DFT investigation of the formation of linear aminols as the first step toward the induction of oxidatively generated interstrand cross-link DNA lesions

Apyrimidinic/apurinic sites feature among the most prevalent DNA lesions. If not repaired, it has been recently evidenced that they are prone to react in situ with vicinal nucleobases, evolving toward more complex and highly mutagenic interstrand cross-links. Information concerning the structure and the multi-step reactivity leading to such clustered defects is scarce due to their low formation yield. This study reports a DFT exploration of the condensation reaction between a ketoaldehyde (derived from an oxidized C4’ abasic site) and three nucleobases featuring an amino group. They are found to present a very similar intrinsic reactivity, indicating in turn that differences of reactivity arise more from the relative positioning of the two reactive fragments within a flexible B-DNA. We also probe the role of a vicinal water molecule for the formation of the aminol and the requirements to reach an adequate estimate of this strongly exothermic reaction, which drives the DNA damage process.     

Determination of the specific heat using laser flash apparatus

Journal of Thermal Analysis and Calorimetry - The main aim of this article was to describe the methodology for the measurement of specific heat using the laser flash apparatus. The obtained values...     

Total Synthesis of Albicidin: A Lead Structure from Xanthomonas albilineans for Potent Antibacterial Gyrase Inhibitors

The peptide antibiotic albicidin, which is synthesized by the plant pathogenic bacterium Xanthomonas albilineans, displays remarkable antibacterial activity against various Gram‐positive and Gram‐negative microorganisms. The low amounts of albicidin obtainable from the producing organism or through heterologous expression are limiting factors in providing sufficient material for bioactivity profiling and structure–activity studies. Therefore, we developed a convergent total synthesis route toward albicidin. The unexpectedly difficult formation of amide bonds between the aromatic amino acids was achieved through a triphosgene‐mediated coupling strategy. The herein presented synthesis of albicidin confirms the previously determined chemical structure and underlines the extraordinary antibacterial activity of this compound. The synthetic protocol will provide multigram amounts of albicidin for further profiling of its drug properties.     

Structure of Framework Aluminum Lewis Sites and Perturbed Aluminum Atoms in Zeolites as Determined by 27Al{1H} REDOR (3Q) MAS NMR Spectroscopy and DFT/Molecular Mechanics

Zeolites are highly important heterogeneous catalysts. Besides Brønsted SiOHAl acid sites, also framework Al_FR Lewis acid sites are often found in their H‐forms. The formation of Al_FR Lewis sites in zeolites is a key issue regarding their selectivity in acid‐catalyzed reactions. The local structures of Al_FR Lewis sites in dehydrated zeolites and their precursors—“perturbed” Al_FR atoms in hydrated zeolites—were studied by high‐resolution MAS NMR and FTIR spectroscopy and DFT/MM calculations. Perturbed framework Al atoms correspond to (SiO)₃AlOH groups and are characterized by a broad ²⁷Al NMR resonance (δ_i=59–62 ppm, C_Q=5 MHz, and η=0.3–0.4) with a shoulder at 40 ppm in the ²⁷Al MAS NMR spectrum. Dehydroxylation of (SiO)₃AlOH occurs at mild temperatures and leads to the formation of Al_FR Lewis sites tricoordinated to the zeolite framework. Al atoms of these (SiO)₃Al Lewis sites exhibit an extremely broad ²⁷Al NMR resonance (δ_i≈67 ppm, C_Q≈20 MHz, and η≈0.1).     

Electrochemical Activity of Wedelolactone and Probing its Interaction with DNA Using Voltammetry at a Carbon Electrode

Wedelolactone (WLA) is a polyphenolic coumestan derivative found in extracts of plants used in traditional medicine. Due to its cytostatic activity, WLA is one of natural compounds tested as potential anticancer drugs. In this work we for the first time studied electrochemical properties of WLA using cyclic (CV) and square‐wave (SWV) voltammetry at the basal‐plane pyrolytic graphite electrode. A reversible pair of peaks, corresponding to catechol/o‐benzoquinone redox system, was observed using CV around 0.275 V vs. Ag|AgCl|3 M KCl reference electrode. Measurements of SWV signal of WLA in the presence of single‐ or double‐stranded DNA suggested a weak interaction without evident preference for double‐stranded DNA. An indirect assay, employing electroactive DNA intercalator doxorubicin as competitor, confirmed absence of intercalative DNA binding of WLA.     

Square‐Wave Voltammetry of Electroinactive Surfactants

Under the influence of previously published and some new theoretical results, potential‐ dependent adsorption and desorption of model electroinactive surfactants Triton X‐100 (T‐X‐100 or polyethylene glycol p‐(1,1,3,3‐tetramethylbutyl)‐phenyl ether) and sodium dodecyl sulfate (SDS) on the static mercury drop electrode (SMDE) were studied by square‐wave voltammetry (SWV). Although (according to the theory) the resulting current – potential curve should consist of two highly separated peaks, only desorption signal could be seen on each experimentally obtained voltammogram, most probably because of the limitations concerning the available potential range. Different properties of the recorded peak are in good agreement with the theory indicating that square‐wave voltammetry could be treated as a potential tool for tensammetric studies of electroinactive surface active substances.     

Arrival time distributions of product ions reveal isomeric ratio of deprotonated molecules in ion mobility–mass spectrometry of hyaluronan‐derived oligosaccharides

Hyaluronic acid is a naturally occurring linear polysaccharide with substantial medical potential. In this work, discrimination of tyramine‐based hyaluronan derivatives was accessed by ion mobility–mass spectrometry of deprotonated molecules and nuclear magnetic resonance spectroscopy. As the product ion mass spectra did not allow for direct isomer discrimination in mixture, the reductive labeling of oligosaccharides as well as stable isotope labeling was performed. The ion mobility separation of parent ions together with the characteristic fragmentation for reduced isomers providing unique product ions allowed us to identify isomers present in a mixture and determine their mutual isomeric ratio. The determination used simple recalculation of arrival time distribution areas of unique ions to areas of deprotonated molecules. Mass spectrometry data were confirmed by nuclear magnetic resonance spectroscopy. Copyright © 2015 John Wiley & Sons, Ltd.     

High‐throughput workflow for identification of phosphorylated peptides by LC‐MALDI‐TOF/TOF‐MS coupled to in situ enrichment on MALDI plates functionalized by ion landing

We report an MS‐based workflow for identification of phosphorylated peptides from trypsinized protein mixtures and cell lysates that is suitable for high‐throughput sample analysis. The workflow is based on an in situ enrichment on matrix‐assisted laser desorption/ionization (MALDI) plates that were functionalized by TiO₂ using automated ion landing apparatus that can operate unsupervised. The MALDI plate can be functionalized by TiO₂ into any array of predefined geometry (here, 96 positions for samples and 24 for mass calibration standards) made compatible with a standard MALDI spotter and coupled with high‐performance liquid chromatography. The in situ MALDI plate enrichment was compared with a standard precolumn‐based separation and achieved comparable or better results than the standard method. The performance of this new workflow was demonstrated on a model mixture of proteins as well as on Jurkat cells lysates. The method showed improved signal‐to‐noise ratio in a single MS spectrum, which resulted in better identification by MS/MS and a subsequent database search. Using the workflow, we also found specific phosphorylations in Jurkat cells that were nonspecifically activated by phorbol 12‐myristate 13‐acetate. These phosphorylations concerned the mitogen‐activated protein kinase/extracellular signal‐regulated kinase signaling pathway and its targets and were in agreement with the current knowledge of this signaling cascade. Control sample of non‐activated cells was devoid of these phosphorylations. Overall, the presented analytical workflow is able to detect dynamic phosphorylation events in minimally processed mammalian cells while using only a short high‐performance liquid chromatography gradient. Copyright © 2015 John Wiley & Sons, Ltd.     

Identification of Structure–Activity Relationships from Screening a Structurally Compact DNA‐Encoded Chemical Library

Methods for the rapid and inexpensive discovery of hit compounds are essential for pharmaceutical research and DNA‐encoded chemical libraries represent promising tools for this purpose. We here report on the design and synthesis of DAL‐100K, a DNA‐encoded chemical library containing 103 200 structurally compact compounds. Affinity screening experiments and DNA‐sequencing analysis provided ligands with nanomolar affinities to several proteins, including prostate‐specific membrane antigen and tankyrase 1. Correlations of sequence counts with binding affinities and potencies of enzyme inhibition were observed and enabled the identification of structural features critical for activity. These results indicate that libraries of this type represent a useful source of small‐molecule binders for target proteins of pharmaceutical interest and information on structural features important for binding.