New insights into structural, electronic, reactivity, spectroscopic and pharmacological properties of Bergenin: Experimental, DFT calculations, MD and docking simulations

Effects of structural characteristics of phenolic compounds on oxidation of glycerol trioleate: Action rule and mechanism

Effects of structural characteristics of phenolic compounds on the oxidation of glycerol trioleate were investigated, and the action rule and mechanism were further explored. By using thermal and multispectral analyses, all tested phenolic compounds significantly inhibited the oxidation of glycerol trioleate, and reduced the decomposition of CC and ester bonds of glycerol trioleate, which were attributed to their capability to inhibit the production of free radicals. Quercetin and gallic acid were the most effective among the condensed and hydrolyzable phenolic compounds in present study, respectively. For condensed phenolic compounds, the hydroxyl groups in B ring, substitution in C ring, and the structure of C ring played a crucial role in their inhibitory action. For hydrolyzable phenolic compounds, the amount of hydroxyl groups and their molecular weight had obvious effects on their inhibitory action. According to the measurement of molecular electrostatic potential and frontier molecular orbitals by density functional theory, the large maximum electrostatic potential and the small energy gap value were beneficial to enhance the inhibitory capability of phenolic compounds on the oxidation of glycerol trioleate. All present results suggested the potential action rule and molecular mechanism about the inhibitory effects of phenolic compounds on the oxidation of glycerol trioleate.

DFT, ADME studies and evaluation of the binding with HSA and MAO-B inhibitory potential of protoberberine alkaloids from Guatteria friesiana: theoretical insights of promising candidates for the treatment of Parkinson's disease

CONTEXT

Parkinson's disease is a chronic neurodegenerative condition that has no cure, characterized by the progressive degeneration of specific brain cells responsible for producing dopamine, a crucial neurotransmitter for controlling movement and muscle coordination. Parkinson's disease is estimated to affect around 1% of the world's population over the age of 60, but it can be diagnosed at younger ages. One of the treatment strategies for Parkinson's disease involves the use of drugs that aim to increase dopamine levels or simulate the action of dopamine in the brain. A class of commonly prescribed drugs are the so-called monoamine oxidase B (MAO-B) inhibitors due to the fact that this enzyme is responsible for metabolizing dopamine, thus reducing its levels in the brain. Studies have shown that berberine-derived alkaloids have the ability to selectively inhibit MAO-B activity, resulting in increased dopamine availability in the brain. In this context, berberine derivatives 13-hydroxy-discretinine and 7,8-dihydro-8-hydroxypalmatine, isolated from Guatteria friesiana, were evaluated via density functional theory followed by ADME studies, docking and molecular dynamic simulations with MAO-B, aiming to evaluate their anti-Parkinson potential, which have not been reported yet. Docking simulations with HSA were carried out aiming to evaluate the transport of these molecules through the circulatory system.

METHODS

The 3D structures of the berberine-derived alkaloids were modeled via the DFT approach at B3LYP-D3(BJ)/6-311 + + G(2df, 2pd) theory level using Gaussian 09 software. Solvation free energies were determined through Truhlar's solvation model. MEP and ALIE maps were generated with Multiwfn software. Autodock Vina software was used for molecular docking simulations and analysis of the interactions in the binding sites. The 3D structure of MAO-B was obtained from the Protein Data Bank website under PDB code 2V5Z. For the interaction of studied alkaloids with human serum albumin (HSA) drug sites, 3D structures with PDB codes 2BXD, 2BXG, and 4L9K were used. Molecular dynamics simulations were carried out using GROMACS 2019.4 software, with the GROMOS 53A6 force field at 100 ns simulation time. The estimation of the ligand's binding free energies was obtained via molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method.

Theoretical and experimental study of the diastereoisomers (2S) and (2R)-naringenin-6-C-β-D-glucopyranoside obtained from Clitoria guianensis

In this work the diastereoisomers (2S) and (2R)-naringenin-6-C-β-D-glucopyroside, isolated for the first time from Clitoria guianensis, were studied using the density functional theory. The frontier molecular orbitals and structural properties showed that the diastereoisomers exhibit the same energy gap 166.61 kcal mol^-1 and structural properties different, where in the S diastereoisomer, the bond length between the chiral carbon and the phenolic group is greater (difference of 0.0126 Å). The HPLC data showed that the retention time of the S-diastereoisomer (16.7 min) is shorter than that of R, suggesting that the S compound is more polar than R. The HPLC results corroborates with the molecular electrostatic potential which showed that in the S configuration, the electronegative density was more intense overall, particularly in the glucose molecule. The reactivity indices showed that the diastereoisomers are good electrophiles and reactive species. Finally, the absolute configuration of the diastereoisomers were determined using electronic circular dichroism (ECD) spectroscopy and the theoretical spectra were similar to the experimental. METHODS : All calculations of Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TDDFT) were performed using the program Gaussian 09 and the structures of the diastereoisomers were generated and analyzed using the GaussView program. The optimization and vibrational frequency calculations were performed using the functional CAM-B3LYP and 6-311 +  + G(2d,2p) basis set. Conformational searches were performed for R configuration, by molecular mechanics using the MM + , MMFF, and OPLS05 force fields; the entire molecular mechanics simulation was performed using the Maestro/MacroModel software. The calculations for the simulations of the ECD spectra were performed for the eight lowest energy conformers obtained in the geometric optimization step, and the TDDFT at the CAM-B3LYP/6-311 +  + G(2d,2p) theory level used. The effects of methanol and chloroform were calculated using the SMD implicit solvent model.