Spectroscopic and molecular modeling studies of binding interaction between the new complex of yttrium and 1,10-phenanthroline derivatives with DNA and BSA.

In this study, the 4,9 diazafluoren-9-one ligand and [Y(Daf)2Cl3.OH2] complex were synthesized. The interaction of this complex with DNA and bovine serum albumin (BSA) was investigated by UV-vis and fluorescence spectroscopy. The molecular docking method was used to confirm the experimental results, investigate the type of interaction, and determine the binding site. The binding constant and Stern-Volmer constant were calculated using spectroscopy techniques. The binding constant of the Y-complex with DNA and BSA obtained using the UV-vis technique was 1.61 × 105 M-1 and 0.49 × 105 M-1, while that obtained using the fluorescence method was 3.39 × 105 M-1 and 3.63 × 105 M-1, respectively. The results of experimental and theoretical data showed that the interaction between the yttrium complex and DNA and BSA is driven by the hydrogen bond and van der Waals interaction, respectively. The yttrium complex communicates with DNA via the groove interaction. This complex has high binding energy with bovine serum albumin. In addition, the molecular docking results showed that the complex binds to the IIA subdomain of BSA (site I). Finally, anticancer activity of the yttrium complex was studied on MCF-7 and A549 cell lines by using the MTT method. The IC50 values obtained showed that the yttrium complex possesses anticancer activity.

Studying the interaction between the new neodymium (Nd) complex with the ligand of 1,10-phenanthroline with FS-DNA and BSA.

To learn more about the chemotherapeutic and pharmacokinetic properties of a neodymium complex containing 1,10-phenanthroline (dafone), In vitro binding was investigated with bovine serum albumin and fish-salmon DNA, using a variety of molecular modeling research and biophysical approaches. A variety of spectroscopic techniques including fluorescence and absorption were used to investigate the interplay between DNA/BSA and the neodymium complex. The findings revealed that the Nd complex had a high affinity for BSA and DNA interplays through van der Waals powers. In addition, the binding of the Nd complex to FS-DNA mainly in the groove binding mode clearly reflects with iodide quenching studies, ethidium bromide (EtBr) exclusion assay, ionic strength effect, and viscosity studies. It was observed that the Nd complex binds to FS-DNA through a minor groove with 3.81 × 105 (M-1). Also, Kb for BSA at 298 K was 5.19×105 (M-1), indicating a relatively high affinity of the Nd complex for DNA and BSA. In addition, a competitive study of a docking investigation revealed that the neodymium complex interacts at BSA site III. The results obtained from the binding calculations are well consistent with the experimental findings. Also, cytotoxicity studies of Nd complex were performed in MCF-7 and A-549 cell lines and the results show that this new complex has a selective inhibitory effect on the growth of various cancer cells.

Malachite Green, the hazardous materials that can bind to Apo-transferrin and change the iron transfer.

Different groups of synthetic dyes might lead to environmental pollution. The binding affinity among hazardous materials with biomolecules necessitates a detailed understanding of their binding properties. Malachite Green might induce a change in the iron transfer by Apo-transferrin. Spectroscopic studies showed malachite green oxalate (MGO) could form the apo-transferrin-MGO complex and change the Accessible Surface Area (ASA) of the key amino acids for iron transfer. According to the ASA results the accessible surface area of Tyrosine, Aspartate, and Histidine of apo-transferrin significantly were changed, which can be considered as a convincing reason for changing the iron transfer. Moreover, based on the fluorescence data MGO could quench the fluorescence intensity of apo-transferrin in a static quenching mechanism. The experimental and Molecular Dynamic simulation results represented that the binding process led to micro environmental changes, around tryptophan residues and altered the tertiary structure of apo-transferrin. The Circular Dichroism (CD) spectra result represented a decrease in the amount of the α-Helix, as well as, increase in the ß-sheet volumes of the apo-transferrin structure. Moreover, FTIR spectroscopy results showed a hypochromic shift in the peaks of amide I and II. Molecular docking and MD simulation confirmed all the computational findings.

QSAR analysis of pyrimidine derivatives as VEGFR-2 receptor inhibitors to inhibit cancer using multiple linear regression and artificial neural network.

BACKGROUND AND PURPOSE: In this study, the pharmacological activity of 33 compounds of furopyrimidine and thienopyrimidine as vascular endothelial growth factor receptor 2 (VEGFR-2) inhibitors to inhibit cancer was investigated. The most important angiogenesis inducer is VEGF endothelial growth factor, which exerts its activity by binding to two tyrosine kinase receptors called VEGFR-1 and VEGFR-2. Due to the critical role of VEGF in the pathological angiogenesis of this molecule, it is a valuable therapeutic target for anti-angiogenesis therapies. EXPERIMENTAL APPROACH: After calculating descriptors using SPSS software and stepwise selection method, 5 descriptors were used for modeling in multiple linear regression (MLR) and artificial neural network (ANN). The calibration series and the test series in this study included 26 and 7 combinations, respectively. FINDINGS/RESULTS: The performance evaluation of models was determined by the R2, RMSE, and Q2 statistic parameters. The R2 values of MLR and ANN models were 0.889 and 0.998, respectively. Also, the value of RMSE in the ANN model was lower and its Q2 value was higher than the MLR model. CONCLUSION AND IMPLICATIONS: The results were evaluated by different statistical methods and it was concluded that the nonlinear neural network method is powerful to predict the pharmacological activity of similar compounds, and because of the complex and nonlinear relationships, the MLR was not capable of establishing a good model with high predictive power.

An insight into the interaction between malachite green oxalate with human serum albumin: Molecular dynamic simulation and spectroscopic approaches.

Cationic triarylmethane dyes such as malachite green are aromatic xenobiotic compounds causing environmental pollution. The affinity between hazardous materials and biomolecules makes it important to understand the properties of such compounds. Accordingly, in this study, the possible molecular interaction between this pollutant and the human serum albumin (HSA) was investigated using a combination of molecular docking, molecular dynamic simulation and multi-spectroscopic approaches. The docking results illustrated that malachite green oxalate (MGO) could bind to some of the HSA amino acids with the estimated free energy = -32.93 kJ/mol. Further, the results of the dynamic simulation revealed that MGO had a steady interaction with the protein though increasing flexibility and decreasing the HSA compactness. These results were, therefore, in agreement with those obtained by spectroscopic techniques. The MGO concentration of 0.0005 mM could quench the HSA's intrinsic fluorescence by %16.88. The protein structural changes also revealed that the binding interaction of MGO-HSA was accompanied by an increase in the α-helix and a decrease in the ß-sheet of the protein. Overall, this study indicated the suitable molecular modeling interaction of MGO and HSA.

In vitro anticancer activity of parent and nano-encapsulated samarium(iii) complex towards antimicrobial activity studies and FS-DNA/BSA binding affinity.

Based on the potential anticancer properties of lanthanide complexes, the anticancer activity of the Sm(iii) complex containing a 2,2'-bipyridine ligand (bpy) and its interaction with FS-DNA (Fish-Salmon DNA) and BSA (Bovine Serum Albumin) were examined experimentally and by molecular docking in this paper. Absorption and fluorescence spectroscopic methods were used to define the thermodynamic parameters, binding constant (K b), and the probable binding mechanism. It was concluded that the Sm complex interacts with FS-DNA through a minor groove with a K b of 105 M-1. Also, the K b for the BSA binding at 298 K was found to be 5.89 × 105 M-1, showing relatively a high tendency of the Sm complex to DNA and BSA. Besides, the Sm complex was docked to BSA and DNA by the autodock program. The results of the docking calculations were in good agreement with the experimental examinations. Additionally, the antifungal and antibacterial properties of this complex were investigated. The anticancer tests on the effect of the Sm complex, starch nano-encapsulation, and lipid nano-encapsulation in MCF-7 and A-549 cell lines were performed by the MTT method. It can be observed that the Sm complex and its nanocarriers presented a selective inhibitory effect on various cancer cell growths.

Experimental and theoretical investigations of Dy(III) complex with 2,2'-bipyridine ligand: DNA and BSA interactions and antimicrobial activity study.

In this study, the interactions of a novel metal complex [Dy(bpy)2Cl3.OH2] (bpy is 2,2'-bipyridine) with fish salmon DNA (FS-DNA) and bovine serum albumin (BSA) were investigated by experimental and theoretical methods. All results suggested significant binding between the Dy(III) complex with FS-DNA and BSA. The binding constants (Kb), Stern-Volmer quenching constants (KSV) of Dy(III)-complex with FS-DNA and BSA at various temperatures as well as thermodynamic parameters using Van't Hoff equation were obtained. The experimental results from absorption, ionic strength, iodide ion quenching, ethidium bromide (EtBr) quenching studies and positive ΔH˚ and ΔS˚ suggested that hydrophobic groove-binding mode played a predominant role in the binding of Dy(III)-complex with FS-DNA. Indeed, the molecular docking results for DNA-binding were in agreement with experimental data. Besides, the results found from experimental and molecular modeling indicated that the Dy(III)-complex bound to BSA via Van der Waals interactions. Moreover, the results of competitive tests by phenylbutazone, ibuprofen, and hemin (as a site-I, site-II and site-III markers, respectively) considered that the site-III of BSA is the most possible binding site for Dy(III)-complex. In addition, Dy(III) complex was concurrently screened for its antimicrobial activities. The presented data provide a promising platform for the development of novel metal complexes that target nucleic acids and proteins with antimicrobial activity.Communicated by Ramaswamy H. Sarma.

Vortex-assisted ionic liquid microextraction coupled to flame atomic absorption spectrometry for determination of trace levels of cadmium in real samples.

A simple and rapid vortex assisted ionic liquid based liquid-liquid microextraction technique (VALLME) was proposed for preconcentration of trace levels of cadmium. According to this method, the extraction solvent was dispersed into the aqueous samples by the assistance of vortex agitator. Cadmium preconcentration was mediated by chelation with the 8-hydroxyquinoline (oxine) reagent and an IL, 1-octyl-3-methylimidazolium hexafluorophosphate ([Omim][PF6]) was chosen as the extraction solvent to extract the hydrophobic complex. Several variables such as sample pH, concentration of oxine, volume of [Omim][PF6] and extraction time were investigated in details and optimum conditions were selected. Under the optimum conditions, the limit of detection (LOD) was 2.9 µg L(-1) for Cd (ІІ) and relative standard deviation (RSD%) for five replicate determinations of 125 µg L(-1) was 4.1%. The method was successfully applied to the determination of cadmium in tap water, apple and rice samples.

Prediction of gas chromatography/electron capture detector retention times of chlorinated pesticides, herbicides, and organohalides by multivariate chemometrics methods.

A quantitative structure-retention relationship (QSRR) study, has been carried out on the gas chromatograph/electron capture detector (GC/ECD) system retention times (t(R)s) of 38 diverse chlorinated pesticides, herbicides, and organohalides by using molecular structural descriptors. Modeling of retention times of these compounds as a function of the theoretically derived descriptors was established by multiple linear regression (MLR) and partial least squares (PLS) regression. The stepwise regression using SPSS was used for the selection of the variables that resulted in the best-fitted models. Appropriate models with low standard errors and high correlation coefficients were obtained. Three types of molecular descriptors including electronic, steric and thermodynamic were used to develop a quantitative relationship between the retention times and structural properties. MLR and PLS analysis has been carried out to derive the best QSRR models. After variables selection, MLR and PLS methods used with leave-one-out cross validation for building the regression models. The predictive quality of the QSRR models were tested for an external prediction set of 12 compounds randomly chosen from 38 compounds. The PLS regression method was used to model the structure-retention relationships, more accurately. However, the results surprisingly showed more or less the same quality for MLR and PLS modeling according to squared regression coefficients R2 which were 0.951 and 0.948 for MLR and PLS, respectively.