Nosrat Madadi Mahani; Maryam Bagherizadeh
Abstract
Tobacco mosaic virus causes great economic damage to tobacco, pepper, cucumber and ornamental flowers all over the world. In the current work, the relationship between the structure and activity of novel series echinopsin derivatives containing acylhydrazone fragments as antiviral activity against tobacco ...
Read More
Tobacco mosaic virus causes great economic damage to tobacco, pepper, cucumber and ornamental flowers all over the world. In the current work, the relationship between the structure and activity of novel series echinopsin derivatives containing acylhydrazone fragments as antiviral activity against tobacco mosaic virus (TMV) was studied using quantitative structure-activity relationship (QSAR) calculations and molecular docking analysis. Molecular docking analysis of echinopsin derivatives with tobacco mosaic virus (2OM3) protein was done using AutoDock software and descriptors such as binding energy, electroestatic energy and hydrogen bond energy were calculated. The negative values of the binding energy illustrated that the binding nature of these derivatives, as the ligand with the 2OM3 protein is strong. For QSAR model first, the dataset was divided into two groups of training and test sets. Then, descriptors were calculated using quantum mechanics, molecular docking and molecular descriptors. Then, modeling was done by multiple linear regression (MLR) method. It was found that of the lowest unoccupied molecular orbital (LUMO) and Gibbs free energy changes play a role in the model. Also, the descriptors of the total energy of van der Waals interactions, hydrogen bond and energy of vdW + H-bond + desolvation of the molecular docking descriptors have an effect in the regression model. This study can play an important role to design anti –TMV inhibitors.
Nosrat Madadi Mahani; Maryam Alibeigi
Abstract
A quantitative Structure-Activity Relationship (QSAR) model was applied to the prediction of the antimicrobial activity of 22 derivatives 2, 4, 6-s-triazine as anti-malarial agents. The antimicrobial activity of 22 2, 4, 6-s-triazine derivatives were modeled with the descriptors of quantum-chemical ...
Read More
A quantitative Structure-Activity Relationship (QSAR) model was applied to the prediction of the antimicrobial activity of 22 derivatives 2, 4, 6-s-triazine as anti-malarial agents. The antimicrobial activity of 22 2, 4, 6-s-triazine derivatives were modeled with the descriptors of quantum-chemical calculations with density functional theory (DFT) method at B3LYP/6‒31G level and topological descriptors. This study was conducted using the multiple linear regressions (MLR), the partial least square analysis (PLS) and the principal component regression (PCR) method. Results displayed that the MLR method predicted of antimicrobial activity good enough. The best model, with six descriptors was selected. Also it indicates very good consistency towards data variations for the validation methods. The predicted values of antimicrobial activity are in suitable agreement with the experimental results. The obtained results suggested that the PLS method could be more helpful to predict the antimicrobial activity of 2, 4, 6-s-triazine derivatives. This study to be usable to predict the activity of other derivatives in the same groups.
Nosrat Madadi Mahani
Abstract
The interactions of 6twk protein with Ectoine drug, Polyamidoamine (PAMAM) /Ectoine and histidine modified PAMAM/Ectoine were investigated using molecular docking and molecular dynamics simulation. Based on the results of molecular docking increasing of binding energy and the decreasing of inhibition ...
Read More
The interactions of 6twk protein with Ectoine drug, Polyamidoamine (PAMAM) /Ectoine and histidine modified PAMAM/Ectoine were investigated using molecular docking and molecular dynamics simulation. Based on the results of molecular docking increasing of binding energy and the decreasing of inhibition constant of the compounds, increase their inhibitory activity. Protein stability in complex with these ligands was investigated using molecular dynamics simulation approach. Results molecular dynamics simulation displayed that histidine modified PAMAM/Ectoine with the lowest mean square displacement (MSD) is the better suitable to deliver the ectoine drug. This causes the most controlled/diffusion of ectoine drug molecule. So, histidine modified PAMAM/Ectoine conjugate can be introduced for further investigations on interaction of ectoine drug and 6twk protein.
Nosrat Madadi Mahani; Khadije Anjomshoaa; Sayed Zia Mohammadi
Abstract
N-salicyloyl tryptamine derivatives as anti-neuroinflammatory agents have a potent strategy to cure neuroinflammatory diseases including Alzheimer and Parkinson. Computational methods of quantitative structure properties relationships (QSPR) and molecular dynamics were successfully used to design of ...
Read More
N-salicyloyl tryptamine derivatives as anti-neuroinflammatory agents have a potent strategy to cure neuroinflammatory diseases including Alzheimer and Parkinson. Computational methods of quantitative structure properties relationships (QSPR) and molecular dynamics were successfully used to design of four novel N-salicyloyl tryptamine with improved properties. The QSPR model of five variables was presented to predict anti- neuroinflammatory activity of N-salicyloyl tryptamine derivatives. The quantum descriptors as Hartree Fock energy, ionization energy, softness, dipole moment and the thermal energy, were calculated with density functional theory at the B3LYP/6-311G level. Cross validation of multivariate linear regression (MLR) was used to build and evaluate the model QSPR. The model possesses coefficients of the highest squared correlation coefficient (R2) of 0.900 for the training set and 0.817 for the test set. The statistical results exhibited high internal and external consistency as demonstrated by the validation methods. Three of designed compounds showed good pharmacokinetic properties by QSPR predictions. These results provided strong guidance for the discovery and design of novel potential anti- neuroinflammatory compounds. Also, the adsorption of the designed compounds on functionalized carbon nanotube (8, 0) was investigated using molecular dynamics simulation with COMPASS force field. Results indicated that the adsorption of designed N-salicyloyl tryptamine derivatives on f-CNT involves a partial π–π interaction and hydrogen bonding. The study of investigation the interactions of N-salicyloyl tryptamine with f-CNT (8, 0) can be useful for finding the main CNT-based carriers for these derrivatives.
Nosrat Madadi Mahani; Azra Horzadeh
Volume 5, Issue 2 , September 2018, , Pages 23-30
Abstract
A quantitative structure activity relationship analysis has been applied to a data set of 34 derivatives of 8-hydroxy-2-iminochromene with inhibitory activities for carbonyl reductase 1. Semi-empirical quantum chemical calculations at the AM1 level were used to find the geometry of the studied molecules. ...
Read More
A quantitative structure activity relationship analysis has been applied to a data set of 34 derivatives of 8-hydroxy-2-iminochromene with inhibitory activities for carbonyl reductase 1. Semi-empirical quantum chemical calculations at the AM1 level were used to find the geometry of the studied molecules. Whole numbers of descriptors were calculated with Dragon software, and a subset of calculated descriptors was selected from 407 Dragon descriptors with the multiple linear regression (MLR), partial least square and principal component analysis methods. Results displayed that the MLR method predicted of activity good enough. The best model of MLR, with seven descriptors was selected. Also it indicates very good consistency towards data variations for the validation methods. The predicted values of activities are in suitable agreement with the experimental results. The obtained results suggested that the PLS method could be more helpful to predict the biological activity of iminochromene derivatives. This study is be useful to predict the activity of other compounds in the same derivatives.
Fatemeh Sabermahani; Leyli Irannejad; Nosrat Madadi Mahani
Volume 5, Issue 1 , March 2018, , Pages 33-38
Abstract
Polyaniline/maghemite magnetic nanocomposite (PANI/γ -Fe2O3 MNC) was used as active agents for removal of lead ions from aqueous media. Chemical co-precipitation method was used to prepare the maghemite nanoparticles. Subsequently, the MNC was synthesized through polymerization of aniline. ...
Read More
Polyaniline/maghemite magnetic nanocomposite (PANI/γ -Fe2O3 MNC) was used as active agents for removal of lead ions from aqueous media. Chemical co-precipitation method was used to prepare the maghemite nanoparticles. Subsequently, the MNC was synthesized through polymerization of aniline. It was characterized by FT-IR.The efficiency of this MNC was estimated for Pb (II) removal by using batch method. The results showed that optimum conditions for lead removal were found to be at pH of 6, adsorbent dosage of 0.04 g and equilibrium contact time of 90 min. The kinetic of adsorption system have been studied based on the assumption of a pseudo-second order rate law. The adsorption isotherms were examined. The Freundlich adsorption isotherm model was found to represent the equilibrium adsorption isotherm better than Langmuir isotherm. The thermodynamic studies indicated that the adsorption was spontaneous and endothermic process for lead.
Nosrat Madadi Mahani; Fatemeh Sabermahani; Peyman Mohammadzadeh Jahani; Nahid Jalali
Volume 2, Issue 2 , September 2015, , Pages 70-76
Abstract
The Quantitative Structure–Activity Relationship of a series of novel Thiazoline derivatives with anticancer activity has been studied by using the density functional theory by B3LYP/ 6-31G. Descriptors of quantum mechanics of 21 thiazoline derivatives with known activity were obtained. Multiple ...
Read More
The Quantitative Structure–Activity Relationship of a series of novel Thiazoline derivatives with anticancer activity has been studied by using the density functional theory by B3LYP/ 6-31G. Descriptors of quantum mechanics of 21 thiazoline derivatives with known activity were obtained. Multiple linear regressions were employed to model the relationships between molecular descriptors and biological activity of molecules using stepwise method. The most model shows not only significant statistical quality, but also predictive ability, with the square of adjusted correlation coefficient (R2=0.945) and standard error (SE=0.586). We find that the anticancer activity expressed that as half maximal inhibitory concentration (IC50), closely relates to the highest occupied molecular orbital, dipole moment, softness, hardness, ionization energy, electron affinity. Accordingly can be offered a quantitative model, and interpret the activity of the compounds relying on the multivariate statistical analysis. This study shows that the prediction results were in excellent agreement with the experimental value. The results can offer some useful references for understanding the action mechanism and designing new compounds with anticancer activity.
