Study of jack bean urease interaction with luteolin by the extended solvation model and docking simulation

Abstract: In this study, the interaction between Luteolin and urease was made at 300 K in aqueous buffer solutions using isothermal titration calorimetry. The extended solvation model was used to calculate the solvation parameters. Moreover, to determine the interaction of Luteolin with Jack Bean Urease (JBU), a molecular docking process was performed. The purpose of this investigation was to measure the inhibitory effects of Luteolin on the activity and structure of urease. Molecular docking analysis confirmed the extended solvation model

Thermodynamic, kinetic and docking studies of some unsaturated fatty acids-quercetin derivatives as inhibitors of mushroom tyrosinase

Inhibition of activity and stability structure of mushroom tyrosinase (MT) is highly important, since it is a key enzyme of melanogenesis playing various roles in organisms. In this study, thermodynamic stability and diphenolase activities were investigated in the presence of quercetin-7-linoleate (ligand I) and quercetin-7-oleate (ligand II) on mushroom tyrosinase by experimental and computational methods. Kinetic analyses showed that the inhibition mechanism of these ligands is reversible and competitive manner. The inhibition constants values (KiI = 0.31 and KiII = 0.43 mM) and the half maximal inhibitory concentration (IC50 = 0.58 and 0.71 mM) were determined for ligand I and ligand II respectively. Thermal denaturation for the sole and modified enzyme were performed by using fluorescence spectroscopy to obtain the thermodynamic parameters of denaturation. Type of interactions and orientation of ligands were determined by molecular docking simulations. The binding affinities of the MT–ligand complexes during docking were calculated. In the computational studies performed using the MT (PDBID: 2Y9X) from which tropolone was removed, we showed that the ligands occupied different pockets in MT other than the active site. The best binding energies with values of −9 and −7.9 kcal/mol were calculated and the MolDock scores of the best poses with the lowest root mean square deviation (RMSD) were obtained as −172.70 and −165.75 kcal/mol for complexes of MT–ligand I and MT–ligand II, respectively. Computational simulations and experimental analysis demonstrated that the ligands increased the mushroom tyrosinase stability by reducing the activity of enzyme. In this regard, ligand I showed the potent inhibitory and played an important role in enzyme stabilit

Activation of apoptosis and G0/G1 cell cycle arrest along with inhibition of melanogenesis by humic acid and fulvic acid: BAX/BCL-2 and Tyr genes expression and evaluation of nanomechanical properties in A375 human melanoma cell line

Objective(s): Humic acid (HA) and Fulvic acid (FA) are major members of humic substances, which are extracted from organic sources including soil and peat. The pro-apoptotic and anti-melanogenic effects of HA and FA at the cellular and molecular levels in the A375 human melanoma cell line were examined in this study. Materials and Methods: The cytotoxicity effect of HA and FA were evaluated by cell viability assay. Apoptosis and cell cycle were investigated by flow cytometry. Real-time PCR was carried out to measure the expression of BAX, BCL-2, and Tyr genes. Moreover, the changes in nanomechanical properties were determined through atomic force microscopy (AFM). Results: It was found that HA and FA decrease cell viability with an IC50 value of 50 µg/ml (dosedependent) for 14 hr, arrested cells in the G0/G1 phase, and increased the sub-G1 phase (induce apoptosis). Based on the AFM analysis, Young’s modulus and adhesion force values were increased, also ultrastructural characteristics of cells were changed. Results of Real-time PCR revealed that HA and FA lead to a decrease in the expressions of BCL-2 and Tyr genes, and increase the BAX gene expression. Conclusion: These results exhibited that HA and FA possess pro-apoptotic effects through increasing the BAX/ BCL-2 expression in A375 cells. These molecular reports were confirmed by cellular nanomechanical assessments using AFM and flow cytometry. In addition, HA and FA inhibited melanogenesis by decreasing the expression of the Tyr gene. It is worthwhile to