Prediction and Validation of a Druggable Site on Virulence Factor of Drug Resistant Burkholderia cenocepacia**

Burkholderia cenocepacia is an opportunistic Gram-negative bacterium that causes infections in patients suffering from chronic granulomatous diseases and cystic fibrosis. It displays significant morbidity and mortality due to extreme resistance to almost all clinically useful antibiotics. The bacterial lectin BC2L-C expressed in B. cenocepacia is an interesting drug target involved in bacterial adhesion and subsequent deadly infection to the host. We solved the first high resolution crystal structure of the apo form of the lectin N-terminal domain (BC2L-C-nt) and compared it with the ones complexed with carbohydrate ligands. Virtual screening of a small fragment library identified potential hits predicted to bind in the vicinity of the fucose binding site. A series of biophysical techniques and X-ray crystallographic screening were employed to validate the interaction of the hits with the protein domain. The X-ray structure of BC2L-C-nt complexed with one of the identified active fragments confirmed the ability of the site computationally identified to host drug-like fragments. The fragment affinity could be determined by titration microcalorimetry. These structure-based strategies further provide an opportunity to elaborate the fragments into high affinity anti-adhesive glycomimetics, as therapeutic agents against B. cenocepacia.     

Improving the Morphological Parameters of Aluminum Foam for Maximum Sound Absorption Coefficient using Genetic Algorithm

Fabricating of metal foams with desired morphological parameters including pore size, porosity and pore opening is possible now using sintering technology. Thus, if it is possible to determine the morphology of metal foam to absorb sound at a given frequency, and then fabricate it through sintering, it is expected to have optimized metal foams for the best sound absorption. Theoretical sound absorption models such as Lu model describe the relationship between morphological parameters and the sound absorption coefficient. In this study, the Lu model was used to optimize the morphological parameters of Aluminum metal foam for the best sound absorption coefficient. For this purpose, the Lu model was numerically solved using written codes in MATLAB software. After validating the proposed codes with benchmark data, the genetic algorithm (GA) was applied to optimize the affecting morphological parameters on the sound absorption coefficient. The optimization was carried out for the thicknesses of 5 mm to 40 mm at the sound frequency range of 250 Hz–8000 Hz. The optimized parameters ranged from 50% to 95% for porosity, 0.1 mm to 4.5 mm for pore size, and 0.07 mm to 0.6 mm for pore opening size. The result of this study was applied to fabricate the desired Aluminum metal foams for the best sound absorption. The novel approach applied in this study, is expected to be successfully applied in for best sound absorption in desired frequencies.     

Virtual Braids, Virtual Temperley-Lieb Algebra and f-Polynomial

The authors study the properties of virtual Temperley-Lieb algebra and show how the f-polynomial of virtual knot can be derived from a representation of the virtual braid group into the virtual Temperley-Lieb algebra,which is an approach similar to Jones's original construction.     

Discovery of potential Zika virus RNA polymerase inhibitors by docking-based virtual screening

Zika virus (ZIKV) infection has been associated with Guillain-Barre syndrome in adults and microcephaly in infants. The existence of insufficient structural data in most of the protein databases hinders the synthesis of anti-ZIKV pharmaceutics. In this work, we attempted to model the catalytic domain of the ZIKV RNA polymerase (RdRpC) along with a detailed assessment of conserved aspartates in ZIKV RdRpC palm domain as potential drug targets. The conserved and catalytically active aspartate residues present in the predicted RdRpC protein were virtually screened against a ZINC database for inhibitors, and the selected potential drug candidates were further filtered based on their ADMET profiles. One of the pharmacokinetically active compounds (Ligand 6) showed a remarkable docking profile against the strictly conserved aspartate residues of the RdRpC active site. We hypothesize that the Ligand 6 may form a potential drug candidate for RdRpC inhibition in the clinical treatment of ZIKV infection.     

Spherical resonator for vapor-phase speed of sound and measurements of 1,1,1,2,2,3,3-heptafluoro-3-methoxypropane (RE347mcc) and trans-1,3,3,3-tetrafluoropropene [R1234ze(E)]

We describe an apparatus to measure the speed of sound of gas samples at temperatures from (265 to 500) K with pressures up to 10 MPa. The speed of sound was determined from the frequency of the three lowest-order radial resonance modes for the gas in a spherical cavity machined from type 321 stainless steel for corrosion resistance. The spherical resonator was contained in an isothermal copper block that was maintained at the temperature of interest by a multilayer thermostat with vacuum insulation. The dimensions of the spherical cavity were characterized as a function of temperature and pressure though calibration measurements with high-purity argon. The performance of the apparatus was demonstrated with measurements of high-purity methane and ethane. Measurements of the sound speed of 1,1,1,2,2,3,3-heptafluoro-3-methoxypropane (RE347mcc) are reported at temperatures from (325 to 500) K with pressures up to 1.6 MPa. Measurements on trans-1,3,3,3-tetrafluoropropene (R1234ze(E)) are reported at temperatures from (280 to 420) K with pressures up to 2.8 MPa. The average relative combined expanded uncertainties of the measured sound speed for RE347mcc and R1234ze(E) are (0.029 and 0.041)%, respectively.     

X射线荧光光谱法测定铁基合金中合金组分的通用工作曲线的制作——基本参数(FP)法虚拟合成标准样品的应用

应用基本参数(FP)法虚拟合成标准样品制作了X射线荧光光谱法测定不同类型的铁基合金中的26种元素的通用工作曲线。选择最佳的仪器工作条件和合理的待测元素的分析线系,测定了9种元素、受共存元素重叠干扰的校正系数,用瑞利散射线扣除背景及通道材料的影响。在设定虚拟合成标准样品中各元素的含量,并算得在此设定值下的理论荧光强度后,用FP法计算各元素在其定值下的最终强度,从而完成了FP法工作曲线。应用此虚拟合成单标工作曲线对多种标准样品进行测定,证明该工作曲线可用于各种类型的铁基合金的分析。     

Identification of potential Tpx inhibitors against pathogen-host interactions

Yersinia organisms cause many infectious diseases by invading human cells and delivering their virulence factors via the type three secretion system (T3SS). One alternative strategy in the fight against these pathogenic organisms is to interfere with their T3SS. Previous studies demonstrated that thiol peroxidase, Tpx is functional in the assembly of T3SS and its inhibition by salicylidene acylhydrazides prevents the secretion of pathogenic effectors. In this study, the aim was to identify potential inhibitors of Tpx using an integrated approach starting with high throughput virtual screening and ending with molecular dynamics simulations of selected ligands. Virtual screening of ZINC database of 500,000 compounds via ligand-based and structure-based pharmacophore models retrieved 10,000 hits. The structure-based pharmacophore model was validated using high-throughput virtual screening (HTVS). After multistep docking (SP and XP), common scaffolds were used to find common substructures and the ligand binding poses were optimized using induced fit docking. The stability of the protein–ligand complex was examined with molecular dynamics simulations and the binding free energy of the complex was calculated. As a final outcome eight compounds with different chemotypes were proposed as potential inhibitors for Tpx. The eight ligands identified by a detailed virtual screening protocol can serve as leads in future drug design efforts against the destructive actions of pathogenic bacteria.     

New peak broadening parameter for the characterization of separation capability in capillary electrophoresis

The influence of separation conditions on peak broadening is usually estimated by the number of theoretical plates. Using the data available in literature and experimental data, it is shown that in pressure‐assisted capillary electrophoresis the plate number is not directly related to the separation capability of conditions used. The experiments at different electrolyte flow velocities demonstrate that a higher plate number (the best separation efficiency) can be obtained with a lower peak resolution. Since ions are separated by electrophoresis due to the difference in electrophoretic mobilities, the peak width in terms of electrophoretic mobility is suggested as a new peak broadening parameter describing the separation capability of the conditions used. The parameter can be calculated using the tailing factor and the temporal peak width at 5% of the peak height. A simple equation for the resolution calculation is derived using the parameter. The advantage of the peak width in terms of mobility over other parameters is shown. The new parameter is recommended to be used not only in pressure‐assisted capillary electrophoresis but also in general capillary electrophoresis when in a number of runs the virtual separative migration distance and separation capability of the conditions used change widely.