Transporters play a vital role in both the resistance mechanisms of existing drugs and effective targeting of their replacements. Melarsoprol and diamidine compounds similar to pentamidine and furamidine are primarily taken up by trypanosomes of the genus Trypanosoma brucei through the P2 aminopurine transporter. In standardized competition experiments with [ 3 H]adenosine, P2 transporter inhibition constants (K i ) have been determined for a diverse dataset of adenosine analogs, diamidines, Food and Drug Administration-approved compounds and analogs thereof, and custom-designed trypanocidal compounds. Computational biology has been employed to investigate compound structure diversity in relation to P2 transporter interaction. These explorations have led to models for inhibition predictions of known and novel compounds to obtain information about the molecular basis for P2 transporter inhibition. A common pharmacophore for P2 transporter inhibition has been identified along with other key structural characteristics. Our model provides insight into P2 transporter interactions with known compounds and contributes to strategies for the design of novel antiparasitic compounds. This approach offers a quantitative and predictive tool for molecular recognition by specific transporters without the need for structural or even primary sequence information of the transport protein.Trypanosoma brucei are unicellular trypanosomal parasites that cause African sleeping sickness in humans and nagana in livestock. These trypanosomes are auxotrophic for purines and thus rely entirely on purine supplies salvaged from the host environment. As such, T. brucei brucei expresses a multitude of purine nucleoside and nucleobase transporters (1). One of these, the T. brucei aminopurine P2 transporter, is unusual as a genuine nucleoside-nucleobase transporter in that it equally transports the nucleoside adenosine and the nucleobase adenine but has virtually no affinity for any other natural purines or pyrimidines (1-3). Yet, despite this apparent high level of selectivity, it has been shown that P2 also mediates cellular uptake of the Food and Drug Administration-approved drugs melarsoprol and pentamidine (2, 4, 5), the main veterinary trypanocides diminazene aceturate (6) and possibly isometamidium (7), and various nucleoside drugs (8).The unusual nature of this transporter has led to efforts to exploit it as an efficient conduit for novel trypanocides (9, 10), but this requires the identification of the exact pharmacophore as well as the physical limitations on size and charge distribution of the extracellular binding site of the transporter. From the structural similarities between known P2 substrates, it could be concluded early on that the so-called amidine motif of adenine, i.e. N(1)ϭC(6)-NH 2 (see Fig. 1), was very likely to play a major role in the high affinity interaction with the transporter (3, 11). However, quantitative information or three-dimensional models explaining the high affinity binding, by one transporter, of such di...