Simulação computacional das interações entre o herbicida Glifosato e a enzima 5-Enolpiruvil-Shikimato-3-Fosfato Sintase (EPSPs) no desenvolvimento de um nanobiossensor

Abstract

This work aims to developed a molecular model that can describe equilibrium properties, as well as the interacting forces involved in an enzyme-inhibitor system, where the enzyme is the 5-Enolpyruvyl-Shikimate-3-Phosphate Synthase (EPSPs) and its inhibitor is the glyphosate herbicide (GPJ). The participation of the substrate Shikimate-3-Phosphate (S3P) was also studied. The stability and distribution of charges along the surface of the EPSPs enzyme were analyzed for the development of a specific nanobiosensor for glyphosate herbicide detection through the functionalization of the tip of an atomic force microscope (AFM) with the enzyme EPSPs. The parameterization of two dihedral angles for the GPJ herbicide was obtained through mechanical-quantum calculations at the Hartree Fock level using the 6-31G* base set. The parameters obtained, related to the Ryckaert-Bellemans coefficients, were implemented in the OPLS-AA force field, used by the GROMACS program. Steered Molecular Dynamics Simulations (SMD) were performed in three possible unbinding pathways, to remove the herbicide from the active site, applying external harmonic forces with a force constant equivalent to that of the AFM cantilever, in order to simulate experiments to detect the herbicide by atomic force microscopy. A second-order cumulant expansion of the Jarzynski’s equation was used to calculate the free energy profile along the reaction coordinate and to obtain the potential of mean force (PMF) of the SMD simulations. The three paths chosen presented different energetic barriers related to the disruption of inhibitor interactions with the enzyme. These energy barriers calculated by the simulations are in the same order of magnitude as the bond free energies for similar systems obtained from the experimental inhibition constants.