A computation model has been developed for the rational design of bioactive pharmacophore sites as anti-Mycobacterium tuberculosis and anti-Trypanosoma cruzi (TC) candidates. The 40 compounds 1–40 analyzed have been previously screened for their antitubercular and antitrypanosomal activity. The highest anti-TC activity is obtained for compounds 8 and 18 which exhibited low IC50 values (9.2 and 10.8 lM), almost equal to clinical drug, nifurtimox (7.7 lM; 100 % Inhib.). This could be attributed to the existence of two synergic (Od-–Nd-) and (Od-–Od-) antitrypanosomal pharmacophore sites. In contrast to compounds 8 and 18 which contain electroattractor groups (R1 , R2 = F), analog compounds 1 and 13 with electro-donor or only hydrogen (R1 , R2 = CH3, H) show best antibacterial activity (MIC = 0.977 and 1.190 lg/mL) very close to antitubercular activity of Rifampicin (MIC = 0.125 lg/mL). This could be attributed to the existence of (Od-–NHd?) antibacterial pharmacophore site.