Comparative chemical genomics reveal that the spiroindolone antimalarial KAE609 (Cipargamin) is a P-type ATPase inhibitor

Abstract

The spiroindolones, a new class of antimalarial medicines discovered in a cellular screen, are rendered less active by mutations in a parasite P-type ATPase, PfATP4. We show here that S. cerevisiae also acquires mutations in a gene encoding a P-type ATPase (ScPMA1) after exposure to spiroindolones and that these mutations are sufficient for resistance. KAE609 resistance mutations in ScPMA1 do not confer resistance to unrelated antimicrobials, but do confer cross sensitivity to the alkyl-lysophospholipid edelfosine, which is known to displace ScPma1p from the plasma membrane. Using an in vitro cell-free assay, we demonstrate that KAE609 directly inhibits ScPma1p ATPase activity. KAE609 also increases cytoplasmic hydrogen ion concentrations in yeast cells. Computer docking into a ScPma1p homology model identifies a binding mode that supports genetic resistance determinants and in vitro experimental structure-activity relationships in both P. falciparum and S. cerevisiae. This model also suggests a shared binding site with the dihydroisoquinolones antimalarials. Our data support a model in which KAE609 exerts its antimalarial activity by directly interfering with P-type ATPase activity.

Rapid Chagas Disease Drug Target Discovery Using Directed Evolution in Drug-Sensitive Yeast

“…Since yeast resistance often evolves through mutations in efflux-pump genes rather than true drug targets, we used the ABC 16 -Monster yeast strain 11 , a recently engineered strain that entirely lacks sixteen efflux-pump genes and is therefore more sensitive to most cytotoxic compounds. Using a similar approach, we recently identified the S. cerevisiae protein PMA1 as the target of the spiroindolone KAE609, a potent antimalarial 10 . The MMV Malaria Box is a set of 400 compounds, including 200 drug-like molecules as well as 200 tool compounds for discovering novel drug-target pathways.…”

“…39 As more resistance profiles are collected, more genes that contribute to the generic resistome will be identified, enabling better discrimination between real signal and background noise. The use of the ABC 16 -Monster S. cerevisiae strain, which lacks sixteen export pumps, also reduces the likelihood of evolved resistance via mutations in general resistance genes.…”

“…9 In addition, directed evolution in yeast showed that that the spiroindolone antimalarial KAE609, which is a P-type ATPase inhibitor in P. falciparum , is also a P-type ATPase inhibitor in S. cerevisiae . 10 …”

WITHDRAWN: Oligomerization of the antimalarial drug targetPfATP4 is essential for parasite survival

“…Interestingly, 7-9% of the collection of antimalarial compounds included in the Malaria and the Pathogen Boxes distributed by Medicines for Malaria Venture (MMV) appear to inhibit PfATP4 as judged by their ability to cause Na + influx into the parasite and disruption of lipid homeostasis within the PPM (12)(13)(14). Resistance to several of these compounds has been shown to be associated with mutations in PfATP4 (5,7,8,15,16). If one were to extrapolate the proportion of PfATP4 inhibitors found in the Malaria and Pathogen Boxes to all the antimalarial compounds identified by the highthroughput screening campaigns, one would predict that thousands of potential antimalarials target PfATP4, making it a highly druggable target in the malaria parasite.…”

A human microdose study of the antimalarial drug GSK3191607 in healthy volunteers

“…It displayed a novel, but already clinically proven mechanism of actioninhibition of the PfATP4 pathway, which has been implicated in the regulation of sodium homeostasis in the parasite P. falciparum [11][12][13][14]. No PfATP4 inhibitors are yet approved for clinical use, although some are in development [14][15][16].…”