Structure-Based Identification of Non-covalent Prolyl Oligopeptidase 80 Inhibitors Targeting <i>Trypanosoma cruzi</i> Cell Entry

Chagas disease remains a persistent public health challenge due to the limited efficacy and significant toxicity of current pharmacological treatments. This highlights the urgent need for novel drugs with innovative mechanisms of action, specifically targeting cell infection pathways. The prolyl oligopeptidase of <i>Trypanosoma cruzi</i> (POPTc80) has emerged as a promising target for developing inhibitors to block the parasite's infection process. In this study, we developed a robust structure-based virtual screening pipeline to discover potent POPTc80 inhibitors. The customized protocol integrated structural analysis of the 3D structure of POPTc80 and enrichment analysis of molecular docking and shape-based models to optimize the selection of potential inhibitors. After optimization, a large-scale virtual screening of 1.3 million compounds prioritized 19 putative hits for experimental validation. Nine of these compounds demonstrated inhibitory activity at nanomolar concentrations. The most potent inhibitors─LC-44 (<i>K</i>_<i>i</i> = 0.175 μM), LC-45 (<i>K</i>_<i>i</i> = 0.054 μM), LC-46 (<i>K</i>_<i>i</i> = 0.513 μM), LC-50 (<i>K</i>_<i>i</i> = 0.44 μM), LC-53 (<i>K</i>_<i>i</i> = 0.158 μM), and LC-55 (<i>K</i>_<i>i</i> = 0.83 μM)─demonstrated superior inhibitory activity, consistent with the competitive inhibition mechanism predicted by our computational protocol. Subsequently, a phenotypic assay confirmed their ability to effectively inhibit <i>T. cruzi</i> entry into host cells in a dose-dependent manner, further validating their mechanism of action. These findings establish these compounds as promising chemical scaffolds for prospective hit-to-lead optimization, offering a unique opportunity to develop novel, mechanism-driven therapeutics targeting a critical step in the parasite's infection process.