Search

The translocation of cephalosporins across enterobacterial OmpF and OmpC channels is monitored in real-time, demonstrating differential permeation of some cephalosporins through OmpF and OmpC.

In the huge field of polymer structure and dynamics, including intrinsically disordered peptides, protein folding, and enzyme activity, many questions remain that cannot be answered by methodology based on artificial intelligence, X-ray, or NMR spectroscopy but maybe by fluorescence spectroscopy. The theory of Förster resonance energy transfer (FRET) describes how an optically excited fluorophore transfers its excitation energy through space to an acceptor moiety—with a rate that depends on the distance between donor and acceptor. When the donor and acceptor moiety are conjugated to different sites of a flexible peptide chain or any other linear polymer, the pair could in principle report on chain structure and dynamics, on the site-to-site distance distribution, and on the diffusion coefficient of mutual site-to-site motion of the peptide chain. However, the dependence of FRET on distance distribution and diffusion is not defined by a closed analytical expression but by a partial differential equation (PDE), by the Haas-Steinberg equation (HSE), which can only be solved by time-consuming numerical methods. As a second complication, time-resolved FRET measurements have thus far been deemed necessary. As a third complication, the evaluation requires a computationally demanding but indispensable global analysis of an extended experimental data set. These requirements have made the method accessible to only a few experts. Here, we show how the Haas-Steinberg equation leads to a closed analytical expression (CAE), the Haas-Steinberg-Jacob equation (HSJE), which relates a diffusion-diagnosing parameter, the effective donor–acceptor distance, to the augmented diffusion coefficient, J, composed of the diffusion coefficient, D, and the photophysical parameters that characterize the used FRET method. The effective donor–acceptor distance is easily retrieved either through time-resolved or steady-state fluorescence measurements. Any global fit can now be performed in seconds and minimizes the sum-of-square difference between the experimental values of the effective distance and the values obtained from the HSJE. In summary, the HSJE can give a decisive advantage in applying the speed and sensitivity of FRET spectroscopy to standing questions of polymer structure and dynamics.

Compared with primary and local tumor, metastasis is more difficult to resect completely and remain the leading cause of death associated with solid tumors. It is therefore pressing to develop effective strategies to prevent and suppress tumor metastasis in its early stages. Heparanase overexpression is significantly associated with increased malignancy and metastasis. Here, we develop a novel heparanase degradable heparin-based microcarrier, HBMA, for specific staining, targeting, and inhibiting tumor cells with high metastatic potential. HBMA is fabricated through self-assembling of three components, positively charged fluorescent gold nanoclusters (KG-AuNCs), heparin polymers (HP), and antisense miRNA-21 oligonucleotides (AM-21), with each component playing multiple roles. Results of confocal microscopy and flow cytometry show that this agent has an excellent capability to label metastatic tumor cells with high selectivity. On the therapeutic side, the results of cell viability assay, wound healing assay, and plate colony formation assay verify that HBMA induces a significant inhibition effect towards the proliferation and migration of the selectively target tumor cells. The heparanase responsive AM-21 delivery, the specific staining, and the efficient tumor cell activity suppression highlight HBMA as a promising cancer theranostic agent to prevent tumor metastasis.

Microcystis aeruginosa is a cyanobacterium that produces a variety of cyclic heptapeptide toxins in freshwater. The protective effects of the macromolecular container cucurbit[7]uril (CB7) were evaluated using mouse models of cyanotoxin-induced liver damage. Biochemical analysis of liver function was performed to gauge the extent of liver damage after exposure to cyanobacterial crude extract [CCE; LD50 = 35 mg/kg body weight; intraperitoneal (i.p.)] in the absence or presence of CB7 (35 mg/kg body weight, i.p.). CCE injection resulted in liver enlargement, potentiated the activities of alanine aminotransferase (ALT) and glutathione S-transferase (GST), increased lipid peroxidation (LPO), and reduced protein phosphatase 1 (PP1) activity. CCE-induced liver enlargement, ALT and GST activities, and LPO were significantly reduced when CB7 was coadministered. Moreover, the CCE-induced decline of PP1 activity was also ameliorated in the presence of CB7. Treatment with CB7 alone did not affect liver function, which exhibited a dose tolerance of 100 mg/kg body wt. Overall, our results illustrated that the addition of CB7 significantly reduced CCE-induced hepatotoxicity (P < 0.05).

Parallel artificial membrane permeability assay (PAMPA) is a screening tool for the evaluation of drug permeability across various biological membrane systems in a microplate format. In PAMPA, a drug candidate is allowed to pass through the lipid layer of a particular well during an incubation period of, typically, 10–16 h. In a second step, the samples of each well are transferred to a UV-Vis–compatible microplate and optically measured (applicable only to analytes with sufficient absorbance) or sampled by mass-spectrometric analysis. The required incubation period, sample transfer, and detection methods jointly limit the scalability of PAMPA to high-throughput screening format. We introduce a modification of the PAMPA method that allows direct fluorescence detection, without sample transfer, in real time (RT-PAMPA). The method employs the use of a fluorescent artificial receptor (FAR), composed of a macrocycle in combination with an encapsulated fluorescent dye, administered in the acceptor chamber of conventional PAMPA microplates. Because the detection principle relies on the molecular recognition of an analyte by the receptor and the associated fluorescence response, concentration changes of any analyte that binds to the receptor can be monitored (molecules with aromatic residues in the present example), regardless of the spectroscopic properties of the analyte itself. Moreover, because the fluorescence of the (upper) acceptor well can be read out directly by fluorescence in a microplate reader, the permeation of the drug through the planar lipid layer can be monitored in real time. Compared with the traditional assay, RT-PAMPA allows not only quantification of the permeability characteristics but also rapid differentiation between fast and slow diffusion events.

We report the use of the macrocyclic host cucurbit[7]uril (CB7) as a supramolecular additive in nanosecond time-resolved fluorescence (Nano-TRF) assays for proteases to enhance the discrimination of substrates and products and, thereby, the sensitivity. A peptide substrate was labeled with 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as a long-lived (>300 ns) fluorescent probe and 3-nitrotyrosine was established as a non-fluorescent fluorescence resonance energy transfer (FRET) acceptor that acts as a “dark quencher.” The substrate was cleaved by the model proteases trypsin and chymotrypsin and the effects of the addition of CB7 to the enzyme assay mixture were investigated in detail using UV/VIS absorption as well as steady-state and time-resolved fluorescence spectroscopy. This also allowed us to identify the DBO and nitrotyrosine residues as preferential binding sites for CB7 and suggested a hairpin conformation of the peptide, in which the guanidinium side chain of an arginine residue is additionally bound to a vacant ureido rim of one of the CB7 hosts.

We introduce herein boron-dipyrromethene (BODIPY) dyes as a new class of fluorophores for the design of reporter dyes for supramolecular host–guest complex formation with cucurbit[7]uril (CB7). The BODIPYs contain a protonatable aniline nitrogen in the meso-position of the BODIPY chromophore, which was functionalized with known binding motifs for CB7. The unprotonated dyes show low fluorescence due to photoinduced electron transfer (PET), whereas the protonated dyes are highly fluorescent. Encapsulation of the binding motif inside CB7 positions the aniline nitrogen at the carbonyl rim of CB7, which affects the pKa value, and leads to a host-induced protonation and thus to a fluorescence increase. The possibility to tune binding affinities and pKa values is demonstrated and it is shown that, in combination with the beneficial photophysical properties of BODIPYs, several new applications of host–dye reporter pairs can be implemented. This includes indicator displacement assays with favourable absorption and emission wavelengths in the visible spectral region, fluorescence correlation spectroscopy, and noncovalent surface functionalization with fluorophores.

The supramolecular chemistry of cucurbit[n]urils (CBn) has been rapidly developing to encompass diverse medicinal applications, including drug formulation and delivery, controlled drug release, and sensing for bioanalytical purposes. This is made possible by their unique recognition properties and very low cytotoxicity. In this review, we summarize the host-guest complexation of biologically important molecules with CBn, and highlight their implementation in medicinal chemistry and chemical biology.

A flexible peptide chain displays structural and dynamic properties that correspond to its folding and biological activity. These properties are mirrored in intrachain site-to-site distances and diffusion coefficients of mutual site-to-site motion. Both distance distribution and diffusion determine the extent of Förster resonance energy transfer (FRET) between two sites labeled with a FRET donor and acceptor. The relatively large Förster radii of traditional FRET methods (R0 > 20 Å) lead to a fairly low contribution of diffusion. We introduced short-distance FRET (sdFRET) where Dbo, an asparagine residue conjugated to 2,3-diazabicyclo[2.2.2]octane, acts as acceptor paired with donors, such as naphtylalanine (NAla), tryptophan, 5-l-fluorotryptophan, or tyrosine. The Förster radii are always close to 10 Å, which makes sdFRET highly sensitive to diffusional motion. We recently found indications that the FRET enhancement caused by diffusion depends symmetrically on the product of the radiative fluorescence lifetime of the donor and the diffusion coefficient. In this study, we varied this product by two orders of magnitude, using both donors of different lifetime, NAla and FTrp, as well as a varying viscogen concentration, to corroborate this statement. We demonstrate the consequences of this relationship in evaluating the impact of viscogenic coadditives on peptide dimensions.

The potential of the supramolecular host molecule cucurbit[7]uril to serve as a stabilizing additive and enhancement agent was investigated for the following dyes in aqueous solution: rhodamine 6G, rhodamine 123, tetramethylrhodamine, cresyl violet, fluorescein, coumarin 102, pyronin B, pyronin Y, two cyanine 5 and one cyanine 3 derivative, and IR140 as well as IR144. For most cationic dyes photostabilization was established, and a pronounced thermal stabilization due to deaggregation and solubilization was observed for the xanthene dyes. The advantageous effects are attributed to the formation of inclusion complexes with different photophysical and photochemical properties. The complexation is accompanied by spectral shifts characteristic for the inclusion in a less polar environment, while the fluorescence quantum yields as well as the brightness show an increase, with few exceptions. As a consequence of the low polarizability inside the cucurbituril cavity, the fluorescence lifetimes of the included dyes increase substantially and systematically. Applications of the new photostabilizing additive for dye lasers, for prolonged storage of dye solutions, in scanning confocal microscopy, and fluorescence correlation spectroscopy are discussed.

Looping rates in short polypeptides can be determined by intramolecular fluorescence quenching of a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) by tryptophan. By this methodology, the looping rates in glycine-serine peptides with the structure Trp-(Gly-Ser)n-Dbo-NH2 of different lengths (n = 0–10) were determined in dependence on temperature in D2O and the activation parameters were derived. In general, the looping rate increases with decreasing peptide length, but the shortest peptide (n=0) shows exceptional behavior because its looping rate is slower than that for the next longer ones (n=1,2). The activation energies increase from 17.5 kJ mol−1 for the longest peptide (n=10) to 20.5 kJ mol−1 for the shortest one (n=0), while the pre-exponential factors (log⁡(A/s−1)) range from 10.20 to 11.38. The data are interpreted in terms of an interplay between internal friction (stiffness of the biopolymer backbone and steric hindrance effects) and solvent friction (viscosity-limited diffusion). For the longest peptides, the activation energies resemble more and more the value expected for solvent viscous flow. Internal friction is most important for the shortest peptides, causing a negative curvature and a smaller than ideal slope (ca. –1.1) of the double-logarithmic plots of the looping rates versus the number of peptide chain segments (N). Interestingly, the corresponding plot for the pre-exponential factors (logA versus logN) shows the ideal slope (–1.5). While the looping rates can be used to assess the flexibility of peptides in a global way, it is suggested that the activation energies provide a measure of the “thermodynamic” flexibility of a peptide, while the pre-exponential factors reflect the “dynamic” flexibility.

Fluorophores based on the azo chromophore 2,3-diazabicyclo[2.2.2]oct-2-ene, referred to as fluorazophores, display an exceedingly long fluorescence lifetime. Besides the use in time-resolved screening assays, where the long-lived fluorescence can be time-gated, thereby improving the signal to background ratio, a distinct application of fluorazophores lies in the area of biopolymer dynamics. For this purpose, one chain end is labeled with a fluorazophore and the other one with an efficient fluorescence quencher. The fluorescence lifetime of the probe/quencher-labeled peptide then reflects the kinetics of intramolecular end-to-end collision. Applications to polypeptides are described and control experiments which establish the nature of the quenching mechanism as a diffusive process requiring intimate probe/quencher contact are described.

The thermodynamic properties of cyclodextrin complexes and knowledge of kinetics of host-guest complexation as well as structural details are studied. The joint study of structural, kinetic and thermodynamic effects was made possible by the application of several independent spectroscopic techniques in aqueous solution and the complex stability appears to be dominated by interplay between hydrophobic and specific structural effects, while the association rate constants are relatively insensitive to substitution.

The complexation behavior of pyropheophorbide-a methyl ester (PPME) with transition metal ions as well as other biologically relevant metal ions has been investigated in water–DMF (2 : 1 v/v) solution. PPME was found to selectively complex Cu2+ions, which leads to a distinct change in its absorption spectrum as well as efficient fluorescence quenching. The degree of fluorescence quenching by Cu2+depended on concentration and time. Upon addition of Cu2+, the fluorescence showed a time-resolved decay on the time scale of minutes to hours, with the decay rate being dependent on the cation concentration. Fitting according to a bimolecular reaction rate law provided a rate constant of 650 ± 90 M−1s−1at 298 K for metallochlorin formation. The potential implications of Cu2+binding for the use of PPME in photodynamic therapy are discussed, along with its use as a fluorescent sensor for detection of micromolar concentrations of Cu2+. [ABSTRACT FROM AUTHOR]

Azoalkanes of the 2,3-diazabicyclo[2.2.2]-oct-2-ene type have been introduced as probes for antioxidants in homogeneous solution as well as in liposomes and micelles. The bimolecular fluorescence quenching of the bridgehead dichloro-substituted 1,4-dichloro-2,3-diazabicyclo[2.2.2]-oct-2-ene (3) was compared with that of the parent compound 2,3-diazabicyclo[2.2.2]-oct-2-ene (1) and the bridgehead-dialkylated compound 4-methyl-1-isopropyl-2,3-diazabicyclo[2.2.2]-oct-2-ene (2). Compound 3showed a more efficient fluorescence quenching in C–H containing solvents (e.g., in n-hexane: 30 ns for 3versus340 ns for 1and 770 ns for 2), but a less efficient quenching in aqueous solution (e.g., in deaerated H2O: 485 ns for 3versus420 ns for 1and 340 ns for 2), and also by molecular oxygen (kq/109M−1s−1= 0.32 for 3versus2.5 for 1and 1.9 for 2). Towards low-molecular weight antioxidants, compound 3showed a significantly higher reactivity (e.g., for reduced glutathione: kq/109M−1s−1= 1.8 for 3versus0.82 for 1and 0.39 for 2), at the expense of a lower differentiation between the investigated antioxidants (lower selectivity). The increased reactivity of 3and lower, as well as qualitatively different, selectivity is attributed to a combination of factors, most importantly the slightly increased excitation energy of 3and its lower excited-state nucleophilicity. The latter was independently corroborated, besides its longer fluorescence lifetime in aqueous solution, through the trends in quenching rate constants of the azoalkanes 1–3towards electron-deficient versuselectron-rich lactone antioxidants of the benzofuranone type. While common inorganic buffer constituents caused no fluorescence quenching, significant quenching was observed, as a curiosity, for hydrogencarbonate (kq/106M−1s−1= 1.7 for 3versus2.4 for 1and 0.45 for 2), with a fully manifested kinetic deuterium isotope effect (kq(H2O)/kq(D2O) = 12) for 3. [ABSTRACT FROM AUTHOR]

The host–guest interactions of the neutral (AO) and cationic (AOH+) forms of the dye acridine orange with the macrocyclic hosts cucurbit[7]uril (CB7) and β-cyclodextrin (β-CD) were investigated by using ground-state absorption and steady-state as well as time-resolved fluorescence measurements. The cationic form undergoes no significant complexation with β-CD, but binds strongly with CB7 (Keq = 2.0 × 105 M−1), causing a large enhancement in fluorescence intensity and lifetime of the dye in the latter host. The strong and selective binding of AOH+ with CB7 is attributed to ion–dipole interactions involving the ureido carbonyl rims of CB7 and the charged AOH+. In contrast, the neutral AO form of the dye shows quite similar binding with both CB7 and β-CD, but the binding constants are lower by more than two orders of magnitude compared to that of the AOH+–CB7 system. CB7 and β-CD show a contrasting behavior in modifying the acid–base character of the dye, shifting its pKa by about 2.6 units upward and about 0.7 units downward, in the two respective cases. These divergent pKa shifts of the dye arise from the differential affinity of the two host molecules to encapsulate the protonated and neutral form of the dye. [ABSTRACT FROM AUTHOR]

The binding affinity of Neutral Red with cucurbit[7]uril (CB7) can be fine-tuned by addition and competitive binding of metal ions, which leads also to a pKa shift of the dye; this can be exploited to relocate the dye from the macrocyclic cavity of CB7 to the biomolecular pocket of bovine serum albumin. [ABSTRACT FROM AUTHOR]

The macrocyclic host cucurbit[7]uril exhibits highly specific inhibitory effects on the activity of proteases, which can be analyzed by a host–substrate complexation model. [ABSTRACT FROM AUTHOR]

Corynebacterium jeikeium, a resident of human skin, is often associated with multidrug resistant nosocomial infections in immunodepressed patients. C. jeikeium K411 belongs to mycolic acid-containing actinomycetes, the mycolata and contains a channel-forming protein as judged from reconstitution experiments with artificial lipid bilayer experiments. The channel-forming protein was present in detergent treated cell walls and in extracts of whole cells using organic solvents. A gene coding for a 40 amino acid long polypeptide possibly responsible for the pore-forming activity was identified in the known genome of C. jeikeium by its similar chromosomal localization to known porH and porA genes of other Corynebacterium strains. The gene jk0268 was expressed in a porin deficient Corynebacterium glutamicum strain. For purification temporarily histidine-tailed or with a GST-tag at the N-terminus, the homogeneous protein caused channel-forming activity with an average conductance of 1.25 nS in 1M KCl identical to the channels formed by the detergent extracts. Zero-current membrane potential measurements of the voltage dependent channel implied selectivity for anions. This preference is according to single-channel analysis caused by some excess of cationic charges located in the channel lumen formed by oligomeric alpha-helical wheels. The channel has a suggested diameter of 1.4 nm as judged from the permeability of different sized hydrated anions using the Renkin correction factor. Surprisingly, the genome of C. jeikeium contained only one gene coding for a cell wall channel of the PorA/PorH type found in other Corynebacterium species. The possible evolutionary relationship between the heterooligomeric channels formed by certain Corynebacterium strains and the homooligomeric pore of C. jeikeium is discussed.

The catalytic activity of L-aspartate α-decarboxylase (ADC) is essential for the growth of several micro-organisms, including Mycobacterium tuberculosis (Mtb), and has triggered efforts for the development of pharmaceutically active compounds against tuberculosis. The present study is a continuation of our recent chemoinformatics-based design approach for identifying potential drug-like inhibitors against MtbADC. We report an NMR-based protocol that allows label-free and direct monitoring of enzymatic conversion, which we have combined with a systematic testing of reported and newly identified potential inhibitors against MtbADC. Quantification of enzymatic conversion in the absence and presence of inhibitors allowed for a relative measure of the inhibitory effect (k(rel)). Among the newly identified compounds, D-tartrate, L-tartrate, and 2,4-dihydroxypyrimidine-5-carboxylate were found to inhibit the enzyme with k(rel) values of 0.36, 0.38, and 0.54, respectively. In addition to the identification of potential building blocks for the development of therapeutic agents, the current study highlights the importance of electrostatic interactions governing enzyme-inhibitor binding.