The Plasmodium falciparum ABC transporter ABCI3 confers parasite strain-dependent pleiotropic antimalarial drug resistance

James M Murithi,Tomas Yeo,Jessica L Bridgford,Jacquin C Niles,Elizabeth A Winzeler,Sachel Mok,Nina F Gnädig,Maëlle Duffey,Amanda K Lukens,Ioanna Deni,Annie N Cowell,Sumanta Dey,Charisse Flerida A Pasaje,Manu Vanaerschot,Eva S Istvan,David A Fidock,Sabine Ottilie,Claire Le Manach,Gavreel F Kalantarov,John Okombo,Kelly Chibale,Benoît Laleu,Rachel L Edwards,Anna Y Burkhard,Dyann F Wirth,Kathryn J Wicht,Olivia Coburn-Flynn,Daniel E Goldberg,Tomoyo Sakata‐Kato ,Francisco‐Javier Gamo ,Audrey Odom John ,Ilya Trakht ,Marı́a G Gómez-Lorenzo

doi:10.1016/j.chembiol.2021.06.006

Abstract

SummaryWidespread Plasmodium falciparum resistance to first-line antimalarials underscores the vital need to develop compounds with novel modes of action and identify new druggable targets. Here, we profile five compounds that potently inhibit P. falciparum asexual blood stages. Resistance selection studies with three carboxamide-containing compounds, confirmed by gene editing and conditional knockdowns, identify point mutations in the parasite transporter ABCI3 as the primary mediator of resistance. Selection studies with imidazopyridine or quinoline-carboxamide compounds also yield changes in ABCI3, this time through gene amplification. Imidazopyridine mode of action is attributed to inhibition of heme detoxification, as evidenced by cellular accumulation and heme fractionation assays. For the copy-number variation-selecting imidazopyridine and quinoline-carboxamide compounds, we find that resistance, manifesting as a biphasic concentration-response curve, can independently be mediated by mutations in the chloroquine resistance transporter PfCRT. These studies reveal the interconnectedness of P. falciparum transporters in overcoming drug pressure in different parasite strains.

Highlights

An estimated 1.5 billion malaria cases and 7.6 million deaths have been averted since 2000 as a result of chemotherapy, vector control, diagnosis, and access to treatment (WHO, 2020)
We describe here a series of experiments including in vitro resistance selections and CRISPR/Cas9 genetic validation, drug susceptibility, conditional knockdown, drug cellular accumulation, protein localization, and heme fractionation assays to characterize culture-adapted P. falciparum resistance to five chemically distinct antiplasmodial compounds studied by the Malaria Drug Accelerator (MalDA) consortium
Whole-genome sequencing results of these clones segregated the compounds into two distinct categories: (1) those that generated copy-number variations (CNVs); and (2) those that generated single-nucleotide polymorphisms (SNPs) in ABCI3 (Figure 1)

Summary

Introduction

An estimated 1.5 billion malaria cases and 7.6 million deaths have been averted since 2000 as a result of chemotherapy, vector control, diagnosis, and access to treatment (WHO, 2020). Despite this extraordinary success, 229 million new cases and 409,000 deaths were reported in 2019 alone (WHO, 2020), underscoring the difficult path to malaria eradication. Plasmodium falciparum resistance to first-line artemisinin-based combination therapies has spread across Southeast Asia and is threatening sub-Saharan Africa (Conrad and Rosenthal, 2019; Imwong et al, 2020; Uwimana et al, 2020) This makes it imperative that we identify new druggable targets in malaria parasites using compounds that have novel modes of antiplasmodial action.

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Conclusion