The Cytotoxic Effect of Thymoquinone Enhance on HepG2 Cell Line due to Induction of Fenton Reaction by Hydrogen Peroxide: An In Vitro and In Silico Study

OBJECTIVE

Thymoquinone (TQ) is a component derived from the volatile oil of Nigella sativa. Fenton reaction induction is a well-known strategy to prevent the growth of cancer cells which can stimulate by hydrogen peroxide. This study was designed to investigate the TQ effects on hydrogen peroxide-induced cytotoxicity.

METHODS

In this study, HepG2 cell survival, reactive oxygen species (ROS) production, cell membrane integrity, and changes of superoxide dismutase (SOD)/ catalase (CAT) activity were evaluated following incubation of HepG2 cells with 31 μM hydrogen peroxide and different concentrations of TQ (18.5, 37 and 75 μM). In addition, molecular docking studies on the interference of TQ with CAT/SOD enzymes were investigated.

RESULTS

Our findings showed that TQ low concentration can increase the survival of HepG2 cells when exposed to hydrogen peroxide, and on the contrary, its high concentration can potentiate cytotoxicity induced by hydrogen peroxide. The TQ alongside hydrogen peroxide increased the production of ROS, which was related to increase CAT and SOD activity in the HepG2 cells. Molecular docking findings showed that TQ effects on the formation of free radicals were not related to its chemical interference with the structure of the SOD/CAT molecules.

CONCLUSION

Fenton reaction induction may increase the effectiveness of TQ in preventing HepG2 cells proliferation.

New molecular insights into the A218V variant impact on the steroidogenic acute regulatory protein (STAR) associated with 46, XY disorders of sexual development

Disorders of sexual development (DSD) are an abnormal congenital conditions associated with atypical development of the urogenital tract and external genital structures. The steroidogenic acute regulatory (STAR) gene, associated with congenital lipoid adrenal hyperplasia (CLAH), is included in the targeted gene panel for the DSD diagnosis. Therefore, the genetic alterations of the STAR gene and their molecular effect were examined in the CLAH patients affected with DSD. Ten different Iranian families including twelve male pseudo-hermaphroditism patients with CLAH phenotype were studied using genetic linkage screening and STAR gene sequencing in the linked families to the STAR locus. Furthermore, the structural, dynamical, and functional impacts of the variants on the STAR in silico were analyzed. Sanger sequencing showed the pathogenic variant p.A218V in STAR gene, as the first report in Iranian population. Moreover, modeling and simulation analysis were performed using tools such as radius of gyration, root mean square deviation (RMSD), root mean square fluctuation (RMSF), and molecular docking showed that p.A218V variant affects the residues interaction in cholesterol-binding site and the proper folding of STAR through increasing H-bound and the amount of α-Helix, deceasing total flexibility and changing fluctuations in some residues, resulting in reduced steroidogenic activity of the STAR protein. The study characterized the structural and functional changes of STAR caused by pathogenic variant p.A218V. It leads to limited cholesterol-binding activity of STAR, ultimately leading to the CLAH disease. Molecular dynamics simulation of STAR variants could help explain different clinical manifestations of CLAH disease.

Ameliorative effects of bilirubin on cell culture model of non-alcoholic fatty liver disease

BACKGROUND

Non-alcoholic fatty liver disease (NAFLD) is defined as the most prevalent hepatic disorder that affects a significant population worldwide. There are several genes/proteins, involving in the modulation of NAFLD pathogenesis; sirtuin1 (SIRT1), TP53-inducible regulator gene (TIGAR), and autophagy-related gene 5 (Atg5) are considered a chief group of these modulators that principally act by regulating the hepatic lipid metabolism, as well as preventing the lipid accumulation. Surprisingly, bilirubin, especially in its unconjugated form, might be able to alleviate NAFLD progression by decreasing lipid accumulation and regulating the expression levels of the above-stated genes.

METHODS AND RESULTS

Herein, the interactions between bilirubin and the corresponding genes' products were first analyzed by docking assessments. Afterwards, HepG2 cells were cultured under the optimum conditions, and then were incubated with high concentrations of glucose to induce NAFLD. After treating normal and fatty liver cells with particular bilirubin concentrations for 24- and 48-hour periods, 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl-tetrazolium bromide (MTT) assay, colorimetric method, and quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) were employed to assess cell viability status, intracellular triglycerides content, and mRNA expression levels of the genes, respectively. Intracellular lipid accumulation of HepG2 cells was significantly decreased after treating with bilirubin. Bilirubin also increased SIRT1 and Atg5 gene expression levels in fatty liver cells. TIGAR gene expression levels were variable upon the conditions and the cell type, suggesting a dual role for TIGAR during the NAFLD pathogenesis.

CONCLUSION

Our findings indicate the potential of bilirubin in the prevention from or amelioration of NAFLD through influencing SIRT1-related deacetylation and the process of lipophagy, as well as decreasing the intrahepatic lipid content. In vitro model of NAFLD was treated with unconjugated bilirubin under the optimal conditions.Desirably, bilirubin moderated the accumulation of triglycerides within the cells possibly through modulation of the expression of SIRT1, Atg5, and TIGAR genes. In the context, bilirubin was shown to increase the expression levels of SIRT1 and Atg5, while the expression of TIGAR was demonstrated to be either increased or decreased, depending on the treatment conditions. Created with BioRender.com.

The effect of metformin on Bad, Bak, and Bim pro-apoptotic factors: A molecular dynamic simulation study

Background:

Recent investigations have demonstrated that metformin treatment can decrease tumor incidence and growth using cell cycle arrest and induction of apoptosis pathway. However, it is not clear how metformin affects the factors involved in the apoptotic process.

Objective:

The present study aimed to determine the effect of metformin on Bak, Bad, and Bim pro-apoptotic proteins using docking and dynamics simulation studies.

Method:

The 3D structure of molecules was retrieved from PubChem and RCSB servers. Simulation and docking studies were conducted by Gromacs and AutoDock software. Next, molecular dynamics analysis was performed using Gromacs software. Moreover, LigPlot+V.4.5.3 software was applied for the determination of the hydrogen and hydrophobic interactions at the binding sites.

Result:

Our findings demonstrated that metformin has the highest affinity for binding the Bak protein. This binding occurred using four amino acid residues within the binding site of Bak with the minimum binding energy (-5.70 kcal/mol). The molecular docking of metformin to these pro-apoptotic factors significantly decreased the total energy and increased the coil secondary structure of Bak protein.

Conclusion:

According to our findings, metformin can alter the molecular dynamics property of these proteins which results in increased activity of these pro-apoptotic proteins and induction of apoptosis.

Apoptotic Effects of Bilirubin on Skin Cancer Cell Lines SK-MEL-3 (Melanoma) and A431 (Non-Melanoma)

BACKGROUND

Bilirubin has long been exclusively considered as a potentially dangerous sign of liver diseases, but it is currently regarded as a reliable signaling molecule as well.

OBJECTIVE

This study investigated the effects of unconjugated bilirubin on survival, proliferation, apoptotic and cell arrest capacities of melanoma SKMEL-3 and non-melanoma A431 skin cancer cells in comparison with normal Human Dermal Fibroblast (HDF) cells.

METHODS

The MTT assay test was used to identify survival and the IC₅₀ at various concentrations of bilirubin on SKMEL-3, A431, and HDF cells for 24h and 48h. The comet assay technique was used to investigate genotoxicity effects, and flow cytometry was run to investigate apoptotic and cell arresting effects of bilirubin on the cells. The gene expression of cyclin D1, cyclin E1, survivin, Bcl-2, and p53 was investigated by qRT-PCR. The molecular docking of bilirubin on CDKs (Cyclin-Dependent Kinases 2, 4, and 6) and pro-apoptotic factors Bad, Bak, Bax, Bid, Bik, and Bim was performed by Autodock software version 2.

RESULTS

The IC₅₀ of bilirubin on HDF, A431, and SKMEL-3 cells was 125, 115, and 95 μM at 24h and 115, 100, and 75 μM at 48h, respectively. Although cell arrest in the G1 phase occurred in all cells, bilirubin induced genotoxicity and apoptosis in SKMEL-3 and A431 cancer cells more pronouncedly than those in normal HDF cells.

CONCLUSION

Bilirubin led to cell arrest in the G₁ phase in SKMEL-3, A431, and HDF cells. Additionally, bilirubin induced apoptotic pathways in SKMEL-3 and A431 cancer cells.

Autophagy and Ubiquitination as Two Major Players in Colorectal Cancer: A Review on Recent Patents

BACKGROUND

As one of the most commonly diagnosed cancers among men and women, Colorectal Cancer (CRC) leads to high rates of morbidity and mortality across the globe. Recent anti- CRC therapies are now targeting specific signaling pathways involved in colorectal carcinogenesis. Ubiquitin Proteasome System (UPS) and autophagy are two main protein quality control systems, which play major roles in the carcinogenesis of colorectal cancer. A balanced function of these two pathways is necessary for the regulation of cell proliferation and cell death.

OBJECTIVE

In this systematic review, we discuss the available evidence regarding the roles of autophagy and ubiquitination in progression and inhibition of CRC.

METHODS

The search terms "colorectal cancer" or "colon cancer" or "colorectal carcinoma" or "colon carcinoma" in combination with "ubiquitin proteasome" and "autophagy" were searched in PubMed, Web of Science, and Scopus databases, and also Google Patents (https://patents.google .com) from January 2000 to Feb 2020.

RESULTS

The most important factors involved in UPS and autophagy have been investigated. There are many important factors involved in UPS and autophagy but this systematic review shows the studies that have mostly focused on the role of ATG, 20s proteasome and mTOR in CRC, and the more important factors such as ATG8, FIP200, and TIGAR factors that are effective in the regulation of autophagy in CRC cells have not been yet investigated.

CONCLUSION

The most important factors involved in UPS and autophagy such as ATG, 20s proteasome and mTOR, ATG8, FIP200, and TIGAR can be considered in drug therapy for controlling or activating autophagy.

Inhibitory Effects of Bilirubin on Colonization and Migration of A431 and SK-MEL-3 Skin Cancer Cells Compared with Human Dermal Fibroblasts (HDF)

This study evaluated the inhibitory effects of bilirubin on colony formation and cell migration of melanoma and non-melanoma skin cancer cell lines SK-MEL-3 and A431, compared with normal human dermal fibroblasts (HDF). The IC₅₀ obtained from the MTT assay was 125, 100, and 75 μM bilirubin for HDF, A431, and SK-MEL-3 cells, respectively. The colony formation and cell migration of cancer cells, treated with 100 μM bilirubin, were reduced significantly (p < 0.05). Bilirubin decreased cell adhesion and inhibited cell colonization via inducing apoptosis and cell death. Also by interaction with migration main factors, bilirubin caused inhibition the cell migration.

Medicinal plant compounds as promising inhibitors of coronavirus (COVID-19) main protease: an in silico study

The novel Coronavirus (COVID-19) has spread rapidly across the globe and has involved more than 215 countries and territories. Due to a lack of effective therapy or vaccine, urgent and concerted efforts are needed to identify therapeutic targets and medications. COVID-19 main protease represents a major target for drug treatment to inhibit viral function. The present study sought to evaluate medicinal plant compounds as potential inhibitors of the COVID-19 main protease using molecular docking and molecular dynamic analysis. The PDB files of COVID-19 main protease and some medicinal plant compounds were retrieved from the Protein Data Bank (http://www.rcsb.org) and Pubchem server, respectively. The Gromacs software was used for simulation studies, and molecular docking analysis was done using Autodock 4.2. The COVID-19 main protease simulation, compared with some phytochemicals docked to the COVID-19 main protease, were analyzed. Glabridin, catechin, and fisetin had the greatest tendency to interact with the COVID-19 main protease by hydrogen and hydrophobic interactions. Docking of these phytochemicals to COVID-19 main protease led to an increase in the radius of gyration (Rg), decrease in the Root mean square fluctuation (RMSF), and induced variation in COVID-19 main protease secondary structure. The high tendency interaction of glabridin, catechin, and fisetin to COVID-19 main protease induced conformational changes on this enzyme. These interactions can lead to enzyme inhibition. This simulated study indicates that these phytochemicals may be considered as potent inhibitors of the viral protease; however, more investigations are required to explore their potential medicinal use.Communicated by Ramaswamy H. Sarma.

In vivo/in silico insight into the effect of titanium dioxide nanoparticle on serum paraoxonase 1 activity in rat

Serum paraoxonase1 (PON1) has special function in human body organism including the antioxidant and anti-atherogenic properties. In the present study, the effect of TiO₂ nanoparticles on the activity and structure of the PON1 has been evaluated through in vivo and in silico methods. After treatments of the rats with different doses of TiO₂ NPs, blood samples were collected and serum PON1 activity was measured by phenylacetate and paraoxon as substrate. In addition, the effects of TiO₂ NP on enzyme structure were analyzed through Molecular dynamic (MD) simulation via Gromacs software package to obtain RMSD, RMSF, Rg, SASA, and secondary structures values. A significant reduction (p < 0.05) in arylesterase & paraoxonase activities of serum PON1 were monitored in Spectrometric assays when rats were treated with 150 and 200 mg/kg doses of TiO₂ NPs. RMSD, RG, RMSF, and SASA values in the presence of TiO₂ have been increased while RMSF values of the L1 and L2 loops (gate of the catalytic site) have been reduced. Moreover, Hydrogen bonds and secondary structure values of the enzyme decreased in the presence of TiO₂ NP. All of these MD simulation results could indicate the instability of the PON1 structure bounded to TiO₂ NP. TiO₂ NP could cause a disturbance in the enzyme structure and function of PON1 based on the results. PON1 prevents oxidation of LDL and can delay atherosclerosis progression while in the presence of TiO₂ NP these protective effects could be endangered.Communicated by Ramaswamy H. Sarma.

Effect of cinnamon supplementation on blood pressure and anthropometric parameters in patients with type 2 diabetes: A systematic review and meta-analysis of clinical trials

BACKGROUND AND AIMS

The present systematic review and meta-analysis was conducted to investigate the effect of cinnamon supplementation on blood pressure and anthropometric indices in patients with type 2 diabetes.

METHODS

PubMed, Embase, Scopus, Web of Science and Cochrane Library were systematically searched to find relevant records up to 22 August 2019. Standard mean difference (SMD) and 95% confidence interval (CI) were used to evaluate the effect of cinnamon supplementation on the outcomes of this study. In the case of heterogeneity, fixed and random effect models were used. The obtained data were analyzed by Stata 13. After excluding irrelevant records, 9 eligible articles were included.

RESULTS

This meta-analysis found a significant reduction in systolic blood pressure (SBP) (SMD: -0.532, 95% CI: [-1.032, -0.033], P = 0.037) and diastolic blood pressure (DBP) (SMD: -0.681, 95% CI: [-1.297, -0.065], P = 0.030) of patients with type 2 diabetes following cinnamon supplementation. Based on the results of the present study, cinnamon supplementation had no significant effect on the body weight (BW) (SMD: -0.309, 95% CI: [-0.793, 0.175], P = 0.211), body mass index (BMI) (SMD: -0.550, 95% CI: [-1.244, 0.144], P = 0.120). and waist circumference (WC) (SMD: -0.235, 95% CI: [-0.518, 0.047], P = 0.103).

CONCLUSIONS

Cinnamon supplementation significantly decreased SBP and DBP of patients with type 2 diabetes. Although cinnamon intake caused changes in anthropometric parameters, the observed changes were not statistically significant.

Biodecomposition of Phenanthrene and Pyrene by a Genetically Engineered Escherichia coli

BACKGROUND

Genetically engineered microorganisms (GEMs) can be used for bioremediation of the biological pollutants into nonhazardous or less-hazardous substances, at lower cost. Polycyclic aromatic hydrocarbons (PAHs) are one of these contaminants that associated with a risk of human cancer development. Genetically engineered E. coli that encoded catechol 2,3- dioxygenase (C230) was created and investigated its ability to biodecomposition of phenanthrene and pyrene in spiked soil using high-performance liquid chromatography (HPLC) measurement. We revised patents documents relating to the use of GEMs for bioremediation. This approach have already been done in others studies although using other genes codifying for same catechol degradation approach.

OBJECTIVE

In this study, we investigated biodecomposition of phenanthrene and pyrene by a genetically engineered Escherichia coli.

METHODS

Briefly, following the cloning of C230 gene (nahH) into pUC18 vector and transformation into E. coli Top10F, the complementary tests, including catalase, oxidase and PCR were used as on isolated bacteria from spiked soil.

RESULTS

The results of HPLC measurement showed that in spiked soil containing engineered E. coli, biodegradation of phenanthrene and pyrene comparing to autoclaved soil that inoculated by wild type of E. coli and normal soil group with natural microbial flora, were statistically significant (p<0.05). Moreover, catalase test was positive while the oxidase tests were negative.

CONCLUSION

These findings indicated that genetically manipulated E. coli can provide an effective clean-up process on PAH compounds and it is useful for bioremediation of environmental pollution with petrochemical products.

Molecular Dynamics Mechanisms of the Inhibitory Effects of Abemaciclib, Hymenialdisine, and Indirubin on CDK-6

BACKGROUND

Cyclin-Dependent Kinases-6 (CDK-6) is a serine/threonine protein kinase with regular activity in the cell cycle. Some inhibitors, such as abemaciclib, hymenialdisine, and indirubin, cause cell arrest by decreasing its activity.

OBJECTIVES

The purpose of this study was to evaluate the Molecular Dynamic (MD) effects of abemaciclib, hymenialdisine, and indirubin on the structure of CDK-6.

METHODS

The PDB file of CDK-6 was obtained from the Protein Data Bank (http://www.rcsb.org). After the simulation of CDK-6 in the Gromacs software, 200 stages of molecular docking were run on CDK-6 in the presence of the inhibitors using AutoDock 4.2. The simulation of CDK-6 in the presence of inhibitors was performed after docking.

RESULTS

Abemaciclib showed the greatest tendency to bind CDK-6 via binding 16 residues in the binding site with hydrogen bonds and hydrophobic bonding. CDK-6 docked to hymenialdisine and indirubin increased the Total Energy (TE) and decreased the radius of gyration (Rg). CDK-6 docked to hymenialdisine significantly decreased the coil secondary structure.

CONCLUSION

CDK-6 is inhibited via high binding affinity to abemaciclib, hymenialdisine, and indirubin inhibitors and induces variation in the secondary structure and Rg in the CDK-6 docked to the three inhibitors. It seems that developing a drug with a binding tendency to CDK6 that is similar to those of abemaciclib, indirubin, and hymenialdisine can change the secondary structure of CDK6, possibly more potently, and can be used to develop anticancer drugs. However, additional studies are needed to confirm this argument.

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.

Evaluating the effects of ellagic acid on pSTAT3, pAKT, and pERK1/2 signaling pathways in prostate cancer PC3 cells

OBJECTIVE

One of the most common malignancies among men is prostate cancer. Ellagic acid (EA), a polyphenol antioxidant, has many pharmacological actions, especially anticancer effects. The purpose of this study was to evaluate the effect of EA treatment on interleukin-6 (IL-6) gene expression, cell viability, IL-6 secretion, phosphorylated STAT3, ERK, and AKT cellular signaling proteins in human prostate cancer cells (PC3).

MATERIALS AND METHODS

The cytotoxic effects of the EA (0-100 µM) on PC3 cells were determined by 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide assay. IL-6 gene expression was down, using real-time quantitative polymerase chain reaction. The cellular concentration of phosphorylated ERK1/2, AKT, and STAT3 signaling pathways was assessed by Western blotting technic.

RESULTS

EA treatment of PC3 cells resulted in a reduction of cell viability and phosphorylated STAT3, ERK, and AKT signaling proteins after 72 h in a dose-dependent manner. IL-6 gene expression and IL-6 levels significantly increased (P < 0.05) in a dose-dependent pattern in treated PC3 with EA. Thus, these data suggested the essential role of signaling proteins in EA-mediated anti-proliferation of PC3 cells.

CONCLUSIONS

Our finding shows that EA can be considered as a potent agent that decreases cell proliferation through a reduction of phosphorylated STAT3, ERK, and AKT cellular signaling proteins.

Comparison between the cultures of human induced pluripotent stem cells (hiPSCs) on feeder-and serum-free system (Matrigel matrix), MEF and HDF feeder cell lines

Human induced pluripotent stem cells (hiPSCs) are a type of pluripotent stem cells artificially derived from an adult somatic cell (typically human fibroblast) by forced expression of specific genes. In recent years, different feeders like inactivated mouse embryonic fibroblasts (MEFs), human dermal fibroblasts (HDFs), and feeder free system have commonly been used for supporting the culture of stem cells in undifferentiated state. In the present work, the culture of hiPSCs and their characterizations on BD Matrigel (feeder-and serum-free system), MEF and HDF feeders using cell culture methods and molecular techniques were evaluated and compared. The isolated HDFs from foreskin samples were reprogrammed to hiPSCs using gene delivery system. Then, the pluripotency ability of hiPSCs cultured on each layer was determined by teratoma formation and immunohistochemical staining. After EBs generation the expression level of three germ layers genes were evaluated by Q-real-time PCR. Also, the cytogenetic stability of hiPSCs cultured on each condition was analyzed by karyotyping and comet assay. Then, the presence of pluripotency antigens were confirmed by Immunocytochemistry (ICC) test and alkaline phosphatase staining. This study were showed culturing of hiPSCs on BD Matrigel, MEF and HDF feeders had normal morphology and could maintain in undifferentiated state for prolonged expansion. The hiPSCs cultured in each system had normal karyotype without any chromosomal abnormalities and the DNA lesions were not observed by comet assay. Moreover, up-regulation in three germ layers genes in cultured hiPSCs on each layer (same to ESCs) compare to normal HDFs were observed (p < 0.05). The findings of the present work were showed in stem cells culturing especially hiPSCs both MEF and HDF feeders as well as feeder free system like Matrigel are proper despite benefits and disadvantages. Although, MEFs is suitable for supporting of stem cell culturing but it can animal pathogens transferring and inducing immune response. Furthermore, HDFs have homologous source with hiPSCs and can be used as feeder instead of MEF but in therapeutic approaches the cells contamination is a problem. So, this study were suggested feeder free culturing of hiPSCs on Matrigel in supplemented media (without using MEF conditioned medium) resolves these problems and could prepare easy applications of hiPSCs in therapeutic approaches of regenerative medicine such as stem-cell therapy and somatic cell nuclear in further researches.