Fig 1.
Shown are selected data from the HeatMap (S1 Table) for the 400 Malaria Box compounds. Each column represents an assay (grouped by category), compounds are represented in rows. The red-green gradient represents higher to lower activity. Favorable PK activities are scored green. Pf: Plasmodium falciparum, Pb: Plasmodium berghei, PK: pharmacokinetics, sol.: solubility, hERG: human ether-a-go-go channel inhibition, DDI: drug-drug interactions (predicted).
Table 1.
Malaria Box compounds with activity in biological assays (malaria, helminths, Wolbachia, and cancer cells) and lacking toxicity at therapeutic levels.
Selectivity Index, SI, is toxicity level/activity level; p, probe-like; d, drug-like.
Fig 2.
Metabolomic and chemogenomic profiling.
(A) Metabolic profiling: Heat map showing metabolic fingerprints of 80 Malaria Box compounds and atovaquone control. Parasite extracts were analyzed by LC-MS, and changes in metabolite pools were calculated for drug-treated parasites as compared to untreated controls. Hierarchical clustering was performed on 2log-fold changes in metabolites (data in S2 Table), scaled from -3 to +3. Six of seven compounds (indicated in red) reported to target PfATP4 [25] showed a distinct metabolic response characterized by the accumulation of dNTPs and a decrease in hemoglobin-derived peptides. A large cluster of compounds (indicated in blue) clustered with the atovaquone control (indicated in orange), and exhibit an atovaquone-like signature characterized by dysregulation of pyrimidine biosynthesis, and showed a distinct metabolic response characterized by the accumulation of dNTPs and a decrease in hemoglobin-derived peptides. (B) Chemogenomic profiling: A collection of 35 P. falciparum single insertion piggyBac mutants were profiled with 53 MMV compounds and 3 artemisinin (ART) compounds [Artesunate (AS), Artelinic acid (AL) and Artemether (AM)] for changes in IC50 relative to the wild-type parent NF54 (data in S3 Table, genes queried in S4 Table). Clone PB58 carried a piggyBac insertion in the promoter region of the K13 gene and has an increased sensitivity to ART compounds as do PB54 and PB55 [33]. Drug-drug relationships based on similarities in IC50 deviations of compounds generated with piggyBac mutants created chemogenomic profiles used to define drug-drug relationships. The significance of similarity in MoA between Malaria Box compounds and ART was evaluated by Pearson’s correlation calculations from pairwise comparisons. The X axis shows the chemogenomic profile correlation between a Malaria Box compound and AS, the Y axis with AM; the color gradient indicates the average correlation with all ART derivatives tested. Five Malaria Box compounds (MMV006087, MMV006427, MMV020492, MMV665876, MMV396797) were identified as having similar drug-drug chemogenomic profiles to the ART sensitivity cluster.
Table 2.
Antiprotozoal Malaria Box compounds with activity in biological assays and lacking toxicity at therapeutic levels.
Selectivity Index, SI, is toxicity level/activity level; p, probe-like; d, drug-like.