Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity

Background  

Virtual screening methods are now well established as effective to identify hit and lead candidates and are fully integrated in most drug discovery programs. Ligand-based approaches make use of physico-chemical, structural and energetics properties of known active compounds to search large chemical libraries for related and novel chemotypes. While 2D-similarity search tools are known to be fast and efficient, the use of 3D-similarity search methods can be very valuable to many research projects as integration of 3D knowledge can facilitate the identification of not only related molecules but also of chemicals possessing distant scaffolds as compared to the query and therefore be more inclined to scaffolds hopping. To date, very few methods performing this task are easily available to the scientific community.     

Topological origins of chromosomal territories

Using freely jointed polymer model we compare equilibrium properties of crowded polymer chains whose segments are either permeable or not permeable for other segments to pass through. In particular, we addressed the question whether non-permeability of long chain molecules, in the absence of excluded volume effect, is sufficient to compartmentalize highly crowded polymer chains, similarly to what happens during formation of chromosomal territories in interphase nuclei. Our results indicate that even polymers without excluded volume compartmentalize and show strongly reduced intermingling when they are mutually non-permeable. Judging from the known fact that chromatin fibres originating from different chromosomes show very limited intermingling in interphase nuclei, we propose that regular chromatin fibres during chromosome decondensation can hardly serve as a substrate of cellular type II DNA topoisomerases.     

How does shoreline development impact the recruitment patterns of coral reef fish juveniles (Moorea Island,French Polynesia)?

The study examined the effects of coastal embankment building on fish recruitment in three habitat types (beach-rock, white sand and muddy sand) in the near shore and fringing reef habitats of Moorea lagoon (French Polynesia). The results showed a positive relationship between the presence of embankments and the density and species richness of juvenile fish along the shoreline (whatever the habitat types). However, embankments deteriorated adjacent fringing reefs (decrease of live coral), which led to a decrease of fish density on beach-rock and white sand sites, and a decrease of fish species richness on muddy sand sites.     

Glutamatergic and GABAergic effects of fipronil on olfactory learning and memory in the honeybee

We investigated here the role of transmissions mediated by GABA and glutamate-gated chloride channels (GluCls) in olfactory learning and memory in honeybees, both of these channels being a target for fipronil. To do so, we combined olfactory conditioning with injections of either the GABA- and glutamate-interfering fipronil alone, or in combination with the blocker of glutamate transporter l-trans-Pyrrolidine-2,4-Dicarboxylicacid (l -trans-PDC), or the GABA analog Trans-4-Aminocrotonic Acid (TACA). Our results show that a low dose of fipronil (0.1 ng/bee) impaired olfactory memory, while a higher dose (0.5 ng/bee) had no effect. The detrimental effect induced by the low dose of fipronil was rescued by the coinjection of l-trans-PDC but was rather increased by the coinjection of TACA. Moreover, using whole-cell patch-clamp recordings, we observed that l-trans-PDC reduced glutamate-induced chloride currents in antennal lobe cells. We interpret these results as reflecting the involvement of both GluCl and GABA receptors in the impairment of olfactory memory induced by fipronil.     

Effects of gleno-humeral joint centre mislocation on gleno-humeral kinematics and kinetics

The gleno-humeral (GH) rotation centre is typically estimated using predictive or functional methods, however these methods may lead to location errors. This study aimed at determining a location error threshold above which statistically significant changes in the values of kinematic and kinetic GH parameters occur. The secondary aims were to quantify the effects of the direction of mislocation (X, Y or Z axis) of the GH rotation centre on GH kinematic and kinetic parameters.

Shoulder flexion and abduction movements of 11 healthy volunteers were recorded using a standard motion capture system (Vicon, Oxford Metrics Ltd, Oxford, UK), then GH kinematic and kinetic parameters were computed. The true position of the GH rotation centre was determined using a low dose x-ray scanner (EOS? imaging, France) and this position was transferred to the motion data. GH angles and moments were re-computed for each position of the GH rotation centre after errors of up to ± 20?mm were added in increments of ± 5?mm to each axis. The three-dimensional error range was 5?mm to 34.65?mm.

GH joint angle and moment values were significantly altered from 10?mm of three-dimensional error, and from 5?mm of error on individual axes. However, errors on the longitudinal and antero-posterior axes only caused very small alterations of GH joint angle and moment values respectively. Future research should develop methods of GH rotation centre estimation that produce three-dimensional location errors of less than 10?mm to reduce error propagation on GH kinematics and kinetics.     

Structure and diversity of the T-cell receptor α chain in the Mexican axolotl

 Polymerase chain reaction was used to isolate cDNA clones encoding putative T-cell receptor (TCR) α chains in an amphibian, the Mexican axolotl (Ambystoma mexicanum). Five TCRα-V chain-encoding segments were identified, each belonging to a separate family. The best identity scores for these axolotl TCRα-V segments were all provided by sequences belonging to the human TCRα-V1 family and the mouse TCRα-V3 and TCRα-V8 families. A total of 14 different TCRA-J segments were identified from 44 TCRA-V/TCRA-J regions sequenced, suggesting that a large repertoire of TCRA-J segments is a characteristic of most vertebrates. The structure of the axolotl CDR3 α chain loop is in good agreement with that of mammals, including a majority of small hydrophobic residues at position 92 and of charged, hydrophilic, or polar residues at positions 93 and 94, which are highly variable and correspond to the TCRA-V/J junction. This suggests that some positions of the axolotl CDR3 α chain loop are positively selected during T-cell differentiation, particularly around residue 93 that could be selected for its ability to makes contacts with major histocompatibility complex-associated antigenic peptides, as in mammals. The axolotl Cα domain had the typical structure of mammalian and avian Cα domains, including the charged residues in the TM segment that are thought to interact with other proteins in the membrane, as well as most of the residues forming the conserved antigen receptor transmembrane motif. Received: 12 June 1996 / Revised: 11 September 1996     

Non‐resource effects of foundation species on meta‐ecosystem stability and function

Ecosystems such as forests and mussel beds, that are driven by foundation species can be characterized by the slow accumulation of matter that affect their structural stability. This non‐resource effect of matter on ecosystems can lead to disturbances and to pulsed release and transport of matter over regional scales. However, non‐resource effects of endogenous pulses of matter on meta‐ecosystem stability and function remain largely unknown. Using a two‐patch meta‐ecosystem model of mussel bed dynamics, we show that non‐resource effects of matter on the structural stability of mussel beds promote pulsed releases of matter and fluctuations in population abundance. These pulsed fluctuations explain the maintenance of meta‐ecosystem heterogeneity in the distribution of abundance and matter through out‐of‐phase synchrony and asynchrony over a broad range of connectivity. These regimes of spatial (a)synchrony explain a tradeoff between the regional retention of matter (ecosystem function) and metapopulation persistence. These results reveal how foundation species can cause local and catastrophic changes that can promote regional asynchrony and stability, even under strong connectivity.     

Long-term CFTR inhibition modulates 15d-prostaglandin J2 in human pulmonary cells

Prostaglandins, the products of arachidonic acid release and oxidation by phospholipase A(2) and cyclooxygenases (COX) 1 and 2 respectively, are known as important inflammation mediators. However, their diversity in structure, properties and cell specificity make their physiological function difficult to define. In the lung, the prostaglandin D(2) (PGD(2)) metabolite 15d-PGJ(2) is known to modulate the properties of a large number of intracellular compounds, leading to both pro- and anti-inflammatory effects. In the lung, the serous sub-mucosal glands, that strongly express CFTR (cystic fibrosis transmembrane conductance regulator), play an important role in the defence against inflammation, and their derivatives Calu-3 cells are largely used in in vitro experiments. The present study was undertaken to determine whether the PGD synthase-PGD(2)-15d-PGJ(2) pathway is active in Calu-3 cells, and whether its activity requires a functional CFTR. Both cellular and released PGD(2) and 15d-PGJ(2) were measured in cells treated with CFTR inhibitors and stimulated or not with inflammatory IL-1β. Pretreatment with either CFTR(inh172) or GlyH101 inhibitors decreased the basal cell content of both prostaglandins, and so did acute stimulation with IL-1β, but the latter was dramatically reversed in CFTR(inh172)-treated cells. CFTR(inh172) also altered the release of inflammation mediators PGE(2) and IL-8, and this effect was blunted by exogenous 15d-PGJ(2). CFTR(inh172)-induced modulation of 15d-PGJ(2) cellular content was not detected in CFTR-silenced Calu-3 cells, but it was reproduced in pulmonary CFBE41o-cells, which express F508del-CFTR. These results show that cellular 15d-PGJ(2) production, which controls PGE(2) and IL-8 release, is disturbed by CFTR dysfunction. In Calu-3 cells, 15d-PGJ(2) production resulted from COX-2-regulated COX-1 activation, while CFTR(inh172)-induced alteration of 15d-PGJ(2) synthesis involved both decreased expression of PGD synthase and disturbed relationships between both COXs. CFTR-mediated regulation of PGD synthase-PGD(2)-15d-PGJ(2) pathway and cellular 15d-PGJ(2) effects may involve a large number of molecular reactive pathways. Their exploration should help understand the development of CF inflammation and might bring new perspectives in its treatment.     

Quantification of Pseudomonas aeruginosa hydrogen cyanide production by a polarographic approach

Pseudomonas aeruginosa is an opportunistic pathogen responsible for numerous infections acquired in hospital especially in persons whose immune systems are weakened, such as with patient suffering from AIDS or cystic fibrosis. This bacterium produces a great diversity of virulence factors among them hydrogen cyanide (HCN) which is one of the most potent and toxic. A precise quantification of HCN or CN(-) ion is essential to understand the involvement of this toxin in the pathogenesis of P. aeruginosa. In the present study, we present a new technique based on a polarographic approach to measure the production kinetics of HCN/CN(-) by P. aeruginosa strains, in several media commonly used in microbiology labs. The method was validated using mutants (hcnB- and hcnC-) which are unable to produce detectable HCN/CN(-). The kinetics of HCN/CN(-) production by P. aeruginosa in Luria Bertani (LB) medium showed a parabolic shape with a peak observed at 4, 5 and 8h for strains PA14, PAO1 and MPAO1, respectively. When bacteria were grown in ordinary nutrient broth (ONB) 2.5% medium, a less adapted medium for bacterial growth, the general profile of the kinetics was conserved but peak production was delayed (10 and 12h for PAO1 and MPAO1, respectively). When the bacteria were cultured in minimum medium MMC, bacterial growth was particularly slow and HCN/CN(-) production was markedly reduced. Taken together, this new polarographic method appears as a useful technique to detect and quantify HCN/CN(-) in routine media where the bacteria can express and regulate high amounts of toxins. With this method, we demonstrate that HCN/CN(-) production by P. aeruginosa is maximal at the end of the exponential growth phase and depends on the richness of the growth medium used.