Structural characterization of the Plasmodium falciparum lactate transporter PfFNT alone and in complex with antimalarial compound MMV007839 reveals its inhibition mechanism

Abstract

Plasmodium falciparum, the deadliest causal agent of malaria, caused more than half of the 229 million malaria cases worldwide in 2019. The emergence and spreading of frontline drug-resistant Plasmodium strains are challenging to overcome in the battle against malaria and raise urgent demands for novel antimalarial agents. The P. falciparum formate–nitrite transporter (PfFNT) is a potential drug target due to its housekeeping role in lactate efflux during the intraerythrocytic stage. Targeting PfFNT, MMV007839 was identified as a lead compound that kills parasites at submicromolar concentrations. Here, we present 2 cryogenic-electron microscopy (cryo-EM) structures of PfFNT, one with the protein in its apo form and one with it in complex with MMV007839, both at 2.3 Å resolution. Benefiting from the high-resolution structures, our study provides the molecular basis for both the lactate transport of PfFNT and the inhibition mechanism of MMV007839, which facilitates further antimalarial drug design.

Discovery and Development of Inhibitors of the Plasmodial FNT-Type Lactate Transporter as Novel Antimalarials

“…Very recently, the protein structure of PfFNT was revealed as a complex with the MMV007839 inhibitor (Figure 7) [28,29]. The data confirm that the vinylogous acid represents the binding tautomer.…”

“…The binding site in the cytoplasmic vestibule and constriction region, as well as the interacting amino acids, were found to be correctly predicted in our models. Eventually, the proposed clash of the hydroxyl moieties from the PfFNT G107S resistance mutation with MMV007839, and the resolution of the collision by removal of the phenyl hydroxyl and formation of a hydrogen bond instead with the BH267.meta compound were found to be highly plausible as deduced from modeling (Figure 7) [29].…”

“…predicted in our models. Eventually, the proposed clash of the hydroxyl moieties from the PfFNT G107S resistance mutation with MMV007839, and the resolution of the collision by removal of the phenyl hydroxyl and formation of a hydrogen bond instead with the BH267.meta compound were found to be highly plausible as deduced from modeling (Figure 7) [29]. Visualization of MMV007839 bound to PfFNT was done using PDB# 7e27 with the Maestro software (Release 2021-3; Schrödinger, New York, USA).…”

“…PfFNT is a homopentameric membrane protein (Figure 2, left) [27][28][29]. Each protomer acts as an individual bidirectional transport unit (Figure 2, center) [30].…”

“…Each protomer acts as an individual bidirectional transport unit (Figure 2, center) [30]. The N-and C-termini are located at the cytoplasmic side, and the protomer fold consists of six transmembrane helices around a symmetrical narrow transport path [28][29][30][31][32]. Two lipophilic constrictions isolate a highly conserved central histidine residue from wider vestibules at both entrance sites (Figure 2, right).…”