Identification of Novel Trypanosoma cruzi Cysteine Protease Inhibitors via Ligand-Based Virtual Screening of FDA-Approved Drugs with Trypanocidal Activity

Background: Chagas disease is a major public health problem, especially in Latin American countries, and benznidazole and nifurtimox are currently the only drugs available for its treatment. However, they present several disadvantages, such as low availability, high toxicity, and limited efficacy, which often result in treatment discontinuation. In recent decades, bioinformatics studies have accelerated the field of drug repurposing, reducing time and costs. In this study, the aim was to identify novel cruzain inhibitors from the analogs of FDA-approved drugs with trypanocidal activity. Methods: A ligand-based virtual screen, along with molecular docking analysis, was carried out, and the selected compounds were evaluated for their trypanocidal activity against trypomastigotes of two endemic Mexican strains and their inhibitory activity on cysteine proteases. Results: A cefsulodin analog (LC50 = 126.18 and 77.50 µM), two flucloxacillin analogs (LC50 = 94.05 and 101.73 µM; 48.74 and 64.49 µM), and one piperacillin analog (LC50 = 48.46 and 83.68 µM) had better trypanocidal activity and selectivity index against the NINOA and INC-5 strains than the reference drugs. Enzymatic evaluation showed that all four compounds inhibited cysteine proteases (IC50 < 840.03 µM). Furthermore, molecular dynamics simulations predicted the stability of the compound–protein complex, while the docking test on human cathepsin L predicted their potential selectivity. Finally, our in silico analysis of ADMET properties showed that all compounds exhibited favorable profiles. Conclusions: These results encourage the development of new and more potent anti-Trypanosoma cruzi agents using FDA-approved drugs as scaffolds.