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High-throughput assays for drug screening applications have to fulfill particular specifications. Besides the capability to identify even compounds with low potency, one of the major issues is to minimize the number of false-positive hits in a screening campaign in order to reduce the logistic effort for the subsequent cherry picking and confirmation procedure. In this respect, fluorescence lifetime (FLT) appears as an ideal readout parameter that is supposed to be robust against autofluorescent and light-absorbing compounds, the most common source of systematic false positives. The extraordinary fluorescence features of the recently discovered [1,3]dioxolo[4,5-f][1,3]benzodioxole dyes were exploited to develop an FLT-based binding assay with exceptionally robust readout. The assay setup was comprehensively validated and shown to comply not only with all requirements for a powerful high-throughput screening assay but also to be suitable to determine accurate binding constants for inhibitors against enzymes of the histone deacetylase family. Using the described binding assay, the first inhibitors against three members of this enzyme family from Pseudomonas aeruginosa were identified. The compounds were characterized in terms of potency and selectivity profile. The novel ligand probe should also be applicable to other homologues of the histone deacetylase family that are inhibited by N-hydroxy-N'-phenyloctandiamide.
Class IIa histone deacetylases (HDACs) show extremely low enzymatic activity and no commonly accepted endogenous substrate is known today. Increasing evidence suggests that these enzymes exert their effect rather through molecular recognition of acetylated proteins and recruiting other proteins like HDAC3 to the desired target location. Accordingly, class IIa HDACs like bromodomains have been suggested to act as “Readers” of acetyl marks, whereas enzymatically active HDACs of class I or IIb are called “Erasers” to highlight their capability to remove acetyl groups from acetylated histones or other proteins. Small-molecule ligands of class IIa histone deacetylases (HDACs) have gained tremendous attention during the last decade and have been suggested as pharmaceutical targets in several indication areas such as cancer, Huntington's disease and muscular atrophy. Up to now, only enzyme activity assays with artificial chemically activated trifluoroacetylated substrates are in use for the identification and characterization of new active compounds against class IIa HDACs. Here, we describe the first binding assay for this class of HDAC enzymes that involves a simple mix-and-measure procedure and an extraordinarily robust fluorescence lifetime readout based on [1,3]dioxolo[4,5-f]benzodioxole-based ligand probes. The principle of the assay is generic and can also be transferred to class I HDAC8.
A new class of fluorescent dyes based on 1,3-benzodioxole and [1,3]-dioxolo[4.5-f]benzodioxole
(2011)
We report on synthesis and photophysical properties of a new class of fluorescent dyes. They are characterized by large Stokes-shifts, long fluorescence lifetimes in organic solvents and a pronounced dependency of the fluorescence lifetime on the solvent polarity. Also worthy of note is the high bleaching stability. To provide access to biochemical and medical applications a series of derivatives were prepared, which exhibit specific reactivity towards different biologically relevant functional groups (carboxylic acids, amines, maleimides, N-hydroxysuccinimide esters). Furthermore, two alkynes were prepared, which could be used in 'Click' chemistry.
In the present study, we describe synthesis and photochemical behaviour of the coumarinylmethyl phenyl ethers 1 and 6-10. Irradiation of the compounds in polar solvents leads to o-, p- and m-hydroxybenzyl substituted coumarins as main products. A side reaction is the photosolvolysis of the ethers that gives the (coumarin-4-yl)methyl alcohol and the corresponding phenol. Detailed studies of the quantum yields and product distributions upon irradiation of 6 as a function of the solvents are indicative of a dominant role of an ionic pathway in photochemical conversions. The found photochemical rearrangement is a useful tool for the preparation of hydroxylated 4-benzylcoumarins. A series of such compounds have been synthesised.
An efficient route from myo- to neo-inositol is described. The key steps of the sequence are oxidation of the hydroxy group at C-5 to the corresponding ketone, followed by a highly (dr = 7.8:1) stereoselective reduction. The route includes nine steps with an overall yield of 51% and is therefore superior to all hitherto reported methods for the preparation of neo-inositol.
Different signal amplification strategies to improve the detection sensitivity of immunoassays have been applied which utilize enzymatic reactions, nanomaterials, or liposomes. The latter are very attractive materials for signal amplification because liposomes can be loaded with a large amount of signaling molecules, leading to a high sensitivity. In addition, liposomes can be used as a cell-like "bioscaffold" to directly test recognition schemes aiming at cell-related processes. This study demonstrates an easy and fast approach to link the novel hydrophobic optical probe based on [1,3]dioxolo[4,5-f]-[1,3]benzodioxole (DBD dye mm239) with tunable optical properties to hydrophilic recognition elements (e.g., antibodies) using liposomes for signal amplification and as carrier of the hydrophobic dye. The fluorescence properties of mm239 (e.g., long fluorescence lifetime, large Stokes shift, high photostability, and high quantum yield), its high hydrophobicity for efficient anchoring in liposomes, and a maleimide bioreactive group were applied in a unique combination to build a concept for the coupling of antibodies or other protein markers to liposomes (coupling to membranes can be envisaged). The concept further allowed us to avoid multiple dye labeling of the antibody. Here, anti-TAMRA-antibody (DC7-Ab) was attached to the liposomes. In proof-of-concept, steady-state as well as time-resolved fluorescence measurements (e.g., fluorescence depolarization) in combination with single molecule detection (fluorescence correlation spectroscopy, FCS) were used to analyze the binding interaction between DC7-Ab and liposomes as well as the binding of the antigen rhodamine 6G (R6G) to the antibody. Here, the Forster resonance energy transfer (FRET) between mm239 and R6G was monitored. In addition to ensemble FRET data, single-molecule FRET (PIE-FRET) experiments using pulsed interleaved excitation were used to characterize in detail the binding on a single-molecule level to avoid averaging out effects.
We developed a new type of molecular rods consisting of two (or more) rigid units linked by a flexible joint. Consequently we called these constructs articulated rods (ARs). The syntheses of ARs were carried out by a flexible and modular approach providing access to a number of compounds with various functionalizations in terminal positions. First applications were presented with pyrene, cinnamoyl and anthracenyl labelled ARs.
An asymmetric variant of the dehydro-Diels-Alder (DDA) reaction has been developed and applied in the atropselective synthesis of various (1,5)naphthalenophanes. Whereas the suitability of the photochemically induced DDA (PDDA) was limited, the thermally induced DDA provided the desired product, depending on the chiral auxiliary used and the length of the linker, with nearly perfect stereoselectivity. Furthermore, the mechanism of the DDA was investigated by means of DFT calculations, and a stepwise mechanism involving 1,4-biradicals was suggested.
Catalytic amounts of a weak base are sufficient to induce the decomposition of anthracene endoperoxides to anthraquinone. The mechanism has been elucidated by isolation of intermediates in combination with DFT calculations. The whole process is suitable for the convenient generation of hydrogen peroxide under very mild conditions.
Catalytic amounts of a weak base are sufficient to induce the decomposition of anthracene endoperoxides to anthraquinone. The mechanism has been elucidated by isolation of intermediates in combination with DFT calculations. The whole process is suitable for the convenient generation of hydrogen peroxide under very mild conditions.
Catalytic amounts of a weak base are sufficient to induce the decomposition of anthracene endoperoxides to anthraquinone. The mechanism has been elucidated by isolation of intermediates in combination with DFT calculations. The whole process is suitable for the convenient generation of hydrogen peroxide under very mild conditions.
Building blocks for oligospiroketal (OSK) rods and evaluation of their influence on rod rigidity
(2012)
We report on the synthesis of three new sleeves and their incorporation in OSK rods. The structures of these sleeves are based on neo-inositol, terephthalaldehyde diacetals, and indacene. To quantify the influence of the sleeves on rod rigidity, we applied the worm-like chain (WLC) model on the new rods and found that this approach is rather disappointing. As the chief cause of this result, we assume that the rigidity of typical molecular rods largely exceeds the rigidity of polymers, which were successfully described by the WLC model. Alternatively, we suggest quantifying the rigidity of molecular rods by fitting an empirical function on the end-to-end distance distribution curve obtained by MD simulations. After checking various function types, the Levy-Martin function proved to be most suitable for this purpose. On the basis of this function, we defined the Levy-Martin parameter and suggest using this parameter for the characterization of the rigidity of molecular rods.
Carbon nanodots revised
(2020)
Luminescent compounds obtained from the thermal reaction of citric acid and urea have been studied and utilized in different applications in the past few years. The identified reaction products range from carbon nitrides over graphitic carbon to distinct molecular fluorophores. On the other hand, the solid, non-fluorescent reaction product produced at higher temperatures has been found to be a valuable precursor for the CO2-laser-assisted carbonization reaction in carbon laser-patterning. This work addresses the question of structural identification of both, the fluorescent and non-fluorescent reaction products obtained in the thermal reaction of citric acid and urea. The reaction products produced during autoclave-microwave reactions in the melt were thoroughly investigated as a function of the reaction temperature and the reaction products were subsequently separated by a series of solvent extractions and column chromatography. The evolution of a green molecular fluorophore, namely HPPT, was confirmed and a full characterization study on its structure and photophysical properties was conducted. The additional blue fluorescence is attributed to oligomeric ureas, which was confirmed by complementary optical and structural characterization. These two components form strong hydrogen-bond networks which eventually react to form solid, semi-crystalline particles with a size of similar to 7 nm and an elemental composition of 46% C, 22% N, and 29% O. The structural features and properties of all three main components were investigated in a comprehensive characterization study.
Prokaryotic solute binding protein-dependent ATP-binding cassette import systems are divided into type land type II and mechanistic differences in the transport process going along with this classification are under intensive investigation. Little is known about the conformational dynamics during the catalytic cycle especially concerning the transmembrane domains. The type I transporter for positively charged amino acids from Salmonella enterica serovar Typhimurium (1A0-Hi5QMP2) was studied by limited proteolysis in detergent solution in the absence and presence of co-factors including ATP, ADP, LAO/arginine, and Mg2+ ions. Stable peptide fragments could be obtained and differentially susceptible cleavage sites were determined by mass spectrometry as Lys-258 in the nucleotide-binding subunit, HisP, and Arg-217/Arg-218 in the transmembrane subunit, HisQ In contrast, transmembrane subunit HisM was gradually degraded but no stable fragment could be detected. HisP and HisQ were equally resistant under pre- and post-hydrolysis conditions in the presence of arginine-loaded solute-binding protein LAO and ATP/ADP. Some protection was also observed with LAO/arginine alone, thus reflecting binding to the transporter in the apo-state and transmembrane signaling. Comparable digestion patterns were obtained with the transporter reconstituted into proteoliposomes and nanodiscs. Fluorescence lifetime spectroscopy confirmed the change of HisQ(R218) to a more apolar microenvironment upon ATP binding and hydrolysis. Limited proteolysis was subsequently used as a tool to study the consequences of mutations on the transport cycle. Together, our data suggest similar conformational changes during the transport cycle as described for the maltose ABC transporter of Escherichia coli, despite distinct structural differences between both systems.
Previously, [1,3]dioxolo[4,5-f][1,3]benzodioxole (DBD)-based fluorophores used as highly sensitive fluorescence lifetime probes reporting on their microenvironmental polarity have been described. Now, a new generation of DBD dyes has been developed. Although they are still sensitive to polarity, in contrast to the former DBD dyes, they have extraordinary spectroscopic properties even in aqueous surroundings. They are characterized by long fluorescence lifetimes (10-20ns), large Stokes shifts (approximate to 100nm), high photostabilities, and high quantum yields (>0.56). Here, the spectroscopic properties and synthesis of functionalized derivatives for labeling biological targets are described. Furthermore, thio-reactive maleimido derivatives of both DBD generations show strong intramolecular fluorescence quenching. This mechanism has been investigated and is found to undergo a photoelectron transfer (PET) process. After reaction with a thiol group, this fluorescence quenching is prevented, indicating successful bonding. Being sensitive to their environmental polarity, these compounds have been used as powerful fluorescence lifetime probes for the investigation of conformational changes in the maltose ATP-binding cassette transporter through fluorescence lifetime spectroscopy. The differing tendencies of the fluorescence lifetime change for both DBD dye generations promote their combination as a powerful toolkit for studying microenvironments in proteins.