Palbociclib (PD 0332991) Interaction with Kinases. Theoretical and Comparative Molecular Docking Study

The optimized geometry of palbociclib, (PD 0332991) (8-cyclopentyl-6-ethanoyl-5-methyl-2-(5-(piperazin-1-yl)pyridin-2-ylamino)pyrido[2,3-d]pyrimidin-7(8H)-one), electrostatic potential map, molecular orbitals were calculated using the density functional theory. The geometry was used in a molecular docking study of palbociclib-kinase complexes, results could be explained by the charge of the nitrogen and oxygen atoms within the palbociclib. Energy gap of HOMO-LUMO surfaces, could help to explain the reactivity of the ligand and the hydrogen bonding with three different kinases, two of CDK6 and one of CDK4 type. Docking results are similar and complementary with literature reports using molecular dynamics, were hydrogen bonding was obtained and analyzed. The promiscuity of three kinases with palbociclib was detected by the docking results, thus, palbociclib could be used in other types of cancer besides myeloid leukemia. Some similarities are found with CDK4/CDK6 kinases which allow us to determine that palbociclib could be used to control other resistant inhibitor types of cancer.     

On the Origin of Extracellular Glutamate Levels Monitored in the Basal Ganglia of the Rat by In Vivo Microdialysis

Abstract: Several putative neurotransmitters and metabolites were monitored simultaneously in the extracellular space of neostriatum, substantia nigra, and cortex and in subcutaneous tissue of the rat by in vivo microdialysis. Glutamate (Glu) and aspartate (Asp) were at submicromolar and γ-aminobutyric acid (GABA) was at nanomolar concentrations in all brain regions. The highest concentration of dopamine (DA) was in the neostriatum. Dynorphin B (Dyn B) was in the picomolar range in all brain regions. Although no GABA, DA, or Dyn B could be detected in subcutaneous tissue, Glu and Asp levels were ≈5 and ≈0.4 µM, respectively. Lactate and pyruvate concentrations were ≈200 and ≈10 µM in all regions. The following criteria were applied to ascertain the neuronal origin of substances quantified by microdialysis: sensitivity to (a) K⁺ depolarization, (b) Na⁺ channel blockade, (c) removal of extracellular Ca²⁺, and (d) depletion of presynaptic vesicles by local administration of α-latrotoxin. DA, Dyn B, and GABA largely satisfied all these criteria. In contrast, Glu and Asp levels were not greatly affected by K⁺ depolarization and were increased by perfusing with tetrodotoxin or with Ca²⁺-free medium, arguing against a neuronal origin. However, Glu and Asp, as well as DA and GABA, levels were decreased under both basal and K⁺-depolarizing conditions by α-latrotoxin. Because the effect of K⁺ depolarization on Glu and Asp could be masked by reuptake into nerve terminals and glial cells, the reuptake blocker dihydrokainic acid (DHKA) or l -trans-pyrrolidine-2,4-dicarboxylic acid (PDC) was included in the microdialysis perfusion medium. The effect of K⁺ depolarization on Glu and Asp levels was increased by DHKA, but GABA levels were also affected. In contrast, PDC increased only Glu levels. It is concluded that there is a pool of releasable Glu and Asp in the rat brain. However, extracellular levels of amino acids monitored by in vivo microdialysis reflect the balance between neuronal release and reuptake into surrounding nerve terminals and glial elements.     

When motion is not perceived: evidence from adaptation and dynamical stability

Adaptation was used to probe the perceiver's activation state when either motion or nonmotion percepts are formed for bistable, single-element apparent motion stimuli. Although adaptation was not observed in every instance, when it was observed its effect was to increase the probability of both motion-to-nonmotion and nonmotion-to-motion switches, the time scale of adaptation corresponding to neurophysiological observations for directionally selective cortical cells (Giaschi et al. 1993). This susceptibility to de-stabilizing adaptation effects indicated that the nonmotion percept was not the result of inadequate stimulation producing subthreshold levels of motion detector activation; if that were the case, activation-dependent adaptation would have decreased the nonmotion-to-motion switching rate by reducing activation further below threshold. Above-threshold activation levels are therefore associated with both nonmotion and motion perceptual states, and the failure to perceive motion despite the presence of adequate motion detector stimulation can be attributed to inhibitory competition between detectors activated by motion-specifying stimulus information and detectors activated to similar levels by motion-independent stimulus information, consistent with the dynamical quality of single-element apparent motion.     

Identification of gene disruptions for increased poly‐3‐hydroxybutyrate accumulation in Synechocystis PCC 6803

Inverse metabolic engineering (IME) is a combinatorial approach for identifying genotypes associated with a particular phenotype of interest. In this study, gene disruptions that increase the biosynthesis of poly‐3‐hydroxybutyrate (PHB) in the photosynthetic bacterium Synechocystis PCC6803 were identified. A Synechocystis mutant library was constructed by homologous recombination between the Synechocystis genome and a mutagenized genomic plasmid library generated through transposon insertion. Using a fluorescence‐activated cell sorting‐based high throughput screen, high PHB accumulating mutants from the library grown in different nutrient conditions were isolated and characterized. While several mutants isolated from the screen had increased PHB accumulation, transposon insertions in only two ORFs could be linked to increased PHB production. Disruptions of sll0461, coding for gamma‐glutamyl phosphate reductase (proA), and sll0565, a hypothetical protein, resulted in increased accumulation in standard growth media and acetate supplemented media. These genetic perturbations have increased PHB accumulation in Synechocystis and serve as markers for engineering increased polymer production in higher photosynthetic organisms. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Comparison of three methods for DNA extraction from bone remains

Extraction of amplifiable DNA is a frequent problem when working with degraded specimens like bone samples. The possibility of obtaining as much information as possible from these samples has a particular significance in many forensic investigations. The present investigation was aimed to assess the efficiency of three organic extraction methods for purifying amplifiable DNA from bone samples. The amount of nucleic acids obtained, the success rate in the amplification of DNA microsatellite (STR) markers and amelogenin by PCR, the influence of PCR inhibitors and environmental conditions, and where the samples were found before their processing in the laboratory, were all evaluated in this investigation for the three methods. Results showed that method A (a modification of FBI method for DNA extraction) performed better in producing not a higher amount but a better quality amplifiable DNA, in comparison with the other two methods evaluated. It was also demonstrated that the quality of the DNA to be amplified by PCR was influenced by the presence of inhibitors and/or contaminants and the environmental conditions where the bone sample was taken from. The worst conditions were observed from aquatic environments. The results suggest that the implementation of some specific modifications in the method A (use of purification columns, reliable quantification methods and different dilutions) would help to obtain better DNA extracts intended to be used in different molecular identification tests.     

Chromatin from two classes of platyhelminthes display both protist H1 and higher eukaryote core histones

Histones from the parasitic platyhelminthes, Echinococcus granulosus and Fasciola hepatica, were systematically characterized. Core histones H2A, H2B, H3 and H4, which were identified on the basis of amino acid sequencing and mass spectrometry data, showed conserved electrophoretic patterns. Histones H1, identified on the basis of physicochemical properties, amino acid composition and amino acid sequencing, showed divergence, both in their number and electrophoretic mobilities, between the two species and among other organisms. According to these data, core histones but not H1 histones, would be stabilized during evolution at the level of platyhelminthes.