Masoomeh Shaghaghi; Samaneh Rashtbari; Laleh Solouki; Somaieh Soltani; Gholamreza Dehghan
Abstract
Danofloxacin (DNF), a synthetic fluoroquinolone, is widely used as an antibacterial agent against a broad spectrum of pathogens. In the present study, the effects of DNF on the structure of bovine serum albumin (BSA) were investigated using UV-Vis absorption and fluorescence spectroscopy, and molecular ...
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Danofloxacin (DNF), a synthetic fluoroquinolone, is widely used as an antibacterial agent against a broad spectrum of pathogens. In the present study, the effects of DNF on the structure of bovine serum albumin (BSA) were investigated using UV-Vis absorption and fluorescence spectroscopy, and molecular docking methods at different temperatures. The obtained results of UV-Vis absorption studies showed that the microenvironment of the fluorophore residues does not significantly change upon interaction with DNF. Also, fluorometric studies revealed BSA-DNF complex formation and fluorescence quenching of BSA in the presence of DNF. The number of binding sites and binding constants were calculated to be ~1 and in the order of 103, respectively. According to thermodynamic parameters, van der Waals forces and hydrogen bonding play the main role in the BSA-DNF complex formation, which is a spontaneous process. The binding distance between DNF and BSA was calculated by the Förster resonance energy transfer (FRET) method. Molecular docking results were in agreement with thermodynamic and spectroscopic data and confirmed the binding mechanism of DNF to BSA.
Zahra Garkani Nejad; Abuozar Ghanbari
Abstract
Three-dimensional quantitative structure-activity relationship (3D-QSAR) techniques are useful methods for ligand-based drug design by correlating physicochemical descriptors from a set of related compounds to their known molecular activity or molecular property values. A novel clubbed triazolyl thiophene ...
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Three-dimensional quantitative structure-activity relationship (3D-QSAR) techniques are useful methods for ligand-based drug design by correlating physicochemical descriptors from a set of related compounds to their known molecular activity or molecular property values. A novel clubbed triazolyl thiophene series of cdk5/p25 inhibitors were selected to establish 3D-QSAR models using Comparative molecular field analysis (CoMFA) and Comparative molecular similarity indices analysis (CoMSIA) methods. The optimum CoMFA and CoMSIA models obtained, were statistically significant with cross-validated correlation coefficients r2cv (q2) of 0.539 and 0.558, and conventional correlation coefficients (r2) of 0.980 and 0.967, respectively. A training set containing 88 molecules and a test set containing 24 molecules served to establish the QSAR models. Independent test set validated the external predictive power of both models with predicted correlation coefficients (r2pred) 0.968 and 0.945 for CoMFA and CoMSIA, respectively. Molecular docking was applied to explore the binding mode between the ligand and the receptor. The information obtained from molecular modeling studies may be helpful to design novel CDK5/P25 inhibitors with desired activity.
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 ...
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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.
