Fragment-similarity-based QSAR (FS-QSAR) algorithm for ligand biological activity predictions

Quantitative structure-activity relationship (QSAR) studies are useful computational tools often used in drug discovery research and in many scientific disciplines. In this study, a robust fragment-similarity-based QSAR (FS-QSAR) algorithm was developed to correlate structures with biological activities by integrating fragment-based drug design concept and a multiple linear regression method. Similarity between any pair of training and testing fragments was determined by calculating the difference of lowest or highest eigenvalues of the chemistry space BCUT matrices of corresponding fragments. In addition to the BCUT-similarity function, molecular fingerprint Tanimoto coefficient (Tc) similarity function was also used as an alternative for comparison. For validation studies, the FS-QSAR algorithm was applied to several case studies, including a dataset of COX2 inhibitors and a dataset of cannabinoid CB2 triaryl bis-sulfone antagonist analogues, to build predictive models achieving average coefficient of determination (r(2)) of 0.62 and 0.68, respectively. The developed FS-QSAR method is proved to give more accurate predictions than the traditional and one-nearest-neighbour QSAR methods and can be a useful tool in the fragment-based drug discovery for ligand activity prediction.

Determination of the magnetic contribution to the heat capacity of cobalt oxide nanoparticles and the thermodynamic properties of the hydration layers

We present low temperature (11 K) inelastic neutron scattering (INS) data on four hydrated nanoparticle systems: 10 nm CoO·0.10H(2)O (1), 16 nm Co(3)O(4)·0.40H(2)O (2), 25 nm Co(3)O(4)·0.30H(2)O (3) and 40 nm Co(3)O(4)·0.026H(2)O (4). The vibrational densities of states were obtained for all samples and from these the isochoric heat capacity and vibrational energy for the hydration layers confined to the surfaces of these nanoparticle systems have been elucidated. The results show that water on the surface of CoO nanoparticles is more tightly bound than water confined to the surface of Co(3)O(4), and this is reflected in the reduced heat capacity and vibrational entropy for water on CoO relative to water on Co(3)O(4) nanoparticles. This supports the trend, seen previously, for water to be more tightly bound in materials with higher surface energies. The INS spectra for the antiferromagnetic Co(3)O(4) particles (2-4) also show sharp and intense magnetic excitation peaks at 5 meV, and from this the magnetic contribution to the heat capacity of Co(3)O(4) nanoparticles has been calculated; this represents the first example of use of INS data for determining the magnetic contribution to the heat capacity of any magnetic nanoparticle system.

The small GTPase Cdc42 promotes membrane protrusion during polar body emission via ARP2-nucleated actin polymerization

Polar body emission is a specialized cell division throughout the animal kingdom, serving to reduce chromosome ploidy while preserving the egg cytoplasm. Critical to polar body emission are the asymmetric positioning of the meiotic spindle prior to anaphase, with one pole attached to the oocyte cortex, and the simultaneous membrane protrusion during subsequent cytokinesis. We have shown that, during Xenopus oocyte maturation, the small GTPase Cdc42 promotes membrane protrusion while a classical RhoA contractile ring forms and constricts at the base of the protrusion. We report here that treating oocytes with low concentrations of nocodazole diminished the size of metaphase I spindles and prevented polar body emission, and yet an active Cdc42 cap of correspondingly diminished size still developed, on time, atop of the spindle pole. Conversely, treating oocytes with low concentrations of taxol resulted in a spindle with multiple poles attached to the cortex, but still each of these poles were associated with activated cortical Cdc42 at the appropriate time. Therefore, the asymmetric positioning of the meiotic spindle with one pole anchored to the cortex is a prerequisite for Cdc42 activation. Furthermore, we demonstrated that the Cdc42-regulated F-actin nucleator ARP2/3 complex was similarly localized at the cortex of the protruding polar body membrane, suggesting that Cdc42 promotes membrane protrusion through an F-actin meshwork mechanism. Finally, we demonstrated that Cdc42 and RhoA formed similarly complementary activity zones during egg activation and that inhibition of Cdc42 prevented second polar body emission. Therefore, Cdc42 activation likely promotes membrane protrusion during polar body emission in widespread systems.

Continuous feeding of antimicrobial growth promoters to commercial swine during the growing/finishing phase does not modify faecal community erythromycin resistance or community structure

AIMS

To investigate the effect of continuous feeding of antimicrobial growth promoters (tylosin or virginiamycin) on the swine faecal community.

METHODS AND RESULTS

The study consisted of two separate on-farm feeding trials. Swine were fed rations containing tylosin (44 or 88 mg kg(-1) of feed) or virginiamycin (11 or 22 mg kg(-1) of feed) continuously over the growing/finishing phases. The temporal impact of continuous antimicrobial feeding on the faecal community was assessed and compared to nondosed control animals through anaerobic cultivation, the analysis of community 16S rRNA gene libraries and faecal volatile fatty acid content. Feeding either antimicrobial had no detectable effect on the faecal community.

CONCLUSIONS

Erythromycin methylase genes encoding resistance to the macrolide-lincosamide-streptogramin B (MLS(B) ) antimicrobials are present at a high level within the faecal community of intensively raised swine. Continuous antimicrobial feeding over the entire growing/finishing phase had no effect on community erm-methylase gene copy numbers or faecal community structure.

SIGNIFICANCE AND IMPACT OF THE STUDY

Antimicrobial growth promoters are believed to function by altering gut bacterial communities. However, widespread MLS(B) resistance within the faecal community of intensively raised swine likely negates any potential effects that these antimicrobials might have on altering the faecal community. These findings suggest that if AGP-mediated alterations to gut communities are an important mechanism for growth promotion, it is unlikely that these would be associated with the colonic community.