Fluorescent Reporter Group Research Articles

Ultra-sensitive and fast nitroreductase-responsive fluorescence probe for real-time bioimaging of hypoxia in tumor cells and zebrafish wound inflammation

Hypoxia is intertwined with the occurrence and progression of tumors and inflammation. To date, various fluorescent probes have been constructed for monitoring degrees of hypoxia in tumor cells, however, efficiently evaluating the degrees of hypoxia caused by inflammation in real-time has been rarely exhibited via fluorescence imaging technique. Hence, an ultra-sensitive and fast-response fluorescent probe R19-NTR using rhodamine 19 as the fluorescent reporter and nitro aromatic groups as the recognition unit was performed to estimate the degrees of hypoxia through assessing the changes in the level of nitroreductase. The probe R19-NTR was basically non-fluorescent on account of the intramolecular photo-induced electron transfer process. Upon selectively reacted with nitroreductase, the R19-NTR featured an ultrafast response (< 1 min), and a significant fluorescence enhancement (ca. 114-fold). Encouraged by these outstanding properties, R19-NTR has been utilized for monitoring the degree of hypoxia in tumor cells and zebrafish wound inflammation. The results revealed that tumor cells under normoxic and different degrees of hypoxic conditions can be distinguished successfully, as well as the differentiation between tumor cells and normal cells. Moreover, the in vivo visualization disclosed that the endogenous nitroreductase of 6–10 days post fertilization zebrafish embryos was mainly focused on the liver and intestine. In particularly, the elevation of hypoxia degrees in zebrafish wound inflammation caused by severed tails were successfully visualized for the first time, as well as the variation of hypoxia degrees in gradually dying zebrafish embryos. The present research may provide a promising methodology for the diagnosis of inflammation-related diseases and tumors.

Biotin-tagged fluorescent probe for in situ visualization of γ-glutamyl transpeptidase in cancerous cells and tissues

γ-Glutamyl transpeptidase (GGT), a cell-surface enzyme, is strongly implicated in mammalian malignancy growth and migration processes including human hepatocarcinogens. However, simply and conveniently detect of GGT on the cell membrane remains highly challenging. In this study, a biotin-tagged fluorescent probe Nap-biotin-glu was developed using glutamic acid, naphthalimide, and biotin as the reaction site, fluorescent reporter, and membrane-targeting group, which required only three steps. Colocalization fluorescence imaging and immunofluorescence analysis indicated that probe Nap-biotin-glu was successfully realized in situ visualizing of GGT on the cell membrane.Owing to the significant over-expressed GGT level in tumor, the probe was successfully applied to distinguish cancer tissues from adjacent normal tissues.

Near-infrared molecular sensor for visualizing and tracking ONOO- during the process of anti-tuberculosis drug-induced liver damage.

Isoniazid (INH) and pyrazinamide (PZA) are both the first-line anti-tuberculosis drugs in clinical treatment. It is notable that there are serious side effects of the drugs along with upregulation of reactive nitrogen species, mainly including peripheral neuritis, gastrointestinal reactions, and acute drug-induced liver injury (DILI). Among them, DILI is the most common clinical symptom as well as the basic reason of treatment interruption, protocol change, and drug resistance. As vital reactive nitrogen species (RNS), peroxynitrite (ONOO-) has been demonstrated as a biomarker for evaluation and pre-diagnosis of drug-induced liver injury (DILI). In this work, we developed a red-emitting D-π-A type fluorescence probe DIC-NP which was based on 4'-hydroxy-4-biphenylcarbonitrile modified with dicyanoisophorone as a fluorescent reporter and diphenyl phosphinic chloride group as the reaction site for highly selective and sensitive sensing ONOO-. Probe DIC-NP displayed a low detection limit (14.9 nM)and 60-fold fluorescent enhancement at 669 nm in the sensing of ONOO-. Probe DIC-NP was successfully applied to monitor exogenous and endogenous ONOO- in living HeLa cells and zebrafish. Furthermore, we verified the toxicity of isoniazid (INH) and pyrazinamide (PZA) by taking the oxidative stress induced by APAP as a reference, and successfully imaged anti-tuberculosis drug-induced endogenous ONOO- in HepG2 cells. More importantly, we developed a series of mice models of liver injury and investigated the hepatotoxicity caused by the treatment of anti-tuberculosis drugs. At the same time, H&E of mice organs (heart, liver, spleen, lung, kidney) further confirmed thecompetence of probe DIC-NP for estimating the degree of drug-induced liver injury, which laid a solid foundation for medical research.

Comparative Photoaffinity Profiling of Omega-3 Signaling Lipid Probes Reveals Prostaglandin Reductase 1 as a Metabolic Hub in Human Macrophages.

The fish oil constituent docosahexaenoic acid (DHA, 22:6 n-3) is a signaling lipid with anti-inflammatory properties. The molecular mechanisms underlying the biological effect of DHA are poorly understood. Here, we report the design, synthesis, and application of a complementary pair of bio-orthogonal, photoreactive probes based on the polyunsaturated scaffold DHA and its oxidative metabolite 17-hydroxydocosahexaenoic acid (17-HDHA). In these probes, an alkyne serves as a handle to introduce a fluorescent reporter group or a biotin-affinity tag via copper(I)-catalyzed azide-alkyne cycloaddition. This pair of chemical probes was used to map specific targets of the omega-3 signaling lipids in primary human macrophages. Prostaglandin reductase 1 (PTGR1) was identified as an interaction partner that metabolizes 17-oxo-DHA, an oxidative metabolite of 17-HDHA. 17-oxo-DHA reduced the formation of pro-inflammatory lipids 5-HETE and LTB4 in human macrophages and neutrophils. Our results demonstrate the potential of comparative photoaffinity protein profiling for the discovery of metabolic enzymes of bioactive lipids and highlight the power of chemical proteomics to uncover new biological insights.

A Nile red-based near-infrared fluorescent probe for the detection of superoxide radical anion in living cells

Reactive oxygen species (ROS) are important products of aerobic metabolism and play important roles in many physiological and pathological processes. Among the ROS, superoxide radical anion (O 2 •‒ ) is a primary ROS and precursor of a few other kinds of ROS. O 2 •‒ is widely involved in regulating cell functions and is a critical biomarker for monitoring cellular stress responses. Thus, a real-time quantitative detection of O 2 •‒ is of great significance in ascertaining the pathological roles of O 2 •‒ in related diseases. Herein we report a near-infrared (NIR) fluorescent probe NR1 for the sensitive detection and imaging of O 2 •‒ , which is rationally designed and synthesized through an esterification reaction of a Nile red dye and the diphenyl phosphinyl group. The NR1 probe exploits the strong nucleophilic mechanism of O 2 •‒ as a novel detection strategy, which leads to the cleavage of NR1 to yield Nile red as the fluorescence reporter and diphenyl phosphinyl functional group as the responsive unit. The developed NR1 probe exhibits highly sensitive, selective and rapid fluorescence turn-on response on addition of O 2 •‒ in the presence of potential ROS interfering species. Furthermore, the probe NR1 is successfully applied in imaging of various cancer cell lines (4T1 and Hela) and excellent imaging ability of O 2 •‒ in vitro is achieved. Biocompability of NR1 is also evaluated through MTS assay. The present study provides a novel strategy for molecular design of NIR fluorescent probe and the resulting probe shows great potential for practical application in complex bio-systems to study the development and progression of related diseases.

Cytotoxic BODIPY-Appended Half-Sandwich Iridium(III) Complex Forms Protein Adducts and Induces ER Stress.

Half-sandwich complexes of iridium(III) are currently being developed as anticancer drug candidates. In this context, we introduce IrBDP for which the C^N chelating phenyloxazoline ligand carries a fluorescent and lipophilic BODIPY reporter group, designed for intracellular tracking and hydrophobic compartment tropism. High-resolution analysis of cells cultured with IrBDP showed that it quickly permeates the plasma membrane and accumulates in the mitochondria and endoplasmic reticulum (ER), generating ER stress, dispersal of the Golgi apparatus, cell proliferation arrest and apoptotic cell death. Moreover, IrBDP forms fluorescent adducts with a subset of amino acids, namely histidine and cysteine, via coordination of N or S donor atoms of their side chains. Consistently, in vivo formation of covalent adducts with specific proteins is demonstrated, providing a molecular basis for the observed cytotoxicity and cellular response. Collectively, these results provide a new entry to the development of half-sandwich iridium-based anticancer drugs.

Cover Feature: A “Three‐in‐One” Multifunctional Probe for Bcl‐2/Mcl‐1 Profiling and Visualizing in Situ (ChemBioChem 2/2021)

Activity-based protein profiling (ABPP) is a powerful approach for profiling and bioimaging many therapeutic targets for bioactive molecules in situ. The cover feature picture shows an activity-based probe for Bcl-2/Mcl-1 profiling and visualizing. Integrating the Bcl-2/Mcl-1 binding ligand, fluorescent reporter group and photoreactive group into the same scaffold creates a multifunctional probe that can label, capture, enrich, and bioimage Bcl-2/Mcl-1 proteins both in vitro and in cells. More information can be found in the communication by Z. Wang, Z. Zhang, et al.

Fragment-Based Identification of Ligands for Bromodomain-Containing Factor 3 of Trypanosoma cruzi.

The Trypanosoma cruzi (T.cruzi) parasite is the cause of Chagas disease, a neglected disease endemic in South America. The life cycle of the T.cruzi parasite is complex and includes transitions between distinct life stages. This change in phenotype (without a change in genotype) could be controlled by epigenetic regulation, and might involve the bromodomain-containing factors 1-5 (TcBDF1-5). However, little is known about the function of the TcBDF1-5. Here we describe a fragment-based approach to identify ligands for T.cruzi bromodomain-containing factor 3 (TcBDF3). We expressed a soluble construct of TcBDF3 in E.coli, and used this to develop a range of biophysical assays for this protein. Fragment screening identified 12 compounds that bind to the TcBDF3 bromodomain. On the basis of this screen, we developed functional ligands containing a fluorescence or 19F reporter group, and a photo-crosslinking probe for TcBDF3. These tool compounds will be invaluable in future studies on the function of TcBDF3 and will provide insight into the biology of T.cruzi.

A "Three-in-One" Multifunctional Probe for Bcl-2/Mcl-1 Profiling and Visualizing in Situ.

Bcl-2 and Mcl-1, the two arms of the anti-apoptotic Bcl-2 family proteins, have been identified as key regulators of apoptosis and effective therapeutic targets of cancer. However, no small-molecular probe is capable of profiling and visualizing both Bcl-2 and Mcl-1 simultaneously in situ. Herein, we report a multifunctional molecular probe (BnN3 -OPD-Alk) by a "three-in-one" molecular designing strategy, which integrated the Bcl-2/Mcl-1 binding ligand, fluorescent reporter group and photoreactive group azido into the same scaffold. BnN3 -OPD-Alk exhibited sub-micromolar affinities to Bcl-2/Mcl-1 and bright green self-fluorescence. It was then successfully applied for Bcl-2/Mcl-1 labeling, capturing, enriching, and bioimaging both in vitro and in cells. This strategy could facilitate the precise early diagnosis and effective therapy of dual Bcl-2/Mcl-1-related diseases.

Transient Deprotonation of the Chromophore Affects Protein Dynamics Proximal and Distal to the Linear Tetrapyrrole Chromophore in Phytochrome Cph1.

Phytochromes are biological red/far-red light sensors found in many organisms. Prototypical phytochromes, including Cph1 from the cyanobacterium Synechocystis 6803, act as photochemical switches that interconvert between stable red (Pr)- and metastable far-red (Pfr)-absorbing states induced by photoisomerization of the bilin chromophore. The connection between photoconversion and the cellular output signal involves light-mediated global structural changes in the interaction between the photosensory module (PAS-GAF-PHY) and the C-terminal transmitter (output) module, usually a histidine kinase, as in the case of Cph1. The chromophore deprotonates transiently during the Pr → Pfr photoconversion in association with extensive global structural changes required for signal transmission. Here, we performed equilibrium studies in the Pr state, involving pH titration of the linear tetrapyrrole chromophore in different Cph1 constructs, and measurement of pH-dependent structural changes at various positions in the protein using picosecond time-resolved fluorescence anisotropy. The fluorescent reporter group was attached at positions 371 (PHY domain), 305 (GAF domain), and 120 (PAS domain), as well as at sites in the PAS-GAF bidomain. We show direct correlation of chromophore deprotonation with pH-dependent conformational changes in the various domains. Our results suggest that chromophore deprotonation is closely associated with a higher protein mobility (conformational space) both in proximal and in distal protein sites, implying a causal relationship that might be important for the global large protein arrangements and thus intramolecular signal transduction.

Conformational Changes in the 5-HT3A Receptor Extracellular Domain Measured by Voltage-Clamp Fluorometry

The 5-hydroxytryptamine (5-HT) type 3 receptor is a member of the cysteine (Cys)-loop receptor super family of ligand-gated ion channels in the nervous system and is a clinical target in a range of diseases. The 5-HT3 receptor mediates fast serotonergic neurotransmission by undergoing a series of conformational changes initiated by ligand binding that lead to the rapid opening of an intrinsic cation-selective channel. However, despite the availability of high-resolution structures of a mouse 5-HT3 receptor, many important aspects of the mechanistic basis of 5-HT3 receptor function and modulation by drugs remain poorly understood. In particular, there is little direct evidence for the specific conformational changes predicted to occur during ligand-gated channel activation and desensitization. In the present study, we used voltage-clamp fluorometry (VCF) to measure conformational changes in regions surrounding the orthosteric binding site of the human 5-HT3A (h5-HT3A) receptor during binding of 5-HT and different classes of 5-HT3 receptor ligands. VCF utilizes parallel measurements of receptor currents with photon emission from fluorescent reporter groups covalently attached to specific positions in the receptor structure. Reporter groups that are highly sensitive to the local molecular environment can, in real time, report conformational changes as changes in fluorescence that can be correlated with changes in receptor currents reporting the functional states of the channel. Within the loop C, D, and E regions that surround the orthosteric binding site in the h5-HT3A receptor, we identify positions that are amenable to tagging with an environmentally sensitive reporter group that reports robust fluorescence changes upon 5-HT binding and receptor activation. We use these reporter positions to characterize the effect of ligand binding on the local structure of the orthosteric binding site by agonists, competitive antagonists, and allosterically acting channel activators. We observed that loop C appears to show distinct fluorescence changes for ligands of the same class, while loop D reports similar fluorescence changes for all ligands binding at the orthosteric site. In contrast, the loop E reporter position shows distinct changes for agonists, antagonists, and allosteric compounds, suggesting the conformational changes in this region are specific to ligand function. Interpretation of these results within the framework of current models of 5-HT3 and Cys-loop mechanisms are used to expand the understanding of how ligand binding in Cys-loop receptors relates to channel gating. SIGNIFICANCE STATEMENT: The 5-HT3 receptor is an important ligand-gated ion channel and drug target in the central and peripheral nervous system. Determining how ligand binding induced conformational changes in the receptor is central for understanding the structural mechanisms underlying 5-HT3 receptor function. Here, we employ voltage-gated fluorometry to characterize conformational changes in the extracellular domain of the human 5-HT3 receptor to identify intrareceptor motions during binding of a range of 5-HT3 receptor agonists and antagonists.

Acid-Regulated Switching of Metal Cation and Anion Guest Binding in Halogen-Bonding Rotaxanes.

The ability of natural enzymes to regulate their guest binding affinities and preferences through the use of co-ligands which alter the features of the binding site is fundamental to biological homeostatic control. Herein, the rarely exploited orthosteric control of guest binding is demonstrated using neutral halogen bonding [2]rotaxanes, in which a chemical stimulus (acid) interacting with the interlocked host binding site switches the host's native guest preference from metal cations to anions. When neutral, the rotaxanes exhibit pronounced transition metal cation affinity and comparatively weak anion binding properties. However, the addition of acid attenuates the rotaxanes' ability to coordinate cations, while concurrently enabling strong binding of halides through charge assisted halogen bonding and hydrogen bonding interactions in competitive aqueous solvent media. The appendage of a fluorescent anthracene reporter group to the rotaxane framework also enables diagnostic sensory responses to cation/anion binding.

Red-Emitting Fluorescent Probe for Detection of γ-Glutamyltranspeptidase and Its Application of Real-Time Imaging under Oxidative Stress in Cells and in Vivo.

γ-Glutamyltranspeptidase (GGT) plays critical roles in regulating various physiological/pathophysiological processes including the intracellular redox homeostasis. However, an effective fluorescent probe for dissecting the relationships between GGT and oxidative stress in vivo remains largely unexplored. Herein, we present a light-up fluorescent probe (DCDHF-Glu) with long wavelength emission (613 nm) for the highly sensitive and selective detection of GGT using dicyanomethylenedihydrofuran derivative as the fluorescent reporter and γ-glutamyl group as the enzyme-active trigger. DCDHF-Glu is competent to real-time image endogenous GGT in live cells and mice. In particular, DCDHF-Glu enables the direct real-time visualization of the upregulation of GGT under drug-induced oxidative stress in the HepG2 cells and the LO2 cells, as well as in vivo, vividly implying its excellent capacity in elucidation of GGT function in GGT-related biological events.

A new fluorescent chemosensor for cadmium(II) based on a pyrene-appended piperidone derivative and its β-cyclodextrin complex.

We report, in this article, a piperidin-4-one derivative carrying pyrenyl fluorescent reporter groups which acts as a Cd2+ ion sensor. The compound is synthesized and characterized using IR and NMR spectral techniques. The compound forms an inclusion complex with β-cyclodextrin. It selectively binds to Cd2+ ions in water and aqueous β-cyclodextrin media. The stoichiometry of the host-guest complex of the compound with β-cyclodextrin is 1:2. The ligand-metal ion binding stoichiometry is 1:1 both in water and in β-cyclodextrin. The linear concentration range of detection of the metal ion is reported. Cyclodextrin complex formation does not affect the metal ion selectivity of the compound.

Fluorescent nanoparticle sensors with tailor-made recognition units and proximate fluorescent reporter groups

Molecular imprinting in micelles followed by covalent modification of the binding pocket yielded fluorescent sensors with precisely constructed binding pockets.

Fluorescent Agonists of the α7 Nicotinic Acetylcholine Receptor Derived from 3‐Amino‐Quinuclidine

Here, we investigated whether fluorescence labeled small molecule agonists of the α7 nicotinic acetylcholine receptor (nAChR) might be identified to enhance receptor studies. Enantiomerically pure 3‐amino‐quinuclidines appended with fluorophores at the 3‐amino group were synthesized and tested by electrophysiology on human α7 nAChR in Xenopus oocytes, uncovering (R)‐4 and (R)‐9 as the first examples of fluorescent α7 nAChR agonists. These molecules elegantly incorporate the fluorescent reporter group as part of the pharmacophore itself and provide a new class of tool compounds for the study of these ligand‐gated ion channels.

Computational modeling of acrylodan-labeled cAMP dependent protein kinase catalytic subunit unfolding

Structure of the cAMP-dependent protein kinase catalytic subunit, where the asparagine residue 326 was replaced with acrylodan-cystein conjugate to implement this fluorescence reporter group into the enzyme, was modeled by molecular dynamics (MD) method and the positioning of the dye molecule in protein structure was characterized at temperatures 300K, 500K and 700K. It was found that the acrylodan moiety, which fluorescence is very sensitive to solvating properties of its microenvironment, was located on the surface of the native protein at 300K that enabled its partial solvation with water. At high temperatures the protein structure significantly changed, as the secondary and tertiary structure elements were unfolded and these changes were sensitively reflected in positioning of the dye molecule. At 700K complete unfolding of the protein occurred and the reporter group was entirely expelled into water. However, at 500K an intermediate of the protein unfolding process was formed, where the fluorescence reporter group was directed towards the protein interior and buried in the core of the formed molten globule state. This different positioning of the reporter group was in agreement with the two different shifts of emission spectrum of the covalently bound acrylodan, observed in the unfolding process of the protein.

Sialic Acid-Imprinted Fluorescent Core-Shell Particles for Selective Labeling of Cell Surface Glycans.

The expression of cell surface glycans terminating with sialic acid (SA) residues has been found to correlate with various disease states there among cancer. We here report a novel strategy for specific fluorescence labeling of such motifs. This is based on sialic acid-imprinted core-shell nanoparticles equipped with nitrobenzoxadiazole (NBD) fluorescent reporter groups allowing environmentally sensitive fluorescence detection at convenient excitation and emission wavelengths. Imprinting was achieved exploiting a hybrid approach combining reversible boronate ester formation between p-vinylphenylboronic acid and SA, the introduction of cationic amine functionalities, and the use of an NBD-appended urea-monomer as a binary hydrogen-bond donor targeting the SA carboxylic acid and OH functionalities. The monomers were grafted from 200 nm RAFT-modified silica core particles using ethylene glycol dimethacrylate (EGDMA) as cross-linker resulting in a shell thickness of ca. 10 nm. The particles displayed strong affinity for SA in methanol/water mixtures (K = 6.6 × 10(5) M(-1) in 2% water, 5.9 × 10(3) M(-1) in 98% water, B(max) ≈ 10 μmol g(-1)), whereas binding of the competitor glucuronic acid (GA) and other monosaccharides was considerably weaker (K (GA) = 1.8 × 10(3) M(-1) in 98% water). In cell imaging experiments, the particles selectively stained different cell lines in correlation with the SA expression level. This was further verified by enzymatic cleavage of SA and by staining using a FITC labeled SA selective lectin.

Kinetics of the ATP and dATP-mediated formation of a functionally-active RecA-ssDNA complex

The kinetics of the ATP and dATP-mediated formation of a functionally-active RecA-ssDNA complex were examined by stopped-flow fluorescence spectroscopy, using a modified version of the RecA protein that contains a fluorescent reporter group in the ssDNA binding site. The results indicated that: i) an active RecA-ssDNA complex was formed more rapidly on dT200 than on dT50 when either ATP or dATP was provided as the nucleotide cofactor, and ii) active complex formation occurred more rapidly with dATP than with ATP on either dT50 or dT200. The dependence on both the identity of the nucleotide cofactor and the length of the ssDNA effector indicated that active complex formation occurs by a cooperative mechanism and that dATP is more effective than ATP in mediating the interactions between RecA monomers that drive this process. Interestingly, the time courses of dATP-mediated active complex formation were closely similar to those that were obtained with ATPγS, an effectively non-hydrolyzable ATP analog that strongly stabilizes the active conformation of the RecA-ssDNA complex. These results provide mechanistic insight into the enhanced ssDNA binding and DNA strand exchange activities that are observed when dATP is provided in place of ATP in RecA biochemical assays.

Synthesis of phospholipids on a glyceric acid scaffold: design and preparation of phospholipase A2 specific substrates

Synthesis of a new series of phospholipid analogues to serve as activity-based probes of secretory phospholipase A2 enzymes is reported. The synthesis is based upon (1) preparation of long-chain esters and amides of glyceric acid, followed by (2) regioselective derivatization of the diol function of the molecule to achieve phosphorylation at the primary hydroxyl group, and to introduce the incipient sn-2-ester group of the target compounds. The sequence has been shown to allow incorporation of fluorescent, paramagnetic, and redox-active reporter groups, leading to phospholipid analogues applicable to detect and measure enzyme activity, to develop highly specific, real-time spectroscopic assay of phospholipase A2 enzymes, as well as to track the metabolic fate of the hydrolysis products. The synthetic method has a great deal of flexibility to open the way to the design and synthesis of activity-probes for other phospholipid metabolizing enzymes as well.