High-throughput matrix screening identifies synergistic and antagonistic antimalarial drug combinations

Abstract

Drug resistance in Plasmodium parasites is a constant threat. Novel therapeutics, especially new drug combinations, must be identified at a faster rate. In response to the urgent need for new antimalarial drug combinations we screened a large collection of approved and investigational drugs, tested 13,910 drug pairs, and identified many promising antimalarial drug combinations. The activity of known antimalarial drug regimens was confirmed and a myriad of new classes of positively interacting drug pairings were discovered. Network and clustering analyses reinforced established mechanistic relationships for known drug combinations and identified several novel mechanistic hypotheses. From eleven screens comprising >4,600 combinations per parasite strain (including duplicates) we further investigated interactions between approved antimalarials, calcium homeostasis modulators, and inhibitors of phosphatidylinositide 3-kinases (PI3K) and the mammalian target of rapamycin (mTOR). These studies highlight important targets and pathways and provide promising leads for clinically actionable antimalarial therapy.

mQC: A Heuristic Quality-Control Metric for High-Throughput Drug Combination Screening

“…We observed some cases in a malaria screen10 where the replicate response matrices varied significantly even when mQC classifies them all as “Good” quality. Implementing a consistent QC metric at matrix-level remains challenging because (1) Combination screening data is still limited in terms of large scale availability; (2) While many synergy metrics have been defined, the question of which metric can serve as a well-defined endpoint, analogous to IC50, EC50 or AUC for single agent dose response, that can be used to compare between independent replicates is still open24.…”

“…To ensure the diversity of the checkerboard pattern, we first separated 127,119 response matrices from NCATS database into 32 groups using the 5 heuristic criteria described by Mott et al 10. (see below).…”

“…The initial version of the platform was used to screen a few hundred drug combinations. However, the platform has expanded to thousands and even tens of thousands of combinations10. Since the platform is based on traditional plate-reader technology, traditional plate-level QC metrics, especially those based on control performance, can be computed to provide an overall determination of the assay performance.…”

Phenotypic Screens in Antimalarial Drug Discovery

“…Compounds in combination should ideally act against different cellular targets to offset the likelihood that a single parasite genome amplification event could render parasites resistant to both drugs. To identify compounds that might act synergistically, Mott et al performed an ABS screen using a small library of 2317 compounds including known and investigational antimalarial compounds [37]. They then performed eleven iterative combination screens, with compounds selected from the single agent screen, identifying compounds pairs that act antagonistically or synergistically, such as the artemisinin and the phosphatidylinositide 3-kinase inhibitors, NVP-BGT226.…”

“…On the other hand, the approach could provide details on a compound's mechanism of action—compounds acting against the same pathway or target (e.g. the cytochrome bc1 inhibitors, atovaquone and decoquinate) tend to synergize [37]. …”