In-Plate Chemical Synthesis of Isopeptide-Linked SUMOylated Peptide Fluorescence Polarization Reagents for High-Throughput Screening of SENP Preferences.

Small ubiquitin-like modifiers (SUMOs) are conjugated to protein substrates in cells to regulate their function. The attachment of SUMO family members SUMO1-3 to substrate proteins is reversed by specific isopeptidases called SENPs (sentrin-specific protease). Whereas SENPs are SUMO-isoform or linkage type specific, comprehensive analysis is missing. Furthermore, the underlying mechanism of SENP linkage specificity remains unclear. We present a high-throughput synthesis of 83 isopeptide-linked SUMO-based fluorescence polarization reagents to study enzyme preferences. The assay reagents were synthesized via a native chemical ligation-desulfurization protocol between 11-mer peptides containing a γ-thiolysine and a SUMO3 thioester. Subsequently, five recombinantly expressed SENPs were screened using these assay reagents to reveal their deconjugation activity and substrate preferences. In general, we observed that SENP1 is the most active and nonselective SENP while SENP6 and SENP7 show the least activity. Furthermore, SENPs differentially process peptides derived from SUMO1-3, who form a minimalistic representation of diSUMO chains. To validate our findings, five distinct isopeptide-linked diSUMO chains were chemically synthesized and proteolysis was monitored using a gel-based read-out.

Development of fluorescent dual-FRET probe for simultaneous detection of caspase-8 and caspase-9 activities and their relative quantification.

A multi-FRET three-fluorophore probe containing coumarin, fluorescein and rhodamine B with two enzymatically cleavable linkers has been synthesized and optimized for the simultaneous activity detection and relative quantification of two proteases - caspase-8 and caspase-9. The probe designed as a ratiometric single-excitation triple-emission system shows specific change in fluorescence intensities upon enzymatic cleavage of individual linkers in model mixtures as well as in a cell lysate. The activation of caspase-8 and caspase-9 is responsible for initiation of extrinsic or intrinsic apoptotic pathway, respectively, and the probe was proposed as a single chemical tool which could help to decipher a mechanism of cell death induced by various stimuli. The main advantage of this probe is the simplicity of its preparation using conventional organic synthesis, easy application for measurement and evaluation of the results.

Synthesis and characterization of a fluorescent steroid dimer linked through C-19 by a 1,4-Bis(phenylethynyl)phenylene fragment.

The synthesis and characterization of a dimer in which two nuclei of 3ß-acetoxy-19-hydroxyandrost-5-en-17-one are linked by the fluorescent 1,4-bis(phenylethynyl)phenylene bridge attached to the oxygenated functions at positions C-19 of each steroid fragment is described. The compound was obtained in five steps and 23 % overall yield and showed a strong blue emission with a quantum yield of 0.66.

An indole-based fluorescent chemosensor targeting the autophagosome.

Autophagy is a process for the degradation and recycling of intracellular components and dysfunctional organelles. We developed an indole-embedded fluorescent naphthalimide for the selective imaging of autophagosomes in live cells. It was shown as intense puncta in the fluorescence confocal images and co-localizes with an autophagosome marker, LC3-RFP. In addition, it was applied to cellular autophagic models based on ER stress and starvation to verify its capability.

A specific esterase and pH logically regulate ESIPT: different kinds of granulocyte sorting.

Simultaneously detecting naphthol AS-D chloroacetate esterase (NAS-DCE) and pH is an effective way to separate different granulocytes, which is of great significance for the analysis of blood. A series of fluorescent small molecules (HBT-ASDs) were designed, whose ESIPT process could be logically regulated by NAS-DCE and pH. One typical molecule, HBT-ASD-2, emits three kinds of fluorescence output signal at 438 nm and 545 nm for NAS-DCE under different pH values (5.0, 7.4 and 10, respectively). According to such differential signals, the acid, neutrophil and alkaline granulocytes can be sorted, and the activity of NAS-DCE can also be simultaneously monitored in real-time. Thus, a simple analytical tool for clinical blood monitoring and analysis is provided.

Optical Study of Solvatochromic Isocyanoaminoanthracene Dyes and 1,5-Diaminoanthracene.

Isocyanoaminoarenes (ICAAr-s) are a novel and versatile group of solvatochromic fluorophores. Despite their versatile applicability, such as antifungals, cancer drugs and analytical probes, they still represent a mostly unchartered territory among intramolecular charge-transfer (ICT) dyes. The current paper describes the preparation and detailed optical study of novel 1-isocyano-5-aminoanthrace (ICAA) and its N-methylated derivatives along with the starting 1,5-diaminoanthracene. The conversion of one of the amino groups of the diamine into an isocyano group significantly increased the polar character of the dyes, which resulted in a significant 50-70 nm (2077-2609 cm-1) redshift of the emission maximum and a broadened solvatochromic range. The fluorescence quantum yield of ICAAs is strongly influenced by the polarity of the solvent. The starting anthracene-diamine is highly fluorescent in every solvent (√f = 12-53%), while the isocyano derivatives are practically nonfluorescent in solvents more polar than dioxane. This phenomenon implies the potential application of ICAAs to probe the polarity of the medium and is favorable in practical applications, such as cell-staining, resulting in a reduced background fluorescence. The ICT character of the emission states of ICAAs are in good agreement with the computational findings presented in TD-DFT calculations and molecular electrostatic potential (MESP) isosurfaces.

Harnessing an emissive guanine surrogate to design small-molecule fluorescent chemosensors of O6-methylguanine-DNA-methyltransferase (MGMT).

The fluorescence properties of an emissive guanine surrogate, thienoguanine (thGN, 2-aminothieno[3,4-d]pyrimidin-4(3H)-one), were exploited to design two real-time chemosensors of O6-methylguanine-DNA-methyltransferase (MGMT), a key DNA repair enzyme involved in the resistance to DNA-alkylating anti-cancer drugs though direct reversal of O6-alkylated guanine adducts.

Sustainable and Green Synthesis of Waste-Biomass-Derived Carbon Dots for Parallel and Semi-Quantitative Visual Detection of Cr(VI) and Fe3.

Carbon dot (CD)-based multi-mode sensing has drawn much attention owing to its wider application range and higher availability compared with single-mode sensing. Herein, a simple and green methodology to construct a CD-based dual-mode fluorescent sensor from the waste biomass of flowers of wintersweet (FW-CDs) for parallel and semi-quantitative visual detection of Cr(VI) and Fe3+ was firstly reported. The FW-CD fluorescent probe had a high sensitivity to Cr(VI) and Fe3+ with wide ranges of linearity from 0.1 to 60 µM and 0.05 to 100 µM along with low detection limits (LOD) of 0.07 µM and 0.15 µM, respectively. Accordingly, the FW-CD-based dual-mode sensor had an excellent parallel sensing capacity toward Cr(VI) and Fe3+ with high selectivity and strong anti-interference capability by co-using dual-functional integration and dual-masking strategies. The developed parallel sensing platform was successfully applied to Cr(VI) and Fe3+ quantitative detection in real samples with high precision and good recovery. More importantly, a novel FW-CD-based fluorescent hydrogel sensor was fabricated and first applied in the parallel and semi-quantitative visual detection of Cr(VI) and ferrous ions in industrial effluent and iron supplements, further demonstrating the significant advantage of parallel and visual sensing strategies.

High-Affinity Ratiometric Fluorescence Probe Based on 6-Amino-2,2'-Bipyridine Scaffold for Endogenous Zn2+ and Its Application to Living Cells.

Zinc is an essential trace element involved in many biological activities; however, its functions are not fully understood. To elucidate the role of endogenous labile Zn2+, we developed a novel ratiometric fluorescence probe, 5-(4-methoxyphenyl)-4-(methylsulfanyl)-[2,2'-bipyridin]-6-amine (6 (rBpyZ)) based on the 6-amino-2,2'-bipyridine scaffold, which acts as both the chelating agent for Zn2+ and the fluorescent moiety. The methoxy group acted as an electron donor, enabling the intramolecular charge transfer state of 6 (rBpyZ), and a ratiometric fluorescence response consisting of a decrease at the emission wavelength of 438 nm and a corresponding increase at the emission wavelength of 465 nm was observed. The ratiometric probe 6 (rBpyZ) exhibited a nanomolar-level dissociation constant (Kd = 0.77 nM), a large Stokes shift (139 nm), and an excellent detection limit (0.10 nM) under physiological conditions. Moreover, fluorescence imaging using A549 human lung adenocarcinoma cells revealed that 6 (rBpyZ) had good cell membrane permeability and could clearly visualize endogenous labile Zn2+. These results suggest that the ratiometric fluorescence probe 6 (rBpyZ) has considerable potential as a valuable tool for understanding the role of Zn2+ in living systems.

Ratiometric Flapping Force Probe That Works in Polymer Gels.

Polymer gels have recently attracted attention for their application in flexible devices, where mechanically robust gels are required. While there are many strategies to produce tough gels by suppressing nanoscale stress concentration on specific polymer chains, it is still challenging to directly verify the toughening mechanism at the molecular level. To solve this problem, the use of the flapping molecular force probe (FLAP) is promising because it can evaluate the nanoscale forces transmitted in the polymer chain network by ratiometric analysis of a stress-dependent dual fluorescence. A flexible conformational change of FLAP enables real-time and reversible responses to the nanoscale forces at the low force threshold, which is suitable for quantifying the percentage of the stressed polymer chains before structural damage. However, the previously reported FLAP only showed a negligible response in solvated environments because undesirable spontaneous planarization occurs in the excited state, even without mechanical force. Here, we have developed a new ratiometric force probe that functions in common organogels. Replacement of the anthraceneimide units in the flapping wings with pyreneimide units largely suppresses the excited-state planarization, leading to the force probe function under wet conditions. The FLAP-doped polyurethane organogel reversibly shows a dual-fluorescence response under sub-MPa compression. Moreover, the structurally modified FLAP is also advantageous in the wide dynamic range of its fluorescence response in solvent-free elastomers, enabling clearer ratiometric fluorescence imaging of the molecular-level stress concentration during crack growth in a stretched polyurethane film.

Improved Cathepsin Probes for Sensitive Molecular Imaging.

Cysteine cathepsin proteases are found under normal conditions in the lysosomal compartments of cells, where they play pivotal roles in a variety of cellular processes such as protein and lipid metabolism, autophagy, antigen presentation, and cell growth and proliferation. As a consequence, aberrant localization and activity contribute to several pathologic conditions such as a variety of malignancies, cardiovascular diseases, osteoporosis, and other diseases. Hence, there is a resurgence of interest to expand the toolkit to monitor intracellular cathepsin activity and better ascertain their functions under these circumstances. Previous fluorescent activity-based probes (ABPs) that target cathepsins B, L, and S enabled detection of their activity in intact cells as well as non-invasive detection in animal disease models. However, their binding potency is suboptimal compared to the cathepsin inhibitor on which they were based, as the P1 positive charge was capped by a reporter tag. Here, we show the development of an improved cathepsin ABP that has a P1 positive charge by linking the tag on an additional amino acid at the end of the probe. While enhancing potency towards recombinant cathepsins, the new probe had reduced cell permeability due to additional peptide bonds. At a second phase, the probe was trimmed; the fluorophore was linked to an extended carbobenzoxy moiety, leading to enhanced cell permeability and superb detection of cathepsin activity in intact cells. In conclusion, this work introduces a prototype design for the next generation of highly sensitive ABPs that have excellent detection of cellular cathepsin activity.

Photoactivatable Fluorescent Tags for Dual-Modality Positron Emission Tomography Optical Imaging.

Fluorescent protein conjugates are vital tools in a wide range of scientific disciplines from basic biochemical research to applications in clinical pathology and intraoperative surgery. We report the synthesis and characterization of photoactivatable fluorophores (PhotoTags) based on the functionalization of coumarin, fluorescein, BODIPY, rhodamine B, and cyanine dyes with a photochemically active aryl azide group. Photochemical labeling experiments using human serum albumin produced fluorescent proteins in high yields under irradiation with ultraviolet light for <15 min. We also synthesized DFO-RhodB-PEG3-ArN3─a photoactivatable compound that can be radiolabeled with 89Zr for applications in optical imaging and positron emission tomography. One-pot 89Zr-radiolabeling and light-induced protein conjugation produced [89Zr]ZrDFO-RhodB-PEG3-azepin-trastuzumab. Proof-of-concept studies in vitro and in vivo confirmed that [89Zr]ZrDFO-RhodB-PEG3-azepin-trastuzumab is a potential dual-modality agent for detecting human epidermal growth factor receptor 2 (HER2/neu) expression. Overall, the PhotoTag technology represents a rapid, synthetically versatile, and user-friendly approach for generating novel protein conjugates.

Development and Characterization of a Fluorescent Ligand for Leukotriene B4 Receptor 2 in Cells and Tissues.

The leukotriene B4 receptor 2 (BLT2) is a G-protein coupled receptor activated by 12(S)-hydroxyheptadeca-5Z,8E,10E-trienoic acid (12-HHT), which has been proposed as a promising therapeutic target for diabetic wound healing and gastrointestinal lesions. In this study, the rational design of a fluorescent probe based on the synthetic BLT2 agonist CAY10583 is described. The synthesis of several derivatives of CAY10583 coupled to fluorescein resulted in a traceable ligand suitable for different fluorescence-based techniques. An HTRF-based displacement assay (Tag-lite) on stably transfected CHO-K1 cells was developed to characterize binding properties of diverse BLT2 ligands. Highly specific binding to the BLT2 receptor was demonstrated in staining experiments on mouse skin tissue, and specific modulation of BLT2-induced cAMP signaling provided further evidence for receptor binding and ligand functionality. In conclusion, the fluorescent ligands developed in this study are suitable to investigate the pharmacology of BLT2 receptor ligands in a variety of assay systems.

Guest-host doped strategy for constructing ultralong-lifetime near-infrared organic phosphorescence materials for bioimaging.

Organic near-infrared room temperature phosphorescence materials have unparalleled advantages in bioimaging due to their excellent penetrability. However, limited by the energy gap law, the near-infrared phosphorescence materials (>650 nm) are very rare, moreover, the phosphorescence lifetimes of these materials are very short. In this work, we have obtained organic room temperature phosphorescence materials with long wavelengths (600/657-681/732 nm) and long lifetimes (102-324 ms) for the first time through the guest-host doped strategy. The guest molecule has sufficient conjugation to reduce the lowest triplet energy level and the host assists the guest in exciton transfer and inhibits the non-radiative transition of guest excitons. These materials exhibit good tissue penetration in bioimaging. Thanks to the characteristic of long lifetime and long wavelength emissive phosphorescence materials, the tumor imaging in living mice with a signal to background ratio value as high as 43 is successfully realized. This work provides a practical solution for the construction of organic phosphorescence materials with both long wavelengths and long lifetimes.

Catalytic Activation of Bioorthogonal Chemistry with Light (CABL) Enables Rapid, Spatiotemporally Controlled Labeling and No-Wash, Subcellular 3D-Patterning in Live Cells Using Long Wavelength Light.

Described is the spatiotemporally controlled labeling and patterning of biomolecules in live cells through the catalytic activation of bioorthogonal chemistry with light, referred to as "CABL". Here, an unreactive dihydrotetrazine (DHTz) is photocatalytically oxidized in the intracellular environment by ambient O2 to produce a tetrazine that immediately reacts with a trans-cyclooctene (TCO) dienophile. 6-(2-Pyridyl)dihydrotetrazine-3-carboxamides were developed as stable, cell permeable DHTz reagents that upon oxidation produce the most reactive tetrazines ever used in live cells with Diels-Alder kinetics exceeding k2 of 106 M-1 s-1. CABL photocatalysts are based on fluorescein or silarhodamine dyes with activation at 470 or 660 nm. Strategies for limiting extracellular production of singlet oxygen are described that increase the cytocompatibility of photocatalysis. The HaloTag self-labeling platform was used to introduce DHTz tags to proteins localized in the nucleus, mitochondria, actin, or cytoplasm, and high-yielding subcellular activation and labeling with a TCO-fluorophore were demonstrated. CABL is light-dose dependent, and two-photon excitation promotes CABL at the suborganelle level to selectively pattern live cells under no-wash conditions. CABL was also applied to spatially resolved live-cell labeling of an endogenous protein target by using TIRF microscopy to selectively activate intracellular monoacylglycerol lipase tagged with DHTz-labeled small molecule covalent inhibitor. Beyond spatiotemporally controlled labeling, CABL also improves the efficiency of "ordinary" tetrazine ligations by rescuing the reactivity of commonly used 3-aryl-6-methyltetrazine reporters that become partially reduced to DHTzs inside cells. The spatiotemporal control and fast rates of photoactivation and labeling of CABL should enable a range of biomolecular labeling applications in living systems.

Fluorescently labelled thioacetazone for detecting the interaction with Mycobacterium dehydratases HadAB and HadBC.

Thioacetazone (TAC) used to be a highly affordable, bacteriostatic anti-TB drug but its use has now been restricted, owing to severe side-effects and the frequent appearance of the TAC resistant M. tuberculosis strains. In order to develop new TAC analogues with fewer side-effects, its target enzymes need to be firmly established. It is now hypothesized that TAC, after being activated by a monooxygenase EthA, binds to the dehydratase complex HadAB that finally leads to a covalent modification of HadA, the main partner involved in dehydration. Another dehydratase enzyme, namely HadC in the HadBC complex, is also thought to be a possible target for TAC, for which definitive evidence is lacking. Herein, using a recently exploited azido naphthalimide template attached to thioacetazone and adopting a photo-affinity based labelling technique, coupled with electrophoresis and in-gel visualization, we have successfully demonstrated the involvement of these enzymes including HadBC along with a possible participation of an alternate mycobacterial monooxygenase MymA. In silico studies also revealed strong interactions between the TAC-probe and the concerned enzymes.

Identification of alternative protein targets of glutamate-ureido-lysine associated with PSMA tracer uptake in prostate cancer cells.

Prostate-specific membrane antigen (PSMA) is highly overexpressed in most prostate cancers and is clinically visualized using PSMA-specific probes incorporating glutamate-ureido-lysine (GUL). PSMA is effectively absent from certain high-mortality, treatment-resistant subsets of prostate cancers, such as neuroendocrine prostate cancer (NEPC); however, GUL-based PSMA tracers are still reported to have the potential to identify NEPC metastatic tumors. These probes may bind unknown proteins associated with PSMA-suppressed cancers. We have identified the up-regulation of PSMA-like aminopeptidase NAALADaseL and the metabotropic glutamate receptors (mGluRs) in PSMA-suppressed prostate cancers and find that their expression levels inversely correlate with PSMA expression and are associated with GUL-based radiotracer uptake. Furthermore, we identify that NAALADaseL and mGluR expression correlates with a unique cell cycle signature. This provides an opportunity for the future study of the biology of NEPC and potential therapeutic directions. Computationally predicting that GUL-based probes bind well to these targets, we designed and synthesized a fluorescent PSMA tracer to investigate these proteins in vitro, where it shows excellent affinity for PSMA, NAALADaseL, and specific mGluRs associated with poor prognosis.

A Double-Site Chemodosimeter for Selective Fluorescence Detection of a Nerve Agent Mimic.

A novel two-site chemodosimeter (SWJT-4) based on fluorescein skeleton to detect diethyl chlorophosphate (DCP) was designed and synthesized. It is a turn-on fluorescent probe for DCP with good selectivity and obvious color change in aqueous solution. Interestingly, the two oxime groups of SWJT-4 as dual response sites initiated different reactions with DCP to form a cyano group and an isoxazole ring, respectively. The corresponding mechanism was confirmed by 1H NMR, MS and DFT calculation. Moreover, SWJT-4 could be used as a fluorescent test paper to detect DCP vapor.

Color-changing fluorescent DNA probe containing solvatochromic Dansyl-nucleoside surrogate for sensing local variation of DNA duplex.

A novel Dansyl-nucleoside surrogate (Dns) based on (±)-trans-4-(hydroxymethyl) piperidin-3-ol was designed and synthesized. The Dns exhibited excellent solvatochromic properties. About 90 nm of red-shift accompanied color change from green to orange could be achieved with an increase of solvent polarity. The Dns was incorporated into oligodeoxynucleotide by phosphoroamidite chemistry. Two kinds of Dns-incorporated fluorescent DNA probes were designed and synthesized for sensing variation of DNA duplexes based on color-changing manner. As a result, the color-changing DNA probe not only can detect complementary oligonucleotide, but also can distinguish mismatch flanked in Dansyl/nucleobase pair by naked eye. Moreover, the change of fluorescence color of sample solutions could be captured by smartphone, and the photographs could be digitalized by image-processing software. Thus, the Dns-incorporated fluorescent DNA probe is expected to open the way to point-of-care assays in the future.

Fluorescent probes for targeting endoplasmic reticulum: design strategies and their applications.

Advances in developing organic fluorescent probes and fluorescence imaging techniques have enhanced our understanding of cell biology. The endoplasmic reticulum (ER) is a dynamic structure that plays a crucial role in protein synthesis, post-translational modifications, and lipid metabolism. The malfunction of ER contributes to several physiological and pathological conditions. Therefore, the investigations on the imaging and role of ER have attracted a lot of attention. Due to their simplicity, synthetic tunability, photostability, high quantum yields, easier cellular uptake, and lower cytotoxicity, organic fluorophores offer invaluable tools for the precision targeting of various cellular organelles and probe ER dynamics. The precision staining is made possible by incorporating specific functional groups having preferential and local organelle biomolecular interactions. For instance, functional moieties such as methyl sulfonamide, sulfonylurea, and pentafluorophenyl assist in ER targeting and thus have become essential tools to probe a deeper understanding of their dynamics. Furthermore, dual-function fluorescent probes that simultaneously image ER and detect specific physiological parameters or biological analytes were achieved by introducing special recognition or chemically reactive sites. This article attempts to comprehensively capture various design strategies currently employed by researchers utilizing small organic molecules to target the ER and detect specific analytes.