Abstract
Malaria caused by Plasmodium falciparum is a disease that is responsible for 880,000 deaths per year worldwide. Vaccine development has proved difficult and resistance has emerged for most antimalarial drugs. To discover new antimalarial chemotypes, we have used a phenotypic forward chemical genetic approach to assay 309,474 chemicals. Here we disclose structures and biological activity of the entire library—many of which showed potent in vitro activity against drug-resistant P. falciparum strains—and detailed profiling of 172 representative candidates. A reverse chemical genetic study identified 19 new inhibitors of 4 validated drug targets and 15 novel binders among 61 malarial proteins. Phylochemogenetic profiling in several organisms revealed similarities between Toxoplasma gondii and mammalian cell lines and dissimilarities between P. falciparum and related protozoans. One exemplar compound displayed efficacy in a murine model. Our findings provide the scientific community with new starting points for malaria drug discovery.
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Acknowledgements
This work was supported by the American Lebanese Syrian Associated Charities (ALSAC) and St Jude Children’s Research Hospital (SJCRH, R.K.G.), the Medicines for Malaria Venture (W.C.V.V. and V.M.A.), National Institute of Allergy and Infectious Diseases (AI772682 (P.H.D.), AI075517 (R.K.G.), AI067921 (W.C.V.V.) and AI080625 (W.C.V.V.), AI28724 (D.S.R.), AI53862 (J.L.D.), AI35707 (P.J.R.), AI053680 (M.A.P. and P.K.R.), AI075594 (M.A.P., P.K.R. and I.B.), AI082617 (P.K.R.) and AI045774 (D.J.S.)), the National Cancer Institute (CA78039 (J.S.L.)), the Welch Foundation (I-1257 (M.A.P.)), the Doris Duke Charitable Foundation (P.J.R.), and the Ellison Medical Foundation (D.S.R.). We acknowledge A. B. Vaidya for providing the parasite strain D10_yDHOD. We acknowledge M. Sigal for assistance in the early leads project coordination, the SJCRH High Throughput Screening Center, particularly J. Cui; the SJCRH Lead Discovery Informatics Center, and the SJCRH High Throughput Analytical Chemistry Center, particularly C. Nelson and A. Lemoff; at UW, F. Buckner, W. Hol and A. Napuli (AI067921, W. Hol); S. Wei and W. Hao in the UT Southwestern HTS Center; and the Australian Red Cross Blood Service for the provision of O+ erythrocytes to Griffith University.
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Contributions
W.A.G. and R.K.G. designed and coordinated the project. A.A.S. wrote the algorithms for the data analysis and generated the figures. Assays were conceived, performed and analysed by W.A.G. and D.B. (P. falciparum phenotypic screen), M.C. (human cell lines), D.C.S. (T. brucei), P.H.D. and D.S.R. (T. gondii), J.S.L. and E.R.S. (L. major), A.K.T. and D.J.S. (haemozoin inhibition), G.J.C. and W.C.V.V. (thermal melt experiments), M.A.P., P.K.R., F.E.M. and I.B. (PfDHOD), J.W.F. and P.K.R. (P. falciparum dihydrofolate reductase), J.G. and P.J.R. (PfFP-2), I.F. and M.K.R. (cytochrome bc1), J.C. (P. falciparum mutant drug sensitivity). E.B.W., S.D., J.L.D. and V.M.A. (independent antimalarial in vitro experiments), F.Z. (in vitro pharmacokinetics), M.B.J.D., M.S.M., I.A.-B. and S.F. (in vivo pharmacokinetics and efficacy), I.B. (coordination of technology development and network development), S.C. and P.L.M. (re-synthesis). W.A.G., A.A.S. and R.K.G. wrote the manuscript. All authors contributed to the design of the experiments and the preparation of the manuscript.
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Supplementary information
Supplementary Information (download PDF )
This file contains Supplementary Information comprising: Compound Library Screened; Parasite and cell-based assay methods; Enzymatic and protein assays; Data processing and screening results; Multiple-lab cross-validation study; Chemical structure network graph; Additional mechanistic studies; Detailed analysis of three early lead compounds; Other high-value compounds; Data availability; Supplementary Tables S1-S8, Supplementary Figures S1-S5 with legends and References. The Supplementary Information file was replaced on 24 June 2010. (PDF 952 kb)
Supplementary Data (download XLS )
This file contains Structural information and Primary screening for 1536 compounds, Screening data from 228 compounds for the Bland-Altman analysis, Calculated medicinal chemistry properties, Cytotoxic activity, Screen sensitivity and Differential activity for 172 compounds, Raw data from the Hemozoin polymerization inhibition assay, summary of activity of 172 compounds in the thermal melt assays and Raw data and calculated Kd for thermal melt assay hits. (XLS 5090 kb)
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Guiguemde, W., Shelat, A., Bouck, D. et al. Chemical genetics of Plasmodium falciparum. Nature 465, 311–315 (2010). https://doi.org/10.1038/nature09099
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DOI: https://doi.org/10.1038/nature09099
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