Crystal Structure of Dihydrofolate Reductase from Plasmodium vivax: Pyrimethamine Displacement Linked with Mutation-Induced Resistance

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 + S...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 102; no. 37; pp. 13046 - 13051
Main Authors Kongsaeree, Palangpon, Khongsuk, Puttapol, Leartsakulpanich, Ubolsree, Chitnumsub, Penchit, Tarnchompoo, Bongkoch, Walkinshaw, Malcolm D., Yuthavong, Yongyuth, Stroud, Robert M.
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 13.09.2005
National Acad Sciences
Subjects
Active sites
Amino Acid Substitution
Animals
Antimalarials - chemistry
Antimalarials - metabolism
Atomic interactions
Atoms
Binding Sites
Biological Sciences
Crystal structure
Crystallography, X-Ray
Crystals
Drug resistance
Drug Resistance - genetics
Enzymes
Folic acid antagonists
Folic Acid Antagonists - chemistry
Folic Acid Antagonists - metabolism
Malaria
Molecular Structure
Mutation
Parasites
Parasitism
Plasmodium vivax
Plasmodium vivax - enzymology
Protein Binding
Pyrimethamine - chemistry
Pyrimethamine - metabolism
Pyrimidines
Tetrahydrofolate Dehydrogenase - chemistry
Tetrahydrofolate Dehydrogenase - genetics
Tetrahydrofolate Dehydrogenase - metabolism
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Summary: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.
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This paper was submitted directly (Track II) to the PNAS office.
Data deposition: The atomic coordinates have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 2bl9, 2blb, 2bla, and 2blc).
Edited by Robert M. Stroud, University of California, San Francisco, CA, and approved July 22, 2005
To whom correspondence should be addressed. E-mail: yongyuth@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.
Abbreviations: DHF, dihydrofolate; DHFR, DHF reductase; Pf, Plasmodium falciparum; Pv, Plasmodium vivax; Pyr, pyrimethamine; rmsd, rms deviation; TS, thymidylate synthase.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0501747102