EGFRisopred: a machine learning-based classification model for identifying isoform-specific inhibitors against EGFR and HER2

The EGFR kinase pathway is one of the most frequently activated signaling pathways in human cancers. EGFR and HER2 are the two significant members of this pathway, which are attractive drug targets of clinical relevance in lung and breast cancer. Therefore, identifying EGFR- and HER2-specific inhibitors is one of the important challenges in cancer drug discovery. To address this issue, a dataset of 519 compounds having inhibitory activity against both the isoforms, i.e., EGFR and HER2, was collected from the literature and developed a knowledge-based computational classification model for predicting the specificity of a molecule for an isoform (EGFR/HER2) with precision. A total of seventy-two classification models using nine fingerprint types, four classifiers (IBK, NB, SMO and RF) and two different datasets (EGFR and HER2 isoform specific) were developed. It was observed that the models developed using random forest and IBK performed better for EGFR- and HER2-specific datasets, respectively. Scaffold and functional group analysis led to the identification of prevalent core and fragments in each of the datasets. The accuracy of the selected best performing models was also evaluated using the decoy dataset. We have also developed an application EGFRisopred, which integrates the best performing models and permits the user to predict the specificity of a compound as an EGFR-/HER2-specific anticancer agent. It is expected that the tool’s availability as a free utility will allow researchers to identify new inhibitors against these targets important in cancer.

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Peroxidase enzyme sensor for on-line monitoring of disinfection processes in the food industry.

For desirable environmental reasons, peroxides have replaced halogenated substances for disinfection purposes in the food and beverage industry. However, cost issues and the requirement to remove these agents completely after disinfection necessitate simple, low-cost and sensitive test methods with a wide dynamic range and on-line capability. The development and performance of such a method is detailed here. Low-cost peroxide sensors were fabricated using a single deposition procedure, in which horseradish peroxidase enzyme and dimethylferrocene mediator were entrapped within a cellulose acetate membrane, over the working electrode area of a screen-printed three-electrode assembly. Optimum performance was obtained using HRP and DMFc loadings of 25 U and 0.03 micromol per electrode, respectively, and a mean cellulose acetate molecular weight of 37,000. The device had a detection limit of 49.5 microM hydrogen peroxide and mean RSD values of 21% across the concentration range 49.5-368 microM. In laboratory studies the sensor was shown to have a stability of > or = 4 d in continuous flow-mode maintaining an accuracy of +/- 16% that was considered acceptable for the intended on-line monitoring of the disinfection process. In a field study, it was successfully used on-line within a flow-cell to measure peroxide levels during disinfection of an industrial fermentation vessel.     

Site directed maleimide bifunctional chelators for the M(CO)3+ core (M =(99m)Tc, Re)

A series of bifunctional chelates containing a tridentate donor set for complexation of the M(CO)3+ core and a maleimide group for site-specific coupling to peptides and proteins containing free thiol groups has been prepared and their Re(CO)3+ complexes and glutathione conjugates structurally characterized. The flexibility of design allows preparation of ligands suitable for both fluorescence imaging, radioimaging and radiotherapeutic studies of proteins and peptides as well as other biopolymers using site specific conjugation.     

Determination of trace concentrations of bromate in municipal and bottled drinking waters using a hydroxide-selective column with ion chromatography

The International Agency for Research on Cancer determined that bromate is a potential human carcinogen, even at low micro/l levels in drinking water. Bromate is commonly produced from the ozonation of source water containing naturally occurring bromide. Traditionally, trace concentrations of bromate and other oxyhalides in environmental waters have been determined by anion exchange chromatography with an IonPac AS9-HC column using a carbonate eluent and suppressed conductivity detection, as described in EPA Method 300.1 B. However, a hydroxide eluent has lower suppressed background conductivity and lower noise compared to a carbonate eluent and this can reduce the detection limit and practical quantitation limit for bromate. In this paper, we examine the effect of using an electrolytically generated hydroxide eluent combined with a novel hydroxide-selective anion exchange column for the determination of disinfection byproduct anions and bromide in municipal and bottled drinking water samples. EPA Methods 300.1 B and 317.0 were used as test criteria to evaluate the new anion exchange column. The combination of a hydroxide eluent with a high capacity hydroxide-selective column allowed sub-microg/l detection limits for chlorite, bromate, chlorate, and bromide with a practical quantitation limit of 1 microg/l bromate using suppressed conductivity detection and 0.5 microg/l using postcolumn addition of o-dianisidine followed by visible detection. The linearity, method detection limits, robustness, and accuracy of the methods for spiked municipal and bottled water samples will be discussed.     

ssDNA binding reveals the atomic structure of graphene

We used AFM to investigate the interaction of polyelectrolytes such as ssDNA and dsDNA molecules with graphene as a substrate. Graphene is an appropriate substrate due to its planarity, relatively large surfaces that are detectable via an optical microscope, and straightforward identification of the number of layers. We observe that in the absence of the screening ions deposited ssDNA will bind only to the graphene and not to the SiO(2) substrate, confirming that the binding energy is mainly due to the π-π stacking interaction. Furthermore, deposited ssDNA will map the graphene underlying structure. We also quantify the π-π stacking interaction by correlating the amount of deposited DNA with the graphene layer thickness. Our findings agree with reported electrostatic force microscopy (EFM) measurements. Finally, we inspected the suitability of using a graphene as a substrate for DNA origami-based nanostructures.     

LiBr: A Mild Lewis Acid Catalyst for Efficient One-Pot Synthesis of α-Amino Nitriles

α-Amino nitriles are synthesized in a one-pot, three-component coupling of aldehydes, amines, and trimethylsilyl cyanide using a catalytic amount of LiBr at ambient temperature.     

Synthetic route for the novel pyrimidine-substituted alkanoate,acetohydrazide, and imines: Synthon for β-lactams

A simple and efficient synthesis of novel pyrimidine-substituted alkanoate, acetohydrazide, and imines is described. The synthesis of novel ethyl 2-(2,6-dimethylpyrimidin-4-yloxy)acetate (EDMPyA) 2 was performed through S_N2 O-alkylation of 2,6-dimethyl-4-hydroxypyrimidine 1 with ethyl haloacetate. The compound EDMPyA 2 was subjected to nucleophilic substitution reaction with hydrazine hydrate to afford novel 2-(2,6-dimethylpyrimidin-4-yloxy)acetohydrazide (DMPyAH) 3. This DMPyAH 3 upon condensation with differently substituted carbonyl compounds (aldehydes/ketones) furnished DMPyAH imines (DMPyAH-I) 4a–d. These imines can be used for the preparation of unique β-lactams. The structure elucidation of all the newly synthesized compounds was performed using spectroscopy (FT-IR, ¹H and ¹³C NMR) and elemental analysis (C, H, N).     

Synthesis and biological activities of 2-methyl-4-N-2′-cyanoethyl-N-substituted benzaldehydes and their derivatives

Synthesis and antiAIDS, anticancer, antitubercular, fungicidal and antibacterial activities of 2-methyl-4-N-2′-cyanoethyl-N-methane/benzenesulphonylaminobenzaldehyde and their hydrazones are reported.     

New Strategy for the Oxidation of Hantzsch 1,4‐Dihydropyridines and Dihydropyrido[2,3‐d]pyrimidines Catalyzed by DMSO under Aerobic Conditions

A novel metal‐salt‐oxidant‐free, efficient, and economical method for the oxidation of Hantzsch 1,4‐dihydropyridines that uses aerial oxygen and solvent‐grade dimethylsulfoxide is described. Also, the synthesis of pyrido[2,3‐d]pyrimidines is achieved from in situ oxidation of dihydropyrido[2,3‐d]pyrimidines that arise from the reaction of 6‐aminouracils and cyano olefins in dimethylsulfoxide.