Exploring the interaction of 5,6-benzocoumarin-3-carboxylic acid with bovine serum albumin at the molecular level: A biophysical investigation using molecular dynamics

Abstract

In this work, molecular dynamics (MD) is used to monitor the conformational space spanned by a ligand when in the binding pocket of a protein. 5,6-benzocoumarin-3-carboxylic acid was chosen as it is a relatively rigid molecule, with only one rotational degree of freedom, useful in its simplicity, whereas bovine serum albumin was used as a model protein. The initial geometry of the protein-ligand complex was obtained by molecular docking. The MD simulation was carried out for 90 ns and the dynamic evolution of the system was explored based on the usual parameters: root mean square deviation (RMSD), radius of gyration (Rg) and root mean square fluctuation (RMSF). The MD trajectory was analysed and interpreted in terms of the hydrogen bonds formed with the surrounding aminoacid residues and the conformational space spanned by the ligand during the interaction process.