A NMR and computational study of Smac mimics targeting both the BIR2 and BIR3 domains in XIAP protein

In this paper we report an extensive NMR analysis of small ligands (Smac mimics) complexed with different constructs of XIAP. The mimics-binding site of XIAP is known as the BIR3 domain - primary, and the linker BIR2 region - secondary site. Interactions between the BIR3 domain and Smac mimics have been extensively studied by X-ray but, as of today, there are scarce data about the interaction between BIR2, or the whole linker-BIR2-BIR3 construct, and Smac mimics. In order to characterize our Smac mimics, we performed a STD NMR study between our 4-substituted, 1-aza-2-oxobicyclo[5.3.0]decane scaffold-based molecules and three different XIAP fragments: single BIR2 and BIR3 domains, and bifunctional linker-BIR2-BIR3. The results were integrated with docking calculations and molecular dynamics simulations. NMR data, which are consistent with biological tests, indicated that the two BIR subunits interact differently with our Smac mimics and suggest that the ligands enter into more intimate contact with the linker-BIR2-BIR3. In conclusion, we observe that the SMAC mimics showed with the construct linker-BIR2-BIR3 a series of NOE contacts that were not observed in the mono-domain ligand:BIR2 or :BIR3 complexes. So, in agreement with the computational models we believe that the linker moieties of the binding site play a key role in the stability of the protein complex.     

Cyclic RGD peptidomimetics containing bifunctional diketopiperazine scaffolds as new potent integrin ligands

The synthesis of eight bifunctional diketopiperazine (DKP) scaffolds is described; these were formally derived from 2,3-diaminopropionic acid and aspartic acid (DKP-1-DKP-7) or glutamic acid (DKP-8) and feature an amine and a carboxylic acid functional group. The scaffolds differ in the configuration at the two stereocenters and the substitution at the diketopiperazinic nitrogen atoms. The bifunctional diketopiperazines were introduced into eight cyclic peptidomimetics containing the Arg-Gly-Asp (RGD) sequence. The resulting RGD peptidomimetics were screened for their ability to inhibit biotinylated vitronectin binding to the purified integrins α(v)β(3) and α(v)β(5), which are involved in tumor angiogenesis. Nanomolar IC(50) values were obtained for the RGD peptidomimetics derived from trans DKP scaffolds (DKP-2-DKP-8). Conformational studies of the cyclic RGD peptidomimetics by (1)H?NMR spectroscopy experiments (VT-NMR and NOESY spectroscopy) in aqueous solution and Monte Carlo/Stochastic Dynamics (MC/SD) simulations revealed that the highest affinity ligands display well-defined preferred conformations featuring intramolecular hydrogen-bonded turn motifs and an extended arrangement of the RGD sequence [Cβ(Arg)-Cβ(Asp) average distance ≥8.8??]. Docking studies were performed, starting from the representative conformations obtained from the MC/SD simulations and taking as a reference model the crystal structure of the extracellular segment of integrin α(v)β(3) complexed with the cyclic pentapeptide, Cilengitide. The highest affinity ligands produced top-ranked poses conserving all the important interactions of the X-ray complex.     

Carbon-Coated SiO2 Composites as Promising Anode Material for Li-Ion Batteries

Porous silica-based materials are a promising alternative to graphite anodes for Li-ion batteries due to their high theoretical capacity, low discharge potential similar to pure silicon, superior cycling stability compared to silicon, abundance, and environmental friendliness. However, several challenges prevent the practical application of silica anodes, such as low coulombic efficiency and irreversible capacity losses during cycling. The main strategy to tackle the challenges of silica as an anode material has been developed to prepare carbon-coated SiO₂ composites by carbonization in argon atmosphere. A facile and eco-friendly method of preparing carbon-coated SiO₂ composites using sucrose is reported herein. The carbon-coated SiO₂ composites were characterized using X-ray diffraction, X-ray photoelectron spectroscopy, thermogravimetry, transmission and scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy, cyclic voltammetry, and charge–discharge cycling. A C/SiO₂-0.085 M calendered electrode displays the best cycling stability, capacity of 714.3 mAh·g⁻¹, and coulombic efficiency as well as the lowest charge transfer resistance over 200 cycles without electrode degradation. The electrochemical performance improvement could be attributed to the positive effect of the carbon thin layer that can effectively diminish interfacial impedance.     

Towards a Bioactive Food Packaging: Poly(Lactic Acid) Surface Functionalized by Chitosan Coating Embedding Clove and Argan Oils

Here we introduce a new method aiming the immobilization of bioactive principles onto polymeric substrates, combining a surface activation and emulsion entrapment approach. Natural products with antimicrobial/antioxidant properties (essential oil from Syzygium aromaticum—clove and vegetal oil from Argania spinosa L—argan) were stabilized in emulsions with chitosan, a natural biodegradable polymer that has antimicrobial activity. The emulsions were laid on poly(lactic acid) (PLA), a synthetic biodegradable plastic from renewable resources, which was previously activated by plasma treatment. Bioactive materials were obtained, with low permeability for oxygen, high radical scavenging activity and strong inhibition of growth for Listeria monocytogenes, Salmonella Typhimurium and Escherichia coli bacteria. Clove oil was better dispersed in a more stable emulsion (no separation after six months) compared with argan oil. This leads to a compact and finely structured coating, with better overall properties. While both clove and argan oils are highly hydrophobic, the coatings showed increased hydrophilicity, especially for argan, due to preferential interactions with different functional groups in chitosan. The PLA films coated with oil-loaded chitosan showed promising results in retarding the food spoilage of meat, and especially cheese. Argan, and in particular, clove oil offered good UV protection, suitable for sterilization purposes. Therefore, using the emulsion stabilization of bioactive principles and immobilization onto plasma activated polymeric surfaces we obtained a bioactive material that combines the physical properties and the biodegradability of PLA with the antibacterial activity of chitosan and the antioxidant function of vegetal oils. This prevents microbial growth and food oxidation and could open new perspectives in the field of food packaging materials.     

A robust metal-organic framework constructed from alkoxo-bridged binuclear nodes and hexamethylenetetramine spacers: crystal structure and sorption studies

A neutral 3D metal-organic framework, (3)(∞)[Cu(2)(mand)(2)(hmt)]·H(2)O (1), was constructed from binuclear Cu(2)O(2) alkoxo-bridged nodes, generated by the doubly deprotonated mandelic acid. The nodes are connected by hexamethylenetetramine (hmt) spacers, which act as biconnective bridging ligands, and by carboxylato groups. Channels are observed along the crystallographic c axis. The water molecules from the channels can be easily removed, preserving the architecture of the crystal, which is stable up to 280 °C. The Langmuir surface area was found to be 610 m(2) g(-1). The sorption ability of 1 was investigated using H(2) and CO(2).     

A comparison study between a disposable electrochemical DNA biosensor and a Vibrio fischeri-based luminescent sensor for the detection of toxicants in water samples

In the present study, a comparison between a disposable electrochemical DNA biosensor and a Vibrio fischeri-based luminescent sensor for the detection of toxicants in water samples was made.In order to realize this study, a disposable electrochemical DNA biosensor has been reported. The DNA biosensor is assembled by immobilizing double stranded Calf Thymus DNA onto the surface of a disposable carbon screen-printed electrode. The oxidation signal of the guanine base, obtained by a square wave voltammetric scan, is used as analytical signal to detect the DNA damage; the presence of low molecular weight compounds with affinity for nucleic acids is measured by their effect on the guanine oxidation peak.Wastewater samples provided during First European Interlaboratory Exercise on water toxicity in the course of the project SWIFT-WFD were analyzed, and biosensor results were compared with a currently used toxicity test ToxAlert^®100 based on the bioluminescence inhibition of Vibrio fischeri. This test have been used because is rapid, easy handling and cost effectively responses for the toxicity assessment in real water samples.The results showed a promising correlation between two tests used for the detection of toxic compounds in water samples.     

Trapping of a Thiolate→Dibromine Charge‐Transfer Adduct by a Macrocyclic Dinickel Complex and Its Conversion into an Arenesulfenyl Bromide Derivative

Stuck on sulfur : The first transition‐metal complexes with S? Br units are surprisingly stable. Solid 3 is stable for at least six months and under vacuum solid 2 does not lose Br₂. The formation of the first structurally characterized transition‐metal arenesulfenyl bromide complex 3 occurs with a change of the spin ground state from S=2 to S=0.

     

Rank-two vector bundles on Hirzebruch surfaces

We survey some parts of the vast literature on vector bundles on Hirzebruch surfaces, focusing on the rank-two case.     

Iron oxide nanoparticle synthesis in aqueous and membrane systems for oxidative degradation of trichloroethylene from water

The potential for using hydroxyl radical (OH^?) reactions catalyzed by iron oxide nanoparticles (NPs) to remediate toxic organic compounds was investigated. Iron oxide NPs were synthesized by controlled oxidation of iron NPs prior to their use for contaminant oxidation (by H₂O₂ addition) at near-neutral pH values. Cross-linked polyacrylic acid (PAA) functionalized polyvinylidene fluoride (PVDF) microfiltration membranes were prepared by in situ polymerization of acrylic acid inside the membrane pores. Iron and iron oxide NPs (80–100 nm) were directly synthesized in the polymer matrix of PAA/PVDF membranes, which prevented the agglomeration of particles and controlled the particle size. The conversion of iron to iron oxide in aqueous solution with air oxidation was studied based on X-ray diffraction, Mössbauer spectroscopy and BET surface area test methods. Trichloroethylene (TCE) was selected as the model contaminant because of its environmental importance. Degradations of TCE and H₂O₂ by NP surface generated OH^? were investigated. Depending on the ratio of iron and H₂O₂, TCE conversions as high as 100 % (with about 91 % dechlorination) were obtained. TCE dechlorination was also achieved in real groundwater samples with the reactive membranes.     

A Cheminformatics Study Regarding the Human Health Risks Assessment of the Stereoisomers of Difenoconazole

Difenoconazole is a chemical entity containing two chiral centers and having four stereoisomers: (2R,4R)-, (2R,4S)-, (2S,4R)- and (2S,4S)-difenoconazole, the marketed product containing a mixture of these isomers. Residues of difenoconazole have been identified in many agricultural products and drinking water. A computational approach has been used to evaluate the toxicological effects of the difenoconazole stereoisomers on humans. It integrates predictions of absorption, distribution, metabolism, excretion and toxicity (ADMET) profiles, prediction of metabolism sites, and assessment of the interactions of the difenoconazole stereoisomers with human cytochromes, nuclear receptors and plasma proteins by molecular docking. Several toxicological effects have been identified for all the difenoconazole stereoisomers: high plasma protein binding, inhibition of cytochromes, possible hepatotoxicity, neurotoxicity, mutagenicity, skin sensitization potential, moderate potential to produce endocrine disrupting effects. There were small differences in the predicted probabilities of producing various biological effects between the distinct stereoisomers of difenoconazole. Furthermore, there were significant differences between the interacting energies of the difenoconazole stereoisomers with plasma proteins and human cytochromes, the spectra of the hydrogen bonds and aromatic donor–acceptor interactions being quite distinct. Some distinguishing results have been obtained for the (2S,4S)-difenoconazole: it registered the highest value for clearance, exposed reasonable probabilities to produce cardiotoxicity and carcinogenicity and negatively affected numerous nuclear receptors.