Synthesis,photochemical synthesis and antitumor evaluation of novel derivatives of thieno[3',2':4,5]thieno[2,3-c]quinolones

The novel derivatives of thieno[3',2':4,5]thieno[2,3-c]quinolones 6a, 6b, 7, 10a and 10b were synthesized in multistep synthesis starting from thiophene-3-carboxaldehyde and malonic acid reacting in aldol condensation or from 3-bromothiophenes or methyl 4-bromothiophene-2-carboxylate reacting in Heck reaction. They resulted in corresponding substituted thienylacrylic acids 3a-c, which were cyclized into thieno[2,3-c]thiophene-2-carbonyl chlorides 4a-c and converted into thieno[2,3-c]thiophene-2-carboxamides 5a-d. Prepared carboxamides were photochemically dehydrohalogenated into corresponding substituted thieno[3',2':4,5]thieno[2,3-c]quinolones 6a-d. Compound 7 was prepared from 6d by alkylation with N-[3-(dimethylamino)propyl]chloride hydrochloride in the presence of NaH. Compounds 10a and 10b were prepared from 6c in the multistep synthesis over acid 8 and acid chloride 9. Compounds 6a, 6b, 7, 10a and 10b were found to exert cytostatic activities against malignant cell lines: pancreatic carcinoma (MiaPaCa2), breast carcinoma (MCF7), cervical carcinoma (HeLa), laryngeal carcinoma (Hep2), colon carcinoma (CaCo-2), melanoma (HBL), and human fibroblast cell lines (WI-38). The compound 6b, which bears the 3-dimethylaminopropyl substituent on quinolone nitrogen and methoxycarbonyl substituent on position 9, exhibited marked antitumor activity. On the contrary, compound 7, which also bears the 3-dimethylaminopropyl substituent on the quinolone nitrogen but anilido substituent on position 9, exhibited less antitumor activity than the others.     

Reconstructing Free Energy Profiles from Nonequilibrium Relaxation Trajectories

Reconstructing free energy profiles is an important problem in bimolecular reactions, protein folding or allosteric conformational changes. Nonequilibrium trajectories are readily measured experimentally, but their statistical significance and relation to equilibrium system properties still call for rigorous methods of assessment and interpretation. Here we introduce methods to compute the equilibrium free energy profile of a given variable from a set of short nonequilibrium trajectories, obtained by externally driving a system out of equilibrium and subsequently observing its relaxation. This protocol is not suitable for the Jarzynski equality since the irreversible work on the system is instantaneous. Assuming that the variable of interest satisfies an overdamped Langevin equation, which is frequently used for modeling biomolecular processes, we show that the trajectories sample a nonequilibrium stationary distribution that can be calculated in closed form. This allows for the estimation of the free energy via an inversion procedure that is analogous to that used in equilibrium and bypasses more complicated path integral methods, which we derive for comparison. We generalize the inversion procedure to systems with a diffusion constant that depends on the reaction coordinate, as is the case in protein folding, as well as to protocols in which the trajectories are initiated at random points. Using only a statistical pool of tens of synthetic trajectories, we demonstrate the versatility of these methods by reconstructing double and multi-well potentials, as well as a proposed profile for the hydrophobic collapse of a protein.     

A new approach to the analysis of nicarbazin and ionophores in eggs by HPLC/MS/MS

An HPLC/MS/MS method has been developed and validated for the quantification and confirmation of nicarbazin and ionophores (lasalocid, monensin, salinomycin, and narasin) in eggs. Nicarbazin is determined in the negative electrospray mode with a basic mobile phase that supports creation of negative ions. Consequently, our ability to maintain instrument sensitivity over time has significantly improved. The analysis of the ionophores is done in the positive electrospray mode using ammonium buffer for HPLC separation. Monitoring ammonium adduct parent ions resulted in enhanced sensitivity and better reproducibility of the ionophore analysis. The validation of this improved HPLC/MS/MS method for the detection of nicarbazin and the ionophores demonstrated excellent precision of below 10% RSD and lower LOD values (microg/kg) for nicarbazin (0.018), lasalocid (0.015), monensin (0.015), salinomycin (0.033), and narasin (0.039).     

A correlation of the limiting viscosity number, molecular mass and composition of statistical linear styrene-methyl methacrylate copolymers

Statistical copolymers of styrene and methyl methacrylate of different compositions were synthesized by the radical solution copolymerization in a batch isothermal reactor. Copolymers were characterized by the size exclusion chromatography (SEC), elemental analysis and dilute solution viscometry. Experimental limiting viscosity numbers were described by the Mark-Houwink-Kuhn-Sakurada correlation as the function of the molar mass and by the Mendelson correlation as the function of both the molar mass and copolymer composition. A new correlation of the intrinsic viscosity number, molar mass and composition was developed, based on semiempirical considerations. The correlation takes into consideration all the effects which affect the dimensions of random linear copolymer coils in solvents. The new equation was found to be superior to the Mendelson’s one in correlating the experimentally obtained intrinsic viscosities.     

Characterization of Mercury Contamination Surrounding a Chloralkali Production Facility in Tuzla,Bosnia and Herzegovina

Tuzla is among the most polluted cities of Bosnia and Herzegovina. The main source of pollution in the area is soil heavily contaminated by mercury released from a former chloralkali plant. This paper is focused on the characterization of mercury contaminated soil and air surrounding the chloralkali plant. In soil, the mobility and transformation of mercury were investigated by sequential extraction, while the methylation and reduction potentials were determined by the use of a radioactive tracer. Mercury emission from soil was determined by laboratory and by flux chamber measurements in the field. In addition, mercury concentrations in air were estimated by the analysis of air and the transplanted lichen Hypogymnia physodes. Mercury in soils in the vicinity of the chloralkali plant exceeded the background value by a factor of more than 3000. The fractionation of mercury in surface soil by sequential extraction showed that the mercury in soil was primarily bound to organic matter and a fraction containing elemental mercury and mercury (I) chloride is also significant. The obtained methylation and reduction potentials are low. The mercury flux from soil was estimated by two approaches. Fluxes of up to 8000?ng/m²/day were measured at the most polluted site; evaporation from soil was shown to be the primary source of elevated mercury in air. Air concentration mapping also revealed other sources of mercury; the most likely is the 715 MW coal power plant in the vicinity of former chloralkali facility.     

Ultrahigh-resolution (1)H-(13)C HSQC spectra of metabolite mixtures using nonlinear sampling and forward maximum entropy reconstruction

To obtain a comprehensive assessment of metabolite levels from extracts of leukocytes, we have recorded ultrahigh-resolution 1H-13C HSQC NMR spectra of cell extracts, which exhibit spectral signatures of numerous small molecules. However, conventional acquisition of such spectra is time-consuming and hampers measurements on multiple samples, which would be needed for statistical analysis of metabolite concentrations. Here we show that the measurement time can be dramatically reduced without loss of spectral quality when using nonlinear sampling (NLS) and a new high-fidelity forward maximum-entropy (FM) reconstruction algorithm. This FM reconstruction conserves all measured time-domain data points and guesses the missing data points by an iterative process. This consists of discrete Fourier transformation of the sparse time-domain data set, computation of the spectral entropy, determination of a multidimensional entropy gradient, and calculation of new values for the missing time-domain data points with a conjugate gradient approach. Since this procedure does not alter measured data points, it reproduces signal intensities with high fidelity and does not suffer from a dynamic range problem. As an example we measured a natural abundance 1H-13C HSQC spectrum of metabolites from granulocyte cell extracts. We show that a high-resolution 1H-13C HSQC spectrum with 4k complex increments recorded linearly within 3.7 days can be reconstructed from one-seventh of the increments with nearly identical spectral appearance, indistinguishable signal intensities, and comparable or even lower root-mean-square (rms) and peak noise patterns measured in signal-free areas. Thus, this approach allows recording of ultrahigh resolution 1H-13C HSQC spectra in a fraction of the time needed for recording linearly sampled spectra.     

On-line sheathless capillary electrophoresis/nanoelectrospray ionization-tandem mass spectrometry for the analysis of glycosaminoglycan oligosaccharides

A novel approach in glycosaminoglycomics, based on sheathless on-line capillary electrophoresis/nanoelectrospray ionization-quadrupole time of flight-mass spectrometry (CE/nanoESI-QTOF-MS) and tandem MS of extended chondroitin sulfate/dermatan (CS/DS) oligosaccharide chains is described. The methodology required the construction of a new sheathless CE/nanoESI-QTOF-MS configuration, its implementation and optimization for the high sensitivity analysis of CS/DS oligosaccharide mixtures from conditioned culture medium of decorin transfected human embryonic kidney (HEK) 293 cells. Under newly established sheathless on-line CE/(-)nanoESI conditions for glycosaminoglycan (GAG) ionization and MS detection, single CS/DS oligosaccharide components of extended chain length and increased sulfation degree were identified. Molecular ions corresponding to species carrying 5 and 6 negative charges could be generated for large GAG oligosaccharide species in the negative ion nanoESI-MS. The optimized on-line conditions enabled the detection of molecular ions assigned to oversulfated tetradeca-, octadeca-, and eicosasaccharide CS/DS molecules, which represent the category of largest sulfated GAG-derived oligosaccharides evidenced by CE/ESI-MS. By on-line CE/ESI tandem MS in data-dependent acquisition mode the oversulfated eicosasaccharide species could be sequenced and the localization of the additional sulfate group along the chain could be determined.