Probing the Open Global Health Chemical Diversity Library for Multistage-Active Starting Points for Next-Generation Antimalarials

Abstract

Most phenotypic screens aiming to discover new antimalarial chemotypes begin with low cost, high-throughput tests against the asexual blood stage (ABS) of the malaria parasite life cycle. Compounds active against the ABS are then sequentially tested in more difficult assays that predict whether a compound has other beneficial attributes. Although applying this strategy to new chemical libraries may yield new leads, repeated iterations may lead to diminishing returns and the rediscovery of chemotypes hitting well-known targets. Here, we adopted a different strategy to find starting points, testing ∼70,000 open source small molecules from the Global Health Chemical Diversity Library for activity against the liver stage, mature sexual stage, and asexual blood stage malaria parasites in parallel. In addition, instead of using an asexual assay that measures accumulated parasite DNA in the presence of compound (SYBR green), a real time luciferase-dependent parasite viability assay was used that distinguishes slow-acting (delayed death) from fast-acting compounds. Among 382 scaffolds with the activity confirmed by dose response (<10 μM), we discovered 68 novel delayed-death, 84 liver stage, and 68 stage V gametocyte inhibitors as well. Although 89% of the evaluated compounds had activity in only a single life cycle stage, we discovered six potent (half-maximal inhibitory concentration of <1 μM) multistage scaffolds, including a novel cytochrome bc1 chemotype. Our data further show the luciferase-based assays have higher sensitivity. Chemoinformatic analysis of positive and negative compounds identified scaffold families with a strong enrichment for activity against specific or multiple stages.

Multistage and transmission-blocking targeted antimalarials discovered from the open-source MMV Pandemic Response Box

“…in place of the paradigm where compounds are only profiled for additional life cycle activity once asexual activity has been established, confirms the possibility of identifying gametocytespecific compounds 7,8,10 . Indeed, we identified several active compounds that have no former documented antimalarial activity, simply because they were previously not screened against the correct life cycle stage of the parasite, where the relevant biology being targeted was essential.…”

“…While this strategy can identify compounds targeting two or more life cycle stages, it does not allow de novo discovery of compounds with selective activity against specific life cycle stages, such as gametocytes. Parallel screening against multiple life cycle stages would best identify such compounds and rely on selective and predictive assays for gametocytocidal activity 4 , transmissionblocking 5,6 , and hepatic development 7 . Recently, parallel screening of diversity sets has resulted in reports of such stage-specific compounds [7][8][9][10] , with the benefit that divergent biology associated with the different life cycle states can be targeted 5,6,11 .…”

Natural Products: A Potential Source of Malaria Transmission Blocking Drugs?

“…Alternative sources are the de novo screen of natural product libraries in medium-to high-throughput format. It is now clearly indicated that driving screens based on asexual stage potency may not identify transmission-blocking specific compounds and as such we recommend parallel screens against different parasite life cycle stages or at the start, screening driven primarily on the transmissible forms, after which activity against other stages can be determined for hits obtained [131,132]. For such natural product libraries, stringent go/no go criteria need to be defined, similar to screening any other small molecule libraries.…”

Molecular approaches to Malaria 2020

“…She also spoke about the malaria drug accelerated program, MalDA, and the benefits of collaborative teams that enable a wide variety of chemogenomic methods to be deployed to identify the targets for a wide variety of compounds with whole cell activity and their mode of action. In addition, she revealed that when the types of evaluation methods for a screen were altered (e.g., short 48 hr and long 96 hr periods of incubation with compound compared to the typical 72 hr screen), new compounds and targets started coming out of the screen (Abraham et al, 2020). She also highlighted that compound scaffolding structuring to group compounds based on structural similarity, showed that compounds with similar structures have similar activities across the lifecycle.…”