Lucia Sessa

YADAMP: yet another database of antimicrobial peptides

This work presents an antimicrobial peptide database (YADAMP) based on an extensive literature search. This database is focused primarily on bacteria, with detailed information for 2133 peptides active against bacteria. YADAMP was created to facilitate access to critical information on antimicrobial peptides (AMPs). The main difference between YADAMP and other web databases of AMPs is the explicit presence of antimicrobial activity against the most common bacterial strains. YADAMP allows complex queries, easily accessible through a web interface. Peptide information can be retrieved based on peptide name, number of amino acids, net charge, hydrophobic percentage, sequence motif, structure and activity against bacteria. YADAMP is suitable for reviewing information on AMPs and for structure-function analyses of peptides. The database can be accessed via a web-based browser at http://www.yadamp.unisa.it.

Small azobenzene derivatives active against bacteria and fungi.

ATP synthase and protein kinase (PKs) are prime targets for drug discovery in a variety of diseases. It is well known that numerous stilbenes are capable to interact and inhibit ATP synthase and PKs. This work focuses on a series of azobenzene based molecules having high structural similarity with antimicrobial stilbenes. An investigation was carried out analyzing the potential toxicity of a large set of molecules by means of computational analysis. A small selection of potential low toxic molecules have been therefore synthesized, characterized and finally microbiologically tested. The synthesized compounds show potent bactericidal activity against Gram+ and a fungus, and are capable of inhibiting biofilm formation. Finally, the compounds demonstrated a thermal stability that makes them potential candidates for incorporation in polymer matrix for application as biomedical devices and food packaging.

Yada: a novel tool for molecular docking calculations

Molecular docking is a computational method employed to estimate the binding between a small ligand (the drug candidate) and a protein receptor that has become a standard part of workflow in drug discovery. Generally, when the binding site is known and a molecule is similar to known ligands, the most popular docking methods are rather accurate in the prediction of the geometry. Unfortunately, when the binding site is unknown, the blind docking analysis requires large computational resources and the results are often not accurate. Here we present Yada, a new tool for molecular docking that is capable to distribute efficiently calculations onto general purposes computer grid and that combines biological and structural information of the receptor. Yada is available for Windows and Linux and it is free to download at www.yada.unisa.it.

Novel Algorithm for Efficient Distribution of Molecular Docking Calculations

Molecular docking is a computational method to study the formation of intermolecular complexes between two molecules. In drug discovery, it is employed to estimate the binding between a small ligand (the drug candidate), and a protein of known three-dimensional structure. Docking is becoming a standard part of workflow in drug discovery. Recently, we have used the software VINA, a de facto standard in molecular docking, to perform extensive docking analysis. Unfortunately, performing a successful blind docking procedure requires large computational resources that can be obtained by the use of clusters or dedicated grid. Here we present a new tool to distribute efficiently a molecular docking calculation onto a grid changing the distribution paradigm: we define portions on the protein surface, named hotspots, and the grid will perform a local docking for each region. Performance studies have been conducted via the software GRIMD.

Structure Modification of an Active Azo-Compound as a Route to New Antimicrobial Compounds

Some novel (phenyl-diazenyl)phenols 3a–g were designed and synthesized to be evaluated for their antimicrobial activity. A previously synthesized molecule, active against bacteria and fungi, was used as lead for modifications and optimization of the structure, by introduction/removal or displacement of hydroxyl groups on the azobenzene rings. The aim of this work was to evaluate the consequent changes of the antimicrobial activity and to validate the hypothesis that, for these compounds, a plausible mechanism could involve an interaction with protein receptors, rather than an interaction with membrane. All newly synthesized compounds were analyzed by 1H-NMR, DSC thermal analysis and UV-Vis spectroscopy. The in vitro minimal inhibitory concentrations (MIC) of each compound was determined against Gram-positive and Gram-negative bacteria and Candida albicans. Compounds 3b and 3g showed the highest activity against S. aureus and C. albicans, with remarkable MIC values of 10 µg/mL and 3 µg/mL, respectively. Structure-activity relationship studies were capable to rationalize the effect of different substitutions on the phenyl ring of the azobenzene on antimicrobial activity.

Synthesis and Antimicrobial Studies of New Antibacterial Azo-Compounds Active against Staphylococcus aureus and Listeria monocytogenes

Some novel (phenyl-diazenyl)phenols (4a–m) were designed and synthesized to be evaluated for their antibacterial activity. Starting from an active previously-synthesized azobenzene chosen as lead compound, we introduced some modifications and optimization of the structure, in order to improve solubility and drug conveyance. Structures of all newly-synthesized compounds were confirmed by 1H nuclear magnetic resonance (NMR), mass spectrometry, and UV-Vis spectroscopy. Antibacterial activity of the new compounds was tested with the dilution method against the bacteria strains Listeria monocytogenes, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa PAO1. All the compounds were selectively active against Gram-positive bacteria. In particular, compounds 4d, 4h, and 4i showed the highest activity against S. aureus and Listeria monocytogenes, reaching remarkable MIC100 values of 4 μg/mL and 8 μg/mL. The relationship between antimicrobial activity and compound structure has suggested that the presence of hydroxyl groups seems to be essential for antimicrobial activity of phenolic compounds.

Antimicrobial azobenzene compounds and their potential use in biomaterials

We recently synthesized a class of active compounds with azobenzene structure [1] and lowest in silico toxicity values. The antimicrobial activity of these molecules and their thermal stability are very promising and indicate that they may have interesting and therapeutically significant applications. This work aims to develop new materials with antibacterial and antifungal activity inserting different percentages of synthetic antimicrobial azo compounds in commercial polymer matrices. We realized thin films using solvent casting and melt compounding techniques. The obtained materials retained the proprieties of the pure matrices. This means that azo dye dissolved in the matrix does not influence the thermal behavior and the morphology of the material. Tested films exhibited the capability to inhibit biofilms formation of S. aureus and C. albicans. Spectrophotometric investigation of the azo compound released from the polymer matrices confirmed that the realized materials might be interesting for biomedic...

A New Flexible Protocol for Docking Studies

A significant prerequisite for computational structure-based drug design is the estimation of the structures of ligand-receptor complexes. For this task, the flexibility of both ligand and receptor backbone is required, but it requires the exploration of an extremely vast conformational space. Here we present a protocol to address the receptor flexibility using complementary strategies and the use of receptor sequence conservation. The method aims to increase the accuracy of predicted ligand orientation in the binding pocket and the receptor-ligand binding affinity. The precision in affinity prediction permits to distinguish between binders and non-binders and to identify binding sites and ligand poses necessary for lead optimization.

Electrical Hole Transport Properties of an Ambipolar Organic Compound With Zn-Atoms on a Crystalline Silicon Heterostructure

In this paper, we investigate the electrical hole transport properties of an organic/inorganic heterostructure consisting of a thin organic film, that combines hole and electron conducting molecules around a bridging Zn-atom, deposited on top of an n-type crystalline silicon substrate. Current-voltage characteristics and capacitance voltage measurements have been used for the determination of the organic layer dielectric and hole conduction parameters.

A novel fluorescent solvatochromic probe for lipid bilayers

Abstract The cell membrane is a heterogeneous system constituted mainly by lipids and proteins in which the physical state is finely regulated to guarantee the regular functions. Among the numerous analytical techniques employed in membrane investigation, a special role is the one of fluorescence microscopy. Fluorescence microscopy allows a fast and non-disruptive investigation of model membranes as well as living samples. Numerous fluorescent probes are known, but most of them are unsuitable for membrane studies, since they either alter the membrane structure or they are internalized in the cell. In this work, we report the rational design and the synthesis of a new fluorescent membrane probe and its characterization in model membranes. The probe consists of a fluorescent aromatic nucleus of 7-nitrobenz-2-oxa-1,3-diazole (NBD) that emits in the visible region of the spectrum. The fluorophore has been linked to a zwitterionic structure and a saturated chain of 18 carbon atoms, to prevent the internalization in the cell and to selectively anchor it to the outer membrane layer. It is worth to notice that the probe shows a certain degree of solvatochromism, a feature that can be exploited to evaluate the liquid-ordered and liquid-disordered composition of biological membranes.