Although phenotypic cellular screening has recently been used to drive antimalarial drug discovery, there continues to be a clear need for rational target-based drug discovery. This is especially true when appropriate high-throughput cellular assays are lacking. Such is the case for drug discovery efforts that aim to provide a replacement for primaquine, a drug with known toxicity that is the only agent that eliminates Plasmodium vivax liver stage infection and blocks gametocyte transmission. At present, there are no known chemically validated parasite protein targets that are critical to replicating or hypnozoite liver stages as well as asexual blood and gametocyte stages, and that could be used in biochemical screens of large compound libraries. The genomes of Plasmodium parasite species encode over 5,500 proteins, many of which remain uncharacterized. Our central hypothesis is that a wealth of novel, chemically validated multi-stage antimalarial targets still remain to be discovered. To test this we propose to focus on five recently discovered, chemically distinct scaffolds with broad ranging activity against the parasite lifecycle, including liver and asexual blood stages. We will further prioritize compounds by determining which of these are active against P. falciparum asexual blood stages from multidrug-resistant strains, gametocytes, and P. vivax hepatic forms. To generate low-level resistance, we will expose P. falciparum parasites (three independent selections, against three members of each scaffold series) to sublethal concentrations of compound. The genomes of drug-resistant clones will be examined by next-generation sequencing with paired-end reads (yielding ~100X coverage) to identify the complete suite of genetic changes that have emerged in each clone during chemical selection. Based on our preliminary data, we expect to find a statistically significant enrichment of newly emerged mutations in only one gene for each scaffold, when considering the whole-genome sequence for all nine resistant strains created per scaffold family. The importance of the candidate targets wil be verified by introducing genetic changes into drug-sensitive P. falciparum parasites and testing for gain of resistance, or conversely removing candidate mutations and testing for loss of resistance. Transfection experiments will include zinc finger nucleases, which constitute a major breakthrough in their ability to mediate highly efficient gene editing in P. falciparum. We will alo seek to determine whether the identified gene is the target of the small molecule or a gene involved in resistance through a detailed molecular characterization. The work will provide the malaria community with a systematic picture of how P. falciparum acquires drug resistance, and is expected to yield several new validated targets that can be used in drug development efforts focused on finding new radical-cure agents. This research, which is consistent with NIAID's mission statement, promises to leverage chemical scaffolds active against Plasmodium parasites to define new targets for the development of broad intervention strategies based on chemoprophylaxis and curative treatment of malarial infections.

Public Health Relevance

Emerging drug resistance creates a constant need to innovate in the discovery of antimicrobial agents. Here, we propose to leverage recent chemical advances in the identification of inhibitors active against the human-specific parasitic pathogen Plasmodium falciparum to define new targets for the development of next-generation drugs that will both prevent and treat malaria.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
1R01AI103058-01A1
Application #
8581051
Study Section
Drug Discovery and Mechanisms of Antimicrobial Resistance Study Section (DDR)
Program Officer
Rogers, Martin J
Project Start
2013-08-14
Project End
2017-07-31
Budget Start
2013-08-14
Budget End
2014-07-31
Support Year
1
Fiscal Year
2013
Total Cost
$648,140
Indirect Cost
$136,127
Name
University of California San Diego
Department
Pediatrics
Type
Schools of Medicine
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
Manary, Micah J; Singhakul, Suriya S; Flannery, Erika L et al. (2014) Identification of pathogen genomic variants through an integrated pipeline. BMC Bioinformatics 15:63
Flannery, Erika L; Fidock, David A; Winzeler, Elizabeth A (2013) Using genetic methods to define the targets of compounds with antimalarial activity. J Med Chem 56:7761-71