Computational evaluation on molecular stability and binding affinity of methyldopa against Lysine-specific demethylase 4D Enzyme through quantum chemical computations and molecular docking analysis

Abstract

For the complete characterization of the molecule, quantum chemical calculations utilizing density functional theory (DFT) were performed at the B3LYP/6–311++G(d,p) level of theory. The quantum theory of atoms in molecules (QTAIM) and the reduced density gradient (RDG) analysis were implemented to investigate non-covalent interactions. The electronic environment of each atom in a molecule was explored using an electron localization function (ELF). Molecular stability of dimer structure due to intermolecular hydrogen bonds: O29-H54⋅⋅⋅O2, O1-H26⋅⋅⋅O30, and O32-H56⋅⋅⋅O4 and their corresponding stabilization energies were predicted by natural bond orbital (NBO) analysis. The energy gap and global and local reactivity parameters were determined to predict the chemical reactivity. The molecular electrostatic potential (MEP) was used to predict the electrophilic and nucleophilic sites. The frontier molecular orbitals (FMOs) were also portrayed using a density of states (DOS). Molecular docking was performed to study the interaction of the molecule with an enzyme, Lysine-specific demethylase 4D-like, a human protein.