In silico study on a formation of intramolecular hydrogen bonding of ligand molecule at a protein aromatic hydrophobic pocket

Abstract

A hydrophobic interaction is one of the most known interactions observed between a protein and a ligand. In general, it is well known that the hydrophobic atoms of a ligand locating on a hydrophobic pocket provide stabilization of the protein and ligand complex. On the other hand, recently, an argadin was discovered as one of the chitinase inhibitor and the binding pose was observed with X-ray crystallographic analysis (PDB ID: 1H0G). In the X-ray analysis, the very interested binding pose was observed. In the hydrophobic pocket formed by aromatic amino acid residues, two hydrophilic charged fragments of argadin forms the intramolecule hydrogen bonding. To our knowledge, however, the role of argadin intramolecule hydrogen bonding in the chitinase hydrophobic pocket is not known, yet. So, in the study, we performed ab initio molecular orbital and density functional theory calculations including the contribution of dispersion interaction to research of the role of argadin intramolecular hydrogen bonding and to reveal the characteristic features of intermolecular interactions.