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Veni, Vidi, Vici: Immobilized Peptide-Based Conjugates as Tools for Capture, Analysis, and Transformation. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10010031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Analysis of peptide biomarkers of pathological states of the organism is often a serious challenge, due to a very complex composition of the cell and insufficient sensitivity of the current analytical methods (including mass spectrometry). One of the possible ways to overcome this problem is sample enrichment by capturing the selected components using a specific solid support. Another option is increasing the detectability of the desired compound by its selective tagging. Appropriately modified and immobilized peptides can be used for these purposes. In addition, they find application in studying the specificity and activity of proteolytic enzymes. Immobilized heterocyclic peptide conjugates may serve as metal ligands, to form complexes used as catalysts or analytical markers. In this review, we describe various applications of immobilized peptides, including selective capturing of cysteine-containing peptides, tagging of the carbonyl compounds to increase the sensitivity of their detection, enrichment of biological samples in deoxyfructosylated peptides, and fishing out of tyrosine–containing peptides by the formation of azo bond. Moreover, the use of the one-bead-one-compound peptide library for the analysis of substrate specificity and activity of caspases is described. Furthermore, the evolution of immobilization from the solid support used in peptide synthesis to nanocarriers is presented. Taken together, the examples presented here demonstrate immobilized peptides as a multifunctional tool, which can be successfully used to solve multiple analytical problems.
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2
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Li Z, Cheng J, Huang L, Li W, Zhao Y, Lin W. Aging Diagnostic Probe for Research on Aging and Evaluation of Anti-aging Drug Efficacy. Anal Chem 2021; 93:13800-13806. [PMID: 34606237 DOI: 10.1021/acs.analchem.1c02391] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aging is a biological process, and its gradual degeneration of physiological functions leads to an increase in morbidity and mortality. At present, more and more studies on aging and anti-aging drugs have been conducted, which are of great significance for promoting human health, treating aging-related diseases, and prolonging human life. In the process of aging research and evaluation of anti-aging drugs, β-galactosidase, as an important criterion of aging, has received extensive attention. However, there is a scarcity of effective and reliable tools for aging research and anti-aging drug evaluation based on the aging markers. Hence, we developed a new highly sensitive fluorescent probe, YDGAL, for β-galactosidase, which exhibited good affinity for β-gal (Km = 12.35 μM), fast response speed (stable within 10 min), and extremely low detection limit (2.185 × 10-6 U/mL). Owing to the above advantages, the robust probe can visualize aging and evaluate the efficacy of anti-aging drugs at the cellular and organ levels by detecting β-galactosidase. Through visual imaging of mouse organs, we found that the organs had different degrees of aging; dasatinib and quercetin combination therapy had a therapeutic effect on the mice, but the different organs showed distinct clearance rates on the senescent cells, which may be the limitation of the drugs. We believe that this interesting finding could provide a powerful guidance for the research on aging and the evaluation of anti-aging drugs in the future.
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Affiliation(s)
- Zihong Li
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P.R. China
| | - Jie Cheng
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P.R. China
| | - Ling Huang
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P.R. China
| | - Wenxiu Li
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P.R. China
| | - Yuping Zhao
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P.R. China
| | - Weiying Lin
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P.R. China
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3
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Affinity‐switchable
biotin probes for the analysis of enzymes and small reactive molecules on microarray platform. J CHIN CHEM SOC-TAIP 2020. [DOI: 10.1002/jccs.202000200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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4
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Miniaturized technologies for high-throughput drug screening enzymatic assays and diagnostics – A review. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115862] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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5
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Żądło-Dobrowolska A, Szczygieł M, Koszelewski D, Paprocki D, Ostaszewski R. Self-immolative versatile fluorogenic probes for screening of hydrolytic enzyme activity. Org Biomol Chem 2018; 14:9146-9150. [PMID: 27714153 DOI: 10.1039/c6ob01488g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Enzyme triggered probes with a self-immolative linker for rapid and sensitive hydrolase detection through a cascade reaction have been reported. Their utility was proved by the preparation of three model compounds and their evaluation as enzyme substrates and demonstration of their applicability as fluorogenic probes for screening lipase, esterase and protease activities. These probes represent a new class of fluorogenic compounds, are stable under aqueous conditions and not susceptible to nonspecific degradation. The utilization of the carbamate cleavable linkage in a probe structure allows moving away of the bulky fluorophore from the enzyme recognition unit and targets different classes of enzymes with the same substrate.
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Affiliation(s)
- Anna Żądło-Dobrowolska
- Institute of Organic Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Martyna Szczygieł
- Institute of Organic Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Dominik Koszelewski
- Institute of Organic Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Daniel Paprocki
- Institute of Organic Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Ryszard Ostaszewski
- Institute of Organic Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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6
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Fulton A, Hayes MR, Schwaneberg U, Pietruszka J, Jaeger KE. High-Throughput Screening Assays for Lipolytic Enzymes. Methods Mol Biol 2018; 1685:209-231. [PMID: 29086311 DOI: 10.1007/978-1-4939-7366-8_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Screening is defined as the identification of hits within a large library of variants of an enzyme or protein with a predefined property. In theory, each variant present in the respective library needs to be assayed; however, to save time and consumables, many screening regimes involve a primary round to identify clones producing active enzymes. Such primary or prescreenings for lipolytic enzyme activity are often carried out on agar plates containing pH indicators or substrates as triolein or tributyrin. Subsequently, high-throughput screening assays are usually performed in microtiter plate (MTP) format using chromogenic or fluorogenic substrates and, if available, automated liquid handling robotics. Here, we describe different assay systems to determine the activity and enantioselectivity of lipases and esterases as well as the synthesis of several substrates. We also report on the construction of a complete site saturation library derived from lipase A of Bacillus subtilis and its testing for detergent tolerance. This approach allows for the identification of amino acids affecting sensitivity or resistance against different detergents.
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Affiliation(s)
- Alexander Fulton
- Institute of Molecular Enzyme Technology, Heinrich-Heine - Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany
- Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark
| | - Marc R Hayes
- Institute of Bioorganic Chemistry, Heinrich-Heine - Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, 52074, Aachen, Germany
- DWI Leibniz-Institute for Interactive Materials at RWTH Aachen University, 52056, Aachen, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich-Heine - Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine - Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany.
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany.
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7
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Kübler D, Bergmann A, Weger L, Ingenbosch KN, Hoffmann-Jacobsen K. Kinetics of Detergent-Induced Activation and Inhibition of a Minimal Lipase. J Phys Chem B 2017; 121:1248-1257. [DOI: 10.1021/acs.jpcb.6b11037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel Kübler
- Department of Chemistry, Niederrhein University of Applied Sciences, Adlerstr. 32, 47798 Krefeld, Germany
| | - Anna Bergmann
- Department of Chemistry, Niederrhein University of Applied Sciences, Adlerstr. 32, 47798 Krefeld, Germany
| | - Lukas Weger
- Department of Chemistry, Niederrhein University of Applied Sciences, Adlerstr. 32, 47798 Krefeld, Germany
| | - Kim N. Ingenbosch
- Department of Chemistry, Niederrhein University of Applied Sciences, Adlerstr. 32, 47798 Krefeld, Germany
| | - Kerstin Hoffmann-Jacobsen
- Department of Chemistry, Niederrhein University of Applied Sciences, Adlerstr. 32, 47798 Krefeld, Germany
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8
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Wang P, Du J, Liu H, Bi G, Zhang G. Small quinolinium-based enzymatic probes via blue-to-red ratiometric fluorescence. Analyst 2017; 141:1483-7. [PMID: 26788553 DOI: 10.1039/c5an02480c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A small fluorescence ratiometric probe consisting of a single dye species, N-methyl-6-hydroxyquinolinium (MHQ), and coupled enzymatic substrates, exhibits a dramatic colour change (deep blue to red) and possesses a huge response ratio (over 2000 fold) upon specific recognition of target enzymes. Such dramatic responses are attributed to the excited-state proton transfer processes of MHQ molecules in water. Here the detection of β-galactosidase and porcine pancreatic lipase is successfully demonstrated and this class of molecules has the potential to be developed as a "naked-eye" probe in vitro.
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Affiliation(s)
- Pan Wang
- Heifei National Laboratory for Physical Sciences at the Microscale and Department of Polymer Science and Engieering, University of Science and Technology of China, 230026 Hefei, P. R. China.
| | - Jiajun Du
- Heifei National Laboratory for Physical Sciences at the Microscale and Department of Polymer Science and Engieering, University of Science and Technology of China, 230026 Hefei, P. R. China.
| | - Huijing Liu
- CAS Key Laboratory of Brain Function and Disease and Department of Neurobiology and Biophysics, School of Life Sciences, University of Science and Technology of China, 230026 Hefei, P. R. China
| | - Guoqiang Bi
- CAS Key Laboratory of Brain Function and Disease and Department of Neurobiology and Biophysics, School of Life Sciences, University of Science and Technology of China, 230026 Hefei, P. R. China
| | - Guoqing Zhang
- Heifei National Laboratory for Physical Sciences at the Microscale and Department of Polymer Science and Engieering, University of Science and Technology of China, 230026 Hefei, P. R. China.
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9
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Array-on-Array Strategy For Activity-Based Enzyme Profiling. Methods Mol Biol 2016. [PMID: 27873204 DOI: 10.1007/978-1-4939-6584-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
We describe a novel array on array strategy intended to enhance the throughput of enzymatic activity screening using microarrays. This strategy consists of spotting a first array with large droplets of enzymes with varying concentrations and subsequently spotting a second array with small droplets of fluorogenic substrate on top of the enzyme array. By varying the array on array spotting patterns of different classes of enzyme (e.g., proteases, phosphatases, kinases) and their corresponding fluorogenic substrates, we have the unprecedented ability for testing enzymes and mixed samples in a multiplexed fashion within a single microarray slide. This new approach enables rapid enzyme characterization building upon a one enzyme on one slide droplet-based screening concept previously established.
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10
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Zadlo A, Koszelewski D, Borys F, Ostaszewski R. Evaluation of Pseudoenantiomeric Mixed Carbonates as Efficient Fluorogenic Probes for Enantioselectivity Screening. Chembiochem 2015; 17:71-6. [DOI: 10.1002/cbic.201500509] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Anna Zadlo
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
| | - Dominik Koszelewski
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
| | - Filip Borys
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
| | - Ryszard Ostaszewski
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
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11
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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] [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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12
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Tang Y, Zhang W, Liu J, Zhang L, Huang W, Huo F, Tian D. A plasmonic nanosensor for lipase activity based on enzyme-controlled gold nanoparticles growth in situ. NANOSCALE 2015; 7:6039-6044. [PMID: 25766647 DOI: 10.1039/c4nr07579j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A plasmonic nanosensor for lipase activity was developed based on one-pot nanoparticle growth. Tween 80 was selected not only as the substrate for lipase recognition but also as the reducing and stabilizing agent for the sensor fabrication. The different molecular groups in Tween 80 could have different roles in the fabrication procedure; the H2O2 produced by the autoxidation of the ethylene oxide subunits in Tween 80 could reduce the AuCl4(-) ions to Au atoms, meanwhile, the lipase could hydrolyze its carboxyl ester bond, which could, in turn, control the rate of nucleation of the gold nanoparticles (AuNPs) and tailor the localized surface plasmon resonance (LSPR) of the AuNP transducers. The color changes, which depend on the absence or presence of the lipase, could be used to sense the lipase activity. A linear response ranging from 0.025 to 4 mg mL(-1) and a detection limit of the lipase as low as 3.47 μg mL(-1) were achieved. This strategy circumvents the problems encountered by general enzyme assays that require sophisticated instruments and complicated assembling steps. The methodology can benefit the assays of heterogeneous-catalyzed enzymes.
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Affiliation(s)
- Yan Tang
- College of Science, Nanjing Tech University, Nanjing 211816, China.
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13
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Tallman KR, Beatty KE. Far-red fluorogenic probes for esterase and lipase detection. Chembiochem 2014; 16:70-5. [PMID: 25469918 DOI: 10.1002/cbic.201402548] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 11/05/2022]
Abstract
Fluorogenic enzyme probes go from a dark to a bright state following hydrolysis and can provide a sensitive, real-time readout of enzyme activity. They are useful for examining enzymatic activity in bacteria, including the human pathogen Mycobacterium tuberculosis. Herein, we describe two fluorogenic esterase probes derived from the far-red fluorophore 7-hydroxy-9H-(1,3-dichloro-9,9-dimethylacridin-2-one) (DDAO). These probes offer enhanced optical properties compared to existing esterase probes because the hydrolysis product, DDAO, excites above 600 nm while retaining a good quantum yield (ϕ=0.40). We validated both probes with a panel of commercially available enzymes alongside known resorufin- and fluorescein-derived esterase substrates. Furthermore, we used these probes to reveal esterase activity in protein gel-resolved mycobacterial lysates. These probes represent new tools for esterase detection and characterization and should find use in a variety of applications.
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Affiliation(s)
- Katie R Tallman
- Department of Physiology and Pharmacology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 SW Moody Avenue, CL3B, Portland, OR 97201 (USA)
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14
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Prajapti SK, Nagarsenkar A, Babu BN. Tris(pentafluorophenyl)borane catalyzed acylation of alcohols, phenols, amines, and thiophenols under solvent-free condition. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.01.124] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Identification of organic solvent-tolerant lipases from organic solvent-sensitive microorganisms. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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The chemistry of small-molecule fluorogenic probes. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 113:1-34. [PMID: 23244787 DOI: 10.1016/b978-0-12-386932-6.00001-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Chemical fluorophores find wide use in biology to detect and visualize different phenomena. A key advantage of small-molecule dyes is the ability to construct compounds where fluorescence is activated by chemical or biochemical processes. Fluorogenic molecules, in which fluorescence is activated by enzymatic activity, light, or environmental changes, enable advanced bioassays and sophisticated imaging experiments. Here, we detail the collection of fluorophores and highlight both general strategies and unique approaches that are employed to control fluorescence using chemistry.
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17
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Liu Y, Li Y, Liu J, Deng C, Zhang X. High throughput enzyme inhibitor screening by functionalized magnetic carbonaceous microspheres and graphene oxide-based MALDI-TOF-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:2188-2198. [PMID: 21952774 DOI: 10.1007/s13361-011-0231-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 08/08/2011] [Accepted: 08/09/2011] [Indexed: 05/31/2023]
Abstract
In this work, a high throughput methodology for screening enzyme inhibitors has been demonstrated by combining enzyme immobilized magnetic carbonaceous microspheres and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with grapheme oxide as matrix. First, model enzyme acetylcholinesterase (AChE) was immobilized onto the 3-glycidoxypropyltrimethoxysilane (GLYMO)-modified magnetic carbonaceous (MC) microspheres, displaying a high enzyme activity and stability, and also facilitating the separation of enzyme from substrate and product. The efficiency of immobilized AChE was monitored by biochemical assay, which was carried out by mixing enzyme-immobilized MC microspheres with model substrate acetylcholine (ACh), and subsequent quantitative determination of substrate ACh and product choline using graphene oxide-based MALDI-TOF-MS with no background inference. The limit of detection (LOD) for ACh was 0.25 fmol/μL, and excellent linearity (R(2)=0.9998) was maintained over the range of 0.5 and 250 fmol/μL. Choline was quantified over the range of 0.05 and 15 pmol/μL, also with excellent linearity (R(2)=0.9994) and low LOD (0.15 fmol/μL). Good accuracy and precision were obtained for all concentrations within the range of the standard curves. All together, eight compounds (four known AChE inhibitors and four control chemical compounds with no AChE inhibit effect) were tested with our promoted methodology, and the obtained results demonstrated that our high throughput screening methodology could be a great help to the routine enzyme inhibitor screening.
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Affiliation(s)
- Yang Liu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
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18
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Maillard N, Babiak P, Syed S, Biswas R, Mandrich L, Manco G, Reymond JL. Five-Substrate Cocktail as a Sensor Array for Measuring Enzyme Activity Fingerprints of Lipases and Esterases. Anal Chem 2011; 83:1437-42. [DOI: 10.1021/ac102994n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Noélie Maillard
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Peter Babiak
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Salahuddin Syed
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Rasomoy Biswas
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Luigi Mandrich
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giuseppe Manco
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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19
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Microarray-based enzyme profiling: Recent advances and applications (Review). Biointerphases 2010; 5:FA24-31. [DOI: 10.1116/1.3462969] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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20
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Schmidt M, Böttcher D, Bornscheuer UT. Directed Evolution of Industrial Biocatalysts. Ind Biotechnol (New Rochelle N Y) 2010. [DOI: 10.1002/9783527630233.ch4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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21
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Yeh JY, Coumar MS, Horng JT, Shiao HY, Kuo FM, Lee HL, Chen IC, Chang CW, Tang WF, Tseng SN, Chen CJ, Shih SR, Hsu JTA, Liao CC, Chao YS, Hsieh HP. Anti-Influenza Drug Discovery: Structure−Activity Relationship and Mechanistic Insight into Novel Angelicin Derivatives. J Med Chem 2010; 53:1519-33. [DOI: 10.1021/jm901570x] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jiann-Yih Yeh
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Mohane Selvaraj Coumar
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | | | - Hui-Yi Shiao
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang Fu Road, Hsinchu 300, Taiwan, ROC
| | - Fu-Ming Kuo
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Hui-Ling Lee
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - In-Chun Chen
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Chun-Wei Chang
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | | | - Sung-Nain Tseng
- Department of Medical Biotechnology and Laboratory Science
- Research Center for Emerging Viral Infections
| | | | - Shin-Ru Shih
- Department of Medical Biotechnology and Laboratory Science
| | - John T.-A. Hsu
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
- Department of Biological Science and Technology, National Chiao Tung University, 1001 University Road, Hsinchu 300, Taiwan, ROC
| | - Chun-Chen Liao
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang Fu Road, Hsinchu 300, Taiwan, ROC
- Department of Chemistry, Chung Yuan Christian University, 200 Chung-Pei Road, Chungli 320, Taiwan, ROC
| | - Yu-Sheng Chao
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Hsing-Pang Hsieh
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
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22
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23
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Abstract
We describe here a method for the continuous assessment of enzymatic activity using microarrays. By uniformly coating fluorogenic substrates on slides, we generated surfaces capable of detecting enzymatic activity. The enzymes were deposited on the arrays in segregated droplets using standard microarrayers. Surfaces were developed for assessing the activities of both proteases and phosphatases, hence capitalizing on microarray technology to perform miniaturized high-throughput screens for these, as well as potentially any other, classes of enzyme. This offers an unprecedented ability for performing solution-phase enzymatic assays in nanoliter volumes on microarrays, in contrast to microliter volumes typically required in microplate-based assays, thereby reducing the amounts of reagent(s) required by anywhere from a hundred to a thousand-fold. This new approach thus provides a potentially more cost-effective, label-free enzyme screening technique. A single slide is able to accommodate several thousand assays, facilitating the assessment of both dose and time-dependent inhibition parameters in a single run.
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Affiliation(s)
- Kang L D Aw
- DSO National Laboratories, Defence Medical and Environmental Research Institute, Singapore, Singapore
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24
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Uttamchandani M, Lu CHS, Yao SQ. Next generation chemical proteomic tools for rapid enzyme profiling. Acc Chem Res 2009; 42:1183-92. [PMID: 19435360 DOI: 10.1021/ar9000586] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sequencing of the human genome provided a wealth of information about the genomic blueprint of a cell. But genes do not tell the entire story of life and living processes; identifying the roles of enzymes and mapping out their interactions is also crucial. Enzymes catalyze virtually every cellular process and metabolic exchange. They not only are instrumental in sustaining life but also are required for its regulation and diversification. Diseases such as cancer can be caused by minor changes in enzyme activities. In addition, the unique enzymes of pathogenic organisms are ripe targets for combating infections. Consequently, nearly one-third of all current drug targets are enzymes. An estimated 18-29% of eukaryotic genes encode enzymes, but only a limited proportion of enzymes have thus far been characterized. Therefore, little is understood about the physiological roles, substrate specificity, and downstream targets of the vast majority of these important proteins. A key step toward the biological characterization of enzymes, as well as their adoption as drug targets, is the development of global solutions that bridge the gap in understanding these proteins and their interactions. We herein present technological advances that facilitate the study of enzymes and their properties in a high-throughput manner. Over the years, our group has introduced and developed a variety of such enabling platforms for many classes of enzymes, including kinases, phosphatases, and proteases. For each of these different types of enzymes, specific design considerations are required to develop the appropriate chemical tools to characterize each class. These tools include activity-based probes and chemical compound libraries, which are rapidly assembled using efficient combinatorial synthesis or "click chemistry" strategies. The resulting molecular assortments may then be screened against the target enzymes in high-throughput using microplates or microarrays. These techniques offer powerful means to study, profile, and discover potent small molecules that can modulate enzyme activity. This Account will describe the concepts involved in designing chemical probes and libraries for comparative enzyme screening and drug discovery applications, as well as highlight how these technologies are changing the way in which enzymes may be rapidly profiled and characterized.
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Affiliation(s)
- Mahesh Uttamchandani
- Defence Medical and Environmental Research Institute, DSO National Laboratories, 27 Medical Drive, Singapore 117510
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25
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Abstract
Enantiopure sulfoxides are prevalent in drugs and are useful chiral auxiliaries in organic synthesis. The biocatalytic enantioselective oxidation of prochiral sulfides is a direct and economical approach for the synthesis of optically pure sulfoxides. The selection of suitable biocatalysts requires rapid and reliable high-throughput screening methods. Here we present four different methods for detecting sulfoxides produced via whole-cell biocatalysis, three of which were exploited for high-throughput screening. Fluorescence detection based on the acid activation of omeprazole was utilized for high-throughput screening of mutant libraries of toluene monooxygenases, but no active variants have been discovered yet. The second method is based on the reduction of sulfoxides to sulfides, with the coupled release and measurement of iodine. The availability of solvent-resistant microtiter plates enabled us to modify the method to a high-throughput format. The third method, selective inhibition of horse liver alcohol dehydrogenase, was used to rapidly screen highly active and/or enantioselective variants at position V106 of toluene ortho-monooxygenase in a saturation mutagenesis library, using methyl-p-tolyl sulfide as the substrate. A success rate of 89% (i.e., 11% false positives) was obtained, and two new mutants were selected. The fourth method is based on the colorimetric detection of adrenochrome, a back-titration procedure which measures the concentration of the periodate-sensitive sulfide. Due to low sensitivity during whole-cell screening, this method was found to be useful only for determining the presence or absence of sulfoxide in the reaction. The methods described in the present work are simple and inexpensive and do not require special equipment.
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26
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Maillard N, Darbre T, Reymond JL. Identification of Catalytic Peptide Dendrimers by “Off-Bead” in Silica High-Throughput Screening of Combinatorial Libraries. ACTA ACUST UNITED AC 2009; 11:667-75. [DOI: 10.1021/cc9000289] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Noélie Maillard
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012, Berne, Switzerland
| | - Tamis Darbre
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012, Berne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012, Berne, Switzerland
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27
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Halim VA, Muck A, Hartl M, Ibáñez AJ, Giri A, Erfurth F, Baldwin IT, Svatoš A. A dual fluorescent/MALDI chip platform for analyzing enzymatic activity and for protein profiling. Proteomics 2009; 9:171-81. [DOI: 10.1002/pmic.200800390] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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28
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Enzyme assay and activity fingerprinting of hydrolases with the red-chromogenic adrenaline test. Nat Protoc 2008; 3:1270-7. [PMID: 18714295 DOI: 10.1038/nprot.2008.106] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The adrenaline test for enzymes is a colorimetric enzyme assay based on the quantification of periodate-sensitive reaction products such as 1,2-diols and 1,2-aminoalcohols by back-titration of the oxidant with adrenaline to produce adrenochrome as an easily detectable red product. The test uses commercial reagents and is suitable for screening the activity of various hydrolases. It is demonstrated here for testing epoxide hydrolases, lipases and esterases, and for activity fingerprinting of these enzymes across substrate series. The complete assay requires 2-3 h.
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29
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Deere J, De Oliveira RF, Tomaszewski B, Millar S, Lalaouni A, Solares LF, Flitsch SL, Halling PJ. Kinetics of enzyme attack on substrates covalently attached to solid surfaces: influence of spacer chain length, immobilized substrate surface concentration and surface charge. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:11762-11769. [PMID: 18817422 DOI: 10.1021/la801932f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The use of alpha-chymotrypsin to cleave covalently bound N-acetyl- l-tryptophan (Ac-Trp-OH) from the surfaces of aminopropylated controlled pore glass (CPG) and the polymer PEGA 1,900 was investigated. Oligoglycine spacer chains were used to present the covalently attached Ac-Trp-OH substrate to the aqueous enzyme. In the absence of the oligoglycine spacer chain, the rate of release was relatively slow, especially from the PEGA 1,900. These slow rates reflect the position of the amino group to which Ac-Trp-OH is covalently attached. On the glass there was a clear optimum with a chain of four glycine residues. For PEGA 1,900 there is no real apparent change beyond two glycine residues. The decline in rate beyond these optima are a possible result of changes in oligoglycine structure. Comparing different surface loadings of bound substrate the rate of release of Ac-Trp-OH from CPG with a pore diameter of 1,200 A was optimal when using 83% of the maximum that can be coupled, then fell again at higher loading. The rate of Ac-Trp-OH release from CPG was the same for surface coverages of 0.4 and 1.0. The introduction of permanent surface charges on CPG 1,200 exhibits a distinct influence on enzymatic cleavage with an increase in the rate of biocatalysis at the surface. Optimal presentation of covalently immobilized substrate on different supports by use of appropriate linkers leads to favorable biocatalysis from the support.
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Affiliation(s)
- Joseph Deere
- Department of Pure and Applied Chemistry, Thomas Graham Building, 295 Cathedral Street, University of Strathclyde, Glasgow, G1 1XL, U.K.
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30
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Abstract
Enzyme assays are analytical tools to visualize enzyme activities. In recent years a large variety of enzyme assays have been developed to assist the discovery and optimization of industrial enzymes, in particular for "white biotechnology" where selective enzymes are used with great success for economically viable, mild and environmentally benign production processes. The present article highlights the aspects of fluorogenic and chromogenic substrates, sensors, and enzyme fingerprinting, which are our particular areas of interest.
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Affiliation(s)
- Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, Berne, 3012, Switzerland.
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31
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Hu F, Zhang H, Lin H, Deng C, Zhang X. Enzyme inhibitor screening by electrospray mass spectrometry with immobilized enzyme on magnetic silica microspheres. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:865-873. [PMID: 18396060 DOI: 10.1016/j.jasms.2008.02.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Revised: 02/19/2008] [Accepted: 02/21/2008] [Indexed: 05/26/2023]
Abstract
In this study, a novel technique for screening inhibitors by electrospray mass spectrometry (ESI-MS) with immobilized enzyme on magnetic microspheres has been demonstrated. First, the model enzyme acetylcholinesterase (AChE) is immobilized onto the 3-glycidoxypropyltrimethoxysilane (GLYMO)-modified magnetic silica microspheres. AChE activity was monitored by biochemical assay that is based on mixing of AChE immobilized microspheres and model substrate acetylcholine, separating and detecting the product through ESI-MS. Stability of the enzyme-immobilized microspheres was investigated. No apparent loss of enzyme activity was observed after fivefold reuse of AChE-immobilized microspheres. The enzyme-immobilized bioassay was used to effectively identify AChE inhibitors among two standard samples, huperzine A and huperzine B, and their source herbal Huperzia serrata, all of which were spiked into the substrate. The inhibition was determined by measuring a decrease of product formation using ESI-MS.
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Affiliation(s)
- Fengli Hu
- Department of Chemistry, Fudan University, Shanghai 200433, China
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32
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Reymond JL. Substrate Arrays for Fluorescence-Based Enzyme Fingerprinting and High-Throughput Screening. Ann N Y Acad Sci 2008; 1130:12-20. [DOI: 10.1196/annals.1430.000] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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Abstract
Small-molecule fluorescent probes embody an essential facet of chemical biology. Although numerous compounds are known, the ensemble of fluorescent probes is based on a modest collection of modular "core" dyes. The elaboration of these dyes with diverse chemical moieties is enabling the precise interrogation of biochemical and biological systems. The importance of fluorescence-based technologies in chemical biology elicits a necessity to understand the major classes of small-molecule fluorophores. Here, we examine the chemical and photophysical properties of oft-used fluorophores and highlight classic and contemporary examples in which utility has been built upon these scaffolds.
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Affiliation(s)
| | - Ronald T. Raines
- Department of Chemistry
- Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706
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34
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Sicart R, Collin MP, Reymond JL. Fluorogenic substrates for lipases, esterases, and acylases using a TIM-mechanism for signal release. Biotechnol J 2007; 2:221-31. [PMID: 17219461 DOI: 10.1002/biot.200600181] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
3-Acyloxyl-2-oxopropyl ethers of umbelliferone were investigated as new fluorogenic substrates for lipases and esterases. The aliphatic primary alcohol-leaving group released the fluorescent product umbelliferone by an enolization/beta-elimination reaction similar to the triose phosphate isomerase (TIM) reaction. A similarly designed phenylacetamide provided a fluorescent probe for penicillin G acylase, whereby the enolization/beta-elimination sequence from the intermediate aminoketone was very fast and spontaneous even under acidic conditions. The corresponding epoxyketone was not fluorogenic with epoxide hydrolases (EH). These substrates represent periodate-free Clips-otrade mark substrates.
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Affiliation(s)
- Renaud Sicart
- Department of Chemistry and Biochemistry, University of Berne, Berne, Switzerland
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35
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Reymond JL, Babiak P. Screening systems. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2007; 105:31-58. [PMID: 17408081 DOI: 10.1007/10_2006_032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Enzyme screening technology has undergone massive developments in recent years, particularly in the area of high-throughput screening and microarray methods. Screening consists of testing each sample of a sample library individually for the targeted reaction. This requires enzyme assays that accurately test relevant parameters of the reaction, such as catalytic turnover with a given substrate and selectivity parameters such as enantio- and regioselectivity. Enzyme assays also play an important role outside of enzyme screening, in particular for drug screening, medical diagnostics, and in the area of cellular and tissue imaging. In the 1990s, methods for high-throughput screening of enzyme activities were perceived as a critical bottleneck. As illustrated partly in this chapter, a large repertoire of efficient screening strategies are available today that allow testing of almost any reaction with high-throughput.
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Affiliation(s)
- Jean-Louis Reymond
- Department of Chemistry & Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland.
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36
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Deere J, McConnell G, Lalaouni A, Maltman BA, Flitsch SL, Halling PJ. Real-Time Imaging of Protease Action on Substrates Covalently Immobilised to Polymer Supports. Adv Synth Catal 2007; 349:1321-1326. [PMID: 19779571 PMCID: PMC2749704 DOI: 10.1002/adsc.200700044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We report for the first time single bead spatially resolved activity measurements of solid-phase biocatalytic systems followed in real-time. Trypsin cleavage of Bz-Arg-OH and subtilisin cleavage of Z-Gly-Gly-Leu-OH each liberate a free amino group on aminocoumarin covalently immobilised to PEGA(1900) beads [a co-polymer of poly(ethylene glycol) with molecular mass of 1900 cross-linked with acrylamide]. This restores fluorescence which is imaged in optical sections by two-photon microscopy. For trypsin cleavage, fluorescence is restricted initially to surface regions, with more than 1 hour needed before reaction is fully underway in the bead centre, presumably reflecting slow enzyme diffusion. In contrast, for subtilisin cleavage fluorescence develops throughout the bead more quickly.
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Affiliation(s)
- Joseph Deere
- Department of Pure and Applied Chemistry, Thomas Graham Building, 295 Cathedral Street, University of Strathclyde, Glasgow, G1 1XL, U.K
| | - Gail McConnell
- Centre for Biophotonics, Strathclyde Institute for Biomedical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow, G4 0NR, U.K
| | - Antonia Lalaouni
- Department of Pure and Applied Chemistry, Thomas Graham Building, 295 Cathedral Street, University of Strathclyde, Glasgow, G1 1XL, U.K
| | - Beatrice A. Maltman
- School of Chemistry and MIB, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Sabine L. Flitsch
- School of Chemistry and MIB, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Peter J. Halling
- Department of Pure and Applied Chemistry, Thomas Graham Building, 295 Cathedral Street, University of Strathclyde, Glasgow, G1 1XL, U.K
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37
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Grasso G, Fragai M, Rizzarelli E, Spoto G, Yeo KJ. A new methodology for monitoring the activity of cdMMP-12 anchored and freeze-dried on Au (111). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:961-9. [PMID: 17368043 DOI: 10.1016/j.jasms.2007.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Revised: 02/02/2007] [Accepted: 02/04/2007] [Indexed: 05/14/2023]
Abstract
Matrix metalloproteinases (MMPs) are cell-secreted soluble and membrane-tethered enzymes that are capable of degrading extracellular matrix proteins, but also can process a number of bioactive molecules. They are involved in the cleavage of cell surface receptors, but are also thought to play a major role on cell behaviors as well as in diverse physiological and pathological processes, including embryonic development, wound repair, inflammatory diseases, and cancer. For these reasons, it is obvious that a control over MMPs activity is highly desirable. Consequently, the frantic search for new inhibitors has been coupled to the development of high-throughput methods able to rapidly screen the effect of possible MMP inhibitors on the activity of these enzymes. In this scenario, solid-state-based methods play a major role because of their compatibility with array formats that are able to extract more information from smaller sample volumes and offer some important advantages that are not available in the standard solution assays. In this work, the catalytic domain of MMP-12 was immobilized on a gold substrate and the surface coverage was measured by FT-SPR experiments. A new experimental procedure was developed to freeze-dry the anchored molecules and their activity was measured by ESI-MS. The kinetics parameters obtained for the immobilized enzyme are in good accordance with those reported for similar systems in solution. Inhibition of the immobilized molecules was also carried out, demonstrating the applicability of the method for rapid screening of MMP inhibitors.
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Affiliation(s)
- Giuseppe Grasso
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici, Bari, Italy
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38
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Grasso G, Fragai M, Rizzarelli E, Spoto G, Yeo KJ. In situ AP/MALDI-MS characterization of anchored matrix metalloproteinases. JOURNAL OF MASS SPECTROMETRY : JMS 2006; 41:1561-9. [PMID: 17094173 DOI: 10.1002/jms.1126] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Several different procedures are available for the immobilization of proteins on solid supports, as many advantages derive from this approach, such as the possibility to develop new protein solid-state assays. Enzymes that are anchored on gold surfaces can interact with several different molecules in a tag-free environment, opening the way to surface plasmon resonance (SPR) investigations. Nevertheless, it is often important to know the identity of the affinity-retained analyte, and mass spectrometric analysis, via its unique molecular mass identification, represents a very valuable complementary method. There are many pieces of evidence to suggest that matrix metalloproteinases (MMPs) are involved in normal and pathological processes, including embryogenesis, wound healing, inflammation, arthritis and cancer, but presumably also exhibiting other functions. The search for new inhibitors of MMPs has prompted research towards the development of new solid-state assays for the rapid evaluation of MMP activity. We have already reported the possibility of measuring the activity of MMP-1 anchored on solid support by coupling SPR with ESI-MS analysis. In this work, we show the in situ atmospheric pressure (AP) MALDI-MS characterization of MMPs anchored on a gold chip with known surface coverage. The study extends the MS analysis to different proteins, and sequence coverage is reported for different digestion and MS procedures.
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Affiliation(s)
- Giuseppe Grasso
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici, Via C. Ulpiani 27, Bari, Italy
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39
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Affiliation(s)
- Luke D. Lavis
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI 53706-1322 (USA)
| | - Tzu-Yuan Chao
- Department of Biochemistry, University of Wisconsin–Madison, 433 Babcock Drive, Madison, WI 53706-1544 (USA), Fax: (+1)608-262-3453
| | - Ronald T. Raines
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI 53706-1322 (USA)
- Department of Biochemistry, University of Wisconsin–Madison, 433 Babcock Drive, Madison, WI 53706-1544 (USA), Fax: (+1)608-262-3453
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40
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Grognux J, Reymond JL. A red-fluorescent substrate microarray for lipase fingerprinting. MOLECULAR BIOSYSTEMS 2006; 2:492-8. [PMID: 17216030 DOI: 10.1039/b609275f] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A lipase substrate microarray was obtained by printing aliphatic C2-C12 monoesters of (5R)- and (5S)-3-(5,6-dihydroxyhexyloxy)benzaldehyde by reductive alkylation on amine-functionalized glass slides coated with bovine serum albumin and a short PEG linker. The microarray features 12 substrates and their 66 possible binary mixtures spotted in a 9 x 36 spot array. Lipase reactions are detected by chemoselective NaIO(4)-oxidation of the 1,2-diol hydrolysis product to form an aldehyde, which is then tagged with the red-fluorescent dye rhodamine B sulfohydrazide . Specific fingerprints are produced by active enzymes. These experiments provide the first example of lipase fingerprinting using microarrays.
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Affiliation(s)
- Johann Grognux
- Department of Chemistry & Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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41
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Reisinger C, van Assema F, Schürmann M, Hussain Z, Remler P, Schwab H. A versatile colony assay based on NADH fluorescence. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.molcatb.2006.01.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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42
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Kumar RA, Clark DS. High-throughput screening of biocatalytic activity: applications in drug discovery. Curr Opin Chem Biol 2006; 10:162-8. [PMID: 16520085 DOI: 10.1016/j.cbpa.2006.02.033] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Accepted: 02/21/2006] [Indexed: 11/23/2022]
Abstract
Enzymes catalyze a diverse set of reactions that propel life's processes and hence serve as valuable therapeutic targets. High-throughput screening methods have become essential for sifting through large chemical libraries in search of drug candidates, and several sensitive and reliable analytical techniques have been specifically adapted to high-throughput measurements of biocatalytic activity. High-throughput biocatalytic assay platforms thus enable rapid screening against enzymatic targets, and have vast potential to impact various stages of the drug discovery process, including lead identification and optimization, and ADME/Tox assessment. These advances are paving the way for the adoption of high-throughput biocatalytic assays as an indispensable tool for the pharmaceutical industry.
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Affiliation(s)
- R Anand Kumar
- Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA
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43
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Yang Y, Babiak P, Reymond JL. New Monofunctionalized Fluorescein Derivatives for the Efficient High-Throughput Screening of Lipases and Esterases in Aqueous Media. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690041] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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44
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Yang Y, Babiak P, Reymond JL. Low background FRET-substrates for lipases and esterases suitable for high-throughput screening under basic (pH 11) conditions. Org Biomol Chem 2006; 4:1746-54. [PMID: 16633567 DOI: 10.1039/b601151a] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
FRET-based fluorogenic substrates for lipases and esterases were prepared in four steps from commercially available building blocks. The substrates are pyrenebutyric acid monoesters of aliphatic 1,2-diols bearing a dinitrophenylamino group as a quencher. The most enzyme-reactive substrate is ester 2a. The substrates do not show any measurable background reaction in the absence of enzyme even at pH 11, but react fast and specifically with lipases and esterases. These substrates offer an unprecedented and practical solution to the long-standing problem of a simple yet efficient high-throughput screening tool for lipase activities under basic conditions.
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Affiliation(s)
- Yongzheng Yang
- Department of Chemistry & Biochemistry, University of Berne, Switzerland
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45
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Uttamchandani M, Wang J, Yao SQ. Protein and small molecule microarrays: powerful tools for high-throughput proteomics. ACTA ACUST UNITED AC 2006; 2:58-68. [PMID: 16880923 DOI: 10.1039/b513935j] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advances in genomics and proteomics have opened up new possibilities for the rapid functional assignment and global characterization of proteins. Large-scale studies have accelerated this effort by using tools and strategies that enable highly parallel analysis of huge repertoires of biomolecules. Organized assortments of molecules on arrays have furnished a robust platform for rapid screening, lead discovery and molecular characterization. The essential advantage of microarray technology is attributed to the massive throughput attainable, coupled with a highly miniaturized platform--potentially driving discovery both as an analytical and diagnostic tool. The scope of microarrays has in recent years expanded impressively. Virtually every biological component--from diverse small molecules and macromolecules (such as DNA and proteins) to entire living cells--has been harnessed on microarrays in attempts to dissect the bewildering complexity of life. Herein we highlight strategies that address challenges in proteomics using microarrays of immobilized proteins and small molecules. Of specific interest are the techniques involved in stably immobilizing proteins and chemical libraries on slide surfaces as well as novel strategies developed to profile activities of proteins on arrays. As a rapidly maturing technology, microarrays pave the way forward in high-throughput proteomic exploration.
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46
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Grasso G, D'Agata R, Rizzarelli E, Spoto G, D'Andrea L, Pedone C, Picardi A, Romanelli A, Fragai M, Yeo KJ. Activity of anchored human matrix metalloproteinase-1 catalytic domain on Au (111) surfaces monitored by ESI-MS. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:1565-71. [PMID: 16320288 DOI: 10.1002/jms.929] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Matrix metalloproteinases (MMPs) are a family of Zn-dependent endo-peptidases known for their ability to cleave several components of the extracellular matrix, but which can also cleave many non-matrix proteins. There are many evidences that MMPs are involved in physiological and pathological processes, and a huge effort has been put in the development of possible inhibitors that could reduce the activity of MMPs, as it is clear that the ability to monitor and control such activity plays a pivotal role in the search for potential drugs aimed at finding a cure for several diseases such as pulmonary emphysema, rheumatoid arthritis, fibrotic disorders and cancer.A powerful method currently available to study enzyme-inhibitor interactions is based on the use of the surface plasmon resonance (SPR) technique. When MMP interactions are studied, a procedure by which inhibitors are normally anchored on sensor chips and SPR technique is used in order to study their interaction with MMPs molecules is usually followed. This is because it is currently believed that MMPs cannot be anchored on the sensor-chip surface without losing their activity. However, this approach gives rise to problems, as the anchoring of low-molecular-weight inhibitors on gold surfaces easily affects their ability to interact with MMPs. For this reason, the anchoring of MMPs is highly desirable.A new experimental protocol that couples the Fourier transform-SPR (FT-SPR) technique with electrospray ionization-mass spectroscopy (ESI-MS) is described here for the evaluation of the activity of MMP-1 catalytic domain (cdMMP-1) anchored on gold surfaces. The cdMMP-1 surface coverage is calculated by using FT-SPR and the enzyme activity is estimated by ESI-MS. The proposed method is label-free.
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Affiliation(s)
- Giuseppe Grasso
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici, Via C. Ulpiani 27, 70126, Bari, Italy
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47
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Abstract
Here we show that a microfluidic sensor based on an array of hydrogel-entrapped enzymes can be used to simultaneously detect different concentrations of the same analyte (glucose) or multiple analytes (glucose and galactose) in real time. The concentration of paraoxon, an acetylcholine esterase inhibitor, can be quantified using the same approach. The hydrogel micropatch arrays and the microfluidic systems are easy to fabricate, and the hydrogels provide a convenient, biocompatible matrix for the enzymes. Isolation of the micropatches within different microfluidic channels eliminates the possibility of cross talk between enzymes.
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Affiliation(s)
- Jinseok Heo
- Department of Chemistry, Texas A&M University, College Station, Texas 77842-3012, USA
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Yongzheng Y, Reymond JL. Protease profiling using a fluorescent domino peptide cocktail. MOLECULAR BIOSYSTEMS 2005; 1:57-63. [PMID: 16880964 DOI: 10.1039/b419446b] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Five hexapeptides were prepared containing, in a domino-type arrangement, all 25 possible dipeptides between (1) aromatic, (2) hydrophobic, (3) positively charged, (4) negatively charged, and (5) small and polar amino acids. The peptides were fluorescence labeled at the N-terminus with a (7-coumaryl)oxyacetyl group, allowing the selective detection of N-terminal cleavage products. The five peptides were used as a cocktail reagent in an HPLC analysis. The cocktail produced specific cleavage patterns, or fingerprints, for a variety of proteases. This domino peptide cocktail can be used as a general reagent for protease identification and functional profiling.
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Affiliation(s)
- Yang Yongzheng
- Department of Chemistry & Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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