High‐Throughput Development of a Hybrid‐Type Fluorescent Glutamate Sensor for Analysis of Synaptic Transmission

Fluorescent sensors are powerful tools for visualizing cellular molecular dynamics. We present a high‐throughput screening system, designated hybrid‐type fluorescence indicator development (HyFInD), to identify optimal position‐specific fluorophore labeling in hybrid‐type sensors consisting of combinations of ligand‐binding protein mutants with small molecular fluorophores. We screened sensors for glutamate among hybrid molecules obtained by the reaction of four cysteine‐reactive fluorescence probes with a set of cysteine‐scanning mutants of the 274 amino acid S1S2 domain of AMPA‐type glutamate receptor GluA2 subunit. HyFInD identified a glutamate‐responsive probe (enhanced glutamate optical sensor: eEOS) with a dynamic range >2400 %, good photostability, and high selectivity. When eEOS was specifically tethered to neuronal surfaces, it reliably visualized the spatiotemporal dynamics of glutamate release at single synapses, revealing synapse‐to‐synapse heterogeneity of short‐term plasticity.     

A FRET Probe for Cell‐Based Imaging of Ganglioside‐Processing Enzyme Activity and High‐Throughput Screening

Gangliosides are important signaling molecules in the cell membrane and are processed by several enzymes. Deficiencies in these enzymes can cause human lysosomal storage diseases. Building an understanding of the pathways of glycosphingolipid catabolism requires methods for the analysis of these enzymatic activities A GM3‐derived FRET probe was synthesized chemoenzymatically for the detection and quantitation of a range of ganglioside‐degrading enzymes, both in cell lysates and in living cells. This is the first substrate that enables the ratiometric fluorogenic assay of sphingolipid ceramide N‐deacylase and endoglycoceramidase and can detect and localize neuraminidase activity in living cells. It is therefore a valuable tool for building a better understanding of membrane‐confined enzymology. It also enables the robust and reliable assay of ganglioside‐degrading enzymes in a microtiter plate, thus opening the door to screening for novel or engineered biocatalysts or for new inhibitors.     

A Quadruplex‐Based,Label‐Free,and Real‐Time Fluorescence Assay for RNase H Activity and Inhibition

We demonstrate a unique quadruplex‐based fluorescence assay for sensitive, facile, real‐time, and label‐free detection of RNase H activity and inhibition by using a G‐quadruplex formation strategy. In our approach, a RNA–DNA substrate was prepared, with the DNA strand designed as a quadruplex‐forming oligomer. Upon cleavage of the RNA strand by RNase H, the released G‐rich DNA strand folds into a quadruplex in the presence of monovalent ions and interacts with a specific G‐quadruplex binder, N‐methyl mesoporphyrin IX (NMM); this gives a dramatic increase in fluorescence and serves as a reporter of the reaction. This novel assay is simple in design, fast in operation, and is more convenient and promising than other methods. It takes less than 30 min to finish and the detection limit is much better or at least comparable to previous reports. No sophisticated experimental techniques or chemical modification for either RNA or DNA are required. The assay can be accomplished by using a common spectrophotometer and obviates possible interference with the kinetic behavior of the catalysts. Our approach offers an ideal system for high‐throughput screening of enzyme inhibitors and demonstrates that the structure of the G‐quadruplex can be used as a functional tool in specific fields in the future.     

Ratiometric and Near‐Infrared Molecular Probes for the Detection and Imaging of Zinc Ions

The detection and imaging of Zn²⁺ in biological samples are of paramount interest owing to the role of this cation in physiological functions. This is possible only with molecular probes that specifically bind to Zn²⁺ and result in changes in emission properties. A “turn‐on” emission or shift in the emission color upon binding to Zn²⁺ should be ideal for in vivo imaging. In this context, ratiometric and near‐IR probes are of particular interest. Therefore, in the area of chemosensors or molecular probes, the design of fluorophores that allow ratiometric sensing or imaging in the near‐IR region is attracting the attention of chemists. The purpose of this Focus Review is to highlight recent developments in this area and stress the importance of further research for future applications.     

Synthesis of Privileged Scaffolds by Using Diversity‐Oriented Synthesis

An elegant reagent‐controlled strategy has been developed for the generation of a diverse range of biologically active scaffolds from a chiral bicyclic lactam. Reduction of the chiral lactam with LAH or alkylation with LHMDS to trigger different cyclization reactions have been shown to generate privileged scaffolds, such as pyrrolidines, indolines, and cyclotryptamines. Their amenability to substitution allows us to create various compound libraries by using these scaffolds. In silico studies were used to estimate the drug‐like properties of these compounds. Selected compounds were subjected to anticancer screening by using three different cell lines. In addition, all these compounds were subjected to antibacterial screening to gauge the spectrum of biological activity that was conferred by our DOS methodology. Gratifyingly, with no additional iterative cycles, our method directly generated anticancer compounds with potency at low nanomolar concentrations, as represented by spiroindoline 14 .     

Supramolecular Chemical Sensors Based on Pyrene Monomer–Excimer Dual Luminescence

The past ten years have seen a spectacular development of chemical sensors based on the monomer–excimer dual luminescence of aromatic systems, such as pyrene. Either in the form of integrated or multicomponent molecular devices these chemosensors have been attracting a high interest above all because of their unique ratiometric properties. This review will focus on the latter systems, which can be classified into two classes: Firstly, the assembly of receptor–effector conjugates is triggerred by the analyte of interest. As a result, the sensor shows monomer to excimer fluorescence switching upon substrate binding. Secondly, the supramolecular assembly that constitutes the sensor is perturbed by interaction with the analyte. This induces a conformational change or the exchange of a component of the system, which is the cause of the luminescence switch effect.     

Rapid Formation of Acrylated Microstructures by Microwave‐Induced Thermal Crosslinking

We present a rapid and highly efficient method to form microstructure of poly(ethylene glycol) (PEG)‐based acrylates by microwave‐induced thermal crosslinking. PEG‐based polymeric microstructures such as polymer microarrays and microwells were fabricated on 3‐(trimethoxysilyl)propyl methacrylate (TMSPMA)‐coated glass slides that were placed on top of a silicon wafer. In comparison to ultraviolet (UV) irradiation curing, microwave‐induced thermal crosslinking could be completed within 10 s, without thermal degradation or oxygen inhibition in the presence of ambient oxygen. Furthermore, the activation of surviving free radical impurities by microwave‐induced heating enabled crosslinking even without an exogenous radical initiator (e.g., 2,2′‐azosisobutyronitrile (AIBN)). This approach can be beneficial for fabricating various PEG‐based microstructures for high‐throughput screening assays, cell‐based biosensors, and biomedical microdevices.

     

Diversity‐oriented synthesis

Diversity‐oriented synthesis (DOS), which describes the synthesis of structurally diverse collections of small molecules, was developed, in part, to address combinatorial chemistry's shortfalls. In this paper, we hope to give an indication of what can be achieved using the DOS approach to library generation. We describe some of the most successful strategies utilized in DOS, with special focus on our own area of interest; DOS from simple, pluripotent starting materials. © 2008 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 8: 129–142; 2008: Published online in Wiley InterScience ( www.interscience.wiley.com ) DOI 10.1002/tcr.20144     

Discovery of Small‐Molecule Interleukin‐2 Inhibitors from a DNA‐Encoded Chemical Library

Libraries of chemical compounds individually coupled to encoding DNA tags (DNA‐encoded chemical libraries) hold promise to facilitate exceptionally efficient ligand discovery. We constructed a high‐quality DNA‐encoded chemical library comprising 30 000 drug‐like compounds; this was screened in 170 different affinity capture experiments. High‐throughput sequencing allowed the evaluation of 120 million DNA codes for a systematic analysis of selection strategies and statistically robust identification of binding molecules. Selections performed against the tumor‐associated antigen carbonic anhydrase IX (CA IX) and the pro‐inflammatory cytokine interleukin‐2 (IL‐2) yielded potent inhibitors with exquisite target specificity. The binding mode of the revealed pharmacophore against IL‐2 was confirmed by molecular docking. Our findings suggest that DNA‐encoded chemical libraries allow the facile identification of drug‐like ligands principally to any protein of choice, including molecules capable of disrupting high‐affinity protein–protein interactions.     

An Activity‐Based Sensing Approach for the Detection of Cyclooxygenase‐2 in Live Cells

Cyclooxygenase‐2 (COX‐2) overexpression is prominent in inflammatory diseases, neurodegenerative disorders, and cancer. Directly monitoring COX‐2 activity within its native environment poses an exciting approach to account for and illuminate the effect of the local environments on protein activity. Herein, we report the development of CoxFluor, the first activity‐based sensing approach for monitoring COX‐2 within live cells with confocal microscopy and flow cytometry. CoxFluor strategically links a natural substrate with a dye precursor to engage both the cyclooxygenase and peroxidase activities of COX‐2. This catalyzes the release of resorufin and the natural product, as supported by molecular dynamics and ensemble docking. CoxFluor enabled the detection of oxygen‐dependent changes in COX‐2 activity that are independent of protein expression within live macrophage cells.     

High‐Performance Quinoline‐Malononitrile Core as a Building Block for the Diversity‐Oriented Synthesis of AIEgens

In vivo fluorescent monitoring of physiological processes with high‐fidelity is essential in disease diagnosis and biological research, but faces extreme challenges due to aggregation‐caused quenching (ACQ) and short‐wavelength fluorescence. The development of high‐performance and long‐wavelength aggregation‐induced emission (AIE) fluorophores is in high demand for precise optical bioimaging. The chromophore quinoline‐malononitrile (QM) has recently emerged as a new class of AIE building block that possesses several notable features, such as red to near‐infrared (NIR) emission, high brightness, marked photostability, and good biocompatibility. In this minireview, we summarize some recent advances of our established AIE building block of QM, focusing on the AIE mechanism, regulation of emission wavelength and morphology, the facile scale‐up and fast preparation for AIE nanoparticles, as well as potential biomedical imaging applications.     

A Pyrene Derivative for Hg2+‐Selective Fluorescent Sensing and Its Application in In Vivo Imaging

An Hg²⁺‐selective fluorescent sensor ( 1 ) bearing pyrene as a fluorophore was synthesized. A sandwich‐stacking binding mode was formed during the binding process, which increased the excimer fluorescence 22‐fold at 490 nm. Compound 1 was successfully applied in in vivo imaging to trace the enrichment and distribution of mercury in the nervous system, digestive system, and reproductive system of Caenorhabditis elegans, as well as the organs of zebrafish.     

Tetrazole‐Based Probes for Integrated Phenotypic Screening,Affinity‐Based Proteome Profiling,and Sensitive Detection of a Cancer Biomarker

Target‐identification phenotypic screening has been a powerful approach in drug discovery; however, it is hindered by difficulties in identifying the underlying cellular targets. To address this challenge, we have combined phenotypic screening of a fully functionalized small‐molecule library with competitive affinity‐based proteome profiling to map and functionally characterize the targets of screening hits. Using this approach, we identified ANXA2, PDIA3/4, FLAD1, and NOS2 as primary cellular targets of two bioactive molecules that inhibit cancer cell proliferation. We further demonstrated that a panel of probes can label and/or image annexin A2 (a cancer biomarker) from different cancer cell lines, thus providing opportunities for potential cancer diagnosis and therapy.     

Ratiometric Single‐Nanoparticle Oxygen Sensors for Biological Imaging

It makes sense : Conjugated polymer nanoparticles doped with a platinum porphyrin dye exhibit bright phosphorescence that is highly sensitive to the concentration of molecular oxygen. The small size, extraordinary brightness, excellent sensitivity, and ratiometric emission, together with the demonstration of single‐particle sensing and cellular uptake, indicate the potential of the nanoparticle sensors for quantitative mapping of local molecular oxygen concentration.