Screening of matrix metalloproteinases available from the protein data bank: insights into biological functions, domain organization, and zinc binding groups

A total of 142 matrix metalloproteinase (MMP) X-ray crystallographic structures were retrieved from the Protein Data Bank (PDB) and analyzed by an automated and efficient routine, developed in-house, with a series of bioinformatic tools. Highly informative heat maps and hierarchical clusterograms provided a reliable and comprehensive representation of the relationships existing among MMPs, enlarging and complementing the current knowledge in the field. Multiple sequence and structural alignments permitted better location and display of key MMP motifs and quantification of the residue consensus at each amino acid position in the most critical binding subsites of MMPs. The MMP active site consensus sequences, the C-alpha root-mean-square deviation (RMSd) analysis of diverse enzymatic subsites, and the examination of the chemical nature, binding topologies, and zinc binding groups (ZBGs) of ligands extracted from crystallographic complexes provided useful insights on the structural arrangements of the most potent MMP inhibitors.     

OLED with Hole-Transporting Layer Fabricated by Ink-Jet Printing

we report about the fabrication of organic light-emitting diodes (OLEDs) ink-jet printing a hole-transporting polymer (PF6, poly(9,9-dihexyl-9H-fluorene-2,7-diyl)) on flexible substrate (PET) and performing the other layers through vacuum thermal evaporation. The aim of the work is to employ the ink-jet printing (IJP) technology, familiar as a method for printing on paper, in optoelectronic applications and to determine how the deposition method affects the functional material film properties and hence the ultimate device performances. In this line of work, ink-jet printed polymer films are compared to same spin-coated polymer from the electro-optical point of view: both prepared materials are adopted as HTLs of electroluminescent devices. All manufactured OLEDs are characterized and their behaviours are investigated and analyzed with theoretical models. The results show differences in current density and optical behaviours between the devices fabricated by means of the above mentioned technologies which can be justified in terms of different trap distribution induced by impurity energy levels associated to each process.     

An integrated approach to ligand- and structure-based drug design: development and application to a series of serine protease inhibitors

A novel approach was developed to rationally interface structure- and ligand-based drug design through the rescoring of docking poses and automated generation of molecular alignments for 3D quantitative structure-activity relationship investigations. The procedure was driven by a genetic algorithm optimizing the value of a novel fitness function, accounting simultaneously for best regressions among binding-energy docking scores and affinities and for minimal geometric deviations from properly established crystal-based binding geometry. The GRID/CPCA method, as implemented in GOLPE, was used to feature molecular determinants of ligand binding affinity for each molecular alignment. In addition, unlike standard procedures, a novel multipoint equation was adopted to predict the binding affinity of ligands in the prediction set. Selectivity was investigated through square plots reporting experimental versus recalculated binding affinities on the targets under examination. The application of our approach to the modeling of affinity data of a large series of 3-amidinophenylalanine inhibitors of thrombin, trypsin, and factor Xa generated easily interpretable and independent models with robust statistics. As a further validation study, our approach was successfully applied to a series of 3,4,7-substituted coumarins, acting as selective MAO-B inhibitors.     

Efficiency and Aging Comparison Between N,N′-Bis (3-methylphenyl)-N,N′-diphenylbenzidine (TPD) and N,N′-Di-[(1-naphthalenyl)-N,N′-diphenyl]-1,1′-biphenyl-4,4′-diamine (NPD) Based OLED Devices

In this paper we present and discuss experimental results to evaluate performances and aging behaviour of two Hole Transporting Material (HTM), TPD and NPD, in Organic Light Emitting Device (OLED) with structure: ITO/HTM/Alq3/Al. For each of these HTMs, devices with several thicknesses have been built, to measure and emphasize behaviours of material-geometry combinations. Electro-optical properties have been measured to estimate and compare brightness, power efficiency and aging decays.     

Phosphorylating reagent-free synthesis of 5'-phosphate oligonucleotides by controlled oxidative degradation of their 5'-end

The 5'-phosphorylated oligonucleotides (5'-pONs) are currently synthesized using expensive and sensitive modified phosphoramidite reagents. In this work, a simple, cost-effective, efficient, and automatable method is presented, based on the controlled oxidation of the 5'-terminal alcohol followed by a β-elimination reaction. The latter reaction leads to the removal of the terminal 5'-nucleoside and subsequent formation of the 5'-phosphate moiety. Thus, chemical phosphorylation of oligonucleotides (DNA or RNA) is achieved without using modified phosphoramidites.     

Screening of benzamidine-based thrombin inhibitors via a linear interaction energy in continuum electrostatics model

Abstract  

A series of 27 benzamidine inhibitors covering a wide range of biological activity and chemical diversity was analysed to derive a Linear Interaction Energy in Continuum Electrostatics (LIECE) model for analysing the thrombin inhibitory activity. The main interactions occurring at the thrombin binding site and the preferred binding conformations of inhibitors were explicitly biased by including into the LIECE model 10 compounds extracted from X-ray solved thrombin-inhibitor complexes available from the Protein Data Bank (PDB). Supported by a robust statistics (r ² = 0.698; q ² = 0.662), the LIECE model was successful in predicting the inhibitory activity for about 76% of compounds (r _ext² ≥ 0.600) from a larger external test set encompassing 88 known thrombin inhibitors and, more importantly, in retrieving, at high sensitivity and with better performance than docking and shape-based methods, active compounds from a thrombin combinatorial library of 10240 mimetic chemical products. The herein proposed LIECE model has the potential for successfully driving the design of novel thrombin inhibitors with benzamidine and/or benzamidine-like chemical structure.     

A Study on Thermal Degradation of Organic LEDs Using IR Imaging

In this paper, we present a correlation study between the working temperature of OLEDs (Organic Light Emitting Diodes) and the electroluminescence and driving voltage changes. The aim is to investigate the relationship between the operating temperature and the aging mechanisms. We have found that performances degradation of devices is strictly related to the glass transition temperature (T_g) of organic layers, and that electrical failure is reached only for temperatures higher than T_g.