The therapeutic index of antimetabolites such as purine analogues is in large part determined by the extent to which it is selectively accumulated by the target cell. In the current study we have compared the transport of purine nucleobase analogues by the H2 transporter of bloodstream form Trypanosoma brucei brucei and the equilibrative nucleobase transporter of human erythrocytes. The H2 transporter forms hydrogen bonds with hypoxanthine at positions N3, N7, N(1)H, and N(9)H of the purine ring, with apparent ⌬G 0 of 7.7-12.6 kJ/mol. The transporter also appears to H-bond with the amine group of adenine. The human transporter forms hydrogen bonds that form to (6)NH 2 and N1 of adenine. An H-bond is also formed with N3 and the 6-keto and amine groups of guanine but not with the protonated N1, thus explaining the low affinity for hypoxanthine. N7 and N9 do not directly interact with the human transporter in the form of H-bonds, and it is proposed that -stacking interactions contribute significantly to permeant binding. The potential for selective uptake of antimetabolites by the parasite transporter was demonstrated.Purine and pyrimidine antimetabolites are widely used to combat a variety of infectious diseases and other pathologies. However, many therapies suffer from a lack of selectivity, leading to severe side effects. The selectivity and efficacy of purine antimetabolites is achieved at two levels: the cell-surface transporters that mediate access to the cell, and the enzymes of the purine metabolic pathways that convert the prodrug to the cytotoxic metabolite, usually a nucleotide analogue. This report elucidates the mechanisms of selectivity at the transporter level.We have chosen Trypanosoma brucei, the etiological agent of sleeping sickness, as a model organism, because it lives freely in the host bloodstream rather than within a host cell. Therefore, the accumulation of most nucleobase and nucleoside drugs depends exclusively on the transporters expressed by the parasite itself. In addition, African trypanosomes are entirely dependent on purine salvage because they lack the capacity for de novo synthesis (1), and they consequently express several proton symporters that actively accumulate nucleosides (2, 3) and nucleobases (4 -6). For trypanosomes, nucleobases may make more efficient drugs than their corresponding nucleosides, because purine ribonucleosides are rapidly hydrolyzed in bloodstream form T. brucei, limiting their incorporation into the nucleotide pool (7). In contrast, nucleobases are efficiently assimilated by one-step reactions of phosphoribosyltransferases for adenine, hypoxanthineguanine, and xanthine (8). The current study therefore focuses on the main T. brucei brucei and human nucleobase transporters. This approach will allow the identification of groups that determine high affinity uptake by either the trypanosome or the cells of its mammalian host. The escalating epidemic of African trypanosomiasis (9) and the onset of drug resistance (10) necessitate the development of a new genera...