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The uremic toxin indoxyl sulfate (IS) has been related to the development of various medical conditions notably chronic kidney disease (CKD). Hence, quantification of this biomarker in biological fluids may be a diagnostic tool to evaluate renal system functionality. Numerous analytical methods including liquid chromatography, gas chromatography, spectroscopy, and electrochemical techniques have since been used to analyze IS in different biological fluids. The current review highlights the relevant studies that assessed IS with a special focus on sample preparation, which is essential to reduce or eliminate the effect of endogenous components from the matrix in bioanalysis.

Abstract A rapid and efficient analytical method was established to quantify indoxyl sulfate (IS) in plasma through extraction technique with a deep eutectic solvent (DES) and spectrofluorimetric method. DES (choline chloride: urea) was mixed with plasma samples for the extraction of IS, followed by the addition of dipotassium hydrogen phosphate (K2HPO4) solution to form an aqueous two-phase system. The fluorescence intensity of IS which was first extracted to the DES-rich-phase and then back-extracted into the salt-rich-phase, was measured by spectrofluorimetric method. Some key factors such as pH, centrifugation speed and time, the volume ratio of DES/salt, and salt concentration were optimized. Under the optimized conditions, the suggested method had a dynamic range between 20 and 160 µg/mL with a coefficient of determination (R2) of 0.99. Precision (relative standard deviation) was less than 15% and accuracy (% relative recovery) was ± 15% at the nominal concentration level. In addition, results showed that IS levels in real samples were higher than 40 µg/mL which was compatible with reported IS levels in end-stage renal disease (ESRD) patients. Overall, all the results reflect the fact that the presented analytical method can potentially be used for the determination of IS in real plasma samples.

Abstract Background According to the increasing trend of COPD, the timely diagnosis and treatment of the disease can reduce the high costs to the health systems. Therefore, by biological calculation methods, signaling pathways and genes involved in this disease can be obtained and used to design drugs and other treatment methods. By using biological calculations, we determined that curcumin can affect this disease and its genes and signaling pathways. Our goal in this study was to find the genes by which curcumin exerts its effect and can maintain the function of corticosteroids against oxidizing agents. Results By finding the genes, it is possible to find precisely the pathways by which curcumin works, which can be used to design other drugs that cause these pathways and minimize their side effects. This study considers healthy samples (with/without curcumin) and oxygen-free radicals (with/without curcumin). Finally, statistical algorithms extract meaningful genes as effective biomarkers to investigate curcumin's effects and signaling pathways in COPD. The results show that the genes finally obtained as the most critical genes confirmed by the literature are effective in COPD. Finally, curcumin was input in SwissTargetPrediction to identify potential protein receptors. We used LigPlot+ software to visualize the receptor–ligand binding result provided by iGEMDOCK. Conclusions The data showed that the most significant genes in each group have been confirmed in other studies to be effective in this disease, and protein–protein interaction networks can be established between them to investigate their roles.

Purpose: Exosomes are natural nanoparticles that participate in intercellular communication through molecular transport. Recently, due to their membrane vesicular structure and surface proteins, exosomes have been used extensively in the research field of drug delivery. Osteoporosis is an inflammation in which the cellular balance of bone tissue is disturbed that reduces bone density and making bone prone to abnormal fractures with small amount of force. Utilizing estrogen is one of the main therapeutic strategies for osteoporosis. Despite the positive effects of estrogen on bone tissue, changes in the natural estrogen levels of the body can cause a number of diseases such as different types of cancer. Therefore, designing a therapeutic system which controls more accurate tissue targeting of estrogen seems to be a rational and promising practical approach. Methods: In this study, bone marrow mesenchymal stem cells (BMMSCs)-derived exosomes were loaded by estradiol using two different methods of drug loading, namely incubation and sonication methods and then the survival effects of the drug loaded exosomes on BMMSCs was investigated. Results: Examination of size, shape, and surface factors of exosomes in different states (pure exosomes and drug-loaded exosomes) showed that the round morphology of exosomes was preserved in all conditions. However, the particles size increased significantly when loaded by sonication method. The increased survival of BMMSCs was noted with estradiol-loaded exosomes when compared to the control group. Conclusion: The results suggest that estradiol-loaded exosomes have potential to be used as nano-drug carriers in the treatment of osteoporosis.

Purpose: Medical usage of L-asparaginase (ASNase), the first-line of acute lymphoblastic leukemia treatment, is linked to allergic responses and toxicities, which necessitates the development of new bio-better ASNases. The aim of the current study was in silico design of a novel ASNase with predicted improved enzymatic properties using strategies encompassing sequence-function analysis of known ASNase mutants. Additionally, current study aimed to show that the new enzyme is active. Methods: Based on 21 experimentally reported mutations for ASNase, a virtual library of mutated enzymes with all 7546 possible combinations of up to 4 mutations was generated. Three-dimensional models of proposed mutant enzymes were built and their in silico stabilities were calculated. The most promising mutant was selected for preparing a genetic construct suitable for expression of the designed ASNase in bacterial cells. Results: Computational study predicted that Y176F/S241C double mutation of Escherichia coli ASNase may increase its folding stability. The designed ASNase was expressed in two different E. coli strains (Origami B(DE3) and BL21(DE3)pLysS) and then the soluble fractions prepared from the cell lysates of the host cells were used in enzyme activity assay. Results showed that enzyme activity of soluble fraction from Origami (95.4±7.5 IU/0.1 mL) was four times higher than that of soluble fraction from pLysS (25.8±2.5 IU/0.1 mL). Conclusion: A novel functional double mutant ASNase with predicted improved enzymatic properties was designed and produced in E. coli. The results of the current study suggest a great commercial potential for the identified enzyme in pharmaceutical and industrial applications.

Purpose: Teduglutide is the first and only FDA-approved drug for long-term treatment of short bowel syndrome (SBS). The current study aimed to present an approach for production of teduglutide using recombinant DNA technology. Methods: The coding gene for teduglutide was cloned into pGEX-2T vector, where coding sequence for factor Xa cleavage site was added between GST and teduglutide coding genes. The GST-teduglutide protein was overexpressed in E. coli BL21 (DE3) strain and affinity purified using glutathione sepharose affinity column. Results: On-column proteolytic activity of factor Xa followed by size exclusion chromatography resulted in the pure teduglutide. Circular dichroism (CD) spectropolarimetry showed that the produced teduglutide folds into mainly α-helical structure (>50%), as expected. In mass spectroscopy analysis, the fragments of teduglutide resulted by cyanogen bromide cleavage as well as those expected theoretically due to mass fragmentation were identified. The functionality of the produced peptide was evaluated by measuring its proliferative effect on Caco2 intestinal epithelial cells, and the results indicated that produced teduglutide induces cell proliferation by 19±0.30 and 33±7.82 % at 1.21 and 3.64 µM concentrations, respectively, compared to untreated cells. Conclusion: Teduglutide was successfully expressed and purified and its functionality and structural integrity were confirmed by in vitro experiments. We believe that the experimental-scale method presented in the current study can be useful for pilot-scale and also industrial-scale production of teduglutide.

Introduction: Non-steroidal anti-inflammatory drugs (NSAIDs) constitute an important class of pharmaceuticals acting on cyclooxygenase COX-1 and COX-2 enzymes. Due to their numerous severe side effects, it is necessary to search for new selective, safe, and effective anti-inflammatory drugs. In silico design of novel therapeutics plays an important role in nowadays drug discovery pipelines. In most cases, the design strategies require the use of molecular docking calculations. The docking procedure may require case-specific condition for a successful result. Additionally, many different docking programs are available, which highlights the importance of identifying the most proper docking method and condition for a given problem. Methods: In the current work, the performances of five popular molecular docking programs, namely, GOLD, AutoDock, FlexX, Molegro Virtual Docker (MVD) and Glide to predict the binding mode of co- crystallized inhibitors in the structures of known complexes available for cyclooxygenases were evaluated. Furthermore, the best performers, Glide, AutoDock, GOLD and FlexX, were further evaluated in docking-based virtual screening of libraries consisted of active ligands and decoy molecules for cyclooxygenase enzymes and the obtained docking scores were assessed by receiver operating characteristics (ROC) analysis. Results: The results of docking experiments indicated that Glide program outperformed other docking programs by correctly predicting the binding poses (RMSD less than 2 Å) of all studied co-crystallized ligands of COX-1 and COX-2 enzymes (i.e., the performance was 100%). However, the performances of the other studied docking methods for correctly predicting the binding poses of the ligands were between 59% to 82%. Virtual screening results treated by ROC analysis revealed that all tested methods are useful tools for classification and enrichment of molecules targeting COX enzymes. The obtained AUCs range between 0.61-0.92 with enrichment factors of 8 – 40 folds. Conclusion: The obtained results support the importance of choosing appropriate docking method for predicting ligand-receptor binding modes, and provide specific information about docking calculations on COXs ligands.

Purpose: Drug repurposing is an approach successfully used for discovery of new therapeutic applications for the existing drugs. The current study was aimed to use the combination of in silico methods to identify FDA-approved drugs with possible S1P1 agonistic activity useful in multiple sclerosis (MS). Methods: For this, a 3D-QSAR model for the known 21 S1P1 agonists were generated based on 3D-QSAR approach and used to predict the possible S1P1 agonistic activity of FDA-approved drugs. Then, the selected compounds were screened by docking into S1P1 and S1P3 receptors to select the S1P1 potent and selective compounds. Further evaluation was carried out by molecular dynamics (MD) simulation studies where the S1P1 binding energies of selected compounds were calculated. Results: The analyses resulted in identification of cobicistat, benzonatate and brigatinib as the selective and potent S1P1 agonists with the binding energies of -85.93, -69.77 and -67.44 kcal. mol-1, calculated using MM-GBSA algorithm based on 50 ns MD simulation trajectories. These values are better than that of siponimod (-59.35 kcal mol-1), an FDA approved S1P1 agonist indicated for MS treatment. Furthermore, similarity network analysis revealed that cobicistat and brigatinib are the most structurally favorable compounds to interact with S1P1 . Conclusion: The findings in this study revealed that cobicistat and brigatinib can be evaluated in experimental studies as potential S1P1 agonist candidates useful in the treatment of MS.

Purpose: Today, the discovery of novel and effective chemotherapeutic compounds is the mainchallenge in cancer therapy. In recent years, the anti-tumoral activity of natural naphthoquinonejuglone (JUG), present in different parts of walnut trees, has received considerable interest. Thepurpose of the current study was to prepare and evaluate the in vitro antiproliferative activity ofJUG-loaded bovine serum albumin nanoparticles (JUG-BSA NPs).Methods: BSA NPs and JUG-BSA NPs were prepared using the desolvation technique. The NPswere characterized for their particle size (PS), zeta potential (ZP), drug loading (DL) capacityand encapsulation efficiency (EE). The anti-proliferative activity of JUG-BSA NPs was evaluatedon A431 and HT29 cancer cell lines using cellular uptake and MTT assays.Results: The PS and ZP values of JUG-BSA NPs were 85 ± 6.55 nm and −29.6 mV, respectively.The DL capacity and EE were 3.7% to 5% and 50.4% to 94.6%, respectively. The cytotoxicityof JUG-BSA NPs was significantly less on both cultured A431 and HT29 cells at the studiedconcentrations when compared to free JUG. However, the effect was not very substantial,particularly at high levels.Conclusion: In conclusion, BSA NPs can be used as a suitable and safe carrier for the deliveryof JUG, a cytotoxic hydrophobic natural compound.

Background: Fibroblast growth factors (FGFs) are involved in angiogenesis, wound healing and embryonic development. However, one of the causes of cancer cell growth in fibroblast-dependent cancers is FGF7 secreted by fibroblasts. Therefore, antibodies against FGF7 can be used for the treatment of these types of cancers. Methods: In the previous studies, a phage displaying single domain antibody, D53, against human FGF7 has been identified using the phage display technique. In the present study, D53 was produced and purified in its isolated form. ELISA experiment was performed to evaluate the binding of D53 to FGF7. The mode of interaction of D53-FGF7 was explored using docking study and molecular dynamics (MD) simulations. Results: The expression and purification processes were verified using western blotting and SDS-PAGE analyses. ELISA experiment showed that D53 is able to recognize and bind FGF7. Docking study and MD simulations indicated that compared to dummy VH, D53 has more affinity towards FGF7. Conclusion: The findings in the current study can be useful for the generation and the development of FGF7 inhibitors with a potential use in fibroblast-dependent cancers.

Purpose: This research introduces a polymeric nanosphere as a new dispersive solid phaseextraction (DSPE) adsorbent for the extraction of methylphenidate (MPH) from urine and itshigh performance liquid chromatography (HPLC) analysis.Methods: Polymeric nanosphere is a kind of copolymeric network obtained by copolymerizationof an ionic liquid monomer and styrene in the presence of vinyltriethoxysilane and2-hydroxyethylmethacrylate. HPLC coupled with ultra violet detector was applied for thedetermination and quantification of MPH. Dominant parameters in extraction were modified bythe one-parameter-at-a-time method. The results are as follow: 10 mg of polymeric nanospheres(PNS), 400 μL of acetonitrile (ACT), 5 mL of urine with the pH value of 9, and the extractionand desorption times of 2 and 5 minutes, respectively, which can be selected as the optimumextraction conditions.Results: Calibration curve was plotted through optimized conditions, and the proposed methodwas validated. The results demonstrated that the method presented linearity in the concentrationrange of 30-1200 ng/mL. Selectivity, matrix effect and metabolites interference effect wereinvestigated and the method presented no obvious interference effect during the analysis runtime. Repeatability, limit of detection (LOD) and limit of quantification (LOQ) values of themethod can be reported in this section as well. The method showed satisfactory results with98.8% relative recovery in the analysis of positive urine samples.Conclusion: The findings convinced the applicability of the introduced method for DSPE andHPLC analysis of the positive urine samples in different laboratories.

Background: Physicochemical properties play important role in fundamental issues likeabsorption and distribution of pharmaceuticals to the target tissue. This is particularly importantfor drugs acting in central nervous system (CNS). In this study, physicochemical properties ofpreviously synthesized thiazole-pyridinium derivatives with anti-acetylcholinesterase activityand possible anti-Alzheimer effect were studied. Methods: Partition coefficient (n-octanol/water) and chromatographic Rf values for the studiedcompounds were determined using shake flask and high performance thin layer chromatography(HPTLC) methods, respectively. Different druglikeness properties of the compounds were alsocalculated using available software and web-servers. Results: The experimentally determined logarithm of partition coefficients (log P) for thestudied compounds were in the range of -1.00 to -0.38. The Rf values for the studied compoundsunder the applied chromatographic condition ranged between 0.38 to 0.58. Moreover, calculatedphysicochemical properties, and druglikeness scores of the studied thiazole-pyridiniumderivatives and matching piperidine analogues were predicted. Furthermore, some ADMETfeatures of studied compounds like toxicity and metabolism by CYP450 (2C9, 2D6, 3A4, 1A2and 2C19) enzymes were predicted. Conclusion: The ranges of experimental and calculated LogP values for the studied thiazolepyridinumswere close. However, the determined Rf values showed relatively better correlationto the predicted LogP values indicating the suitability of used chromatographic method forcomparing the lipophilicity of the positively charged pyridinium derivatives. The studiedcompounds were predicted to pass GI membrane and reach the CNS where they can exerttheir effects. In silico studies indicate that the piperidine counterparts of the studied thiazolepyridiniumsmay represent anti-Alzheimer agents with improved druglikeness properties.

Purpose: This paper established the application of synthesized graphitic carbon nitride nanosheets (GCNNs) as an influential dispersive solid phase extraction (DSPE) adsorbent in extracting methamphetamine from complicated urine media coupled with high performance liquid chromatography. Methods: The graphitic carbon nitride nanosheets (GCNNs) was synthesized easily and applied as adsorbent in the extraction process. The effective extraction parameters were investigated by one-parameter-at-a-time. Under optimized conditions the method was validated. Results: The calibration curve was plotted in the concentration range of 50-1500 ng/mL through the optimized conditions and the proposed method was validated. The method was used for the analysis of positive urine samples and showed satisfactory results with the average 99.7% relative recovery. Conclusion: The results persuade the capability of this novel method in analyzing of the positive urine samples in diverse clinical and forensic laboratories.

Purpose: DOF (DNA-binding with One Finger) proteins are plant-specific transcription factors which mediate numerous biological processes. The purpose of the current study is to report new naturally occurring mutations in the gene encoding for one of the members of DOF proteins named DOF 4.2. Methods: The expression of zinc finger domain of DOF 4.2 (DOF 4.2-ZF) was investigated by first synthesis of cDNA library using different parts of Arabidopsis thaliana plant. Then the coding sequence for zinc finger domain of DOF 4.2 protein was prepared using nested PCR experiment and cloned into pGEX-6P-1 expression vector. Finally, the prepared construct was used for protein expression. Furthermore, molecular dynamics (MD) simulation was carried out to predict DNA binding affinity of DOF 4.2-ZF using AMBER package. Results: For the first time a new variant of DOF 4.2-ZF protein with three mutations was detected. One of the mutations is silent while the other two mutations lead to amino acid replacement (S18G) as well as introduction of a stop codon ultimately resulting in a truncated protein production. In order to investigate whether the truncated form is able to recognize DNA binding motif, MD simulations were carried out and the results showed that the chance of binding of DOF 4.2-ZF protein to cognate DNA in its truncated form is very low. Conclusion: The findings demonstrated that the observed mutations adversely affect the DNA binding ability of the truncated form of DOF4.2 if it is expressed in the mutant variant of A. thaliana used in this study.

Background: Application of natural-based herbal medicine is on a growing trend in some countries and people prefer to use plant-originated drugs rather than chemical-based ones. The present study describes an interesting sample preparation method for extraction and determination of cyproheptadine in herbal supplements as appetizing stimulant by using carbon nitride nanosheets as dispersive solid phase extraction method coupled with HPLCUV. Methods: Various techniques used for characterization of adsorbent such as: Infrared spectroscopy (IR), scanning electron microscopy (SEM), Zeta potential analysis and powder X-ray diffraction (XRD). Optimization of the important extraction parameters were conducted by one parameter-at-a time method. Next, method validation was carried out. Results: The optimized cyproheptadine extraction parameters were introduced and under optimized conditions the method presented a good linearity in the concentration range of 300-2000 ng/g. The limit of detection (LOD) was 100 ng/g for the introduced method. Conclusion: Quantitative analysis of fifteen real samples (Tablets or capsules) by proposed method confirmed the illegal presence of cyproheptadine in herbal appetizing stimulants supplements of the markets.

Background: In the recent years, histamine H3 receptor (H3R) has been receiving increasing attention in pharmacotherapy of neurological disorders. The aim of the current study was to investigate structural requirements for the prediction of H3 antagonistic activity using quantitative structure-activity relationship (QSAR) and molecular docking techniques. Methods: To this end, genetic algorithm coupled partial least square and stepwise multiple linear regression methods were employed for developing a QSAR model. The obtained QSAR model was stringently assessed using different validation criteria. Results: The generated model indicated that connectivity information and mean absolute charge are two important descriptors for the prediction of H3 antagonistic activity of the studied compounds. To gain insight into the mechanism of interaction between studied molecules and H3R, molecular docking was performed. The most important residues involved in the ligand-receptor interactions were identified. Conclusion: The result of current study can be used for designing of new H3 antagonist and proposing structural modifications to improve H3 inhibitory potency.

Background: Uncontrolled activity of tumor necrosis factor alpha (TNF-α) as pro-inflammatory cytokine has been linked with pathogenesis of autoimmune/inflammatory diseases. Therefore, modulating of TNF-α associated biological pathways is a promising strategy for alleviating of such diseases. In view of this, the use of antibody fragments such as single-chain variable fragments (scFv) in therapeutic applications has been gained much attention in terms of pharmacokinetic as well as production and therapeutic costs. Methods: In the current investigation, the previously designed and humanized hD2 antibody was modeled and docked onto the TNF-α structure. The binding free energy was predicted for the complex of hD2-TNF-α using molecular dynamics calculation followed by per-residue energy decomposition for residues of hD2. In addition in silico mutations of important amino acids at the binding site of enzyme were performed and the binding free energy was calculated for mutant forms of scFv in complex with TNF-α. Results: The analyses of the results proposed Y27F mutation in heavy chain CDR1 of hD2 scFv antibody may be considered as a promising substitution. Conclusion: The results may be used for designing new anti-TNF-α antibody with improved activity.

Purpose: Despite the discovery and synthesis of several anticancer drugs, cancer is still a major life threatening incident for human beings after cardiovascular diseases. Toxicity, severe side effects, and drug resistance are serious problems of available commercial anticancer drugs. Coumarins are synthetic and natural heterocycles that show promising antiproliferative activities against various tumors. The aim of this research is to computationally study the coumarin derivatives in order to develop reliable quantitative structure-activity relationship (QSAR) models for predicting their anticancer activities. Methods: A data set of thirty one coumarin analogs with significant antiproliferative activities toward HepG2 cells were selected from the literature. The molecular descriptors for these compounds were calculated using Dragon, HyperChem, and ACD/Labs programs. Genetic algorithm (GA) accompanied by multiple linear regression (MLR) for simultaneous feature selection and model development was employed for generating the QSAR models. Results: Based on the obtained results, the developed linear QSAR models with three and four descriptors showed good predictive power with r2 values of 0.670 and 0.692, respectively. Moreover, the calculated validation parameters for the models confirmed the reliability of the QSAR models. Conclusion: The findings of the current study could be useful for the design and synthesis of novel anticancer drugs based on coumarin structure.

Objective(s): Hypercholesterolemia is a common metabolic disorder in developing and developed countries and is associated with the increased rates of chronic kidney disease (CKD). Statin therapy could reduce cholesterol synthesis as well as progression of CKD. Diversity between statins causes variety in pharmacokinetics and pharmacodynamics and also their pleiotropic effects. In the present investigation we aimed to evaluate the protective potentials of both atorvastatin (Ator) (as lipid-soluble statin) and rosuvastatin (Ros) (as water-soluble statin) against renal histopathological damages in the high cholesterol diet induced hypercholesterolemic rats (HCDIHR).Materials and Methods: Serum lipid profile, oxidized low density lipoprotein (OX-LDL), malondialdehyde (MDA), urea and creatinine levels, as well as renal histopathology were evaluated.Results: While Ros acted better than Ator to reduce serum low density lipoprotein cholesterol (LDL-C) (PConclusion: The findings underline that the lipophilic Ator may performs better than Ros in attenuating renal damages in HCDIHR.

Objective(s): Empagliflozin, a sodium-glucose cotransporter-2 (SGLT-2) inhibitor, possesses verified anti-inflammatory and anti-oxidative stress effects against diabetic nephropathy. The present investigation aims to examine empagliflozin effects on the renal levels of high mobility group box-1 (HMGB1), a potent inflammatory cytokine, and its respective receptor toll-like receptor-4 (TLR-4) in STZ-induced diabetic rats.Materials and Methods: Empagliflozin at 10 mg/kg per os (p.o.) was administered for 4 weeks, starting 8 weeks after the induction of diabetes. Renal function, kidney inflammation, oxidative stress, and apoptosis markers as well as renal HMGB1, receptor for advanced glycation end products (RAGE), and TLR-4 levels were assessed.Results: In addition to down-regulating NF-κB activity in renal cortices, empagliflozin reduced renal levels of HMGB1, RAGE, and TLR-4. It alleviated renal inflammation as indicated by diminished renal expressions of inflammatory cytokines and chemokines like tumor necrosis factor-alpha (TNF-α) and monocyte chemoattractant protein-1 (MCP-1) and also decreased urinary levels of interleukin-6 (IL-6) and alpha-1 acid glycoprotein (AGP). Moreover, empagliflozin ameliorated renal oxidative stress as demonstrated by decreased renal malondialdehyde (MDA) and elevated renal activities of superoxide dismutase (SOD) and glutathione peroxidase (GPX). It also suppressed renal caspase-3, the marker of apoptosis; and furthermore, enhanced renal function noticed by the declined levels of serum urea and creatinine.Conclusion: These findings underline that empagliflozin is able to attenuate diabetes-related elevations in renal HMGB1 levels, an influential inflammatory cytokine released from the necrotic and activated cells, and its correspondent receptors, i.e., RAGE and TLR-4.

Objective(s): Cisplatin is an effective antineoplastic agent; its clinical utility, however, is limited by a few salient toxic side effects like nephrotoxicity. This study aimed to determine the potential protective effects of tangeretin, a citrus-derived flavonoid, against renal tubular cell injury in cisplatin-induced renal toxicity of rats.Materials and Methods: Tangeretin was injected intraperitoneally at 2.5 and 5 mg/kg doses for 10 days, and a single dose of cisplatin (8 mg/kg) was injected on the 7th day. Tests of kidney function and tubular injury in renal tissues and urine together with oxidative stress and inflammation markers were examined.Results: Tangeretin ameliorated cisplatin-induced elevations in serum creatinine, BUN, and histopathologic changes. It also attenuated kidney oxidative stress elicited by cisplatin as demonstrated by reduced MDA and increased GSH, CAT, and SOD activities, elevated Nrf2 expression and protein levels of its downstream effectors, HO-1 and NQO-1. Tangeretin further alleviated inflammation evoked by cisplatin as indicated by reduced NF-κB p65 subunit phosphorylation with a simultaneous decrement in its downstream effectors IL-1β and TNF-α expression and protein levels. Moreover, it declined caspase-3 protein levels and TUNEL positive cells in the kidneys, the markers of apoptosis and DNA fragmentation, thus improving renal endurance. Additionally, tangeretin mitigated renal levels of KIM-1 and NGAL, as well as urinary cystatin C and β2-microglobulin concentrations, the markers of renal tubular injury.Conclusion: Collectively, these data signify the binary profit of tangeretin: enhancement of renal protective mechanisms against cisplatin and attenuation of renal tubular cell injuries induced by the agent.

Introduction: The bacterial enzyme has gained more attention in therapeutic application because of the higher substrate specificity and longer half-life. L-asparaginase is an important enzyme with known antineoplastic effect against acute lymphoblastic leukemia (ALL). Methods: Novel L-asparaginase genes were identified from a locally isolated halo-thermotolerant Bacillus strain and the recombinant enzymes were overexpressed in modified E. coli strains, OrigamiTM B and BL21. In addition, the biochemical properties of the purified enzymes were characterized, and the enzyme activity was evaluated at different temperatures, pH, and substrate concentrations. Results: The concentration of pure soluble enzyme obtained from Origami strain was ~30 mg/L of bacterial culture, which indicates the significant improvement compared to L-asparaginase produced by E. coli BL21 strain. The catalytic activity assay on the identified L-asparaginases (ansA1 and ansA3 genes) from Bacillus sp. SL-1 demonstrated that only ansA1 gene codes an active and stable homologue (ASPase A1) with high substrate affinity toward L-asparagine. The Kcat and Km values for the purified ASPase A1 enzyme were 23.96s-1 and 10.66 µM, respectively. In addition, the recombinant ASPase A1 enzyme from Bacillus sp. SL-1 possessed higher specificity to L-asparagine than L-glutamine. The ASPase A1 enzyme was highly thermostable and resistant to the wide range of pH 4.5–10. Conclusion: The biochemical properties of the novel ASPase A1 derived from Bacillus sp. SL-l indicated a great potential for the identified enzyme in pharmaceutical and industrial applications.

Introduction: Iron-regulated outer membrane virulence protein (IrgA) involved in the initial step of iron uptake by binding ferric- iron chelation siderophore that allows the bacterium to extract iron from the environment. IrgA homologue adhesion (Iha) revealed as a novel adherence conferring molecule. In this study, homology modeling, fold recognition and Ab-initio approaches along with their combination were invoked to determine the tertiary structure of Iha. Material and Methods: Specific bioinformatics methods were used to forecast their immunological, biochemical and functional properties. Results: The results showed that IrgA constitutes beta barrel structures. The immunological, biochemical and functional analyzes led us to pick a region of every antigen with the highest immunogenic properties. Comparison of antigenicity scores for selected regions and the whole proteins showed that the antigenicity of the selected regions is considerably higher than the whole antigen. Conclusion: Our strategy for prediction of the 3D structure and epitopes could be deemed as an amenable approach for efficient vaccine design. These approaches used could provide the basis for future functional studies to design and development of a suitable vaccine. In this regard, a region includes residues 200-340, covering a part of barrel, was chosen as vaccine candidate against Iha protein in Escherichia Coli.

Introduction: DOF proteins are a family of plant-specific transcription factors with a conserved zinc finger (ZF) DNA-binding domain. Although several studies have demonstrated their specific DNA binding, quantitative affinity data is not available for the binding of DOF domains to their binding sites. Methods: ZF domains of DOF2.1, DOF3.4, and DOF5.8 from Arabidopsis thaliana were expressed and purified. Their DNA binding affinities were assessed using gel retardation assays and microscale thermophoresis with two different oligonucleotide probes containing one and two copies of recognition sequence AAAG. Results: DOF zinc finger domains (DOF-ZFs) were shown to form independently folded structures. Assessments using microscale thermophoresis demonstrated that DOF-ZFs interact more tightly (~ 100 fold) with double-motif probe than the single-motif probe. The overall Kd values for the DOF3.4-ZF and DOF5.8-ZF to the double-motif probe were ~2.3±1 and 2.5±1 µM, respectively. Conclusion: Studied DOF-ZF domains formed stable complexes with the double-motif probe. Although DOF3.4-ZF and DOF5.8-ZF do not dimerize with an appreciable affinity in the absence of DNA (judging from size-exclusion and multiangle laser light scattering data), it is possible that these ZFs form protein-protein contacts when bound to this oligonucleotide, consistent with previous reports that DOF proteins can homo- and hetero-dimerize.

Objective(s): The interaction of DNA with iron oxide nanoparticles (SPIONs) was studied to find out the interaction mechanism and design new drug delivery systems. Materials and Methods: The interaction of calf thymus DNA (ctDNA) with SPIONs doped with 2H-chromene via dopamine as cross linker (SPIONs@DA-Chr) was studied using the UV absorption spectroscopy, viscosity measurement, circular dichroism, fluorescence and FT-IR spectroscopic techniques. Results: UV absorption study showed hyperchromic effect in the spectra of DNA. Few changes were observed in the viscosity of ctDNA in the presence of different concentration of SPIONs@DA-Chr. The result of circular dichroism (CD) suggested that SPIONs@DA-Chr can change the secondary structure of DNA. Further, fluorescence quenching reaction of ctDNA with SPIONs@DA-Chr and competitive fluorescence spectroscopy studied by using methylene blue, have shown that the SPIONs@DA-Chr can bind to ctDNA through non-intercalative mode. FT-IR spectroscopy confirmed the binding of SPIONs@DA-Chr and ctDNA. Conclusion: These results suggested that SPIONs@DA-Chr binds to DNA via groove binding mode.

Purpose: Receptor tyrosine kinase (RTK) inhibitors are widely used pharmaceuticals in cancer therapy. Fibroblast growth factor receptors (FGFRs) are members of RTK superfamily which are highly expressed on the surface of carcinoma associate fibroblasts (CAFs). The involvement of FGFRs in different types of cancer makes them promising target in cancer therapy and hence, the identification of novel FGFR inhibitors is of great interest. In the current study we aimed to develop an alignment independent three dimensional quantitative structure-activity relationship (3D-QSAR) model for a set of 26 FGFR2 kinase inhibitors allowing the prediction of activity and identification of important structural features for these inhibitors. Methods: Pentacle software was used to calculate grid independent descriptors (GRIND) for the active conformers generated by docking followed by the selection of significant variables using fractional factorial design (FFD). The partial least squares (PLS) model generated based on the remaining descriptors was assessed by internal and external validation methods. Results: Six variables were identified as the most important probes-interacting descriptors with high impact on the biological activity of the compounds. Internal and external validations were lead to good statistical parameters (r2 values of 0.93 and 0.665, respectively). Conclusion: The results showed that the model has good predictive power and may be used for designing novel FGFR2 inhibitors.

Abstract LIM-Homeodomain (LIM-HD) transcription factors are highly conserved in animals where they are thought to act in a transcriptional ‘LIM code’ that specifies cell types, particularly in the central nervous system. In chick and mammals the interaction between two LIM-HD proteins, LHX3 and Islet1 (ISL1), is essential for the development of motor neurons. Using yeast two-hybrid analysis we showed that the Caenorhabditis elegans orthologs of LHX3 and ISL1, CEH-14 and LIM-7 can physically interact. Structural characterisation of a complex comprising the LIM domains from CEH-14 and a LIM-interaction domain from LIM-7 showed that these nematode proteins assemble to form a structure that closely resembles that of their vertebrate counterparts. However, mutagenic analysis across the interface indicates some differences in the mechanisms of binding. We also demonstrate, using fluorescent reporter constructs, that the two C. elegans proteins are co-expressed in a small subset of neurons. These data show that the propensity for LHX3 and Islet proteins to interact is conserved from C. elegans to mammals, raising the possibility that orthologous cell specific LIM-HD-containing transcription factor complexes play similar roles in the development of neuronal cells across diverse species.

Tumor necrosis factor-alpha (TNF-α) is a pro-inflammatory cytokine produced by a variety of cells, including hematopoietic and non-hematopoietic cells, malignant cells, macrophages, B lymphocytes, T lymphocytes, natural killer cells, neutrophils, astrocytes, endothelial cells, and smooth muscle cells. TNF-α is a homo-trimeric molecular whose individual subunits are composed of antiparallel beta-sheets, forming a regular triangular prism shape. TNF-α binds to three receptor molecules through its receptor-binding sites, which are at the base of its pyramid structure. Biological responses to TNF-α are mediated through two different receptors: TNFR1 and TNFR2. These receptors are transmembrane glycoproteins with extracellular domains containing multiple cysteine-rich repeats that are structurally and functionally homologous, and the intracellular domains that are discrete and transduce their signals through both overlapping and distinct pathways. However, though TNF-α was initially discovered as an anti-tumor agent, it has been revealed that TNF-α and other ligands of this family are involved in some diseases like cancer, neurological, pulmonary, cardiovascular and autoimmune diseases and metabolic disorders. In general, TNF-α activates the control systems involved in cell proliferation, differentiation, inflammation and cell death, and the regulation of immune system. Although a normal level of TNF-α is very important for the regulation of immune responses, the persistence of the immune response as a result of inappropriate and excessive production of TNF-α can cause some inflammatory or autoimmune diseases. Accordingly, either neutralization TNF-α or blockade of its receptors using TNF-α inhibitors can be an effective therapeutic strategy to prevent or treat such inflammatory diseases. Several methods have been used to inhibit TNF-α, including the production of chimeric or fully human antibodies, soluble TNF-α receptors, or anti-TNF-α small molecules. The two previous agents are mostly capable of inhibiting the binding of TNF-α to its associated receptors, while anti-TNF-α small molecules, in addition to the above, inhibit the biosynthesis of TNF-α by blocking TNF-α mRNA biosynthesis, through the inhibition of its post-translational processing, or by blocking TNF-α receptors. Therefore, in this review article, we discuss the structure and characteristics of TNF-α and its related receptors: TNF-α signaling, TNF-α-mediated inflammatory diseases as well as TNF-α inhibition strategies.

Purpose: Implication of protein-protein interactions (PPIs) in development of many diseases such as cancer makes them attractive for therapeutic intervention and rational drug design. RON (Recepteur d’Origine Nantais) tyrosine kinase receptor has gained considerable attention as promising target in cancer therapy. The activation of RON via its ligand, macrophage stimulation protein (MSP) is the most common mechanism of activation for this receptor. The aim of the current study was to perform in silico alanine scanning mutagenesis and to calculate binding energy for prediction of hot spots in protein-protein interface between RON and MSPβ chain (MSPβ). Methods: In this work the residues at the interface of RON-MSPβ complex were mutated to alanine and then molecular dynamics simulation was used to calculate binding free energy. Results: The results revealed that Gln193, Arg220, Glu287, Pro288, Glu289, and His424 residues from RON and Arg521, His528, Ser565, Glu658, and Arg683 from MSPβ may play important roles in protein-protein interaction between RON and MSP. Conclusion: Identification of these RON hot spots is important in designing anti-RON drugs when the aim is to disrupt RON-MSP interaction. In the same way, the acquired information regarding the critical amino acids of MSPβ can be used in the process of rational drug design for developing MSP antagonizing agents, the development of novel MSP mimicking peptides where inhibition of RON activation is required, and the design of experimental site directed mutagenesis studies.

Purpose: Robust pharmaceutical and industrial enzymes from extremophile microorganisms are main source of enzymes with tremendous stability under harsh conditions which make them potential tools for commercial and biotechnological applications. Methods: The genome of a Gram-positive halo-thermotolerant Bacillus sp. SL1, new isolate from Saline Lake, was investigated for the presence of genes coding for potentially pharmaceutical enzymes. We determined gene sequences for the enzymes laccase (CotA), l-asparaginase (ansA3, ansA1), glutamate-specific endopeptidase (blaSE), l-arabinose isomerase (araA2), endo-1,4-β mannosidase (gmuG), glutaminase (glsA), pectate lyase (pelA), cellulase (bglC1), aldehyde dehydrogenase (ycbD) and allantoinases (pucH) in the genome of Bacillus sp. SL1. Results: Based on the DNA sequence alignment results, six of the studied enzymes of Bacillus sp. SL-1 showed 100% similarity at the nucleotide level to the same genes of B. licheniformis 14580 demonstrating extensive organizational relationship between these two strains. Despite high similarities between the B. licheniformis and Bacillus sp. SL-1 genomes, there are minor differences in the sequences of some enzyme. Approximately 30% of the enzyme sequences revealed more than 99% identity with some variations in nucleotides leading to amino acid substitution in protein sequences. Conclusion: Molecular characterization of this new isolate provides useful information regarding evolutionary relationship between B. subtilis and B. licheniformis species. Since, the most industrial processes are often performed in harsh conditions, enzymes from such halo-thermotolerant bacteria may provide economically and industrially appealing biocatalysts to be used under specific physicochemical situations in medical, pharmaceutical, chemical and other industries.

Introduction: Nephrotoxicity as a side effect caused by the immunosuppressive drug, cyclosporine-A (CsA), can be a major problem in transplant medicine. Oxidative stress may play an important role in the CsA-induced nephrotoxicity. It has been shown that the antihypertensive drug, valsartan (Val), has also renoprotective effects but, its molecular mechanism is largely unknown. In the present study, it was aimed to evaluate the Val effect in the alleviation of CsA nephrotoxicity via probable renal glutathione peroxidase (GPx) upregulation and oxidative stress decrease. Methods: Thirty-two Sprague-Dawley rats were divided into four groups based on CsA and/or Val administration: group A (Control, 1 mL/kg/day of olive oil as vehicle), group B (CsA, 30 mg/kg/day), group C (CsA+Val, 30+30 mg/kg/day), and group D (Val, 30 mg/kg/day). After the administration period (six weeks), renal GPx expression was evaluated by real-time polymerase chain reaction (PCR). Plasma levels of GPx and 8-Hydroxydeoxyguanosine (8-OHdG) were measured by enzyme-linked immunosorbent assay (ELISA). Malondialdehyde (MDA) and protein carbonyl groups (PCG) were measured by spectrophotometer. Plasma levels of urea and creatinine were measured by an autoanalyzer. Results: CsA treatment led to the decrease in renal expression and plasma levels of GPx in comparison to other study groups. Rats received CsA were detected to have significantly (p

Purpose: Tumor necrosis factor alpha (TNF-α) is an inflammatory cytokine, involved in both physiological and pathological pathways. Because of central role of TNF-α in pathogenesis of inflammatory diseases, in the current study, we aimed to identify novel scFv antibodies against TNF-α using phage display technology. Methods: Using libraries composed of phagemid displaying scFv antibodies, four rounds of biopanning against TNF-α were carried out, which led to identification of scFvs capable of binding to TNF-α. The scFv antibody with appropriate binding affinity towards TNF-α, was amplified and used in ELISA experiment. Results: Titration of phage achieved from different rounds of biopanning showed an enrichment of specific anti-TNF-α phages during biopanning process. Using ELISA experiment, a binding constant (Kd) of 1.11 ± 0.32 nM was determined for the phage displaying J48 scFv antibody. Conclusion: The findings in the current work revealed that the identified novel scFv antibody displayed at the N-terminal of minor coat proteins of phagemid binds TNF-α with suitable affinity. However, the soluble form of the antibody is needed to be produced and evaluated in more details regarding its binding properties to TNF-α.

Purpose: TNF-α is an inflammatory cytokine with a key role in initiation of inflammatory responses. Anti-TNF-α antibodies are being used in clinic for the purpose of diagnosis and treatment due to their high specificity. The objective of the current study was to express and purify an anti-TNF-α scFv antibody identified by phage display technology. Methods: The DNA coding sequence of the identified scFv was cloned into pET28a vector and the corresponding protein was expressed as 6×His tagged using E.coli BL21 (DE3) pLysS expression system followed by affinity purification on Ni-Sepharose affinity column. Results: The J44 scFv antibody was cloned into the expression vector and successfully expressed and purified. The purity of the scFv fraction was confirmed using SDS-PAGE analysis. Western blotting technique was used to detect expression of 6×His tagged protein. Conclusion: In the current study an anti-TNF-α scFv antibody was successfully expressed in bacterial expression system and purified on affinity column. The purified protein can be used in different in vitro and in vivo experiments in order to elucidate its functionality.

Purpose: The bacterial cultivation conditions for obtaining anti-TNF-α single chain variable fragment (scFv) antibody as the soluble product in E. coli was investigated. Methods: To avoid the production of inclusion bodies, the effects of lactose, IPTG, incubation time, temperature, shaking protocol, medium additives (Mg+2, sucrose), pH, osmotic and heat shocks were examined. Samples from bacterial growth conditions with promising results of soluble expression of GST-hD2 scFv were affinity purified and quantified by SDS-PAGE and image processing for further evaluation. Results: The results showed that cultivation in LB medium under induction by low concentrations of lactose and incubation at 10 °C led to partial solubilization of the expressed anti-TNF-α scFv (GST-hD2). Other variables which showed promising increase in soluble expression of GST-hD2 were osmotic shock and addition of magnesium chloride. Furthermore, addition of sucrose to medium suppressed the expression of scFv completely. The other finding was that the addition of sorbitol decreased the growth rate of bacteria. Conclusion: It can be concluded that low cultivation temperature in the presence of low amount of inducer under a long incubation time or addition of magnesium chloride are the most effective environmental factors studied for obtaining the maximum solubilization of GST-hD2 recombinant protein.

Purpose: The mutagenic potency of materials used in dentistry is of great concern. The Ames test is a bacterial reverse mutation assay, which is used to determine the mutagenicity potential of chemicals. In this study, the Ames test was used to compare mutagenic effects of three pulpotomy agents, namely, CEM cement, formocresol and ferric sulfate. Methods: TA100 strain of Salmonella typhimurium was used to evaluate mutagenicity of different concentrations of pulpotomy materials in the presence and absence of enzymatic system found in rat liver S9 fraction. Negative controls were 1% dimethyl sulfoxide and water. The positive controls were sodium azide and 2-aminoanthracene. The number of colonies per plate was counted. The material was regarded mutagenic if the number of histidine revertant colonies was twice or more than the spontaneous revertant colonies (Ames mutagenicity ratio). Results: Ferric sulfate was found mutagenic in the concentrations prepared by addition of 50 μL of its 1 in 100 and 1 in 1000 times diluted solutions to the culture medium in the absence of S9 fraction (Ames test ratios of 2.8 and 2.2, respectively). Formocresol showed strong toxicity toward TA100 strain of S. typhimurium up to the concentration as low achieved using 1000 times diluted solution of the original preparation, particularly in the presence of S9 fraction. Ames assay failed to detect significant reverse mutations in all the concentrations of CEM cement. Conclusion: In contrast to formocresol and ferric sulfate, CEM cement is a less toxic and non-mutagenic agent.

This paper1 was simultaneously submitted by the authors to "Transplantation" journal under the title "The Effects of Valsartan on Renal Klotho Expression and Oxidative stress in Alleviation of Cyclosporine Nephrotoxicity" and was accepted for publication in that journal. On the basis of BioImpacts policy in accordance with the Committee on Publication Ethics (COPE), any duplicate submission is considered as an ethical misconduct. The accepted manuscript in Transplantation shared considerable overlapping text and data (identical images and materials) with the published paper1 in BioImpacts. The Editor-in-Chief of BioImpacts, Prof. Y. Omidi, was alerted by the Editor-in-Chief of Transplantation, Prof. Jeremy R. Chapman, on such duplication. A comprehensive investigation through comparison of both papers was conducted by the editorial office of BioImpacts along with the Ethics Committee of Tabriz University of Medical Sciences (TUOMS) under Prof. M. R. Rashidi, who also acts as Director-in-Charge of BioImpacts and TUOMS Vice Chancellor of Research and Technology Affairs. As a result, they decided to retract this paper in line with the COPE recommendations. The authors were informed and advised on this serious ethical breach. Therefore, the paper is retracted at the request of authors, the aforementioned committee and the Editor-in-Chief of BioImpacts, even though the corresponding author believed that two papers were different in their aims, studied animals, and factors. By the way, they apologize for any inconvenience this may have caused. One of the conditions of submission of a paper to BioImpacts is that authors declare explicitly that "This manuscript has been exclusively submitted to this journal and is not under review or accepted for publication elsewhere". As such, this paper represents abuse of the scientific publishing system. As a peer-review multidisciplinary international "Publish Free" and "Access Free" journal, BioImpacts strongly adheres to the "Publication Ethics", and its foremost goal is to preserve the integrity of the scientific reports in the highest standards, therefore the journal takes all issues of publication misconduct seriously.

PURPOSE. Interleukin-12 (Il-12) as a cytokine has been proved to possess antitumor effects via stimulating the immune system. Non-viral gene delivery systems exhibit low toxicity and are easier to prepare compared to their viral counterparts. In this study, we aimed to prepare plasmid DNA loaded chitosan nanoparticles for expression of Il-12 and to evaluate their physicochemical characteristics, cytotoxicity and transfection efficiency in Murine CT-26 colon carcinoma cells. METHODS. Nanoparticles were prepared using a complex coacervation process at different N/P ratios and characterized in terms of size, zeta potential, polydispersity index, morphology, encapsulation efficiency and polyplex formation. The cytotoxicities and transfection efficiencies of the prepared polyplexes were evaluated by MTT assay and ELISA (for hIL-12, p70), respectively. RESULTS. Size and zeta potential varied from 76.73 to 867.03 nm and between 5.68 and 16.77 mV, respectively. Strong attachment of the DNA to chitosan was observed after polyplex preparation. Encapsulation efficiencies were high (72.97–94.87%). The transfection efficiencies of the prepared complexes were obviously higher than those of naked pDNA when N/P ratios were between 16 and 60. Maximum level of phIL-12 expression was obtained at (N/P = 16) with mean particle size of 381.83±82.77 nm (polydispersity index=0.44) indicating the improved transfection of pUMVC3-hIL12 about 2.80 times compared to that of the naked pUMVC3-hIL12. Prepared polyplexes were nontoxic to CT-26 cells. CONCLUSIONS. Chitosan-DNA nanoparticles at N/P = 16 with minimal cytotoxicity, can be used as suitable candidate for Il-12 delivery. This article is open to POST-PUBLICATION REVIEW. Registered readers (see “For Readers”) may comment by clicking on ABSTRACT on the issue’s contents page.