Identifying molecular targets of next-generation antimalarials using a genome-wide suppressor screen

Malaria remains a major global health challenge, causing over 250 million cases and 600,000 deaths annually. This infectious disease is caused by Plasmodium parasites that infect red blood cells and can lead to severe cardiovascular and cerebrovascular complications. The emergence of widespread resistance to current antimalarial drugs threatens control efforts and highlights the urgent need for new therapeutics with novel mechanisms of action. The two next-generation antimalarials, ganaplacide and cipargamin, have demonstrated potent activity in clinical trials. However, their molecular targets and resistance mechanisms remain poorly understood. FosSeq is a genome-wide gain-of-function screen that systematically overexpresses genes to identify resistance drivers, achieved by introducing additional gene copies on high-capacity cloning vectors called fosmids. This method leverages the genetically tractable zoonotic malaria parasite Plasmodium knowlesi, whose genome composition and high transfection efficiency enable the creation of overexpression mutant libraries covering nearly all protein-coding genes. Specifically, this project will generate a dual-selectable fosmid library capable of introducing more than ten additional gene copies per cell for functional genomic screening of ganaplacide and cipargamin (aim 1). It will then identify direct drug-protein interactions via CETSA (aim 2), followed by validation of high-confidence targets using chemical-genetic approaches (aim 3). Understanding these mechanisms will inform the rational design of combination therapies, enable early detection of resistance, and accelerate development of more effective treatments to overcome antimalarial resistance and reduce the global disease burden.

Drug Resistance
Genetics and Genomics

Jul 2026 — Jun 2028

$156,172

United States