Mapping the malaria parasite druggable genome by using in vitro evolution and chemogenomics

Abstract

Chemogenetic characterization through in vitro evolution combined with whole-genome analysis can identify antimalarial drug targets and drug-resistance genes. We performed a genome analysis of 262 Plasmodium falciparum parasites resistant to 37 diverse compounds. We found 159 gene amplifications and 148 nonsynonymous changes in 83 genes associated with drug-resistance acquisition, where gene amplifications contributed to one-third of resistance acquisition events. Beyond confirming previously identified multidrug-resistance mechanisms, we discovered hitherto unrecognized drug target–inhibitor pairs, including thymidylate synthase and a benzoquinazolinone, farnesyltransferase and a pyrimidinedione, and a dipeptidylpeptidase and an arylurea. This exploration of the P. falciparum resistome and druggable genome will likely guide drug discovery and structural biology efforts, while also advancing our understanding of resistance mechanisms available to the malaria parasite.

The transportome of the malaria parasite

“…It is becoming increasingly evident that transporters play a major role in the phenomenon of drug resistance in the malaria parasite. In their recent exploration of the P. falciparum resistome and druggable genome, the MalDA Consortium employed chemogenomics, in vitro evolution of drug resistance, and whole-genome sequencing to uncover the genetic determinants of the parasite's resistance to a diverse selection of lead candidate antimalarials (Cowell et al, 2018). Examination of the resulting data sets reveals that a substantial number of transporters serve as drug targets and/or mediators of drug resistance in the parasite; transporter genes accounted for 75% of the copy-number variations and 45% of the non-synonymous single nucleotide polymorphisms.…”

“…Consistent with their importance to all aspects of Plasmodium biology, transporters are increasingly being identified as mediators of antimalarial drug resistance as well as drug targets themselves (e.g. Lim et al, 2016;Richards et al, 2016;Cowell et al, 2018). In this review, several large data sets as well as the findings from many smaller-scale studies of Plasmodium transporters -including investigations of gene essentiality, protein subcellular localisation, predicted or observed function, and associations with drug resistance -have been collated and analysed to expand and deepen our understanding of the parasite's transportome.…”

Microbial esterases and ester prodrugs: An unlikely marriage for combating antibiotic resistance

“…PfPARE prodrug activation was also transferrable to the intracellular activation of another malaria drug (MMV011438; Figure g) (Istvan et al, ). Conversely, resistance mutations were also developed in PfPARE that inactivated the antimalarial activity of ester‐protected pepstatin, illustrating the difficulty in generally applying this prodrug strategy (Cowell et al, ; Istvan et al, ). This resistance has also been confirmed by combined evolution and chemogenomics, with PfPARE only showing resistance mutations against the two ester‐containing antimalarial drugs (Cowell et al, ).…”

Rapid emergence of clonal interference during malaria parasite cultivation

“…During in vitro culture malaria parasites are maintained in a suspension of red blood cells (RBCs) obtained from a donor, supplied with the necessary nutrients from culture media and serum and housed in a low oxygen environment at normal body temperature (37C˚). By regular changes in media and replenishing RBCs parasite cultures can be maintained indefinitely, and subject to drug testing, genetic manipulation (Ghorbal et al, 2014), and placed under selective pressures to understand adaptation (Cowell et al, 2018).…”