Parasites of the genus Plasmodium are responsible for 300-500 million cases of human malaria and cause about one million deaths every year. The search for new novel antimalarials relies on a number of approaches including natural products, high-throughput screens, small chemical libraries directed at important pathways, or just structural modification of previously active antimalarials. Prioritization, optimization, and advancement of a good experimental antimalarial to a clinically useful drug may be greatly facilitated by knowledge of the target or the pathway. Chemistry and Chemical Biology based approaches can be powerful for target identification and validation, especially when tightly linked to open-ended biological tools. We will study the Structure Activity Relationships (SAR) of select bioactive molecules. For each compound class, we will (i) establishment isogenic sensitive and resistant strains to help develop confidence in the chemistry-biology links, before genomic DNA sequencing on the isogenic strains for each chemical classes (ii) separately, develop a ligand-binding proteomics approach to identify drug targets. To gain confidence in our approach, we will use escalating challenge in our specific aims.
In Specific Aim 1, to establish a well-grounded set of protocols, we will first establish and validate genome-sequence and proteomics- based approaches for target identification, using new antimalarial chemicals from our team with proven targets.
In Specific Aim 2, our genome-wide target identification approaches will be expanded to new anti-metabolites where the mechanisms of action are different and unknown, compared to what was expected.
In Aim 3, we will apply the genomic tools to completely new antimalarials whose mechanisms of action are completely unknown. Together, these carefully developed and controlled studies, involving small chemical molecules and genomic tools, will lead to generally applicable, streamlined approaches for establishing connections between good antimalarials and their high-value targets in the parasite.

Public Health Relevance

Malaria parasites infect over 500 million people and are responsible for over 1 million deaths per year. Cell-based assays and other approaches have revealed thousands of molecules with anti-proliferative activity in culture, but their optimization and advancement to drug-like molecules is often limited by inefficient strategies for target identification and validation. This project will address this need through a multidisciplinary approach combining chemical biology with parasite genetics, and genomics.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
Project #
Application #
Study Section
Special Emphasis Panel (ZAI1-LG-M (J3))
Program Officer
Rogers, Martin J
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Washington
Schools of Arts and Sciences
United States
Zip Code
Kumar, Shiva; Mudeppa, Devaraja G; Sharma, Ambika et al. (2016) Distinct genomic architecture of Plasmodium falciparum populations from South Asia. Mol Biochem Parasitol 210:1-4
Deng, Xiaoyi; Matthews, David; Rathod, Pradipsinh K et al. (2015) The X-ray structure of Plasmodium falciparum dihydroorotate dehydrogenase bound to a potent and selective N-phenylbenzamide inhibitor reveals novel binding-site interactions. Acta Crystallogr F Struct Biol Commun 71:553-9
Mudeppa, Devaraja G; Kumar, Shiva; Kokkonda, Sreekanth et al. (2015) Topoisomerase II from Human Malaria Parasites: EXPRESSION, PURIFICATION, AND SELECTIVE INHIBITION. J Biol Chem 290:20313-24
Kumar, Shiva; Krishnamoorthy, Kalyanaraman; Mudeppa, Devaraja G et al. (2015) Structure of Plasmodium falciparum orotate phosphoribosyltransferase with autologous inhibitory protein-protein interactions. Acta Crystallogr F Struct Biol Commun 71:600-8
Guler, Jennifer L; White 3rd, John; Phillips, Margaret A et al. (2015) Atovaquone tolerance in Plasmodium falciparum parasites selected for high-level resistance to a dihydroorotate dehydrogenase inhibitor. Antimicrob Agents Chemother 59:686-9
Herricks, Thurston; Avril, Marion; Janes, Joel et al. (2013) Clonal variants of Plasmodium falciparum exhibit a narrow range of rolling velocities to host receptor CD36 under dynamic flow conditions. Eukaryot Cell 12:1490-8
Guler, Jennifer L; Freeman, Daniel L; Ahyong, Vida et al. (2013) Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications. PLoS Pathog 9:e1003375
Mudeppa, Devaraja G; Rathod, Pradipsinh K (2013) Expression of functional Plasmodium falciparum enzymes using a wheat germ cell-free system. Eukaryot Cell 12:1653-63
Mailu, Boniface M; Ramasamay, Gowthaman; Mudeppa, Devaraja G et al. (2013) A nondiscriminating glutamyl-tRNA synthetase in the plasmodium apicoplast: the first enzyme in an indirect aminoacylation pathway. J Biol Chem 288:32539-52