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Structural Studies of Polyamine Biosynthesis Enzymes: Potential Targets for Drugs against Tropical Parasites

Tamu Dufe, Veronica LU (2007)
Abstract
Two enzymes involved in the biosynthesis of polyamines, ornithine decarboxylase (ODC, from human and Leishmania donovani) and spermidine synthase (SPDS, from Plasmodium falciparum and Caenorhabditis elegans) were studied using biochemical methods, homology modelling and X-ray crystallography.



ODC catalyses the first and committed step in polyamine biosynthesis, the decarboxylation of ornithine to putrescine. Kinetic parameters were different between L. donovani and human ODC. 3-aminooxy-1-aminopropane (APA) was a potent inhibitor of both human and L. donovani ODC with a Ki value of around 1.0 nM. The structure of human ODC in complex with its inhibitor, APA, revealed the binding mode of APA with no oxime formed between... (More)
Two enzymes involved in the biosynthesis of polyamines, ornithine decarboxylase (ODC, from human and Leishmania donovani) and spermidine synthase (SPDS, from Plasmodium falciparum and Caenorhabditis elegans) were studied using biochemical methods, homology modelling and X-ray crystallography.



ODC catalyses the first and committed step in polyamine biosynthesis, the decarboxylation of ornithine to putrescine. Kinetic parameters were different between L. donovani and human ODC. 3-aminooxy-1-aminopropane (APA) was a potent inhibitor of both human and L. donovani ODC with a Ki value of around 1.0 nM. The structure of human ODC in complex with its inhibitor, APA, revealed the binding mode of APA with no oxime formed between APA and pyridoxal 5'-phosphate.



SPDS catalyses the transfer of an aminopropyl group from decarboxylated S-adenosylmethionine, (dcAdoMet) to putrescine, forming spermidine. Analysis of the crystal structure of C. elegans SPDS confirmed a homo-dimeric organisation of the nematode enzyme and revealed a high degree of conservation of the overall fold when compared to the structure of other SPDSs. Furthermore, a nematode-specific insertion that has been identified close to the N-terminus of the C. elegans and other nematode SPDSs was found to be located in close proximity to the substrate binding site.



The structure of the apo-enzyme as well as the structures with the substrate dcAdoMet and the inhibitors, S-adenosyl-1,8-diamino-3-thio-octane (AdoDATO) and trans-4-methylcyclohexylamine (4MCHA) of P. falciparum SPDS were determined. Comparison of the apo- and dcAdoMet structures suggests that the binding of dcAdoMet is necessary for the binding of the second substrate, putrescine. AdoDATO and 4MCHA bind such that the proximal negatively charged putrescine binding pocket is not occupied. The complex with 4MCHA clearly demonstrates why it is a better inhibitor of P. falciparum than cyclohexylamine and suggests a way for the development of new inhibitors of higher potency. (Less)
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supervisor
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  • unknown], [unknown
organization
publishing date
type
Thesis
publication status
published
subject
keywords
inhibitors, protein crystallography, Molecular biophysics, Molekylär biofysik, tropical parasites, polyamine biosynthesis enzymes
pages
112 pages
publisher
Department of Molecular Biophysics, Lund University
defense location
N/A
defense date
2007-04-25 10:15
ISBN
978-91-7422-154-1
language
English
LU publication?
yes
id
cf0472ad-690f-435f-84d6-a60d5a0cd358 (old id 548390)
date added to LUP
2007-10-10 10:54:03
date last changed
2016-09-19 08:45:07
@misc{cf0472ad-690f-435f-84d6-a60d5a0cd358,
  abstract     = {Two enzymes involved in the biosynthesis of polyamines, ornithine decarboxylase (ODC, from human and Leishmania donovani) and spermidine synthase (SPDS, from Plasmodium falciparum and Caenorhabditis elegans) were studied using biochemical methods, homology modelling and X-ray crystallography.<br/><br>
<br/><br>
ODC catalyses the first and committed step in polyamine biosynthesis, the decarboxylation of ornithine to putrescine. Kinetic parameters were different between L. donovani and human ODC. 3-aminooxy-1-aminopropane (APA) was a potent inhibitor of both human and L. donovani ODC with a Ki value of around 1.0 nM. The structure of human ODC in complex with its inhibitor, APA, revealed the binding mode of APA with no oxime formed between APA and pyridoxal 5'-phosphate.<br/><br>
<br/><br>
SPDS catalyses the transfer of an aminopropyl group from decarboxylated S-adenosylmethionine, (dcAdoMet) to putrescine, forming spermidine. Analysis of the crystal structure of C. elegans SPDS confirmed a homo-dimeric organisation of the nematode enzyme and revealed a high degree of conservation of the overall fold when compared to the structure of other SPDSs. Furthermore, a nematode-specific insertion that has been identified close to the N-terminus of the C. elegans and other nematode SPDSs was found to be located in close proximity to the substrate binding site.<br/><br>
<br/><br>
The structure of the apo-enzyme as well as the structures with the substrate dcAdoMet and the inhibitors, S-adenosyl-1,8-diamino-3-thio-octane (AdoDATO) and trans-4-methylcyclohexylamine (4MCHA) of P. falciparum SPDS were determined. Comparison of the apo- and dcAdoMet structures suggests that the binding of dcAdoMet is necessary for the binding of the second substrate, putrescine. AdoDATO and 4MCHA bind such that the proximal negatively charged putrescine binding pocket is not occupied. The complex with 4MCHA clearly demonstrates why it is a better inhibitor of P. falciparum than cyclohexylamine and suggests a way for the development of new inhibitors of higher potency.},
  author       = {Tamu Dufe, Veronica},
  isbn         = {978-91-7422-154-1},
  keyword      = {inhibitors,protein crystallography,Molecular biophysics,Molekylär biofysik,tropical parasites,polyamine biosynthesis enzymes},
  language     = {eng},
  pages        = {112},
  publisher    = {ARRAY(0xa5ab100)},
  title        = {Structural Studies of Polyamine Biosynthesis Enzymes: Potential Targets for Drugs against Tropical Parasites},
  year         = {2007},
}