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Malaria, mainly caused byPlasmodium falciparumandPlasmodium vivax,has been a growing cause of morbidity and mortality.P. falciparumis more lethal than isP. vivax, but there is a vital need for effective drugs against both species. Geranylgeranyl diphosphate synthase (GGPPS) is an enzyme involved in the biosynthesis of quinones and in protein prenylation and has been proposed to be a malaria drug target. However, the structure ofP. falciparumGGPPS(PfGGPPS) has not been determined, due to difficulties in crystallization. Here, we created aPfGGPPSmodel using the homologousP.vivaxGGPPSX‐ray structure as a template. We simulated the modeledPfGGPPSas well asPvGGPPSusing conventional and Gaussian accelerated molecular dynamics in bothapo‐andGGPP‐bound states. TheMDsimulations revealed a striking similarity in the dynamics of both enzymes with loop 9‐10 controlling access to the active site. We also found thatGGPPstabilizesPfGGPPSandPvGGPPSinto closed conformations andviasimilar mechanisms. Shape‐based analysis of the binding sites throughout the simulations suggests that the two enzymes will be readily targeted by the same inhibitors. Finally, we produced threeMD‐validated conformations ofPfGGPPSto be used in future virtual screenings for potential new antimalarial drugs acting on bothPvGGPPSandPfGGPPS.