A common method for the determination of several calcium channel blockers using an HPLC system with ultraviolet detection

We report a common HPLC method for the single or simultaneous determination of four calcium channel blockers (CCB), namely diltiazem (DTZ), verapamil (VER), nifedipine (NIF) and nitrendipine (NIT) and their active metabolites demetildiltiazem and deacetildiltiazem (MA and M1), norverapamil (NOR), and dehydronifedipine (DHN). DHN was first synthesised in our laboratory and different pH values of the mobil phase were subsequently prepared and tested for chromatographic separation. The detection system and the environmental light conditions were optimised. The best separations of all analytes were obtained using a C₁₈ column and a mobile phase of methanol, 0.04 M ammonium acetate, acetonitrile and triethylamine (2:2:1:0.04 v/v). Quantitation was performed using imipramine (IMI) as the internal standard. For DTZ and its metabolites (M1 and MA), the wavelength chosen was 237 nm; for VER and its metabolite NOR, it was 210 nm; and, finally for NIF and its metabolite DHN and NIT it was 216 nm. When a simultaneous analysis was carried out the wavelength was of 230 nm. The optimum pH were 7.90 and 7.10 when the separation of NIT and DTZ or VER and NIF were carried out, respectively, and 7.90 when a simultaneous separation was carried out. The detection limit of the assay was less than 8 ng ml⁻¹ for all compounds, with coefficients of variation less than 7% (for inter- and intra-day) over the concentration range of 1–1000 ng ml⁻¹. The retention times were less than 11 min. When NIF or NIT were studied, it was necessary to use a sodium vapour lamp in order to avoid the photodegradation which takes place under daylight conditions.     

A comparative multivariate analysis of nitrilase enzymes: An ensemble based computational approach

Nitrilases, member of nitrilase superfamily catalyse the hydrolysis of different nitriles to corresponding amides and acids. In this article, we demonstrate two-fold computational comparative analysis on coding gene sequences, amino acid sequences, three-dimensional structure of the nitrilases from different species and discovered conserved motifs linked with related species. A large ensemble-based dataset was utilized from bacteria, fungi, plants and animals. Here, we used comparative genomics, motif analyses and Bayesian phylogenetic analyses in combination with structural analyses [molecular dynamics simulation, principal component analysis (PCA), dynamic cross correlation (DCCM), root mean squared inner product (RMSIP), free energy surface (FES)] to investigate the evolution, ecological relationship and structure-function association of nitrilase family. The inferred evolutionary tree displayed nitrilase gene clusters to be shared among bacteria, fungi and plants. Structural analysis revealed that the folding of catalytic sites is similar among species; however, the loop region varies. We provide evidence based on PCA that the nitrilases are clustered into different clades due to variation in side chains. Numerous of significant correlations were found between sequence clades and the structural discriminating properties of nitrilases originating from different species. The results are consistent with the hypothesis that bacterial nitrilases are in ecological and evolutionary relationships with fungi and plants during plant-pathogen interaction to large extent. This compact and detail results also open new dimensions for further studying and improvement of industrially important nitrilase enzymes.     

Analysis of multiblock datasets using ComDim: Overview and extension to the analysis of (K + 1) datasets

ComDim analysis was designed to assess the relationships between individuals and variables within a multiblock setting where several variables, organized in blocks, are measured on the same individuals. An overview of this method is presented together with some of its properties. Furthermore, we discuss a new extension of the method of analysis to the case of (K+1) datasets. More precisely, the aim is to explore the relationships between a response dataset and K other datasets. An illustration of this latter strategy of analysis on the basis of a case study involving Time Domain ‐ Nuclear Magnetic Resonance data is outlined and the outcomes are compared with those of Multiblock Partial Least Squares regression.     

Comparative molecular modelling study of the calcium channel blockers nifedipine and black mamba toxin FS2

The identification and structural determination of the criticalamino acid residues causing the calcium channel blocking effects of theangusticeps type III toxin FS₂ is described. Alignments withmore than 200 different short and long neuro-, cyto-, muscarinic and otherangusticeps-type toxins yielded 12 amino acid residues at the tips of loopsII and III which are unique to the type III toxins. The competitive bindingbehaviour between the 1,4-dihydropyridine derivative nifedipine and toxinFS₂ was used for a further delimitation of the relevant toxinbinding domain. Using the ab initio geometry optimized nifedipine X-raystructure as a template, a model based on the sequenceMet⁴⁵-Trp⁴⁶-cis-Pro⁴⁷-Tyr⁴⁸has been elaborated. This sequence shows the same hydrophobic andhydrogen bond forming properties as nifedipine. In addition, qualitativelysimilar molecular electrostatic potentials are observed for both structures,leading to the assumption that these amino acid residues of the toxin act asthe potential attachment region at the calcium channel receptor site.     

Inhibitors of prolyl endopeptidase: Characterization of the pharmacophoric pattern using conformational analysis and 3D-QSAR

Summary A structure-activity study has been carried out on several compounds known as inhibitors of the serine protease prolyl endopeptidase. Conformational analysis has been done using different molecular mechanics methods such as molecular dynamics, or a randomized conformational search method. The conformers obtained were classified using geometric and energetic criteria. A pattern recognition analysis was done in order to divide conformers according to families. The resulting dominant families, for all compounds investigated, showed very similar geometric features. Based on the lowest energy conformers obtained after randomized conformational analysis, a 3D-QSAR model was established using the CoMFA approach. The validity of this model was verified by prediciting correctly the activity of other molecules not used in the construction of this model.     

Gas phase and water solution conformational analysis of the herbicide diuron (DCMU): an ab initio study

In the present work, the conformational equilibrium for the herbicide diuron (DCMU) has been investigated using high level ab initio calculations. The solvent effect was included through two different continuum models: (1) the real cavity IPCM method and (2) the standard dipole Onsager model SCRF. The effect due to solute-solvent hydrogen-bond interactions was analyzed considering a hybrid discreet-continuum model. At the Hartree-Fock level, the gas phase results showed that only the trans forms (A and B) are present in the equilibrium mixture, with the relative concentrations found to be 33% (A) and 67% (B) (HF/6-311+G**//6-31G**). When the electronic correlation effect is included (MP2/6-31G*//HF/6-31G*), a relative stabilization of the cis forms was observed, with the conformational distribution calculated as 38% (A), 50% (B), 6% (C) and 6% (D). The trans conformations were found to be completely planar, which has been considered to be a prerequisite for the herbicide binding. In water solution, the trans conformation A should be the most abundant conformer, the IPCM and SCRF values being ca. 100% and ca. 85% respectively. The IPCM calculations with the isodensity level set to 0.0005 present a conformational distribution close to that obtained from the hybrid model [92% (A) and 8% (B)], which has been considered our best solvent approach. Regarding the biological action of urea-type herbicides, the results presented here are important, because some QSAR studies have suggested that the partition coefficient is related to the herbicide activity, so the conformational equilibrium may play a role in the biological action. Received: 23 February 1998 / Accepted: 28 May 1998 / Published online: 19 August 1998     

Esters of 2,5-multisubstituted-1,3-dioxane-2-carboxylic acid: their conformational analysis and selective hydrolysis

The carbomethoxy group at the C2 position of the 2,5-multisubstituted 1,3-dioxanes prefers the axial conformation rather than the equatorial one due to an anomeric effect. The trans isomers of the 5-monosubstituted compounds are more selectively hydrolyzed than the cis isomers. Based on the calculated results, hydrolysis to the trans isomers is attributed to the larger carbonyl charges of the trans than those of the cis isomers. The anomeric and homoanomeric effects will explain the axial preference of the carbomethoxy group and selective hydrolysis to the trans isomers. Furthermore, the calculated stability between the cis and trans isomers is in good agreement with the experimental results in the equilibrium state.     

Differentiating diterpene resin acids using ToF‐SIMS and principal component analysis: new tools for assessing the geochemistry of amber

Amber is a polymerized plant resin having remarkable preservation potential in the geological record. Numerous analytical techniques have been applied to the study of amber organic chemistry in order to extract paleobotanical information. However, only exploratory work has been conducted using time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS), despite its immense potential due to the high mass resolution and range that can be analyzed concurrently. Detailed assessments of ion fragmentation patterns are prerequisite, given that amber is comprised of a challenging range of terpenoids, carboxylic acids, alcohols, and associated esters. In recent work, we demonstrated the applicability and efficiency of ToF‐SIMS as a tool to investigate amber chemical composition. However, only two diterpene resin acid standards were considered in this preliminary study, namely abietic acid and communic acid. We now extend this work by documenting the ToF‐SIMS spectra of ten additional diterpene resin acids and ask whether ToF‐SIMS analysis can distinguish subtle differences within a larger set of diterpenoids. Both positive and negative ToF‐SIMS spectra were produced, although negative polarity appears particularly promising for differentiating diterpene resin acids. Principal component analysis (PCA) was used to distill the data and verified that purified diterpenes have distinct ToF‐SIMS spectra that can be applied to amber chemotaxonomy as well as to the analysis of modern resins of known botanical origin. While this work is pertinent to the study of the composition and histories of ambers, the mass spectra of the 12 diterpene standards could prove valuable to any system where diterpenoid chemistry plays a role. Copyright © 2014 John Wiley & Sons, Ltd.     

Conformational analysis 29: Preparation and1H and13C NMR,FTIR, MS,and crystallographic conformational and configurational study of 3-Oxo-1,3-oxathiane and its monomethyl derivatives

3-Oxo-1,3-oxathiane (1) and its monomethyl derivatives were prepared by oxidation of the corresponding 1,3-oxathianes. The structural analysis was carried out by¹H and¹³C NMR, FTIR, and mass spectrometry. At 298 K compound1 was a 1 1 (at 173 K a 3 1) mixture of the SO(ax) and SO(eq) chair forms. The major oxidation products of methyl 1,3-oxathianes attained exclusively the SO(ax), Me(eq) chair forms except that of the 5-methyl derivative, which consisted of 7% of the SO(eq), Me(ax) chair conformation in CDCl₃ solution. The minor products of oxidation existed in anancomeric SO(eq), Me(eq) chair conformations. The oxidation of 2-methyl- 1,3-oxathiane, however, led to 3,3-dioxo derivative (6) in addition to thetrans [SO(eq)] monoxide. The crystal structures of6 andtrans-3-oxo-5-methyl-1,3-oxathiane were solved by X-ray diffractometry.     

NMR and chemometric methods: a powerful combination for characterization of Balsamic and Traditional Balsamic Vinegar of Modena

This work presents the capability of NMR spectroscopy combined with Chemometrics in predicting the ageing of Balsamic and Traditional Balsamic Vinegar of Modena. The need of an analytical method is an important requirement for both research oriented and commercial evaluation of these very valuable products. ¹H NMR spectroscopy, based on the advantage of rapid sample analysis without any manipulation or derivatization, is here proposed as a valid tool to describe Balsamic and Traditional Balsamic Vinegar of Modena. For this purpose, 72 reliable samples, were divided into three different groups according to their ageing process: young (<12 years), old (>12 and <25 years) and extra old (>25 years). Hierarchical Projection to Latent Structures Discriminant Analysis (PLS-DA) allowed us to characterize the ageing process. Variables showing the largest VIP (Variable Importance in the Projection) were extracted from PLS-DA model, thus shedding lights onto the role played by specific compounds in this complex ageing process. Two robust classification models, were built by PLS-DA and Naïve Bayes classifier and compared to prove the accuracy of the representation on both training and test sets. The predictions obtained for 41 “unknown” vinegar samples with these both methods gave more than 80% agreement among them.     

Quantum chemical study on the interaction of some bisphosphonates and Ca2+: The role of molecular electrostatic potentials in the prediction of binding geometry

Summary Molecular electrostatic potentials have been used to model the calcium binding properties of some bisphosphonate drugs, which are used to treat various bone diseases. The mechanism of action involves the binding of bisphosphonates to the bone surface, where calcium plays an important role. Electrostatic potential maps derived from ab initio partial charges have been compared with both the crystal structure and the fully optimized ab initio structure of (dichloro)methylenebisphosphonate-calcium ion complex. Molecular electrostatic potentials can correctly predict the calcium binding geometry of bisphosphonate-type compounds and this type of information can be used in the practical drug design work.     

CpRuCl- and CpCo-catalyzed or mediated cyclotrimerizations of alkynes and [2+2+2] cycloadditions of alkynes to alkenes: A comparative DFT study

Computational methods have been used to better understand both the CpRuCl- and CpCo-catalyzed and mediated cyclotrimerization of alkynes and the [2+2+2] cycloaddition of alkynes to alkenes. These studies have allowed more accurate mechanisms to be proposed for each of these transformations and for some previously proposed intermediates to be discarded. The mechanistic rationale of these processes depends on the nature of the metal, ligands and substrate partners.     

Synthesis and conformational analysis of naphth[1′,2′:5,6][1,3]oxazino[3,2-c][1,3]benzoxazine and naphth[1′,2′:5,6][1,3]oxazino[3,4-c][1,3]benzoxazine derivatives

A new functional group, the hydroxy group, was inserted into a Betti base by reaction with salicylaldehyde, and the naphthoxazine derivatives thus obtained were converted by ring-closure reactions with formaldehyde, acetaldehyde, propionaldehyde or phosgene to the corresponding naphth[1′2′:5,6][1,3]oxazino[3,2-c][1,3]benzoxazine derivatives. Further, the conformational analysis of these polycyclic compounds by NMR spectroscopy and an accompanying molecular modelling are reported; especially, both quantitative anisotropic ring current effects of the aromatic moieties in these compounds and steric substituent effects were employed to determine the stereochemistry of the naphthoxazinobenzoxazine derivatives.     

Application of partial least squares discriminant analysis and variable selection procedures: a 2D-PAGE proteomic study

2D gel electrophoresis is a tool for measuring protein regulation, involving image analysis by dedicated software (PDQuest, Melanie, etc.). Here, partial least squares discriminant analysis was applied to improve the results obtained by classic image analysis and to identify the significant spots responsible for the differences between two datasets. A human colon cancer HCT116 cell line was analyzed, treated and not treated with a new histone deacetylase inhibitor, RC307. The proteins regulated by RC307 were detected by analyzing the total lysates and nuclear proteome profiles. Some of the regulated spots were identified by tandem mass spectrometry. The preliminary data are encouraging and the protein modulation reported is consistent with the antitumoral effect of RC307 on the HCT116 cell line. Partial least squares discriminant analysis coupled with backward elimination variable selection allowed the identification of a larger number of spots than classic PDQuest analysis. Moreover, it allows the achievement of the best performances of the model in terms of prediction and provides therefore more robust and reliable results. From this point of view, the multivariate procedure applied can be considered a good alternative to standard differential analysis, also taking into account the interdependencies existing among the variables.     

Molecular structure of 2-Amino-5-(1-methyl-5-nitro-2-imidazolyl)-1,3,4-thiadiazol (Megazol) and related compounds: A concerted study using X-ray crystallography,molecular mechanics,and semiempirical methods

A structural study of three nitroimidazoles was carried out using molecular mechanics, semiempirical methods, and X-ray crystallography. Structural features which might account for the high efficiency of1 (Megazol) as an antiparasitic drug and its opposite, the inactivity of its regiomers2 and3 were examined, i.e., coplanarity of the two rings, preferred conformations, and rotational barriers around the pivot bond between the two rings. For the three compounds an antiperiplanar conformation is preferred for the N(CH₃) and C-S bonds. For compounds1 and3, the rings are coplanar, with2 being somewhat twisted. The geometry obtained by molecular mechanics for compound1 is in excellent agreement with the X-ray structure, and greater confidence can be placed in this method than in semiempirical ones. Similarities observed on the LUMO positions, as well as rotational barriers lead to the conclusion that the differences in biological activity of these compounds do not rely on their ground state properties but rather on their subsequent reactions with oxygen. In addition, the calculations revealed significant structural information of a family of biological importance (nitroimidazoles) and constitute a comparative test for the MM2, AM1, and PM3 methods.     

A comparative study of laser induced breakdown spectroscopy analysis for element concentrations in aluminum alloy using artificial neural networks and calibration methods

A comparative study of analysis methods (traditional calibration method and artificial neural networks (ANN) prediction method) for laser induced breakdown spectroscopy (LIBS) data of different Al alloy samples was performed. In the calibration method, the intensity of the analyte lines obtained from different samples are plotted against their concentration to form calibration curves for different elements from which the concentrations of unknown elements were deduced by comparing its LIBS signal with the calibration curves. Using ANN, an artificial neural network model is trained with a set of input data of known composition samples. The trained neural network is then used to predict the elemental concentration from the test spectra. The present results reveal that artificial neural networks are capable of predicting values better than traditional method in most cases.     

Investigation on transition States of [Alanine + M2+] (M = Ca,Cu, and Zn) complexes: A quantum chemical study

The ground state geometries of [Alanine (Ala) + M²⁺] [M = Ca, Cu, and Zn) complexes were calculated in gas phase at B3LYP/6‐311++G(d,p) level of theory. Transition states (TSs) between different stable conformers of [Ala + M²⁺] complexes were also calculated. Among the different [Ala + M²⁺] complexes, the complex where metal cations coordinated to carboxylate group (? COO^?) is found to be energetically most favorable. To calculate TSs, the ground state structures of any two conformers of [Ala + M²⁺] complexes were used. The ground state energies of two stable conformers and their TS structures were used to calculate the activation energy. The reactivity of different conformers of [Ala + M²⁺] complexes have been discussed in terms of energy difference between their highest occupied molecular orbital and lowest unoccupied molecular orbital. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Understanding the inactivation process of organophosphorus herbicides: A DFT study of glyphosate metallic complexes with Zn2+, Ca2+, Mg2+, Cu2+, Co3+, Fe3+, Cr3+, and Al3+

Glyphosate is the active component of one of the top‐selling herbicides, which is also a potent EPSP synthase inhibitor. The herbicide is absorbed by living tissue and translocated via the phloem, to plant roots and rhizomes. When applied directly into the soil it has low activity, due to the high adsorption by soil constituents. Understanding the specific interactions between metals in the soil and glyphosate is the main step in understanding the low activity of the herbicide when applied directly into the ground and not pulverized. We can observe there is a stability order for both tetrahedral and octahedral complexes between glyphosate and metals: Zn>Cu>Co>Fe>Cr>Al>Ca>Mg. © 2012 Wiley Periodicals, Inc.