Investigation of the bindings of a class of inhibitors with GSK3ß kinase using thermodynamic integration MD simulation and kinase assay.

GSK3ß kinase is a noteworthy target for discovery of the drugs that will be used to treat several diseases. In the effort to identify a new inhibitor lead compound, we utilized thermodynamic integration (TI)-molecular dynamics (MD) simulation and kinase assay to investigate the bindings between GSK3ß kinase and five compounds that were analogous to a known inhibitor with an available crystal structure. TI-MD simulations of the first two compounds (analogs 1 and 2) were used for calibration. The computed binding affinities of analogs 1 and 2 agreed well with the experimental results. The rest three compounds (analogs 3-5) were newly obtained from a database search, and their affinity data were newly measured in our labs. TI-MD simulations predicted the binding modes and the computed ΔΔG values have a reasonably good correlation with the experimental affinity data. These newly identified inhibitors appear to be new leads according to our survey of GSK3ß inhibitors listed in recent review articles. The predicted binding modes of these compounds should aid in designing new derivatives of these compounds in the future.

Identifying GSK-3ß kinase inhibitors of Alzheimer's disease: Virtual screening, enzyme, and cell assays.

Glycogen synthase kinase 3ß (GSK-3ß) is widely known as a critical target protein for treating Alzheimer's disease (AD). We utilized virtual screening to search databases for compounds with the potential to be used in drugs targeting GSK-3ß kinase, and kinase as well as cell assays to investigate top-scored, selected compounds. Virtual screening of >1.1 million compounds in the ZINC and in-house databases was conducted using an optimized computational protocol in the docking program GOLD. Of the top-ranked compounds, 16 underwent a luminescent kinase assay and a cell assay using HEK293 cells expressing DsRed-tagged ΔK280 in the repeat domain of tau (tauRD). The compounds VB-003 (a potent GSK-3ß inhibitor) and VB-008 (AM404, an anandamide transport inhibitor), with determined IC50 values of 0.25 and 5.4µM, respectively, were identified as reducing tau aggregation. Both compounds increased expression of phospho-GSK-3ß (Ser9) and reduced endogenous tau phosphorylation at the sites of Ser202, Thr231, and Ser396. In the ∆K280 tauRD-DsRed SH-SY5Y cells, VB-008, but not VB-003, enhanced HSPB1 and GRP78 expression, increased ∆K280 tauRD-DsRed solubility, and promoted neurite outgrowth. Thus VB-008 performed best to the end of the present study. The identified compound VB-008 may guide the identification and synthesis of potential inhibitors analogous to this compound.

Investigation of differences in the binding affinities of two analogous ligands for untagged and tagged p38 kinase using thermodynamic integration MD simulation.

Thermodynamic integration (TI) molecular dynamics (MD) simulations for the binding of a pair of a reference ("ref") ligand and an analogous ("analog") ligand to either tagged (with six extra residues at the N-terminus) or untagged p38 kinase proteins were carried out in order to probe how the binding affinity is influenced by the presence or absence of the peptide tag in p38 kinase. This possible effect of protein length on the binding affinity of a ligand-which is seldom addressed in the literature-is important because, even when two labs claim to have performed experiments with the same protein, they may actually have studied variants of the same protein with different lengths because they applied different protein expression conditions/procedures. Thus, if we wanted to compare ligand binding affinities measured in the two labs, it would be necessary to account for any variation in ligand binding affinity with protein length. The pair of ligand-p38 kinase complexes examined in this work (pdb codes: 3d7z and 3lhj, respectively) were ideal for investigating this effect. The experimentally determined binding energy for the ref ligand with the untagged p38 kinase was -10.9 kcal mol(-1), while that for the analog ligand with the tagged p38 kinase was -11.9 kcal mol(-1). The present TI-MD simulation of the mutation of the ref ligand into the analog ligand while the ligand is bound to the untagged p38 kinase predicted that the binding affinity of the analog ligand is 2.0 kcal mol(-1) greater than that of the ref ligand. A similar simulation also indicated that the same was true for ligand binding to the tagged protein, but in this case the binding affinity for the analog ligand is 2.5 kcal mol(-1) larger than that for the ref ligand. These results therefore suggest that the presence of the peptide tag on p38 kinase increased the difference in the binding energies of the ligands by a small amount of 0.5 kcal mol(-1). This result supports the assumption that the presence of a peptide tag has only a minor effect on ΔG values. The error bars in the computed ΔG values were then estimated via confidence interval analysis and a time autocorrelation function for the quantity dV/dλ. The estimated correlation time was ~0.5 ps and the error bar in the ΔG values estimated using nanosecond-scale simulations was ±0.3 kcal mol(-1) at a confidence level of 95%. These predicted results can be verified in future experiments and should prove useful in subsequent similar studies. Graphical Abstract Thermodynamic cycles for binding of two analogous ligands with untagged and tagged p38 kinases and associated Gibbs free energy.

Using thermodynamic integration MD simulation to compute relative protein-ligand binding free energy of a GSK3ß kinase inhibitor and its analogs.

Thermodynamic integration molecular dynamics simulation was used to investigate how TI-MD simulation preforms in reproducing relative protein-ligand binding free energy of a pair of analogous GSK3ß kinase inhibitors of available experimental data (see Fig. 1), and to predict the affinity for other analogs. The computation for the pair gave a ΔΔG of 1.0 kcal/mol, which was in reasonably good agreement with the experimental value of -0.1 kcal/mol. The error bar was estimated at 0.5 kcal/mol. Subsequently, we employed the same protocol to proceed with simulations to find analogous inhibitors with a stronger affinity. Four analogs with a substitution at one site inside the binding pocket were the first to be tried, but no significant enhancement in affinity was found. Subsequent simulations for another 7 analogs was focused on substitutions at the benzene ring of another site, which gave two analogs (analogs 9 and 10) with ΔΔG values of -0.6 and -0.8 kcal/mol, respectively. Both analogs had a OH group at the meta position and another OH group at the ortho position at the other side of the benzene ring, as shown in Table 3. To explore further, another 4 analogs with this characteristic were investigated. Three analogs with ΔΔG values of -2.2, -1.7 and -1.2 kcal/mol, respectively, were found. Hydrogen bond analysis suggested that the additional hydrogen bonds of the added OH groups with Gln185 and/or Asn64, which did not appear in the reference inhibitor or as an analog with one substitution only in the examined cases, were the main contributors to an enhanced affinity. A prediction for better inhibitors should interest experimentalists of enzyme and/or cell assays. Analysis of the interactions between GSK3ß kinase and the investigated analogs will be useful in the design of GSK3ß kinase inhibitors for compounds of this class.

Filtration of dust particulates with a moving granular bed filter.

The goal of this study was to evaluate the performance of a moving granular bed filter designed for cold test to filter coal particulates. A series of experiments were carried out at room temperature to demonstrate the collection efficiency of this method of filtration technology (i.e., the moving granular bed filter) at different filtration superficial velocities and mass flow rates of filter granules but with a fixed inlet dust concentration. The dynamic characteristics of the filter system were evaluated by measuring variations in the outlet concentration and size distribution of dust particulates. The collection mechanisms of the filter granules in the moving granular bed filter were also studied. Experimental results showed that the collection efficiency could be enhanced by using a filtration superficial velocity of 30 cm/s and mass flow rate of 450 g/min. The results of this study indicate this type of method could be useful for application in different cross-flow filter systems for gas cleanup. The focus in the current study is essentially the development of a moving granular bed filter that could be applied in a high-temperature environment. The results are expected to serve as the basis for future research.

Development of a reliable assay protocol for identification of diseases (RAPID)-bioactive amplification with probing (BAP) for detection of Newcastle disease virus.

Due to appearance of new genotypes of Newcastle disease virus (NDV) with no cross-protection and with vaccine strains, some outbreaks have been reported in Taiwan that caused significant damage to the poultry industry. A reliable assay protocol, (RAPID)-bioactive amplification with probing (BAP), for detection of NDV that uses a nested PCR and magnetic bead-based probe to increase sensitivity and specificity, was developed. Primers and probes were designed based on the conserved region of the F protein-encoding gene sequences of all NDV Taiwan isolates. The optimal annealing temperature for nested reverse transcription-polymerase chain reaction (RT-PCR) to amplify the gene was 61 degrees C and optimal hybridization occurred when buffer 1x SSC and 0.5% SDS were used at 50 degrees C. The sensitivity of RAPID-BAP was 1 copy/microl for standard plasmids and 10 copy/mul for transcribed F protein-encoding gene of NDV with comparable linearity (R(2)=0.984 versus R(2)=0.99). This sensitivity was superior to that of other techniques currently used. The assay was also highly specific because the negative controls, including classical swine fever virus, avian influenza virus, avian reovirus, and infectious bursa disease virus could not be detected. Thirty-four field samples were tested using conventional RT-PCR, nested RT-PCR, real-time quantitative RT-PCR, and RAPID-BAP assay and the positive rates were 24%, 30%, 41%, and 53%, respectively. The developed assay allows for rapid, correct, and sensitive detection of NDV and fulfils all of the key requirements for clinical applicability. It could reliably rule out false negative results from antibody-based assays and also facilitate a rapid diagnosis in the early phase of the disease for emergency quarantine that may help prevent large-scale outbreaks.

Magnetic viscosity and microstructure of GePt/FePt films.

We found various GePt/FePt microstructures at different post-annealing temperatures. The Ge(2)Pt(3) compound was formed when the annealing temperature was 800 °C and the particle-like structure was able to relax the growth stress between Ge(2)Pt(3) and quartz. After deposition of FePt film, a discontinuous L1(0) FePt layer was formed when it was post-annealed at 400 °C. However, isolated L1(0) FePt particles were observed at 800 °C post-annealing temperature, and each particle contains many grains. Furthermore, the magnetic viscosity was measured to investigate the different GePt/FePt morphology effects on thermal activation behaviour. When the applied field was less than the coercivity field H(c), we found smaller activation volume (V(a) = 0.5 × 10(-18) cm(3)) for a film with 400 °C post-annealing. This is because smaller FePt grains are in between GePt islands and the moments in these grains are hard to reverse. In contrast, a larger V(a) (= 1.9 × 10(-18) cm(3)) was found in samples post-annealed at 600-800 °C. This is because the GePt islands agglomerate to become particle-like at high temperature and larger FePt grains were distributed on each GePt particle.