Harnessing evolutionary fitness in Plasmodium falciparum for drug discovery and suppressing resistance

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 111; no. 2; pp. 799 - 804
• Main Authors: Lukens, Amanda K., Ross, Leila Saxby, Heidebrecht, Richard, Gamo, Francisco Javier, Lafuente-Monasterio, Maria J., Booker, Michael L., Hartl, Daniel L., Wiegand, Roger C., Wirth, Dyann F.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 14.01.2014; National Acad Sciences
• Subjects: Analysis of Variance; Antimalarials; Base Sequence; Biological Sciences; Chloroquine - pharmacology; Dehydrogenases; Drug Discovery - methods; Drug Evaluation, Preclinical; Drug resistance; Drug Resistance - genetics; Ecological competition; Evolution; Genetic Fitness - genetics; Genetic mutation; Genome - genetics; Genomics; Inhibitor drugs; Malaria; Malaria - drug therapy; Molecular Sequence Data; Mutation; Oxidoreductases Acting on CH-CH Group Donors - antagonists & inhibitors; Oxidoreductases Acting on CH-CH Group Donors - genetics; Parasites; Plasmodium falciparum; Plasmodium falciparum - genetics; Point Mutation - genetics; Pyrimidines; R&D; Research & development; Sequence Analysis, DNA; Sequencing; Small Molecule Libraries; Triazoles; combination therapy; target identification; evolution
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1320886110

Drug resistance emerges in an ecological context where fitness costs restrict the diversity of escape pathways. These pathways are targets for drug discovery, and here we demonstrate that we can identify small-molecule inhibitors that differentially target resistant parasites. Combining wild-type and mutant-type inhibitors may prevent the emergence of competitively viable resistance. We tested this hypothesis with a clinically derived chloroquine-resistant (CQ ʳ) malaria parasite and with parasites derived by in vitro selection with Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors. We screened a chemical library against CQ ˢ and CQ ʳ lines and discovered a drug-like compound (IDI-3783) that was potent only in the CQ ʳ line. Surprisingly, in vitro selection of Plasmodium falciparum resistant to IDI-3783 restored CQ sensitivity, thereby indicating that CQ might once again be useful as a malaria therapy. In parallel experiments, we selected P. falciparum lines resistant to structurally unrelated PfDHODH inhibitors (Genz-666136 and DSM74). Both selections yielded resistant lines with the same point mutation in PfDHODH:E182D. We discovered a compound (IDI-6273) more potent against E182D than wild-type parasites. Selection of the E182D mutant with IDI-6273 yielded a reversion to the wild-type protein sequence and phenotype although the nucleotide sequence was different. Importantly, selection with a combination of Genz-669178, a wild-type PfDHODH inhibitor, and IDI-6273, a mutant-selective PfDHODH inhibitor, did not yield resistant parasites. These two examples demonstrate that the compromise between resistance and evolutionary fitness can be exploited to design therapies that prevent the emergence and spread of resistant organisms.