Molecular modeling elucidates parasite-specific features of polyamine pathway enzymes of Plasmodium falciparus

Abstract

Malaria remains a debilitating disease, especially in developing countries of the tropics and sub-tropics. Increasing drug resistance and the rising cost of drug development calls for methods that can cost-effectively identify new drugs. The proteins of the malaria causing Plasmodium parasites often exhibit unique features compared to their mammalian counterparts. Such features invite discovery of parasite-specific drugs. In this study computational methods were applied to understand unique structural features of enzymes from the Plasmodium polyamine biosynthesis pathways. Molecular modeling of P. falciparum arginase was used to explore the structural metal dependency between enzyme activity and trimer formation. This dependency is not observed in the mammalian host. A novel inter-monomer salt-bridge was discovered between Glu 295 and Arg 404 that helps mediate the structural metal dependency. Removal of the active site metal atoms promoted breaking of the Glu 295á::Arg 404b interaction during simulation. The involvement of this salt-bridge was further confirmed by site-directed mutagenesis of the recombinantly expressed enzyme and subsequent simulation of the mutants in silico. Mutations designed to break the salt-bridge resulted in decreased enzyme activity and oligomerisation. Furthermore, simulation of the mutants indicated potential loss of metal co-ordination within the active site. The interface around Glu 295á::Arg 404b could thus serve as a novel therapeutic target. In Plasmodium the usually separate activities S-adenosylmethionine decarboxylase and ornithine decarboxylase occur in a single bifunctional enzyme. Previous studies have established the importance of complex formation and protein-protein interactions for correct enzyme functioning. Disturbing these interactions within the complex may therefore have inhibitory potential. In the second aspect of this study the potential quarternary structure of AdoMetDC/ODC was studied by homology modeling of the domains followed by protein-protein docking. The results from five Plasmodium species suggest that one face of each domain is favoured for complex formation. The predicted faces concur with existing experimental results, suggesting the direct involvement of Plasmodium-specific inserts in maintaining complex formation. Further fine-grained analysis revealed potentially conserved residue pairs between AdoMetDC/ODC that can be targeted during experimental follow-up. In both aspects of this study computational methods yielded useful insights into the parasite-specific features of polyamine biosynthesis enzymes from Plasmodium. Exploitation of these features may lead to novel parasite-specific drugs. Furthermore, this study highlights the importance of simulation and computational methods in the current and future practice of Science.