The use of the permeable cells system for study trans-splicing reaction in trypanosomes, as described for Ullu & Tschudi (1990) and standardized for T. cruzi by Ambrósio et al. (2004), it helps in the inquiry of the synthesis, processing and regulation of mRNAs in trypanosomes. In this work, the activities of two substances derived from the cubebin were evaluated, hinokynin (HQ) and 6,6' - dinitrohinokynin (DNH), using Y strain of T. cruzi epimastigote permeable cells. Initially, for screening the activity of these derivatives, the non-radioactive trans-splicing reaction was done and submitted to the polyacrilamide gels and silver stain. To confirm the results and evaluate the activity of substances in the RNA maturation process, an anti-sense probe using the SL RNA was transcribed and used with permeable cells radioactive reaction to make the RNase protection. The results showed that both substances were active on the transcription reaction of the parasites. DNH caused a reduction in the amount of the RNA (detected by densitometry), which it was not proportional to the increase of its concentration, when compared with HQ, which demonstrated that when the concentration raised, the optical densities of the RNA bands were diminishing. The results of RNase protection reaction showed that RNA bands just synthesized were more evident after the addition of substances, allowing to conclude that, HQ and DNH modified the RNA metabolism of these parasites promoting an increase of the transcription and, consequently, the mRNA synthesis. These substances seem, still, to affect the posterior stage of mRNAs maturation, the trans-splicing reaction itself. Because of the analysis of the trans-splicing products occurred at 20 minutes after drug incubation with the cells, these results suggest that their trypanocidal activity would promote accumulation in the cell of any kind of mRNA, in the attempt to supply some vital enzymatic blockade in the metabolism of the parasite. Further studies are in progress in our laboratory to better understand these findings.