Computational study of quercetin effect on pre-apoptotic factors of Bad, Bak and Bim

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

THE LACK OF CORRELATION BETWEEN TP53 MUTATIONS AND GASTRIC CANCER: A REPORT FROM A PROVINCE OF IRAN

Gastric cancer ranks second cause of cancer death worldwide after lung cancer. Its etiology is heterogeneous and genetic factors including protooncogenes and tumor suppressor genes always contribute to the progression of cancer. The TP53 tumor suppressor gene has a broad role in genomic stability and DNA repair. The aim of this study was to determine the TP53 gene mutations in gastric cancer specimens in Chaharmahal Va Bakhtiari province of Iran. In this descriptive-lab based study, we investigated the promoter and exons of TP53 gene mutations in 38 paraffin-embedded gastric cancer specimens. DNA was extracted following a standard phenol-chloroform protocol. The TP53 gene mutations were determined using PCR-SSCP & PCR-RFLP procedures. The present study revealed no TP53 gene mutation in the promoter and exons in the gastric cancer subjects studied. While TP53 gene mutations have been reported as the most frequent genetic alterations and are found in about 50% of the human malignancies, no mutation was detected in this study. This may be due to mutations in other related genes in the same pathway or epigenetic factors

The study of apoptosis-inducing effects of three pre-apoptotic factors by gallic acid, using simulation analysis and the comet assay technique on the prostatic cancer cell line PC3

Background: In this study, we demonstrated the effects of the Gallic Acid (GA) molecule on the prostate cancer cells line PC3 using the comet assay (Alkaline electrophoresis) technique and its effects on some important apoptotic factors including BAD (Bcl-2-Associated Death promoter), BAK (Bcl-2 homologous Antagonist/Killer), and BIM (Bcl-2-like protein 11) via simulation analysis by using the Auto Dock and Gromacs software. Methods: Following the MTT assay on the PC3 cells, and determining IC50, we used three concentrations of GA to around IC50 to treat PC3 cells. 100 comet pictures were obtained by alkaline electrophoresis and have been analysed with the CASP version 1.2.2 software; all the results were thereafter analysed by the SPSS version 21 statistical software. Results: The IC50 value for GA was determined to be 35 µM. The ratio of tail to head in alkaline electrophoresis for the three concentrations below the IC50 of GA in 25, 30, and 35 µM were measured as 24.7 (2.7), 44.5 (1.8), and 57.3 (1.3) percent, respectively. The results of the preapoptotic factors (BAD, BAK, and BIM) in the performed simulation in the absence and presence of GA showed that the GA protein causes the structural instability in the BAD protein, and the effect of GA can be explained by the creation of hydrogen bonds with proteins. Conclusion: GA is a polyphenol compound in plants that can suppress cell growth and induce apoptosis in PC3 cells in prostate cancer in the range of IC50 concentrations. The apoptotic properties of GA induce pre-apoptotic factors

Effects of Phenanthrene and Pyrene on Cytogenetic Stability of Human Dermal Fibroblasts Using Alkaline Comet Assay Technique

In the present study, the influence of phenanthrene and pyrene on cytogenetic stability of human dermal fibroblasts using alkaline comet assay was evaluated. The cells were isolated from foreskin samples obtained from healthy male infants and in low passages (P 1–3) were exposed to various concentrations (0.0900, 0.0625, 0.0320, and 0.0066 ppm) of phenanthrene and pyrene. Then, alkaline comet assay was performed to investigate the influence of these compounds on DNA damage and cytogenetic stability of human dermal fibroblasts. In the present work H2O2 treatment was used as a positive control of comet assay to create DNA damages. The analysis of alkaline comet assay parameters by CaspLab software showed the tail DNA% in high concentration (0.0900 ppm) of phenanthrene and pyrene in the exposed cells got increased as compared to normal cells, while head DNA% decreased. Also, similar to positive control (H2O2), DNA damage with long tail comet was observed in high concentration of these compounds as compared to normal cells. The comparison of comet assay parameters specially head DNA% and tail DNA% between each concentrations of phenanthrene and pyrene with other groups (healthy cells and H2O2 treatment) by ANOVA and post hoc Tukey test showed that these parameters were more significantly different (p < 0.05). These results indicated that phenanthrene and pyrene even in low dosage are dangerous and can increase the DNA damage and affect on cytogenetic stability of dermal fibroblasts. These findings suggested that phenanthrene and pyrene could increase the related diseases and risk of skin cancer in exposed individuals

Cytogentic analysis of human dermal fibroblasts (HDFs) in early and late passages using both karyotyping and comet assay techniques

Human dermal fibroblasts (HDFs) are a potential source of somatic cells for genetic manipulation and tissue engineering. Confirmation of cytogenetic stability of these cells is an essential step for cell nuclear transfer and generation of a suitable and functional induced pluripotent stem cells line. HDF cells were isolated and cultured from human foreskin samples. Cytogenetic stability of these cells was evaluated in early (3-4) and late (10-15) passages using karyotype test and alkaline comet assay techniques. HDF cells in early and late passages showed normal karyotype but by comet assay abnormality and DNA damages in late passages of HDFs were observed. Also, the parameters of alkaline comet assay in early passages of HDFs compared with late passages and positive control groups more significantly were different (p < 0.05). These findings indicate that single-strand breaks or DNA damage after many passages may have occurred in HDF cells. Our results demonstrate that only early passages of HDF cells maintain cytogenetic stability and are good candidates for gene reprogramming. In conclusion, karyotype testing alone can not be used for detection of all signs of cytogenetic abnormality and DNA damages of cells. So, for precise evaluation of DNA damage and cytogenetic instability of fibroblast cells comet assay and karyotype techniques could complement each other

Insilco study of the effect of hesperetin on three pre-apoptotic factors Bad, Bak, Bim

Background and Aim Many compounds derived from medicinal plants, such as antioxidants and polyphenols have significant roles in prevention and treatment of various cancers. Activation of apoptosis related pathways is one of the mechanisms for inhibition of cancer progression. In this study, we investigated the effect of molecular dynamics simulation of hesperetin on the pre-apoptotic factors of Bad, Bak, and Bim. Material and Methods In this study we collected data about 3 dimensional structure and Protein Data Bank (PDB) files of three apoptotic factors of Bad, Bak, and Bim from Protein Data Bank (http://www.rscb.org/pdb). Using VMD v1.9.2, AutoDock v.4.2, and Gromacs v.4.5.4 softwares, we started processes such as optimization, simulation, molecular docking and molecular dynamics calculations. Results Binding of Bad molecule to hesperetin led to release of the highest amount of energy and reduced changes in the radius of gyration of Bad protein. But after binding of Bim and Bak proteins to hesperetin, changes in the radius of gyration, increased. The most frequent change in the secondary protein structure was related to increased amount of Bent structure and decreased amount of β-sheet structure in Bim molecule. Conclusion Hesperetin can affect the activities of pre-apoptotic factors of Bad, Bak, and Bim by influencing their molecular dynamics. It seems that hesperetin has the highest effect on the activation of Bad molecule. Also, it can activate Bim protein and induce apoptosis via inducing alternations in the secondary structure of the protein. Keywords: Molecular dynamic , Apoptosis , Hespereti

Effects of lentiviral vectors on DNA damage of human dermal fibroblasts (HDFs)

In present study we evaluated the DNA damages and cytogenetic stability of transducted and non-transducted human dermal fibroblasts (HDFs) by enhanced green fluorescent protein (eGFP) lentiviral vector using karyotyping, comet assay, and molecular techniques. HDFs were isolated from human foreskin samples and eGFP-expressing lentiviral vector were transfected into HEK-293T cells to produce lentiviruses. Then, HDFs at passage 2 were transducted with concentrated eGFP lentivirus and transducted HDFs were detected by fluorescent microscope. The expression levels of cell cycle genes include two subunits of anaphase promoting complex (APC) in transducted and nontransducted HDFs were measured by quantitative real-time PCR and finally, karyotype test and comet assay was performed to evaluate the DNA damages and cytogenetic stability in both groups. The results of karyotype analysis were not showed any abnormalities in karyotype of transducted HDFs by eGFP in compared to normal cells. The mean values of alkaline comet assay parameters on non-transducted (normal cells), eGFP-transducted group and positive control (H2O2 treatment) were calculated by CaspLab software. The comparison of mean difference of comet assay parameters include tail length, comet length, tail moment, and Olive tail moment by T test between eGFP-transducted HDFs and other groups (positive control and non-transducted HDFs) were statistically significant (p≤0.05). The alkaline comet assay on HDFs in eGFP-transducted group was showed small tail and indicated slight genetic damage compared with non-transducted group. Furthermore, the analysis of real-time PCR on expression of APC2 and APC7 genes in non-transducted HDFs compared with eGFP-transducted HDFs were not significant (p≤0.05). These findings indicated that integration of lentiviral vectors in first passage of transducted HDFs could not disturb the DNA structure and create chromosome instability. So in genetic engineering and gene transformation these vectors in first passages are useful

The Effects of Thymoquinone on Viability, and Anti-apoptotic Factors (BCL-XL, BCL-2, MCL-1) in Prostate Cancer (PC3) Cells: An In Vitro and Computer-Simulated Environment Study

Purpose: Since active plant ingredients can induce apoptosis in many tumors, in this study we evaluate the apoptotic effects of thymoquinone (TQ) on PC3 cells. Also, we predicted the interaction of TQ with BCL-XL, BCL-2, and MCL-1anti-apoptotic factors by computer-simulated environment. Methods: PC3 cells were treated with different concentrations of TQ (0- 80 mu M) and IC50 was determined using 3-(4, 5-dimethylthiaztol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay. Apoptotic and cytotoxicity effects of TQ were analyzed using flowcytometry and comet assay, respectively. Changes in energy and the molecular interactions of TQ with BCL-XL, BCL-2 and MCL-1 anti-apoptotic factors were investigated using simulation. Results: IC50 value was 40 mu M. TQ led to the destruction of the genome of PC3 cells and inducing apoptosis. Molecular dynamics (MD) revealed that the root mean-square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), and the number of hydrogen and hydrophobic bonds between TQ and residues of BCL-2, BCL-XL and MCL-lwere significantly (P<0.001) changed. TQ makes a more stable and stronger connection with BCL-XL compared to BCL-2 and MCL-1 and inhibits BCL-XL non-competitively. Conclusion: Our results demonstrated that TQ not only led to apoptosis, at least partly, due to reduction in the Coil, Turn, and Bend structure of BCL-XL but also caused a decrease in the Rg and RMSD value of BCL-XL, MCL-1, and BCL-2. Keywords Author Keywords:Thymoquinone; Apoptosis; Cancer; Simulation KeyWords Plus:PATHWAYS; DOCKING; GLUTATHIONE; ACTIVATION; PROTEINS; INVASION; GROWT

A study of cytogenetic stability of induced pluripotent stem cells using karyotyping and comet assay techniques

Background & Aims: Induced pluripotent stem cells (iPSCs) have the capability to undergo unlimited selfrenewal and differentiation into all cell types in the body. These cells are artificially derived from a nonpluripotent cell, typically human dermal fibroblasts (HDFs). The study of cytogenetic stability of these cells, in order to use iPS cells and apply studies in therapeutic applications, is essential. Methods: In the present experimental study, HDFs were isolated and cultured from human foreskin samples. The cytogenetic stability of these cells was evaluated in early passages (1-3) of HDFs using karyotype test and alkaline comet assay technique. The HDF cells treatment with hydrogen peroxide (H2O2) was used as a positive control for alkaline comet assay. The iPS cells with low passage (4-7) derived from reprogrammed HDFs were cultured on mouse embryonic fibroblast (MEF) feeder layer and cytogenetic stability of these cells were evaluated in early passages using karyotype test and alkaline comet assay technique. Results: The iPS cells in early passages (4-7) had normal karyotype (46, XY) and DNA damage and comet were not observed in these cells. In addition, HDF cells showed normal karyotype in early passages (1-3), but using comet assay, abnormality and DNA damages were observed in positive control (HDFs treated with H2O2). The comparison of alkaline comet assay parameters of iPS and HDF cells with positive control group showed statistically significant differences (P < 0.05). Conclusion: Since the comet assay is a sensitive technique for finding DNA damage, it is best if cytogenetic stability of these cells were evaluated before performing functional experiments on iPS cells. Therefore, for the precise evaluation of DNA damage and cytogenetic stability of iPS cells, the two techniques could complement each other. © 2015, Kerman University of Medical Sciences. All rights reserved

The study of drug resistance properties of ABCG2 (ATP-binding cassette G2) in contact with thymoquinone, gallic acid, and hesperetin antioxidants

Introduction: ATP-binding cassette (ABC) transporters are a group of intra membrane proteins that play key roles in the transmission and exchange of vital compounds on both sides of the membrane. These proteins can specially transport anti-cancer drugs out of cancer cells. ABCG2 is a member of this family that is extremely expressed in many cancers. This study, aims to evaluate the binding affinity of three antioxidants thymoquinone (TQ), gallic acid (GA), and hesperetin (HP) to ABCG2 compared with an anti-cancer drug, mitoxantrone (Mit), to export cells. Methods: The PDB file of ABCG2 was obtained from the protein data bank server (http://www.rcsb.org) with ID: 5NJ3. After 200 stages of molecular docking running on ABCG2 protein in AutoDock v.4.2 software, the amino acids involved in the binding site of each compound were identified using the LigPlot+ software. Results: HP had the lowest (-6.36 kcal/mol) and GA had the highest (-3.93 kcal/mol) binding energy in comparison with Mit (-0.06 kcal/mol) for binding to ABCG2. Effective concentration required to perform the reaction between ABCG2 was higher in GA (1.31 mM) than TQ (42.69 μM) and HP (21.74 μM). GA, HP, and TQ formed 17, 18, and 22 hydrogen and hydrophobic bonds at the binding site of ABCG2. Conclusion: It seems that GA has the lowest affinity to make contact with ABCG2 binding site. So, GA tends to remain in the cell but TQ and HP tend to leave the cell easily via ABCG2 transporter