Characterization of the interaction of glycyrrhizin and glycyrrhetinic acid with bovine serum albumin by spectrophotometric-gradient flow injection titration technique and molecular modeling simulations.

In this research, the interactions of glycyrrhizin (GL) and glycyrrhetinic acid (GA) with bovine serum albumin (BSA) have been investigated by the novel method of spectrophotometric- gradient flow injection titration technique. The hard-modeling multivariate approach to binding was used for calculation of binding constants and estimation of concentration-spectral profiles of equilibrium species. The stoichiometric ratio of binding was estimated using eigenvalue analysis. Results showed that GL and GA bind BSA with overall binding constants of KGL-BSA=3.85 (±0.09)×104Lmol-1, KGA-BSA=3.08 (±0.08)×104Lmol-1. Ligand-BSA complexes were further analyzed by combined docking and molecular dynamics (MD) simulations. Docking simulations were performed to obtain a first guess on the binding structure of the GL/GA-BSA complex, and subsequently analyzed by 20 ns MD simulations in order to evaluate interactions of GL/GA with BSA in detail. Results of MD simulations indicated that GL-BSA complex forms mainly on the basis of hydrogen bonds, while, GA-BSA complex forms on the basis of hydrophobic interactions. Also, water molecules can bridge between the ligand and protein by hydrogen bonds, which are stable during the entire simulation and play an important role in stabilization of the GL/GA-BSA complexes.

Experimental, computational and chemometrics studies of BSA-vitamin B6 interaction by UV-Vis, FT-IR, fluorescence spectroscopy, molecular dynamics simulation and hard-soft modeling methods.

The interaction of pyridoxine (Vitamin B6) with bovine serum albumin (BSA) is investigated under pseudo-physiological conditions by UV-Vis, fluorescence and FTIR spectroscopy. The intrinsic fluorescence of BSA was quenched by VB6, which was rationalized in terms of the static quenching mechanism. According to fluorescence quenching calculations, the bimolecular quenching constant (kq), dynamic quenching (KSV) and static quenching (KLB) at 310K were obtained. The efficiency of energy transfer and the distance between the donor (BSA) and the acceptor (VB6) were calculated by Foster's non-radiative energy transfer theory and were equal to 41.1% and 2.11nm. The collected UV-Vis and fluorescence spectra were combined into a row-and column-wise augmented matrix and resolved by multivariate curve resolution-alternating least squares (MCR-ALS). MCR-ALS helped to estimate the stoichiometry of interactions, concentration profiles and pure spectra for three species (BSA, VB6 and VB6-BSA complex) existed in the interaction procedure. Based on the MCR-ALS results, using mass balance equations, a model was developed and binding constant of complex was calculated using non-linear least squares curve fitting. FT-IR spectra showed that the conformation of proteins was altered in presence of VB6. Finally, the combined docking and molecular dynamics (MD) simulations were used to estimate the binding affinity of VB6 to BSA. Five-nanosecond MD simulations were performed on bovine serum albumin (BSA) to study the conformational features of its ligand binding site. From MD results, eleven BSA snapshots were extracted, at every 0.5ns, to explore the binding affinity (GOLD score) of VB6 using a docking procedure. MD simulations indicated that there is a considerable flexibility in the structure of protein that affected ligand recognition. Structural analyses and docking simulations indicated that VB6 binds to site I and GOLD score values depend on the conformations of both BSA and ligand. Molecular modeling results showed that VB6-BSA complex formed not only on the basis of electrostatic forces, but also on the basis of π-π staking and hydrogen bond. There was an excellent agreement between the experimental and computational results. The results presented in this paper, will offer a reference for detailed and systematic studies on the biological effects and action mechanism of small molecules with proteins.

Combined docking, molecular dynamics simulations and spectroscopic studies for the rational design of a dipeptide ligand for affinity chromatography separation of human serum albumin.

A computational approach to designing a peptide-based ligand for the purification of human serum albumin (HSA) was undertaken using molecular docking and molecular dynamics (MD) simulation. A three-step procedure was performed to design a specific ligand for HSA. Based on the candidate pocket structure of HSA (warfarin binding site), a peptide library was built. These peptides were then docked into the pocket of HSA using the GOLD program. The GOLDscore values were used to determine the affinity of peptides for HSA. Consequently, the dipeptide Trp-Trp, which shows a high GOLDscore value, was selected and linked to a spacer arm of Lys[CO(CH2)5NH] on the surface of ECH-lysine sepharose 4 gel. For further evaluation, the Autodock Vina program was used to dock the linked compound into the pocket of HSA. The docking simulation was performed to obtain a first guess of the binding structure of the spacer-Trp-Trp-HSA complex and subsequently analyzed by MD simulations to assess the reliability of the docking results. These MD simulations indicated that the ligand-HSA complex remains stable, and water molecules can bridge between the ligand and the protein by hydrogen bonds. Finally, absorption spectroscopic studies were performed to illustrate the appropriateness of the binding affinity of the designed ligand toward HSA. These studies demonstrate that the designed dipeptide can bind preferentially to the warfarin binding site.

Adsorption properties of tetracycline onto graphene oxide: equilibrium, kinetic and thermodynamic studies.

Graphene oxide (GO) nanoparticle is a high potential effective absorbent. Tetracycline (TC) is a broad-spectrum antibiotic produced, indicated for use against many bacterial infections. In the present research, a systematic study of the adsorption and release process of tetracycline on GO was performed by varying pH, sorption time and temperature. The results of our studies showed that tetracycline strongly loads on the GO surface via π-π interaction and cation-π bonding. Investigation of TC adsorption kinetics showed that the equilibrium was reached within 15 min following the pseudo-second-order model with observed rate constants of k2 = 0.2742-0.5362 g/mg min (at different temperatures). The sorption data has interpreted by the Langmuir model with the maximum adsorption of 323 mg/g (298 K). The mean energy of adsorption was determined 1.83 kJ/mol (298 K) based on the Dubinin-Radushkevich (D-R) adsorption isotherm. Moreover, the thermodynamic parameters such as ΔH°, ΔS° and ΔG° values for the adsorption were estimated which indicated the endothermic and spontaneous nature of the sorption process. The electrochemistry approved an ideal reaction for the adsorption under electrodic process. Simulation of GO and TC was done by LAMMPS. Force studies in z direction showed that tetracycline comes close to GO sheet by C8 direction. Then it goes far and turns and again comes close from amine group to the GO sheet.

The effect of Se salts on DNA structure.

There is considerable interest in the role of selenium in cancer prevention. Various organic and inorganic Se compounds are considered to be antioxidants. In the present study, the binding modes, the binding constants and the stability of Se-DNA complexes have been determined by Fourier transform infrared (FTIR) and UV-Visible spectroscopic methods. Spectroscopic evidence showed that Na(2)SeO(4) and Na(2)SeO(3) bind to the minor and major grooves of DNA and the backbone phosphate (PO(2)) with overall binding constants of K(Na(2)SeO(4)-DNA)=5.20×10(4) M(-1) and K(Na(2)SeO(3)-DNA)=1.87×10(3) M(-1). DNA aggregations occurred at high selenium concentrations. No biopolymer conformational changes were observed upon Na(2)SeO(3) and Na(2)SeO(4) interactions, while DNA remained in the B-family structure.

Study on the interaction of glycyrrhizin and glycyrrhetinic acid with RNA.

Glycyrrhizin is a well known pharmacologically bioactive natural glycoside. Glycyrrhizin (GL) has been widely used as a therapeutic agent for chronic active liver diseases. Glycyrrhetinic acid is an aglycone and an active metabolite of glycyrrhizin. This study is the first attempt to locate the binding sites of glycyrrhizin and glycyrrhetinic acid to RNA. The effect of the ligand complexation on RNA aggregation was investigated in aqueous solution at physiological conditions, using constant RNA concentration (6.25 mM) and various ligand/polynucleotide (phosphate) ratios of 1/280, 1/240, 1/120, 1/80, 1/40, 1/20, 1/10, 1/5, 1/2 and 1/1. Fourier transform infrared (FTIR) and UV-Visible spectroscopic methods as well as molecular modeling were used to determine the ligand binding modes, the binding constants, and the stability of ligands-RNA complexes in aqueous solution. Spectroscopic evidence showed that glycyrrhizin and glycyrrhetinic acid bind RNA via G-C and A-U base pairs as well as the backbone phosphate group with overall binding constants of K(GL-RNA)=3.03×10(3)M(-1), K(GA-RNA)=2.71×10(3)M(-1). The affinity of ligands-RNA binding is in the order of glycyrrhizin>glycyrrhetinic acid. RNA remains in the A-family structure, while biopolymer aggregation occurred at high triterpenoid concentrations.

Interaction of glycyrrhizin and glycyrrhetinic acid with DNA.

Glycyrrhizin (GL), a molecule of glycyrrhetinic acid (GA), is an aqueous extract from licorice root. These compounds are well known for their anti-inflammatory, hepatocarcinogenesis, antiviral, and interferon-inducing activities. This study is the first attempt to investigate the binding of GL and GA with DNA. The effect of ligand complexation on DNA aggregation and condensation was investigated in aqueous solution at physiological conditions, using constant DNA concentration (6.25 mM) and various ligands/polynucleotide (phosphate) ratios of 1/240, 1/120, 1/80, 1/40, 1/20, 1/10, 1/5, 1/2, and 1/1. Fourier transform infrared and ultraviolet (UV)-visible spectroscopic methods were used to determine the ligand binding modes, the binding constants, and the stability of ligand-DNA complexes in aqueous solution. Spectroscopic evidence showed that GL and GA bind DNA via major and minor grooves as well as the backbone phosphate group with overall binding constants of K(GL-DNA)=5.7×10(3) M(-1), K(GA-DNA)=5.1×10(3) M(-1). The affinity of ligand-DNA binding is in the order of GL>GA. DNA remained in the B-family structure, whereas biopolymer aggregation occurred at high triterpenoid concentrations.

Beta-carboline alkaloids bind DNA.

Beta-carboline alkaloids present in Peganum harmala (harmal) have recently drawn attention due to their antitumor activities. The mechanistic studies indicate that beta-carboline derivatives inhibit DNA topoisomerases and interfere with DNA synthesis. They interact with DNA via both groove binding and intercalative modes and cause major DNA structural changes. The aim of this study was to examine the interactions of five beta-carboline alkaloids (harmine, harmane, harmaline, harmalol and tryptoline) with calf-thymus DNA in aqueous solution at physiological conditions, using constant DNA concentration (6.25 mM) and various alkaloids/polynucleotide (phosphate) ratios of 1/240, 1/160, 1/80, 1/40, 1/20, 1/10, 1/5, 1/2 and 1/1. Fourier transform infrared (FTIR) and UV-visible spectroscopic methods were used to determine the ligand binding modes, the binding constants, and the stability of alkaloids-DNA complexes in aqueous solution. Spectroscopic evidence showed major binding of alkaloids to DNA with overall binding constants of K(harmine)-DNA=3.44x10(7) M(-1), K(harmane)-DNA=1.63x10(5) M(-1), K(harmaline)-DNA=3.82x10(5) M(-1), K(harmalol)-DNA=6.43x10(5) M(-1) and K(tryptoline)-DNA=1.11x10(5) M(-1). The affinity of alkaloids-DNA binding is in the order of harmine>harmalol>harmaline>harmane>tryptoline. No biopolymer secondary structural changes were observed upon alkaloid interaction and DNA remains in the B-family structure in these complexes.