bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the Minimal Steric Difference (MTD) and Comparative Molecular Field Analysis (CoMFA) Methods for Analysis of Binding of Steroids to Carrier Proteins
Authors: Oprea Tudor I. , Ciubotariu Dan , Sulea Traian I. , Simon Zeno 
Published: October 2006

AbstractCross validation and results with test series indicate similar predictive power for the CoMFA and the much less CPU‐time consuming MTD method. We present an MTD analysis for the binding of a series of 21 steroids to Corticosteroid Binding Globulin (CBG) and to Testosterone Binding Globulin (TeBG) series previously analyzed by CoMFA. For the construction of the hypermolecule we used crystal structures of available steroids retrieved from the Cambridge Crystallographic Data Center (CCDC) and the COSMIC software for structural manipulation and molecular superposition. The correlation results of MTD were r2 = 0.93 for CBG binding and r2 = 0.85 for TeBG binding. The distribution of cavity and wall vertices of the MTD receptor maps present some similarities with the CoMFA coefficient contour maps. Cross validation results of MTD (50% of data in one subseries and 50% in the second), with r2 = 0.70 for CBG and r2 = 0.72 for TeBG binding, are somewhat better than CoMFA results, r2 = 0.66 and r2 = 0.555 respectively, while CoMFA predictions for a separate series of 10 steroids are better. In CoMFA, the equation derived for the molecule receptor affinity corresponds to molecules which interact with “receptor” atoms in fixed positions by electrostatic and van der Waals 6–12 potentials. Repulsions are thereby very high for some of the van der Waals terms – while in reality the overlapping of the ligand and receptor van der Waals envelopes are circumvented by conformational transitions at lower energy costs. This may explain why the elegant CoMFA method indicates only receptor regions whose occupation by the ligand molecules have a favorable or unfavorable effect upon binding.
Modelling the Ionization Potential of Halogenated Aliphatics
Authors: Chiorboli Claudio , Piazza Rossano , Carassiti Vittorio , Passerini Laura , Tosato Maria Livia 
Published: October 2006

AbstractA multivariate QSAR for estimating the ionization potential (IP) of halo‐alkanes has been constructed. 69 compounds, including 47 for which experimental IP data in the 10 to 13.6 eV were available were parametrized with 12 structural descriptors. The data analysis to correlate IP to these descriptors was carried out by PLS that gave a tri‐dimensional model explaining over 80% of the variance of IP. The reliability of the model was evaluated on the basis of predictions by using two different approaches. These were (a) a modified PLS version providing the Standard Deviation of Errors of Prediction, the SDEP parameter, which was found to be +/− 0.45 eV, and (b) an “external” validation process where the standard deviation was computed on the basis of the predicted IP.s for 17 compounds kept outside the training set, and was found to be +/− 0.39 eV.
Multivariate Characterization and Modelling of the Chemical Reactivity of Epoxides. Part II: Extension to Di‐ and Trisubstitution
Authors: Eriksson Lennart , Verhaar Henk J. M. , Sjöström Michael , Hermens Joop L. M. 
Published: October 2006

AbstractThe chemical reactivity toward 4‐nitrobenzylpyridine (4‐NBP) of a series of twelve mono‐, di‐ and trisubstituted epoxides has been modelled by means of multivariate quantitative structure‐property relationships (QSPRs). The models were established using theoretical descriptor variables and partial least squares (PLS) analysis. It was found that a multivariate set of eleven descriptor variables was sufficient to adequately model the chemical reactivity. Furthermore, there existed a non‐linear relationship between the theoretical descriptors and the chemical reactivity. Two‐component PLS models were generally required, using the second component to compensate for non‐linearity in the first. The nature of the non‐linearity suggests that different physico‐chemical factors are regulating the chemical reactivity among two observed subgroups of epoxides. The reactivity of one group of five epoxides with one non‐substituted ring carbon is regulated by the electronegative properties of the substituent on the other ring carbon, whereas the reactivity of seven di‐ and trisubstituted epoxides depends on a combination of the substitution pattern around the epoxide ring and the size of these substituents. Two additional points of general relevance for QSPR modelling are also addressed, namely predictor variable selection and appropriate transformation of the dependent variable.
Relation between the Odor of (R)‐Ethyl Citronellyl Oxalate and its Stable Conformations
Authors: Yoshii Fumiko , Hirono Shuichi , Moriguchi Ikuo 
Published: October 2006

AbstractThe complex odor of (R)‐ethyl citronellyl oxalate (ECO) was investigated based on its stable conformations. ECO, a flexible chain‐type compound, mainly has a musk‐like odor, but also has a rose‐like odor. The rose‐like odor recalls citronellol according to a perfumer's sensory evaluation. The conformational analyses of ECO and (S)‐citronellol were performed using CACheTM (Computer Aided Chemistry) system. Structure optimization of selected conformers was performed with the PM3 method in succession. Twenty‐three conformers of ECO were obtained and were compared with the three‐dimensional structure model for benzenoid musks previously proposed and also with 22 stable conformers of (S)‐citronellol. As a result, we found that the two most stable compact conformers of ECO, which were quite similar, fit the structure model for benzenoid musks, and that a three‐dimensional partial structure of another conformer of ECO was similar to one conformer of (S)‐citronellol. Thus, the main odor quality of ECO, the musk‐like odor, could be explained by the most stable compact conformers. We also showed that the secondary odor quality of ECO, a rose‐like odor, was possibly due to one of the stable conformers of ECO that is partially similar to the conformer of (S)‐citronellol.
Quantitative Structure‐Activity Relationships of 2‐Benzamido‐5‐Nitrothiazole Molluscicidal Derivatives
Authors: Vignoles Philipp , Clédat Dominique , Dreyfuss Gilles , Rondelaud Daniel , Pénicaut Bernard 
Published: October 2006

AbstractThe pharmacologic action of 2‐benzamido‐5‐nitrothiazole and eleven derivatives was studied in Lymnaea peregra ovata Müller, Gammarus pulex pulex L., and Euglena gracilis Klebs. The toxicity parameters (50 % lethal concentration, 50 % inhibitory concentration) were correlated with the physicochemical parameters of the compounds (lipophilicity, stability). The toxicity of the molecule was related to its lipophilicity and stability. By combining these parameters it was possible to establish specific equations for each species studied. Linear equations of the overall parameters of the molecule were obtained with L. p. ovata and E. gracilis, whereas second‐degree relationships were found with G. p. pulex. Using these pharmacokinetics models, it is possible to predict the pharmacologic action of these compounds knowing only the physicochemical parameters of each molecule.
Physicochemical Significance of Topological Parameters, Connectivity Indices and Information Content. Part 1: Correlation Studies in the Sets with Aromatic and Aliphatic Substituents
Authors: Saxena Anil K. 
Published: October 2006

AbstractTopological parameters like 1x, 2xv and IC1 are used in QSAR studies because of their simplicity of calculation. In the absence of their physicochemical significance, it is difficult to interpret the results of such QSAR studies in terms of mode or mechanism of action of the bioactive molecule. Keeping this in view, attempts have been made to interpret the empiricism of these parameters. The physicochemical significance of these parameters has been studied in different sets of compounds having one physicochemical parameter constant in each set. It has been observed that the connectivity index correlated to a greater extent with molar refractivity (MR) than with hydrophobic (π) or logP which may be due to the inherent relationship between MR, molecular weight, numbers of non‐hydrogen atoms in the molecule, surface, volume 1x and 2xv values. The information content did not show correlation with any of the physicochemical parameter considered.
Quantitative Structure‐Time‐Activity Relationships (QSTAR): Growth Inhibition of Escherichia coli by Nonionizable Kojic Acid Derivatives
Authors: Piršelová Katarína , Baláž Štefan , Ujhelyová Regina , Šturdík Ernest , Veverka Miroslav , Uher Michal , Brtko Július 
Published: October 2006

AbstractA semi‐empirical model for quantitative structure‐time‐activity relationships (QSTAR) has been applied to the data on inhibition of Escherichia coli in a batch culture in seven media of different acidity (pH 5.6 – 8.0) by twenty one nonionizable derivatives of kojic acid (5‐hydroxy‐2‐hydroxymethyl‐4H‐pyrane‐4‐one). The antibacterial potency of individual derivatives was characterized by the equieffective concentrations causing the 50%‐decrease in the specific growth rate in comparison with the untreated control. The QSTAR models satisfactorily describe toxicity of the studied compounds as a model‐based non‐linear function of hydrophobicity, the size of the substituents in the position 2, and the time of exposure. The dependence of the antibacterial activity on hydrophobicity at a fixed exposure time exhibits a broad maximum: the decrease for hydrophilic compounds is caused by their diminished ability for binding to the receptors and that for hydrophobic compounds is elicited by their lower concentrations in the aqueous phases and their slower inactivation. Inactivation is probably enzymatic because its rate depends on the size of the molecules. The size has a positive effect also on the binding to the receptor.
Comparative Molecular Field Analysis (CoMFA) of MX Compounds using different Semi‐empirical Methods: LUMO Field and its Correlation with Mutagenic Activity
Authors: Navajas Cecil , Poso Antti , Tuppurainen Kari , Gynther Jukka 
Published: October 2006

AbstractIn the present paper we make a comparison among three different semi‐empirical methods (AMI, MNDO and PM3) for the optimization of the geometries and calculation of different properties of MX compounds. The results were used to develop a CoMFA model to correlate the TA100 mutagenicity of these compounds with the LUMO field. The correlations between the LUMO field and steric, electrostatic and CoMFA fields generated automatically by the SYBYL CoMFA program, were explored. A comparison among different values of grid spacing for the lattice and standard deviation thresholds for column filtering was carried out to select the best values for this and future work.The results indicate that AM1 and PM3 methods represent a real improvement over MNDO in respect to QSAR studies relating electronic properties and mutagenicity for these compounds.
Inhibition of Bilirubin UDP‐glucuronosyltransferase: A Comparative Molecular Field Analysis (CoMFA)
Authors: Said Mourad , Ziegler Jean‐Claude , Magdalou Jacques , Elass Abdelaziz , Vergoten Gérard 
Published: October 2006

AbstractTwo series of compounds structurally related to phenolphthalein and triphenylalkyl carboxylic acid were tested as inhibitors of bilirubin glucuronidation catalyzed by rat liver microsomal UDP‐glucuronosyltransferase, and analyzed by the CoMFA method in order to predict the inhibitory potency of these structures and afford a three dimensional structure of the bilirubin binding site. These substances could inhibit bilirubin glucuronidation to different extents. Their inhibitory potency was quantitated in terms of I50 values. The best inhibitors exhibited competitive inhibition. The 3D‐QSAR results led to a fairly good prediction of the inhibitory potency of these two series of compounds. They indicate a correlation between the inhibitory activity of the glucuronidation reaction and the steric and electrostatic fields with a relative contribution of 43% and 57%, respectively.
Comparative Molecular Field Analysis of HIV‐1 Reverse Transcriptase Inhibitors in the Class of 1[(2‐Hydroxyethoxy)‐methyl]‐6‐(phenylthio)thymine
Authors: Hannongbua Supa , Lawtrakul Luckhana , Sotriffer Christoph A. , Rode Bernd M. 
Published: October 2006

AbstractA Comparative Molecular Field Analysis of 40 HEPT (1‐[(2‐Hydroxyethoxy)‐methyl]‐6‐(phenylthio)thymine) analogues was performed. The 3D‐QSAR study correlates steric and electrostatic fields of the compounds with HIV‐1 RT inhibition, resulting in a model which has a high predictive ability. CoMFA results revealed that steric interaction explains a majority (70%) of the variance in the data. Using only steric interaction energy in the analyses provided a better predictive model. Inclusion of electrostatic descriptors in terms of coulomb interaction energies deteriorates the results. However, it was found in this study that variation of sp3 O charges had some influence on r and that the interaction energies using sp3 O probe with a charge of −0.3 led to the best predictive model.
Test Series Selection from Nonlinear Neural Mapping
Authors: Domine Daniel , Devillers James , Wienke Dietrich , Buydens Lutgarde 
Published: October 2006

AbstractA new nonlinear neural mapping (N2M) technique based on the combined use of Kohonen self‐organizing map (KSOM), minimum spanning tree (MST), and nonlinear mapping (NLM) is introduced for optimal test series selection. With the N2M method, KSOM results are enhanced by the visualization of the actual distances between the loaded neurons from MST and NLM. N2M provides an easily interpretable and comprehensible graphical display which guides the selection of representative test series especially when the number of individuals is high. In addition, structure‐activity relationships can be derived. The approach is open since any information useful for data interpretation can be plotted by means of graphical tools.
Quantitative Structure‐Property Relationships of Azurin Mutants from Pseudomonas Aeruginosa
Authors: Norinder Ulf , Karlsson B. Göran , Sjölin Lennart , Pascher Torbjörn , Bonander Nicklas 
Published: October 2006

AbstractThe method of partial least squares projections to latent structures (PLS) has been used to derive quantitative relationships between measured reduction potentials and structures of some Pseudomonas aeruginosa azurin mutants with changes in position 121. The models indicate that relatively few properties of the amino acids explain the experimental results obtained. Electronic characteristics exert a major influence on the models but also factors associated with acid‐base strength, lipophilicity as well as with hydrogen bonding have large impact. The calculations also show that no single amino acid, natural or synthetic, can meet all of the optimum requirements of position 121 but indicate that a fine balance between various factors is a necessary prerequisite for a proper choice of residue to obtain a mutant with the desired properties.
Stepwise Leave‐One‐Isomer‐Out Free‐Wilson Approaches as Preprocessing Tools in QSAR Analysis of Racemates
Authors: Dove Stefan , Buschauer Armin 
Published: October 2006

AbstractQSAR analysis of racemates is complicated if specific substituent‐receptor interactions and, by that, specific spatial fits to the binding site result in individual but unknown activity differences of enantiomers, and even in structure‐dependent changes of which is the more active configuration. In a first approximation, additivity of substituent contributions should be assumed instead of major conformational effects. Then, Free‐Wilson analysis (FWA) can be used as preprocessing tool to reduce a starting set of all pairs of enantiomers into a final series of the probably (more) active configurations. A stepwise “leave‐one‐isomer‐out” approach is applied, where the model is successively improved by checking all remaining pairs and leaving out one enantiomer, determined by a special criterion of poorest prediction, in each step. The final model is given by the maximal F value. This approach was applied to histamine H1 antagonistic activity (pKB, guinea pig ileum) of 19 racemic and six non‐chiral phenyl‐halogenated N‐(diphenylpropyl)‐N′‐(imidazolylpropyl)guanidines. Based on only eight variables because of additivity of meta and para contributions, the starting model with n = 44, r2 = 0.29, s = 0.52, F = 1.8, r2‐PRESS = −0.14 has been improved to a final one with n = 31 (only six remaining pairs), r2 = 0.84, s = 0.24, F=14.0, r2‐PRESS = 0.65. Additionally, each of the successive series was submitted to CoMFA. Statistical parameters of the parallel CoMFA and FWA models are closely related. QSAR results obtained with both methods correspond to well‐known structure‐activity relationships of diphenhydramine‐like H1 antagonists. A direct application of the leave‐one‐isomer‐out strategy to CoMFA was less successful.
Quantitative Structure‐Activity Relationship Studies on Some Acyclouridine Derivatives Acting as Anti‐HIV‐1 Drugs
Authors: Garg Rajni , Kurup Alka , Gupta S. P. 
Published: October 2006

AbstractThe anti‐HIV‐1 activity of some derivatives of 1‐[2‐hydroxyethoxy]‐6‐(phenylthio)thymine(HEPT) is analyzed in relation to their physicochemical and molecular properties. The activities of the compounds are found to be significantly correlated with hydrophobic constant π and the van der Waals volume Vw. The results are found to be useful in discussing the mechanism of drug‐receptor interaction.
Modelling of the CCK Antagonist Activity of Benzodiazepines on Pancreatic Receptors
Authors: Huché Michel , Legendre Jean‐Jacques 
Published: October 2006

AbstractThe pancreatic CCK antagonist activity of 73 benzodiazepines was studied by molecular modelling. Construction and optimisation by GenMol and MOPAC allowed us to obtain molecules of absolute minimum energy. Seven geometrical parameters and pharmacophores were selected for a processing by neuronal system. They allow a good prediction of activity of a compound belonging to this series: the correlation coefficients are 0.971 for the calculation and 0.952 for the prediction. A second database, limited to 23 compounds, constituted by a sample of the former one, allowed us, by selecting four parameters to obtain a satisfactory linear and not‐linear correlation for these compounds. The correlation coefficients obtained by neuronal system are 0.977 for the calculation and 0.967 for the prediction.
Mutual view sharing system for real‐time telecommunication
Authors: Nishikawa Atsushi , Kijima Shigeo , Katoh Tomohiro , Maruya Masachika , Yamaguchi Satoshi , Yamazaki Fumio 
Published: October 2006

AbstractOwing to the widespread use of the Internet and portable phones, long‐distance human communication is becoming convenient and is being widely used in daily life. In particular, with portable phones, real‐time voice communications can be realized between widely separated locations, regardless of where, and at any time. This paper proposes a real‐time remote communications support system (mutual view‐sharing system) in which the views seen by the parties can be shared in real time by means of an eyeglass‐type face‐mounted display, a small camera attached above the eye of the user, and a wearable PC. When this system is used to communicate with another party at a distant location, the displays on both sides maintain the same “shared view.” The “shared view,” in which one party's view is shared with the other party, contains the image obtained from one party's face‐mounted camera and also an image of the hand of the other party. When the view of the other party is shared, the “shared view” combines the image obtained from the face‐mounted camera of the other party and also the speaker's own hand image. This mechanism makes it possible, even if the other party is at a distant location, to share a view of the subject of the conversation visually and to transmit positional information on the subject by means of pointing gestures. The system is completely wearable, and the parties communicate while appropriately switching between the shared views. Thus, the system can be considered as an extension of the portable phone. This system was used to perform a real‐time remote communications experiment with the content of “asking the other party to find an object.” It was shown that the system is especially useful compared to voice‐only communications when the shape of the subject of the conversation is complex and the other party has no knowledge of the subject. © 2006 Wiley Periodicals, Inc. Syst Comp Jpn, 37(14): 73–86, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.20460
Noise reduction of speech signals by running spectrum filtering
Authors: Fujioka Kazuma , Hayasaka Noboru , Miyanaga Yoshikazu , Yoshida Norinobu 
Published: October 2006

AbstractThis paper proposes a new noise reduction method intended for noise reduction in speech. The method combines running spectrum filtering (RSF) based on the different time variations of the power spectrum between speech and noise, and postprocessing to reduce musical noise. RSF is a filter which is realized in the modulation spectrum and can effectively reduce noise when applied to the running spectrum of speech. In this paper, it is shown that the segmental SNR of the speech with noise used in the experiment can be improved. A subjective listening experiment shows that the quality of speech degraded by noise is improved. © 2006 Wiley Periodicals, Inc. Syst Comp Jpn, 37(14): 52–61, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.20529
ARXPS characterisation of plasma polymerised surface chemical gradients
Authors: Parry K. L. , Shard A. G. , Short R. D. , White R. G. , Whittle J. D. , Wright A. 
Published: October 2006

AbstractThe aim of this paper is twofold: first to report on the lateral and vertical characterisation of a surface chemical gradient of carboxylic‐acid functionality and second, to demonstrate the use of said gradient to probe the passive adsorption of immunoglobulin G (IgG) as a function of the density of surface carboxylic‐acid groups.A surface chemical gradient of carboxylic‐acid functionality was fabricated by the plasma copolymerisation of octadiene (OD) and acrylic acid (AA). The plasma‐polymerised gradient was over 12 mm, with 2 mm of plasma‐polymerised OD at one end and 2 mm of plasma‐polymerised AA at the other. By means of linescan angle resolved x‐ray photoelectron spectroscopy (ARXPS) it is shown precisely how acid functionality varies from the 2 mm position (OD end) on the gradient to the 10 mm position (AA end). By recording data from 16 angles at each of the 25 sampling points along the gradient, it is shown that the surface gradient also changes vertically, most notably in the thickness of the plasma polymer. At the OD end the plasma‐polymerised layer is 6.3 nm thick, while at the AA end the plasma‐polymerised layer is 5 nm. More subtle changes in chemistry through the plasma‐polymerised layer are shown at the 7.5 and 10 mm points.An identical gradient is used to probe IgG adsorption along the length of the gradient. ARXPS is used to monitor the nitrogen 1s (N1s) signal at 25 points, the N1s signal being unique to adsorbed IgG. It is demonstrated that IgG adsorbs in far greater amount (IgG per unit area) at the OD end, and the amount of adsorbed IgG decreases along the length of the gradient. It is estimated that >200 ng/cm2 adsorbed at the OD, while at the AA the amount adsorbed was <20 ng/cm2. Copyright © 2006 John Wiley & Sons, Ltd.