Disaggregation-Activated pan-COX Imaging Agents for Human Soft tissue Sarcoma.

Cancer stem cells are pivotal players in tumors initiation, growth, and metastasis. While several markers have been identified, there remain challenges particularly in heterogeneous malignancies like adult soft tissue sarcomas, where conventional markers are inherently overexpressed. Here, we designed BODIPY scaffold fluorescence probes (BD-IMC-1, BD-IMC-2) that activate via disaggregation targeting for cyclooxygenase (COX), a potential marker for CSCs in sarcoma in clinical pathology. Based on their structures, BD-IMC-1 showcased higher susceptibility to disaggregation compared to BD-IMC-2, consistent with their selective interaction with COX. Notably, the BD-IMC-1 revealed positive cooperativity binding to COX-2 at sub-micromolar ranges. Both probes showed significant fluorescence turn-on upon LPS or PMA triggered COX-2 upregulation in live RAW264.7, HeLa, and human sarcoma cell line (Saos-LM2) up to 2-fold increase with negligible toxicity. More importantly, the BD-IMC-1 demonstrated their practical imaging for COX-2 positive cells in paraffin-fixed human sarcoma tissue. Considering the fixed tissues are most practiced pathological sample, our finding suggests a potential of disaggregation activated chemosensor for clinical applications.

Chemical Probes and Activity-Based Protein Profiling for Cancer Research.

Chemical probes can be used to understand the complex biological nature of diseases. Due to the diversity of cancer types and dynamic regulatory pathways involved in the disease, there is a need to identify signaling pathways and associated proteins or enzymes that are traceable or detectable in tests for cancer diagnosis and treatment. Currently, fluorogenic chemical probes are widely used to detect cancer-associated proteins and their binding partners. These probes are also applicable in photodynamic therapy to determine drug efficacy and monitor regulating factors. In this review, we discuss the synthesis of chemical probes for different cancer types from 2016 to the present time and their application in monitoring the activity of transferases, hydrolases, deacetylases, oxidoreductases, and immune cells. Moreover, we elaborate on their potential roles in photodynamic therapy.

Role of microRNA and Oxidative Stress in Influenza A Virus Pathogenesis.

MicroRNAs (miRNAs) are non-coding RNAs that regulate diverse cellular pathways by controlling gene expression. Increasing evidence has revealed their critical involvement in influenza A virus (IAV) pathogenesis. Host-IAV interactions induce different levels of oxidative stress (OS) by disrupting the balance between reactive oxygen species (ROS) and antioxidant factors. It is thought that miRNA may regulate the expression of ROS; conversely, ROS can induce or suppress miRNA expression during IAV infection. Thus, miRNA and OS are the two key factors of IAV infection and pathogenesis. Accordingly, interactions between OS and miRNA during IAV infection might be a critical area for further research. In this review, we discuss the crosstalk between miRNAs and OS during IAV infection. Additionally, we highlight the potential of miRNAs as diagnostic markers and therapeutic targets for IAV infections. This knowledge will help us to study host-virus interactions with novel intervention strategies.

Recent Developments in Metal-Catalyzed Bio-orthogonal Reactions for Biomolecule Tagging.

With the rapid advances in single-molecule and live-cell imaging studies to investigate biological problems, the role of chemical probes to monitor reactions in a live cell has considerably increased. However, selective labeling of a target protein or a specific residue is highly challenging due to the high complexity of the biological system. In particular, biological macromolecules (such as proteins, DNA, or RNA) share many functional groups that potentially cross-react with exogenous chemical probes. Thus, there are high demands for perfect biocompatible reactions utilizing biologically unavailable chemistry. Metal-catalyzed reactions have been extensively investigated as synthetic methodology studies, including initial attempts in applying the chemistry in aqueous solutions in vitro or even in biological conditions. Herein, the latest developments and progress in metal-catalyzed bio-orthogonal reactions for biomolecule labeling are summarized.

Crosstalk between Oxidative Stress and Tauopathy.

Tauopathy is a collective term for neurodegenerative diseases associated with pathological modifications of tau protein. Tau modifications are mediated by many factors. Recently, reactive oxygen species (ROS) have attracted attention due to their upstream and downstream effects on tauopathy. In physiological conditions, healthy cells generate a moderate level of ROS for self-defense against foreign invaders. Imbalances between ROS and the anti-oxidation pathway cause an accumulation of excessive ROS. There is clear evidence that ROS directly promotes tau modifications in tauopathy. ROS is also highly upregulated in the patients' brain of tauopathies, and anti-oxidants are currently prescribed as potential therapeutic agents for tauopathy. Thus, there is a clear connection between oxidative stress (OS) and tauopathies that needs to be studied in more detail. In this review, we will describe the chemical nature of ROS and their roles in tauopathy.

Reinvestigation of an O-Salicylaldehyde Ester Functional Group in Aqueous Buffer and Discovery of a Coumarin Scaffold Probe for Selective N-Terminal Cysteine Labeling.

Many intracellular proteins are metabolically unstable, and their half-life was known to be controlled by the "N-end rule," that is, the N-terminal residue controlled protein stability. To visualize or measure the cellular stability of a protein, depending on the N-terminal residues, attention is being paid to the development of selective labeling methods for individual N-terminal amino acids. However, there are only a limited number of functional groups available for specific N-terminal amino acid labeling in a biological environment. Herein, we report a re-examination of salicylaldehyde ester for selective N-terminal residue tagging. Salicylaldehyde ester has been used for chemical ligation to N-terminal serine or threonine under pyridine/acetic acid conditions. Inspired by previous selective serine/threonine labeling, N-terminal labeling of salicylaldehyde ester in aqueous buffer has been examined by using boron-dipyrromethene (BODIPY), rhodamine, and coumarin probes. Surprisingly, the selectivity not only significantly differed, depending on the fluorophore incorporated in salicylaldehyde, but was also perturbed by the addition of a small fraction of phosphate-buffered saline. In particular, the coumarin-based salicylaldehyde ester probe showed notable selectivity against N-terminal cysteine under aqueous buffer conditions. This result reveals the serendipitous discovery of a new N-terminal cysteine labeling strategy.

Chloro-Functionalized Photo-crosslinking BODIPY for Glutathione Sensing and Subcellular Trafficking.

Glutathione (GSH) is one of major antioxidants inside cells that regulates oxidoreduction homeostasis. Recently, there have been extensive efforts to visualize GSH in live cells, but most of the probes available today are simple detection sensors and do not provide details of cellular localization. A new fluorescent probe (pcBD2-Cl), which is cell permeable and selectively reacts with GSH in situ, has been developed. The in situ GSH-labeled probe (pcBD2-GSH) exhibited quenches fluorescence, but subsequent binding to cellular abundant glutathione S-transferase (GST) recovers the fluorescence intensity, which makes it possible to image the GSH-GST complex in live cells. Interactions between probe and GST were confirmed by means of photo-crosslinking under intact live-cell conditions. Interestingly, isomers of chloro-functionalized 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) compounds behaved very distinctively inside the cells. Following co-staining imaging with MitoTracker and mitochondria fractionation upon lipopolysaccharide-mediated reactive oxygen species induction experiments showed that pcBD2-GSH accumulated in mitochondria. This is the first example of a live-cell imaging probe to visualize translocation of GSH from the cytosol to mitochondria.

Discrimination of Avian Influenza Virus Subtypes using Host-Cell Infection Fingerprinting by a Sulfinate-based Fluorescence Superoxide Probe.

The current gold-standard diagnosis method for avian influenza (AI) is an embryonic egg-based hemagglutination assay followed by immunoblotting or PCR sequencing to confirm subtypes. It requires, however, specialized facilities to handle egg inoculation and incubation, and the subtyping methods relied on costly reagents. Now, the first differential sensing approach to distinguish AI subtypes is demonstrated using series of cell lines and a fluorescent sensor. Susceptibility of AI virus differs depending on genetic backgrounds of host cells. Cells were examined from different organ origins, and the infection patterns against a panel of cells were utilized for AI virus subtyping. To quantify AI infection, a highly cell-permeable fluorescent superoxide sensor was designed to visualize infection. This differential sensing strategy successfully proved discriminations of AI subtypes and demonstrated as a useful primary screening platform to monitor a large number of samples.

Bulk Aggregation Based Fluorescence Turn-On Sensors for Selective Detection of Progesterone in Aqueous Solution.

Steroids are polycyclic compounds that share tetracyclic ring as core scaffold, and selective detection of a steroid is challenging owing to their structural similarities. The discovery of chemosensors that recognize progesterone by alteration of self-aggregation state is described, and these show significant fluorescence turn-on. A self-aggregated 48-membered dansyl library was screened against a series of metabolites in aqueous buffer and discovered two compounds (PG-1, PG-2) exhibited exceptional selectivity for progesterone. Following studies of aggregation properties of probes using dynamic light scattering and transmission electron microscopy supports progesterone recognition lead to the generation of bulk aggregates that induce fluorescence enhancement. Though many fluorescence sensing mechanisms have been proposed, a sensing mode based on the bulk aggregate formation of fluorophore has never been reported, and this may open a new avenue of chemosensor design.

Photo-affinity labeling (PAL) in chemical proteomics: a handy tool to investigate protein-protein interactions (PPIs).

Protein-protein interactions (PPIs) trigger a wide range of biological signaling pathways that are crucial for biomedical research and drug discovery. Various techniques have been used to study specific proteins, including affinity chromatography, activity-based probes, affinity-based probes and photo-affinity labeling (PAL). PAL has become one of the most powerful strategies to study PPIs. Traditional photocrosslinkers are used in PAL, including benzophenone, aryl azide, and diazirine. Upon photoirradiation, these photocrosslinkers (Pls) generate highly reactive species that react with adjacent molecules, resulting in a direct covalent modification. This review introduces recent examples of chemical proteomics study using PAL for PPIs.

Novel reversible and selective nerve agent simulant detection in conjunction with superoxide "turn-on" probing.

Herein, we present fluorescein as a reversible fluorescent sensor for nerve agent simulants diethylchlorophosphate (DCP), diethyl methylphosphonate (DEMP), and diethyl cyanophosphonate (DECP). The superoxide allows for an "off-on" mechanism to regenerate fluorescein. The order of decrease in fluorescence intensity for nerve agent simulants is DCP > DEMP ≫ DECP.

Extremely selective "turn-on" fluorescence detection of hypochlorite confirmed by proof-of-principle neurological studies via esterase action in living cells.

Highly specific and sensitive fluorescence detection of hypochlorite in nonbiotic pure water (rapid "turn-on", ~400 fold, λ(em) ~ 560 nm) as well as in living neuronal cell cultures (neutral pH) involves oxidation of a 2-sulfide-2-benzoic acid pendent group in a new meso-thienyl-BODIPY donor-acceptor probe.

An efficient chemodosimeter for the detection of Hg(II) via diselenide oxidation.

Mercury ions are toxic and exhibit hazardous effects on the environment and biological systems, and thus demand for the selective and sensitive detection of mercury has become considerably an important issue. Here, we have developed a diselenide containing coumarin-based probe 3 for the selective detection of Hg(II) with a "turn-on" response (a 48 fold increase in fluorescence intensity) at 438 nm. The probe could quantitatively detect Hg(II) with a detection limit of 1.32 µM in PBS solution. Moreover, the probe has operable efficiency over the physiological range with an increase in the quantum yield from 1.2% to 57.3%. The reaction of the probe with Hg(II) yielded a novel monoselenide based coumarin 4via diselenide oxidation, which was confirmed by single crystal XRD. Furthermore, the biological use of the probe for the detection of Hg(II) was confirmed in the MCF-7 cell line. To the best of our knowledge, this is the first reaction-based probe for Hg(II) via diselenide oxidation.

Temporal control of protein labeling by a photo-caged benzaldehyde motif and discovery of host cell factors of avian influenza virus infection.

Photo-caged benzaldehyde probes using o-nitrophenylethylene glycol were designed for photo-activated electrophile generation. Using photo-activated electrophile generating probes, we successfully revealed under-represented host cell response factors using an avian influenza virus infection model.

Correction: Temporal control of protein labeling by a photo-caged benzaldehyde motif and discovery of host cell factors of avian influenza virus infection.

Correction for 'Temporal control of protein labeling by a photo-caged benzaldehyde motif and discovery of host cell factors of avian influenza virus infection' by Nicholas Asiimwe et al., Chem. Commun., 2022, https://doi.org/10.1039/d2cc04091c.

Structure-activity relationship of cyclic thiacarbocyanine tau aggregation inhibitors.

Macrocyclic bis-thiacarbocyanines are efficacious inhibitors of tau protein aggregation. To extend the structure-activity relationship of this inhibitor class, N,N'-alkylene bis-thiacarbocyanines linked by chains of three to eight methylene carbons were synthesized and examined for inhibitory activity against recombinant human tau aggregation in vitro. At 10 micromolar concentration, inhibitory activity varied with linker length, with four methylene units being most efficacious. On the basis of absorbance spectroscopy measurements, linker length also affected compound folding and aggregation propensity, with a linker length of four methylene units being optimal for preserving open monomer conformation. These data suggest that inhibitory potency can be optimized through control of linker length, and that a contributory mechanism involves modulation of compound folding and aggregation.

Combinatorial Dansyl Library and its Applications to pH-Responsive Probes.

Herein, we report the first 48-membered, dansyl-based, combinatorial fluorescent library. From the electronic and structural properties of the probes, we analyzed their optical properties and chemical yields, with an average of 49 %. The molecules were examined for their pH responses, and DS-2 and DS-45 showed blue-shifts, whereas DS-7 and DS-40 showed red-shifts in wavelength with increasing pH. Finally, cell permeability was investigated by treating SNU-2292 cells. Our results demonstrate the potential application of this library in biosensors, bio-imaging and pH indicators.

Rational design of a photo-crosslinking BODIPY for in situ protein labeling.

Photo-crosslinking agents have emerged as critical tools to investigate protein-protein interactions in complex proteomes, but there are few photocrosslinkers available at the moment. Here, we report the first rational design of a photo-crosslinking BODIPY fluorophore (pcBD) and its biological application for biomolecule labeling. As a photosensitizing functional motif, an aryl ketone group was incorporated into the BODIPY fluorophore, and a series of proteins were labeled by pcBD compounds upon UV irradiation. In order to investigate protein-protein interactions in a protein mixture, amino-functionalized pcBD was prepared and covalently attached to a ubiquitin ligase binding peptide. Upon UV irradiation, we could successfully visualize the substrates in the total lysate. These results provided a proof of concept for spatially controllable tagging via photo-activation of the pcBD scaffold, and demonstrated its potential usage for in situ labeling applications.

H(+)-Assisted fluorescent differentiation of Cu(+) and Cu(2+): effect of Al(3+)-induced acidity on chemical sensing and generation of two novel and independent logic gating pathways.

A novel Schiff base probe exhibited strong 'turn-ON' fluorescence for Cu(2+) at 345 nm, Al(3+) at 445 nm, and Cu(+) at 360 nm in the presence of Al(3+) in organic solvent (acetonitrile), which allowed for construction of molecular logic gates 'INH' and '1:2 DEMULTIPLEXING.' H(+) generated from Al(3+) contributed greatly to Cu(+) chemosensing based on a redox non-innocence mechanism.

Fluorescence probing of the ferric Fenton reaction via novel chelation.

A new probe-chelator PET dyad was synthesised, which can be used to detect Fe(3+)via fluorescence enhancement to discriminate between Fe(2+) and Fe(3+)via Fenton chemistry involving hydrogen peroxide. This is the first BODIPY which works as a 2 : 1 multiplexer for Fe(3+), Fe(2+) and H2O2.