A simple and general approach to assay protease activity with electrochemical technique

The multifaceted role of proteases and modern analytical methods for investigation of their catalytic activity

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.

Protease detection in the biosensor era: A review

Proteases have been proposed as potential biomarkers for several pathological conditions including cancers, multiple sclerosis and cardiovascular diseases, due to their ability to break down the components of extracellular matrix and basement membrane. The development of protease biosensors opened up the possibility to investigate the proteolytic activity of dysregulated proteases with higher efficiency over the traditional detection assays due to their quick detection capability, high sensitivity and selectivity, simple instrumentation and cost-effective fabrication processes. In contrast to the recently published review papers that primarily focused on one specific class of proteases or one specific detection method, this review article presents different optical and electrochemical detection methods that can be used to design biosensors for all major protease families. The benefits and drawbacks of various transducer techniques integrated into protease biosensing platforms are analyzed and compared. The main focus is on activity-based biosensors that use peptides as biorecognition elements. The effects of nanomaterials on biosensor performance are also discussed. This review should help readers to select the biosensor that best fits their needs, and contribute to the further development of this research field. Protease biosensors may allow better comprehension of protease overexperession and potentially enable novel devices for point-of-care testing.

Ultrafast one-minute electronic detection of SARS-CoV-2 infection by 3CLpro enzymatic activity in untreated saliva samples

Since its onset in December 2019, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, has caused over 6.5 million deaths worldwide as of October 2022. Attempts to curb viral transmission rely heavily on reliable testing to detect infections since a large number of transmissions are carried through asymptomatic individuals. Many available detection methods fall short in terms of reliability or point-of-care applicability. Here, we report an electrochemical approach targeting a viral proteolytic enzyme, 3CLpro, as a marker of active infection. We detect proteolytic activity directly from untreated saliva within one minute of sample incubation using a reduction-oxidation pH indicator. Importantly, clinical tests of saliva samples from 50 subjects show accurate detection of SARS-CoV-2, with high sensitivity and specificity, validated by PCR testing. These, coupled with our platform's ultrafast detection, simplicity, low cost and point-of-care compatibility, make it a promising method for the real-world SARS-CoV-2 mass-screening.

Peptide probes for proteases - innovations and applications for monitoring proteolytic activity

Proteases are excellent biomarkers for a variety of diseases, offer multiple opportunities for diagnostic applications and are valuable targets for therapy. From a chemistry-based perspective this review discusses and critiques the most recent advances in the field of substrate-based probes for the detection and analysis of proteolytic activity both in vitro and in vivo.

Colorimetric and Electrochemical Methods for the Detection of SARS-CoV-2 Main Protease by Peptide-Triggered Assembly of Gold Nanoparticles

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) has been regarded as one of the ideal targets for the development of antiviral drugs. The currently used methods for the probing of Mpro activity and the screening of its inhibitors require the use of a double-labeled peptide substrate. In this work, we suggested that the label-free peptide substrate could induce the aggregation of AuNPs through the electrostatic interactions, and the cleavage of the peptide by the Mpro inhibited the aggregation of AuNPs. This fact allowed for the visual analysis of Mpro activity by observing the color change of the AuNPs suspension. Furthermore, the co-assembly of AuNPs and peptide was achieved on the peptide-covered electrode surface. Cleavage of the peptide substrate by the Mpro limited the formation of AuNPs/peptide assembles, thus allowing for the development of a simple and sensitive electrochemical method for Mpro detection in serum samples. The change of the electrochemical signal was easily monitored by electrochemical impedance spectroscopy (EIS). The detection limits of the colorimetric and electrochemical methods are 10 and 0.1 pM, respectively. This work should be valuable for the development of effective antiviral drugs and the design of novel optical and electrical biosensors.

Fluorescence-Based On-Resin Detection of Three Model Proteases

A new approach to on-resin detection of three model proteases (trypsin, chymotrypsin, and thrombin) has been developed, while at the same time already described methodology for simultaneous detection of two enzymes (trypsin and chymotrypsin) has been additionally generalized. Appropriate immobilized substrates, comprising specifically cleavable peptide sequences capped with fluorescent dyes, have been synthesized on Rink Amide PEGA resin or Amino PEGA resin modified with backbone amide linker (BAL). Resulting solid support-bound probes were then dispersed into Tris-HCl buffer solution (pH = 8.0) and subjected to enzymatic cleavage. Liberated fluorophores have been tracked by fluorescence measuring. The competitive activities of studied proteases towards the thrombin probe have been efficiently limited and controlled by employing a Bowman-Birk inhibitor into a system.

Coenzyme-Mediated Electro-RAFT Polymerization for Amplified Electrochemical Interrogation of Trypsin Activity

Trypsin is a key proteolytic enzyme in the digestive system and its abnormal levels are indicative of some pancreatic diseases. Taking advantage of the coenzyme-mediated electrografting of ferrocenyl polymers as a novel strategy for signal amplification, herein, a signal-on cleavage-based electrochemical biosensor is reported for the highly selective interrogation of trypsin activity at ultralow levels. The construction of the trypsin biosensor involves (i) the immobilization of peptide substrates (without free carboxyl groups) via the N-terminus, (ii) the tryptic cleavage of peptide substrates, (iii) the site-specific labeling of the reversible addition-fragmentation chain transfer (RAFT) agents, and (iv) the grafting of ferrocenyl polymers through the electro-RAFT (eRAFT) polymerization, which is mediated by potentiostatic reduction of nicotinamide adenine dinucleotide (NAD⁺) coenzymes. Through the NAD⁺-mediated eRAFT (NAD⁺-eRAFT) polymerization of ferrocenylmethyl methacrylate (FcMMA), the presence of a few tryptic cleavage events can eventually result in the recruitment of a considerable amount of ferrocene redox tags. Obviously, the NAD⁺-eRAFT polymerization is low-cost and easy to operate as a highly efficient strategy for signal amplification. As expected, the as-constructed biosensor is highly selective and sensitive toward the signal-on interrogation of trypsin activity. Under optimal conditions, the detection limit can be as low as 18.2 μU/mL (∼72.8 pg/mL). The results also demonstrate that the as-constructed electrochemical trypsin biosensor is applicable to inhibitor screening and the interrogation of enzyme activity in the presence of complex sample matrices. Moreover, it is low-cost, less susceptible to false-positive results, and relatively easy to fabricate, thus holding great potential in diagnostic and therapeutic applications.

A novel electrochemical assay for chymosin determination using a label-free peptide as a substrate

Chymosin is a predominant enzyme in rennet and is used in cheese production because of its excellent milk-clotting activity. Herein, we proposed a facile and label-free electrochemical method for determining chymosin activity based on a peptide-based enzyme substrate. The synthesized substrate peptide for chymosin was assembled onto the surface of the Au-deposited grassy carbon electrode. The current was proportional to chymosin activity, and thus chymosin activity could be determined. The detection ranges of chymosin activity were 2.5 to 25 U mL^-1. The detection limit of chymosin activity was 0.8 U mL^-1. The sensing platform was used to quantify chymosin activity in commercial rennet with high selectivity, excellent stability, and satisfactory reproducibility. We developed a facile, fast, and effective electrochemical assay for detecting chymosin activity, which has potential applications in cheesemaking.

Giant magnetoresistive biosensors for real-time quantitative detection of protease activity

Proteases are enzymes that cleave proteins and are crucial to physiological processes such as digestion, blood clotting, and wound healing. Unregulated protease activity is a biomarker of several human diseases. Synthetic peptides that are selectively hydrolyzed by a protease of interest can be used as reporter substrates of unregulated protease activity. We developed an activity-based protease sensor by immobilizing magnetic nanoparticles (MNPs) to the surface of a giant magnetoresistive spin-valve (GMR SV) sensor using peptides. Cleavage of these peptides by a protease releases the magnetic nanoparticles resulting in a time-dependent change in the local magnetic field. Using this approach, we detected a significant release of MNPs after 3.5 minutes incubation using just 4 nM of the cysteine protease, papain. In addition, we show that proteases in healthy human urine do not release the MNPs, however addition of 20 nM of papain to the urine samples resulted in a time-dependent change in magnetoresistance. This study lays the foundation for using GMR SV sensors as a platform for real-time, quantitative detection of protease activity in biological fluids.

Fluorescent microsphere probe for rapid qualitative and quantitative detection of trypsin activity

Current technologies still face a big challenge to achieve simultaneous rapid qualitative and quantitative detection of trypsin. In our present study, we developed a simple and effective strategy to sensitively, qualitatively and quantitatively analyze the activity of trypsin using a fluorescent polystyrene (PS) microsphere probe. PS spheres were first functionalized by the surface coating of polyethylene glycol (PEG), which could significantly decrease the possibility of nonspecific physical adsorption of the fluorescein isothiocyanate isomer-modified peptide (peptide-FITC). Then, the obtained PS-PEG spheres were chemically interacted with peptide-FITC, which were then employed to monitor the real-time activity of trypsin. The peptide used in our work contained rich lysine and arginine residues, which were the recognition sites of trypsin. When trypsin interacted with the PS-FITC-peptide microspheres, the peptide-FITC rapidly decomposed into free small fragments in solution, resulting in a gradual decrease in the fluorescence of the PS spheres. By taking advantage of the fluorescence changes using confocal microscopy imaging and fluorescence spectrum intensity, it is easy to achieve the qualitative and quantitative detection of trypsin, with a highly sensitive detection limit as low as 0.5 ng mL^-1 and high selectivity. Thus, the designed fluorescent PS microsphere probe would be very promising in various applications such as food safety inspection, personal healthcare and on-site environmental monitoring.

A ratiometric electrochemical strategy for sensitive determination of Furin activity based on dual signal amplification and antifouling nanosurfaces

Developing a sensitive and accurate method for Furin activity is still the bottleneck for understanding the role played by Furin in cell-surface systems and even in Alzheimer's disease. In this work, a ratiometric electrochemical biosensor was developed for sensitive and accurate determination of Furin activity in the cell based on dual signal amplification stemming from a peptide with multiple response sites and the antifouling gold nano-bellflowers (GBFs). A new peptide, HS-CMRVRR↓YKDFDFG (P3), was designed for the first time to be selectively cleaved by Furin at site↓. More importantly, this peptide P3 constitutes three amino acid residues with the -COOH group subsequently used to bind with the response molecule of ferrocene, and can remarkably improve the determination sensitivity by about 2.3 fold. Meanwhile, GBFs stabilized by PEG were taken as a second element to magnify the signal of the ferrocene group via a large ratio surface area and good conductivity, as well as an antibiofouling nanosurface to reduce the biofouling of the electrode surface in cells. This double amplification strategy can greatly enhance the sensitivity of Furin detection by 6.5-fold, which is favorable for detection of low amounts of Furin. In addition, 5'-MB-GGCGCGA(T)₁₃-SH-3' was co-assembled as an inner reference to provide a built-in element to correct the determination error resulting from a complicated analysis environment. Finally, this sensitive and accurate Furin biosensor was successfully applied to detect Furin activity in Furin overexpressed U251 and MDA-MB-468 cells. As far as we know, this is the first report to mention an electrochemical strategy to detect Furin activity in cells.

Recent developments in protease activity assays and sensors

Proteases play a pivotal role in regulating important physiological processes from food digestion to blood clotting. They are also important biomarkers for many diseases such as cancers. The importance of proteases has led to extensive efforts in the screening of proteases and their inhibitors as potential drug molecules. For example, human immunodeficiency virus (HIV) patients have been treated with HIV-1 protease inhibitors to prolong the life expectancy of patients. Such a close relationship between diseases and proteases provides a strong motivation for developing sensitive, selective, and robust protease assays and sensors, which can be exploited to discover new proteases and inhibitors. In this aspect, protease assays based on levels of proteolytic activities are more relevant than protease affinity assays such as immunoassays. In this review, recent developments of protease activity assays based on different detection principles are discussed and compared. For homogenous assays, fluorescence-based techniques are the most popular due to their high sensitivity and quantitative results. However, homogeneous assays have limited multiplex sensing capabilities. In contrast, heterogeneous assays can be employed to detect multiple proteases simultaneously, given the microarray technology that is already available. Among them, electrochemical methods, surface spectroscopy techniques, and enzyme-linked peptide protease assays are commonly used. Finally, recent developments in liquid crystal (LC)-based protease assays and their applications for detecting proteases and their inhibitors are discussed.

A novel fluorescence strategy for mercury ion and trypsin activity assay based on nitrogen-doped graphene quantum dots

Fluorescent detection of Hg²⁺ and trypsin based on trypsin-modulated competition between Hg²⁺, N-GQDs and HSA.

Preparation of a Peptide-Modified Electrode for Capture and Voltammetric Determination of Endotoxin

Endotoxin is the major structural constituent of the outer membrane of Gram-negative bacteria, which is a great threat to human health. Herein, a sensitive electrochemical biosensor for the detection of endotoxin is established by recording the voltammetric responses of the peptide-modified electrode. The utilized peptide has a high affinity for the target endotoxin, which ensures the high selectivity of this method. After the capture of endotoxin on the electrode surface, a negatively charged layer is formed, and the electron-transfer process is significantly hindered because of the increased steric hindrance and the electrostatic repulsion. The declined electrochemical signal could be used to indicate the concentration of endotoxin. This method is simple but effective, which requires limited reagents. Another highlight of this method is its user-friendly operation. Moreover, its applicability in human blood plasma promises its great potential utility in the near future.

Ultrasensitive Protease Sensors Using Selective Affinity Binding, Selective Proteolytic Reaction, and Proximity-Dependent Electrochemical Reaction

The development of a fast and ultrasensitive protease detection method is a challenging task. This paper reports ultrasensitive protease sensors exploiting (i) selective affinity binding, (ii) selective proteolytic reaction, and (iii) proximity-dependent electrochemical reaction. The selective affinity binding to capture IgG increases the concentration of the target protease (trypsin as a model protease) near the electrode, and the selective proteolytic reaction by trypsin increases the concentration of the redox-active species near the electrode. The electrochemical reaction, which is more sensitive to the concentration of the redox-active species near the electrode than to its bulk concentration, provides an increased electrochemical signal, which is further amplified by the electrochemical-chemical redox cycling. An indium-tin oxide electrode modified with reduced graphene oxide, avidin, and biotinylated capture IgG is used as the electrode, and p-aminophenol liberated from an oligopeptide is used as the redox-active species. The new sensor scheme using no washing process is compared with the new sensor scheme using washing process, and with the conventional scheme using only proteolytic reaction. The new scheme provides a higher signal-to-background ratio and a lower detection limit. Moreover, the increased electrochemical signal offers a more selective protease detection. Trypsin can be detected in phosphate-buffered saline and in artificial serum containing l-ascorbic acid with a low detection limit of 0.5 pg/mL, over a wide range of concentrations, and with an incubation period of only 30 min without washing process. The washing-free electrochemical protease sensor is highly promising for simple, fast, ultrasensitive, and selective point-of-care testing of low-abundance proteases.

Sensitive and low-background electrochemical assay of corin activity via supramolecular recognition and rolling circle amplification

Corin is an important member of type II transmembrane serine proteases that is involved in a variety of cardiovascular and pregnancy-related diseases. Herein, a sensitive and low-background electrochemical method is proposed to assay the activity of corin. In principle, a peptide comprising both the substrate motif of corin and binding site of cucurbit[8]uril (CB[8]) is first designed and immobilized on the electrode surface. Thereafter, via CB[8]-mediated supramolecular recognition, a DNA-primer is recruited, subsequently triggering the rolling circle amplification (RCA) reaction. In this way, a succeeding propagation of DNA strands is achieved on the electrode surface, which would produce remarkable repelling effect against the electrochemical species [Fe(CN)6](3-/4-), and thereby yield a highly minimized background signal. However, in the presence of activated corin, the peptide is specifically recognized and cleaved, breaching the recruitment of DNA primer as well as the RCA reaction, which decreases the repulsion to [Fe(CN)6](3-/4-), leading to a remarkable electrochemical response. As a result, the proposed assay method can sensitively determine the activity of corin with a detection limit of 0.92 pM, and can further be directly used in maternal plasma samples. Therefore, this method may provide a promising tool for pathological research and clinical diagnosis of corin-related diseases.

SERS determination of protease through a particle-on-a-film configuration constructed by electrostatic assembly in an enzymatic hydrolysis reaction

We describe a simple and universal method for trypsin determination with the surface-enhanced Raman scattering (SERS) technique.

An aptasensor for detection of potassium ions based on RecJ(f) exonuclease mediated signal amplification

An electrochemical biosensor for potassium has been developed combining specific potassium-aptamer binding and RecJf exonuclease mediated signal amplification. Generally, the DNA probe with a stem-loop structure containing an anti-K(+) aptamer sequence is designed and modified on a gold electrode. K(+) can specifically bind to the aptamer and a G-quadruplex structure forms, which breaks the original stem-loop structure. The induced single-stranded 5' end can be further digested by RecJf exonuclease, releasing K(+) which can bind to another DNA probe on the electrode. After cycles of RecJf exonuclease cleavage initiated by K(+), the electrochemical signal intensity is significantly decreased, and can be used to determine the concentration of K(+). This aptasensor shows high sensitivity, selectivity as well as excellent stability and accuracy, which provides possibilities for further applications of K(+) assay in clinical diagnosis.