Application of thin-layer chromatographic data in quantitative structure-activity relationship assay of thiazole and benzothiazole derivatives with H1-antihistamine activity. I

A quantitative structure-activity relationship analysis of H1-antihistamine activity and chromatographic data of 2-[2-(phenylamino)thiazol-4-yl]ethanamine; 2-(2-benzyl-4-thiazolyl)ethanamine; 2-(2-benzhydrylthiazol-4-yl)ethylamine derivative; 2-(1-piperazinyl- and 2-(hexahydro-1H-1,4-diazepin-1-yl)benzothiazole derivatives was made. The RP2 thin-layer chromatography (TLC) plates (silica gel RP2 60F254 silanised precoated), impregnated with solutions of selected amino acid mixtures (L-Asp, L-Asn, L-Thr and L-Lys), were used in two developing solvents as hH1R antagonistic interaction models. Using regression analysis, the relationships between chromatographic and biological activity data were found. The correlations obtained in regression analysis for the examined thiazole and benzothiazole derivatives with H1-antihistamine activity [pA2(H1)] represent their interaction with all the proposed biochromatographic models (S1-S7). Some of the calculated equations can be applied to predict the pharmacological activity of new drug candidates. The best multivariate relationships useful in predicting the pharmacological activity of thiazole and benzothiazole derivatives were obtained under the condition of experiment with RP2 TLC plates using the developing solvent acetonitrile-methanol-buffer (40:40:20, v/v). The log P values of particular compounds are extremely important for this kind of activity.     

The modified hartree-fock self-consistent field equation

The electron density at the pyridine nitrogen atom and the π-electron density of the pyridine ring were calculated by the CNDO /2-MO method assuming standard bond lengths and angles. The indices were found to correlate with the pK_a values of pyridine derivatives and with the electronic substituent constants of the Hammett type. The correlations were best for four-substituted pyridines, making the routine CNDO /2-MO calculations useful for studies of quantitative relations between structure and biological activity of the compounds.     

QSAR and mode of action studies of insecticidal ecdysone agonists†

A series of our SAR and QSAR studies of synthetic moulting hormone agonists, dibenzoylhydrazines (DBH), exhibiting insecticidal/larvicidal activity are reviewed in this article. We prepared a number of analogues where various substituents are introduced into the two benzene rings of DBH and measured their biological activity using various biological systems. Larvicidal activity was against larvae of the rice stem borer Chilo suppressalis and the moulting hormone activity was in terms of the stimulation of N-acetylglucosamine incorporation in a cultured integument system of the same insect species. Binding affinity to the ecdysone receptor was assayed with intact Sf-9 cell lines in which the ADME processes are negligible as well as using receptor proteins obtained by in vitro translation of the responsible cDNA cloned from cell-free preparation of integumentary tissue of C. suppressalis. Variations in the biological activity indices were either correlated between two types of activity or correlated using physicochemical molecular and substituent parameters in terms of the classical QSAR. Comparisons among correlations and with recently revealed X-ray crystallographic findings clearly indicate the physicochemical meaning of parameters significant in the correlation equations to help understanding molecular mechanism of the moulting hormonal action.     

QSAR modeling based on the bias/variance compromise: a harmonious

Modeling quantitative structure–activity relationships (QSAR) is considered with an emphasis on prediction. An abundance of methods are available to develop such models. Using a harmonious approach that balances the bias and variance of predictions, the best calibration models are identified relative to the bias and variance criteria used. Criteria utilized to determine the adequacy of models are the root mean square error of calibration (RMSEC) and validation (RMSEV), respective R ² values, and the norm of the regression vector. QSAR data from the literature are used to demonstrate concepts. For these data sets and criteria used, it is suggested that models obtained by ridge regression (RR) are more harmonious and parsimonious than models obtained by partial least squares (PLS) and principal component regression (PCR) when the data is mean-centered. The most harmonious RR models have the best bias/variance tradeoff reflected by the smallest RMSEC, RMSEV, and regression vector norms and the largest calibration and validation R ² values. The most parsimonious RR models have the smallest effective rank.     

Computational studies of the corrosion‐inhibition efficiency of iron by triazole surfactants

The corrosion‐inhibition efficiency of N‐decyl‐1,2,4‐triazole, N‐undecyl‐1,2,4‐triazole, and N‐dodecyl‐1,2,4‐triazole surfactants and the corresponding protonated molecules have been studied computationally using density functional theory and second‐order Møller–Plesset calculations. Corrosion‐inhibition properties and the strength of the affinity of the iron‐surfactant molecules were estimated by using an appropriate cluster model. The iron‐surfactant complexes were constructed by attaching the triazole ring to the iron surface modeled by one and five iron atoms, respectively. Relations between molecular properties and corrosion‐inhibition efficiency were determined by using linear regression and quantitative structure–activity relationship (QSAR). The QSAR analysis yielded significant correlations between the corrosion‐inhibition activity of the studied molecules with molecular properties such as the highest occupied molecular orbital, the lowest unoccupied molecular orbital, dipole moments (μ), and the total atomic charges. Fukui indexes were also calculated for assessing correlations between them and experimental corrosion‐inhibition efficiencies. Solvent effects were investigated by using the polarized continuum model. The effects of the acidity medium and the local reactivity of the triazole derivatives with iron were also analyzed. The calculated binding energy of 276 kJ/mol for the Fe₅‐N‐dodecyl‐1,2,4‐triazole cluster shows that the surfactant molecules bind strongly to iron surfaces, which is in agreement with experimental data. © 2012 Wiley Periodicals, Inc.     

Synthesis,Characterization, and Molecular Docking of Novel bis‐thiazolyl Thienothiophene Derivatives as Promising Cytotoxic Antitumor Drug

A novel, facile reaction for the synthesis of series of bis‐thiazole derivatives has been developed from the reaction of the appropriate thiosemicarbazone derivatives and bis‐2‐bromoacetylthieno[2,3‐b ]thiophene derivatives in ethanol under reflux. The structures of the newly synthesized products were established on the basis of spectral data (mass, IR, and ¹H and ¹³C NMR) and elemental analyses. Fifteen compounds of the synthesized compounds were evaluated for their anticancer activity against human liver hepatocellular carcinoma cell line (HepG2). All compounds showed anticancer activity but differs in potency comparable with the reference drug Cisplatin. Moreover, molecular docking study using MOE software predicted the best binding mode between the most active compound 5o into the active site of human heat‐shock protein 90. The computational studies are confirming the results in biological activity.     

Joint assessment of responses of biomonitors to airborne nickel and vanadium through nuclear and non-nuclear techniques

This study deals with the influence of the exposure conditions on biological uptake, by looking into concentrations of Ni and V in lichen thalli and tree bark after continuous and discontinuous field trials at littoral sites impacted by anthropogenic emissions. Biomonitors were assessed by k ₀-INAA and AAS. Correlations at Sines are more apparent than at Viana or Lisboa. When data from all sites are pooled, V shows correlations for practically every situation while Ni shows none, which may indicate a dissimilar uptake mechanism for each element. At Sines, V/Ni ratios reach values that comply with emissions from oil-related industries.     

Tuning Peptide Structure and Function through Fluorobenzene Stapling

Cyclic peptides are promising next-generation therapeutics with improved biological stability and activity. A catalyst-free stapling method for cysteine-containing peptides has been developed that enables fine-tuning of the macrocycle by using the appropriate regioisomers of fluorobenzene linkers. Stapling was performed on the unprotected linear peptide or, more conveniently, directly on-resin after peptide synthesis. NMR spectroscopy and circular dichroism studies demonstrate that the type of stapling can tune the secondary structures of the peptides. The method was applied to a set of potential agonists for melanocortin receptors, generating a library of macrocyclic potent ligands with ortho, meta or para relationships between the thioethers. Their small but significant differences in potency and efficacy demonstrate how the method allows facile fine-tuning of macrocyclic peptides towards biological targets from the same linear precursor.     

β-Lactam ring stability and antibacterial potency: A novel eigenvalue problem

Low inoculum potency data in vitro for 16 clinical β-lactam antibiotics have been analyzed, and a physical model for interpreting the results of a number of bacterial strains has been derived. An analytic criterion for performing a unitary transformation on the potency data is developed following the identification of a physical vector present within the data which is attributable to an activation energy required for the transport of the β-lactam into a biological membrane. This vector has inverse slope relations in Gram positive and Gram negative bacteria and provides the basis for the analytic criterion for the unitary transformation. Compounds with similar potency spectra which differ only in the absolute magnitude of their effect will possess similar transport properties. It is shown that a slow rate of membrane entry for the β-lactam has overriding consequences on differences in fast rates of binding to the target enzymes and to β-lactamases, and a second primary vector is established directly from the biological data related to the ease of β-lactam ring opening. This vector offers precise evidence for testing the solvational and theoretical requirements for predicting the biological stability of novel β-lactam ring compounds.     

Study of the surface properties and surface concentration of ionic liquid–alcohol mixtures

Surface properties for three binary mixtures containing a 1-butyl-3-methylimidazolium thiocyanate ([BMIM][SCN]) and a long-chain alcohol (1-butanol, 1-pentanol and 1-hexanol) were determined by surface tension data at the following temperatures: (298.15, 308.15, 318.15, 328.15 and 338.15) K. The surface tension data over the entire mole fraction range are correlated by the Fu et al.(FLW) and Myers-Scott (MS) models. There is good agreement between the experimental data and the results of correlations for 15 binary systems (the three systems at five temperatures) with an average relative error below 1.5%. In addition, the UNIFAC group contribution method is applied for calculation of activity coefficients of components in solution. Moreover, the relative adsorptions of alcohol at the air/liquid interface are determined using Gibbs adsorption isotherm. The obtained results show that the values of adsorption for mixtures of alcohols/[BMIM][SCN] increase with increasing the alkyl chain length of alcohol and decreasing temperature.     

3-Aryl-5-[(aryloxy)methyl]-3-[(1H-1,2,4-triazol-1-yl)methyl]-2-methylisoxazolidine derivatives. Synthesis and antifungal activity

The synthesis and antifungal activity of a novel series of 3-aryl-5-[(aryloxy)methyl]-3-[(1H-1,2,4-triazol-1-yl)-methyl]-2-methylisoxazolidines are described. The in vitro activity was evaluated in solid agar cultures against a variety of dermatophytes and yeast fungi, while in vivo activity was measured in an immune-compromised mouse model of systemic candidiasis. The activity of the title series was compared to that of ketoconazole and one derivative, the cis-3-(4-chlorophenyl)-5-(4-chlorophenyloxy)methyl analogue 5f was found to possess a similar potency in the in vivo assay. Structure-activity relationship correlations are also discussed.     

Computational analysis of the cathepsin B inhibitors activities through LR‐MMPBSA binding affinity calculation based on docked complex

Cathepsin B, a ubiquitous lysosomal cysteine protease, is involved in many biological processes related to several human diseases. Inhibitors targeting the enzyme have been investigated as possible diseases treatments. A set of 37 compounds were recently found active in a high throughput screening assay to inhibit the catalytic activity of Cathepsin B, with chemical structures and biological test results available to the public in the PubChem BioAssay Database (AID 820). In this study, we compare these experimental activities to the results of theoretical predictions from binding affinity calculation with a LR‐MM‐PNSA approach based on docked complexes. Strong correlations (r² = 0.919 and q² = 0.887 for the best) are observed between the theoretical predictions and experimental biological activity. The models are cross‐validated by four independent predictive experiments with randomly split compounds into training and test sets. Our results also show that the results based on protein dimer show better correlations with experimental activity when compared to results based on monomer in the in silico calculations. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

In silico fragment-based drug design using a PASS approach

Fragment-based drug design integrates different methods to create novel ligands using fragment libraries focused on particular biological activities. Experimental approaches to the preparation of fragment libraries have some drawbacks caused by the need for target crystallization (X-ray and nuclear magnetic resonance) and careful immobilization (surface plasmon resonance). Molecular modelling (docking) requires accurate data on protein-ligand interactions, which are difficult to obtain for some proteins. The main drawbacks of QSAR application are associated with the need to collect large homogeneous datasets of chemical structures with experimentally determined self-consistent quantitative values (potency). We propose a ligand-based approach to the selection of fragments with positive contribution to biological activity, developed on the basis of the PASS algorithm. The robustness of the PASS algorithm for heterogeneous datasets has been shown earlier. PASS estimates qualitative (yes/no) prediction of biological activity spectra for over 4000 biological activities and, therefore, provides the basis for the preparation of a fragment library corresponding to multiple criteria. The algorithm for fragment selection has been validated using the fractions of intermolecular interactions calculated for known inhibitors of nine enzymes extracted from the Protein Data Bank database. The statistical significance of differences between fractions of intermolecular interactions corresponds, for several enzymes, to the estimated positive and negative contribution of fragments in enzyme inhibition.     

Optimisation of the extraction of olive (Olea europaea) leaf phenolics using water/ethanol-based solvent systems and response surface methodology

An experimental setup based on a 2³ full-factorial, central-composite design was implemented with the aim of optimising the recovery of polyphenols from olive leaves by employing reusable and nontoxic solutions composed of water/ethanol/citric acid as extracting media. The factors considered were (i) the pH of the medium, (ii) the extraction time and (iii) the ethanol concentration. The model obtained produced a satisfactory fit to the data with regard to total polyphenol extraction (R ² = 0.91, p = 0.0139), but not for the antiradical activity of the extracts (R ² = 0.67, p = 0.3734). The second-order polynomial equation obtained after analysing the experimental data indicated that ethanol concentration and time mostly affected the extraction yield, but that increased pH values were unfavourable in this regard. The maximum theoretical yield was calculated to be 250.2 ± 76.8 mg gallic acid equivalent per g of dry, chlorophyll-free tissue under optimal conditions (60% EtOH, pH 2 and 5 h). Liquid chromatography–electrospray ionisation mass spectrometry of the optimally obtained extract revealed that the principal phytochemicals recovered were luteolin 7-O-glucoside, apigenin 7-O-rutinoside and oleuropein, accompanied by smaller amounts of luteolin 3′,7-O-diglucoside, quercetin 3-O-rutinoside (rutin), luteolin 7-O-rutinoside and luteolin 3′-O-glucoside. Simple linear regression analysis between the total polyphenol and antiradical activity values gave a low and statistically insignificant correlation (R ² = 0.273, p > 0.05), suggesting that it is not the sheer amount of polyphenols that provides high antioxidant potency; instead, this potency is probably achieved through interactions among the various phenolic constituents.