Structure-Based Discovery of Non-Covalent Triazole-Based Cruzipain Inhibitors with Improved Bioactivity Translation

Abstract

Chagas disease is a neglected tropical condition with limited treatment options, emphasizing the need for new antichagasic agents. Cruzipain (CZP), the main cysteine protease of Trypanosoma cruzi, is a validated target; however, achieving strong trypanocidal activity through CZP inhibition remains challenging. In this work, we report a series of novel triazole-based noncovalent CZP inhibitors designed by applying state-of-the-art molecular modeling techniques, showing good potency against isolated CZP combined with effective trypanocidal activity. Structure–activity relationships that define key pharmacodynamic features were elucidated, enabling analogues to translate enzymatic inhibition into cellular effects. The computer-aided design workflow combining molecular docking, molecular dynamics simulations, and binding free-energy calculations was key to reveal conserved interaction patterns within the oxyanion hole and the S1/S1′ subsites (Gln19, His162, Trp184) of CZP for the most effective inhibitors. Overall, our findings introduce new 1,2,3-triazole-based antichagasic candidates and clarify molecular determinants influencing the translational gap between enzymatic and cellular activity, contributing with a predictive framework for the rational design of CZP-targeted inhibitors for Chagas disease therapy.