Introduction: Quercetin is an effective compound which is found in many medicinal plants. Quercetin antioxidant properties against cancerous tumors and apoptosis induction have been demonstrated. This study is aimed to investigate the molecular dynamics of quercetin with regard to activating the pre-apoptotic factors such as Bim, bak, and Bad using simulation software.Methods: In this study, the thermodynamic properties of flavonoid molecule of quercetin on three important factors in apoptotic pathway such as Bim, bak, and Bad were investigated. After the three-dimensional structure of these molecules was obtained from NCBI and simulation was done by Gromacs software, docking stages were performed by AutoDock software and then the molecular dynamics of the complexes were investigated by Gromacs software.Results: The number of hydrogen bonds between quercetin and Bad was higher than bak and Bim, which causes Bad to have lower energy than bak and Bim. Mean root-mean-square deviation at 10 ns of simulation increased for Bad and bak and decreased for Bim in quercetin presence. Root-mean-square fluctuation investigations indicated that Bim had the highest flexibility in quercetin presence compared to free state.Conclusion: Computational studies indicated that quercetin could have a greater effect on Bad compared to bak and Bim. However it is necessary to investigate the effect mechanism of quercetin on these three pre-apoptotic factors in experimental studies.

Muscari armeniacum is one of the important ornamental cut flower in floriculture industry which native to Southern Europe, North Africa, Western Asia and Asia Minor. In this study, bulb explants (basal plate of bulb having meristem), bulb scales and leaf segments from in vitro derived bulblets were culture in Murashige and Skoog (MS) medium with different plant growth regulator concentrations and combinations to assess growth regulators effect on different bulblet organogenesis pathways in vitro. The results demonstrated that cytokinin in combination with auxin is required for both axillary and adventitious bulblet regeneration. Benzyladenine (BA)-α-naphthalene acetic acid (NAA) combination, showed significant effects compared to other growth regulator combinations tested. 4. 0 μ M BA + 2. 0 μ M NAA was the found to the best for axillary bulblet formation from bulb explants. Likewise, bulb and leaf segments showed the best response in adventitious bulblet organogenesis when they were cultured in BANAA combinations. Out of several concentrations of BA with NAA, 4. 0 μ M BA + 1. 0 μ M NAA was optimum for adventitious bulblet regeneration. Bulblets, properly isolated from both axillary and adventitious proliferation systems, showed maximum percentage of rooting on half strength MS medium containing 2. 0 μ M Indole-3-butyric acid (IBA). However, the higher concentration of all the auxins showed either callus formation at the base of shoots or malformation of roots. All the in vitro regenerated plantlets were successfully acclimatized under ex vitro environment in the garden soil with 60% survival rate.

Background: Apoptosis is one of the most vital mechanisms in the removal of old and damaged cells, especially cancer cells. Many polyphenolic and antioxidant compounds can inhibit the growth and proliferation of cancer cells by inducing apoptosis. This study intended to evaluate the effect of the thymoquinone (TQ) on the three pre-apoptotic factors Bad, bak, and Bim in the simulation environment. Methods: The Protein Data Bank (PDB) files of three pre-apoptotic proteins Bad, bak, and Bim were obtained from PDB database and the molecular structure of TQ from PubChem database. The optimization, simulation, molecular docking, and molecular dynamics (MD) computation were performed using AutoDock, VMD, and GROMACS packages on each one of the proteins in free mode and ligand binding mode. Results: The number and type of hydrogen and hydrophobic bonds at the binding site of TQ and preapoptotic factors Bad, bak, and Bim were detected at the lowest level of energy. The lowest binding energy level of TQ had the highest tendency to bind to the BAD molecule. After the binding of TQ to proteins, the radius of gyration (Rg) of Bim increased while the Rg of Bad and bak decreased. However, the secondary structures (Turn, Coil, Helix, and Bend) were greatly affected in the binding of TQ to Bad, bak, and Bim. Conclusion: The variations of binding energy indicated that TQ can affect the three pre-apoptotic factors Bad, bak, and Bim. This bond seems to increase their activity by variation in the secondary structure of the Bim specific residues.