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 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

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

Damage intensity of carvacrol on prostatic cancer cells lineDu145 and molecular dynamic simulation of it effect on apoptotic factors

Prostatic cancer is one of the most dangerous diseases in men worldwide. The apoptotic factors such as BID, BIM and APAF1 have a main role in inducing apoptotic pathways. On the other hand, some compounds can active this apoptotic factors. In this study, this notion was investigated by the use of the comet assay technique and molecular dynamics simulations. In the comet assay technique, different concentrations including 130, 230, and 360 μM of Carvacrol were selected according to IC50 using MTT assay on the cell line DU145. Then, alkaline electrophoresis was performed and 100 comet pictures were analyzed using CASP software. Data were analyzed by SPSS statistical software and also using molecular dynamics simulations, wherein protein and Carvacrol were studied, thus avoiding the necessity for quantum mechanical calculations. Molecular dynamics simulations were carried out using with Carvacrol closed in a fully hydrated simulation box with a protein (Bak, Bax, Bim, Apaf1, Bid and P38). The IC50 for Carvacrol was determined at 360μM by MTT test. Rate of tail to head in alkaline electrophoresis at 130, 230, and 360 μM of Carvacrol concentrations were 13. 8±0. 3, 40. 6±0. 3, and 47. 6±0. 5 percent, respectively. Statistical analysis of the molecular dynamics and calculated potential energy, radius of gyration (Rg), temperature, root mean square fluctuation (RMSF) and root mean square deviation (RMSD) indicated that Carvacrol affected protein which stimulated the apoptosis cascade. Therefore, both experimental and theoretical results demonstrate carvacrol directly affects factors initiating apoptosis. © 2016, Sphinx Knowledge House. All rights reserved

Molecular dynamics simulation study of the effect of hesperetin on pre-apoptotic factors of bad, bak, and 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

Expression levels of mRNA cytokines of IL-17 and IL-23 in epithelialfiber of stomach inpatients with Helicobacter pylori using Real-Time PCR in Chahar Mahal and Bakhtiari province

زمینه و هدف: اینترلوکین های 17 و 23 در دفاع بر علیه برخی عفونت‌های مخاطی دستگاه گوارش نقش دارند و IL-17 باعث جذب نوتروفیل ها به محل عفونت شده و در ایجاد التهاب نقش دارد. مطالعه حاضر میزان بیان mRNA سیتوکاین های IL-17و IL-23در دو گروه بیماران گاستریتی با عفونت هلیکوباکترپیلوری و فاقد عفونت را به وسیله روش کمی Real-Time PCR بررسی می‌کند. روش بررسی: در این مطالعه مورد- شاهدی، از 58 بیمار دارای گاستریت با عفونت هلیکوباکترپیلوری و 50 بیمار مبتلا به گاستریت که فاقد عفونت بودند، توسط آندوسکوپی بیوپسی تهیه شد. بعد از استخراجmRNA و تبدیل آن به cDNA، میزان بیانmRNA مربوط به IL-17و IL-23در نمونه‌ها توسط Real-Time PCR اندازه گیری شد و بیان سایتوکاین ها در دو گروه آلوده و غیر آلوده با استفاده از تست Mann–Whitney مورد آنالیز قرار گرفت. یافته‌ها: ارتباط معنی‌داری بین میزان بیانIL-17 mRNA در افراد دارای گاستریت با عفونت هلیکوباکترپیلوری و افراد دارای گاستریت فاقد عفونت دیده نشد (941/0P=). همچنین ارتباط بین میزان بیان mRNA IL-23در بیماران دارای گاستریت با عفونت هلیکوباکترپیلوری و بیماران دارای گاستریت فاقد عفونت معنی دار نبود (076/0 P=). نتیجه‌گیری: نتایج این مطالعه نشان داد که میزان بیان mRNA سیتوکاین های IL-17و IL-23در بیماران دارای گاستریت با عفونت هلیکوباکترپیلوری در مقایسه با بیماران گاستریتی بدون عفونت بالاتر نمی‌باشد و در نتیجه ارتباط معنی داری بین دو گروه مورد مطالعه در این استان وجود ندارد؛ لذا می طلبد تا نقش دقیق سایتوکاین ‌های دیگر درگیر در بروز بیماری گاستریت جهت تعیین پیش آگهی و ارزیابی برنامه های درمانی بیشتر مشخص شود

Exact solution for frequency equations of radial and transverse vibration of a circular plate with various boundary conditions

In this study, closed-form relations are obtained for the frequency equations of radial (in-plane) and transverse (out-ofâplane) free vibration of a circular plate with free, simply-support, and clamped boundary conditions. Governing equations are obtained using Hamilton's principal. In the case of radial vibration, governing equations are coupled to each other. So, they are decoupled using Helmholtz decomposition technique and solved using separation of variables method. In the case of transverse vibration, governing equations are analytically solved using separation of variables method. Finally, natural frequencies obtained from the frequency equations are compared with finite element results for an isotropic homogeneous circular plate with various boundary conditions

Mutation analysis of VSX1 and SOD1 in Iranian patients with keratoconus

Purpose: To evaluate mutations in the visual system homeobox gene 1 (VSX1) and superoxide dismutase 1 (SOD1) genes with keratoconus (KTCN), direct sequencing was performed in an Iranian population. Methods: One hundred and twelve autosomal dominant KTCN patients and fifty-two unaffected individuals from twentysix Iranian families, as well as one hundred healthy people as controls were enrolled. Genomic DNA was extracted from whole blood sample. Then to study the possible linkage between KTCN and six known loci linkage analysis was performed using 12 short tandem repeat (STR) markers. Also, the entire coding region and intron-exon boundaries of VSX1 and SOD1 were amplified by the PCR technique in each proband. Subsequently, PCR products were subjected to direct sequencing. Co-segregation analysis of the identified mutation was conducted in the family members. An Amplification Refractory Mutation System PCR (ARMS-PCR) was additionally employed for detection of the identified mutation in healthy controls. Results: Linkage analysis of aforementioned loci did not detect evidence for linkage to KTCN. Direct PCR sequencing revealed two single nucleotide polymorphisms (SNPs; g.1502T>G and g.9683C>T), as well as two missense mutations that have been previously reported (R166W and H244R) in VSX1. We also found three undescribed SNPs (g.4886G>A, g.4990C>G, and g.9061T>A) in SOD1. The R166W and H244R mutations were co-segregated in affected family members but not in those that were unaffected. Moreover, the ARMS-PCR strategy did not detect the identified mutations in controls. Conclusions: Our data suggest a significant association between KTCN patients and VSX1 genetic alterations (p.R166W and p.H244R). Although our findings support VSX1 as a plausible candidate gene responsible for keratoconus, other chromosomal loci and genes could be involved in KTCN development. Taken together, our results suggest that p.R166W and p.H244R could have possible pathogenic influences on KTCN