A computation model has been developed forthe rational design of bioactive pharmacophore sites as anti-Mycobacterium tuberculosis and anti-Trypanosomacruzi (TC) candidates. The 40 compounds 1–40 analyzed have been previously screened for their antitubercular andantitrypanosomal activity. The highest anti-TC activity is obtained for compounds 8 and 18 which exhibited low IC50values (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. Incontrast to compounds 8 and 18 which contain electro-attractor groups (R1with electro-donor or only hydrogen (R1show best antibacterial activity (MIC = 0.977 and 1.190lg/mL) very close to antitubercular activity of Rifampicin, R2 = F), analog compounds 1 and 13, R2 = CH3, H).