This study investigated the functioning of the E protein using molecular docking and molecular dynamics techniques. Furthermore, five inhibitors were also proposed using computational simulations. The root-mean-square deviations (RMSDs) analysis confirmed the equilibration of all five complexes within the simulation time. The study compared the electrostatic potentials (ESPs), secondary structures, non-covalent interactions, root-mean-square fluctuations (RMSF), and inhibitors binding free energies to discuss the preferential binding of these inhibitors and the coordination flexibility of the enzyme.