Cruzain Inhibitor Discovery Stalled by Affinity-First Optimization, Needs Multiparametric Framework for Clinical Translation

Chagas disease, caused by Trypanosoma cruzi, remains a life-threatening illness with uncertain efficacy for guideline-recommended treatments, particularly in heart failure with reduced ejection fraction (HFrEF). Cruzain, the principal cysteine protease of T. cruzi, is a validated drug target. Despite decades of research yielding numerous potent inhibitors, none have advanced to clinical candidates, highlighting a significant translational gap in drug discovery for this neglected tropical disease.

This review analyzed over 215 cruzain inhibitors with IC50 ≤ 1 μM and 30+ crystal structures, examining their translational failures over three decades. It synthesized insights from diverse chemical classes, including peptidyl vinyl sulfones, non-peptidic scaffolds, and thiosemicarbazones. The authors assessed the application of computational approaches like docking, molecular dynamics, free-energy perturbation, and machine-learning QSAR in relation to their affinity-centered objectives.

The review identifies a 'translational paradox' where 215 cruzain inhibitors with IC50 ≤ 1 μM and 30+ crystal structures have yielded no clinical candidates for Chagas disease. This failure stems from a persistent strategic mismatch: enzymatic potency has been systematically prioritized over crucial determinants of intracellular efficacy. Specifically, inhibitors across peptidyl vinyl sulfones, non-peptidic scaffolds, and thiosemicarbazones fail due to poor permeability, inadequate metabolic stability, or insufficient cathepsin selectivity. > Computational approaches, despite increasing sophistication, have been misdirected towards affinity-centered objectives, underrepresenting exposure constraints. The authors propose a multiparametric optimization framework, including provisional viability benchmarks and a feasibility-envelope concept, reframing discovery as a constraint-satisfaction problem rather than potency maximization. This framework outlines quantitative criteria for future cruzain leads, explaining why structurally tractable intracellular cysteine protease targets can remain clinically unrealized.