Molecular design and synthesis of reversible cruzain inhibitors

Abstract

The cruzain, a major Trypanosoma cruzi cysteine protease, is an enzyme essential for the life cycle of the parasite and has been used as a viable target for the search of enzyme inhibitors as drug candidates. The peptide-mimetic compound K11777 inhibits cruzain in nanomolar concentration and acts by a mechanism of irreversible inhibition. This strong interaction seems to be essential for the inhibition process and death of the parasite since several studies have shown that irreversible cruzain inhibition by small molecules, eradicate the infection caused by the parasite in cell cultures and animal models. Analogs or derivatives K11777 generally contain electrophilic functional groups known as "warheads" that can bind covalently to the active site via nucleophilic attack by the catalytic cysteine. Although this mechanism has been extensively studied, few other studies have explored the influence of the nature of the covalent bond in the process of reversible covalent inhibition in cruzain. This work will be carried out to a detailed computational study using 3D-QSAR (CoMFA / CoMSIA), covalent docking, molecular dynamics and free energy calculations of interaction for known inhibitors of cruzain to better understand the process of reversibility associated with inhibition and death of the parasite. Initially, a model will be developed with the goal of mapping the essential features for disclosing of any structure-activity relationships (SAR). The evaluation of this model will be carried out using data from both our laboratory as well as the current literature. Based on these results, new commercially putative cruzain inhibitors will be purchased and assayed to validate the model. Cysteine protease inhibitors are also susceptible to electrophilic nitriles to achieve potency at nanomolar concentrations. However, such inhibitors may have higher or lower off-target effects depending on the nature of the electrophilic substituted nitriles. Thus, in this project analogs and/or derivatives of bioactive compounds present in the models will be synthesized, when acceptable reactivity against thiol-nucleophiles is likely to be found. Compounds will be tested by fluorimetric methods, time-dependent, in order to experimentally quantify the contribution of the molecular changes in potency and selectivity against cruzain and cathepsin L. (AU)