Transition state analogues of plasmodium falciparum and human orotate phosphoribosyltransferases

Yong Zhang, Gary B. Evans, Keith Clinch, Douglas R. Crump, Lawrence D. Harris, Richard F G Fröhlich, Peter C. Tyler, Keith Z. Hazleton, María B. Cassera, Vern L. Schramm

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

The survival and proliferation of Plasmodium falciparum parasites and human cancer cells require de novo pyrimidine synthesis to supply RNA and DNA precursors. Orotate phosphoribosyltransferase (OPRT) is an indispensible component in this metabolic pathway and is a target for antimalarials and antitumor drugs. P. falciparum (Pf) and Homo sapiens (Hs) OPRTs are characterized by highly dissociative transition states with ribocation character. On the basis of the geometrical and electrostatic features of the PfOPRT and HsOPRT transition states, analogues were designed, synthesized, and tested as inhibitors. Iminoribitol mimics of the ribocation transition state in linkage to pyrimidine mimics using methylene or ethylene linkers gave dissociation constants (Kd) as low as 80 nM. Inhibitors with pyrrolidine groups as ribocation mimics displayed slightly weaker binding affinities for OPRTs. Interestingly, p-nitrophenyl riboside 5'-phosphate bound to OPRTs with Kd values near 40 nM. Analogues designed with a C5-pyrimidine carbon-carbon bond to ribocation mimics gave Kd values in the range of 80-500 nM. Acyclic inhibitors with achiral serinol groups as the ribocation mimics also displayed nanomolar inhibition against OPRTs. In comparison with the nucleoside derivatives, inhibition constants of their corresponding 5'-phosphorylated transition state analogues are largely unchanged, an unusual property for a nucleotide-binding site. In silico docking of the best inhibitor into the HsOPRT active site supported an extensive hydrogen bond network associated with the tight binding affinity. These OPRT transition state analogues identify crucial components of potent inhibitors targeting OPRT enzymes. Despite their tight binding to the targets, the inhibitors did not kill cultured P. falciparum.

Original languageEnglish (US)
Pages (from-to)34746-34754
Number of pages9
JournalJournal of Biological Chemistry
Volume288
Issue number48
DOIs
StatePublished - Nov 29 2013

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Orotate Phosphoribosyltransferase
Plasmodium falciparum
Carbon
RNA Precursors
Antimalarials
Metabolic Networks and Pathways
Static Electricity
Nucleosides
Computer Simulation
Antineoplastic Agents
Hydrogen
Electrostatics
Catalytic Domain
Hydrogen bonds
Parasites
Nucleotides
Phosphates
Binding Sites
Cells
RNA

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

Cite this

Transition state analogues of plasmodium falciparum and human orotate phosphoribosyltransferases. / Zhang, Yong; Evans, Gary B.; Clinch, Keith; Crump, Douglas R.; Harris, Lawrence D.; Fröhlich, Richard F G; Tyler, Peter C.; Hazleton, Keith Z.; Cassera, María B.; Schramm, Vern L.

In: Journal of Biological Chemistry, Vol. 288, No. 48, 29.11.2013, p. 34746-34754.

Research output: Contribution to journalArticle

Zhang, Y, Evans, GB, Clinch, K, Crump, DR, Harris, LD, Fröhlich, RFG, Tyler, PC, Hazleton, KZ, Cassera, MB & Schramm, VL 2013, 'Transition state analogues of plasmodium falciparum and human orotate phosphoribosyltransferases', Journal of Biological Chemistry, vol. 288, no. 48, pp. 34746-34754. https://doi.org/10.1074/jbc.M113.521955
Zhang, Yong ; Evans, Gary B. ; Clinch, Keith ; Crump, Douglas R. ; Harris, Lawrence D. ; Fröhlich, Richard F G ; Tyler, Peter C. ; Hazleton, Keith Z. ; Cassera, María B. ; Schramm, Vern L. / Transition state analogues of plasmodium falciparum and human orotate phosphoribosyltransferases. In: Journal of Biological Chemistry. 2013 ; Vol. 288, No. 48. pp. 34746-34754.
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AB - The survival and proliferation of Plasmodium falciparum parasites and human cancer cells require de novo pyrimidine synthesis to supply RNA and DNA precursors. Orotate phosphoribosyltransferase (OPRT) is an indispensible component in this metabolic pathway and is a target for antimalarials and antitumor drugs. P. falciparum (Pf) and Homo sapiens (Hs) OPRTs are characterized by highly dissociative transition states with ribocation character. On the basis of the geometrical and electrostatic features of the PfOPRT and HsOPRT transition states, analogues were designed, synthesized, and tested as inhibitors. Iminoribitol mimics of the ribocation transition state in linkage to pyrimidine mimics using methylene or ethylene linkers gave dissociation constants (Kd) as low as 80 nM. Inhibitors with pyrrolidine groups as ribocation mimics displayed slightly weaker binding affinities for OPRTs. Interestingly, p-nitrophenyl riboside 5'-phosphate bound to OPRTs with Kd values near 40 nM. Analogues designed with a C5-pyrimidine carbon-carbon bond to ribocation mimics gave Kd values in the range of 80-500 nM. Acyclic inhibitors with achiral serinol groups as the ribocation mimics also displayed nanomolar inhibition against OPRTs. In comparison with the nucleoside derivatives, inhibition constants of their corresponding 5'-phosphorylated transition state analogues are largely unchanged, an unusual property for a nucleotide-binding site. In silico docking of the best inhibitor into the HsOPRT active site supported an extensive hydrogen bond network associated with the tight binding affinity. These OPRT transition state analogues identify crucial components of potent inhibitors targeting OPRT enzymes. Despite their tight binding to the targets, the inhibitors did not kill cultured P. falciparum.

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