Drug resistance in the malaria parasite, Plasmodium falciparum, poses a major threat to global plans for the control and elimination of malaria. Resistance has been reported against all the currently approved antimalarial agents, although the underlying mechanisms associated with resistance are poorly understood. Most current drugs act by inhibiting cellular metabolism (e.g. atovaquone and antifolates) or act in the digestive vacuole (e.g. artemisinin and quinolines). Therefore, it is likely that a system-wide approach to monitor metabolism and protein turnover will reveal novel aspects of drug resistance for existing antimalarials. In order to identify key features associated with a delayed parasite clearance phenotype, we have developed a multi-omics platform based on high-resolution mass spectrometry combining proteomics, peptidomics and metabolomics to analyse global differences between drug-resistant and drug-sensitive isolates.

When applied to P. falciparum infected red blood cells, our multi-omics platform facilitated the identification of approximately 3000 proteins, 1000 metabolites and 10,915 naturally abundant peptides and integration of these data has provided a detailed view of protein expression and regulation associated with drug resistance. Preliminary findings for artemisinin-resistant isolates revealed that artemisinin resistance is associated with increased expression of proteins associated with the stress response and the unfolded protein response, as well as the accumulation of specific peptides and small molecule metabolites. These findings shed light on the biochemical pathways that are targeted by this critical antimalarial compound, and reveal the molecular adaptions that allow parasites to overcome the antimalarial effects of these front-line therapies.