3-Amino-2(5H)furanones as inhibitors of subgenomic hepatitis C virus RNA replication

A new class of compounds able to block the replication of subgenomic HCV RNA in liver cells is described. 3-Amino-2(5H)furanones 4 may be regarded as diketoacid analogues and were obtained by basic rearrangement of the isoxazolidine nucleus.     

An efficient conformational sampling method for homology modeling

The structural refinement of protein models is a challenging problem in protein structure prediction (Moult et al., Proteins 2003;53(Suppl 6):334-339). Most attempts to refine comparative models lead to degradation rather than improvement in model quality, so most current comparative modeling procedures omit the refinement step. However, it has been shown that even in the absence of alignment errors and using optimal templates, methods based on a single template have intrinsic limitations, and that refinement is needed to improve model accuracy. It is thought that failure of current methods originates on one hand from the inaccuracy of the effective free energy functions adopted, which do not represent properly the energetic balance in the native state, and on the other hand from the difficulty to sample the high dimensional and rugged free energy landscape of protein folding, in the search for the global minimum. Here, we address this second issue. We define the evolutionary and vibrational armonics subspace (EVA), a reduced sampling subspace that consists of a combination of evolutionarily favored directions, defined by the principal components of the structural variation within a homologous family, plus topologically favored directions, derived from the low frequency normal modes of the vibrational dynamics, up to 50 dimensions. This subspace is accurate enough so that the cores of most proteins can be represented within 1 A accuracy, and reduced enough so that Replica Exchange Monte Carlo (Hukushima and Nemoto, J Phys Soc Jpn 1996;65:1604-1608; Hukushima et al., Int J Mod Phys C: Phys Comput 1996;7:337-344; Mitsutake et al., J Chem Phys 2003;118:6664-6675; Mitsutake et al., J Chem Phys 2003;118:6676-6688) (REMC) can be applied. REMC is one of the best sampling methods currently available, but its applicability is restricted to spaces of small dimensionality. We show that the combination of the EVA subspace and REMC can essentially solve the optimization problem for backbone atoms in the reduced sampling subspace, even for rather rugged free energy landscapes. Applications and limitations of this methodology are finally discussed.     

Relations between the mitogen-activated protein kinase and the cAMP-dependent protein kinase pathways: comradeship and hostility

Inter- and intracellular communications and responses to environmental changes are pivotal for the orchestrated and harmonious operation of multi-cellular organisms. These well-tuned functions in living organisms are mediated by the action of signal transduction pathways, which are responsible for receiving a signal, transmitting and amplifying it, and eliciting the appropriate cellular responses. Mammalian cells posses numerous signal transduction pathways that, rather than acting in solitude, interconnect with each other, a phenomenon referred to as cross-talk. This allows cells to regulate the distribution, duration, intensity and specificity of the response. The cAMP/cAMP-dependent protein kinase (PKA) pathway and the mitogen-activated protein kinase (MAPK) cascades modulate common processes in the cell and multiple levels of cross-talk between these signalling pathways have been described. The first- and best-characterized interconnections are the PKA-dependent inhibition of the MAPKs ERK1/2 mediated by RAF-1, and PKA-induced activation of ERK1/2 interceded through B-RAF. Recently, novel interactions between components of these pathways and new mechanisms for cross-talk have been elucidated. This review discusses both known and novel interactions between compounds of the cAMP/PKA and MAPKs signalling pathways in mammalian cells.     

In vitro comparison of the prebiotic effects of two inulin-type fructans

Faecal cultures were used to compare the prebiotic effects of a new fructan containing high solubility inulin (HSI) and of a well-established prebiotic containing oligofructose (OF) with a negative control (CT). Changes in the intestinal microbiota, pH, ammonia, volatile organic acids and lactic acid were monitored during incubation. Molecular techniques for microbial enumeration indicated that both HSI and OF led to a significant increase in bifidobacteria (P< or =0.05) and lactobacilli (P< or =0.05) compared to the control. Significant changes in the pH and levels of ammonia with both inulin-type fructans were observed, as well as higher levels of acetic, lactic and formic acids (P< or =0.05). The fermentative metabolism appeared to be faster on OF than on HSI. Both OF and HSI showed clear prebiotic effects, but had differences in fermentation kinetics because of to the different degree of polymerization (DP). This study provides proof for the prebiotic effectiveness of HSI, and shows that inulin-type fructans with higher DP might have a prolonged bifidogenic effect, thus could extend the saccharolytic metabolism and low pH to the distal parts of the colon.     

Combined effect of hemostatic gene polymorphisms and the risk of myocardial infarction in patients with advanced coronary atherosclerosis

Background

Relative little attention has been devoted until now to the combined effects of gene polymorphisms of the hemostatic pathway as risk factors for Myocardial Infarction (MI), the main thrombotic complication of Coronary Artery Disease (CAD). The aim of this study was to evaluate the combined effect of ten common prothrombotic polymorphisms as a determinant of MI.

Methodology/Principal Findings

We studied a total of 804 subjects, 489 of whom with angiographically proven severe CAD, with or without MI (n = 307; n = 182; respectively). An additive model considering ten common polymorphisms [Prothrombin 20210G>A, PAI-1 4G/5G, Fibrinogen β -455G>A, FV Leiden and “R2”, FVII -402G>A and -323 del/ins, Platelet ADP Receptor P2Y12 -744T>C, Platelet Glycoproteins Ia (873G>A), and IIIa (1565T>C)] was tested. The prevalence of MI increased linearly with an increasing number of unfavorable alleles (χ² for trend = 10.68; P = 0.001). In a multiple logistic regression model, the number of unfavorable alleles remained significantly associated with MI after adjustment for classical risk factors. As compared to subjects with 3-7 alleles, those with few (≤2) alleles had a decreased MI risk (OR 0.34, 95%CIs 0.13–0.93), while those with more (≥8) alleles had an increased MI risk (OR 2.49, 95%CIs 1.03–6.01). The number of procoagulant alleles correlated directly (r = 0.49, P = 0.006) with endogenous thrombin potential.

Conclusions

The combination of prothrombotic polymorphisms may help to predict MI in patients with advanced CAD.