Hit clustering can improve virtual fragment screening: CDK2 and PARP1 case studies

Virtual fragment screening could be a promising alternative to existing experimental screening techniques. However, reliable methods of in silico fragment screening are yet to be established and validated. In order to develop such an approach we first checked how successful the existing molecular docking methods can be in predicting fragment binding affinities and poses. Using our Lead Finder docking software the RMSD of the binding energy prediction was observed to be 1.35 kcal/mol(-1) on a set of 26 experimentally characterized fragment inhibitors, and the RMSD of the predicted binding pose from the experimental one was <1.5 ?. Then, we explored docking of 68 fragments obtained from 39 drug molecules for which co-crystal structures were available from the PDB. It appeared that fragments that participate in oriented non-covalent interactions, such as hydrogen bonds and metal coordination, could be correctly docked in 70-80% of cases suggesting the potential success of rediscovering of corresponding drugs by in silico fragment approach. Based on these findings we've developed a virtual fragment screening technique which involved structural filtration of protein-ligand complexes for specific interactions and subsequent clustering in order to minimize the number of preferable starting fragment candidates. Application of this method led to 2 millimolar-scale fragment PARP1 inhibitors with a new scaffold.     

Natural causes of programmed death of yeast Saccharomyces cerevisiae

The existence of cell death program in unicellular organisms has been reported for a number of species. Nevertheless, the question why the ability to commit suicide has been maintained throughout evolution is far from being solved. While it is believed that altruistic death of individual yeast cells could be beneficial for the population, it is generally not known (i) what is wrong with the individuals destined for elimination, (ii) what is the critical value of the parameter that makes a cell unfit and (iii) how the cell monitors this parameter. Studies performed on yeast Saccharomyces cerevisiae allow us to hypothesize on ways of possible solutions of these problems. Here we argue that (a) the main parameter for life-or-death decision measured by the cell is the degree of damage to the genetic material, (b) its critical value is dictated by quorum sensing machinery, and (c) it is measured by monitoring delays in cell division.     

Thrips (Thysanoptera) identification using artificial neural networks

We studied the use of a supervised artificial neural network (ANN) model for semi-automated identification of 18 common European species of Thysanoptera from four genera: Aeolothrips Haliday (Aeolothripidae), Chirothrips Haliday, Dendrothrips Uzel, and Limothrips Haliday (all Thripidae). As input data, we entered 17 continuous morphometric and two qualitative two-state characters measured or determined on different parts of the thrips body (head, pronotum, forewing and ovipositor) and the sex. Our experimental data set included 498 thrips specimens. A relatively simple ANN architecture (multilayer perceptrons with a single hidden layer) enabled a 97% correct simultaneous identification of both males and females of all the 18 species in an independent test. This high reliability of classification is promising for a wider application of ANN in the practice of Thysanoptera identification.     

Types of Systemic Reactions of Human Hemodynamics and Hemostasis to Multiple Occupational Migrations to the Polar Circle Regions

Effects of meridional migrations in shuttle from middle latitudes to regions beyond the Polar Circle, where an expedition and the organization of work shifts were being conducted, were studied. Three main types of systemic reactions of human hemodynamics and hemostasis were established. The first type was characterized by a moderate increase in the arterial blood pressure (BP) at the beginning of the shift with its subsequent normalization; by hypocoagulemia; and by an increase in the total phospholipid content, with a significant increase in the content of lysolecithins (an adaptive type). The second type was characterized by hypertension throughout the whole shift, by hypercoagulemia with significant changes in the phospholipid spectrum, and with a pronounced increase in the lysolecithin and cardiolipin fractions (a hypertensive type). The third type was characterized by a decrease in BP and an increase in heart rate (HR), by hypocoagulemia and an asthenic state associated with sleep disorders, and a decreased mental capacity (an asthenic type).     

Role of blood lipoproteins in adaptive reorganization of the rat liver mitochondria

It was shown in experiments in vitro that high density lipids (HDL), very low density lipids (VLDL) and cAMP taken separately did not affect the kinetics of mitochondrial swelling in the liver of control and 72-hr-fasting rats. ApoHDL and particularly ApoVLDL obtained by delipidation of appropriate lipoproteins had pronounced capacities to stimulate the process of swelling. Mitochondrial swelling increased to an ever greater degree under the action of cAMP coupled with apoproteins. The maximum stimulation of the swelling was attained as a result of administering apoVLDL in conjunction with cAMP. The effects of enhanced swelling were the most remarkable in experiments with mitochondria from the control animals.     

Anticataleptic effect of delta sleep-inducing peptide and its action on brain monoamine oxidase in rats genetically predisposed to catalepsy

Rats with genetic susceptibility to catalepsy (GC strain) were compared with Wistar rats (W). After an intraperitoneal administration of 120 micrograms/100 g delta sleep-inducing peptide (DSIP) in GC rats the duration of cataleptic freezing was shortened (13.8 +/- 9.5 sec against 27.2 +/- 7.5 sec in control). MAO-B activity decreased due to DSIP administration both in GC and W rats. It is hypothesized that the DSIP effect MAO-B in GC rats may correct the lost MAO-A function in deamination of dopamine, a common MAO-A and MAO-B substrate, and the dopaminergic neurotransmission in catalepsy.     

Kinetics of hairpin ribozyme cleavage in yeast.

Hairpin ribozymes catalyze a self-cleavage reaction that provides a simple model for quantitative analyses of intracellular mechanisms of RNA catalysis. Decay rates of chimeric mRNAs containing self-cleaving ribozymes give a direct measure of intracellular cleavage kinetics in yeast. Intracellular ribozyme-mediated cleavage occurs at similar rates and shows similar inhibition by ribozyme mutations as ribozyme-mediated reactions in vitro, but only when ribozymes are located in a favorable mRNA sequence context. The impact of cleavage on mRNA abundance is shown to depend directly on intrinsic mRNA stability. Surprisingly, cleavage products are no more labile than uncleaved mRNAs despite the loss of terminal cap structures or poly (A).     

A DEAD-box RNA helicase promotes thermodynamic equilibration of kinetically trapped RNA structures in vivo

RNAs must assemble into specific structures in order to carry out their biological functions, but in vitro RNA folding reactions produce multiple misfolded structures that fail to exchange with functional structures on biological time scales. We used carefully designed self-cleaving mRNAs that assemble through well-defined folding pathways to identify factors that differentiate intracellular and in vitro folding reactions. Our previous work showed that simple base-paired RNA helices form and dissociate with the same rate and equilibrium constants in vivo and in vitro. However, exchange between adjacent secondary structures occurs much faster in vivo, enabling RNAs to quickly adopt structures with the lowest free energy. We have now used this approach to probe the effects of an extensively characterized DEAD-box RNA helicase, Mss116p, on a series of well-defined RNA folding steps in yeast. Mss116p overexpression had no detectable effect on helix formation or dissociation kinetics or on the stability of interdomain tertiary interactions, consistent with previous evidence that intracellular factors do not affect these folding parameters. However, Mss116p overexpression did accelerate exchange between adjacent helices. The nonprocessive nature of RNA duplex unwinding by DEAD-box RNA helicases is consistent with a branch migration mechanism in which Mss116p lowers barriers to exchange between otherwise stable helices by the melting and annealing of one or two base pairs at interhelical junctions. These results suggest that the helicase activity of DEAD-box proteins like Mss116p distinguish intracellular RNA folding pathways from nonproductive RNA folding reactions in vitro and allow RNA structures to overcome kinetic barriers to thermodynamic equilibration in vivo.