In situ and multisubstrate detection of elastase enzymatic activity external to microdialysis sampling probes using LC-ESI-MS

First Insight into the Degradome of Aspergillus ochraceus: Novel Secreted Peptidases and Their Inhibitors

Aspergillus fungi constitute a pivotal element within ecosystems, serving as both contributors of biologically active compounds and harboring the potential to cause various diseases across living organisms. The organism's proteolytic enzyme complex, termed the degradome, acts as an intermediary in its dynamic interaction with the surrounding environment. Using techniques such as genome and transcriptome sequencing, alongside protein prediction methodologies, we identified putative extracellular peptidases within Aspergillus ochraceus VKM-F4104D. Following manual annotation procedures, a total of 11 aspartic, 2 cysteine, 2 glutamic, 21 serine, 1 threonine, and 21 metallopeptidases were attributed to the extracellular degradome of A. ochraceus VKM-F4104D. Among them are enzymes with promising applications in biotechnology, potential targets and agents for antifungal therapy, and microbial antagonism factors. Thus, additional functionalities of the extracellular degradome, extending beyond mere protein substrate digestion for nutritional purposes, were demonstrated.

Coumarin-based turn-on fluorescence probe with a large Stokes shift for detection of endogenous neutrophil elastase in live cells and zebrafish

Neutrophil elastase (NE), a serine proteinase, is a significant biomarker which is closely related to the progress of diseases. However, only few probes have been reported for detection of NE activity and cell imaging. And these probes have exhibited small Stokes shift, which leads to high fluorescence interferences. Furthermore, only one probe among them is able to image NE in vivo successfully. To overcome the above problems, we designed a novel coumarin-based fluorescent probe HNCOU-NE with large Stokes shift to visualize NE activity in living cells and zebrafish. The new probe HNCOU-NE for NE contains fluorophore HNCOU as the reporter and pentafluoroethyl as the enzyme-active trigger moiety. As expected, HNCOU-NE displays perfect detecting performance for sensing of NE, including good water solubility, large Stokes shift, high affinity and wide linear response concentration. In addition, HNCOU-NE has been successfully utilized for NE real-time detection and imaging in different living cells, exhibiting low cytotoxicity and excellent biocompatibility. Most importantly, endogenous NE fluorescence imaging experiments reveals that HNCOU-NE can distinguish liver cancer cells (HepG2) and other cells (293T, HeLa and SKOV3), illustrating its specific ability to diagnose liver cancer cells. Besides, probe HNCOU-NE also has the ability to specifically detect endogenous NE activity in living zebrafish. All the results indicate that HNCOU-NE is a valuable probe for qualitative and quantitative sensing of NE activity in vitro and in vivo.

Engineering Molecular Probes for In Vivo Near-Infrared Fluorescence/Photoacoustic Duplex Imaging of Human Neutrophil Elastase

Early detection of human neutrophil elastase (HNE), the potential biomarker of lung cancer, is crucial for the accurate diagnosis and evaluation of lung cancer. Currently, little progress of HNE-activated probes has been made for in vivo imaging. Herein, assisted by probe-active pocket match engineering, we synthesized a series of near-infrared fluorescence (NIRF) and photoacoustic (PA) duplex imaging probes by conjugating diverse fluorinated amide chains onto hemi-cyanine. Finally, we identified that probe 2 (denoted as LET-8), with the pentafluoroethyl group, is a superior probe to detect HNE with the best selectivity as well as good response ability and thus successfully realized NIRF/PA duplex imaging of HNE activity both in vitro and in vivo.

Electroosmotic Perfusion-Microdialysis Probe Created by Direct Laser Writing for Quantitative Assessment of Leucine Enkephalin Hydrolysis by Insulin-Regulated Aminopeptidase in Vivo

There are many processes that actively alter the concentrations of solutes in the extracellular space. Enzymatic reactions, either by soluble enzymes or membrane-bound ectoenzymes, and uptake or clearance are two such processes. Investigations of ectoenzymatic reactions in vivo is challenging, particularly in the brain. Studies using microdialysis have revealed some qualitative information about what enzymes may be present, but microdialysis is a sampling technique so it is not designed to control conditions such as a substrate concentration outside the probe. Micropush-pull perfusion has been used to determine which nitric oxide synthase enzymes are active in discrete regions of the rat retina. Ectopeptidases are a particularly important class of ectoenzymes. As far as it is known, the extracellular activity of active peptides in the brain is controlled by ectopeptidases. To understand ectopeptidase activity, we developed a physical probe and an accompanying method. The probe has a two-channel source that supplies substrate or substrate plus inhibitor using electroosmotic perfusion (EOP). It also has a microdialysis probe to collect products and unreacted substrate. The method provides quantitative estimates of substrate-to-product conversion and the influence of inhibitors on this process. The quantitative estimates are made possible by including a d-amino acid-containing peptide analog of the substrate in the substrate-containing solution infused. Quantitative analysis of substrate, substrate analog, and products is carried out by quantitative, online capillary liquid chromatography-tandem mass spectrometry. The electroosmotic perfusion-microdialysis probe and associated method were used to determine the effect of the selective inhibitor HFI-419 on insulin-regulated aminopeptidase (EC 3.4.11.3) in the rat neocortex.

Activity-based ratiometric fluorescent small-molecule probe for endogenously monitoring neutrophil elastase in living cells

Neutrophil elastase (NE), a representative protease which is closely related to many diseases, acts an indispensable role in inflammatory diseases and clinical medicine. In this work, one activity-based non-peptide ratiometric fluorescent probe DCDF was designed with pentafluoropropionic anhydride as identification group. To our knowledge, this is the first probe capable of detecting NE in ratio. After the addition of the NE, the emission spectrum of DCDF has obvious bathochromic-shift phenomenon, and there is large Stokes shifts of ∼60 nm. Compared to only a few reported NE probes, DCDF is sensitive and selective and has very low detection limit (0-14 μg/mL, DL = 30.8 ng/mL). A possible response mechanism was proposed and verified by HPLC and HRMS spectra. What's more, DCDF is capable of endogenous recognition imaging in biological cells without interference from other enzymes under the ratio signal. A549 and HeLa cells were used for endogenous cell imaging experiments of NE and the feasibility of DCDF for the specific detection of NE in cells was proved. This experimental result makes probe DCDF a very promising tool for the clinical diagnosis and treatment of NE related diseases.

Protein Encapsulation: A Nanocarrier Approach to the Fluorescence Imaging of an Enzyme-Based Biomarker

Here, we report a new pentafluoropropanamido rhodamine fluorescent probe (ACS-HNE) that allows for the selective detection of neutrophil elastase (NE). ACS-HNE displayed high sensitivity, with a low limit of detection (<5.3 nM), and excellent selectivity toward elastase over other relevant biological analytes and enzymes. The comparatively poor solubility and cell permeability of neat ACS-HNE was improved by creating an ACS-HNE-albumin complex; this approach allowed for improvements in the in situ visualization of elastase activity in RAW 264.7 cells relative to ACS-HNE alone. The present study thus serves to demonstrate a simple universal strategy that may be used to overcome cell impermeability and solubility limitations, and to prepare probes suitable for the cellular imaging of enzymatic activity in vitro.

Design of a chromogenic substrate for elastase based on split GFP system-Proof of concept for colour switch sensors

Recent studies have demonstrated that human neutrophil elastase (HNE) can be used as marker for inflammation/infection of chronic wounds since it was found to be present in high concentration in exudate collected from chronic wounds. Biosensors used in wound care benefit from a chromogenic signalling due to the readiness of signal interpretation, but the most common use faint yellow chromogenic molecules such as p-nitroaniline (pNa). In addition, if to be converted into smart dressings, the colour of the detection system should not be masked by the exudate's colour. In this work, we designed a chromogenic substrate for HNE aiming to be incorporated in a smart dressing as a colour switch sensor. The substrate was developed using the GFP-like chromoprotein ultramarine (UM), following the split GFP technology. The cleavage sequence for HNE (Ala-Ala-Pro-Val) was embedded into the sensing moiety of the substrate corresponding to the 11th β-sheet. In the presence of HNE, the 11th β-sheet is able to interact to the signalling moiety composed of the β1-β10 incomplete barrel, allowing the re-establishment of the chromophore environment and, hence, the colour production. Structural homology and molecular dynamics simulations were conducted to aid on the disclosure of the structural changes that are the base of the mechanism of action of this HNE switch substrate. Our findings explore the possible application of GFP-like chromogenic sensors in point-of-care devices for the evaluation of the wounds status, representing a major step in the medical field.

A real-time fluorescence assay for protease activity and inhibitor screening based on the aggregation-caused quenching of a perylene probe

We have established a real-time and label-free fluorescence turn-on strategy for protease activity detection and inhibitor screening via peptide-induced aggregation-caused quenching of a perylene probe. Because of electrostatic interactions and high hydrophilicity, poly-l-glutamic acid sodium salt (PGA; a negatively charged peptide) could induce aggregation of a positively charged perylene probe (probe 1) and the monomer fluorescence of probe 1 was effectively quenched. After a protease was added, PGA was enzymatically hydrolyzed into small fragments and probe 1 disaggregated. The fluorescence recovery of probe 1 was found to be proportional to the concentration of protease in the range from 0 to 1 mU/ml. The detection limit was down to 0.1 mU/ml. In the presence of a protease inhibitor, protease activity was inhibited and fluorescence recovery reduced. Moreover, we demonstrated the potential application of our method in a complex mixture sample including 1% human serum. Our method is simple, fast and cost effective.

Aggregation-deaggregation-triggered, tunable fluorescence of an assay ensemble composed of anionic conjugated polymer and polypeptides by enzymatic catalysis of trypsin

We prepared a water-soluble conjugated polymer composed of electron-donating units and electron-accepting groups in the backbone. The polymer exhibits a short wavelength (blue) emission in aqueous solution and long wavelength (red) emission in the solid state, because of intermolecular energy transfer. Considering this, we develop a new approach for the sensitive detection of trypsin, which is known to control pancreatic exocrine function, using an ensemble system composed of the anionically charged conjugated polymer and cationically charged polypeptides (such as polylysine and polyarginine). The blue-emitting, water-soluble conjugated polymer becomes aggregated upon exposure to the polypeptides, leading to a red-emitting assay ensemble. The red-emitting assay ensemble becomes dissociated in the conjugated polymer and polypeptide fragments by selective degradation of trypsin, which then exhibits recovery of blue emission. This emission-tuning assay ensemble allows for detection of trypsin at nanomolar concentrations, which enables naked-eye detection. Importantly, this strategy can be employed for label-free, continuous assay for trypsin.

Electroosmotic sampling. Application to determination of ectopeptidase activity in organotypic hippocampal slice cultures

We hypothesize that peptide-containing solutions pulled through tissue should reveal the presence and activity of peptidases in the tissue. Using the natural zeta-potential in the organotypic hippocampal slice culture (OHSC), physiological fluids can be pulled through the tissue with an electric field. The hydrolysis of the peptides present in the fluid drawn through the tissue can be determined using capillary HPLC with electrochemical detection of the biuret complexes of the peptides following a postcolumn reaction. We have characterized this new sampling method by measuring the flow rate, examining the use of internal standards, and examining cell death caused by sampling. The sampling flow rate ranges from 60 to 150 nL/min with a 150 microm (ID) sampling capillary with an electric field (at the tip of the capillary) from 30 to 60 V/cm. Cell death can be negligible with controlled sampling conditions. Using this sampling approach, we have electroosmotically pulled Leu-enkephalin through OHSCs to identify ectopeptidase activity in the CA3 region. These studies show that a bestatin-sensitive aminopeptidase may be critical for the hydrolysis of exogenous Leu-enkephalin, a neuropeptide present in the CA3 region of OHSCs.

In vivo monitoring of the transfer kinetics of trace elements in animal brains with hyphenated inductively coupled plasma mass spectrometry techniques

The roles of metal ions to sustain normal function and to cause dysfunction of neurological systems have been confirmed by various studies. However, because of the lack of adequate analytical method to monitor the transfer kinetics of metal ions in the brain of a living animal, research on the physiopathological roles of metal ions in the CNS remains in its early stages and more analytical efforts are still needed. To explicitly model the possible links between metal ions and physiopathological alterations, it is essential to develop in vivo monitoring techniques that can bridge the gap between metalloneurochemistry and neurophysiopathology. Although inductively coupled plasma mass spectrometry (ICP-MS) is a very powerful technique for multiple trace element analyses, when dealing with chemically complex microdialysis samples, the detection capability is largely limited by instrumental sensitivity, selectivity, and contamination that arise from the experimental procedure. As a result, in recent years several high efficient and clean on-line sample pretreatment systems have been developed and combined with microdialysis and ICP-MS for the continuous and in vivo determination of the concentration-time profiles of metal ions in the extracellular space of rat brain. This article reviews the research relevant to the development of analytical techniques for the in vivo determination of dynamic variation in the concentration levels of metal ions in a living animal.

Detection of in vivo matrix metalloproteinase activity using microdialysis sampling and liquid chromatography/mass spectrometry

Matrix metalloproteinases (MMPs) are a family of endoproteases that break down extracellular matrix and whose upregulation contributes to several diseases. A liquid chromatography/tandem mass spectrometry (LC/MS/MS) method was developed to quantify MMP-1 and MMP-9 substrates and their N-terminal peptide products in samples obtained from implanted microdialysis sampling probes. In vitro studies with purified human MMP-1 and MMP-9 were used to optimize the assay and determine the effectiveness of the local delivery of a broad-spectrum MMP inhibitor, GM 6001. Localized delivery of GM 6001 at 10 microM was sufficient to completely inhibit product formation in vitro. In vivo studies in male Sprague-Dawley rats were performed with microdialysis probes implanted into the subcutaneous tissue. Directly after microdialysis probe implantation, infusions of the MMP-1 and MMP-9 substrates (50 microM each) resulted in recovered product concentrations of approximately 2 microM. During a 50 microM GM 6001 coinfusion with the substrates, a 30% and 25% reduction in product formation for the MMP-1 and MMP-9 substrates was obtained, respectively. Blank dialysates were negative for enzymatic activity that could cleave the MMP substrates. This method allowed for the activity of different MMPs surrounding the microdialysis probe to be observed during in vivo sampling.

Mass spectrometry for monitoring protease reactions

More than 560 genes are annotated as proteases in the human genome. About half of the genes are not or are only marginally characterized. Over the past decade, mass spectrometry has become the basis for proteomics, especially for protein identification, performed in a high-throughput manner. This development was also very fruitful for exploring the complex systems associated with protease functions, as briefly reviewed here. Mass spectrometry is an ideal tool for monitoring protease reactions, as will be highlighted in this review.