dUTPase as a Platform for Antimalarial Drug Design: Structural Basis for the Selectivity of a Class of Nucleoside Inhibitors

Abstract

Pyrimidine metabolism is a major route for therapeutic intervention against malaria. Here we report inhibition and structural studies on the deoxyuridine nucleotidohydrolase from the malaria parasite Plasmodium falciparum (PfdUTPase). We have identified a series of triphenylmethane derivatives of deoxyuridine with antimalarial activity in vitro which inhibit specifically the Plasmodium dUTPase versus the human enzyme. A 2.4 Angstrom crystal structure of PfdUTPase in complex with one of these inhibitors reveals an atypical trimeric enzyme in which the triphenylmethane derivative can be seen to select for PfdUTPase by way of interactions between the trityl group and the side chains of residues Phe46 and Ile117. Immunofluorescence microscopy studies of parasitized red blood cells reveal that enzyme concentrations are highest during the trophozoite/schizont stages, suggesting that PfdUTPase has a major role in DNA replication. Taken together the data show that PfdUTPase may be considered as an antimalarial drug target.

Rational Inhibitors of DNA Base Excision Repair Enzymes: New Tools for Elucidating the Role of BER in Cancer Chemotherapy

“…However, a secondary plot of the Lineweaver-Burk slopes against [3-(3)-27] showed a parabolic response consistent with the presence of at least two inhibitor binding sites ( Figure 6A, inset). 36 Global discrimination fitting of the inhibition data by computer simulation with the program Dynafit using competitive, noncompetitive, uncompetitive, mixed-type, two-site competitive-noncompetitive, and two-site competitive-uncompetitive inhibition mechanisms unambiguously confirmed the presence of two inhibitory binding sites for 3-(3)-27 (see Supporting Information). 37 Simulations clearly indictated that the first tight site is competitive with respect to substrate.…”

Preventive DNA repair by sanitizing the cellular (deoxy)nucleoside triphosphate pool

“…The interest in these enzymes is highly motivated on the one hand by the peculiar active site architecture and, on the other hand, by the possibility of using these dUTPases as targets for developing drugs against neoplastic, as well as infectious diseases [31,[56][57][58][59][60][61][62][63][64][65] [100]. All-b dUTPases also include monomeric dUTPases [40].…”

“…Differences of dUTPase enzymes from parasites and the human host were suggested to contribute to different drug-enzyme recognition characteristics that can be exploited in the design of drugs against protozoan infections [64]. Human dUTPase is also an important target for chemotherapeutic agents that combat a variety of neoplastic diseases [58,110].…”

A Protein in the palm of your hand through augmented reality

“…The computer's camera detects the movement of the trigger card (one of six) and automatically superimposes the image of a specific molecule. Molecular structure of the dUTPase from Plasmodium falciparum (PDB entry 1VYQ) [9] is shown with the subunits colored green, cyan, and magenta and the inhibitor molecules, bound at the subunit interfaces, are colored red. Figure prepared using the Chimera program [10][11][12].…”