Optical Modulation of Antibiotic Resistance by Photoswitchable Cystobactamids

The rise of antibiotic resistance causes a serious health care problem, and its counterfeit demands novel, innovative concepts. The combination of photopharmacology, enabling a light-controlled reversible modulation of drug activity, with antibiotic drug design has led to first photoswitchable antibiotic compounds derived from established scaffolds. In this study, we converted cystobactamids, gyrase-inhibiting natural products with an oligoaryl scaffold and highly potent antibacterial activities, into photoswitchable agents by inserting azobenzene in the N-terminal part and/or an acylhydrazone moiety near the C-terminus, yielding twenty analogs that contain mono- as well as double-switches. Antibiotic and gyrase inhibition properties could be modulated 3.4-fold and 5-fold by light, respectively. Notably, the sensitivity of photoswitchable cystobactamids towards two known resistance factors, the peptidase AlbD and the scavenger protein AlbA, was light-dependent. While irradiation of an analog with an N-terminal azobenzene with 365 nm light led to less degradation by AlbD, the AlbA-mediated inactivation was induced. This provides a proof-of-principle that resistance towards photoswitchable antibiotics can be optically controlled.     

Structure of Zinc and Nickel Histidine Complexes in Solution Revealed by Molecular Dynamics and Raman Optical Activity

The histidine residue has an exceptional affinity for metals, but solution structure of its complexes are difficult to study. For zinc and nickel complexes, Raman and Raman optical activity (ROA) spectroscopy methods to investigate the link between spectral shapes and the geometry were used. The spectra were recorded and interpreted on the basis of ionic equilibria, molecular dynamics, ab initio molecular dynamics, and density functional theory. For zwitterionic histidine the dominant tautomer was determined by the decomposition of experimental spectra into calculated subspectra. An octahedral structure was found to prevail for the ZnHis₂ complex in solution, in contrast to a tetrahedral arrangement in the crystal phase. The solution geometry of NiHis₂ is more similar to the octahedral structure found by X-ray. The Raman and ROA structural determinations of metal complexes are dependent on extensive computations, but reveal unique information about the studied systems.     

Monitoring of circulating amino acids in patients with pancreatic cancer and cancer cachexia using capillary electrophoresis and contactless conductivity detection

Branched chain amino acids (BCAAs), alanine and glutamine are determined in human plasma by capillary electrophoresis with contactless conductivity detection (CE/C⁴D). The baseline separation of five amino acids from other plasma components is achieved on the short capillary effective length of 18 cm in 3.2 mol/L acetic acid with addition of 13% v/v methanol as background electrolyte. Migration times range from 2.01 min for valine to 2.84 min for glutamine, and LODs for untreated plasma are in the interval 0.7–0.9 μmol/L. Sample treatment is based on the addition of acetonitrile to only 15 μL of plasma and supernatant is directly subjected to CE/C⁴D. Circulating amino acids are measured in patients with pancreatic cancer and cancer cachexia during oral glucose tolerance test. It is shown that patients with pancreatic cancer and cancer cachexia syndrome exhibit low basal circulating BCAAs and glutamine levels and loss of their insulin-dependent suppression.     

Ultrasound as a Promising Tool for the Green Extraction of Specialized Metabolites from Some Culinary Spices

Spices are a popular food of plant origin, rich in various phytochemicals and recognized for their numerous properties. The aim of the study was to evaluate the antioxidant and antimicrobial activity, as well as the content of specialized metabolites, of aqueous extracts of three spice species––garlic (Allium sativum L.), ginger (Zingiber officinalle L.) and turmeric (Curcuma longa L.)––prepared by green extraction methods. Ultrasound treatment increased the chromaticity parameter b value of turmeric and ginger extracts, thus indicating a higher yellow color predominantly due to curcuminoids characteristic of these species. Ultrasound-assisted extraction significantly increased the content of total soluble solids, phenolic compounds, total carotenoids and vitamin C. The temperature of the system was also an important factor, with the highest (70 °C) conditions in ultrasound-assisted extraction having a positive effect on thermolabile compounds (vitamin C, phenolics, total carotenoids). For example, turmeric extract treated with ultrasound at 70 °C had up to a 67% higher vitamin C content and a 69.4% higher total carotenoid content compared to samples treated conventionally at the same temperature, while ginger extracts had up to 40% higher total phenols. All different concentrations of spice extracts were not sufficient for complete inhibition of pathogenic bacterial strains of Salmonella, L. monocytogenes and S. aureus; however, only garlic extracts had an effect on slowing down the growth and number of L. monocytogenes colonies. Spice extracts obtained by ultrasonic treatment contained a significantly higher level of bioactive compounds and antioxidant capacity, suggesting that the extracts obtained have significant nutritional potential and thus a significant possibility for phytotherapeutic uses.     

Expanding the Topological Landscape by a G-Column Flip of a Parallel G-Quadruplex

Canonical G-quadruplexes can adopt a variety of different topologies depending on the arrangement of propeller, lateral, or diagonal loops connecting the four G-columns. A novel intramolecular G-quadruplex structure is derived through inversion of the last G-tract of a three-layered parallel fold, associated with the transition of a single propeller into a lateral loop. The resulting (3+1) hybrid fold features three syn⋅anti⋅anti⋅anti G-tetrads with a 3’-terminal all-syn G-column. Although the ability of forming a duplex stem-loop between G-tracts seems beneficial for a propeller-to-lateral loop rearrangement, unmodified G-rich sequences resist folding into the new (3+1) topology. However, refolding can be driven by the incorporation of syn-favoring guanosine analogues into positions of the fourth G-stretch. The presented hybrid-type G-quadruplex structure as determined by NMR spectroscopy may provide for an additional scaffold in quadruplex-based technologies.     

“Anti-electrostatic” halogen bonding in solution

Halogen-bonded (XB) complexes between halide anions and a cyclopropenylium-based anionic XB donor were characterized in solution for the first time. Spontaneous formation of such complexes confirms that halogen bonding is sufficiently strong to overcome electrostatic repulsion between two anions. The formation constants of such “anti-electrostatic” associations are comparable to those formed by halides with neutral halogenated electrophiles. However, while the latter usually show charge-transfer absorption bands, the UV-Vis spectra of the anion–anion complexes examined herein are determined by the electronic excitations within the XB donor. The identification of XB anion–anion complexes substantially extends the range of the feasible XB systems, and it provides vital information for the discussion of the nature of this interaction.

Spontaneous formation of “anti-electrostatic” complexes in solution demonstrates that halogen bonding can be sufficiently strong to overcome anion–anion repulsion when the latter is attenuated by the polar medium.

Halogen bonding (XB) is an attractive interaction between a Lewis base (LB) and a halogenated compound, exhibiting an electrophilic region on the halogen atom.¹ It is most commonly related to electrostatic interaction between an electron-rich species (XB acceptor) and an area of positive electrostatic potential (σ-holes) on the surface of the halogen substituent in the electrophilic molecule (XB donor).² Provided that mutual polarization of the interacting species is taken into account, the σ-hole model explains geometric features and the variation of stabilities of XB associations, especially in the series of relatively weak complexes.³ Based on the definition of halogen bonding and its electrostatic interpretation, this interaction is expected to involve either cationic or neutral XB donors. Electrostatic interaction of anionic halogenated species with electron-rich XB acceptors, however, seems to be repulsive, especially if the latter are also anionic. Yet, computational analyses predicted that halogen bonding between ions of like charges, called “anti-electrostatic” halogen bonding (AEXB),⁴ can possibly be formed^5–12 and the first examples of AEXB complexes formed by different anions, i.e. halide anions and the anionic iodinated bis(dicyanomethylene)cyclopropanide derivatives 1 (see Scheme 1) or the anionic tetraiodo-p-benzoquinone radical, were characterized recently in the solid state.^13,14 The identification of such complexes substantially extends the range of feasible XB systems, and it provides vital information for the discussion of the nature of this interaction. Computational results, however, significantly depend on the used methods and applied media (gas phase vs. polar environment and solvation models) and the solid state arrangements of the XB species might be affected by crystal forces and/or counterions. Unambiguous confirmation of the stability of the halogen-bonded anion–anion complexes and verification of their thermodynamic characteristics thus requires experimental characterization of the spontaneous formation of such associations in solution. Still, while the solution-phase complexes formed by hydrogen bonding between two anionic species were reported previously,^15–17 there is currently no example of “anti-electrostatic” XB in solution.Open in a separate windowScheme 1Structures of the XB donor 1 and its hydrogen-substituted analogue 2.To examine halogen bonding between two anions in solution, we turn to the interaction between halides and 1,2-bis(dicyanomethylene)-3-iodo-cyclopropanide 1 (Scheme 1).^‡ Even though this compound features a cationic cyclopropenylium core, it is overall anionic, and calculations have demonstrated that its electrostatic potential is universally negative across its entire surface.¹³ The solution of 1 (with tris(dimethylamino)cyclopropenium (TDA) as counterion) in acetonitrile is characterized by an absorption band at 288 nm with ε = 2.3 × 10⁴ M⁻¹ cm⁻¹ (Fig. 1). As LB, we first applied iodide anions taken as a salt with n-tetrabutylammonium counter-ion, Bu₄NI. This salt does not show absorption bands above 290 nm, but its addition to a solution of 1 led to a rise of absorption in the 290–350 nm range (Fig. 1). Subtraction of the absorption of the individual components from that of their mixture produced a differential spectrum which shows a maximum at about 301 nm (insert in Fig. 1). At constant concentration of the XB donor (1) and constant ionic strength, the intensity of the absorption in the range of 280–300 nm (and hence differential absorbance, ΔAbs) rises with increasing iodide concentration (Fig. S1 in the ESI^†). This suggests that the interaction of iodide with 1 results in the formation of the [1, I⁻]-complex which shows a higher absorptivity in this spectral range (eqn (1)):1 + X⁻ ⇌ [1, X⁻]1Open in a separate windowFig. 1Spectra of acetonitrile solutions with constant concentration of 1 (0.60 mM) and various concentrations of Bu₄NI (6.0, 13, 32, 49, 75, 115 and 250 mM, solid lines from the bottom to the top). The dashed lines show spectra of the individual solutions 1 (c = 0.60 mM, red line) and Bu₄NI (c = 250 mM, blue line). The ionic strength was maintained using Bu₄NPF₆. Insert: Differential spectra of the solutions obtained by subtraction of the absorption of the individual components from the spectra of their corresponding mixtures.To clarify the mode of interaction between 1 and iodide in the complex, we also performed analogous measurements with the hydrogen-substituted compound 2 (see Scheme 1). The addition of iodide to a solution of 2 in acetonitrile did not increase the absorption in the 280–300 nm spectral range. Instead, some decrease of the absorption band intensity of 2 with the increase of concentration of I⁻ anions was observed (Fig. S2 in the ESI^†). Such changes are related to a blue shift of this band resulting from the hydrogen bonding between 2 and iodide (formation of hydrogen-bonded [2, I⁻] complex is corroborated by the observation of the small shift of the NMR signal of the proton of 2 to the higher ppm values in the presence of I⁻ anions, see Fig. S3 in the ESI^†).^§ Furthermore, since H-compound 2 should be at least as suitable as XB donor 1 to form anion–π complexes with the halide, this finding (as well as solid-state and computational data^¶) rules out that any increase in absorption in this region observed with the I-compound 1 may be due to this alternative interaction.Likewise, the addition of NBu₄I to a solution of TDA cations taken as a salt with Cl⁻ anions did not result in an increase in the relevant region. Hence, we could also rule out anion–π interactions with the TDA counter-ions as source of the observed changes, which is in line with previous reports on the electron-rich nature of TDA.¹⁸All these observations (supported by the computational analysis, vide infra) indicate that the [1, I⁻] complex (eqn (1)) is formed via halogen bonding of I⁻ with iodine substituents in 1. The changes in the intensities of the differential absorption ΔAbs as a function of the iodide concentration (with constant concentration of XB donor (1) as well as constant ionic strength) are well-modelled by the 1 : 1 binding isotherm (Fig. S1 in the ESI^†). The fit of the absorption data produced a formation constant of K = 15 M⁻¹ for the [1, I⁻] complex (Table 1).^|| The overlap with the absorption of the individual XB donor hindered the accurate evaluation of the position and intensity of the absorption band of the corresponding complex which is formed upon LB-addition to 1. As such, the values of Δλ_max shown in Table 1 represent a wavelength of the largest difference in the absorptivity of the [1, I⁻] complex and individual anion 1, and Δε reflects the difference of their absorptivity at this point (see the ESI^† for the details of calculations).Equilibrium constants and spectral characteristics of the complexes of 1 with halide anions X⁻

Mechanistic insights into dopaminergic and serotonergic neurotransmission – concerted interactions with helices 5 and 6 drive the functional outcome

Brain functions rely on neurotransmitters that mediate communication between billions of neurons. Disruption of this communication can result in a plethora of psychiatric and neurological disorders. In this work, we combine molecular dynamics simulations, live-cell biosensor and electrophysiological assays to investigate the action of the neurotransmitter dopamine at the dopaminergic D₂ receptor (D₂R). The study of dopamine and closely related chemical probes reveals how neurotransmitter binding translates into the activation of distinct subsets of D₂R effectors (i.e.: G_i2, G_oB, G_z and β-arrestin 2). Ligand interactions with key residues in TM5 (S5.42) and TM6 (H6.55) in the D₂R binding pocket yield a dopamine-like coupling signature, whereas exclusive TM5 interaction is typically linked to preferential G protein coupling (in particular G_oB) over β-arrestin. Further experiments for serotonin receptors indicate that the reported molecular mechanism is shared by other monoaminergic neurotransmitter receptors. Ultimately, our study highlights how sequence variation in position 6.55 is used by nature to fine-tune β-arrestin recruitment and in turn receptor signaling and internalization of neurotransmitter receptors.

Neurotransmitter contacts within the receptor binding site differentially contribute to the overall functional response: transmembrane helix (TM) 5 contacts promote G protein coupling whereas concerted TM5–TM6 contacts enhance β-arrestin recruitment.     

Immunomagnetic separation and detection of Salmonella cells using newly designed carriers

A new method for simultaneous determination of alkoxyethanols (2-methoxyethanol, 2-ethoxyethanol, 2-isopropoxyethanol, and 2-butoxyethanol) by high-performance liquid chromatography (HPLC) with fluorescence detection has been developed. The alkoxyethanols and an internal standard (2-phenoxyethanol) were derivatized by treatment with 1-anthroylnitrile to give the anthroyl esters. The esterification was completed in 30 min in the presence of quinuclidine as base catalyst at room temperature. After stopping the reaction, an aliquot of the final solution was injected into the HPLC. The resulting anthroyl esters of the alkoxyethanols and the internal standard were separated on a C18 reversed-phase column with acetonitrile-water-acetic acid (65:35:0.1, v/v) as the mobile phase and detected fluorimetrically at excitation and emission wavelengths of 360 nm and 460 nm, respectively. The detection limits of the derivatives as alkoxyethanols at a signal-to-noise ratio of 3 were in the range of 1-3 pg per injection. The minimal amounts of alkoxyethanols derivatized in the reaction mixture for derivatization to determine the limits of detection were approximately 0.5 ng. This HPLC method was applied to the determination of some of alkoxyethanols in the air of the workplace where the thinner containing alkoxyethanols was used for painting.     

Aggregation and decomposition of a pseudoisocyanine dye in dispersions of layered silicates

The optical properties of reaction systems composed from a pseudoisocyanine (PIC) solution and dispersed layered silicates were studied using visible spectroscopy. Two series of reduced-charge montmorillonites were used as the silicate materials. Each series consisted of eight samples with different layer charges, which were prepared from one parent material. Observed trends were verified with another series of dioctahedral and trioctahedral smectites of different layer charges, structure, and origin. The layer charge density of the silicates significantly affected the aggregation of PIC cations. In addition to the formation of J-aggregates, dye spectral bleaching was also observed. Silicates with very low charge densities induced neither significant aggregation nor spectral bleaching of the dye. The highest levels of PIC J-aggregate formation were found in dispersions of the layered silicates with a medium surface charge. However, reversible spectral bleaching was also observed in some cases. PIC dye cations probably change their conformations during the adsorption process, due to the tension resulting from the large size of the cations and the relatively high charge density at the silicate surface. The bleached dye recovers, at least partially, with the rearrangement and redistribution of the dye cations over the time. In contrast, the presence of silicates with very high charge densities (synthetic taeniolite and fluorohectorite) led to the very fast and irreversible decomposition of the PIC. Perhaps, the tension in adsorbed dye cations, induced by the high charge density at the silicate surface, resulted in significant destabilization and a decomposition reaction of the chromophore.