Chagas disease is caused by the protozoan Trypanosoma cruzi and is widely distributed throughout Latin America. Because it is a pathology neglected by the pharmaceutical industry and existing drugs have low efficacy and several side effects, interest in new drugs has been increasing. Due to the necessity of the discovery of new active compounds, the aim of this work was to relate the biological activity of natural and semi-synthetic aromatic compounds that inhibit glyceraldehyde 3-phosphate dehydrogenase enzyme. Molecular descriptors such as HOMO-LUMO frontier orbitals, partition coefficient (LogP), water solubility (LogS) and ionization potential, were calculated by molecular modeling, in addition to performing a molecular docking simulation to obtain a better molecular view of the interaction of the aromatic compounds with the active site of the enzyme. It was observed that the compounds involved in the study interacted attractively with the enzyme, in accordance with experimental studies, and had adequate solubility for good pharmacokinetics. It was also possible to relate the pharmacological activity of some compounds with the energy of the LUMO orbital. The study showed that the methodology used in this work can be used to understand the interaction of active compounds with their respective targets, saving time and resources.