Abstract In this research, using nonequilibrium green's function (NEGF) integrated with densi... more Abstract In this research, using nonequilibrium green's function (NEGF) integrated with density functional theory (DFT), we investigated the electronic transport properties of a bicyclic aziridine (2-nIiitro-4-(6-(4-nitrophenyl)-4-phenyl-1,3-diaza-bicyclo[3.1.0]hex-3-en-2-yl)phenol) molecular wire. The title molecule can be converted between two open and closed forms. The electronic transmission factors, spatial spreading of molecular projected self-consistent Hamiltonian (MPSH) orbitals, on-off ratio, I–V characteristics, the alteration of the electrode materials, Y, (Y = Au, Ag, and Pt), and HOMO–LUMO gaps relevant to these forms are thoroughly discussed. It can be concluded that due to the deformation of the title molecule (open → closed), there is a noticeable change in conductivity.
AbstractMethylglycine, also known sarcosine, is dramatically used in drug molecules and its metal... more AbstractMethylglycine, also known sarcosine, is dramatically used in drug molecules and its metal complexes can interact to DNA and also do cleavage. Hence, to study the influence of methylglycine ligand on biological behavior of metal complexes, two water-soluble platinum (II) complexes with the formula cis-[Pt(NH3)2(CH3-gly)]NO3 and cis-[Pt(NH2-CH3)2(CH3-gly)]NO3 (where CH3-gly is methylglycine) have been synthesized and characterized by spectroscopic methods, molar conductivity measurements, and elemental analyzes. The anticancer activity of synthesized complexes was tested against human breast adenocarcinoma cell line of MCF7 using MTT assay and results showed excellent anticancer activity with Cc50 values of 126 and 292 μM after 24 h incubation time, for both complexes of cis-[Pt(NH3)2(CH3gly)]NO3 and cis-[Pt(NH2-CH3)2(CH3gly)]NO3, respectively. Also, the interaction between Pt(II) complexes with calf thymus DNA was extensively studied by means of absorption spectroscopy, fluorescence titration spectra displacement with ethidium bromide (EtBr), and circular dichroism studied in Tris-buffer. The obtained spectroscopic results revealed that two complexes can bind to highly polymerized calf thymus DNA cooperatively and denature at micromolar concentrations. The fluorescence data indicate that quenching effect for cis-[Pt(NH3)2(CH3gly)]NO3 (Ksv = 9.48 mM−1) was higher than that of cis-[Pt(NH2-CH3)2(CH3gly)]NO3 (Ksv = 1.98 mM−1). These results were also confirmed by circular dichrosim spectra. Consequently, docking data showed that cis-[Pt(NH3)2(CH3gly)]NO3 with more interaction energy binds on DNA via groove binding which is more compatible with experimental results. Graphical AbstractᅟTwo anticancer Pt(II) complexes, cis-[Pt(NH3)2(CH3gly)]NO3 and cis-[Pt(NH2−CH3)2(CH3gly)]NO3, have been synthesized and interacted with calf thymus DNA. Improving solubility of these compounds reduce side effects and increase anticancer activity against human breast cell line. Modes of binding have been studied by electronic absorption, fluorescence, and CD measurements. Results show that both Pt(II) complexes can interact to DNA via groove binding.
The aggregation of 85 porphyrin derivatives and a report on a kinetic and thermodynamic study of ... more The aggregation of 85 porphyrin derivatives and a report on a kinetic and thermodynamic study of such aggregation behavior on varying the derivatives of porphyrin was carried out using molecular dynamics simulation and Docking. Distance diagrams of simulated compounds were obtained and decrease of curves is a clear evidence of the aggregation. Aggregation rates were studied by origin software. In order to calculate interaction energies of derivatives, compounds were docked and the equilibrium constant of porphyrin-porphyrin interaction were obtained. Quantitative Structure-Property Relationship (QSPR) studies were performed for the sets of 85 Porphyrin derivatives. Multiple Linear Regression method (MLR) and Principal Component Analysis (PCA) were used and resulted in useful models with good prediction ability. This models were able to predict the kinetic and equilibrium constant for all sets of our compounds. The correlation coefficients for prediction of rate and logarithm of equi...
ABSTRACT Kinetic study of the reaction of flavonoid naringenin with the stable free radical 2,2-d... more ABSTRACT Kinetic study of the reaction of flavonoid naringenin with the stable free radical 2,2-diphenyl-1-picrylhydrazyl (DPPH) was performed in different percentage compositions of aqueous ethanol (50-90% v/v) using spectrophotometric method. The reaction, which follows the mixed second-order rate law, was investigated under pseudo firstorder conditions with respect to the DPPH radical, at (25.0 +/- 0.1) degrees C and an ionic strength of 0.1 mol dm(-3). The rate of reaction was found to decrease with increasing organic solvent content in binary mixture. The reaction mechanism was inferred from the stoichiometry, kinetics, and product identification. Furthermore, the effects of solvent composition on the reaction rate in the mixed solvents were analyzed in terms of Reichardt parameter (E-T(N)), and Kamlet, Abboud and Taft (KAT) solvatochromic parameters (alpha, beta, and pi*). To further investigate the solvent effects we theoretically studied the three antioxidant action mechanisms of naringenin using density functional theory (DFT) method. Reaction enthalpies related to these mechanisms were calculated in gas-phase, water, ethanol and 50-90% (by v/v) ethanol-water. It was found that theoretical findings are in good agreement with experimental results.
Abstract We analyze the transport properties of 4-(6-(4-chlorophenyl)-4-phenyl-1,3-diaza-bicyclo[... more Abstract We analyze the transport properties of 4-(6-(4-chlorophenyl)-4-phenyl-1,3-diaza-bicyclo[3.1.0]hex-3-en-2-yl)-2-nitrophenol molecular optical switch using first-principles calculations. Molecule consisting switch can transform among closed and open forms by visible or ultraviolet irradiation. We have studied multiple attributes such as I–V characteristics, electronic transmission coefficients T(E), the effect of electrode materials (Au, Ag, and Pt) on electronic transport properties, on-off ratio and spatial distribution of molecular projected self-consistent Hamiltonian (MPSH) orbitals corresponding to the closed and open forms. The physical origin of switching behavior is interpreted based on the different molecular geometries, location and size of the frontier molecular orbitals and the HOMO–LUMO gap. According to the theoretical results, one can found that when the open form converts to the closed form, there is a switch from low resistance (on state) to high resistance (off state). We hope that the results of this study can help researchers to design new functional molecular devices.
Nucleic acids play an important role in biological systems and carry out a broad range of biologi... more Nucleic acids play an important role in biological systems and carry out a broad range of biological functions. In recent years, metal Schiff-base complexes have also found important applications in the biological field. Therefore, the interaction of these complexes with DNA has attracted much attention.In this work, the interaction between a new nickel complex containing tetradentate Schiff base ligand with calf thymus DNA (CT-DNA) was measured by Viscometry method and UV-Vis spectrophotometry in physiological buffer (pH=7.4). The viscosity of DNA enhanced with increasing in the ratio of complex to DNA indicated the intercalative mode of binding. The midpoint of thermal transition (T m ) of DNA in the absence and presence of complex was measured. Data showed that by addition of complex, T m of DNA increased, and confirmed type of complex intercalation. The results indicated that nickel Schiff base complex can bind to DNA and the major binding mode was intercalative binding.
Electrochemical behavior of some anthraquinone (Aq) derivatives were investigated in acetonitrile... more Electrochemical behavior of some anthraquinone (Aq) derivatives were investigated in acetonitrile (AN), N,N-dimethyl formamide (DMF) and dimethylsulfoxide (DMSO) by cyclic voltammetry (CV), quantum mechanics and statistical methods. A reasonable correlation between the computational and experimental standard reduction potential ( o E ) for electron transfer was obtained. It was concluded that the first step reduction potential, o 1 E in acetonitrile, increases with hydrogen bonding, aromaticity and HOMO energy and decreases with size and polarity of anthraquinone. Trend of average values for o 1 E in three solvents is AN < DMSO < DMF, while the trend of o 2 E is inversely. The o 1 E values increase with polarity, dielectric constant, molecular size and hydrogen bonding of solvent and this trend is reverse in the case of o 2 E values. Difference in trend of reduction potential is related to solutesolvent and solvent interactions. Solvent effect in the explicit model presents be...
To investigate the interaction and adsorption of drug and carbon nanotube on human serum albumin,... more To investigate the interaction and adsorption of drug and carbon nanotube on human serum albumin, three anti-cancer drugs ([Pd(phen)(R-gly)]NO3, R = methyl, propyl and amyl) with different hydrophobic tails and anticancer activities were selected. These drugs have better anti-tumor activity and less side effects than that known cis-platinum drug. Human serum albumin is also important for drug delivery and release and acts as carrier of internal biological molecules and external drugs that bind to many drugs in blood route and carry them. Drug binding to human serum albumin can change its helicity and this can affect on the drug release and distribution. Thus, study of this aspect can provide structural features determining the therapeutic efficiency of drug that has the least effect on human serum albumin helix structure. Interaction of three drugs with human serum albumin was investigated by molecular dynamics simulation and the best drug with the least denaturation effect was sele...
Interactions of 3,3',4,4'-tetrahydroxybiphenyl (BPT) and three isomeric 3,3",4,4&quo... more Interactions of 3,3',4,4'-tetrahydroxybiphenyl (BPT) and three isomeric 3,3",4,4"-tetrahydroxyterphenyls (OTT, MTT, PTT) with Alzheimer’s amyloid-β peptide (Aβ) were studied by molecular dynamics simulation and molecular docking. Structural parameters such as Root-mean-square derivations (RMSD), radial distribution function (RDF), helix percentage and other physical parameters were obtained. These inhibitors have been evaluated and compared for their activity against aggregation of Aβ. The results showed that all four compounds successfully inhibit association of Aβ and reduce aggregation of protein. For the tetrahydroxyterphenyls efficacy varies with linker geometry: the ortho-position affords the most successful inhibition and the para-geometry the least perhaps due to differing abilities of these inhibitors to bind amyloid-β peptide. Of the four small inhibitors studied 3,3',4,4'-tetrahydroxybiphenyl (BPT) is the most effective inhibitor. Molecular docki...
ABSTRACT: Quantitative structure-activity relationship (QSAR) study on the piperidone-grafted mon... more ABSTRACT: Quantitative structure-activity relationship (QSAR) study on the piperidone-grafted mono- and bis-spirooxindole-hexahydropyrrolizines as potent butyrylcholinestrase (BuChE) inhibitors were carried out using statistical methods, molecular dynamics and molecular docking simulation. QSAR methodologies, including classification and regression tree (CART), multiple linear regression (MLR), principal component analysis (PCA) and principal component regression analysis (PCRA). Three descriptors in three classes: 3D-Morse, WHIM and GETAWAY descriptors were selected by SPSS software and then applied in the final tree structure to describe the inhibitory activities. Docking simulations were carried out using AutoDock Vina softwares for all inhibitors. Docking results showed that the studied BuChE inhibitors have two commons binding modes. Molecular dynamics results obtained by Gromacs showed that the more potent inhibitor has more interaction with the enzyme and higher effect on the...
The heat capacity has played a major role in proteins. Its calculation by atomistic simulation me... more The heat capacity has played a major role in proteins. Its calculation by atomistic simulation methods remains a significant challenge due to the complex and dynamic nature of protein structures and this work compares the denaturation effect of bovine carbonic anhydrase (BCA) by heat, pH and scan rate dependence of protein denaturation by molecular dynamics (MD) simulation. To better understand this factor on calculating a protein heat capacity and Tm, we have provided a comparative analysis of simulation models that differ in their scan rate and pH description. Our model protein system is the carbonic anhydrase, and a series of 20 ns simulated DSC with different scan rate (v= 0.10, 0.0125, 0.015 and 0.02 K/ps) and pH have been reported by simulated annealing performed at temperatures ranging from 250 to 575 K, starting from the carbonic anhydrase native structure. It was observed that, our systems were quite sensitive to the description and the calculated melting temperature (Tm) v...
Mutations of surface residues as well as of amino acides in the interior of proteins can affect t... more Mutations of surface residues as well as of amino acides in the interior of proteins can affect their stability. Even single residue substitutions can influence stability as has been observed for, e.g., interacellulary fatty acid-binding proteins, lysozyme, apoflavodoxin and crystallins. In the present work, thermal denaturation of 2 genetic variants of human serum albumin (HSA) , 573 Lys→Glu and 82 Glu→Lys hve been studied by molecular dynamics simulation. structure of HSA has been taken from protein data bank (RCSB:1AO6 pdb id code). The thermal stability of these alloalbumins, as compared with that of wild-type albumin, was monitored by analyzing the CD results at 222 nm in the temperature range of 285 to 360 K by Gromacs software. Stability was quantitated in terms of midpoint of the denaturation curve (T m ) and vant Hoff enthalpy. In addition, the changes in T m were related to changes in helical content as is confirmed with structural results and is in good agreement with pre...
Molecular dynamic simulation is a powerful method that monitors all variations in the atomic leve... more Molecular dynamic simulation is a powerful method that monitors all variations in the atomic level in explicit solvent. By this method we can calculate many chemical and biochemical properties of large scale biological systems. In this work, all-atom molecular dynamic simulation of polyalanine (PA) was investigated in the presence of 0.224, 0.448, 0.673, 0.897 and 1.122 M of guanidinium chloride (GdmCl) at 273-395 K by molecular dynamics simulation. Analysis of surface area, radial distribution function, radius of gyration, heat capacity, hydrogen bond, helix, coil and beta contents showed that an intermediate appears on the way of helix to coil transition. GdmCl at low concentration increases the midpoint of transition temperature (Tm), number of solvent molecules in the hydration layer and interapeptide hydrogen bond as well as decreases in rate of helix to coil transition. Thus, the role of guanidine at low concentration is as the same as osmolytes which decreases the beta form a...
Abstract In the present study, poly (aniline-co-pyrrole) nano-sphere (PACPNS) was synthesized by ... more Abstract In the present study, poly (aniline-co-pyrrole) nano-sphere (PACPNS) was synthesized by micro-emulsion polymerization technique. The PACPNS was examined as a strong absorbent for lead(II) removal from aqueous media. The FTIR spectroscopy, TGA and XRD characterization were used for confirmation of construction, phase identification and thermal stability of PACPNS, respectively. FESEM images of the PACPNS showed a nanosphere structure with diameter ∼90 nm. The experimental data revealed that the sorption isotherm of lead(II) onto the PACPNS was in well agreement with Langmuir equation. The Lagergren pseudo-second order equation was in well agreement with adsorption data of kinetic for lead(II). According to results, the maximum adsorption capacity (Qmax) of lead(II) was determined 119.02 mg/g, under optimized conditions. The thermodynamic data implied that the adsorption procedure of lead(II) was feasible, endothermic and spontaneous in nature. Also, the adsorption of lead(II) onto the PACPNS was investigated using molecular dynamics simulation (MDS) by DL-poly software. According to experimental and theoretical data a probable mechanism for sorption of lead(II) was proposed where electrostatic interfaces controlled the lead(II) adsorption.
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
Photconversion of an anthraquinone photochrome (AQP) from Trans to Ana forms were studied by diff... more Photconversion of an anthraquinone photochrome (AQP) from Trans to Ana forms were studied by different methods and techniques. Solution of AQP was irradiated under UV light in buffer condition, pH = 7.5, 10 mM phosphate buffer in the absence and presence of human serum albumin at 27 and 37 °C. The results showed that a new peak at higher wavelength was observed that indicative of producing the Ana form. Rate of Trans to Ana conversion increases in the presence of human serum albumin (HSA). Electron transport calculations were carried out from the first principles with a method based on non-equilibrium Green's functions (NEGF) combined with DFT. The results showed that electron transport is easier in Ana form due to increasing the resonance length and electron delocalization. Binding study by docking and spectroscopy showed that Trans form has more tendency to interact with HSA due to higher number of HSA-Trans hydrogen bond. Structural studies by circular dichroism and molecular dynamics results show that at lower concentration of AQP, percentage of helix was increased and then decreases at higher concentration. In addition structural parameters such as RMSD, accessible surface area, hydrogen bond, in associated with experimental results showed that protein folded at low concentration.
Abstract In this research, using nonequilibrium green's function (NEGF) integrated with densi... more Abstract In this research, using nonequilibrium green's function (NEGF) integrated with density functional theory (DFT), we investigated the electronic transport properties of a bicyclic aziridine (2-nIiitro-4-(6-(4-nitrophenyl)-4-phenyl-1,3-diaza-bicyclo[3.1.0]hex-3-en-2-yl)phenol) molecular wire. The title molecule can be converted between two open and closed forms. The electronic transmission factors, spatial spreading of molecular projected self-consistent Hamiltonian (MPSH) orbitals, on-off ratio, I–V characteristics, the alteration of the electrode materials, Y, (Y = Au, Ag, and Pt), and HOMO–LUMO gaps relevant to these forms are thoroughly discussed. It can be concluded that due to the deformation of the title molecule (open → closed), there is a noticeable change in conductivity.
AbstractMethylglycine, also known sarcosine, is dramatically used in drug molecules and its metal... more AbstractMethylglycine, also known sarcosine, is dramatically used in drug molecules and its metal complexes can interact to DNA and also do cleavage. Hence, to study the influence of methylglycine ligand on biological behavior of metal complexes, two water-soluble platinum (II) complexes with the formula cis-[Pt(NH3)2(CH3-gly)]NO3 and cis-[Pt(NH2-CH3)2(CH3-gly)]NO3 (where CH3-gly is methylglycine) have been synthesized and characterized by spectroscopic methods, molar conductivity measurements, and elemental analyzes. The anticancer activity of synthesized complexes was tested against human breast adenocarcinoma cell line of MCF7 using MTT assay and results showed excellent anticancer activity with Cc50 values of 126 and 292 μM after 24 h incubation time, for both complexes of cis-[Pt(NH3)2(CH3gly)]NO3 and cis-[Pt(NH2-CH3)2(CH3gly)]NO3, respectively. Also, the interaction between Pt(II) complexes with calf thymus DNA was extensively studied by means of absorption spectroscopy, fluorescence titration spectra displacement with ethidium bromide (EtBr), and circular dichroism studied in Tris-buffer. The obtained spectroscopic results revealed that two complexes can bind to highly polymerized calf thymus DNA cooperatively and denature at micromolar concentrations. The fluorescence data indicate that quenching effect for cis-[Pt(NH3)2(CH3gly)]NO3 (Ksv = 9.48 mM−1) was higher than that of cis-[Pt(NH2-CH3)2(CH3gly)]NO3 (Ksv = 1.98 mM−1). These results were also confirmed by circular dichrosim spectra. Consequently, docking data showed that cis-[Pt(NH3)2(CH3gly)]NO3 with more interaction energy binds on DNA via groove binding which is more compatible with experimental results. Graphical AbstractᅟTwo anticancer Pt(II) complexes, cis-[Pt(NH3)2(CH3gly)]NO3 and cis-[Pt(NH2−CH3)2(CH3gly)]NO3, have been synthesized and interacted with calf thymus DNA. Improving solubility of these compounds reduce side effects and increase anticancer activity against human breast cell line. Modes of binding have been studied by electronic absorption, fluorescence, and CD measurements. Results show that both Pt(II) complexes can interact to DNA via groove binding.
The aggregation of 85 porphyrin derivatives and a report on a kinetic and thermodynamic study of ... more The aggregation of 85 porphyrin derivatives and a report on a kinetic and thermodynamic study of such aggregation behavior on varying the derivatives of porphyrin was carried out using molecular dynamics simulation and Docking. Distance diagrams of simulated compounds were obtained and decrease of curves is a clear evidence of the aggregation. Aggregation rates were studied by origin software. In order to calculate interaction energies of derivatives, compounds were docked and the equilibrium constant of porphyrin-porphyrin interaction were obtained. Quantitative Structure-Property Relationship (QSPR) studies were performed for the sets of 85 Porphyrin derivatives. Multiple Linear Regression method (MLR) and Principal Component Analysis (PCA) were used and resulted in useful models with good prediction ability. This models were able to predict the kinetic and equilibrium constant for all sets of our compounds. The correlation coefficients for prediction of rate and logarithm of equi...
ABSTRACT Kinetic study of the reaction of flavonoid naringenin with the stable free radical 2,2-d... more ABSTRACT Kinetic study of the reaction of flavonoid naringenin with the stable free radical 2,2-diphenyl-1-picrylhydrazyl (DPPH) was performed in different percentage compositions of aqueous ethanol (50-90% v/v) using spectrophotometric method. The reaction, which follows the mixed second-order rate law, was investigated under pseudo firstorder conditions with respect to the DPPH radical, at (25.0 +/- 0.1) degrees C and an ionic strength of 0.1 mol dm(-3). The rate of reaction was found to decrease with increasing organic solvent content in binary mixture. The reaction mechanism was inferred from the stoichiometry, kinetics, and product identification. Furthermore, the effects of solvent composition on the reaction rate in the mixed solvents were analyzed in terms of Reichardt parameter (E-T(N)), and Kamlet, Abboud and Taft (KAT) solvatochromic parameters (alpha, beta, and pi*). To further investigate the solvent effects we theoretically studied the three antioxidant action mechanisms of naringenin using density functional theory (DFT) method. Reaction enthalpies related to these mechanisms were calculated in gas-phase, water, ethanol and 50-90% (by v/v) ethanol-water. It was found that theoretical findings are in good agreement with experimental results.
Abstract We analyze the transport properties of 4-(6-(4-chlorophenyl)-4-phenyl-1,3-diaza-bicyclo[... more Abstract We analyze the transport properties of 4-(6-(4-chlorophenyl)-4-phenyl-1,3-diaza-bicyclo[3.1.0]hex-3-en-2-yl)-2-nitrophenol molecular optical switch using first-principles calculations. Molecule consisting switch can transform among closed and open forms by visible or ultraviolet irradiation. We have studied multiple attributes such as I–V characteristics, electronic transmission coefficients T(E), the effect of electrode materials (Au, Ag, and Pt) on electronic transport properties, on-off ratio and spatial distribution of molecular projected self-consistent Hamiltonian (MPSH) orbitals corresponding to the closed and open forms. The physical origin of switching behavior is interpreted based on the different molecular geometries, location and size of the frontier molecular orbitals and the HOMO–LUMO gap. According to the theoretical results, one can found that when the open form converts to the closed form, there is a switch from low resistance (on state) to high resistance (off state). We hope that the results of this study can help researchers to design new functional molecular devices.
Nucleic acids play an important role in biological systems and carry out a broad range of biologi... more Nucleic acids play an important role in biological systems and carry out a broad range of biological functions. In recent years, metal Schiff-base complexes have also found important applications in the biological field. Therefore, the interaction of these complexes with DNA has attracted much attention.In this work, the interaction between a new nickel complex containing tetradentate Schiff base ligand with calf thymus DNA (CT-DNA) was measured by Viscometry method and UV-Vis spectrophotometry in physiological buffer (pH=7.4). The viscosity of DNA enhanced with increasing in the ratio of complex to DNA indicated the intercalative mode of binding. The midpoint of thermal transition (T m ) of DNA in the absence and presence of complex was measured. Data showed that by addition of complex, T m of DNA increased, and confirmed type of complex intercalation. The results indicated that nickel Schiff base complex can bind to DNA and the major binding mode was intercalative binding.
Electrochemical behavior of some anthraquinone (Aq) derivatives were investigated in acetonitrile... more Electrochemical behavior of some anthraquinone (Aq) derivatives were investigated in acetonitrile (AN), N,N-dimethyl formamide (DMF) and dimethylsulfoxide (DMSO) by cyclic voltammetry (CV), quantum mechanics and statistical methods. A reasonable correlation between the computational and experimental standard reduction potential ( o E ) for electron transfer was obtained. It was concluded that the first step reduction potential, o 1 E in acetonitrile, increases with hydrogen bonding, aromaticity and HOMO energy and decreases with size and polarity of anthraquinone. Trend of average values for o 1 E in three solvents is AN < DMSO < DMF, while the trend of o 2 E is inversely. The o 1 E values increase with polarity, dielectric constant, molecular size and hydrogen bonding of solvent and this trend is reverse in the case of o 2 E values. Difference in trend of reduction potential is related to solutesolvent and solvent interactions. Solvent effect in the explicit model presents be...
To investigate the interaction and adsorption of drug and carbon nanotube on human serum albumin,... more To investigate the interaction and adsorption of drug and carbon nanotube on human serum albumin, three anti-cancer drugs ([Pd(phen)(R-gly)]NO3, R = methyl, propyl and amyl) with different hydrophobic tails and anticancer activities were selected. These drugs have better anti-tumor activity and less side effects than that known cis-platinum drug. Human serum albumin is also important for drug delivery and release and acts as carrier of internal biological molecules and external drugs that bind to many drugs in blood route and carry them. Drug binding to human serum albumin can change its helicity and this can affect on the drug release and distribution. Thus, study of this aspect can provide structural features determining the therapeutic efficiency of drug that has the least effect on human serum albumin helix structure. Interaction of three drugs with human serum albumin was investigated by molecular dynamics simulation and the best drug with the least denaturation effect was sele...
Interactions of 3,3',4,4'-tetrahydroxybiphenyl (BPT) and three isomeric 3,3",4,4&quo... more Interactions of 3,3',4,4'-tetrahydroxybiphenyl (BPT) and three isomeric 3,3",4,4"-tetrahydroxyterphenyls (OTT, MTT, PTT) with Alzheimer’s amyloid-β peptide (Aβ) were studied by molecular dynamics simulation and molecular docking. Structural parameters such as Root-mean-square derivations (RMSD), radial distribution function (RDF), helix percentage and other physical parameters were obtained. These inhibitors have been evaluated and compared for their activity against aggregation of Aβ. The results showed that all four compounds successfully inhibit association of Aβ and reduce aggregation of protein. For the tetrahydroxyterphenyls efficacy varies with linker geometry: the ortho-position affords the most successful inhibition and the para-geometry the least perhaps due to differing abilities of these inhibitors to bind amyloid-β peptide. Of the four small inhibitors studied 3,3',4,4'-tetrahydroxybiphenyl (BPT) is the most effective inhibitor. Molecular docki...
ABSTRACT: Quantitative structure-activity relationship (QSAR) study on the piperidone-grafted mon... more ABSTRACT: Quantitative structure-activity relationship (QSAR) study on the piperidone-grafted mono- and bis-spirooxindole-hexahydropyrrolizines as potent butyrylcholinestrase (BuChE) inhibitors were carried out using statistical methods, molecular dynamics and molecular docking simulation. QSAR methodologies, including classification and regression tree (CART), multiple linear regression (MLR), principal component analysis (PCA) and principal component regression analysis (PCRA). Three descriptors in three classes: 3D-Morse, WHIM and GETAWAY descriptors were selected by SPSS software and then applied in the final tree structure to describe the inhibitory activities. Docking simulations were carried out using AutoDock Vina softwares for all inhibitors. Docking results showed that the studied BuChE inhibitors have two commons binding modes. Molecular dynamics results obtained by Gromacs showed that the more potent inhibitor has more interaction with the enzyme and higher effect on the...
The heat capacity has played a major role in proteins. Its calculation by atomistic simulation me... more The heat capacity has played a major role in proteins. Its calculation by atomistic simulation methods remains a significant challenge due to the complex and dynamic nature of protein structures and this work compares the denaturation effect of bovine carbonic anhydrase (BCA) by heat, pH and scan rate dependence of protein denaturation by molecular dynamics (MD) simulation. To better understand this factor on calculating a protein heat capacity and Tm, we have provided a comparative analysis of simulation models that differ in their scan rate and pH description. Our model protein system is the carbonic anhydrase, and a series of 20 ns simulated DSC with different scan rate (v= 0.10, 0.0125, 0.015 and 0.02 K/ps) and pH have been reported by simulated annealing performed at temperatures ranging from 250 to 575 K, starting from the carbonic anhydrase native structure. It was observed that, our systems were quite sensitive to the description and the calculated melting temperature (Tm) v...
Mutations of surface residues as well as of amino acides in the interior of proteins can affect t... more Mutations of surface residues as well as of amino acides in the interior of proteins can affect their stability. Even single residue substitutions can influence stability as has been observed for, e.g., interacellulary fatty acid-binding proteins, lysozyme, apoflavodoxin and crystallins. In the present work, thermal denaturation of 2 genetic variants of human serum albumin (HSA) , 573 Lys→Glu and 82 Glu→Lys hve been studied by molecular dynamics simulation. structure of HSA has been taken from protein data bank (RCSB:1AO6 pdb id code). The thermal stability of these alloalbumins, as compared with that of wild-type albumin, was monitored by analyzing the CD results at 222 nm in the temperature range of 285 to 360 K by Gromacs software. Stability was quantitated in terms of midpoint of the denaturation curve (T m ) and vant Hoff enthalpy. In addition, the changes in T m were related to changes in helical content as is confirmed with structural results and is in good agreement with pre...
Molecular dynamic simulation is a powerful method that monitors all variations in the atomic leve... more Molecular dynamic simulation is a powerful method that monitors all variations in the atomic level in explicit solvent. By this method we can calculate many chemical and biochemical properties of large scale biological systems. In this work, all-atom molecular dynamic simulation of polyalanine (PA) was investigated in the presence of 0.224, 0.448, 0.673, 0.897 and 1.122 M of guanidinium chloride (GdmCl) at 273-395 K by molecular dynamics simulation. Analysis of surface area, radial distribution function, radius of gyration, heat capacity, hydrogen bond, helix, coil and beta contents showed that an intermediate appears on the way of helix to coil transition. GdmCl at low concentration increases the midpoint of transition temperature (Tm), number of solvent molecules in the hydration layer and interapeptide hydrogen bond as well as decreases in rate of helix to coil transition. Thus, the role of guanidine at low concentration is as the same as osmolytes which decreases the beta form a...
Abstract In the present study, poly (aniline-co-pyrrole) nano-sphere (PACPNS) was synthesized by ... more Abstract In the present study, poly (aniline-co-pyrrole) nano-sphere (PACPNS) was synthesized by micro-emulsion polymerization technique. The PACPNS was examined as a strong absorbent for lead(II) removal from aqueous media. The FTIR spectroscopy, TGA and XRD characterization were used for confirmation of construction, phase identification and thermal stability of PACPNS, respectively. FESEM images of the PACPNS showed a nanosphere structure with diameter ∼90 nm. The experimental data revealed that the sorption isotherm of lead(II) onto the PACPNS was in well agreement with Langmuir equation. The Lagergren pseudo-second order equation was in well agreement with adsorption data of kinetic for lead(II). According to results, the maximum adsorption capacity (Qmax) of lead(II) was determined 119.02 mg/g, under optimized conditions. The thermodynamic data implied that the adsorption procedure of lead(II) was feasible, endothermic and spontaneous in nature. Also, the adsorption of lead(II) onto the PACPNS was investigated using molecular dynamics simulation (MDS) by DL-poly software. According to experimental and theoretical data a probable mechanism for sorption of lead(II) was proposed where electrostatic interfaces controlled the lead(II) adsorption.
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
Photconversion of an anthraquinone photochrome (AQP) from Trans to Ana forms were studied by diff... more Photconversion of an anthraquinone photochrome (AQP) from Trans to Ana forms were studied by different methods and techniques. Solution of AQP was irradiated under UV light in buffer condition, pH = 7.5, 10 mM phosphate buffer in the absence and presence of human serum albumin at 27 and 37 °C. The results showed that a new peak at higher wavelength was observed that indicative of producing the Ana form. Rate of Trans to Ana conversion increases in the presence of human serum albumin (HSA). Electron transport calculations were carried out from the first principles with a method based on non-equilibrium Green's functions (NEGF) combined with DFT. The results showed that electron transport is easier in Ana form due to increasing the resonance length and electron delocalization. Binding study by docking and spectroscopy showed that Trans form has more tendency to interact with HSA due to higher number of HSA-Trans hydrogen bond. Structural studies by circular dichroism and molecular dynamics results show that at lower concentration of AQP, percentage of helix was increased and then decreases at higher concentration. In addition structural parameters such as RMSD, accessible surface area, hydrogen bond, in associated with experimental results showed that protein folded at low concentration.
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Papers by Davood Ajloo