Antitrypanosomal Potential of Chalcone-Based Ursolic Acid Derivatives via Ligand-Based Virtual Screening, DMPK Analyses, Molecular Dynamics Simulation, and MM/GBSA Binding Energy

Chagas disease, caused by the protozoan parasite Trypanosoma cruzi and transmitted mainly by triatomine insects, represents a significant challenge to public health, especially in impoverished regions. Current treatments, such as benznidazole and nifurtimox, have limitations, including serious side effects and reduced efficacy in the chronic phase. This work aims to evaluate the antitrypanosomal activity of ursolic acid-derived chalcones (UACD) using a ligand-based virtual screening approach. To this end, a series of independent molecular docking simulations were carried out (via AutoDock Vina code) with the parasite proliferation cycle enzymes TcGAPDH and cruzain. The most favorable candidates underwent drug metabolism and pharmacokinetics (DMPK) analyses and molecular dynamics (MD) simulations to estimate the pharmacokinetic and pharmacodynamic profile. Molecular docking simulations showed that the UACD derivatives showed better specificity for the TcGAPDH enzyme, emphasizing the ursolic acid and UACD3 derivatives (affinity energy = −9.4 kcal/mol for each). The DMPK prediction showed that the derivatives present viable apparent permeability (P_app) that promotes an excellent absorbed fraction (in 10⁻⁶ cm/s). MD simulations showed that the UACD3 derivative showed better free energy when binding to the TcGAPDH enzyme (−13.27 ± 1.87 kcal/mol) and interacting with the active site residues Cys166 and Thr167. However, both ligands appear to be alternative therapies in treating Chagas disease.