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

Abstract

Hydroxyanthraquinones and anthraquinone glucoside derivatives are always considered as the active antibacterial components. Comprehensive comparison and analysis of these compounds were performed for their structure characteristics and antibacterial effect by applying quantum chemical calculations, atoms in molecules theory, molecular docking and dynamics simulation procedure. The molecular geometric con guration, stability, electrostatic potential, the frontier orbital energies and topological properties were analyzed. 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. The type of carboxyl, hydroxyl, hydroxylmethyl groups on phenyl ring and the substituent glucose rings are important to the interactions with the topoisomerase type II enzyme DNA gyrase B.

Synthesis of a New Series of Anthraquinone-Linked Cyclopentanone Derivatives: Investigating the Antioxidant, Antibacterial, Cytotoxic and Tyrosinase Inhibitory Activities of the Mushroom Tyrosinase Enzyme Using Molecular Docking

“…Molecular dynamics simulations were performed by Desmond and Schrödinger to dock the complex structures of ligand compound 2 with 2Y9X proteins. 48 In previous studies, we compared the molecular dynamics simulations to examine the interactions and stability of compounds with native ligands and kojic acid. 49 The stability and simulation of the complexes were analysed and are depicted in…”

Role of anthraquinones in combating insulin resistance

“…Additionally, they are also found in the metabolites of lichens and fungi ( Li and Jiang, 2018 ). It is now well established that anthraquinones exhibit a wide range of biological activities, such as anticancer ( Zhang et al, 2021 ), anti-inflammatory ( Xie et al, 2022 ), antibacterial ( Qi et al, 2022 ), anti-oxidant ( Yin et al, 2022 ), and antiviral effects ( Dai et al, 2017 ). They have also been shown to have great potential in the prevention and treatment of various diseases, including cancer and diabetes.…”