Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 1789

Search results for: molecular descriptors

1789 Quantitative Structure–Activity Relationship Analysis of Some Benzimidazole Derivatives by Linear Multivariate Method

Authors: Strahinja Z. Kovačević, Lidija R. Jevrić, Sanja O. Podunavac Kuzmanović

Abstract:

The relationship between antibacterial activity of eighteen different substituted benzimidazole derivatives and their molecular characteristics was studied using chemometric QSAR (Quantitative Structure–Activity Relationships) approach. QSAR analysis has been carried out on inhibitory activity towards Staphylococcus aureus, by using molecular descriptors, as well as minimal inhibitory activity (MIC). Molecular descriptors were calculated from the optimized structures. Principal component analysis (PCA) followed by hierarchical cluster analysis (HCA) and multiple linear regression (MLR) was performed in order to select molecular descriptors that best describe the antibacterial behavior of the compounds investigated, and to determine the similarities between molecules. The HCA grouped the molecules in separated clusters which have the similar inhibitory activity. PCA showed very similar classification of molecules as the HCA, and displayed which descriptors contribute to that classification. MLR equations, that represent MIC as a function of the in silico molecular descriptors were established. The statistical significance of the estimated models was confirmed by standard statistical measures and cross-validation parameters (SD = 0.0816, F = 46.27, R = 0.9791, R2CV = 0.8266, R2adj = 0.9379, PRESS = 0.1116). These parameters indicate the possibility of application of the established chemometric models in prediction of the antibacterial behaviour of studied derivatives and structurally very similar compounds.

Keywords: antibacterial, benzimidazole, molecular descriptors, QSAR

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1788 A DFT-Based QSARs Study of Kovats Retention Indices of Adamantane Derivatives

Authors: Z. Bayat

Abstract:

A quantitative structure–property relationship (QSPR) study was performed to develop models those relate the structures of 65 Kovats retention index (RI) of adamantane derivatives. Molecular descriptors derived solely from 3D structures of the molecular compounds. The usefulness of the quantum chemical descriptors, calculated at the level of the DFT theories using 6-311+G** basis set for QSAR study of adamantane derivatives was examined. The use of descriptors calculated only from molecular structure eliminates the need to experimental determination of properties for use in the correlation and allows for the estimation of RI for molecules not yet synthesized. The prediction results are in good agreement with the experimental value. A multi-parametric equation containing maximum Four descriptors at B3LYP/6-31+G** method with good statistical qualities (R2train=0.913, Ftrain=97.67, R2test=0.770, Ftest=3.21, Q2LOO=0.895, R2adj=0.904, Q2LGO=0.844) was obtained by Multiple Linear Regression using stepwise method.

Keywords: DFT, adamantane, QSAR, Kovat

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1787 Chemometric QSRR Evaluation of Behavior of s-Triazine Pesticides in Liquid Chromatography

Authors: Lidija R. Jevrić, Sanja O. Podunavac-Kuzmanović, Strahinja Z. Kovačević

Abstract:

This study considers the selection of the most suitable in silico molecular descriptors that could be used for s-triazine pesticides characterization. Suitable descriptors among topological, geometrical and physicochemical are used for quantitative structure-retention relationships (QSRR) model establishment. Established models were obtained using linear regression (LR) and multiple linear regression (MLR) analysis. In this paper, MLR models were established avoiding multicollinearity among the selected molecular descriptors. Statistical quality of established models was evaluated by standard and cross-validation statistical parameters. For detection of similarity or dissimilarity among investigated s-triazine pesticides and their classification, principal component analysis (PCA) and hierarchical cluster analysis (HCA) were used and gave similar grouping. This study is financially supported by COST action TD1305.

Keywords: chemometrics, classification analysis, molecular descriptors, pesticides, regression analysis

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1786 Evaluation of Newly Synthesized Steroid Derivatives Using In silico Molecular Descriptors and Chemometric Techniques

Authors: Milica Ž. Karadžić, Lidija R. Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Z. Kovačević, Anamarija I. Mandić, Katarina Penov-Gaši, Andrea R. Nikolić, Aleksandar M. Oklješa

Abstract:

This study considered selection of the in silico molecular descriptors and the models for newly synthesized steroid derivatives description and their characterization using chemometric techniques. Multiple linear regression (MLR) models were established and gave the best molecular descriptors for quantitative structure-retention relationship (QSRR) modeling of the retention of the investigated molecules. MLR models were without multicollinearity among the selected molecular descriptors according to the variance inflation factor (VIF) values. Used molecular descriptors were ranked using generalized pair correlation method (GPCM). In this method, the significant difference between independent variables can be noticed regardless almost equal correlation between dependent variable. Generated MLR models were statistically and cross-validated and the best models were kept. Models were ranked using sum of ranking differences (SRD) method. According to this method, the most consistent QSRR model can be found and similarity or dissimilarity between the models could be noticed. In this study, SRD was performed using average values of experimentally observed data as a golden standard. Chemometric analysis was conducted in order to characterize newly synthesized steroid derivatives for further investigation regarding their potential biological activity and further synthesis. This article is based upon work from COST Action (CM1105), supported by COST (European Cooperation in Science and Technology).

Keywords: generalized pair correlation method, molecular descriptors, regression analysis, steroids, sum of ranking differences

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1785 Quantitative Structure-Property Relationship Study of Base Dissociation Constants of Some Benzimidazoles

Authors: Sanja O. Podunavac-Kuzmanović, Lidija R. Jevrić, Strahinja Z. Kovačević

Abstract:

Benzimidazoles are a group of compounds with significant antibacterial, antifungal and anticancer activity. The studied compounds consist of the main benzimidazole structure with different combinations of substituens. This study is based on the two-dimensional and three-dimensional molecular modeling and calculation of molecular descriptors (physicochemical and lipophilicity descriptors) of structurally diverse benzimidazoles. Molecular modeling was carried out by using ChemBio3D Ultra version 14.0 software. The obtained 3D models were subjected to energy minimization using molecular mechanics force field method (MM2). The cutoff for structure optimization was set at a gradient of 0.1 kcal/Åmol. The obtained set of molecular descriptors was used in principal component analysis (PCA) of possible similarities and dissimilarities among the studied derivatives. After the molecular modeling, the quantitative structure-property relationship (QSPR) analysis was applied in order to get the mathematical models which can be used in prediction of pKb values of structurally similar benzimidazoles. The obtained models are based on statistically valid multiple linear regression (MLR) equations. The calculated cross-validation parameters indicate the high prediction ability of the established QSPR models. This study is financially supported by COST action CM1306 and the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina.

Keywords: benzimidazoles, chemometrics, molecular modeling, molecular descriptors, QSPR

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1784 QSAR Modeling of Germination Activity of a Series of 5-(4-Substituent-Phenoxy)-3-Methylfuran-2(5H)-One Derivatives with Potential of Strigolactone Mimics toward Striga hermonthica

Authors: Strahinja Kovačević, Sanja Podunavac-Kuzmanović, Lidija Jevrić, Cristina Prandi, Piermichele Kobauri

Abstract:

The present study is based on molecular modeling of a series of twelve 5-(4-substituent-phenoxy)-3-methylfuran-2(5H)-one derivatives which have potential of strigolactones mimics toward Striga hermonthica. The first step of the analysis included the calculation of molecular descriptors which numerically describe the structures of the analyzed compounds. The descriptors ALOGP (lipophilicity), AClogS (water solubility) and BBB (blood-brain barrier penetration), served as the input variables in multiple linear regression (MLR) modeling of germination activity toward S. hermonthica. Two MLR models were obtained. The first MLR model contains ALOGP and AClogS descriptors, while the second one is based on these two descriptors plus BBB descriptor. Despite the braking Topliss-Costello rule in the second MLR model, it has much better statistical and cross-validation characteristics than the first one. The ALOGP and AClogS descriptors are often very suitable predictors of the biological activity of many compounds. They are very important descriptors of the biological behavior and availability of a compound in any biological system (i.e. the ability to pass through the cell membranes). BBB descriptor defines the ability of a molecule to pass through the blood-brain barrier. Besides the lipophilicity of a compound, this descriptor carries the information of the molecular bulkiness (its value strongly depends on molecular bulkiness). According to the obtained results of MLR modeling, these three descriptors are considered as very good predictors of germination activity of the analyzed compounds toward S. hermonthica seeds. This article is based upon work from COST Action (FA1206), supported by COST (European Cooperation in Science and Technology).

Keywords: chemometrics, germination activity, molecular modeling, QSAR analysis, strigolactones

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1783 Non-Linear Assessment of Chromatographic Lipophilicity of Selected Steroid Derivatives

Authors: Milica Karadžić, Lidija Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Anamarija Mandić, Aleksandar Oklješa, Andrea Nikolić, Marija Sakač, Katarina Penov Gaši

Abstract:

Using chemometric approach, the relationships between the chromatographic lipophilicity and in silico molecular descriptors for twenty-nine selected steroid derivatives were studied. The chromatographic lipophilicity was predicted using artificial neural networks (ANNs) method. The most important in silico molecular descriptors were selected applying stepwise selection (SS) paired with partial least squares (PLS) method. Molecular descriptors with satisfactory variable importance in projection (VIP) values were selected for ANN modeling. The usefulness of generated models was confirmed by detailed statistical validation. High agreement between experimental and predicted values indicated that obtained models have good quality and high predictive ability. Global sensitivity analysis (GSA) confirmed the importance of each molecular descriptor used as an input variable. High-quality networks indicate a strong non-linear relationship between chromatographic lipophilicity and used in silico molecular descriptors. Applying selected molecular descriptors and generated ANNs the good prediction of chromatographic lipophilicity of the studied steroid derivatives can be obtained. This article is based upon work from COST Actions (CM1306 and CA15222), supported by COST (European Cooperation and Science and Technology).

Keywords: artificial neural networks, chemometrics, global sensitivity analysis, liquid chromatography, steroids

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1782 Molecular Modeling of Structurally Diverse Compounds as Potential Therapeutics for Transmissible Spongiform Encephalopathy

Authors: Sanja O. Podunavac-Kuzmanović, Strahinja Z. Kovačević, Lidija R. Jevrić

Abstract:

Prion is a protein substance whose certain form is considered as infectious agent. It is presumed to be the cause of the transmissible spongiform encephalopathies (TSEs). The protein it is composed of, called PrP, can fold in structurally distinct ways. At least one of those 3D structures is transmissible to other prion proteins. Prions can be found in brain tissue of healthy people and have certain biological role. The structure of prions naturally occurring in healthy organisms is marked as PrPc, and the structure of infectious prion is labeled as PrPSc. PrPc may play a role in synaptic plasticity and neuronal development. Also, it may be required for neuronal myelin sheath maintenance, including a role in iron uptake and iron homeostasis. PrPSc can be considered as an environmental pollutant. The main aim of this study was to carry out the molecular modeling and calculation of molecular descriptors (lipophilicity, physico-chemical and topological descriptors) of structurally diverse compounds which can be considered as anti-prion agents. Molecular modeling was conducted applying ChemBio3D Ultra version 12.0 software. The obtained 3D models were subjected to energy minimization using molecular mechanics force field method (MM2). The cutoff for structure optimization was set at a gradient of 0.1 kcal/Åmol. The Austin Model 1 (AM-1) was used for full geometry optimization of all structures. The obtained set of molecular descriptors is applied in analysis of similarities and dissimilarities among the tested compounds. This study is an important step in further development of quantitative structure-activity relationship (QSAR) models, which can be used for prediction of anti-prion activity of newly synthesized compounds.

Keywords: chemometrics, molecular modeling, molecular descriptors, prions, QSAR

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1781 Molecular Modeling of 17-Picolyl and 17-Picolinylidene Androstane Derivatives with Anticancer Activity

Authors: Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Lidija Jevrić, Evgenija Djurendić, Jovana Ajduković

Abstract:

In the present study, the molecular modeling of a series of 24 17-picolyl and 17-picolinylidene androstane derivatives whit significant anticancer activity was carried out. Modelling of studied compounds was performed by CS ChemBioDraw Ultra v12.0 program for drawing 2D molecular structures and CS ChemBio3D Ultra v12.0 for 3D molecular modelling. The obtained 3D structures were subjected to energy minimization using molecular mechanics force field method (MM2). The cutoff for structure optimization was set at a gradient of 0.1 kcal/Åmol. Full geometry optimization was done by the Austin Model 1 (AM1) until the root mean square (RMS) gradient reached a value smaller than 0.0001 kcal/Åmol using Molecular Orbital Package (MOPAC) program. The obtained physicochemical, lipophilicity and topological descriptors were used for analysis of molecular similarities and dissimilarities applying suitable chemometric methods (principal component analysis and cluster analysis). These results are the part of the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina and CMST COST Action CM1306.

Keywords: androstane derivatives, anticancer activity, chemometrics, molecular descriptors

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1780 Application of Artificial Neural Network for Prediction of Retention Times of Some Secoestrane Derivatives

Authors: Nataša Kalajdžija, Strahinja Kovačević, Davor Lončar, Sanja Podunavac Kuzmanović, Lidija Jevrić

Abstract:

In order to investigate the relationship between retention and structure, a quantitative Structure Retention Relationships (QSRRs) study was applied for the prediction of retention times of a set of 23 secoestrane derivatives in a reversed-phase thin-layer chromatography. After the calculation of molecular descriptors, a suitable set of molecular descriptors was selected by using step-wise multiple linear regressions. Artificial Neural Network (ANN) method was employed to model the nonlinear structure-activity relationships. The ANN technique resulted in 5-6-1 ANN model with the correlation coefficient of 0.98. We found that the following descriptors: Critical pressure, total energy, protease inhibition, distribution coefficient (LogD) and parameter of lipophilicity (miLogP) have a significant effect on the retention times. The prediction results are in very good agreement with the experimental ones. This approach provided a new and effective method for predicting the chromatographic retention index for the secoestrane derivatives investigated.

Keywords: lipophilicity, QSRR, RP TLC retention, secoestranes

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1779 Quantitative Structure-Activity Relationship Analysis of Binding Affinity of a Series of Anti-Prion Compounds to Human Prion Protein

Authors: Strahinja Kovačević, Sanja Podunavac-Kuzmanović, Lidija Jevrić, Milica Karadžić

Abstract:

The present study is based on the quantitative structure-activity relationship (QSAR) analysis of eighteen compounds with anti-prion activity. The structures and anti-prion activities (expressed in response units, RU%) of the analyzed compounds are taken from CHEMBL database. In the first step of analysis 85 molecular descriptors were calculated and based on them the hierarchical cluster analysis (HCA) and principal component analysis (PCA) were carried out in order to detect potential significant similarities or dissimilarities among the studied compounds. The calculated molecular descriptors were physicochemical, lipophilicity and ADMET (absorption, distribution, metabolism, excretion and toxicity) descriptors. The first stage of the QSAR analysis was simple linear regression modeling. It resulted in one acceptable model that correlates Henry's law constant with RU% units. The obtained 2D-QSAR model was validated by cross-validation as an internal validation method. The validation procedure confirmed the model’s quality and therefore it can be used for prediction of anti-prion activity. The next stage of the analysis of anti-prion activity will include 3D-QSAR and molecular docking approaches in order to select the most promising compounds in treatment of prion diseases. These results are the part of the project No. 114-451-268/2016-02 financially supported by the Provincial Secretariat for Science and Technological Development of AP Vojvodina.

Keywords: anti-prion activity, chemometrics, molecular modeling, QSAR

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1778 Molecular Topology and TLC Retention Behaviour of s-Triazines: QSRR Study

Authors: Lidija R. Jevrić, Sanja O. Podunavac-Kuzmanović, Strahinja Z. Kovačević

Abstract:

Quantitative structure-retention relationship (QSRR) analysis was used to predict the chromatographic behavior of s-triazine derivatives by using theoretical descriptors computed from the chemical structure. Fundamental basis of the reported investigation is to relate molecular topological descriptors with chromatographic behavior of s-triazine derivatives obtained by reversed-phase (RP) thin layer chromatography (TLC) on silica gel impregnated with paraffin oil and applied ethanol-water (φ = 0.5-0.8; v/v). Retention parameter (RM0) of 14 investigated s-triazine derivatives was used as dependent variable while simple connectivity index different orders were used as independent variables. The best QSRR model for predicting RM0 value was obtained with simple third order connectivity index (3χ) in the second-degree polynomial equation. Numerical values of the correlation coefficient (r=0.915), Fisher's value (F=28.34) and root mean square error (RMSE = 0.36) indicate that model is statistically significant. In order to test the predictive power of the QSRR model leave-one-out cross-validation technique has been applied. The parameters of the internal cross-validation analysis (r2CV=0.79, r2adj=0.81, PRESS=1.89) reflect the high predictive ability of the generated model and it confirms that can be used to predict RM0 value. Multivariate classification technique, hierarchical cluster analysis (HCA), has been applied in order to group molecules according to their molecular connectivity indices. HCA is a descriptive statistical method and it is the most frequently used for important area of data processing such is classification. The HCA performed on simple molecular connectivity indices obtained from the 2D structure of investigated s-triazine compounds resulted in two main clusters in which compounds molecules were grouped according to the number of atoms in the molecule. This is in agreement with the fact that these descriptors were calculated on the basis of the number of atoms in the molecule of the investigated s-triazine derivatives.

Keywords: s-triazines, QSRR, chemometrics, chromatography, molecular descriptors

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1777 Computational Study of Chromatographic Behavior of a Series of S-Triazine Pesticides Based on Their in Silico Biological and Lipophilicity Descriptors

Authors: Lidija R. Jevrić, Sanja O. Podunavac-Kuzmanović, Strahinja Z. Kovačević

Abstract:

In this paper, quantitative structure-retention relationships (QSRR) analysis was applied in order to correlate in silico biological and lipophilicity molecular descriptors with retention values for the set of selected s-triazine herbicides. In silico generated biological and lipophilicity descriptors were discriminated using generalized pair correlation method (GPCM). According to this method, the significant difference between independent variables can be noticed regardless almost equal correlation with dependent variable. Using established multiple linear regression (MLR) models some biological characteristics could be predicted. Established MLR models were evaluated statistically and the most suitable models were selected and ranked using sum of ranking differences (SRD) method. In this method, as reference values, average experimentally obtained values are used. Additionally, using SRD method, similarities among investigated s-triazine herbicides can be noticed. These analysis were conducted in order to characterize selected s-triazine herbicides for future investigations regarding their biodegradability. This study is financially supported by COST action TD1305.

Keywords: descriptors, generalized pair correlation method, pesticides, sum of ranking differences

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1776 A Machine Learning-Based Model to Screen Antituberculosis Compound Targeted against LprG Lipoprotein of Mycobacterium tuberculosis

Authors: Syed Asif Hassan, Syed Atif Hassan

Abstract:

Multidrug-resistant Tuberculosis (MDR-TB) is an infection caused by the resistant strains of Mycobacterium tuberculosis that do not respond either to isoniazid or rifampicin, which are the most important anti-TB drugs. The increase in the occurrence of a drug-resistance strain of MTB calls for an intensive search of novel target-based therapeutics. In this context LprG (Rv1411c) a lipoprotein from MTB plays a pivotal role in the immune evasion of Mtb leading to survival and propagation of the bacterium within the host cell. Therefore, a machine learning method will be developed for generating a computational model that could predict for a potential anti LprG activity of the novel antituberculosis compound. The present study will utilize dataset from PubChem database maintained by National Center for Biotechnology Information (NCBI). The dataset involves compounds screened against MTB were categorized as active and inactive based upon PubChem activity score. PowerMV, a molecular descriptor generator, and visualization tool will be used to generate the 2D molecular descriptors for the actives and inactive compounds present in the dataset. The 2D molecular descriptors generated from PowerMV will be used as features. We feed these features into three different classifiers, namely, random forest, a deep neural network, and a recurring neural network, to build separate predictive models and choosing the best performing model based on the accuracy of predicting novel antituberculosis compound with an anti LprG activity. Additionally, the efficacy of predicted active compounds will be screened using SMARTS filter to choose molecule with drug-like features.

Keywords: antituberculosis drug, classifier, machine learning, molecular descriptors, prediction

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1775 Binding Studies of Complexes of Anticancer Drugs with DNA and Enzymes Involved in DNA Replication Using Molecular Docking and Cell Culture Techniques

Authors: Fouzia Perveen, Rumana Qureshi

Abstract:

The presently studied twelve anticancer drugs are the cytotoxic agents which inhibit the replication of DNA and activity of enzymes involved in DNA replication namely topoisomerase-II, polymerase and helicase and have shown remarkable anticancer activity in clinical trials. In this study, we performed molecular docking studies of twelve antitumor drugs against DNA and DNA enzymes in the presence and absence of ascorbic acid (AA) and developed the quantitative structure-activity relationship (QSAR) model for anticancer activity screening. A number of electronic and steric descriptors were calculated using MOE software package. QSAR was established showing a correlation of binding strength with various physicochemical descriptors. Out of these twelve, eight cytotoxic drugs were tested on Non-Small Cell Lung Cancer cell lines (H-157 and H-1299) in the absence and presence of ascorbic acid and experimental IC50 values were calculated. From the docking studies, binding constants were calculated indicating the strength of drug-DNA and drug-enzyme complex formation and it was correlated to the IC50 values (both experimental and theoretical). These results can offer useful references for directing the molecular design of DNA enzyme inhibitor with improved anticancer activity.

Keywords: ascorbic acid, binding constant, cytotoxic agents, cell culture, DNA, DNA enzymes, molecular docking

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1774 A 7 Dimensional-Quantitative Structure-Activity Relationship Approach Combining Quantum Mechanics Based Grid and Solvation Models to Predict Hotspots and Kinetic Properties of Mutated Enzymes: An Enzyme Engineering Perspective

Authors: R. Pravin Kumar, L. Roopa

Abstract:

Enzymes are molecular machines used in various industries such as pharmaceuticals, cosmetics, food and animal feed, paper and leather processing, biofuel, and etc. Nevertheless, this has been possible only by the breath-taking efforts of the chemists and biologists to evolve/engineer these mysterious biomolecules to work the needful. Main agenda of this enzyme engineering project is to derive screening and selection tools to obtain focused libraries of enzyme variants with desired qualities. The methodologies for this research include the well-established directed evolution, rational redesign and relatively less established yet much faster and accurate insilico methods. This concept was initiated as a Receptor Rependent-4Dimensional Quantitative Structure Activity Relationship (RD-4D-QSAR) to predict kinetic properties of enzymes and extended here to study transaminase by a 7D QSAR approach. Induced-fit scenarios were explored using Quantum Mechanics/Molecular Mechanics (QM/MM) simulations which were then placed in a grid that stores interactions energies derived from QM parameters (QMgrid). In this study, the mutated enzymes were immersed completely inside the QMgrid and this was combined with solvation models to predict descriptors. After statistical screening of descriptors, QSAR models showed > 90% specificity and > 85% sensitivity towards the experimental activity. Mapping descriptors on the enzyme structure revealed hotspots important to enhance the enantioselectivity of the enzyme.

Keywords: QMgrid, QM/MM simulations, RD-4D-QSAR, transaminase

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1773 Computing Some Topological Descriptors of Single-Walled Carbon Nanotubes

Authors: Amir Bahrami

Abstract:

In the fields of chemical graph theory, molecular topology, and mathematical chemistry, a topological index or a descriptor index also known as a connectivity index is a type of a molecular descriptor that is calculated based on the molecular graph of a chemical compound. Topological indices are numerical parameters of a graph which characterize its topology and are usually graph invariant. Topological indices are used for example in the development of quantitative structure-activity relationships (QSARs) in which the biological activity or other properties of molecules are correlated with their chemical structure. In this paper some descriptor index (descriptor index) of single-walled carbon nanotubes, is determined.

Keywords: chemical graph theory, molecular topology, molecular descriptor, single-walled carbon nanotubes

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1772 Bag of Words Representation Based on Fusing Two Color Local Descriptors and Building Multiple Dictionaries

Authors: Fatma Abdedayem

Abstract:

We propose an extension to the famous method called Bag of words (BOW) which proved a successful role in the field of image categorization. Practically, this method based on representing image with visual words. In this work, firstly, we extract features from images using Spatial Pyramid Representation (SPR) and two dissimilar color descriptors which are opponent-SIFT and transformed-color-SIFT. Secondly, we fuse color local features by joining the two histograms coming from these descriptors. Thirdly, after collecting of all features, we generate multi-dictionaries coming from n random feature subsets that obtained by dividing all features into n random groups. Then, by using these dictionaries separately each image can be represented by n histograms which are lately concatenated horizontally and form the final histogram, that allows to combine Multiple Dictionaries (MDBoW). In the final step, in order to classify image we have applied Support Vector Machine (SVM) on the generated histograms. Experimentally, we have used two dissimilar image datasets in order to test our proposition: Caltech 256 and PASCAL VOC 2007.

Keywords: bag of words (BOW), color descriptors, multi-dictionaries, MDBoW

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1771 Assisted Video Colorization Using Texture Descriptors

Authors: Andre Peres Ramos, Franklin Cesar Flores

Abstract:

Colorization is the process of add colors to a monochromatic image or video. Usually, the process involves to segment the image in regions of interest and then apply colors to each one, for videos, this process is repeated for each frame, which makes it a tedious and time-consuming job. We propose a new assisted method for video colorization; the user only has to colorize one frame, and then the colors are propagated to following frames. The user can intervene at any time to correct eventual errors in color assignment. The method consists of to extract intensity and texture descriptors from the frames and then perform a feature matching to determine the best color for each segment. To reduce computation time and give a better spatial coherence we narrow the area of search and give weights for each feature to emphasize texture descriptors. To give a more natural result, we use an optimization algorithm to make the color propagation. Experimental results in several image sequences, compared to others existing methods, demonstrates that the proposed method perform a better colorization with less time and user interference.

Keywords: colorization, feature matching, texture descriptors, video segmentation

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1770 Determining the Octanol-Water Partition Coefficient for Armchair Polyhex BN Nanotubes Using Topological Indices

Authors: Esmat Mohammadinasab

Abstract:

The aim of this paper is to investigate theoretically and establish a predictive model for determination LogP of armchair polyhex BN nanotubes by using simple descriptors. The relationship between the octanol-water partition coefficient (LogP) and quantum chemical descriptors, electric moments, and topological indices of some armchair polyhex BN nanotubes with various lengths and fixed circumference are represented. Based on density functional theory (DFT) electric moments and physico-chemical properties of those nanotubes are calculated. The DFT method performed based on the Becke’s 3-parameter formulation with the Lee-Yang-Parr functional (B3LYP) method and 3-21G standard basis sets. For the first time, the relationship between partition coefficient and different properties of polyhex BN nanotubes is investigated.

Keywords: topological indices, quantum descriptors, DFT method, nanotubes

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1769 QSRR Analysis of 17-Picolyl and 17-Picolinylidene Androstane Derivatives Based on Partial Least Squares and Principal Component Regression

Authors: Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Lidija Jevrić, Evgenija Djurendić, Jovana Ajduković

Abstract:

There are several methods for determination of the lipophilicity of biologically active compounds, however chromatography has been shown as a very suitable method for this purpose. Chromatographic (C18-RP-HPLC) analysis of a series of 24 17-picolyl and 17-picolinylidene androstane derivatives was carried out. The obtained retention indices (logk, methanol (90%) / water (10%)) were correlated with calculated physicochemical and lipophilicity descriptors. The QSRR analysis was carried out applying principal component regression (PCR) and partial least squares regression (PLS). The PCR and PLS model were selected on the basis of the highest variance and the lowest root mean square error of cross-validation. The obtained PCR and PLS model successfully correlate the calculated molecular descriptors with logk parameter indicating the significance of the lipophilicity of compounds in chromatographic process. On the basis of the obtained results it can be concluded that the obtained logk parameters of the analyzed androstane derivatives can be considered as their chromatographic lipophilicity. These results are the part of the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina and CMST COST Action CM1105.

Keywords: androstane derivatives, chromatography, molecular structure, principal component regression, partial least squares regression

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1768 Evaluation of Robust Feature Descriptors for Texture Classification

Authors: Jia-Hong Lee, Mei-Yi Wu, Hsien-Tsung Kuo

Abstract:

Texture is an important characteristic in real and synthetic scenes. Texture analysis plays a critical role in inspecting surfaces and provides important techniques in a variety of applications. Although several descriptors have been presented to extract texture features, the development of object recognition is still a difficult task due to the complex aspects of texture. Recently, many robust and scaling-invariant image features such as SIFT, SURF and ORB have been successfully used in image retrieval and object recognition. In this paper, we have tried to compare the performance for texture classification using these feature descriptors with k-means clustering. Different classifiers including K-NN, Naive Bayes, Back Propagation Neural Network , Decision Tree and Kstar were applied in three texture image sets - UIUCTex, KTH-TIPS and Brodatz, respectively. Experimental results reveal SIFTS as the best average accuracy rate holder in UIUCTex, KTH-TIPS and SURF is advantaged in Brodatz texture set. BP neuro network works best in the test set classification among all used classifiers.

Keywords: texture classification, texture descriptor, SIFT, SURF, ORB

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1767 Non-Linear Assessment of Chromatographic Lipophilicity and Model Ranking of Newly Synthesized Steroid Derivatives

Authors: Milica Karadzic, Lidija Jevric, Sanja Podunavac-Kuzmanovic, Strahinja Kovacevic, Anamarija Mandic, Katarina Penov Gasi, Marija Sakac, Aleksandar Okljesa, Andrea Nikolic

Abstract:

The present paper deals with chromatographic lipophilicity prediction of newly synthesized steroid derivatives. The prediction was achieved using in silico generated molecular descriptors and quantitative structure-retention relationship (QSRR) methodology with the artificial neural networks (ANN) approach. Chromatographic lipophilicity of the investigated compounds was expressed as retention factor value logk. For QSRR modeling, a feedforward back-propagation ANN with gradient descent learning algorithm was applied. Using the novel sum of ranking differences (SRD) method generated ANN models were ranked. The aim was to distinguish the most consistent QSRR model that can be found, and similarity or dissimilarity between the models that could be noticed. In this study, SRD was performed with average values of retention factor value logk as reference values. An excellent correlation between experimentally observed retention factor value logk and values predicted by the ANN was obtained with a correlation coefficient higher than 0.9890. Statistical results show that the established ANN models can be applied for required purpose. This article is based upon work from COST Action (TD1305), supported by COST (European Cooperation in Science and Technology).

Keywords: artificial neural networks, liquid chromatography, molecular descriptors, steroids, sum of ranking differences

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1766 Prediction of Anticancer Potential of Curcumin Nanoparticles by Means of Quasi-Qsar Analysis Using Monte Carlo Method

Authors: Ruchika Goyal, Ashwani Kumar, Sandeep Jain

Abstract:

The experimental data for anticancer potential of curcumin nanoparticles was calculated by means of eclectic data. The optimal descriptors were examined using Monte Carlo method based CORAL SEA software. The statistical quality of the model is following: n = 14, R² = 0.6809, Q² = 0.5943, s = 0.175, MAE = 0.114, F = 26 (sub-training set), n =5, R²= 0.9529, Q² = 0.7982, s = 0.086, MAE = 0.068, F = 61, Av Rm² = 0.7601, ∆R²m = 0.0840, k = 0.9856 and kk = 1.0146 (test set) and n = 5, R² = 0.6075 (validation set). This data can be used to build predictive QSAR models for anticancer activity.

Keywords: anticancer potential, curcumin, model, nanoparticles, optimal descriptors, QSAR

Procedia PDF Downloads 231
1765 Development of DNA Fingerprints in Selected Medicinal Plants of India

Authors: V. Verma, Hazi Raja

Abstract:

Conventionally, morphological descriptors are routinely used for establishing the identity of varieties. But these morphological descriptors suffer from many drawbacks such as influence of environment on trait expression, epistatic interactions, pleiotrophic effects etc. Furthermore, the paucity of a sufficient number of these descriptors for unequivocal identification of increasing number of reference collection varieties enforces to look for alternatives. Therefore, DNA based finger-print based techniques were selected to define the systematic position of the selected medicinal plants like Plumbago zeylanica, Desmodium gangeticum, Uraria picta. DNA fingerprinting of herbal plants can be useful in authenticating the various claims of medical uses related to the plants, in germplasm characterization and conservation. In plants it has not only helped in identifying species but also in defining a new realm in plant genomics, plant breeding and in conserving the biodiversity. With world paving way for developments in biotechnology, DNA fingerprinting promises a very powerful tool in our future endeavors. Data will be presented on the development of microsatellite markers (SSR) used to fingerprint, characterize, and assess genetic diversity among 12 accessions of both Plumbago zeylanica, 4 accessions of Desmodium gengaticum, 4 accessions of Uraria Picta.

Keywords: Plumbago zeylanica, Desmodium gangeticum, Uraria picta, microsaetllite markers

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1764 QSAR Study and Haptotropic Rearrangement in Estradiol Derivatives

Authors: Mohamed Abd Esselem Dems, Souhila Laib, Nadjia Latelli, Nadia Ouddai

Abstract:

In this work, we have developed QSAR model for Relative Binding Affinity (RBA) of a large diverse set of estradiol among these derivatives, the organometallic derivatives. By dividing the dataset into a training set of 24 compounds and a test set of 6 compounds. The DFT method was used to calculate quantum chemical descriptors and physicochemical descriptors (MR and MLOGP) were performed using E-Dragon. All the validations indicated that the QSAR model built was robust and satisfactory (R2 = 90.12, Q2LOO = 86.61, RMSE = 0.272, F = 60.6473, Q2ext =86.07). We have therefore apply this model to predict the RBA, for two isomers β and α wherein Mn(CO)3 complex with the aromatic ring of estradiol, and the two isomers show little appreciation for the estrogenic receptor (RBAβ = 1.812 and RBAα = 1.741).

Keywords: DFT, estradiol, haptotropic rearrangement, QSAR, relative binding affinity

Procedia PDF Downloads 206
1763 Resource Framework Descriptors for Interestingness in Data

Authors: C. B. Abhilash, Kavi Mahesh

Abstract:

Human beings are the most advanced species on earth; it's all because of the ability to communicate and share information via human language. In today's world, a huge amount of data is available on the web in text format. This has also resulted in the generation of big data in structured and unstructured formats. In general, the data is in the textual form, which is highly unstructured. To get insights and actionable content from this data, we need to incorporate the concepts of text mining and natural language processing. In our study, we mainly focus on Interesting data through which interesting facts are generated for the knowledge base. The approach is to derive the analytics from the text via the application of natural language processing. Using semantic web Resource framework descriptors (RDF), we generate the triple from the given data and derive the interesting patterns. The methodology also illustrates data integration using the RDF for reliable, interesting patterns.

Keywords: RDF, interestingness, knowledge base, semantic data

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1762 Investigation of the Mechanism, Régio and Sterioselectivity Using the 1,3-Dipolar Cycloaddition Reaction of Fused 1h-Pyrrole-2,3-Diones with Nitrones: Molecular Electron Density Theory Study

Authors: Ameur Soukaina, Zeroual Abdellah, Mazoir Noureddine

Abstract:

Molecular Electron Density Theory (MEDT) elucidates the regioselectivity of the [4+2] cycloaddition reaction between 3-aroylpyrrolo[1,2-α]quinoxaline-1,2,4(5H)-trione and butyl vinyl ether Regioselectivity and stereoselectivity. The regioselectivity mechanisms of these reactions were investigated by evaluating potential energy surfaces calculated for cycloaddition processes and DFT density-based reactivity indices. These methods have been successfully applied to predict preferred regioisomers for different method alternatives. Reactions were monitored by performing transition state optimizations, calculations of intrinsic reaction coordinates, and activation energies. The observed regioselectivity was rationalized using DFT-based reactivity descriptors such as the Parr function. Solvent effects were also investigated in 1,4-dioxane solvent using a field model for self-consistent reactions. The results were compared with experimental data to find good agreement.

Keywords: cycloaddition, DFT, ELF, MEDT, parr, stereoselectivité

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1761 2D Fingerprint Performance for PubChem Chemical Database

Authors: Fatimah Zawani Abdullah, Shereena Mohd Arif, Nurul Malim

Abstract:

The study of molecular similarity search in chemical database is increasingly widespread, especially in the area of drug discovery. Similarity search is an application in the field of Chemoinformatics to measure the similarity between the molecular structure which is known as the query and the structure of chemical compounds in the database. Similarity search is also one of the approaches in virtual screening which involves computational techniques and scoring the probabilities of activity. The main objective of this work is to determine the best fingerprint when compared to the other five fingerprints selected in this study using PubChem chemical dataset. This paper will discuss the similarity searching process conducted using 6 types of descriptors, which are ECFP4, ECFC4, FCFP4, FCFC4, SRECFC4 and SRFCFC4 on 15 activity classes of PubChem dataset using Tanimoto coefficient to calculate the similarity between the query structures and each of the database structure. The results suggest that ECFP4 performs the best to be used with Tanimoto coefficient in the PubChem dataset.

Keywords: 2D fingerprints, Tanimoto, PubChem, similarity searching, chemoinformatics

Procedia PDF Downloads 211
1760 Retrieving Similar Segmented Objects Using Motion Descriptors

Authors: Konstantinos C. Kartsakalis, Angeliki Skoura, Vasileios Megalooikonomou

Abstract:

The fuzzy composition of objects depicted in images acquired through MR imaging or the use of bio-scanners has often been a point of controversy for field experts attempting to effectively delineate between the visualized objects. Modern approaches in medical image segmentation tend to consider fuzziness as a characteristic and inherent feature of the depicted object, instead of an undesirable trait. In this paper, a novel technique for efficient image retrieval in the context of images in which segmented objects are either crisp or fuzzily bounded is presented. Moreover, the proposed method is applied in the case of multiple, even conflicting, segmentations from field experts. Experimental results demonstrate the efficiency of the suggested method in retrieving similar objects from the aforementioned categories while taking into account the fuzzy nature of the depicted data.

Keywords: fuzzy object, fuzzy image segmentation, motion descriptors, MRI imaging, object-based image retrieval

Procedia PDF Downloads 299