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Filippova TA, Masamrekh RA, Khudoklinova YY, Shumyantseva VV, Kuzikov AV. The multifaceted role of proteases and modern analytical methods for investigation of their catalytic activity. Biochimie 2024; 222:169-194. [PMID: 38494106 DOI: 10.1016/j.biochi.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/19/2024]
Abstract
We discuss the diverse functions of proteases in the context of their biotechnological and medical significance, as well as analytical approaches used to determine the functional activity of these enzymes. An insight into modern approaches to studying the kinetics and specificity of proteases, based on spectral (absorption, fluorescence), mass spectrometric, immunological, calorimetric, and electrochemical methods of analysis is given. We also examine in detail electrochemical systems for determining the activity and specificity of proteases. Particular attention is given to exploring innovative electrochemical systems based on the detection of the electrochemical oxidation signal of amino acid residues, thereby eliminating the need for extra redox labels in the process of peptide synthesis. In the review, we highlight the main prospects for the further development of electrochemical systems for the study of biotechnologically and medically significant proteases, which will enable the miniaturization of the analytical process for determining the catalytic activity of these enzymes.
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Affiliation(s)
- Tatiana A Filippova
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Rami A Masamrekh
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Yulia Yu Khudoklinova
- Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Victoria V Shumyantseva
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Alexey V Kuzikov
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia.
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Filippova TA, Masamrekh RA, Shumyantseva VV, Latsis IA, Farafonova TE, Ilina IY, Kanashenko SL, Moshkovskii SA, Kuzikov AV. Electrochemical biosensor for trypsin activity assay based on cleavage of immobilized tyrosine-containing peptide. Talanta 2023; 257:124341. [PMID: 36821964 DOI: 10.1016/j.talanta.2023.124341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/13/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023]
Abstract
In this work, we proposed a biosensor for trypsin proteolytic activity assay using immobilization of model peptides on screen-printed electrodes (SPE) modified with gold nanoparticles (AuNPs) prepared by electrosynthetic method. Sensing of proteolytic activity was based on electrochemical oxidation of tyrosine residues of peptides. We designed peptides containing N-terminal cysteine residue for immobilization on an SPE, modified with gold nanoparticles, trypsin-specific cleavage site and tyrosine residue as a redox label. The peptides were immobilized on SPE by formation of chemical bonds between mercapto groups of the N-terminal cysteine residues and AuNPs. After the incubation with trypsin, time-dependent cleavage of the immobilized peptides was observed by decline in tyrosine electrochemical oxidation signal. The kinetic parameters of trypsin, such as the catalytic constant (kcat), the Michaelis constant (KM) and the catalytic efficiency (kcat/KM), toward the CGGGRYR peptide were determined as 0.33 ± 0.01 min-1, 198 ± 24 nM and 0.0016 min-1 nM-1, respectively. Using the developed biosensor, we demonstrated the possibility of analysis of trypsin specificity toward the peptides with amino acid residues disrupting proteolysis. Further, we designed the peptides with proline or glutamic acid residues after the cleavage site (CGGRPYR and CGGREYR), and trypsin had reduced activity toward both of them according to the existing knowledge of the enzyme specificity. The developed biosensor system allows one to perform a comparative analysis of the protease steady-state kinetic parameters and specificity toward model peptides with different amino acid sequences.
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Affiliation(s)
- Tatiana A Filippova
- Pirogov Russian National Research Medical University, 1 Ostrovityanova st., Moscow 117997, Russia; Institute of Biomedical Chemistry, 10, Pogodinskaya st., Moscow, 119121, Russia
| | - Rami A Masamrekh
- Pirogov Russian National Research Medical University, 1 Ostrovityanova st., Moscow 117997, Russia; Institute of Biomedical Chemistry, 10, Pogodinskaya st., Moscow, 119121, Russia
| | - Victoria V Shumyantseva
- Pirogov Russian National Research Medical University, 1 Ostrovityanova st., Moscow 117997, Russia; Institute of Biomedical Chemistry, 10, Pogodinskaya st., Moscow, 119121, Russia
| | - Ivan A Latsis
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a Malaya Pirogovskaya st., Moscow, 119435, Russia
| | | | - Irina Y Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a Malaya Pirogovskaya st., Moscow, 119435, Russia
| | - Sergey L Kanashenko
- Institute of Biomedical Chemistry, 10, Pogodinskaya st., Moscow, 119121, Russia
| | - Sergei A Moshkovskii
- Pirogov Russian National Research Medical University, 1 Ostrovityanova st., Moscow 117997, Russia; Federal Research and Clinical Center of Physical-Chemical Medicine, 1a Malaya Pirogovskaya st., Moscow, 119435, Russia.
| | - Alexey V Kuzikov
- Pirogov Russian National Research Medical University, 1 Ostrovityanova st., Moscow 117997, Russia; Institute of Biomedical Chemistry, 10, Pogodinskaya st., Moscow, 119121, Russia.
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Wang M, Li L, Zhang L, Zhao J, Jiang Z, Wang W. Peptide-Derived Biosensors and Their Applications in Tumor Immunology-Related Detection. Anal Chem 2021; 94:431-441. [PMID: 34846861 DOI: 10.1021/acs.analchem.1c04461] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Small-molecular targeting peptides possess features of biocompatibility, affinity, and specificity, which is widely applied in molecular recognition and detection. Moreover, peptides can be developed into highly ordered supramolecular assemblies with boosting binding affinities, diverse functions, and enhanced stabilities suitable for biosensors construction. In this Review, we summarize recent progress of peptide-based biosensors for precise detection, especially on tumor-related analysis, as well as further provide a brief overview of the progress in tumor immune-related detection. Also, we are looking forward to the prospective future of peptide-based biosensors.
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Affiliation(s)
- Minxuan Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Lingyun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Limin Zhang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Jinge Zhao
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Zhenqi Jiang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Weizhi Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People's Republic of China
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Ucar A, González-Fernández E, Staderini M, Avlonitis N, Murray AF, Bradley M, Mount AR. Miniaturisation of a peptide-based electrochemical protease activity sensor using platinum microelectrodes. Analyst 2020; 145:975-982. [PMID: 31829318 DOI: 10.1039/c9an02321f] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Proteases are ideal target biomarkers as they have been implicated in many disease states, including steps associated with cancer progression. Electrochemical peptide-based biosensors have attracted much interest in recent years. However, the significantly large size of the electrodes typically used in most of these platforms has led to performance limitations. These could be addressed by the enhancements offered by microelectrodes, such as rapid response times, improved mass transport, higher signal-to-noise and sensitivity, as well as more localised and less invasive measurements. We present the production and characterisation of a miniaturised electrochemical biosensor for the detection of trypsin, based on 25 μm diameter Pt microelectrodes (rather than the ubiquitous Au electrodes), benchmarked by establishing the equivalent Pt macroelectrode response in terms of quantitative response to the protease, the kinetics of cleavage and the effects of non-specific protein binding and temperature. Interestingly, although there was little difference between Au and Pt macroelectrode response, significant differences were observed between the responses of the Pt macroelectrode and microelectrode systems indicative of increased reproducibility in the microelectrode SAM structure and sensor performance between the electrodes, increased storage stability and a decrease in the cleavage rate at functionalised microelectrodes, which is mitigated by measurement at normal body temperature. Together, these results demonstrate the robustness and sensitivity of the miniaturised sensing platform and its ability to operate within the clinically-relevant concentration ranges of proteases in normal and disease states. These are critical features for its translation into implantable devices.
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Affiliation(s)
- Ahmet Ucar
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, The King's Buildings, Mayfield Road, Edinburgh EH9 3JL, UK
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Hu Q, Bao Y, Gan S, Zhang Y, Han D, Niu L. Electrochemically controlled grafting of polymers for ultrasensitive electrochemical assay of trypsin activity. Biosens Bioelectron 2020; 165:112358. [DOI: 10.1016/j.bios.2020.112358] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/26/2020] [Accepted: 06/01/2020] [Indexed: 12/18/2022]
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González-Fernández E, Staderini M, Yussof A, Scholefield E, Murray AF, Mount AR, Bradley M. Electrochemical sensing of human neutrophil elastase and polymorphonuclear neutrophil activity. Biosens Bioelectron 2018; 119:209-214. [DOI: 10.1016/j.bios.2018.08.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/04/2018] [Accepted: 08/08/2018] [Indexed: 10/28/2022]
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4-Mercaptophenylboronic acid-induced in situ formation of silver nanoparticle aggregates as labels on an electrode surface. Electrochem commun 2017. [DOI: 10.1016/j.elecom.2016.11.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Parnsubsakul A, Safitri RE, Rijiravanich P, Surareungchai W. Electrochemical assay of proteolytically active prostate specific antigen based on anodic stripping voltammetry of silver enhanced gold nanoparticle labels. J Electroanal Chem (Lausanne) 2017. [DOI: 10.1016/j.jelechem.2016.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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González-Fernández E, Avlonitis N, Murray AF, Mount AR, Bradley M. Methylene blue not ferrocene: Optimal reporters for electrochemical detection of protease activity. Biosens Bioelectron 2016; 84:82-8. [DOI: 10.1016/j.bios.2015.11.088] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/24/2015] [Accepted: 11/27/2015] [Indexed: 01/08/2023]
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Biela A, Watkinson M, Meier UC, Baker D, Giovannoni G, Becer CR, Krause S. Disposable MMP-9 sensor based on the degradation of peptide cross-linked hydrogel films using electrochemical impedance spectroscopy. Biosens Bioelectron 2015; 68:660-667. [PMID: 25660510 DOI: 10.1016/j.bios.2015.01.060] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 01/23/2015] [Accepted: 01/26/2015] [Indexed: 11/17/2022]
Abstract
Matrix metalloproteinase-9 (MMP-9) plays an important role in both physiological and pathological processes. This enzyme is a peripheral biomarker of neuroinflammation in multiple sclerosis (MS), a chronic autoimmune disease of the central nervous system. Presently, expensive magnetic resonance imaging (MRI) studies are used to monitor subclinical disease activity in MS. An alternative to costly MRI scans could be the detection of MMP-9, using a low-cost, disposable sensor system for MMP-9 suitable for home-monitoring of inflammation. This would allow an early prediction of the failure of anti-inflammatory therapies and more timely clinical intervention to limit neuronal damage and prevent disability. Herein we present the development of a disposable sensor for fast and straightforward detection of MMP-9. Biosensors were produced by coating electrodes with oxidized dextran and subsequent cross-linking with peptides containing specific cleavage sites for MMP-9. Exposure of the films to the enzyme resulted in the degradation of the films, which was monitored using impedance measurements. Sensor response was rapid, a significant impedance change was usually observed within 5 min after the addition of MMP-9. Sensors showed a negligible response to matrix metalloproteinase-2 (MMP-2), a protease which may interfere with MMP-9 detection. The peptide sequence with the highest sensitivity and selectivity Leu-Gly-Arg-Met-Gly-Leu-Pro-Gly-Lys was selected to construct calibration curves. MMP-9 was successfully detected in a clinically relevant range from 50 to 400 ng/ml. Two different processes of hydrogel degradation were observed on electrode surfaces with different roughness, and both appeared suitable to monitor MMP-9 activity. The sensor materials are generic and can be easily adopted to respond to other proteases by selecting peptide cross-linkers with suitable cleavage sites.
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Affiliation(s)
- Anna Biela
- School of Engineering and Materials Science, Queen Mary University of London, UK
| | - Michael Watkinson
- School of Biological and Chemical Sciences, Queen Mary University of London, UK
| | - Ute C Meier
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, UK
| | - David Baker
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, UK
| | - Gavin Giovannoni
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, UK
| | - C Remzi Becer
- School of Engineering and Materials Science, Queen Mary University of London, UK
| | - Steffi Krause
- School of Engineering and Materials Science, Queen Mary University of London, UK.
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Challier L, Miranda-Castro R, Marchal D, Noël V, Mavré F, Limoges B. Kinetic Rotating Droplet Electrochemistry: A Simple and Versatile Method for Reaction Progress Kinetic Analysis in Microliter Volumes. J Am Chem Soc 2013; 135:14215-28. [DOI: 10.1021/ja405415q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Lylian Challier
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Rebeca Miranda-Castro
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Damien Marchal
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Vincent Noël
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - François Mavré
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Benoît Limoges
- ITODYS, UMR 7086 CNRS, and ‡Laboratoire d’Electrochimie Moléculaire,
UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
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Monney A, Albrecht M. Transition metal bioconjugates with an organometallic link between the metal and the biomolecular scaffold. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.12.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Shin DS, Liu Y, Gao Y, Kwa T, Matharu Z, Revzin A. Micropatterned surfaces functionalized with electroactive peptides for detecting protease release from cells. Anal Chem 2013; 85:220-7. [PMID: 23181468 PMCID: PMC3677045 DOI: 10.1021/ac302547p] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Matrix metalloproteinases (MMPs) regulate composition of the extracellular matrix and play a critical role in cancer, fibrosis, and wound healing. This article describes a novel peptide-based electrochemical biosensor for detecting activity of cell-secreted protease MMP9. In this sensing strategy, a peptide specific to MMP9 was modified with a redox label (methylene blue (MB)) and immobilized on microfabricated 300 μm diameter Au electrodes. Challenging the electrodes with known concentrations of MMP9 resulted in the cleavage of the MB containing peptide fragment and caused a decrease in electrical signal measured by square wave voltammetry (SWV). The limit of detection for MMP9 was determined to be 60 pM with a linear range extending to 50 nM. In preparation to detect cell-secreted MMP9, glass surfaces with Au electrode arrays were further micropatterned with poly(ethylene glycol) (PEG) gel to define annular cell adhesive regions next to electrodes and render the remainder of the surface nonfouling. The surfaces were further modified with CD14 antibody to promote attachment of monocytes. The peptide-modified electrode arrays were integrated into PDMS microfluidic devices and incubated with U-937 cells, transformed monocytes known to produce MMPs. These studies revealed a 3-fold higher electrochemical signal from ∼400 activated monocytes after 10 min activation compared to nonactivated monocytes. Whereas this article focuses on MMP9 detection, the general strategy of employing redox-labeled peptides on electrodes should be broadly applicable for detection of other proteases and should have clinical as well as basic science applications.
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Affiliation(s)
- Dong-Sik Shin
- Department of Biomedical Engineering, University of California, Davis, CA 95616, USA
| | - Ying Liu
- Department of Biomedical Engineering, University of California, Davis, CA 95616, USA
| | - Yandong Gao
- Department of Biomedical Engineering, University of California, Davis, CA 95616, USA
| | - Timothy Kwa
- Department of Biomedical Engineering, University of California, Davis, CA 95616, USA
| | - Zimple Matharu
- Department of Biomedical Engineering, University of California, Davis, CA 95616, USA
| | - Alexander Revzin
- Department of Biomedical Engineering, University of California, Davis, CA 95616, USA
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Anne A, Demaille C. Kinetics of enzyme action on surface-attached substrates: a practical guide to progress curve analysis in any kinetic situation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:14665-14671. [PMID: 22978617 DOI: 10.1021/la3030827] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In the present work, exact kinetic equations describing the action of an enzyme in solution on a substrate attached to a surface have been derived in the framework of the Michaelis-Menten mechanism but without resorting to the often-used steady-state approximation. The here-derived kinetic equations are cast in a workable format, allowing us to introduce a simple and universal procedure for the quantitative analysis of enzyme surface kinetics that is valid for any kinetic situation. The results presented here should allow experimentalists studying the kinetics of enzyme action on immobilized substrates to analyze their data in a perfectly rigorous way.
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Affiliation(s)
- Agnès Anne
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
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