Polynomial neural network for linear and non-linear model selection in quantitative-structure activity relationship studies on the internet

This article presents a self-organising multilayered iterative algorithm that provides linear and non-linear polynomial regression models thus allowing the user to control the number and the power of the terms in the models. The accuracy of the algorithm is compared to the partial least squares (PLS) algorithm using fourteen data sets in quantitative-structure activity relationship studies. The calculated data show that the proposed method is able to select simple models characterized by a high prediction ability and thus provides a considerable interest in quantitative-structure activity relationship studies. The software is developed using client-server protocol (Java and C++ languages) and is available for world-wide users on the Web site of the authors.     

A new computer program for QSAR-analysis: ARTE-QSAR

A new computer program has been designed to build and analyze quantitative-structure activity relationship (QSAR) models through regression analysis. The user is provided with a range of regression and validation techniques. The emphasis of the program lies mainly in the validation of QSAR models in chemical applications. ARTE-QSAR produces an easy interpretable output from which the user can conclude if the obtained model is suitable for prediction and analysis.     

α1-AR拮抗剂DDPH类似物的比较分子力场分析

利用比较分子力场分析(CoMFA)方法, 建立苯(氧)烷胺类α1-肾上腺素受体拮抗剂DDPH及其类似物的三维定量构效关系模型。交叉验证回归系数q2、非交叉验证回归系数r2和标准偏差SEE分别为0.457, 0.953, 0.208,研究结果显示立体场比静电场对活性的影响更大。所得模型具有一定的预测能力,可用来指导设计新的苯氧烷胺类α1-肾上腺素受体拮抗剂 ,并为以后进一步的工作提供依据。     

Larvicidal and structural studies of some triphenyl- and tricyclohexyltin para-substituted benzoates

Several new triphenyl- and tricyclohexyltin para-substituted benzoates were synthesized. Their structures were characterized by IR and Mössbauer spectroscopies. The structures were determined to be four-coordinated monomers. Larvicidal activities of the new compounds as well as other benzoates were evaluated against the 2nd larval instar of the Anopheles stephensi and Aedes aegypti mosquitoes. Results from the screening studies indicated that the triphenyltin benzoates were more toxic towards the Ae. aegypti larvae. A quantitative-structure activity relationship was also developed for the An. stephensi larvae.     

Variable selection for QSAR by artificial ant colony systems

Derivation of quantitative structure-activity relationships (QSAR) usually involves computational models that relate a set of input variables describing the structural properties of the molecules for which the activity has been measured to the output variable representing activity. Many of the input variables may be correlated, and it is therefore often desirable to select an optimal subset of the input variables that results in the most predictive model. In this paper we describe an optimization technique for variable selection based on artificial ant colony systems. The algorithm is inspired by the behavior of real ants, which are able to find the shortest path between a food source and their nest using deposits of pheromone as a communication agent. The underlying basic self-organizing principle is exploited for the construction of parsimonious QSAR models based on neural networks for several classical QSAR data sets.     

Mechanism of the Oxidation of 3,3′,5,5′-Tetramethylbenzidine Catalyzed by Peroxidase-Like Pt Nanoparticles Immobilized in Spherical Polyelectrolyte Brushes: A Kinetic Study

Experimental and kinetic modelling studies are presented to investigate the mechanism of 3,3′,5,5′-tetramethylbenzidine (TMB) oxidation by hydrogen peroxide (H₂O₂) catalyzed by peroxidase-like Pt nanoparticles immobilized in spherical polyelectrolyte brushes (SPB−Pt). Due to the high stability of SPB−Pt colloidal, this reaction can be monitored precisely in situ by UV/VIS spectroscopy. The time-dependent concentration of the blue-colored oxidation product of TMB expressed by different kinetic models was used to simulate the experimental data by a genetic fitting algorithm. After falsifying the models with abundant experimental data, it is found that both H₂O₂ and TMB adsorb on the surface of Pt nanoparticles to react, indicating that the reaction follows the Langmuir–Hinshelwood mechanism. A true rate constant k, characterizing the rate-determining step of the reaction and which is independent on the amount of catalysts used, is obtained for the first time. Furthermore, it is found that the product adsorbes strongly on the surface of nanoparticles, thus inhibiting the reaction. The entire analysis provides a new perspective to study the catalytic mechanism and evaluate the catalytic activity of the peroxidase-like nanoparticles.     

Excess Enthalpy Data in Some Binary Systems Containing Non Electrolyte Solution and Their Correlations at 298.15K

Abstract

Excess enthalpy data measured at 298.15K were collected from the literature. The data contains 48 binary systems (812 data points). The experimental data were correlated by Redlich-Kister equation. In this work the following thermodynamics models were also tested. Wilson, NRTL models: and their parameters were calculated. A modified NRTL with a composition-dependent (α₁₂) parameter was also proposed. The correlation of excess enthalpy data in the systems using this model provides good results.     

Conformational studies on the four stereoisomers of the novel anticholinergic 4-(dimethylamino)-2-phenyl-2-(2-pyridyl)pentanamide

Summary To interpret differences in the anticholinergic activity among the four steroisomers of 4-(dimethylamino)-2-phenyl-2-(2-pyridyl)pentanamide (1–4), we performed conformational studies using the semiempirical molecular orbital method. The structures of the global minimum-energy conformations obtained for 1–4, however, could not explain the different activities, particularly in terms of distances between the essential pharmacophores. We thus implemented superimposition studies, using the energetically stable conformations of the most active stereoisomer, 1(2S,4R), as a template. The energy penalties for a conformation change of the less active stereoisomers 2–4 from their global minimum-energy structure to a new conformation, fitting onto the global minimum-energy conformation of 1, appear to account for the differences in the pharmacological potency better than using the other conformations of 1 as a template. We thus presume that the global minimum-energy conformation of 1 is closely related to the bioactive conformation for these anticholinergics, and also that the pharmacological potency is linked to how readily these substances can change their conformations to fit the muscarinic receptor.     

k‐Nearest neighbors optimization‐based outlier removal

Datasets of molecular compounds often contain outliers, that is, compounds which are different from the rest of the dataset. Outliers, while often interesting may affect data interpretation, model generation, and decisions making, and therefore, should be removed from the dataset prior to modeling efforts. Here, we describe a new method for the iterative identification and removal of outliers based on a k‐nearest neighbors optimization algorithm. We demonstrate for three different datasets that the removal of outliers using the new algorithm provides filtered datasets which are better than those provided by four alternative outlier removal procedures as well as by random compound removal in two important aspects: (1) they better maintain the diversity of the parent datasets; (2) they give rise to quantitative structure activity relationship (QSAR) models with much better prediction statistics. The new algorithm is, therefore, suitable for the pretreatment of datasets prior to QSAR modeling. © 2014 Wiley Periodicals, Inc.     

Simultaneous feature selection and parameter optimisation using an artificial ant colony: case study of melting point prediction

Background  

We present a novel feature selection algorithm, Winnowing Artificial Ant Colony (WAAC), that performs simultaneous feature selection and model parameter optimisation for the development of predictive quantitative structure-property relationship (QSPR) models. The WAAC algorithm is an extension of the modified ant colony algorithm of Shen et al. (J Chem Inf Model 2005, 45: 1024–1029). We test the ability of the algorithm to develop a predictive partial least squares model for the Karthikeyan dataset (J Chem Inf Model 2005, 45: 581–590) of melting point values. We also test its ability to perform feature selection on a support vector machine model for the same dataset.     

Studies on molecular mechanism between SHP2 and pyridine derivatives by 3D-QSAR,molecular docking and MD simulations

BackgroundSrc homology 2 (SH2)-containing protein tyrosine phosphatase 2 (SHP2) as a major phosphatase would affect the development of tumors by regulating several cellular processes, and is a significant potential target for cancer treatment.MethodsIn the present work, a series of pyridine derivatives possessing a wide range of inhibitory activity was employed to investigate the structural requirements by developing three dimensional quantitative structure–activity relationship (3D-QSAR) models using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods. The results show that CoMFA (R²_cv = 0.646, R²_pred = 0.5587) and CoMSIA (R²_cv = 0.777, R²_pred = 0.7131) have excellent stability and predictability. The relationship between the inhibitory activity and structure of the inhibitors was analyzed by the derived contour maps. Furthermore, the QSAR models were validated by molecular docking and molecular dynamics simulations, which were also applied to reveal the potential molecular mechanism of these inhibitors.FindingsIt was found that Arg110, Asn216, Thr218, Thr252 and Pro490 play a crucial role in stabilizing the inhibitors. Additionally, MM/PBSA calculations provided the binding free energy were also conducted to explain the discrepancy of binding activities. Overall, the outcomes of this work could provide useful information and theoretical guidance for the development of novel and potent SHP2 inhibitors.     

Synthesis of novel fluorophenylpyrazole-picolinamide derivatives and determination of their anticancer activity

Abstract

A series of fluorophenylpyrazole-picolinamide derivatives were synthesized in high yields using a cross-coupling reaction catalyzed by in situ formed palladium-N-heterocyclic carbenes (Pd-NHCs). The synthesized novel derivatives were evaluated for in vitro anticancer activity against a panel of four human tumor cell lines, HeLa (cervical), A-549 (lung), MCF-7 (breast), and IMR-32 (neuroblastoma). Four compounds, 11c, 11e, 11j, and 11k, showed growth inhibition (low µM) comparable with the standard drug cisplatin, providing a preliminary structure–activity relationship for the series. The present procedure is operationally simple and works with a wide range of substrates and may thus be useful in further compound optimization.     

Bayesian Models Leveraging Bioactivity and Cytotoxicity Information for Drug Discovery

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Highlights? Including efficacy and cytotoxicity data improves performance of computational models ? Antitubercular hits, leads, and chemical probes were identified using Bayesian models ? The most advanced compound provides significant in vitro activity and in vivo safety ? Demonstrated orders-of-magnitude higher hit rates than current HTS practices     

Synthesis,crystal structures and spectral characterization of Cu(II) and Mn(II) complexes of 4-hydroxy-3-methoxybenzaldehyde: antioxidant properties and molecular docking studies

[Cu(L)₂(H₂O)₂] (1) and [Mn(L)₂(H₂O)₂] (2) (HL = 4-hydroxy-3-methoxybenzaldehyde) were synthesized and characterized using elemental, spectral (FTIR, ESI-MS, UV–visible, fluorescence and EPR), thermal, cyclic voltammetric, powder, and single crystal X-ray crystallographic studies. Spectral and X-ray data ascertained the structural features, binding modes of ligand and distorted octahedral geometry around the metal ions. Cyclic voltammetric studies confirmed the formation of a quasi reversible redox couple in solution. Crystal structure analysis of 1 and 2 reveal the presence of non-covalent interactions, resulting in a 1-D polymeric chain. Antioxidant properties (using DPPH and hydrogen peroxide assay) and molecular docking studies (using 1BNA) are also examined. The binding free energies (calculated from docked models), ?270 (1) and ?295 kJ mol^?1 (2), suggest that the complexes reasonably bind to DNA, and the DNA-binding affinity of 2 is stronger than that of 1.     

Acetyl- and O-alkyl- derivatives of β-mangostin from Garcinia mangostana and their anti-inflammatory activities

Pure β-mangostin (1) was isolated from the stem bark of Garcinia mangostana L. One monoacetate (2) and five O-alkylated β-mangostin derivatives (3–7) were synthesised from β-mangostin. The structures of these compounds were elucidated and determined using spectroscopic techniques such as 1D NMR and MS. The cytotoxicities and anti-inflammatory activities of these five compounds against RAW cell 264.7 were tested. The structural-activity relationship studies indicated that β-mangostin showed a significant activity against the LPS-induced RAW cell 264.7, while the acetyl- as well as the O-alkyl- β-mangostin derivatives did not give good activity. Naturally occurring β-mangostin demonstrated comparatively better anti-inflammatory activity than its synthetic counterparts.