The Third-Generation Sequencing Challenge: Novel Insights for the Omic Sciences.

The understanding of the human genome has been greatly improved by the advent of next-generation sequencing technologies (NGS). Despite the undeniable advantages responsible for their widespread diffusion, these methods have some constraints, mainly related to short read length and the need for PCR amplification. As a consequence, long-read sequencers, called third-generation sequencing (TGS), have been developed, promising to overcome NGS. Starting from the first prototype, TGS has progressively ameliorated its chemistries by improving both read length and base-calling accuracy, as well as simultaneously reducing the costs/base. Based on these premises, TGS is showing its potential in many fields, including the analysis of difficult-to-sequence genomic regions, structural variations detection, RNA expression profiling, DNA methylation study, and metagenomic analyses. Protocol standardization and the development of easy-to-use pipelines for data analysis will enhance TGS use, also opening the way for their routine applications in diagnostic contexts.

Modulation of proteasome machinery by natural and synthetic analogues of the marine bioactive compound petrosaspongiolide M.

Natural or synthetic? Several petrosaspongiolide M natural and synthetic analogues have been tested as proteasome inhibitors and apoptosis modulators. The natural petrosaspongiolide M congeners gave a consistent decrease in activity. Among the synthetic analogues, the introduction of the benzothiophene ring resulted in a bioequivalent alternative of the petrosaspongiolide M terpenoid system.

Identification of new γ-hydroxybutenolides that preferentially inhibit the activity of mPGES-1.

Microsomal prostaglandin E(2) synthase-1 (mPGES-1) has been recognized as novel, promising drug target for anti-inflammatory and anticancer drugs. mPGES-1 catalyzes the synthesis of the inducible prostaglandin E(2) in response to pro-inflammatory stimuli, rendering this enzyme extremely interesting in drug discovery process owing to the drastic reduction of the severe side effects typical for traditional non-steroidal anti-inflammatory drugs. In the course of our investigations focused on this topic, we identified two interesting molecules bearing the γ-hydroxybutenolide scaffold which potently inhibit the activity of mPGES-1. Notably, the lead compound 2c that inhibited mPGES-1 with IC(50) = 0.9 µM, did not affect other related enzymes within the arachidonic acid cascade.

[Effects of two Sicilian red wines on some cardiovascular risk factors]. / Effetto di due vini rossi siciliani su alcuni fattori di rischio cardiovascolare.

BACKGROUND: The aim of this study was to evaluate whether Sicilian red wine consumption is associated with a lower cardiovascular risk. METHODS: Forty-eight subjects of both sexes (age range 35-65 years) nondrinkers or rarely drinkers of moderate red wine intake were selected. Subjects were divided into two groups (group A and group B), assigned to receive with a crossover design 250 ml/die (during the meals) of one of two types of Sicilian red wines (Nero d'Avola and Etna Torrepalino respectively). At all visits (-15 days, basal, +4 and +8 weeks) the following parameters were measured: blood glucose, total cholesterol and triglycerides (by enzyme kit methods, Boehringer Mannheim, Milan, Italy), HDL cholesterol (by selective precipitation with dextran-magnesium chloride), LDL cholesterol (by calculation with the Friedewald formula), LDL/HDL ratio, apolipoproteins A1 and B (by radial immunodiffusion, Behring Institute, Scoppito, Italy), lipoprotein(a) (ELISA, Technoclone, Vienna, Austria), plasma C-reactive protein (high-sensitivity, Dade Behring, Marburg, Germany), D-dimer (Turbiquant, Dade Behring), factor VII (coagulant activity, Dade Behring), plasminogen activator inhibitor antigen (ELISA), tissue-type plasminogen activator antigen (ELISA), fibrinogen (coagulant), oxidized LDL antibody (ELISA), total plasma antioxidant capacity (FRAP method). RESULTS: At the end of the red wine intake period, HDL cholesterol was significantly increased (p < 0.01) and the LDL/HDL ratio was significantly decreased (p < 0.05) in both study groups, while apolipoprotein A1 was significantly increased (p < 0.05) only in group A. In both group A and group B fibrinogen (p < 0.01 and p < 0.005, respectively), factor VII (p < 0.01 and p < 0.05, respectively), plasma C-reactive protein (p < 0.005 and p < 0.05, respectively) and oxidized LDL antibody (p < 0.05) were significantly decreased, while tissue-type plasminogen activator (p < 0.005), plasminogen activator inhibitor (p < 0.005) and total plasma antioxidant capacity (p < 0.005) were significantly increased. CONCLUSIONS: Our results show a positive effect of these Sicilian red wines on many risk factors, suggesting a moderate consumption of red wine in the adult population as a component of the Mediterranean diet.

Design and synthesis of a second series of triazole-based compounds as potent dual mPGES-1 and 5-lipoxygenase inhibitors.

Microsomal prostaglandin E(2) synthase (mPGES)-1 and 5-lipoxygenase (5-LO) are pivotal enzymes in the biosynthesis of the pro-inflammatory PGE(2) and leukotrienes, respectively. The design and synthesis of a second series of mPGES-1 inhibitors based on a triazole scaffold are described. Our studies allowed us to draw a tentative SAR profile and to optimize this series with the identification of compounds 10, 11 and 14-15 which displayed potent mPGES-1 inhibition in a cell-free assay. In addition, compounds 5, 10, 12 and 14-16 also blocked 5-LO activity in cell-free and cell-based test systems, emerging as very promising candidates for the development of safer and more effective anti-inflammatory drugs.

Structure-based discovery of inhibitors of microsomal prostaglandin E2 synthase-1, 5-lipoxygenase and 5-lipoxygenase-activating protein: promising hits for the development of new anti-inflammatory agents.

Microsomal prostaglandin E(2) synthase (mPGES)-1 catalyzes the transformation of PGH(2) to PGE(2) that is involved in several pathologies like fever, pain, and inflammatory disorders. To identify novel mPGES-1 inhibitors, we used in silico screening to rapidly direct the synthesis, based on the copper-catalyzed 3 + 2 Huisgen's reaction (click chemistry), of potential inhibitors. We designed 26 new triazole-based compounds in accordance with the pocket binding requirements of human mPGES-1. Docking results, in agreement with ligand efficiency values, suggested the synthesis of 15 compounds that at least in theory were shown to be more efficient in inhibiting mPGES-1. Biological evaluation of these selected compounds has disclosed three new potential anti-inflammatory drugs: (I) compound 4 displaying selectivity for mPGES-1 with an IC(50) value of 3.2 µM, (II) compound 20 that dually inhibits 5-lipoxygenase and mPGES-1, and (III) compound 7 apparently acting as 5-lipoxygenase-activating protein inhibitor (IC(50) = 0.4 µM).

Toward the discovery of new agents able to inhibit the expression of microsomal prostaglandin E synthase-1 enzyme as promising tools in drug development.

In our recent studies, we focused our attention on the synthesis of several gamma-hydroxybutenolides designed on the basis of petrosaspongiolide M 1 (PM) structure that has been recognized to potently inhibit the inflammatory process through the selective PLA(2) enzyme inhibition. By means of a combination of computational methods and efficient synthetic strategies, we generated small collections of PM modified analogs to identify new potent PLA(2) inhibitors, suitable for clinical development. In the course of the biological screening of our compounds, we discovered a potent and selective inhibitor of mPGES-1 expression, the benzothiophene gamma-hydroxybutenolide 2, which so far represents the only product, together with resveratrol, able to reduce PGE(2) production through the selective downregulation of mPGES-1 enzyme. In consideration that microsomal prostaglandin E synthase 1 (mPGES-1) is one of the most strategic target involved both in inflammation and in carcinogenesis processes, we decided to explore the biological effects of some structural changes of the gamma-hydroxybutenolide 2, hoping to improve its biological profile. This optimization process led to the identification of three strictly correlated compounds 14g, 16g, and 18 with higher inhibitory potency on PGE(2) production on mouse macrophage cell line RAW264.7 through the selective modulation of mPGES-1 enzyme expression.