Planejamento de inibidores da cruzaína baseado em fragmentos
Fonseca, Emanuella Maria Barreto
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The Chagas disease, described in 1909 by the Brazilian sanitary physician, scientist and bacteriologist Dr. Carlos Chagas, is caused by the Trypanosomatid parasite Trypanosoma cruzi. Current treatments involve the use of drugs benznidazole and nifurtimox, which are effective only in the early stage of the disease (acute phase), but have severe side effects. The enzyme cruzain is a validated target for searching small molecules to act against Chagas disease. Cruzain inhibition has been studied for the discovery and development of new drugs. In this work, the planning strategy was based on molecular fragments, using a computational approach for selecting them. Using GRID/CPCA, important residues such as Ser207 and Asp69 were identified in an adjacent cavity to the S2 sub-site of the enzyme. These residues can take part on hydrogen-bond interactions and have not been explored in the search for inhibitors for this target. In addition, we identified patterns of molecular recognition of the enzyme, based on the structures deposited in the Protein Data Bank, which are co-crystallized with inhibitors at the site of the enzyme. These inhibitors were used to guide the search via SMARTS pattern to build a fragment database. Docking and molecular dynamics were used to select the fragments for an in vitro assay. Many fragments were acquired and tested against cruzain using the technique of fluorescence spectroscopy. One fragment (Nequimed147) showed activity, inhibiting the enzyme with IC50 equal to 2.39 mM, resulting in a ligand efficiency of 0.23 kcal mol-1 weight atom-1. Based on this fragment, new inhibitors were identified with IC50 between 1.25 and 4.29 mM. Their ligand efficiencies were in the range of 0.21 and 0.26 kcal mol-1 weight atom-1 whose molecular recognition features are suitable for the search of new enzyme inhibitors likely to bind the cavity near the S2 sub-site that has not been explored yet.