Abdol-Khalegh Bordbar | California Polytechnic State University at San Luis Obispo (original) (raw)

Papers by Abdol-Khalegh Bordbar

Journal of Molecular Structure, 2017

In the first part of this paper, docking method was employed in order to study the binding mechan... more In the first part of this paper, docking method was employed in order to study the binding mechanism of breast cancer resistance protein (BCRP) with a group of previously synthesized TPS-A derivatives which known as potent inhibitors of this protein to get insight into drug binding site of BCRP and to explore structure-activity relationship of these compounds. Molecular docking results showed that most of these compounds bind in the binding site of BCRP at the interface between the membrane and outer environment. In the second part, a group of designed TPS-A derivatives which showed good binding energies in the binding site of αβtubulin in the previous study were chosen to study their binding energies in the binding site of BCRP to investigate their simultaneous inhibitory effect on both αβ-tubulin and BCRP. The results showed that all of these compounds bind to the binding site of BCRP with relatively suitable binding energies and therefore could be potential inhibitors of both αβ-tubulin and BCRP proteins. Finally, virtual consensus docking method was utilized with the aim of design of new 2,5-diketopiperazine derivatives with significant inhibitory effect on both αβ-tubulin and BCRP proteins. For this purpose binding energies of a library of 2,5-diketopiperazine derivatives in the binding sites of αβ-tubulin and BCRP was investigated by using AutoDock and AutoDock vina tools. Molecular docking results revealed that a group of 36 compounds among them exhibit strong anti-tubulin and anti-BCRP activity.

Heliyon, 2019

In this study, we analyzed the capability of unmodified b-cyclodextrin (b-CD) to form the stable ... more In this study, we analyzed the capability of unmodified b-cyclodextrin (b-CD) to form the stable complex with serotonin hydrochloride (SER), as an important neurotransmitter in the brain. The stable b-CD: SER formulation was prepared and characterized using spectroscopic, thermal, molecular docking, and molecular dynamics techniques, revealing the phenomenon of H-bond formations and the domination of hydrophobic forces between the host molecule and its guest via the amine group of SER and the narrow side of b-CD. The complexation mechanism was mainly enthalpy-driven, representing the improvement in SER photo-stability. Overall, the results highlighted the possibility to use this formulation with improved stability in clinical practice for treatment and prevention of various depressive conditions, such as anxiety disorders.

The European Physical Journal Plus

Heliyon, 2020

Density (ρ), viscosity (η) and surface tension (γ) of three amino acids (valine, alanine, and gly... more Density (ρ), viscosity (η) and surface tension (γ) of three amino acids (valine, alanine, and glycine) have been measured at a different mass fraction (0.002-0.009) of aqueous hydroxypropyl-β-cyclodextrin (HPβCD) mixtures and different temperatures (278.15-295.15 K). The formation of inclusion complexes has been analyzed via evaluating the amounts of apparent and limiting apparent molar volumes, limiting apparent molar expansibilities, activation energy, kinematic, relative, intrinsic, spatial, and dynamic viscosities. The surface tension studies indicated that the inclusion complexes have been formed with 1:1 stoichiometry and mediated by hydrophobic effects and electrostatic forces. Additionally, the ρ and η parameters were evaluated by molecular modeling experiments to provide more details on the mechanisms of the complexation.

Journal of Biotherapy, 2014

α-lactalbumin (α-La) is one of the major milk proteins that in addition of nutritional value it c... more α-lactalbumin (α-La) is one of the major milk proteins that in addition of nutritional value it can get many other useful novel functions such as antiviral and tumoricidal activities via structural modifications by enzyme or chemical methods. Several researches show antiviral activity of esterified milk proteins because of their new functional properties followed by structural modifications. In this research, the hypothesis based on antibacterial activity of esterified α-La was examined. The esterification reaction as an important tool for modifying food proteins was employed in this study by using different alcohols under strong acidic condition at 4 °C for 3 days. α-La was esterified to the extent of 53.8%, 34.95%, 32.2% , 6.07% and 46.8% with methanol, ethanol, 1butanol, 2-pentanol and 1-hexanol, respectively, showed the influence of molar ratio, type of used alcohol and time of reaction on the reaction yield. Then the effects of esterified derivatives of α-La were tested on the growth of some positive and negative gram bacteria (including Bacillus cereus, methicylin resistant Staphylococcus aureus (MRSA), Escherichia coli, and Klebsiella) by disc assay. After 24-48 h incubation, no inhibition zone surrounding the discs was observed which represents the fail of any antibacterial activity of α-La and its esterified derivatives.

Curcumin (CUR) is the active curcuminoid with many physiological, biochemical, and pharmacologica... more Curcumin (CUR) is the active curcuminoid with many physiological, biochemical, and pharmacological properties. Solubility and stability of CUR is the limiting factors for realizing its therapeutic potential. Bovine β-casein is an abundant milk protein that is highly amphiphilic and self-assembles into stable micellar nanoparticles in aqueous solution. β-Casein nanoparticle can solubilize CUR molecules. In the present study, we introduced a drug-delivery system comprising hydrophobic anticancer drug, CUR, entrapped within β-casein-based nanoparticles. The interaction of CUR with β-casein was investigated using steady-state fluorescence spectroscopy and molecular docking calculation. Results showed that at pH 7, CUR molecules bind to β-casein micelle and formed complexes through hydrophobic interactions. Forster energy transfer measurements and molecular docking studies suggested that CUR molecules bind to the hydrophobic core of βcasein. The binding parameters including number of sub...

Physical Chemistry Research, 2017

Because of participation in many aspects of human life, and due to oxidation-sensitive characteri... more Because of participation in many aspects of human life, and due to oxidation-sensitive characteristics of dopamine (DA) and arachidonoyl dopamine (AA-DA), the necessity of biocompatible carrier to keep them against oxidation is of importance. In this work, we explored the putative binding sites of DA and AA-DA to -lactoglobulin (BLG) as potent carrier. Docking results identified the binding sites, involved residues and driving forces to the binding process of these ligands. The dissimilar binding site of AA-DA in comparison with DA has been designated by different values of Gibbs free energy, biding constants and contact residues. Molecular dynamics simulation outcomes confirmed that both compounds stayed in their predicted binding sites during the entire time of simulation with no major secondary and tertiary protein structural changes which pointed that BLG might be considered as a suitable oxidation-protective carrier for these compounds.

Physical Chemistry Research, 2018

This paper is designed to examine the binding behavior of Coumarin with bovine -casein (βCN) thr... more This paper is designed to examine the binding behavior of Coumarin with bovine -casein (βCN) through fluorescence spectroscopy and molecular modeling techniques. The data analysis on fluorescence titration experiments at various temperatures represents the enthalpy driven nature for the formation of Coumarin–βCN complex and the prevailed role of hydrogen bonds and van der Waals interactions in the binding process. The results also represent the static quenching of tryptophan and dynamics quenching of tyrosine and phenylalanine residues due to the binding of Coumarin. It can be concluded from molecular docking studies that Coumarin binds to several polar and non-polar residues in the hydrophobic core of βCN with the binding energy of -6.96 kcal mol-1. Finally, analysis of molecular dynamics (MD) simulation results suggested that the interactions between βCN and Coumarin are very stable and the binding of Coumarin restricted the flexibility of important residues in the binding site o...

Thermal denaturation of p-Iactoglobulin type B in the absence and pteNcno: of g arious concentrat... more Thermal denaturation of p-Iactoglobulin type B in the absence and pteNcno: of g arious concentrations of trehalo5e, sucrose and sork toles sugar osmolytes and twlyols were nuyoured hy monitoring changes in the absorption coefficients at pH 2.0. These measurements gave aliss, or I. mpdpDint of denaturation), Al-fis (enthalpy change at Ty). and ACp (consttun-pressure heal capaciit eh.iltgtii under a gisen solvent condition Using these valuer of Ali,, r s, and AC, , AG D° (Gibbs Dieu:, chantiet was determined at a given concentration of each sugar. Ii has been obsessed that each sugar glafili se. the 13-lac toglob B m terns of 3. and AGn a. The temperature that corresponds to rtmirntim proiv in Rahflits.. I s is increased G the presence of these osmulytes. The same rend was also obsessed for fir,. the temperanirc corresponding to nun eat-haler change of denaturation.

In order to shed more light on the effect of peripheral groups of porphyrin core intophysicochemi... more In order to shed more light on the effect of peripheral groups of porphyrin core intophysicochemical properties and DNA binding behavior of porphyrins, we have chosen toinvestigate solution properties and calf thymus DNA binding behavior of meso-tetrakis (4-Nbenzyl-pyridyl) porphyrin (TBZPyP) and its Mn (III), Co (III), Ni (II) and Cu (II) complexesderivatives have been studied in thermodynamic viewpoint using Uv/Vis spectroscopy. They havebeen chosen because of their good solubility in physiological solution as well as moderatelyhydrophobic property, so that we may consider them as promising compounds for clinicalapplications. The measurements were done in 1mM phosphate buffer, pH 7.0 and varioustemperatures. The optical absorption spectra of porphyrins were analyzed in order to obtainbinding constants and stoichiometries using SQUAD software. The results show that the bestfitting corresponds to a 1:1 complex model between base pair of DNA and porphyrins. Theestimation of binding c...

Informatics in Medicine Unlocked, 2021

Abstract The molecular nature, antioxidant, and anticancer actions of the dietary flavonoid daidz... more Abstract The molecular nature, antioxidant, and anticancer actions of the dietary flavonoid daidzein binding to two types of β-lactoglobulin (βLG) are investigated in this work by using different kinds of spectroscopic techniques, electrochemical analysis, molecular docking, and molecular dynamics simulation. The results showed that hydrogen bonds and van der Waals interactions played a major role in the development of the stable complex. It may be deduced from molecular docking studies and competitive assays that daidzein binds to the outer surface of βLG with appropriate binding energies. The results of molecular dynamics showed the creation of a relatively stable complex in which daidzein binding reduced the flexibility of key residues in the binding site. In terms of the masking effect of βLG, the best antioxidant activity was found at low concentrations of the βLG-daidzein complex. After 48 hours of exposure to a 50 μM mixture of βLG and daidzein, the complexes showed increased anticancer activity with maximal mortalities of 38.62 and 47.08% for HeLa and MCF-7 cells, respectively. The improvement of daidzein's solubility and anticancer activity as a result of its complexation with βLG, as well as its light and heat stability, could be a beneficial approach in the food and pharmaceutical industries.

ACS Omega, 2021

This study focused on the inclusion of levodopa (LVDP) into β-cyclodextrin (BCD) using various co... more This study focused on the inclusion of levodopa (LVDP) into β-cyclodextrin (BCD) using various computational methods such as quantum mechanics (QM), molecular dynamics/ steered molecular dynamics (MD/SMD), and QM/molecular mechanics/Poison−Boltzmann surface area (QM/MM/PBSA). The QM results assigned the most significant charge-transfer atoms and the higher stability of LVDP in the aqueous phase. The MD results indicate the formation of a 1:1 complex with a reasonable estimation of the effective radius of the complex, the significant contribution of hydrogen bonding in the binding energy, and the enhancement of the water solubility of LVDP. By accounting for the water hydrogen bonds and their dipolar effects, QM/MM calculations lead to the more accurate IR spectrum and binding energy of the BCD−LVDP complex. By considering carboxylic and amine functional groups' more precise arrangement, QM/MM assigns stronger hydrogen bonds between LVDP and BCD. While all the methods provide a reasonable estimation of the binding energy, the most accurate value (−4.14 kcal/mol) is obtained from QM/MM/PBSA.

Industrial & Engineering Chemistry Research, 2020

A simple method was introduced to determine the activity of activated carbonsupported palladium (... more A simple method was introduced to determine the activity of activated carbonsupported palladium (Pd/AC) catalysts in the hydrogenation of cinnamic acid (CA). Catalytic transfer hydrogenation (CTH) of CA to hydrocinnamic acid (HCA) with assistance of simple Bayer's test is chosen for this purpose. The ability of this method for accurate measurement of the catalyst activity is proved by comparing its results with data obtained from the catalytic hydrogenation (CH) reaction of CA to HCA. Four commercial 10%Pd/AC catalysts were used which their characterization are determined. The reliability of correlation between the obtained activity from catalysts in two CH and CTH reactions is confirmed by high and low values of the coefficient of determination (R 2 =0.9895) and standard error (s=2.84), respectively. It is indicated

Journal of Membrane Science, 2020

Abstract Recently, membrane-immobilized enzyme as an affordable bioreactor has been explored in v... more Abstract Recently, membrane-immobilized enzyme as an affordable bioreactor has been explored in various fields such as biodiesel production and biosensing because of the reusability of the biocatalyst, increasing its stability and being a low-cost separating unit for producing pure products. Usually, membrane modification could affect the surface morphology and hydrophilicity to make them appropriate for enzyme immobilization. In this context, the modified nanocomposite membranes of polyethersulfone (PES) with various percentages (x: 0.00, 0.25, 0.50, 1.00, 2.00, 3.00) of the graphene oxide nanosheets (GON) named (PGx) are synthesized through the phase inversion technique. The enzymatic hybrid membrane reactors (EHMRs) are provided through the Candida rugosa lipase (CRL) immobilization on the synthesized hybrid membranes. The structure and surface functionalities of the synthesized GON and hybrid membrane are characterized by X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy and attenuated total reflection (ATR), respectively. The effect of the GON incorporation and CRL immobilization on the morphology of the membrane are explored through field emission scanning electron microscopy (FE-SEM), atomic force microscopy (AFM), contact angle goniometry, and surface free energy analysis. After measuring the porosity of the hybrid membranes with different amounts of GON, their performance, before and after CRL immobilization, are studied through pure water flux. The effective parameters on the activity and performance of EHMR such as GON percentages, CRL initial concentration, immobilization time, and storage condition are accurately optimized. The examination of the relative activity, reusability, and product permeability display that EHMR with 1.00% of GON (EHMR1) is the most efficient between EHMRs with different percentages of GON. Moreover, EHMR1 exhibits the enhancement in pH and thermal stability compared with free CRL and even the immobilized CRL on GON. While the storage stability of the wet- EHMR1 is higher than that of the dry-EHMR1, the stored wet- EHMR1 at 4 °C is more stable than room temperature. Because of these advantages, it is recommended that this bioactive membrane could be a passable candidate for application in the environmental, analytical, and industrial processes.

Bulletin of the Korean Chemical Society, 2003

In the present work, the interaction of three water soluble porphyrins, tetra(p-trimethyle) ammon... more In the present work, the interaction of three water soluble porphyrins, tetra(p-trimethyle) ammonium phenyl porphyrin iodide (TAPP) as a cationic porphyrin, tetra sodium meso-tetrakis (p-sulphonato phenyle) porphyrin (TSPP) as an anionic porphyrin and manganese tetrakis (p-sulphonato phenyl) porphinato acetate (MnTSPP) as a metal porphyrin, with histone H 2 B have been studied by isothermal titration microcalorimetry at 8 mM phosphate buffer, pH 6.8 and 27 °C. The values of binding constant, entropy, enthalpy and Gibbs free energy changes for binding of the first MnTSPP, and first and second TSPP and TAPP molecules were estimated from microcalorimetric data analysis. The results represent that the process is both entropy and enthalpy driven and histone induces self-aggregation of the porphyrins. The results indicate that both columbic and hydrophobic interactions act as self-aggregation driving forces for the formation of aggregates around histone.

Journal of Molecular Liquids, 2017

Gold/silver decorated magnetic nanostructures as theranostic agents: Synthesis, characterization ... more Gold/silver decorated magnetic nanostructures as theranostic agents: Synthesis, characterization and in-vitro study. The address for the corresponding author was captured as affiliation for all authors. Please check if appropriate. Molliq(2017),

Acta Biochimica Polonica, 2006

The binding data for oxygenation of human hemoglobin, Hb, at various temperatures and in the abse... more The binding data for oxygenation of human hemoglobin, Hb, at various temperatures and in the absence and presence of 2,3-diphosphoglycerate, DPG, and inositol hexakis phosphate, IHP, were analyzed for extraction of mean intrinsic Gibbs free energy, DeltaGo, enthalpy, DeltaHo, and entropy, DeltaSo, of binding at various partial oxygen pressures. This method of analysis considers all the protein species present such as dimer and tetramer forms which were not considered by Imai et al. (Imai K et al., 1970, Biochim Biophys Acta 200: 189-196), in their analysis which was based on Adair equation. In this regard, the values of Hill equation parameters were estimated with high precision at all points of the binding curve and used for calculation of DeltaGo, DeltaHo and DeltaSo were also calculated by analysis of DeltaGo values at various temperatures using van't Hoff equation. The results represent the enthalpic nature of the cooperativity in Hb oxygenation and the compensation effect o...

Monatshefte für Chemie - Chemical Monthly, 2017

The interaction mechanism of adrenaline and arachidonoyl adrenalin with b-casein milk protein as ... more The interaction mechanism of adrenaline and arachidonoyl adrenalin with b-casein milk protein as a nanocarrier was investigated by fluorescence spectroscopy, molecular docking, and molecular dynamics simulation approaches. The results of fluorescence studies and thermodynamic parameters revealed the negative values of enthalpy and entropy changes for both compounds which illustrate the vital role of hydrogen bond and van der Waals interaction in stabilizing protein-ligand complexes. The docking studies showed that adrenaline binds to several polar and non-polar residues in the inner hydrophobic core of b-casein with binding energy of-27.25 kJ mol-1 but arachidonoyl adrenalin binds in a core near the surface of this protein with the binding energy of-28.67 kJ mol-1. Finally, the molecular dynamics simulation results suggested that the interactions between protein and both compounds are very stable and during the whole simulation time no significant protein structure changes were observed, consequently b-casein can be considered as a suitable carrier for adrenaline and arachidonoyl adrenalin.