The antiparasitic activity of two tetrahydrodiisoquinoline alkaloids 2, 3, β-allocryptopine (4), protopine (5), and a substituted phenylethylamine 6 was studied. Compounds 2 and 6 inhibited the growth of the parasite Leishmania donovani. The capability of the examined compounds to bind DNA was estimated by molecular modeling. It has been shown that binding occurs in the small groove and primarily at the AT-enriched part of the oligonucleotide.Protoberberine compounds include an important class of isoquinoline alkaloids (IQA) that exhibit a broad spectrum of pharmacological activity [1,2]. The type of IQA is currently of great interest because of the characteristic manifestation of high cytotoxicity and antiparasite activity (for example, berberine is known in folk medicine as a powerful agent for treating many parasite-borne diseases) [3]. Considering the demand for new promising antiparasite and antitumor preparations [4,5], the present work is very timely.The antitumor activity of berberine (1) and its cytotoxic analogs is related to their ability to inactivate topoisomerase I (and topoisomerase II in certain instances). It is assumed that the key step in this process is the specific binding of the alkaloid to DNA that stabilizes the ternary complex DNA-topoisomerase-alkaloid [6][7][8]. Under normal conditions (without alkaloid), topoisomerase I performs one of its key tasks related to the cleavage of two DNA chains (introduces a single-strand break into the DNA chain), thereby preparing for the subsequent processes of replication and transcription. Fluorescence analysis and NMR spectroscopy have now established that berberine exhibits high affinity toward DNA [9]. Studies of the interaction of protoberberine alkaloids with oligonucleotides confirm the hypothesis that the alkaloid binds primarily to the small groove (SG) of the DNA helix [7,9,10].The mechanism of the antiparasite activity of berberine and its analogs cannot be unambiguously determined by experimental data. In particular, it cannot be determined if this is a consequence of binding with kinetoplast DNA. However, it has been reported that compounds that are cytotoxic or have the capability to interact with human DNA typically exhibit antiparasite activity. The interaction with the SG or intercalation are usually examined because both of these types of interaction affect DNA and/or topoisomerase of parasites [11][12][13]. The alkaloid camptothecine, on the basis of which many antitumor preparations have been created and tested clinically, provides an example. Camptothecine, like berberine, forms ternary complexes with DNA and topoisomerase. it has been shown experimentally that camptothecine can form covalent DNA-topoisomerase complexes with human (nuclear) DNA and kinetoplast DNA isolated from trypanosomes, leischmania, and other parasites [6].