Crystal structure of phosphoethanolamine methyltransferase from Plasmodium falciparum in complex with amodiaquine

Abstract

Phosphoethanolamine N-methyltransferase (PMT) is essential for phospholipid biogenesis in the malarial parasite Plasmodium falciparum. PfPMT catalyzes the triple methylation of phosphoethanolamine to produce phosphocholine, which is then used for phosphatidylcholine synthesis. Here we describe the 2.0Å resolution X-ray crystal structure of PfPMT in complex with amodiaquine. To better characterize inhibition of PfPMT by amodiaquine, we determined the IC(50) values of a series of aminoquinolines using a direct radiochemical assay. Both structural and functional analyses provide a possible approach for the development of new small molecule inhibitors of PfPMT.

Figure 1

Structure of PfPMT in complex with amodiaquine. (A) Chemical structure of amodiaquine with the quinoline group indicated. (B) Electron density (2F_o-F_c omit map contoured at 1.0 σ) of amodiaquine in binding site 2 of PfPMT. Oxygen, nitrogen, and chloride atoms are shown in red, blue, and green, respectively. (C) Ribbon diagram of the PfPMT•SAH•PO₄^2-•amodiaquine complex with α-helices and β-strands colored gold and blue, respectively. Green stick molecules indicate SAH in the SAM/SAH binding site and PO₄^2- in the phosphobase binding site. Pink stick molecules indicate amodiaquine molecule in each binding site.

Figure 2

View of the amodiaquine binding sites in PfPMT. (A) Surface view of amodiaqine binding site 1. PfPMT is shown as a surface rendering. Surfaces for acidic residues (Glu42 and Glu217) and hydrophobic residues (Phe29, Ile30, Phe31, Tyr209, Leu213, Val216, and Tyr 220) are highlighted in red and gold, respectively. (B) Residues in amodiaquine binding site 1. Side-chains for residues in the site are shown as stick drawings. Two water molecules that mediate hydrogen bonds between the ligand and protein are shown as red spheres. (C) Surface view of amodiaqine binding site 2. Surfaces for acidic residues (Glu171 and Glu174) and Tyr175 are highlighted in red and gold, respectively. (D) Residues in amodiaquine binding site 2. Side-chains for residues in the site are shown as stick drawings. The water molecule that mediate hydrogen bonds between the ligand and protein is shown as a red sphere.

Figure 3

Structure comparison of PfPMT in the presence (white) and absence (gold) of amodiaquine. The region around amodiaqione binding site 2, which is adjacent to the active site is shown.