Crystal structure of dihydrofolate reductase from Plasmodium vivax: Pyrimethamine displacement linked with mutation-induced resistance

doi:10.1073/pnas.0501747102

Crystal structure of dihydrofolate reductase from Plasmodium vivax: Pyrimethamine displacement linked with mutation-induced resistance

^†Department of Chemistry and Center for Protein Structure and Function, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand; ^‡BIOTEC, National Science and Technology Development Agency, 113 Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand; and ^§Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland

Edited by Robert M. Stroud, University of California, San Francisco, CA, and approved July 22, 2005 (received for review March 3, 2005)

Abstract

Pyrimethamine (Pyr) targets dihydrofolate reductase of Plasmodium vivax (PvDHFR) as well as other malarial parasites, but its use as antimalarial is hampered by the widespread high resistance. Comparison of the crystal structures of PvDHFR from wild-type and the Pyr-resistant (SP21, Ser-58 → Arg + Ser-117 → Asn) strain as complexes with NADPH and Pyr or its analog lacking p-Cl (Pyr20) clearly shows that the steric conflict arising from the side chain of Asn-117 in the mutant enzyme, accompanied by the loss of binding to Ser-120, is mainly responsible for the reduction in binding of Pyr. Pyr20 still effectively inhibits both the wild-type and SP21 proteins, and the x-ray structures of these complexes show how Pyr20 fits into both active sites without steric strain. These structural insights suggest a general approach for developing new generations of antimalarial DHFR inhibitors that, by only occupying substrate space of the active site, would retain binding affinity with the mutant enzymes.

Footnotes

↵ ¶ To whom correspondence should be addressed. E-mail: yongyuth{at}biotec.or.th.
Author contributions: P. Kongsaeree, U.L., P.C., M.D.W., and Y.Y. designed research; P. Kongsaeree, P. Khongsuk, U.L., and P.C. performed research; B.T. contributed new reagents/analytic tools; P. Kongsaeree, P. Khongsuk, U.L., P.C., and Y.Y. analyzed data; and P. Kongsaeree, U.L., P.C., M.D.W., and Y.Y. wrote the paper.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: DHF, dihydrofolate; DHFR, DHF reductase; Pf, Plasmodium falciparum; Pv, Plasmodium vivax; Pyr, pyrimethamine; rmsd, rms deviation; TS, thymidylate synthase.
Data deposition: The atomic coordinates have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 2bl9, 2blb, 2bla, and 2blc).