Improving performance of docking-based virtual screening by structural filtration

In the current study an innovative method of structural filtration of docked ligand poses is introduced and applied to improve the virtual screening results. The structural filter is defined by a protein-specific set of interactions that are a) structurally conserved in available structures of a particular protein with its bound ligands, and b) that can be viewed as playing the crucial role in protein-ligand binding. The concept was evaluated on a set of 10 diverse proteins, for which the corresponding structural filters were developed and applied to the results of virtual screening obtained with the Lead Finder software. The application of structural filtration resulted in a considerable improvement of the enrichment factor ranging from several folds to hundreds folds depending on the protein target. It appeared that the structural filtration had effectively repaired the deficiencies of the scoring functions that used to overestimate decoy binding, resulting into a considerably lower false positive rate. In addition, the structural filters were also effective in dealing with some deficiencies of the protein structure models that would lead to false negative predictions otherwise. The ability of structural filtration to recover relatively small but specifically bound molecules creates promises for the application of this technology in the fragment-based drug discovery.     

On the origin of the sweet-smelling Parma violet cultivars (Violaceae): wide intraspecific hybridization, sterility, and sexual reproduction

Parma violets are reputed for their double, fragrant flowers and have been cultivated for centuries in Europe. However, due to a rather atypical morphology their taxonomic affinity has not been clarified. Authors have proposed an origin from three possible species, Viola alba, V. odorata, or V. suavis, or a hybrid origin. Using both ITS sequence variation and allozyme variation in 14 putative loci, we showed that the Parma violet cultivars have their origin within Viola alba and that they are best included in the Mediterranean subsp. dehnhardtii. There is no trace of interspecific hybridization. However, the cultivars appear to have a single origin in a wide hybrid within V. alba, involving parental plants from the eastern and western Mediterranean region; historical literature sources seem to indicate Turkey and Italy, respectively. The Parma violet cultivars possess high levels of allozyme heterozygosity and to some extent also within-individual ITS sequence variation. Losses of heterozygosity and within-individual ITS sequence variation in some of the cultivars indicate subsequent rare events of sexual reproduction, presumably through cleistogamous seed set. We unambiguously identify the closest wild relative of this group of cultivars, allowing growers to develop new selection procedures, and show a peculiar molecular process associated with human selection.     

Luminescent studies of binuclear ternary europium(III) pyridineoxide tetrazolate complexes containing bis‐phosphine oxide as auxiliary co‐ligands

A new class of antenna chromophores so called ‘tetrazolates’ have not been explored much for lanthanide luminescencent complexes. However, we have already published several articles considering pyridineoxide tetrazolates as sensitizer with lanthanide ions. Although this class of antenna attracted much less attention because of its poor photoluminescence quantum yields (tris‐pyridineoxide tetrazolate europium complex = 13% in solution) we tried and successfully achieved to improve the photoluminescence quantum yields for this particular antenna molecule by replacing coordinated water from the inner coordination sphere of europium ion by introducing phosphine oxides as additional chromophore. In the present article the two bis‐phosphine oxides attach two molecules of tris‐pyridineoxide tetrazolate europium(III) complex which leads to the improvement of the overall molar absorption coefficients as well as photo‐physical properties of the complexes. We found more than two‐fold increase (31% in solution) in photoluminescence quantum yield with one of the coordinated phosphine oxides comparing with that of tris‐pyridineoxide tetrazolate europium(III) complex.     

Survival of Bifidobacterium animalis DN-173 010 in the faecal microbiota after administration in lyophilised form or in fermented product - a randomised study in healthy adults

The survival of Bifidobacterium animalis strain DN-173 010 was assessed after its ingestion in a fermented product or in a lyophilised form. Twelve healthy subjects were included in a randomised, open study with 2 parallel groups. The composition and activities of the faecal microbiota were monitored before (10-day baseline step), during (1-week product administration step) and after (10-day follow-up step) the ingestion of 1 of the 2 products. A colony immunoblotting method, fluorescent in situ hybridisation with group-specific DNA probes, and temporal temperature gradient gel electrophoresis using group-specific primers were carried out to compare survival of B. animalis strain DN-173 010 after ingestion of the 2 products, together with analyses of enzyme activities and faecal metabolites. At the end of the supplementation step, the mean number of B. animalis DN-173 010 quantified by immunodetection in the faeces of 5 of 6 subjects in each treatment group was >/=10(8) colony-forming units/g faeces. These numbers corresponded to an average survival of 22% for the lyophilised form and 20% for the fermented product. At the same step, the PCR temporal temperature gradient gel electrophoresis profiles showed a double band corresponding to the B. animalis DN-173 010 pattern for 11 subjects. No major modification was observed during the trial in either the dominant members of the faecal microbiota assessed by fluorescent in situ hybridisation or their activities. In conclusion, we show that the lyophilised form of B. animalis DN-173 010 survives transit and could represent a more convenient form to administer for long-term clinical trials.     

Demasculinization of male Japanese quail by prenatal estrogen treatment

Genetic male Japanese quail were administered sex hormones or the oil vehicle on Day 10 of incubation and were caponized 3 weeks after hatching. As adults, the capons were injected with testosterone propionate daily for 2 weeks and then were tested for masculine sexual behavior in response to sexually receptive females. Males that had received as little as 2 μg of estradiol-17β in ovo failed to exhibit the head grabbing and mounting typical of the normal masculine sexual response to females. In a second experiment, this demasculinization was produced by prenatal treatment with 2 μg of estradiol-17α, estrone, estriol, or diethylstilbestrol, but not by this quantity of testosterone. These data suggest that an estrogen is the agent of behavioral demasculinization in the normal female, and that endogenous testosterone poses no difficulty for proper sexual development in the normal male.     

Effects of Sodium Selenite and Dithiothreitol on Expression of Endoplasmic Reticulum Selenoproteins and Apoptosis Markers in MSF7 Breast Adenocarcinoma Cells

Molecular Biology - The endoplasmic reticulum (ER) stress inducers dithiothreitol (DTT) and sodium selenite (SS) were tested for effect on expression of ER selenoproteins and apoptosis markers in...