Quantitative electrochemical detection of cathepsin B activity in complex tissue lysates using enhanced AC voltammetry at carbon nanofiber nanoelectrode arrays

A highly sensitive NanoLuc-based protease biosensor for detecting apoptosis and SARS-CoV-2 infection

Proteases play critical roles in various biological processes, including apoptosis and viral infection. Several protease biosensors have been developed; however, obtaining a reliable signal from a very low level of endogenous protease activity remains a challenge. In this study, we developed a highly sensitive protease biosensor, named FlipNanoLuc, based on the Oplophorus gracilirostris NanoLuc luciferase. The flipped β-strand was restored by protease activation and cleavage, resulting in the reconstitution of luciferase and enzymatic activity. By making several modifications, such as introducing NanoBiT technology and CL1-PEST1 degradation tag, the FlipNanoLuc-based protease biosensor system achieved more than 500-fold luminescence increase in the corresponding protease-overexpressing cells. We demonstrated that the FlipNanoLuc-based caspase sensor can be utilized for the detection of staurosporine-induced apoptosis with sixfold increase in luminescence. Furthermore, we also demonstrated that the FlipNanoLuc-based coronavirus 3CL-protease sensor can be used to detect human coronavirus OC43 with tenfold increase in luminescence and severe acute respiratory syndrome-coronavirus-2 infections with 20-fold increase in luminescence by introducing the stem-loop 1 sequence to prevent the virus inducing global translational shutdown.

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.

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.

Quantitative Detection of Cathepsin B Activity in Neutral pH Buffers Using Gold Microelectrode Arrays: Toward Direct Multiplex Analyses of Extracellular Proteases in Human Serum

Proteases are critical signaling molecules and prognostic biomarkers for many diseases including cancer. There is a strong demand for multiplex bioanalytical techniques that can rapidly detect the activity of extracellular proteases with high sensitivity and specificity. This study demonstrates an activity-based electrochemical biosensor of a 3 × 3 gold microelectrode array for the detection of cathepsin B activity in human serum diluted in a neutral buffer. Proteolysis of ferrocene-labeled peptide substrates functionalized on 200 × 200 μm microelectrodes is measured simultaneously over the nine channels by AC voltammetry. The protease activity is represented by the inverse of the exponential decay time constant (1/τ), which equals to (k_cat/K_M)[CB] based on the Michaelis-Menten model. An enhanced activity of the recombinant human cathepsin B (rhCB) is observed in a low-ionic-strength phosphate buffer at pH = 7.4, giving a very low limit of detection of 8.49 × 10^-4 s^-1 for activity and 57.1 pM for the active rhCB concentration that is comparable to affinity-based enzyme-linked immunosorbent assay (ELISA). The cathepsin B presented in the human serum sample is validated by ELISA, which mainly detects the inactive proenzyme, while the electrochemical biosensor specifically measures the active cathepsin B and shows significantly higher decay rates when rhCB and human serum are activated. Analyses of the kinetic electrochemical measurements with spiked active cathepsin B in human serum provide further assessment of the protease activity in the complex sample. This study lays the foundation to develop the gold microelectrode array into a multiplex biosensor for rapid detection of the activity of extracellular proteases toward cancer diagnosis and treatment assessment.

A comprehensive review summarizing the recent biomedical applications of functionalized carbon nanofibers

Since the discovery and fabrication of carbon nanofibers (CNFs) over a decade ago, scientists foster to discover novel myriad potential applications for this material in both biomedicine and industry. The unique economic viability, mechanical, electrical, optical, thermal, and structural properties of CNFs led to their rapid emergence. CNFs become an artificial intelligence platform for different uses, including a wide range of biomedical applications. Furthermore, CNFs have exceptionally large surface areas that make them flexible for tailoring and functionalization on demand. This review highlights the recent progress and achievements of CNFs in a wide range of biomedical fields, including cancer therapy, biosensing, tissue engineering, and wound dressing. Besides the synthetic techniques of CNFs, their potential toxicity and limitations, as biomaterials in real clinical settings, will be presented. This review discusses CNF's future investigations in other biomedical fields, including gene delivery and bioimaging and CNFs risk assessment.

Nucleolin-Targeted Ratiometric Fluorescent Carbon Dots with a Remarkably Large Emission Wavelength Shift for Precise Imaging of Cathepsin B in Living Cancer Cells

As one of the most promising biomarkers for numerous malignant tumors, accurate and reliable reporting of Cathepsin B (CTSB) activity is of great significance to achieve efficient diagnosis of cancers at an early stage and predicting metastasis. Here, we report a vigorous ratiometric fluorescent method integrating a cancer-targeting recognition moiety with a remarkably large emission wavelength shift into a single matrix to report CTSB activity sensitively and specifically. As a proof of concept, we synthesized amine-rich carbon quantum dots (CQDs) with a blue fluorescence, which offered an efficient scaffolding to covalently assemble the nucleolin-targeting recognition nucleic acid aptamer AS1411 and a CTSB-cleavable peptide substrate Gly-Arg-Arg-Gly-Lys-Gly-Gly-Cys-COOH that tethered with a near-infrared (NIR) fluorophore chlorin e6 (Ce6-GRRGKGGC, Ce6-Pep), enabling a cancer-targeting and CTSB stimulus-responsive ratiometric nanoprobe AS1411-Ce6-CQDs. Owing to the efficient fluorescence resonance energy transfer (FRET) process from the CQDs to Ce6 inside the assembly of nanoprobe, the blue fluorescence of CQDs at ∼450 nm was remarkably quenched, along with an obvious NIR fluorescence enhancement of Ce6 at ∼650 nm. After selective entry into cancer cells via nucleolin-mediated endocytosis, the overexpressed CTSB in lysosome could cleave Ce6-Pep and trigger the Ce6 moiety dissociation from AS1411-Ce6-CQDs, thus leading to the termination of FRET process, achieving the efficient ratiometric fluorescence response toward endogenous CTSB with a remarkably large emission wavelength shift of ∼200 nm from NIR to blue emission region. Notably, the nanoprobe AS1411-Ce6-CQDs exhibited an excellent specificity for ratiometric fluorescent sensing of CTSB activity with an ultralow detection limit of 0.096 ng/mL, demonstrating its promising use for early precise cancer diagnosis in the near future.

Magnetic nanoparticle decorated anodic alumina nanotubes for fluorescent detection of cathepsin B

In this work, we present the process to provide anodic alumina nanotubes with magnetic responsivity based on magnetic nanoparticles. We demonstrate the possibility to cause the motion of these composite nanotubes under magnetic field, providing them with guided mobility. The obtained magnetic anodic alumina nanotubes are completely characterized and their potential to undergo selective and effective functionalization, and stimuli-responsive load release is demonstrated. For this purpose, protease-triggered release of fluorescent molecules loaded inside the magnetic anodic alumina nanotubes (MAANTs) by selective functionalization is performed. The inner walls of the MAANTs were selectively covered with protein padding of albumin-fluorescein isothiocyanate conjugate (FITC-BSA) through means of silanization. Protein functionalization was designed to undergo proteolytic hydrolysis in presence of cathepsin B- protease highly expressed during growth and initial stages of tumor metastasis - in order to cleave peptide bond of albumin and release fluorescent fragments of the protein. Proteolytic reaction with the enzyme is performed under acidic conditions. Presented arrangement is an exemplary combination of functionalities - which are vast - and of value for applications like drug delivery and biosensing applications.

Integration of a peptide–DNA conjugate with multiple cyclic signal amplification for the ultrasensitive detection of cathepsin B activity

We integrate a peptide–DNA conjugate with multiple cyclic signal amplification for the sensitive detection of cathepsin B activity.

Electrochemical Activity Assay for Protease Analysis Using Carbon Nanofiber Nanoelectrode Arrays

There is a strong demand for bioanalytical techniques to rapidly detect protease activities with high sensitivity and high specificity. This study reports an activity-based electrochemical method toward this goal. Nanoelectrode arrays (NEAs) fabricated with embedded vertically aligned carbon nanofibers (VACNFs) are functionalized with specific peptide substrates containing a ferrocene (Fc) tag. The kinetic proteolysis curves are measured with continuously repeated ac voltammetry, from which the catalytic activity is derived as the inverse of the exponential decay time constant based on a heterogeneous Michaelis-Menten model. Comparison of three peptide substrates with different lengths reveals that the hexapeptide H2N-(CH2)4-CO-Pro-Leu-Arg-Phe-Gly-Ala-NH-CH2-Fc is the optimal probe for cathepsin B. The activity strongly depends on temperature and is the highest around the body temperature. With the optimized peptide substrate and measuring conditions, the limit of detection of cathepsin B activity and concentration can reach 2.49 × 10-4 s-1 and 0.32 nM, respectively. The peptide substrates show high specificity to the cognate proteases, with negligible cross-reactions among three cancer-related proteases cathepsin B, ADAM10, and ADAM17. This electrochemical method can be developed into multiplex chips for rapid profiling of protease activities in cancer diagnosis and treatment monitoring.

Nanofiber-integrated miniaturized systems: an intelligent platform for cancer diagnosis

Cancer diagnostic tools enabling screening, diagnosis, and effective disease management are essential elements to increase the survival rate of diagnosed patients. Low abundance of cancer markers present in large amounts of interferences remains the major issue. Moreover, current diagnostic technologies are restricted to high-resourced settings only. Integrating nanofibers into miniaturized analytical systems holds a significant promise to address these challenges as demonstrated by recent publications. A large surface area, three-dimensional porous network, and diverse range of functional chemistries make nanofibers an excellent candidate as immobilization support and/or transduction elements, enabling high capture yield and ultrasensitive detection in miniaturized devices. Functional nanofibers have thus been used to isolate and detect various cancer-related biomarkers with a high degree of success in both on-chip and off-chip platforms. In fact, the chemical and functional adaptability of nanofibers has been exploited to address the technical challenges unique to each of the cancer markers in body fluids, where circulating tumor cells are prominently investigated among others (proteins, nucleic acids, and exosomes). So far, none of the work has exploited the nanofibers for cancer-derived exosomes, opening an avenue for further research effort. The trend and future prospects signal possibilities to strengthen the implementation of nanofiber-miniaturized system hybrid for a next generation of cancer diagnostic platforms both in clinical and point-of-care testing.

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.

Titania-Coated Gold Nano-Bipyramids for Blocking Autophagy Flux and Sensitizing Cancer Cells to Proteasome Inhibitor-Induced Death

Targeting protein degradation is recognized as a valid approach to cancer therapy. The ubiquitin-proteasome system (UPS) and the autophagy-lysosome pathway are two major pathways for intracellular protein degradation. Proteasome inhibitors such as bortezomib are clinically approved for treating malignancies, but to date, they are still unsatisfactory for cancer therapy. This study identifies titania-coated gold nano-bipyramid (NBP/TiO2) nanostructures as an autophagic flux inhibitor, as the smallest NBP/TiO2 nanostructures induce significant autophagosome accumulation in human glioblastoma U-87 MG cells via blocking the autophagosome-lysosome fusion process and inhibiting lysosomal degradation. Further study indicates that NBP/TiO2 nanostructures reduce the intracellular level of mature cathepsin B and directly inhibit the proteolytic activity of cathepsin B, thereby further inhibiting trypsin-like proteolytic activity, which is a potential cotarget for UPS inhibition. NBP/TiO2 nanostructures interact synergistically with bortezomib to suppress the viability of U-87 MG cells, as the combined treatment synergistically induces the intracellular accumulation of ubiquitinated protein and endoplasmic reticulum stress. In addition, photothermal therapy further synergistically reduces the cell viability. In summary, this study suggests that NBP/TiO2 nanostructures function as a promising anticancer agent in combination with proteasome inhibitors.

Quantitative electrochemical detection of cathepsin B activity in breast cancer cell lysates using carbon nanofiber nanoelectrode arrays toward identification of cancer formation

The proteolytic activity of cathepsin B in complex breast cell lysates has been measured with alternating current voltammetry (ACV) using ferrocene (Fc)-labeled-tetrapeptides immobilized on nanoelectrode arrays (NEAs) fabricated with vertically aligned carbon nanofibers (VACNFs). Four types of breast cells have been tested, including normal breast cells (HMEC), transformed breast cells (MCF-10A), breast cancer cells (T47D), and metastatic breast cancer cells (MDA-MB-231). The detected protease activity was found increased in cancer cells, with the MDA-MB-231 metastatic cancer cell lysate showing the highest cathepsin B activity. The equivalent cathepsin B concentration in MDA-MB-231 cancer cell lysate was quantitatively determined by spiking recombinant cathepsin B into the immunoprecipitated MDA-MB-231 lysate and the HMEC whole cell lysate. The results illustrated the potential of this technique as a portable multiplex electronic device for cancer diagnosis and treatment monitoring through rapid profiling the activity of specific cancer-relevant proteases.

FROM THE CLINICAL EDITOR

Breast cancer is the most common cancer in women. In this report, the authors applied the technique of nanoelectrode arrays to try to detect and compare cathepsin B activities in normal and breast cancer cells. It was found that protease activity correlated positively with the degree of malignancy cancer cells. Taking this further, this technique may be useful for rapid diagnosis of cancer in the future.

Carbon nanomaterial-based electrochemical biosensors: an overview

Carbon materials on the nanoscale exhibit diverse outstanding properties, rendering them extremely suitable for the fabrication of electrochemical biosensors. Over the past two decades, advances in this area have continuously emerged. In this review, we attempt to survey the recent developments of electrochemical biosensors based on six types of carbon nanomaterials (CNs), i.e., graphene, carbon nanotubes, carbon dots, carbon nanofibers, nanodiamonds and buckminsterfullerene. For each material, representative samples are introduced to expound the different roles of the CNs in electrochemical bioanalytical strategies. In addition, remaining challenges and perspectives for future developments are also briefly discussed.