Heterocyclic Substitutions Greatly Improve Affinity and Stability of Folic Acid towards FRα. an In Silico Insight

Folate receptor alpha (FRα) is known as a biological marker for many cancers due to its overexpression in cancerous epithelial tissue. The folic acid (FA) binding affinity to the FRα active site provides a basis for designing more specific targets for FRα. Heterocyclic rings have been shown to interact with many receptors and are important to the metabolism and biological processes within the body. Nineteen FA analogs with substitution with various heterocyclic rings were designed to have higher affinity toward FRα. Molecular docking was used to study the binding affinity of designed analogs compared to FA, methotrexate (MTX), and pemetrexed (PTX). Out of 19 FA analogs, analogs with a tetrazole ring (FOL03) and benzothiophene ring (FOL08) showed the most negative binding energy and were able to interact with ASP81 and SER174 through hydrogen bonds and hydrophobic interactions with amino acids of the active site. Hence, 100 ns molecular dynamics (MD) simulations were carried out for FOL03, FOL08 compared to FA, MTX, and PTX. The root mean square deviation (RMSD) and root mean square fluctuation (RMSF) of FOL03 and FOL08 showed an apparent convergence similar to that of FA, and both of them entered the binding pocket (active site) from the pteridine part, while the glutamic part was stuck at the FRα pocket entrance during the MD simulations. Molecular mechanics Poisson-Boltzmann surface accessible (MM-PBSA) and H-bond analysis revealed that FOL03 and FOL08 created more negative free binding and electrostatic energy compared to FA and PTX, and both formed stronger H-bond interactions with ASP81 than FA with excellent H-bond profiles that led them to become bound tightly in the pocket. In addition, pocket volume calculations showed that the volumes of active site for FOL03 and FOL08 inside the FRα pocket were smaller than the FA–FRα system, indicating strong interactions between the protein active site residues with these new FA analogs compared to FA during the MD simulations.     

Nanosecond laser ablation and deposition of silicon

Nanosecond-pulsed KrF (248 nm, 25 ns) and Nd:YAG (1064 nm, 532 nm, 355 nm, 5 ns) lasers were used to ablate a polycrystalline Si target in a background pressure of <10⁻⁴ Pa. Si films were deposited on Si and GaAs substrates at room temperature. The surface morphology of the films was characterized using scanning electron microscopy (SEM) and atomic force microscopy (AFM). Round droplets from 20 nm to 5 μm were detected on the deposited films. Raman Spectroscopy indicated that the micron-sized droplets were crystalline and the films were amorphous. The dependence of the properties of the films on laser wavelengths and fluence is discussed.     

QSAR classification of metabolic activation of chemicals into covalently reactive species

Metabolic activation of chemicals into covalently reactive species might lead to toxicological consequences such as tissue necrosis, carcinogenicity, teratogenicity, or immune-mediated toxicities. Early prediction of this undesirable outcome can help in selecting candidates with increased chance of success, thus, reducing attrition at all stages of drug development. The ensemble modelling of mixed features was used for the development of a model to classify the metabolic activation of chemicals into covalently reactive species. The effects of the quality of base classifiers and performance measure for sorting were examined. An ensemble model of 13 naive Bayes classifiers was built from a diverse set of 1,479 compounds. The ensemble model was validated internally with five-fold cross validation and it has achieved sensitivity of 67.4% and specificity of 93.4% when tested on the training set. The final ensemble model was made available for public use.     

Consensus QSAR model for identifying novel H5N1 inhibitors

Due to the importance of neuraminidase in the pathogenesis of influenza virus infection, it has been regarded as the most important drug target for the treatment of influenza. Resistance to currently available drugs and new findings related to structure of the protein requires novel neuraminidase 1 (N1) inhibitors. In this study, a consensus QSAR model with defined applicability domain (AD) was developed using published N1 inhibitors. The consensus model was validated using an external validation set. The model achieved high sensitivity, specificity, and overall accuracy along with low false positive rate (FPR) and false discovery rate (FDR). The performance of model on the external validation set and training set were comparable, thus it was unlikely to be overfitted. The low FPR and low FDR will increase its accuracy in screening large chemical libraries. Screening of ZINC library resulted in 64,772 compounds as probable N1 inhibitors, while 173,674 compounds were defined to be outside the AD of the consensus model. The advantage of the current model is that it was developed using a large and diverse dataset and has a defined AD which prevents its use on compounds that it is not capable of predicting. The consensus model developed in this study is made available via the free software, PaDEL-DDPredictor.     

Graphene-based Q-switched pulsed fiber laser in a linear configuration

A pulsed laser system is realized with graphene employed as a Q-switch.The graphene is exfoliated from its solution using an optical deposition and the optical tweezer effect.A fiber ferrule that already has the graphene deposited on it is inserted into an erbium-ytterbium laser(EYL)system with linear cavity configuration.We successfully demonstrate a pulsed EYL with a pulse duration of approximately 5.9μs and a repetition rate of 20.0 kHz.     

Reaction of NiBr2(DME) with 2-pyridinal-methyl-N-2,6-diisopropylphenylimine. The first crystal structure of an α-diimine nickel(II) complex of the NiL2X2 type

NiBr₂ (DME) (DME = ethylene glycol dimethyl ether) reacts with 2-pyridinal-methyl-N-2,6-diisopropylphenylimine (L) in a 1:1 molar ratio in CH₂Cl₂ to give NiBr₂(L) and [NiBrL₂]Br · 4CH₂Cl₂ in 52% and 14% yield, respectively. The crystal of [NiBrL₂]Br · 4CHCl₃ obtained from CHCl₃ was structurally characterized.     

Evolutionary snowdrift game incorporating costly punishment in structured populations

The role of punishment and the effects of a structured population in promoting cooperation are important issues. Within a recent model of snowdrift game (SG) incorporating a costly punishing strategy (P), we study the effects of a population connected through a square lattice. The punishers, who carry basically a cooperative (C) character, are willing to pay a cost α$\alpha$ so as to punish a non-cooperative (D) opponent by β$\beta$. Depending on α$\alpha$, β$\beta$, the cost-to-benefit ratio r$r$ in SG, and the initial conditions, the system evolves into different phases that could be homogeneous or inhomogeneous. The spatial structure imposes geometrical constraint on how one agent is affected by neighboring agents. Results of extensive numerical simulations, both for the steady state and the dynamics, are presented. Possible phases are identified and discussed, and isolated phases in the r–β$r\text{–}\beta$ space are identified as special local structures of strategies that are stable due to the lattice structure. In contrast to a well-mixed population where punishers are suppressed due to the cost of punishment, the altruistic punishing strategy can flourish and prevail for appropriate values of the parameters, implying an enhancement in cooperation by imposing punishments in a structured population. The system could evolve to a phase corresponding to the coexistence of C, D, and P strategies at some particular payoff parameters, and such a phase is absent in a well-mixed population. The pair approximation, a commonly used analytic approach, is extended from a two-strategy system to a three-strategy system. We show that the pair approximation can, at best, capture the numerical results only qualitatively. Due to the improper way of including spatial correlation imposed by the lattice structure, the approximation does not give the frequencies of C, D, and P accurately and fails to give the homogeneous AllD and AllP phases.     

Routine screening and quantitation of urinary corticosteroids using bench-top gas chromatography-mass-selective detection.

A method was developed for the routine screening, confirmation and quantitation of corticosteroids in human urine using bench top capillary gas chromatography (GC)-mass-selective detection. The free and conjugated corticosteroid fractions were isolated by liquid-liquid partition. After evaporation to dryness under vacuum the corticosteroid residues were derivatized to form the methyloxime trimethylsilyl ether derivatives. Both GC retention data and characteristic spectral data based on authentic reference standards were used for the identification and quantitation of cortisol, cortisone, tetrahydrocortisol and tetrahydrocortisone in the ppb (ng/ml) concentration range. The method is simpler and more efficient than the other GC-mass spectrometric (MS) techniques. It is also more sensitive than the liquid chromatographic-MS method.