Near-infrared small molecular fluorescent dyes for photothermal therapy

This review aims to provide a summary of the progress in fluorescent dyes for photothermal therapy in recent years and it is classified according to the structure of organic molecules including cyanines, phthalocyanines, rhodamine analogues and BODIPYs.     

Photodynamic therapy based on organic small molecular fluorescent dyes

This review aims to provide a summary of the progress in organic small molecular fluorescent dyes for photodynamic therapy in recent years and it is classified according to the structures of dyes including cyanines, phthalocyanine, BODIPYs and other agents.     

Photodynamic therapy based on organic small molecular fluorescent dyes

Photodynamic therapy (PDT) has shown promise as an effective treatment modality for cancer and other localized diseases due to its noninvasive properties and spatiotemporal selectivity. Near-infrared (NIR) fluorescent dyes based on organic small molecules are characterized with low cytotoxicity, good biocompatibility and excellent phototoxicity, which are widely used in PDT. In this review, we attempt to summarize the development of imaging-induced PDT based on organic small molecules and classify it according to the structures of dyes including cyanines, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) analogues, phthalocyanine and other agents such as rhodamine analogues.     

Recent progress in small molecule fluorescent probes for nitroreductase

This review aims to provide a summary of the progress in fluorescent probes for nitroreductase (NTR) in recent years and displays the main fluorescent mechanisms that have been applied to design probes.     

Design strategy and bioimaging of small organic molecule multicolor fluorescent probes

Science China Chemistry - Multicolor fluorescent probes based on small organic molecules have the advantages of low cost, good biocompatibility, easily modifiable molecular structures and...     

Efficient synthesis of small molecule macroarrays: optimization of the macroarray synthesis platform and examination of microwave and conventional heating methods

We report a method for the efficient construction of small molecule macroarrays using microwave-assisted SPOT-synthesis. Macroarrays of 1,3-diphenylpropenones (chalcones) were synthesized rapidly and in high purity starting from robust, Wang-linker-derivatized planar supports. We have optimized the entire chalcone macroarray construction process and evaluated the efficiency and utility of microwave-assisted reactions in array synthesis. Microwave heating was found to be most beneficial for reactions that require temperatures greater than the boiling points of the solvents. These microwave-assisted conditions permitted straightforward access to macroarrays of 2,4,6-triarylpyridines derived from the original chalcone scaffold.     

Recent progress in two-photon small molecule fluorescent probes for enzymes

This review aims to provide a summary of the progress in TP small molecule fluorescent probes for enzymes in recent years and displays the main fluorescent mechanisms that have been applied to design probes.     

Recent progress in two-photon small molecule fluorescent probes for enzymes

Enzymes are macromolecular biological catalysts which can accelerate chemical reactions in living organisms. Almost all the physiological metabolism activities in the cell need enzymes to sustain life via rapid catalysis. Currently, medical research has proved that abnormal enzyme activity is associated with numerous diseases, such as Parkinson’s disease (PD), Alzheimer's disease (AD) and cancers. On the other hand, early diagnosis of those diseases is of great significance to improve the survival rate and cure rate. In the current diagnostic tools, two-photon fluorescent probes (TPFPs) are developing rapidly due to their unique advantages, such as higher spatial resolution, deeper imaging depth, and lower biotoxicity. Therefore, the design and synthesis of two-photon (TP) small molecule enzymatic probes have broad prospects for early diagnosis and treatment of diseases. As of now, scientists have developed many TP small molecule enzymatic probes. This review aims to summarize the TP small molecule enzymatic probes and expound the reaction mechanism.     

Electrophoretic mobility measurements of fluorescent dyes using on-chip capillary electrophoresis

We present an experimental study of the effect of pH, ionic strength, and concentrations of the electroosmotic flow (EOF)-suppressing polymer polyvinylpyrrolidone (PVP) on the electrophoretic mobilities of commonly used fluorescent dyes (fluorescein, Rhodamine 6G, and Alexa Fluor 488). We performed on-chip capillary zone electrophoresis experiments to directly quantify the effective electrophoretic mobility. We use Rhodamine B as a fluorescent neutral marker (to quantify EOF) and CCD detection. We also report relevant acid dissociation constants and analyte diffusivities based on our absolute estimate (as per Nernst-Einstein diffusion). We perform well-controlled experiments in a pH range of 3-11 and ionic strengths ranging from 30 to 90 mM. We account for the influence of ionic strength on the electrophoretic transport of sample analytes through the Onsager and Fuoss theory extended for finite radii ions to obtain the absolute mobility of the fluorophores. Lastly, we briefly explore the effect of PVP on adsorption-desorption dynamics of all three analytes, with particular attention to cationic R6G.     

Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches

Essential for viral replication and highly conserved among poxviridae, the vaccinia virus I7L ubiquitin-like proteinase (ULP) is an attractive target for development of smallpox antiviral drugs. At the same time, the I7L proteinase exemplifies several interesting challenges from the rational drug design perspective. In the absence of a published I7L X-ray structure, we have built a detailed 3D model of the I7L ligand binding site (S2-S2' pocket) based on exceptionally high structural conservation of this site in proteases of the ULP family. The accuracy and limitations of this model were assessed through comparative analysis of available X-ray structures of ULPs, as well as energy based conformational modeling. The 3D model of the I7L ligand binding site was used to perform covalent docking and VLS of a comprehensive library of about 230,000 available ketone and aldehyde compounds. Out of 456 predicted ligands, 97 inhibitors of I7L proteinase activity were confirmed in biochemical assays ( approximately 20% overall hit rate). These experimental results both validate our I7L ligand binding model and provide initial leads for rational optimization of poxvirus I7L proteinase inhibitors. Thus, fragments predicted to bind in the prime portion of the active site can be combined with fragments on non-prime side to yield compounds with improved activity and specificity.     

Discovery of an entropically-driven small molecule streptavidin binder from nucleic acid-encoded libraries

Dehydrocholic acid was identified as a selective streptavidin binder from a PNA-tagged library. Isothermal calorimetry titration measurements showed this interaction to be entropically driven. Peptides tagged with dehydrocholic acid can be captured on a streptavidin resin and released under thermal conditions.     

Discovery of a potent small molecule IL-2 inhibitor through fragment assembly

Using a site-directed fragment discovery method called tethering, we have identified a 60 nM small molecule antagonist of a cytokine/receptor interaction (IL-2/IL2Ralpha) with cell-based activity. Starting with a low micromolar hit, we employed a combination of tethering, structural biology, and computational analysis to design a focused set of 20 compounds. Eight of these compounds were at least 5-fold more active than the original hit. One of these compounds showed a 50-fold enhancement and represents the highest affinity inhibitor reported against this protein-protein target class. This method of coupling selected fragments with a low micromolar hit shows great potential for generating high-affinity lead compounds.     

Subcellular localised small molecule fluorescent probes to image mobile Zn2+

Zn²⁺, as the second most abundant d-block metal in the human body, plays an important role in a wide range of biological processes, and the dysfunction of its homeostasis is related to many diseases, including Type 2 diabetes, Alzheimer''s disease and prostate and breast cancers. Small molecule fluorescent probes, as effective tools for real-time imaging, have been widely used to study Zn²⁺ related processes. However, the failure to control their localisation in cells has limited their utility somewhat, as they are generally incapable of studying individual processes in a specific cellular location. This perspective presents an overview of the recent developments in specific organelle localised small molecule fluorescent Zn²⁺ probes and their application in biological milieu, which could help to extend our understanding of the mechanisms that cells use to respond to dysfunction of zinc homeostasis and its roles in disease initiation and development.

A number of recently developed subcellular localised small molecule fluorescent probes to image mobile Zn²⁺ are reviewed in this perspective.     

Synthesis of fluorescent rhodamine dyes using an extension of the Heck reaction

Both benzo[b]thiophene and indole containing rhodamine dyes were synthesized according to a new pathway requiring a Heck-type coupling and a Pictet-Spengler reaction. The electron-rich indolic dye was shown to have noteworthy absorption and emission maximum.     

Spectroscopic studies of fluorescent perylene dyes

The lowest electronic transition of the fluorescent perylene dye bis-(3,5-di-tertbutylphenyl)-perylene-3, 4:9,10-biscarboximide has been investigated b     

Kinetics of small molecule adsorption studied using precision ellipsometry

On the basis of a miniature polarisation modulator, a precision ellipsometry system has been made, enabling real-time measurement of subnanometre thin layers on reflecting substrates. This system monitored the kinetics of adsorption and desorption of propanol, or ethanol, or methanol on oxidised Si substrates. While adsorption of propanol and ethanol increased the thickness, adsorption of methanol showed surprising kinetics: the thickness first increased, then decreased. To explain this, a model of substitutional (or competitive) adsorption has been used, where the target molecule is adsorbed only when it substitutes another one leaving an adsorption site. The model fits the experimental data quantitatively and can predict processes involving several components on solid surfaces. Precision ellipsometry demonstrated its high analytical potential in investigation of surfaces at molecular level.     

Quantitative inhibitor fingerprinting of metalloproteases using small molecule microarrays

Current methods to identify interactions on small molecule microarrays (SMMs) introduce false positives that are difficult to dissect from the "real" binding events without tedious downstream re-evaluation. To specifically elucidate only activity-dependent ligand binding interactions, we have developed a technique that can be universally applied to present SMM systems. Our method makes use of a dual-color application strategy and is based on the simultaneous application of differentially treated samples. Overcoming the limitations of slide-to-slide variation, this method directly revealed activity-dependent interactions through a one-step application of protein samples on SMMs. Besides providing lead molecules for further development, the high-throughput screening results confer activity-dependent fingerprints for quantitative characterization and differentiation of proteins. The procedure was tested using a synthetic hydroxamate peptide library with 1400 discrete sequences permuted combinatorially across P1', P2', and P3' positions. Functional profiling across a panel of metalloproteases provided 44,800 datapoints within just eight SMM slides. These data were globally analyzed for activities, specificity, potency, and hierarchical clustering providing unique insights into inhibitor design and preference within this group of enzymes. Quantitative K(D) measurements performed on SMMs using one of the enzymes in the panel, Anthrax Lethal Factor, the toxic component of a notorious bioterror agent, unraveled several lead micromolar binders for further development. Overall, the effectiveness of the SMM platform is shown to be enhanced and extended using the strategy presented in this work.     

7-Triazolylcoumarin-based fluorescent tag system for stepwise,comparative assessment of small molecule microarrays

The potential use of a fluorescent tag system based on 7-(1H-1,2,3-triazol-4-yl)coumarin fluorophore having a fluorous moiety and a polyethylene glycol (PEG) spacer at opposite ends as a tool for a stepwise and comparative evaluation of the fabrication process of small molecule microarrays was illustrated by the qualitative analysis of the results of the fluorescence detection obtained from the microarray experiments using the tagged biotins and streptavidin-Cy3 (and avidin-Cy5) as the binding partners.     

Towards highly fluorescent and water-soluble perylene dyes

A systematic approach towards highly fluorescent, water-soluble perylene-3,4:9,10-tetracarboxylic acid diimide chromophores is presented. Water solubility was introduced first through the attachment of four hydrophilic substituents onto the bay region of the perylene dye. Positively and negatively charged groups were then applied to the chromophore, and their number and their distance from the aromatic scaffold were systematically varied. To suppress aggregation, the chromophore was further isolated within a dendritic shell. Such variation of structural features and a thorough investigation of the resulting optical properties facilitated the first synthesis of perylene-3,4:9,10-tetracarboxylic acid diimides combining the properties of water solubility and fluorescence quantum yields (FQYs) close to unity, which makes them attractive as high-performance fluorescence probes in aqueous media.