Frog: a FRee Online druG 3D conformation generator

In silico screening methods based on the 3D structures of the ligands or of the proteins have become an essential tool to facilitate the drug discovery process. To achieve such process, the 3D structures of the small chemical compounds have to be generated. In addition, for ligand-based screening computations or hierarchical structure-based screening projects involving a rigid-body docking step, it is necessary to generate multi-conformer 3D models for each input ligand to increase the efficiency of the search. However, most academic or commercial compound collections are delivered in 1D SMILES (simplified molecular input line entry system) format or in 2D SDF (structure data file), highlighting the need for free 1D/2D to 3D structure generators. Frog is an on-line service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions. Given the atomic constitution of the molecules and connectivity information, Frog can identify the different unambiguous isomers corresponding to each compound, and generate single or multiple low-to-medium energy 3D conformations, using an assembly process that does not presently consider ring flexibility. Tests show that Frog is able to generate bioactive conformations close to those observed in crystallographic complexes. Frog can be accessed at http://bioserv.rpbs.jussieu.fr/Frog.html

Burden and risk factors for Pseudomonas aeruginosa community-acquired pneumonia:a Multinational Point Prevalence Study of Hospitalised Patients

Pseudornonas aeruginosa is a challenging bacterium to treat due to its intrinsic resistance to the antibiotics used most frequently in patients with community-acquired pneumonia (CAP). Data about the global burden and risk factors associated with P. aeruginosa-CAP are limited. We assessed the multinational burden and specific risk factors associated with P. aeruginosa-CAP. We enrolled 3193 patients in 54 countries with confirmed diagnosis of CAP who underwent microbiological testing at admission. Prevalence was calculated according to the identification of P. aeruginosa. Logistic regression analysis was used to identify risk factors for antibiotic-susceptible and antibiotic-resistant P. aeruginosa-CAP. The prevalence of P. aeruginosa and antibiotic-resistant P. aeruginosa-CAP was 4.2% and 2.0%, respectively. The rate of P. aeruginosa CAP in patients with prior infection/colonisation due to P. aeruginosa and at least one of the three independently associated chronic lung diseases (i.e. tracheostomy, bronchiectasis and/or very severe chronic obstructive pulmonary disease) was 67%. In contrast, the rate of P. aeruginosa-CAP was 2% in patients without prior P. aeruginosa infection/colonisation and none of the selected chronic lung diseases. The multinational prevalence of P. aeruginosa-CAP is low. The risk factors identified in this study may guide healthcare professionals in deciding empirical antibiotic coverage for CAP patients

Stabilization of protein-protein interaction complexes through small molecules

Most of the small molecules that have been identified thus far to modulate protein-protein interactions (PPIs) are inhibitors. Another promising way to interfere with PPI-associated biological processes is to promote PPI stabilization. Even though PPI stabilizers are still scarce, stabilization of PPIs by small molecules is gaining momentum and offers new pharmacological options. Therefore, we have performed a literature survey of PPI stabilization using small molecules. From this, we propose a classification of PPI stabilizers based on their binding mode and the architecture of the complex to facilitate the structure-based design of stabilizers

A critical role for Gly25 in the B chain of human thrombin

We have recently identified (Akhavan S et al., Thromb Haemost 2000; 84: 989-97) a patient with a mild bleeding diathesis associated to an homozygous mutation in the thrombin B chain (Gly25Ser, chymotrypsinogen numbering, i.e. position 330 in human prothrombin numbering). Transient transfection of wild-type prothrombin (FII-WT) and mutant prothrombin (designated FII-G25((330))S) cDNA in COS-7 cells showed a mild reduction (50%) in FII-G25((330))S production. Recombinant proteins, stably expressed in Chinese hamster ovary cells, were isolated and activated by TaYpan snake or Echis carinatus venoms. We show that the G25((330))S mutation results in a decrease in the rate of prothrombin proteolytic activation. The mutation also significantly decreases (i) the catalytic activity of thrombin with a 9-fold reduction in catalytic efficiency of the mutant toward S-2238; (ii) the interaction with benzamidine; (iii) the rate of inhibition by TLCK and antithrombin; and (iv) the rate of hydrolysis of macromolecular substrates (fibrinogen, protein C). In contrast, exosite I does not appear to be affected by the molecular defect. These results, together with molecular modeling and dynamics, indicate that Gly25((330)) is important for proper expression and probably proper folding of prothrombin, and also plays a critical role in both the alignment of the catalytic triad and the flexibility of one of the activation segments of prothrombi

Abundance, viability and diversity of the indigenous microbial populations at different depths of the NEEM Greenland ice core

The 2537-m-deep North Greenland Eemian Ice Drilling (NEEM) core provided a first-time opportunity to perform extensive microbiological analyses on selected, recently drilled ice core samples representing different depths, ages, ice structures, deposition climates and ionic compositions. Here, we applied cultivation, small subunit (SSU) rRNA gene clone library construction and Illumina next-generation sequencing (NGS) targeting the V4–V5 region, to examine the microbial abundance, viability and diversity in five decontaminated NEEM samples from selected depths (101.2, 633.05, 643.5, 1729.75 and 2051.5 m) deposited 300–80 000 years ago. These comparisons of the indigenous glacial microbial populations in the ice samples detected significant spatial and temporal variations. Major findings include: (a) different phylogenetic diversity of isolates, dominated by Actinobacteria and fungi, compared to the culture-independent diversity, in which Proteobacteria and Firmicutes were more frequent; (b) cultivation of a novel alphaproteobacterium; (c) dominance of Cyanobacteria among the SSU rRNA gene clones from the 1729.75-m ice; (d) identification of Archaea by NGS that are rarely detected in glacial ice; (e) detection of one or two dominant but different genera among the NGS sequences from each sample; (f) finding dominance of Planococcaceae over Bacillaceae among Firmicutes in the brittle and the 2051.5-m ice. The overall beta diversity between the studied ice core samples examined at the phylum/class level for each approach showed that the population structure of the brittle ice was significantly different from the two deep clathrated ice samples and the shallow ice core

The role of pannexin 1 in the purinergic regulation of synaptic transmission in mouse motor synapses

The role of pannexin 1 in the release to the extracellular space of ATP/adenosine modulating the acetylcholine (ACh) secretion was studied in mouse diaphragm motor synapses. Using neuromuscular preparations obtained from wild-type and pannexin-1 knockout mice, the miniature endplate potential (MEPPs) and evoked endplate potentials (EPPs) were recorded in combination with pharmacological modulation of P2-type ATP receptors and A1-type adenosine receptors. Selective inhibition of A1 receptors with DPCPX or P2 receptors with PPADS increased quantal content of EPPs in wild-type mice. MRS 2211, selective antagonist of P2Y13 receptors, produced the same effect. Activation of receptors A1 or P2Y13 by their agonists (2-CADO and IDP, respectively) decreased the EPP quantal content. It means that the activity of endogenous ATP and adenosine is synergistic and directed to depression of the ACh release. ARL67156, an inhibitor of synaptic ecto-ATPases, which blocks the hydrolysis of ATP to adenosine and increases the level of ATP in the synaptic cleft, prolonged EPPs without changing their quantal content. In pannexin-1 knockout mice there were no changes in the EPP quantal content and in other parameters of synaptic transmission as compared to wildtype mice. However, downregulation of purinergic effects with antagonists of A1 or P2 receptors (DPCPX, PPADS, MRS 2211) did not change EPP quantal content and any other parameters of spontaneous or evoked ACh release in all cases. ARL67156 did not alter the temporal parameters of EPPs, either. Nevertheless, 2-CADO, the A1-type receptor agonist, decreased the EPP quantal content, while the agonist of P2Y13 receptors decreased the MEPP amplitude. Thus, in mice lacking pannexin 1, procedures revealing the presence and regulatory activity of synaptic ATP/adenosine did not change the parameters of synaptic transmission. The obtained data substantiate a mandatory role of pannexin 1 in the purinergic regulation of motor synapse activity by endogenous ATP/adenosine

Relationship between Solar Energetic Particles and Properties of Flares and CMEs: Statistical Analysis of Solar Cycle 23 Events

A statistical analysis of the relationship between solar energetic particles (SEPs) and properties of solar flares and coronal mass ejections (CMEs) is presented. SEP events during Solar Cycle 23 are selected that are associated with solar flares originating in the visible hemisphere of the Sun and that are at least of magnitude M1. Taking into account all flares and CMEs that occurred during this period, the probability for the occurrence of an SEP event near Earth is determined. A strong rise of this probability is observed for increasing flare intensities, more western locations, higher CME speeds, and halo CMEs. The correlations between the proton peak flux and these solar parameters are derived for a low (> 10 MeV) and high (> 60 MeV) energy range excluding any flux enhancement due to the passage of fast interplanetary shocks. The obtained correlation coefficients are 0.55±0.07 (0.63±0.06) with flare intensity, and 0.56±0.08 (0.40±0.09) with CME speed for E>10 MeV (E>60 MeV). For both energy ranges, the correlations with flare longitude and CME width are very weak or non-existent. Furthermore, the occurrence probabilities, correlation coefficients, and mean peak fluxes are derived in multi-dimensional bins combining the aforementioned solar parameters. The correlation coefficients are also determined in different proton energy channels ranging from 5 to 200 MeV. The results show that the correlation between the proton peak flux and the CME speed decreases with energy, while the correlation with the flare intensity shows the opposite behaviour. Furthermore, the correlation with the CME speed is stronger than the correlation with the flare intensity below 15 MeV and becomes weaker above 20 MeV. When the enhancements in the flux profiles due to interplanetary shocks are not excluded, only a small but not very significant change is observed in the correlation coefficients between the proton peak flux below 7 MeV and the CME speed