Towards an understanding of drug resistance in malaria: three-dimensional structure of Plasmodium falciparum dihydrofolate reductase by homology building.

A three-dimensional (3-D) model of dihydrofolate reductase (DHFR) from Plasmodium falciparum has been constructed by homology building. The model building has been based on a structural alignment of five X-ray structures of DHFR from different species. The 3-D model of the plasmodial DHFR was obtained by amino acid substitution in the human DHFR, which was chosen as template, modification of four loops (two insertions, two deletions) and subsequent energy minimization. The active site of P. falciparum DHFR was analyzed and compared to human DHFR with respect to sequence variations and structural differences. Based on this analysis the molecular consequences of point mutations known to be involved in drug resistance were discussed. The significance of the most important point mutation causing resistance, S108N, could be explained by the model, whereas the point mutations associated with enhanced resistance, N51I and C59R, seem to have a more indirect effect on inhibitor binding.

[1]  Winona C. Barker,et al.  Protein sequence database. , 1990 .

[2]  F. Winkler,et al.  Crystal structure of human dihydrofolate reductase complexed with folate. , 1988, European journal of biochemistry.

[3]  P. Kollman,et al.  An all atom force field for simulations of proteins and nucleic acids , 1986, Journal of computational chemistry.

[4]  Ioan Motoc,et al.  Three-Dimensional Quantitative Structure-Activity Relationships. 2. Conformational Mimicry and Topographical Similarity of Flexible Molecules , 1986 .

[5]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[6]  J Deisenhofer,et al.  Crystallographic refinement at 2.3 A resolution and refined model of the photosynthetic reaction centre from Rhodopseudomonas viridis. , 1989, Journal of molecular biology.

[7]  M. Perkins,et al.  Chapter 15. Chemotherapy of Malaria , 1996 .

[8]  J. Greer.  Comparative modeling methods: Application to the family of the mammalian serine proteases , 1990, Proteins.

[9]  R. Wade,et al.  New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure. , 1989, Journal of medicinal chemistry.

[10]  W Pangborn,et al.  Comparison of ternary complexes of Pneumocystis carinii and wild-type human dihydrofolate reductase with coenzyme NADPH and a novel classical antitumor furo[2,3-d]pyrimidine antifolate. , 1997, Acta crystallographica. Section D, Biological crystallography.

[11]  A. Cowman,et al.  Amino acid changes linked to pyrimethamine resistance in the dihydrofolate reductase-thymidylate synthase gene of Plasmodium falciparum. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[12]  David A. Matthews,et al.  Structure of and kinetic channelling in bifunctional dihydrofolate reductase–thymidylate synthase , 1994, Nature Structural Biology.

[13]  W. Lipscomb,et al.  Molecular structure of leucine aminopeptidase at 2.7-A resolution. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[14]  T. Wellems,et al.  Evidence that a point mutation in dihydrofolate reductase-thymidylate synthase confers resistance to pyrimethamine in falciparum malaria. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[15]  L. Kuyper.  Receptor-Based Design of Dihydrofolate Reductase Inhibitors , 1990 .

[16]  W. Sirawaraporn,et al.  Antifolate-resistant mutants of Plasmodium falciparum dihydrofolate reductase. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[17]  M Read,et al.  Rational drug design approach for overcoming drug resistance: application to pyrimethamine resistance in malaria. , 1998, Journal of medicinal chemistry.

[18]  F. Jørgensen,et al.  Molecular mechanics calculations of proteins. Comparison of different energy minimization strategies. , 1997, Journal of biomolecular structure & dynamics.

[19]  G. Poste,et al.  Protein Design and the Development of New Therapeutics and Vaccines , 1990, New Horizons in Therapeutics.

[20]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[21]  R. Griffin,et al.  Regioselective deacylation of 2,4-diacylaminopyrimidine derivatives by Lewis acids and crystal structures of two products , 1992 .

[22]  J. Kraut,et al.  Investigation of the functional role of tryptophan-22 in Escherichia coli dihydrofolate reductase by site-directed mutagenesis. , 1994, Biochemistry.

[23]  Peter A. Kollman,et al.  AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions , 1981 .

[24]  A. Cowman,et al.  Antifolate drug selection results in duplication and rearrangement of chromosome 7 in Plasmodium chabaudi , 1989, Molecular and cellular biology.

[25]  G. Marshall.  Computer-aided drug design. , 1987, Annual review of pharmacology and toxicology.

[26]  J. Thornton,et al.  Stereochemical quality of protein structure coordinates , 1992, Proteins.

[27]  T. Horii,et al.  Molecular cloning and sequence analysis of the Plasmodium falciparum dihydrofolate reductase-thymidylate synthase gene. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[28]  P. Goodford.  A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. , 1985, Journal of medicinal chemistry.

[29]  M G Rossmann,et al.  The NADPH binding site on beef liver catalase. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[30]  C. L. Propst,et al.  Computer-Aided Drug Design: Methods and Applications , 1989 .

[31]  G. Cohen,et al.  Structure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis. , 1987, Journal of molecular biology.

[32]  M. Sippl.  Recognition of errors in three‐dimensional structures of proteins , 1993, Proteins.