Quantum chemical calculations on elucidation of molecular structure and spectroscopic insights on 2-amino-4-methoxy-6-methylpyrimidine and 2-amino-5-bromo-6-methyl-4-pyrimidinol--a comparative study

Comparative antibacterial analysis of the anthraquinone compounds based on the AIM theory, molecular docking, and dynamics simulation analysis

BACKGROUND

Hydroxyanthraquinones and anthraquinone glucoside derivatives are always considered as the active antibacterial components.

METHODS

Comparison of structure characteristics and antibacterial effect of these compounds was performed by applying quantum chemical calculations, atoms in molecules theory, molecular docking, and dynamics simulation procedure. Density functional theory calculation with B3LYP using 6-31G (d, p) basis set has been used to determine ground state molecular geometries.

RESULTS

The molecular geometric stability, electrostatic potential, frontier orbital energies, and topological properties were analyzed at the active site. Once glucose ring is introduced into the hydroxyanthraquinone rings, almost all of the positive molecular potentials are distributed among the hydroxyl hydrogen atoms of the glucose rings. In addition, low electron density ρ (r) and positive Laplacian value of the O-H bond of the anthraquinone glucoside are the evidences of the highly polarized and covalently decreased bonding interactions. The anthraquinone glucoside compounds have generally higher intermolecular binding energies than the corresponding aglycones due to the strong interaction between the glucose rings and the surrounding amino acids. Molecular dynamics simulations further explored the stability and dynamic behavior of the anthraquinone compound and protein complexes through RMSD, RMSF, SASA, and Rg.

CONCLUSION

The type of carboxyl, hydroxyl, and hydroxymethyl groups on phenyl ring and the substituent glucose rings is important to the interactions with the topoisomerase type II enzyme DNA gyrase B.

Comparative analysis of interactions between the hydropyridine dicarboxylate derivatives and different proteins by molecular docking and charge density analysis

Molecular docking and charge density analysis were carried out to understand the geometry, charge density distribution and electrostatic properties of one of newly synthesized 4-substituted-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylates (PDE), which is regarded as the best [Formula: see text]-Glucosidase inhibitor among the hydropyridine dicarboxylate derivatives. The different bonding models of the PDE molecule in the active sites of proteins Human serum albumin (HSA) and Saccharomyces cerevisiae [Formula: see text]-glucosidase (SAG) are firstly compared, which is important to understand the different intermolecular interactions between drug-transport protein and drug-target protein. The deformation density maps suggest that the electron densities of the PDE molecule are redistributed when it presents in the active sites. When the molecule presents in the active site of the SAG, it is evident to find that the negative region does not appear at the vicinity of the oxygen atoms on one of the carboxylic acid dimethyl ester group. Frontier molecular orbital density distributions for the PDE molecule are similar in all forms. The highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital (LUMO) energy gaps in the active sites are higher than that of the molecule in pure solution phase. It is generally noticed that all of the orientations of the dipole moment vectors are reoriented in both active sites. These fine details at electronic level allow to better understand the exact drug-transport protein and drug-target protein interactions.