Synthesis of N epsilon-(7-diethylaminocoumarin-3-carboxyl)- and N epsilon-(7-methoxycoumarin-3-carboxyl)-L-Fmoc lysine as tools for protease cleavage detection by fluorescence

Design, synthesis, and spectroscopic profiling of novel coumarin dyes: Investigating solvent sensitivity and photophysical properties

Coumarin dyes are highly versatile and widely employed as fluorescent chemosensors in a variety of fields, including molecular imaging, bioorganic chemistry, analytical chemistry, materials chemistry, biology, and medical science. Thanks to their outstanding photostability and high quantum yield, they represent an ideal choice for developing sensitive and selective sensing platforms. In this study, we successfully designed and synthesized four new dyes based on the coumarin dye molecular skeleton, investigating their solvent sensitivity and spectroscopic properties. Our novel coumarin dyes were synthesized by a straightforward approach, reacting coumarin-3-carboxylic acid succinimidyl ester derivatives with corresponding amines in 1,4-dioxane as a solvent. We carefully monitored the completion of the reactions using thin-layer chromatography (TLC) and characterized these dyes using spectral and elemental analyses. We further investigated the UV, fluorescence, time-correlated single photon counting (TCSPC) technique and time-resolved spectroscopy (TRES) of these dyes in different solvents and on polymer film poly(methyl methacrylate) (PMMA). The quantum yield of the synthesized dyes was determined, with values observed to range between 0.55 and 0.94. Most of the dye-solvent and dye-polymer combinations exhibited single exponential decay, with lifetimes ranging from 2.3 to 3 ns. Minor deviations from single exponential behavior were observed for most of the dyes in toluene, while significant deviations were observed for coumarin dyes with piperazine moiety. We have provided a rationalization of these results in terms of the chemical functionalities of the various dyes. Furthermore, we investigated the effect of interactions between 7-methoxy-2-oxo-N-(2-(piperazin-1-yl)ethyl)-2H-chromene-3-carboxamide and silica nanoparticles (Ludox) on the spectroscopic properties of these dyes, with charge transfer being one possible mechanism contributing to the behavior of the dyes. Additionally, we explored the effect of trifluoroacetic acid (TFA) on the dyes' emission intensity and fluorescence decay. Based on our UV and fluorescence measurements of the dyes in different solvents, we have concluded that these dyes can create excellent donor-acceptor pairs for our upcoming fluorescence resonance energy transfer (FRET) experiments.

New Azido Coumarins as Potential Agents for Fluorescent Labeling and Their "Click" Chemistry Reactions for the Conjugation with closo-Dodecaborate Anion

Novel fluorescent 7-methoxy- and 7-(diethylamino)-coumarins modified with azido-group on the side chain have been synthesized. Their photophysical properties and single crystals structure characteristics have been studied. In order to demonstrate the possibilities of fluorescent labeling, obtained coumarins have been tested with closo-dodecaborate derivative bearing terminal alkynyl group. Cu^I catalyzed Huisgen 1,3-dipolar cycloaddition reaction has led to fluorescent conjugates formation. The absorption-emission spectra of the formed conjugates have been presented. The antiproliferative activity and uptake of compounds against several human cell lines were evaluated.

Co-assembly of a multicomponent network of nanofiber-wrapped nanotubes

Strategies to create organized multicomponent nanostructures composed of discrete, self-sorted domains are important for developing materials that mimic the complexity and multifunctionality found in biological systems. These structures can be challenging to achieve due to the required balance of molecular self-recognition and supramolecular attraction needed between the components. Herein, we report a strategy to construct a two-component nanostructure via a hierarchical assembly process whereby two monomeric building blocks undergo self-sorting assembly at the molecular level followed by a supramolecular association to form a nanofiber-wrapped nanotube. The two molecules self-sorted into respective nanofiber and nanotube assemblies, yet assembly of the nanofibers in the presence of the nanotube template allowed for directed integration into a hierarchical multilayer structure via electrostatic interactions. The fiber-wrapped nanotube co-assembly was characterized using transmission electron microscopy (TEM), atomic force microscopy (AFM) and Förster resonance energy transfer (FRET) between the components. Strategies to co-assemble multicomponent nanostructures composed of discrete, spatially sorted domains with controllable higher level interactions will be critical for the development of novel, functionally competent nanomaterials.

Tagging synthetic polymers with coumarin group for study nucleic acid interaction with gene delivery agents

Polymeric amines and complex amine containing system are actively studied and applied as gene delivery agents in gene therapy and genetic engineering. Optimizing polymer – nucleic acid ratio is the key stage in elaboration of procedures in this area. Application of fluorescent tagged oligonucleotides is widespread approach which allows to visualize nucleic acid in gel electrophoresis experiments and to find conditions of the full binding of the nucleic acid. We suggest to use succinimidyl ester of 7-(diethylamino)coumarin-3-carboxylic acid as an agent for fluorescent labeling of polymeric amines and to use the tagged polymers in optimizing polymer – nucleic acid ratio. This approach allows to see unbound polymer and to study various nucleic acids in interaction with the same polymer.

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Labeling of gene delivery agents with fluorescence groups increases efficiency of optimization of gene delivery compositions.

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Polymeric amines tagged with succinimidyl ester of 7-(diethylamino)coumarin-3-carboxylic acid are suitable for study polymer – nucleic acid interaction with gel electrophoresis.

Diffusion of chiral molecules and propagation of structural chirality in anisotropic liquids

Diffusion in nature is usually considered as a smooth redistribution process. However, it appears that the diffusion of chiral molecules and the propagation of chirality may proceed in quite different ways. Indeed, in the present work, unexpected quantization of the spatial concentration of chiral molecules is discovered in self-aligned molecular liquids. It is shown that the interpenetration of two liquids is forming discrete diffusion barrier walls resulting in steplike concentration distribution of chiral molecules in space. The concentration gradient is at least an order of magnitude stronger from both sides of the barrier wall compared to the gradient between those walls. It is also shown that this microscopic diffusion process may be controlled by macroscopic boundary conditions imposed on the host molecular system. Both of those phenomena are related to the collective long-range orientational "elastic" interactions of molecules of the host. The observed phenomena may radically change our understanding of diffusion of chiral molecules, among others, in biological tissue, which contains many examples of self-aligned molecular liquids. This, in turn, has the potential to revolutionize drug design and delivery techniques.

A coumarin-labeled vinyl sulfone as tripeptidomimetic activity-based probe for cysteine cathepsins

A coumarin-tetrahydroquinoline hydride 8 was synthesized as a chemical tool for fluorescent labeling. The rigidified tricyclic coumarin structure was chosen for its suitable fluorescence properties. The connection of 8 with a vinyl sulfone building block was accomplished by convergent synthesis thereby leading to the coumarin-based, tripeptidomimetic activity-based probe 10, containing a Gly-Phe-Gly motif. Probe 10 was evaluated as inactivator of the therapeutically relevant human cysteine cathepsins S, L, K, and B: it showed particularly strong inactivation of cathepsin S. The detection of recombinant and native cathepsin S was demonstrated by applying 10 to in-gel fluorescence imaging.

Minimalist Approaches to Protein Labelling: Getting the Most Fluorescent Bang for Your Steric Buck

Fluorescence methods allow one to monitor protein conformational changes, protein–protein associations, and proteolysis in real time, at the single molecule level and in living cells. The information gained in such experiments is a function of the spectroscopic techniques used and the strategic placement of fluorophore labels within the protein structure. There is often a trade-off between size and utility for fluorophores, whereby large size can be disruptive to the protein’s fold or function, but valuable characteristics, such as visible wavelength absorption and emission or brightness, require sizable chromophores. Three major types of fluorophore readouts are commonly used: (1) Förster resonance energy transfer (FRET); (2) photoinduced electron transfer (PET); and (3) environmental sensitivity. This review focuses on those probes small enough to be incorporated into proteins during ribosomal translation, which allows the probes to be placed on the interiors of proteins as they are folded during synthesis. The most broadly useful method for doing so is site-specific unnatural amino acid (UAA) mutagenesis. We discuss the use of UAA probes in applications relying on FRET, PET, and environmental sensitivity. We also briefly review other methods of protein labelling and compare their relative merits to UAA mutagenesis. Finally, we discuss small probes that have thus far been used only in synthetic peptides, but which have unusual value and may be candidates for incorporation using UAA methods.

Activatable Optical Probes for the Detection of Enzymes

The early detection of many human diseases is crucial if they are to be treated successfully. Therefore, the development of imaging techniques that can facilitate early detection of disease is of high importance. Changes in the levels of enzyme expression are known to occur in many diseases, making their accurate detection at low concentrations an area of considerable active research. Activatable fluorescent probes show immense promise in this area. If properly designed they should exhibit no signal until they interact with their target enzyme, reducing the level of background fluorescence and potentially endowing them with greater sensitivity. The mechanisms of fluorescence changes in activatable probes vary. This review aims to survey the field of activatable probes, focusing on their mechanisms of action as well as illustrating some of the in vitro and in vivo settings in which they have been employed.

Synthesis and evaluation of self-calibrating ratiometric viscosity sensors

We describe the design, synthesis and fluorescent profile of a family of self-calibrating dyes that provide ratiometric measurements of fluid viscosity. The design is based on covalently linking a primary fluorophore (reference) that displays a viscosity-independent fluorescence emission with a secondary fluorophore (sensor) that exhibits a viscosity-sensitive fluorescence emission. Characterization of fluorescent properties was made with separate excitation of the units and through Resonance Energy Transfer from the reference to the sensor dye. The chemical structures of both fluorophores and the linker length have been evaluated in order to optimize the overall brightness and sensitivity of the viscosity measurements. We also present an application of such ratiometric dyes for the detection of membrane viscosity changes in a liposome model.

A Hg2+-selective chemodosimeter based on desulfurization of coumarin thiosemicarbazide in aqueous media

A fluorescence-enhanced chemodosimeter 1 based on coumarin thiosemicarbazide for Hg(2+) was developed via a Hg(2+)-induced desulfurization reaction. Spectroscopic results reveal that chemodosimeter 1 exhibits high sensitivity and selectivity for Hg(2+) in comparison to common interfering metal ions in aqueous media at room temperature.

Novel cyclopeptides for the design of MMP directed delivery devices: a novel smart delivery paradigm

PURPOSE

Matrix metalloproteinases (MMP) are a family of proteolytic enzymes, the expression of which in a key step of tumor progression has been better defined recently. The studies highlighted the ongoing need for very specific inhibitors, substrates or release devices designed to be selective for one or at least very few MMPs.

METHODS

This report deals with the design, synthesis and in vitro evaluation of linear and especially novel cyclic peptidic moieties, embodying MMP cleavable sequences designed to answer these questions. FRET (fluorescence resonance energy transfer) labelling via chromophore-modified amino-acids was used to give access to enzyme kinetics.

RESULTS

Evaluation of these peptides showed that cyclisation gives rise to high specificity for certain MMP, suggesting that this approach could provide very specific MMP substrate. Moreover, cyclic structures present a very good plasma stability.

CONCLUSIONS

These original derivatives could allow the design of MMP-controlled delivery devices, the specificity of which will be retained in complex biological media and in vivo.

Mechanism-based profiling of MMPs

The recognition that the successful clinical use of MMP inhibitors will require quantitative correlation of MMP activity with disease type, and to disease progression, has stimulated intensive effort toward the development of sensitive assay methods, improved analytical methods for the determination of the structural profile for MMP-sub-type inhibition, and the development of new methods for the determination - in both quantitative and qualitative terms - of MMP activity. This chapter reviews recent progress toward these objectives, with particular emphasis on the quantitative and qualitative profiling of MMP activity in cells and tissues. Quantitative determination of MMP activity is made from the concentration of the MMP from the tissue, using immobilization of a broad-spectrum MMP inhibitor on a chromatography resin. Active MMP, to the exclusion of MMP zymogens and endogenous TIMP-inhibited MMPs, is retained on the column. Characterization of the MMP sub-type(s) follows from appropriate analysis of the active MMP eluted from the resin. Qualitative determination of MMP involvement in disease can be made using an MMP sub-type-selective inhibitor. The proof of principle, with respect to this qualitative determination of the disease involvement of the gelatinase MMP-2 and MMP-9 sub-types, is provided by the class of thiirane-based MMP mechanism-based inhibitors (SB-3CT as the prototype). Positive outcomes in animal models of disease having MMP-2 and/or -9 dependency follow administration of this MMP inhibitor, whereas this inhibitor is inactive in disease models where other MMPs (such as MMP-14) are involved.

Aryldithioethyloxycarbonyl (Ardec): A New Family of Amine Protecting Groups Removable under Mild Reducing Conditions and Their Applications to Peptide Synthesis

The development of phenyldithioethyloxycarbonyl (Phdec) and 2-pyridyldithioethyloxycarbonyl (Pydec) protecting groups, which are thiol-labile urethanes, is described. These new disulfide-based protecting groups were introduced onto the epsilon-amino group of L-lysine; the resulting amino acid derivatives were easily converted into N alpha-Fmoc building blocks suitable for both solid- and solution-phase peptide synthesis. Model dipeptide(Ardec)s were prepared by using classical peptide couplings followed by standard deprotection protocols. They were used to optimize the conditions for complete thiolytic removal of the Ardec groups both in aqueous and organic media. Phdec and Pydec were found to be cleaved within 15 to 30 min under mild reducing conditions: i) by treatment with dithiothreitol or beta-mercaptoethanol in Tris.HCl buffer (pH 8.5-9.0) for deprotection in water and ii) by treatment with beta-mercaptoethanol and 1,8-diazobicyclo[5.4.0]undec-7-ene (DBU) in N-methylpyrrolidinone for deprotection in an organic medium. Successful solid-phase synthesis of hexapeptides Ac-Lys-Asp-Glu-Val-Asp-Lys(Ardec)-NH2 has clearly demonstrated the full orthogonality of these new amino protecting groups with Fmoc and Boc protections. The utility of the Ardec orthogonal deprotection strategy for site-specific chemical modification of peptides bearing several amino groups was illustrated firstly by the preparation of a fluorogenic substrate for caspase-3 protease containing the cyanine dyes Cy 3.0 and Cy 5.0 as FRET donor/acceptor pair, and by solid-phase synthesis of an hexapeptide bearing a single biotin reporter group.

Design, synthesis, and evaluation of original carriers for targeting vascular endothelial growth factor receptor interactions

PURPOSE

Angiogenesis is a key event in tumor growth and metastasis, chronic inflammatory disease, and cardiovascular disease. It is controlled by positive and negative regulators, which include vascular endothelial growth factor (VEGF) as the most active of these. VEGF/VEGF receptors are important targets not only for therapy but also for imaging. Based on the structural study of VEGF, we developed a novel cyclopeptide (cyclo-VEGI) that exhibits powerful antitumor properties. We herein report the design of novel molecules derived from cyclo-VEGI as potential targeting agents in cancer and other angiogenesis-related diseases.

METHODS

We performed selective chemical modification of the most active VEGF-derived cyclopeptide (cyclo-VEGI). Original hydrophilic linkers were synthesized and coupled to cyclo-VEGI. These reactions provide nanocarriers for delivery. The inhibitory effect of the different compounds on VEGF binding was evaluated in competition assays with 125I-VEGF. A fluorescent cyclo-VEGI peptide was synthezised to assess direct binding and internalization of cyclo-VEGI.

RESULTS

Chemical modifications of cyclo-VEGI do not diminish the biological activity of cyclo-VEGI as measured in competition assays; in fact, it is even increased. Moreover there is a strong cellular accumulation of the fluorescent-labeled cyclo-VEGI. Conjugates synthesized in this study may be useful leads to design delivery systems for targeting approaches in cancer and other angiogenesis-related diseases.

CONCLUSION

The modified cyclo-VEGIs may have a wide range of applications and represent a useful tool to develop delivery/carrier systems for therapeutic targeting or imaging.