Discovery of Specific Nonpeptide Probe for Chymotrypsin via Molecular Docking-Based Virtual Screening and the Application

Unravelling the stabilization mechanism of mono-, di- and tri-cholinium citrate-ethylene glycol DESs towards α-chymotrypsin for preservation and activation of the enzyme

Deep eutectic solvents (DESs) are considered as designer solvents that serve as alternatives to traditional solvents. Numerous favourable properties and advantageous characteristics promote their utility in bio-catalysis. Therefore, they have emerged as attractive sustainable media for different biomacromolecules. In the present work, we have synthesized cholinium-based DESs having a hydrogen bond acceptor (HBA) : hydrogen bond donor (HBD) molar ratio of 1 : 2 by varying the cationic ratio in the HBA, which led to the formation of the DESs such as monocholinium citrate ([Chn][Cit]), dicholinium citrate ([Chn]2[Cit]) and tricholinium citrate ([Chn]3[Cit]), keeping the HBD ethylene glycol (EG) constant to study their suitability for α-chymotrypsin (α-CT). Herein, we have systematically evaluated the influence of DES-1 ([Chn][Cit]-[EG]), DES-2 ([Chn]2[Cit]-[EG]) and DES-3 ([Chn]3[Cit]-[EG]) on the structural and thermal stability, thermodynamic profile, colloidal stability and enzymatic activity of α-CT using different spectroscopic techniques. The spectroscopic results explicitly show enhanced structural stability and activity of the enzyme as the cationic ratio in the HBA increases. Fascinatingly, temperature-dependent studies through both fluorescence and activity measurements showed that DES-2 and DES-3 have highly beneficial effects on α-CT stability. The transition temperature (Tm) of α-CT was augmented by 12.0 °C in DES-2, 10.0 °C in DES-3 and 9.1 °C in DES-1 when compared to the enzyme in buffer. Furthermore, transmission electron microscopy (TEM) analysis revealed that the morphology of α-CT in DES-2 and DES-3 closely mirrored the structure of α-CT, while DES-1 exhibited only minor structural deviations. These findings were corroborated by hydrodynamic size (dH) measurements and average decay time analysis, which confirmed the observed morphological similarities and perturbations. The long-term preservation ability and kinetics of DES-3 were eventually confirmed by Michaelis-Menten kinetics. Ultimately, these outcomes demonstrate that increasing the molar ratio of the cholinium cation in the HBA can enhance the ability of DESs to stabilize the α-CT structure. Our results also suggest that the effect imparted by DESs was due to DESs themselves rather than their constituent elements. Altogether, the present investigation provides a new insight into the dependence of protein's stability and conformational alterations on DES composition. Also, the biocompatibility of DESs towards enzymes can be varied by changing the molar ratios of the constituent components of DESs to facilitate the expansion of applicability of DESs in biocatalysis.

Dual-Locked Chemiluminescent Probe Enables Precise Imaging and Timely Diagnosis of Colitis via Chymotrypsin/Vanin-1 Cascade Activation

The development of precise diagnosis and the discovery of individualized drugs go together to provide effective therapy against inflammatory bowel disease (IBD). The exploitation of the unique imaging advantages of chemiluminescent probes represents a pivotal strategy for achieving this goal. Nevertheless, the dual-locked strategy, which is believed to enhance precision, is rarely employed in the design of chemiluminescent probes. A novel dual-locked chemiluminescent probe, BPan-CL, was designed based on IBD candidate biomarkers chymotrypsin (CHT) and vanin-1. BPan-CL exhibited specific reactivity and chemiluminescence response when subjected to simultaneous stimulation of CHT and vanin-1, with a signal-to-noise ratio superior to that of the fluorescent probe with the same dual-locked mode. In both live cell and IBD mice imaging, BPan-CL demonstrated superior sensitivity compared to its single-locked counterpart, Pan-CL. In contrast to Pan-CL, BPan-CL was able to more accurately identify IBD and healthy mice by in vivo imaging and allowed for early prediction of IBD using a noninvasive fecal test. BPan-CL has identified CHT and vanin-1 as valuable combinatorial biomarkers for accurate and early IBD diagnosis. This strategy has significant potential for use in biomedical imaging and future individualized therapies.

Molecular docking studies of isolated marine natural products against α-chymotrypsin

The α-chymotrypsin is widely present in the digestive system of prokaryotes and eukaryotes that helps in the digestion by the hydrolysis of the peptide bond. It is serine protease enzyme (E.C. 3.4.21.1) and involves in many biological processes as well as in pancreatic disorders. In the previous study, marine red alga namely Jolyna laminariodes was used for the isolation of succinylanthranilic acid ester (2). Further, analogues were synthesised from anthranilic acid by using succinic anhydride, maleic anhydride and glutaric anhydride into corresponding dicarboxylic acids and further into acid ester including succinylanthranilic acid (1), succinylanthranilic acid ester (2), maleinylanthranilic acid (3), maleinylanthranilic acid ester (4), glutarnylanthranilic acid (5) and glutarnylanthranilic acid ester (6). For all natural products analogues percent inhibition against α-chymotrypsin have been calculated. In this study, molecular docking is used to estimate the binding energy of natural product analogues against α-chymotrypsin enzyme. The docking energies are in good agreement with experimental findings.

Rational Design of Esterase-Insensitive Fluorogenic Probes for In Vivo Imaging

Small-molecule fluorogenic probes are indispensable tools for performing research in biomedical fields and chemical biology. Although numerous cleavable fluorogenic probes have been developed to investigate various bioanalytes, few of them meet the baseline requirements for in vivo biosensing for disease diagnosis due to their insufficient specificity resulted from the remarkable esterase interferences. To address this critical issue, we developed a general approach called fragment-based fluorogenic probe discovery (FBFPD) to design esterase-insensitive probes for in vitro and in vivo applications. With the designed esterase-insensitive fluorogenic probe, we successfully achieved light-up in vivo imaging and quantitative analysis of cysteine. This strategy was further extended to design highly specific fluorogenic probes for other representative targets, sulfites, and chymotrypsin. The present study expands the bioanalytical toolboxes available and offers a promising platform to develop esterase-insensitive cleavable fluorogenic probes for in vivo biosensing and bioimaging for the early diagnosis of diseases.

De Novo Design of a Highly Selective Nonpeptide Fluorogenic Probe for Chymotrypsin Activity Sensing in a Living System

Chymotrypsin, an extensively known proteolytic enzyme, plays a substantial role in maintaining physiological functions, including protein digestion, immune response, and tissue repair. To date, intense attention has been focused on the invention of efficient and sensitive chemical tools for chymotrypsin activity measurement. Among them, the "nonpeptide"-based chymotrypsin probe design strategy utilizing the esterase activity of chymotrypsin has been well-developed due to its low cost and high atom-economy feature. However, the ester-bond-based nature of these probes make them possibly vulnerable to esterases and active chemicals. These defects strictly restricted the application of the previously reported probes, especially for imaging in living systems. Therefore, to acquire fluorogenic probes with sufficient stability and specificity for chymotrypsin sensing in a complicated biological environment, a more stable skeleton for nonpeptide-based chymotrypsin probe construction is urgently needed. Herein, a novel nonpeptide-based fluorogenic probe for specific chymotrypsin activity sensing was designed and synthesized by the substitution of an ester-based linker with a heptafluorobutylamide moiety. The acquired probe, named TMBIHF, showed high selectivity toward various enzymes and reactive chemicals, while it retained high sensitivity and catalytic efficiency toward chymotrypsin. Moreover, TMBIHF was successfully applied for monitoring chymotrypsin activity and pancreas development in live zebrafish, specific sensing of exogenous and endogenous chymotrypsin in nude mice, and visualizing chymotrypsin-like activity-dependent cellular apoptosis, thus providing an alternative and reliable way for chymotrypsin-targeted biosensor or prodrug construction.

Activatable endoplasmic reticulum-targeted NIR fluorescent probe with a large Stokes shift for detecting and imaging chymotrypsin

In this work, the first endoplasmic reticulum-targeted near-infrared fluorescent probe, ISO-Chy, with a large Stokes shift is reported by introducing a recognition group of 4-bromobutyl for chymotrypsin detection.

Development of Efficient One-Pot Methods for the Synthesis of Luminescent Dyes and Sol-Gel Hybrid Materials

This paper presents a comparison of the simultaneous preparation of di-O-alkylated and ether-ester derivatives of fluorescein using different methods (conventional or microwave heating). Shortening of the reaction time and increased efficiency were observed when using a microwave reactor. Moreover, described here for the first time is the application of a fast, simple, and eco-friendly ball-assisted method to exclusively obtain ether-ester derivatives. We also demonstrate that fluorescein can be effectively functionalized by O-alkylation carried out under microwave or ball-milling conditions, saving time and energy and affording the desired products with good yields and minimal byproduct formation. All the synthesized products as well as pH-dependent (prototropic) forms trapped in the SiO2 matrix were examined using UV-Vis and fluorescence spectroscopy.

A non-peptide probe for detecting chymotrypsin activity based on protection-deprotection strategy in living systems

Chymotrypsin (CHT) plays a vital role in the metabolism of organisms and affects cell proliferation and apoptosis. Abnormal levels of CHT will lead to a variety of diseases, such as inflammatory arthritis, diabetes, pharyngitis, indigestion, and pancreatic cancer. Therefore, it is significant to design an effective method for the detection of CHT in living systems. Here, we synthesized a specific deep-red non-peptide probe DT by effectively combining isophorone and p-hydroxybenzaldehyde for the detection of CHT using 3-phenylpropionate chloride as the recognition group based on a protection-deprotection strategy. The DT probe exhibited an emission range of 525-700 nm and showed excellent photostability, high sensitivity (LOD = 0.071 U mL^-1), and selectivity for CHT detection. The cellular experiments demonstrated that DT could sensitively recognize CHT activity in three cell lines and the content of CHT was much higher in P815 cells than in MCF-7 and 3T3 cells. Also, DT was successfully used to visualize the endogenous CHT in zebrafish. Notably, the DT probe provided an intuitive way to visualize endogenous CHT in mouse pancreas for the first time, demonstrating the potential for application in the future clinical diagnosis of pancreatic diseases. Therefore, the small-molecule probe DT is expected to be a useful molecular tool for CHT-related disease diagnosis and drug discovery.

Review on the recent progress in the development of fluorescent probes targeting enzymes

Enzymes are very important for biological processes in a living being, performing similar or multiple tasks in and out of cells, tissues and other organisms at a particular location. The abnormal activity of particular enzyme usually caused serious diseases such as Alzheimer's disease, Parkinson's disease, cancers, diabetes, cardiovascular diseases, arthritis etc. Hence, nondestructive and real-time visualization for certain enzyme is very important for understanding the biological issues, as well as the drug administration and drug metabolism. Fluorescent cellular probe-based enzyme detectionin vitroandin vivohas become broad interest for human disease diagnostics and therapeutics. This review highlights the recent findings and designs of highly sensitive and selective fluorescent cellular probes targeting enzymes for quantitative analysis and bioimaging.

Multienzyme-Targeted Fluorescent Probe as a Biosensing Platform for Broad Detection of Pesticide Residues

Pesticide residues, significantly hampering the overall environmental and human health, have become an increasingly severe issue. Thus, developing rapid, cost-effective, and sensitive tools for monitoring the pesticide residues in food and water is extremely important. Compared to the conventional and chromatographic techniques, enzyme inhibition-based biosensors conjugated with the fluorogenic probes provide effective alternative methods for detecting pesticide residues due to the inherent advantages including high selectivity and sensitivity, simple operation, and capability of providing in situ and real-time information. However, the detection efficiency of a single enzyme-targeted biosensor in practical samples is strongly impeded by the structural diversity of pesticides and their distinct targets. In this work, we developed a strategy of multienzyme-targeted fluorescent probe design and accordingly obtained a novel fluorescent probe (named as 3CP) for detecting the presence of wide variety of pesticides. The designed probe 3CP, targeting cholinesterases, carboxylesterases, and chymotrypsin simultaneously, yielded intense fluorescence in the solid state upon the enzyme-catalyzed hydrolysis. It showed excellent sensitivity against organophosphorus and carbamate pesticides, and the detection limit for dichlorvos achieved 1.14 pg/L. Moreover, it allowed for the diffusion-resistant in situ visualization of pesticides in live cells and zebrafish and the sensitive measurement of organophosphorus pesticides in fresh vegetables, demonstrating the promising potential for tracking the pesticide residues in environment and biological systems.

Thermodynamics, Kinetics and Mechanisms of Noncompetitive Allosteric Inhibition of Chymotrypsin by Dihydrolipoic Acid-Coated Gold Nanoclusters

Enzymes are an important class of biomacromolecules which catalyze many metabolic processes in living systems. Nanomaterials can be synthesized with tailored sizes as well as desired surface modifications, thus acting as promising enzyme regulators. Fluorescent gold nanoclusters (AuNCs) are a representative class of ultrasmall nanoparticles (USNPs) with sizes of ∼2 nm, smaller than most of proteins including enzymes. In this work, we chose α-chymotrypsin (ChT) and AuNCs as the model system. Activity assays and inhibition kinetics studies showed that dihydrolipoic acid (DHLA)-coated AuNCs (DHLA-AuNCs) had a high inhibitory potency (IC₅₀ = 3.4 μM) and high inhibitory efficacy (>80%) on ChT activity through noncompetitive inhibition mechanism. In distinct contrast, glutathione (GSH)-coated AuNCs (GSH-AuNCs) had no significant inhibition effects. Fluorescence spectroscopy, agarose gel electrophoresis and circular dichroism (CD) spectroscopy were conducted to explore the underlying mechanisms. A two-step interaction model was proposed. First, both DHLA-AuNCs and GSH-AuNCs might be bound to the positively charged sites of ChT through electrostatic forces. Second, further hydrophobic interactions occurred between three tyrosine residues of ChT and the hydrophobic carbon chain of DHLA, leading to a significant structural change thus to deactivate ChT on the allosteric site. On the contrary, no such interactions occurred with GSH of zwitterionic characteristic, which explained no inhibitory effect of GSH-AuNCs on ChT. To the best of our knowledge, this is the first example of the allosteric inhibition of ChT by nano regulators. These findings provide a fundamental basis for the design and development of nano regulators.

Perspective on chymotrypsin detection

Chymotrypsin is one of the most extensively known proteases participating in the pathogenesis of various diseases, which can be used in drug discovery and clinical diagnosis.

Ultrafast 2,7-Naphthyridine-Based fluorescent probe for detection of thiophenol with a remarkable Stokes shift and its application In vitro and in vivo

2,7-Naphthyridine derivatives were developed as fluorophores for the first time to design two fluorescence probes, AND-DNP and ND-DNP, which can be applied for detecting thiophenol in aqueous media. Comparing with ND-DNP, AND-DNP showed more favorable properties such as lower background, larger Stokes shift, and higher fluorescence quantum yield for detecting thiophenol. Moreover, the experimental results were verified by theoretical calculations. Hence, AND-DNP was selected as the superior fluorescence probe to detect thiophenol because of its high sensitivity and selectivity. Based on the experimental results, AND-DNP showed a remarkably larger Stokes shift (225 nm), faster response speed (30 s) and higher fluorescence enhancement (240-fold) than most other fluorescent probes for thiophenol reported in the literature. For an extended application, AND-DNP was applied to detect thiophenol quantitatively in real water samples. Meanwhile, AND-DNP also detected thiophenol via red emission in living A549 cells and zebrafish. All these results proved AND-DNP's potential value as an accurate probe for imaging thiophenol in different environments.