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

Sci Rep. 2016 Jun 13;6:27806. doi: 10.1038/srep27806.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Antimalarials / chemistry
  • Antimalarials / metabolism*
  • Antimalarials / pharmacology
  • Binding Sites
  • CRISPR-Cas Systems / genetics
  • Cytosol / chemistry
  • Cytosol / drug effects
  • Drug Resistance, Fungal
  • Indoles / chemistry
  • Indoles / metabolism*
  • Indoles / pharmacology
  • Inhibitory Concentration 50
  • Molecular Docking Simulation
  • P-type ATPases / antagonists & inhibitors
  • P-type ATPases / genetics
  • P-type ATPases / metabolism*
  • Plasmodium falciparum / drug effects
  • Plasmodium falciparum / enzymology
  • Protein Structure, Tertiary
  • Proton-Translocating ATPases / antagonists & inhibitors
  • Proton-Translocating ATPases / genetics
  • Proton-Translocating ATPases / metabolism
  • Protozoan Proteins / antagonists & inhibitors
  • Protozoan Proteins / metabolism
  • Saccharomyces cerevisiae / drug effects
  • Saccharomyces cerevisiae / enzymology
  • Saccharomyces cerevisiae Proteins / antagonists & inhibitors
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Spiro Compounds / chemistry
  • Spiro Compounds / metabolism*
  • Spiro Compounds / pharmacology
  • Structure-Activity Relationship
  • Whole Genome Sequencing

Substances

  • Antimalarials
  • Indoles
  • NITD 609
  • Protozoan Proteins
  • Saccharomyces cerevisiae Proteins
  • Spiro Compounds
  • PMA1 protein, S cerevisiae
  • P-type ATPases
  • Proton-Translocating ATPases