Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond

Abstract

A major cause of the paucity of new starting points for drug discovery is the lack of interaction between academia and industry. Much of the global resource in biology is present in universities, whereas the focus of medicinal chemistry is still largely within industry. Open source drug discovery, with sharing of information, is clearly a first step towards overcoming this gap. But the interface could especially be bridged through a scale-up of open sharing of physical compounds, which would accelerate the finding of new starting points for drug discovery. The Medicines for Malaria Venture Malaria Box is a collection of over 400 compounds representing families of structures identified in phenotypic screens of pharmaceutical and academic libraries against the Plasmodium falciparum malaria parasite. The set has now been distributed to almost 200 research groups globally in the last two years, with the only stipulation that information from the screens is deposited in the public domain. This paper reports for the first time on 236 screens that have been carried out against the Malaria Box and compares these results with 55 assays that were previously published, in a format that allows a meta-analysis of the combined dataset. The combined biochemical and cellular assays presented here suggest mechanisms of action for 135 (34%) of the compounds active in killing multiple life-cycle stages of the malaria parasite, including asexual blood, liver, gametocyte, gametes and insect ookinete stages. In addition, many compounds demonstrated activity against other pathogens, showing hits in assays with 16 protozoa, 7 helminths, 9 bacterial and mycobacterial species, the dengue fever mosquito vector, and the NCI60 human cancer cell line panel of 60 human tumor cell lines. Toxicological, pharmacokinetic and metabolic properties were collected on all the compounds, assisting in the selection of the most promising candidates for murine proof-of-concept experiments and medicinal chemistry programs. The data for all of these assays are presented and analyzed to show how outstanding leads for many indications can be selected. These results reveal the immense potential for translating the dispersed expertise in biological assays involving human pathogens into drug discovery starting points, by providing open access to new families of molecules, and emphasize how a small additional investment made to help acquire and distribute compounds, and sharing the data, can catalyze drug discovery for dozens of different indications. Another lesson is that when multiple screens from different groups are run on the same library, results can be integrated quickly to select the most valuable starting points for subsequent medicinal chemistry efforts.

Screening for potential prophylactics targeting sporozoite motility through the skin

“…1a). However, due to reported toxic effects on hepatocytes [9] and a lack of a currently available topical treatment, these compounds were not further tested in vivo.

Fig. 1Overview of previous and current screening strategies.

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Esterase mutation is a mechanism of resistance to antimalarial compounds

“…There are now thousands of antimalarial hits from whole parasite compound screens. A survey of 125 compounds with antimalarial activity from the pathogen box and 400 compounds from the malaria box reveals 26 esters17. Consideration should be given to the possibility that some are prodrugs subject to rapid resistance development.…”

Identification of inhibitors that dually target the new permeability pathway and dihydroorotate dehydrogenase in the blood stage of Plasmodium falciparum

“…These metabolites are intermediates in the essential and non-redundant pathway of pyrimidine synthesis in the parasite. The rate-limiting step in pyrimidine biosynthesis is the oxidation of dihydroorotate to orotate by the enzyme Pf DHODH, which is a promising drug target with the inhibitor DSM265 under clinical development34.…”