Identification of small molecule synthetic inhibitors of DNA polymerase β by NMR chemical shift mapping

Hong Yu Hu, Julie K. Horton, Michael R. Gryk, Rajendra Prasad, Jana M. Naron, Di An Sun, Sidney Hecht, Samuel H. Wilson, Gregory P. Mullen

Research output: Contribution to journalArticle

76 Citations (Scopus)

Abstract

DNA polymerase β (β-pol) plays a central role in repair of damaged DNA bases by base excision repair (BER) pathways. A predominant phenotype of β-pol null mouse fibroblasts is hypersensitivity to the DNA-methylating agent methyl methanesulfonate. Residues in the 8-kDa domain of β-pol that seem to interact with a known natural product β-pol inhibitor, koetjapic acid, were identified by NMR chemical shift mapping. The data implicate the binding pocket as the hydrophobic cleft between helix-2 and helix-4, which provides the DNA binding and deoxyribose phosphate lyase activities of the enzyme. Nine structurally related synthetic compounds, containing aromatic or other hydrophobic groups in combination with two carboxylate groups, were then tested. They were found to bind to the same or a very similar region on the surface of the enzyme. The ability of these compounds to potentiate methyl methanesulfonate cytotoxicity, an indicator of cellular BER capacity, in wild-type and β-pol null mouse fibroblasts, was next ascertained. The most active and β-pol-specific of these agents, pamoic acid, was further characterized and found to be an inhibitor of the deoxyribose phosphate lyase and DNA polymerase activities of purified β-pol on a BER substrate. Our results illustrate that NMR-based mapping techniques can be used in the design of small molecule enzyme inhibitors including those with potential use in a clinical setting.

Original languageEnglish (US)
Pages (from-to)39736-39744
Number of pages9
JournalJournal of Biological Chemistry
Volume279
Issue number38
DOIs
StatePublished - Sep 17 2004
Externally publishedYes

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Nucleic Acid Synthesis Inhibitors
Chemical shift
DNA Repair
Repair
Nuclear magnetic resonance
Methyl Methanesulfonate
Deoxyribose
Molecules
Lyases
DNA-Directed DNA Polymerase
Fibroblasts
DNA
Phosphates
Enzyme Inhibitors
Enzymes
Cytotoxicity
Biological Products
Hypersensitivity
Phenotype
Substrates

ASJC Scopus subject areas

  • Biochemistry

Cite this

Hu, H. Y., Horton, J. K., Gryk, M. R., Prasad, R., Naron, J. M., Sun, D. A., ... Mullen, G. P. (2004). Identification of small molecule synthetic inhibitors of DNA polymerase β by NMR chemical shift mapping. Journal of Biological Chemistry, 279(38), 39736-39744. https://doi.org/10.1074/jbc.M402842200

Identification of small molecule synthetic inhibitors of DNA polymerase β by NMR chemical shift mapping. / Hu, Hong Yu; Horton, Julie K.; Gryk, Michael R.; Prasad, Rajendra; Naron, Jana M.; Sun, Di An; Hecht, Sidney; Wilson, Samuel H.; Mullen, Gregory P.

In: Journal of Biological Chemistry, Vol. 279, No. 38, 17.09.2004, p. 39736-39744.

Research output: Contribution to journalArticle

Hu, HY, Horton, JK, Gryk, MR, Prasad, R, Naron, JM, Sun, DA, Hecht, S, Wilson, SH & Mullen, GP 2004, 'Identification of small molecule synthetic inhibitors of DNA polymerase β by NMR chemical shift mapping', Journal of Biological Chemistry, vol. 279, no. 38, pp. 39736-39744. https://doi.org/10.1074/jbc.M402842200
Hu, Hong Yu ; Horton, Julie K. ; Gryk, Michael R. ; Prasad, Rajendra ; Naron, Jana M. ; Sun, Di An ; Hecht, Sidney ; Wilson, Samuel H. ; Mullen, Gregory P. / Identification of small molecule synthetic inhibitors of DNA polymerase β by NMR chemical shift mapping. In: Journal of Biological Chemistry. 2004 ; Vol. 279, No. 38. pp. 39736-39744.
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