx.doi.org/10.1002/cbic.201900771.

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