Structural basis for multiple binding modes of antimalarial ligands targeting Plasmodium falciparum NCR1

PfNCR1 is a Plasmodium falciparum cholesterol transporter at the plasma membrane-parasitophorous vacuole interface, which has recently emerged as a promising antimalarial target. Despite an immense interest in development of novel antimalarial compounds targeting PfNCR1, the molecular mechanism of PfNCR1 inhibition remains elusive. Here, we report cryo-EM structures of PfNCR1 in its apo state and bound to three inhibitors: MMV009108, MMV019662 and MMV028038. MMV009108 binds to the ''neck'' site at the ectodomain-membrane domain inter-face. MMV028038 displaces the sterol at the ectodomain ''ecto'' site. Remarkably, MMV019662 binds both sites: it associates near the bound sterol molecule at the ecto site and targets the neck site, thereby altering the sterol-sensing domain conformation. Importantly, we identify a novel antimalarial compound, G856-4236, which targets the ecto site exclusively. These four distinct modes of PfNCR1 inhibition advance our understanding of its conformational plasticity and es-tablish a framework for rational drug discovery targeting PfNCR1 and related transporters.