BACKGROUND : Plasmodium falciparum is the most pathogenic of the human malaria parasite species and a major
cause of death in Africa. It’s resistance to most of the current drugs accentuates the pressing need for new
chemotherapies. Polyamine metabolism of the parasite is distinct from the human pathway making it an attractive
target for chemotherapeutic development. Plasmodium falciparum spermidine synthase (PfSpdS) catalyzes the
synthesis of spermidine and spermine. It is a major polyamine flux-determining enzyme and spermidine is a
prerequisite for the post-translational activation of P. falciparum eukaryotic translation initiation factor 5A (elF5A).
The most potent inhibitors of eukaryotic SpdS’s are not specific for PfSpdS.
METHODS : ‘Dynamic’ receptor-based pharmacophore models were generated from published crystal structures of
SpdS with different ligands. This approach takes into account the inherent flexibility of the active site, which reduces
the entropic penalties associated with ligand binding. Four dynamic pharmacophore models were developed and
two inhibitors, (1R,4R)-(N1-(3-aminopropyl)-trans-cyclohexane-1,4-diamine (compound 8) and an analogue,
N-(3-aminopropyl)-cyclohexylamine (compound 9), were identified.
RESULTS : A crystal structure containing compound 8 was solved and confirmed the in silico prediction that its
aminopropyl chain traverses the catalytic centre in the presence of the byproduct of catalysis, 5′-methylthioadenosine.
The IC50 value of compound 9 is in the same range as that of the most potent inhibitors of PfSpdS,
S-adenosyl-1,8-diamino-3-thio-octane (AdoDATO) and 4MCHA and 100-fold lower than that of compound 8.
Compound 9 was originally identified as a mammalian spermine synthase inhibitor and does not inhibit mammalian
SpdS. This implied that these two compounds bind in an orientation where their aminopropyl chains face the putrescine
binding site in the presence of the substrate, decarboxylated S-adenosylmethionine. The higher binding affinity
and lower receptor strain energy of compound 9 compared to compound 8 in the reversed orientation explained
their different IC50 values.
CONCLUSION : The specific inhibition of PfSpdS by compound 9 is enabled by its binding in the additional cavity
normally occupied by spermidine when spermine is synthesized. This is the first time that a spermine synthase
inhibitor is shown to inhibit PfSpdS, which provides new avenues to explore for the development of novel inhibitors of PfSpdS.
Additional file 1: Additional compounds identified from virtual
screening that were docked and tested in vitro against PfSpdS.
Additional file 2: Phase space sampling: A 5 ns molecular dynamics
(MD) simulation used to capture the flexibility of the active site.
Additional file 3: An illustration of the conformational change
Gln229 undergoes upon binding of 4MCHA and AdoDATO as well
Additional file 4: Average B factor values for the Cα backbone and
gate-keeping loop of three different PfSpdS crystal structures.
Additional file 5: Inhibition kinetics of PfSpdS treated with
Additional file 6: Superimposition of the human spermine synthase
(grey ribbon) and PfSpdS (blue ribbon).
Additional file 7: Two different binding poses spermine assumes
when co-crystallized with MTA within PfSpdS.