Estimation of the PPARα agonism of fibrates by a combined MM-docking approach.

Fibrates are peroxisome proliferator-activated alpha receptor (PPARα) activators derived from fibric acid and are the most clinically used therapeutics in the treatment of hypertriglyceridemia. Recently, we reported a computational approach for the investigation of the binding properties of fibrates, characterized by similar carboxylic heads but differing in the size and orientation of the hydrophobic portion. This procedure is based on a combination of standard docking and molecular mechanics approaches to better describe the adaptation of the protein target to the bound ligand. The application of our approach to a set of 23 fibrates and the use of an effective regression procedure, allowed the development of predictive models of the PPARα agonism. The obtained models are characterized by good performances realizing a fair trade-off between accuracy and computational costs. The best model is more specialized in the ranking of fibrate agonists whose binding is mainly controlled by steric rather than by electronic modulation. Here, we describe in details the application of this computational procedure for the prediction of PPARα agonism of fibrate ligands.

Bovine lactoferrin-derived peptides as novel broad-spectrum inhibitors of influenza virus.

Bovine lactoferrin (bLf) is a multifunctional glycoprotein that plays an important role in innate immunity against infections, including influenza. Here we have dissected bLf into its C- and N-lobes and show that inhibition of influenza virus hemagglutination and cell infection is entirely attributable to the C-lobe and that all major virus subtypes, including H1N1 and H3N2, are inhibited. By far-western blotting and sequencing studies, we demonstrate that bLf C-lobe strongly binds to the HA(2) region of viral hemagglutinin, precisely the highly conserved region containing the fusion peptide. By molecular docking studies, three C-lobe fragments were identified which inhibited virus hemagglutination and infection at fentomolar concentration range. Besides contributing to explain the broad anti-influenza activity of bLf, our findings lay the foundations for exploiting bLf fragments as source of potential anti-influenza therapeutics.

Binding of GSH conjugates to π-GST: a cross-docking approach.

The high degree of flexibility characterizing the members of the GST protein family is supposed to be an evolution-resolved feature related to the detoxifying role of these enzymes. Many evidences suggest that overexpression of these enzymes may be implicated in the development of acquired resistance to antitumor agents. Among the most effective GST inhibitors, GSH conjugates have been found to be particularly promising because of their low toxicity. Here, we used a cross docking approach based on an ensemble of X-ray structures of GST bound complexes to model the effects of protein flexibility on the binding of GSH conjugates. We showed that our multitarget approach, allows to analyze the impact of protein flexibility and induced fit effects in GSH conjugate docking to GST. Moreover, the inclusion of conserved water molecules in the model allowed to include a further source of target variability and improve the performances in the docking of GSH conjugates through an enhanced description of the GSH moiety interactions. Therefore, a map of ligand-protein interactions reflecting the target variability included in the docking model was retraced and used to gain a thorough insight about the way GSH conjugates bind to GST.

Prediction of the PPARα agonism of fibrates by combined MM-docking approaches.

Fibrates are peroxisome proliferator-activated alpha receptor (PPARα) activators derived from fibric acid and are the most clinically used therapeutics in the treatment of hypertriglyceridemia. Long standing studies on these drugs have accumulated a large body of experimental data about their biological activity and, more recently, on the molecular mechanism mediating their PPARα agonism. An immense interest for the discovery of new fibrates with improved potency and PPARα selectivity has stimulated many investigations toward a deeper understanding of structure-activity relationships controlling their activity. The present study aimed at investigating the binding properties of a set of 23 fibrates, characterized by similar carboxylic heads but differing in the size and orientation of the hydrophobic portion, using computational approaches. We combined standard docking and molecular mechanics approaches to better describe the adaptation of the protein target to the bound ligand. The agonist potencies were then regressed against the calculated binding energies to elaborate predictive model equations. The obtained models were characterized by good performances realizing a fair trade-off between accuracy and computational costs. The best model was obtained with a regression procedure allowing automatic generation of a training subset from the whole set of trials and filtering out outliers, thus highlighting the importance of regression strategies.

N-Substituted acetamidines and 2-methylimidazole derivatives as selective inhibitors of neuronal nitric oxide synthase.

A series of N-substituted acetamidines and 2-methylimidazole derivatives structurally related to W1400 were synthesized and evaluated as Nitric Oxide Synthase (NOS) inhibitors. Analogs with sterically hindering isopropyl and phenyl substituents on the benzylic carbon connecting the aromatic core of W1400 to the acetamidine nitrogen, showed good inhibitory potency for nNOS (IC(50)=0.2 and 0.3 µM) and selectivity over eNOS (500 and 1166) and to a lesser extent over iNOS (50 and 100). A molecular modeling study allowed to shed light on the effects of the structural modifications on the selectivity of the designed inhibitors toward the different NOS isoforms.

Synthesis and biological evaluation of 2-heteroarylthioalkanoic acid analogues of clofibric acid as peroxisome proliferator-activated receptor alpha agonists.

A series of 2-heteroarylthioalkanoic acids were synthesized through systematic structural modifications of clofibric acid and evaluated for human peroxisome proliferator-activated receptor alpha (PPARalpha) transactivation activity, with the aim of obtaining new hypolipidemic compounds. Some thiophene and benzothiazole derivatives showing a good activation of the receptor alpha were screened for activity against the PPARgamma isoform. The gene induction of selected compounds was also investigated in the human hepatoma cell line.