Two crystal structures of the FK506-binding domain ofPlasmodium falciparumFKBP35 in complex with rapamycin at high resolution

Abstract

Antimalarial chemotherapy continues to be challenging in view of the emergence of drug resistance, especially artemisinin resistance in Southeast Asia. It is critical that novel antimalarial drugs are identified that inhibit new targets with unexplored mechanisms of action. It has been demonstrated that the immunosuppressive drug rapamycin, which is currently in clinical use to prevent organ-transplant rejection, has antimalarial effects. The Plasmodium falciparum target protein is PfFKBP35, a unique immunophilin FK506-binding protein (FKBP). This protein family binds rapamycin, FK506 and other immunosuppressive and non-immunosuppressive macrolactones. Here, two crystallographic structures of rapamycin in complex with the FK506-binding domain of PfFKBP35 at high resolution, in both its oxidized and reduced forms, are reported. In comparison with the human FKBP12-rapamycin complex reported previously, the structures reveal differences in the β4-β6 segment that lines the rapamycin binding site. Structural differences between the Plasmodium protein and human hFKBP12 include the replacement of Cys106 and Ser109 by His87 and Ile90, respectively. The proximity of Cys106 to the bound rapamycin molecule (4-5 Å) suggests possible routes for the rational design of analogues of rapamycin with specific antiparasitic activity. Comparison of the structures with the PfFKBD-FK506 complex shows that both drugs interact with the same binding-site residues. These two new structures highlight the structural differences and the specific interactions that must be kept in consideration for the rational design of rapamycin analogues with antimalarial activity that specifically bind to PfFKBP35 without immunosuppressive effects.

The antimalarial action of FK506 and rapamycin: evidence for a direct effect on FK506-binding protein PfFKBP35

“…PfFKBP35 and its Plasmodium vivax homologue PvFKBP35 have received attention as potential antimalarial drug targets, with reports of ligands with potent antimalarial activity (Monaghan et al 2005; Harikishore et al 2013 a , b ) and atomic-level structures in complex with ligands (Kotaka et al 2008; Alag et al 2009; Bianchin et al 2015). Our understanding of the function of the protein in the parasite has however lagged behind.…”

Targeted Covalent Inhibition of Plasmodium FK506 Binding Protein 35

“…Next, we turned to SLF as a starting point . As there are no structures of SLF -bound FKBP35 we used the structure of the related compound SLFb bound to human FKBP51­(PDB 4DRK) aligned with rapamycin-bound Pf FKBP35 (PDB 4QT2) as the basis for docking. We noted two groups proximal to C106: the aryl ring of the benzylic ester (for Series 1) and the tert -pentyl group adjacent to the ketoamide (for Series 2, Figure a), and compounds from both series were modeled (Table S2).…”

Structural insights into Plasmodium PPIases

“…The crystal structures showed that this is a reactive cysteine and being a unique residue of the Plasmodium FKBPs, it was proposed to be an attractive site for designing covalent inhibitors which can enhance the specificity of Plasmodium FKBP35 (Kotaka et al, 2008). Toward this end, the rapamycin-bound PfFKBD35 was determined in the oxidized and reduced forms (Bianchin et al, 2015). Monomeric units were captured in the crystal.…”