A small molecule discrimination map of the antibiotic resistance kinome

Kinase-mediated resistance to antibiotics is a significant clinical challenge. These enzymes share a common protein fold characteristic of Ser/Thr/Tyr protein kinases. We screened 14 antibiotic resistance kinases against 80 chemically diverse protein kinase inhibitors to map resistance kinase chemical space. The screens identified molecules with both broad and narrow inhibition profiles, proving that protein kinase inhibitors offer privileged chemical matter with the potential to block antibiotic resistance. One example is the flavonol quercetin, which inhibited a number of resistance kinases in vitro and in vivo. This activity was rationalized by determination of the crystal structure of the aminoglycoside kinase APH(2″)-IVa in complex with quercetin and its antibiotic substrate kanamycin. Our data demonstrate that protein kinase inhibitors offer chemical scaffolds that can block antibiotic resistance, providing leads for co-drug design.     

Cascade and commutative self-assembles of nanoscale three-component systems controlled by the conformation of thiacalix[4]arene

In this work, the formation of two- and three-component supramolecular systems based on cone, partial cone, 1,3-alternate stereoisomers of heteroditopic "hosts": p-tert-butylthiacalix[4]arene containing 4-amidopyridine fragments with silver(I) cations and dicarboxylic acids in liquid and solid phases were studied by UV spectroscopy, dynamic light scattering, and atomic force microscopy methods. It has been shown that these macrocycles are coreceptors, capable of simultaneously binding silver(I) cations, dicarboxylic acids (oxalic, malonic, succinic, maleic, fumaric acids), and hydroxyl acids (glycol, tartaric acids). For the first time, by the dynamic light scattering method, it has been shown that the conformation of p-tert-butyl thiacalix[4]arenes significantly affects the type of three-component system formed: cone is characterized by the formation of cascade systems; for partial cone, intermediate systems; and for the 1,3-alternate stereoisomers, three types of three-component systems (cascade, intermediate, and commutative) were observed.     

Fast quantitation of 5-hydroxymethylfurfural in honey using planar chromatography

An approach for rapid quantitation of 5-hydroxymethylfurfural (HMF) in honey using planar chromatography is suggested for the first time. In high-performance thin-layer chromatography (HPTLC) the migration time is approximately 5 min. Detection is performed by absorbance measurement at 290 nm. Polynomial calibration in the matrix over a range of 1:80 showed correlation coefficients, r, of ≥ 0.9997 for peak areas and ≥ 0.9996 for peak heights. Repeatability in the matrix confirmed the suitability of HPTLC–UV for quantitation of HMF in honey. The relative standard deviation (RSD, %, n = 6) of HMF at 10 ng/band was 2.9% (peak height) and 5.2% (peak area); it was 0.6% and 1.0%, respectively, at 100 ng/band. Other possible detection modes, for example fluorescence measurement after post-chromatographic derivatization and mass spectrometric detection, were also evaluated and can coupling can be used as an additional tool when it is necessary to confirm the results of prior quantitation by HPTLC–UV. The confirmation is provided by monitoring the HMF sodium adduct [M + Na]⁺ at m/z 149 followed by quantitation in TIC or SIM mode. Detection limits for HPTLC–UV, HPTLC–MS (TIC), and HPTLC–MS (SIM) were 0.8 ng/band, 4 ng/band, and 0.9 ng/band, respectively. If 12 μL honey solution was applied to an HPTLC plate, the respective detection limits for HMF in honey corresponded to 0.6 mg kg⁻¹. Thus, the developed method was highly suitable for quantitation of HMF in honey at the strictest regulated level of 15 mg kg⁻¹. Comparison of HPTLC–UV detection with HPTLC–MS showed findings were comparable, with a mean deviation of 5.1 mg kg⁻¹ for quantitation in SIM mode and 6.1 mg kg⁻¹ for quantitation in TIC mode. The mean deviation of the HPTLC method compared with the HPLC method was 0.9 mg kg^-1 HMF in honey. Re-evaluation of the same HPTLC plate after one month showed a deviation of 0.5 mg kg⁻¹ HMF in honey. It was demonstrated that the proposed HPTLC method is an effective method for HMF quantitation in honey.      

An approximation of the Cioslowski–Mixon bond order indexes using the AlteQ approach

Fast and reliable prediction of bond orders in organic systems based upon experimentally measured quantities can be performed using electron density features at bond critical points (J Am Chem Soc 105:5061–5068, 1983; J Phys Org Chem 16:133–141, 2003; Acta Cryst B 61:418–428, 2005; Acta Cryst B 63:142–150, 2007). These features are outcomes of low-temperature high-resolution X-ray diffraction experiments. However, a time-consuming procedure of gaining these quantities makes the prediction limited. In the present work we have employed an empirical approach AlteQ (J Comput Aided Mol Des 22:489–505, 2008) for evaluation of electron density properties. This approach uses a simple exponential function derived from comparison of electron density, gained from high-resolution X-ray crystallography, and distance to atomic nucleus what allows calculating density distribution in time-saving manner and gives results which are very close to experimental ones. As input data AlteQ accepts atomic coordinates of isolated molecules or molecular ensembles (for instance, protein–protein complexes or complexes of small molecules with proteins, etc.). Using AlteQ characteristics we have developed regression models predicting Cioslowski–Mixon bond order (CMBO) indexes (J Am Chem Soc 113(42):4142–4145, 1991). The models are characterized by high correlation coefficients lying in the range from 0.844 to 0.988 dependently on the type of covalent bond, thereby providing a bonding quantification that is in reasonable agreement with that obtained by orbital theory. Comparative analysis of CMBOs approximated using topological properties of AlteQ and experimental electron densities has shown that the models can be used for fast determination of bond orders directly from X-ray crystallography data and confirmed that AlteQ characteristics can replace experimental ones with satisfactory extent of accuracy.     

Heat capacity of methacetin in a temperature range of 6 to 300 K

Heat capacity of methacetin (N-(4-methoxyphenyl)-acetamide) has been measured in the temperature range 5.8–300 K. No anomalies in the C _p(T) dependence were observed. Thermodynamic functions were calculated. At 298.15 K, the values of entropy and enthalpy are equal to 243.1 J K⁻¹ mol⁻¹ and 36360 J mol⁻¹, respectively. The heat capacity of methacetin in the temperature range 6–10 K is well fitted by Debye equation C _p = AT ³. The thermodynamic data obtained for methacetin are compared with those for the monoclinic and orthorhombic polymorphs of paracetamol.     

Atomistic Insight Into the Host–Guest Interaction of a Photoresponsive Metal–Organic Framework

Photoresponsive functional materials have gained increasing attention due to their externally tunable properties. Molecular switches embedded in these materials enable the control of phenomena at the atomic level by light. Metal–organic frameworks (MOFs) provide a versatile platform to immobilize these photoresponsive units within defined molecular environments to optimize the intended functionality. For the application of these photoresponsive MOFs (pho-MOFs), it is crucial to understand the influence of the switching state on the host–guest interaction. Therefore, we present a detailed insight into the impact of molecular switching on the intermolecular interactions. By performing atomistic simulations, we revealed that due to different interactions of the guest molecules with the two isomeric states of an azobenzene-functionalized MOF, both the adsorption sites and the orientation of the molecules within the pores are modulated. By shedding light on the host–guest interaction, our study highlights the unique potential of pho-MOFs to tailor molecular interaction by light.     

Ferromagnetically Coupled S=1 Chains in Crystals of Verdazyl-Nitronyl Nitroxide Diradicals

Thermally stable organic diradicals with a triplet ground state along with large singlet-triplet energy gap have significant potential for advanced technological applications. A series of phenylene-bridged diradicals with oxoverdazyl and nitronyl nitroxide units were synthesized via a palladium-catalyzed cross-coupling reaction of iodoverdazyls with a nitronyl nitroxide-2-ide gold(I) complex with high yields. The diradicals exhibit high stability and do not decompose in an inert atmosphere up to 180 °C. For the diradicals, both substantial AF (ΔE_ST≈−64 cm⁻¹) and FM (ΔE_ST≥25 and 100 cm⁻¹) intramolecular exchange interactions were observed. The sign of the exchange interaction is determined both by the bridging moiety (para- or meta-phenylene) and by the type of oxoverdazyl block (C-linked or N-linked). Upon crystallization, diradicals with the triplet ground state form unique one-dimensional exchange-coupled chains with strong intra- and weak inter-diradical ferromagnetic coupling.     

UV absorption cross sections between 230 and 350 nm and pressure dependence of the photolysis quantum yield at 308 nm of CF3CH2CHO

Ultraviolet (UV) absorption cross sections of CF(3)CH(2)CHO were determined between 230 and 350 nm by gas-phase UV spectroscopy. The forbidden n → π* transition was characterized as a function of temperature (269-323 K). In addition, the photochemical degradation of CF(3)CH(2)CHO was investigated at 308 nm. The possible photolysis channels are: CF(3)CH(2) + HCO , CF(3)CH(3) + CO , and CF(3)CH(2)CO + H . Photolysis quantum yields of CF(3)CH(2)CHO at 308 nm, Φ(λ=308nm), were measured as a function of pressure (25-760 Torr of synthetic air). The pressure dependence of Φ(λ=308nm) can be expressed as the following Stern-Volmer equation: 1/Φ(λ=308nm) = (4.65 ± 0.56) + (1.51 ± 0.04) × 10(-18) [M] ([M] in molecule cm(-3)). Using the absorption cross sections and the photolysis quantum yields reported here, the photolysis rate coefficient of this fluorinated aldehyde throughout the troposphere was estimated. This calculation shows that tropospheric photolysis of CF(3)CH(2)CHO is competitive with the removal initiated by OH radicals at low altitudes, but it can be the major degradation route at higher altitudes. Photodegradation products (CO, HC(O)OH, CF(3)CHO, CF(3)CH(2)OH, and F(2)CO) were identified and also quantified by Fourier transform infrared spectroscopy. CF(3)CH(2)C(O)OH was identified as an end-product as a result of the chemistry involving CF(3)CH(2)CO radicals formed in the OH + CF(3)CH(2)CHO reaction. In the presence of an OH-scavenger (cyclohexane), CF(3)CH(2)C(O)OH was not detected, indicating that channel (R1c) is negligible. Based on a proposed mechanism, our results provide strong evidences of the significant participation of the radical-forming channel (R1a).     

Synthesis, structure and magnetic properties of Nd3+ and Pr3+ 2D polymers with tetrafluoro-p-phthalate

Two lanthanide tetrafluoro-p-phthalate (L(2-)) complexes, Ln(L)(1.5)·DMF·H(2)O (Ln = Pr(3+) (1), Nd(3+) (2)), were synthesized using pyridine as a base. The compounds were found to be isostructural, and the structure of 1 has been determined by single crystal X-ray diffraction (monoclinic, space group C2, a = 22.194(2) ?, b = 11.4347(12) ?, c = 11.7160(12) ?, β = 94.703(2)°, V = 2963.3(5) ?(3), Z = 4). The crystal structure of 1 consists of dinuclear Pr(3+) units, which are connected by tetrafluoro-p-phthalate, forming separate 2D polymeric layers. The Ln(3+) ions in the dinuclear Ln(2) units are linked by two μ-O atoms and by two bridging O-C-O groups. The structure is porous with DMF and water molecules located between layers. Non-coordinated DMF molecules occupy about 27% of the unit cell volume. A systematic analysis of reported structures of Ln(III) polymers with p-phthalate and its derivatives shows that the ca. known 60 structures can be divided into six possible structural types depending on the presence of certain structural motifs. The magnetic properties of compounds 1 and 2 were studied. The dependence of χ(M)T on T (where χ(M) is magnetic susceptibility per dinuclear lanthanide unit) for 1 and 2 was simulated using two different models, based on: (i) the Hamiltonian ? = Δ?(z)(2)+ μ(B)g(J)H?, which utilises an axial splitting parameter Δ and temperature-independent paramagnetism (tip) and (ii) crystal field splitting. It was found that both models gave satisfactory fits, indicating that the Ln-Ln exchange interactions are small and the symmetry of the coordination environment is the main factor influencing the magnetic properties of these compounds.     

Modified synthesis of Ru–Rh heterobimetallic metallacarboranes based on ruthenium exo-nido complexes and not accompanied by exo-nido → closo rearrangement

1. Download high-res image (125KB)
2. Download full-size image