Accessibility of substituted cysteines in TM2 and TM10 transmembrane segments in the Plasmodium falciparum equilibrative nucleoside transporter PfENT1

Putative purine nucleoside interacting residues in the malaria parasite purine uptake transporter PfENT1 are critical for transporter function

Malaria remains a major public health threat for billions of people worldwide. Infection with obligate intracellular, unicellular parasites from the genus Plasmodium causes malaria. Plasmodium falciparum causes the deadliest form of human malaria. Plasmodium parasites are purine auxotrophic. They rely on purine import from the host red blood cell cytoplasm via equilibrative nucleoside transporters to supply substrates to the purine salvage pathway. We previously developed a high throughput screening assay to identify inhibitors of the P. falciparum Equilibrative Nucleoside Transporter Type 1 (PfENT1). Screening a small molecule library identified PfENT1 inhibitors that blocked proliferation of P. falciparum parasites in in vitro culture. The goal of the current work was to validate a high-resolution model of PfENT1 predicted by the AlphaFold protein structure prediction program. We superimposed the predicted PfENT1 structure on the human homologue structure, hENT1, and developed a structure-based sequence alignment. We mutated the residues in PfENT1 aligned with and flanking the residues in hENT1 that interact with the purine analog, nitrobenzylthioinosine (NBMPR). Mutation of the PfENT1 residues Q135, D287, and R291 that are predicted to form hydrogen bonds to purine nucleosides eliminated purine and pyrimidine transport function in various yeast-based growth and radiolabeled substrate uptake assays. Mutation of two flanking residues, W53 and S290, also resulted in inactive protein. Mutation of L50 that forms hydrophobic interactions with the purine nucleobase reduced transport function. Based on our results the AlphaFold predicted structure for PfENT1 may be useful in guiding medicinal chemistry efforts to improve the potency of our PfENT1 inhibitors.

Impact of Field Isolate Identified Nonsynonymous Single Nucleotide Polymorphisms on Plasmodium falciparum Equilibrative Nucleoside Transporter 1 Inhibitor Efficacy

Plasmodium falciparum causes the most severe form of malaria and causes approximately 500 000 deaths per year. P. falciparum parasites resistant to current antimalarial treatments are spreading. Therefore, it is imperative to develop new antimalarial drugs. Malaria parasites are purine auxotrophic. They rely on purine import from the host erythrocyte via Equilibrative Nucleoside Transporters (ENTs). Recently, inhibitors of the P. falciparum ENT1 (PfENT1) that inhibit proliferation of malaria parasites in culture have been identified as promising starting points for antimalarial drug development. Genome sequencing of P. falciparum field isolates has identified nonsynonymous single nucleotide polymorphisms (SNPs) in the gene encoding PfENT1. Here we evaluate the impact of these PfENT1 SNPs on purine substrate affinity and inhibitor efficacy. We expressed each PfENT1-SNP in Saccharomyces cerevisiae. Using PfENT1-SNP-expressing yeast, we characterized the PfENT1 purine substrate affinity using radiolabeled substrate uptake inhibition experiments. Four of the 13 SNPs altered affinity for one or more purines by up to 7-fold. Three of the SNPs reduced the potency of a subset of the inhibitors by up to 7-fold. One SNP, Q284E, reduced the potency of all six inhibitor chemotypes. We tested drug efficacy in available parasite strains containing PfENT1 SNPs. While PfENT1-SNP-expressing yeast had decreased sensitivity to PfENT1 inhibitors, parasite strains containing SNPs showed similar or more potent inhibition of proliferation with all PfENT1 inhibitors. Thus, parasite strains bearing PfENT1 SNPs are not resistant to these PfENT1 inhibitors. This supports PfENT1 as a promising target for further development of novel antimalarial drugs.