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Structural parasitology is the study of structures of parasitic proteins. Among protozoan parasites, the phylum of Apicomplexa includes organisms responsible for malaria, toxoplasmosis and cryptosporidiosis. Trypanosoma and Leishmania parasites, belonging to the phylum of Kinetoplastida, cause Chagas disease, African Sleeping Disease and visceral leishmaniasis. For some of these diseases, such as malaria, existing drugs face the threat of resistance. For others, such as cryptosporidiosis, there is no effective chemotherapy.
Structural biology involves protein expression, protein purification and crystallography. Proteins from different families and genomes often present different challenges. Parasitic proteins, particularly those in the Plasmodium genomes, have proven to be more difficult than most to express. The complicating factors include AT-rich genomes (e.g. Plasmodium falciparum), long unconserved inserts in the middle of otherwise highly conserved domains (both Plasmodium and Toxoplasma proteins) and largely disparate codon usages compared to E. coli (the most commonly used heterologous expression host). The SGC, along with other labs (e.g. MSGPP), have overcome these challenges for some parasitic proteins and have solved a number of structures to date. The totals, however, remain low compared to other species. For example, close to 8,000 distinct human structures out of 20,000 plus have been solved and deposited in the PDB. In contrast, only 135 distinct Plasmodium falciparum structures in a genome numbering over 5,000 have been solved – less than 5%. The structures from other parasites are even fewer in numbers. Simply put, structural parasitology remains a largely unexplored field.
Despite the relatively low number of structures, there have been a few significant structure-guided discoveries. Plasmodium DHODH is an enzyme in the essential de novo pyrimidine biosynthetic pathway and considered a highly promising anti-malarial target [McRobert and McConkey, Mol. & Biochem Parasitology, 2002; Phillips and Rathod, Infect. Disorder. Drug Targets, 2010]. The structures of this dehydrogenase have elucidated its interaction with novel inhibitors and their mechanism of action. Some of these compounds are now in Phase 1 clinical trial. In another example, the structure of Toxoplasma gondii CDPK1 revealed a hydrophobic pocket in the gatekeeper position [Ojo et al, Nature Struct. & Mol. Biology, 2010]. Inhibitors that targeted this pocket were used to confirm this kinase's role in host invasion [Lourido et al, Nature, 2010].
In addition to protein expression and crystallography, screening is an essential part of structural parasitology when it is carried out on a genomic scale. By screening parasitic proteins against focused libraries of small molecules, potential ligands can be found. In many cases, these ligands can improve the stability of the proteins in solution and promote crystallization. In specific cases, they may be potent inhibitors and candidates as chemical probes.
