The search of useful plants to human health is of great importance to science once they area reservoir of active principles that can be used as a medicine for a variety of pathologies. The family Rutaceae is well known for the numerous quantity and diversity of secondary metabolites that can be potential new drugs. Metrodorea stipularis (Rutaceae) is a plant endemic to Brazil, it is popularly known by arco de pipa, laranjeira-do-mato and limoeira-do-mato, caputuna and cataguá. In our investigation for enzimatic inhibitors we have found the extracts of the stems of M. stipularis inhibited the activity of cathepsins and cruzain. Cruzain is an enzyme that participates in the pathway of proteolytic digestion of the parasite Trypanosoma cruzi, and plays an essential role in its life process; therefore, it is an interesting biological target for the search for new compounds Chagas disease. The isolation procedures have led to the pure alkaloids 1, 2, 3 and 4. Compounds 1-4 displayed IC50 values of cruzain inhibition ranging from 22-99 µM. Compounds 3 and 4 have not been described in the literature yet, and are proposed to be intermediate in biosynthesis route of 1 and 2.