Computational study on human sphingomyelin synthase 1 (hSMS1).

Human sphingomyelin synthase 1 (hSMS1) is the last enzyme for sphingomyelin (SM) biosynthesis. It has been discovered that in different human tumor tissues the SM levels are lower compared to normal tissues and the activation of hSMS1, to restore the normal levels of SM, inhibits cell cycle proliferation of cancer cells. Since the importance of SM and other lipid metabolism genes in the malignant transformation, we decided to explore the hSMS1 mechanism of action. Enzymes capable to regulate the formation of lipids are therefore of paramount importance. Here we present a computational study on sphingomyelin synthases hSMS1. The full structure of the enzyme was obtained by means of homology and ab initio techniques. Further molecular dynamics and docking studies permitted to identify putative binding sites and to identify the key residues for binding. This article is part of a Special Issue entitled: Membrane Lipid Therapy: Drugs Targeting Biomembranes edited by Pablo V. Escribá.

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.

Differential effect of 2-hydroxyoleic acid enantiomers on protein (sphingomyelin synthase) and lipid (membrane) targets.

The complex dual mechanism of action of 2-hydroxyoleic acid (2OHOA), a potent anti-tumor compound used in membrane lipid therapy (MLT), has yet to be fully elucidated. It has been demonstrated that 2OHOA increases the sphingomyelin (SM) cell content via SM synthase (SGMS) activation. Its presence in membranes provokes changes in the membrane lipid structure that induce the translocation of PKC to the membrane and the subsequent overexpression of CDK inhibitor proteins (e.g., p21(Cip1)). In addition, 2OHOA also induces the translocation of Ras to the cytoplasm, provoking the silencing of MAPK and its related pathways. These two differential modes of action are triggered by the interactions of 2OHOA with either lipids or proteins. To investigate the molecular basis of the different interactions of 2OHOA with membrane lipids and proteins, we synthesized the R and S enantiomers of this compound. A molecular dynamics study indicated that both enantiomers interact similarly with lipid bilayers, which was further confirmed by X-ray diffraction studies. By contrast, only the S enantiomer was able to activate SMS in human glioma U118 cells. Moreover, the anti-tumor efficacy of the S enantiomer was greater than that of the R enantiomer, as the former can act through both MLT mechanisms. The present study provides additional information on this novel therapeutic approach and on the magnitude of the therapeutic effects of type-1 and type-2 MLT approaches. This article is part of a Special Issue entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy.

Design and synthesis of spirotryprostatin-inspired diketopiperazine systems from prolyl spirooxoindolethiazolidine derivatives.

Based on the spirotryprostatin-A structure, we designed, synthesized, and evaluated different series of compounds belonging to the diketopiperazine structural class as potential cell cycle modulators and cytotoxic agents. Starting from the spirooxoindolthiazolidine scaffold, amide coupling with Pro derivatives and intramolecular cyclization reactions are suitable synthetic methods to generate chemically diverse diketopiperazine system, such as hexahydropyrrolo[1,2-a][1,3]thiazolo[3,2-d]pyrazine-5,10-dione (structure I), hexahydropyrrolo[1,2-a] [1,3]thiazolo[3,4-d]pyrazine-5,10-dione (structure II) and spiroindol-2-one[3,3']hexahydro-5,10H-pyrrolo[1,2-a][1,3]thiazolo[3,4-d]pyrazine-5,10-dione (structure III). Some of these compounds, especially those who belong to the series I and II, showed interesting cytotoxic activity.

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.

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.