Structural studies on bioactive compounds. 30. Crystal structure and molecular modeling studies on the Pneumocystis carinii dihydrofolate reductase cofactor complex with TAB, a highly selective antifolate

Vivian Cody, David Chan, Nikolai Galitsky, Dawn Rak, Joseph R. Luft, Walter Pangborn, Sherry F. Queener, Charles A. Laughton, Malcolm F.G. Stevens

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

The crystal structure of the ternary complex of NADPH, the potent antifolate [2,4-diamino-5-{3-[3-(2-acetyloxyethyl)-3-benzyltriazen-1-yl]-4- chlorophenyl}-6-ethylpyrimidine] (TAB, 1) and Pneumocystis carinii dihydrofolate reductase (pcDHFR), refined to 2.1 Å resolution, reveals that TAB binds similar to the antifolates trimethoprim and methotrexate. These data also reveal multiple conformations for the binding geometry of TAB with two preferred orientations of the acetyloxy and benzyl groups that results from a 180°rotation about the N2-N3 triazenyl bond. The methyl of the acetyloxy and benzyl ring of TAB probes large hydrophobic regions of the p- aminobenzoyl folate binding pocket of the active site, in particular the region near Phe69, which is unique to the pcDHFR sequence. These results confirm prior molecular modeling investigations of the binding of TAB to pcDHFR that identified four low, energy binding geometries, two involving rotations about the terminal N(2)-N(3) triazenyl linkage and two involving atropisomerism about the pivotal pyrimethamine-phenyl bond. The primary differences in the molecular dynamics (MD) models and those observed in this crystal complex result from small conformational changes in active-site residues on energy minimization. However, two MD models place the acetyloxy and benzyl ring groups in a region of the active site between the cofactor- binding region and the p-aminobenzoyl folate pocket; an orientation never observed in any DHFR crystal structure to date. These conformers interact with solvent near the enzyme surface and are probably not observed due to the loss of specific hydrogen bonds with the enzyme. The high species pcDHFR selectivity of TAB could be the result of ligand flexibility that enables multiple binding orientations at the enzyme active site. Further modification of the acetyloxy region of TAB could increase its potency and selectivity for pcDHFR.

Original languageEnglish (US)
Pages (from-to)3556-3564
Number of pages9
JournalBiochemistry
Volume39
Issue number13
DOIs
StatePublished - Apr 4 2000

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Folic Acid Antagonists
Pneumocystis carinii
Tetrahydrofolate Dehydrogenase
Molecular modeling
Molecular Structure
Crystal structure
Catalytic Domain
Molecular Models
Molecular Dynamics Simulation
Folic Acid
Molecular dynamics
Dynamic models
Enzymes
Pyrimethamine
Trimethoprim
Geometry
Binding energy
NADP
Methotrexate
Crystal orientation

ASJC Scopus subject areas

  • Biochemistry

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Structural studies on bioactive compounds. 30. Crystal structure and molecular modeling studies on the Pneumocystis carinii dihydrofolate reductase cofactor complex with TAB, a highly selective antifolate. / Cody, Vivian; Chan, David; Galitsky, Nikolai; Rak, Dawn; Luft, Joseph R.; Pangborn, Walter; Queener, Sherry F.; Laughton, Charles A.; Stevens, Malcolm F.G.

In: Biochemistry, Vol. 39, No. 13, 04.04.2000, p. 3556-3564.

Research output: Contribution to journalArticle

Cody, Vivian ; Chan, David ; Galitsky, Nikolai ; Rak, Dawn ; Luft, Joseph R. ; Pangborn, Walter ; Queener, Sherry F. ; Laughton, Charles A. ; Stevens, Malcolm F.G. / Structural studies on bioactive compounds. 30. Crystal structure and molecular modeling studies on the Pneumocystis carinii dihydrofolate reductase cofactor complex with TAB, a highly selective antifolate. In: Biochemistry. 2000 ; Vol. 39, No. 13. pp. 3556-3564.
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abstract = "The crystal structure of the ternary complex of NADPH, the potent antifolate [2,4-diamino-5-{3-[3-(2-acetyloxyethyl)-3-benzyltriazen-1-yl]-4- chlorophenyl}-6-ethylpyrimidine] (TAB, 1) and Pneumocystis carinii dihydrofolate reductase (pcDHFR), refined to 2.1 {\AA} resolution, reveals that TAB binds similar to the antifolates trimethoprim and methotrexate. These data also reveal multiple conformations for the binding geometry of TAB with two preferred orientations of the acetyloxy and benzyl groups that results from a 180°rotation about the N2-N3 triazenyl bond. The methyl of the acetyloxy and benzyl ring of TAB probes large hydrophobic regions of the p- aminobenzoyl folate binding pocket of the active site, in particular the region near Phe69, which is unique to the pcDHFR sequence. These results confirm prior molecular modeling investigations of the binding of TAB to pcDHFR that identified four low, energy binding geometries, two involving rotations about the terminal N(2)-N(3) triazenyl linkage and two involving atropisomerism about the pivotal pyrimethamine-phenyl bond. The primary differences in the molecular dynamics (MD) models and those observed in this crystal complex result from small conformational changes in active-site residues on energy minimization. However, two MD models place the acetyloxy and benzyl ring groups in a region of the active site between the cofactor- binding region and the p-aminobenzoyl folate pocket; an orientation never observed in any DHFR crystal structure to date. These conformers interact with solvent near the enzyme surface and are probably not observed due to the loss of specific hydrogen bonds with the enzyme. The high species pcDHFR selectivity of TAB could be the result of ligand flexibility that enables multiple binding orientations at the enzyme active site. Further modification of the acetyloxy region of TAB could increase its potency and selectivity for pcDHFR.",
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T1 - Structural studies on bioactive compounds. 30. Crystal structure and molecular modeling studies on the Pneumocystis carinii dihydrofolate reductase cofactor complex with TAB, a highly selective antifolate

AU - Cody, Vivian

AU - Chan, David

AU - Galitsky, Nikolai

AU - Rak, Dawn

AU - Luft, Joseph R.

AU - Pangborn, Walter

AU - Queener, Sherry F.

AU - Laughton, Charles A.

AU - Stevens, Malcolm F.G.

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