Homology modeling and molecular docking of heme peroxidase from Euphorbia tirucalli: Substrate specificity and thiol inhibitor interactions

Abstract

The crystal structure of peroxidase from Barley Grain Peroxidase 1 (1BGP) provides a good template for modeling the three dimensional structure of Euphorbia tirucalli peroxidase (ETP). Homologous three dimensional structure of ETP was built on the basis of the crystal structure of 1BGP. The reliability of the model was assessed by Ramachandran plot, Profile-3D, PROCHECK, ERRAT and PROSA analysis. The overall structure of the resulting ETP model is similar to those of the template structure. The three dimensional structure of peroxidase was docked with heme and the peroxidase-heme complex was further docked with substrates of peroxidase as well as thiol inhibitors (β-mercaptoethanol and l-cysteine) using Autodock 4.2. software. The modeled peroxidase exhibited substrate specificity in the order of pyrogallol˂guaiacol˂O-dianisidine. The inhibition kinetics of peroxidase in presence of these inhibitors were investigated. IC50 values for these inhibitors were calculated and used for kinetic studies. These studies revealed that β-mercaptoethanol is more potent inhibitor on peroxidase activity as compared to l-cysteine. To explore the binding model of the substrates with the ETP model was docked into the active site of the model and hydrophobic interaction and hydrogen bonding were found to play an important role in substrate recognition and orientation.