Decomposition of the interaction energy of several flavonoids with Escherichia coli DNA Gyr using the SAPT (DFT) method: The relation between the interaction energy components, ligand structure, and biological activity

Abstract

In this study, the SAPT (DFT) method is used to determine the components of the electronic interaction energies (electrostatic (E_ele), exchange (E_ex), induction (E_ind), exchange-induction (E_ex-ind), dispersion (E_disp), and exchange-dispersion (E_ex-disp)) between the several selected flavonoids and the important residues of the active site of Escherichia coli DNA Gyr determined by molecular docking. A significant linear correlation between the calculated SAPT (DFT) interaction energies of flavonoids and their experimental pIC50 values is found, which is not observed for the free binding energies (ΔG_b) of flavonoids obtained from molecular docking. The variation of the interaction energy components of flavonoids with their structural differences is investigated to find the relation between the flavonoids structures and their biological activity based on the interaction energy components.

Keywords: Energy decomposition analysis (EDA); Flavonoid; Molecular docking; Protein-ligand interaction; SAPT (DFT).