Fragment-based discovery of inhibitors of the bacterial DnaG-SSB interaction

Zorik Chilingaryan, Stephen J. Headey, Allen T.Y. Lo, Zhi Qiang Xu, Gottfried Otting, Nicholas E. Dixon, Martin J. Scanlon, Aaron J. Oakley

Research output: Contribution to journalArticleResearchpeer-review

5 Citations (Scopus)

Abstract

In bacteria, the DnaG primase is responsible for synthesis of short RNA primers used to initiate chain extension by replicative DNA polymerase(s) during chromosomal replication. Among the proteins with which Escherichia coli DnaG interacts is the single-stranded DNA-binding protein, SSB. The C-terminal hexapeptide motif of SSB (DDDIPF; SSB-Ct) is highly conserved and is known to engage in essential interactions with many proteins in nucleic acid metabolism, including primase. Here, fragment-based screening by saturation-transfer difference nuclear magnetic resonance (STD-NMR) and surface plasmon resonance assays identified inhibitors of the primase/SSB-Ct interaction. Hits were shown to bind to the SSB-Ct-binding site using15N–1H HSQC spectra. STD-NMR was used to demonstrate binding of one hit to other SSB-Ct binding partners, confirming the possibility of simultaneous inhibition of multiple protein/SSB interactions. The fragment molecules represent promising scaffolds on which to build to discover new antibacterial compounds.

Original languageEnglish
Article number14
Pages (from-to)1-12
Number of pages12
JournalAntibiotics
Volume7
Issue number1
DOIs
Publication statusPublished - 1 Mar 2018

Keywords

  • Antibacterial agents
  • Fragment-based screening
  • Primase
  • Protein
  • Protein interactions
  • SSB

Cite this

Chilingaryan, Z., Headey, S. J., Lo, A. T. Y., Xu, Z. Q., Otting, G., Dixon, N. E., ... Oakley, A. J. (2018). Fragment-based discovery of inhibitors of the bacterial DnaG-SSB interaction. Antibiotics, 7(1), 1-12. [14]. https://doi.org/10.3390/antibiotics7010014
Chilingaryan, Zorik ; Headey, Stephen J. ; Lo, Allen T.Y. ; Xu, Zhi Qiang ; Otting, Gottfried ; Dixon, Nicholas E. ; Scanlon, Martin J. ; Oakley, Aaron J. / Fragment-based discovery of inhibitors of the bacterial DnaG-SSB interaction. In: Antibiotics. 2018 ; Vol. 7, No. 1. pp. 1-12.
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abstract = "In bacteria, the DnaG primase is responsible for synthesis of short RNA primers used to initiate chain extension by replicative DNA polymerase(s) during chromosomal replication. Among the proteins with which Escherichia coli DnaG interacts is the single-stranded DNA-binding protein, SSB. The C-terminal hexapeptide motif of SSB (DDDIPF; SSB-Ct) is highly conserved and is known to engage in essential interactions with many proteins in nucleic acid metabolism, including primase. Here, fragment-based screening by saturation-transfer difference nuclear magnetic resonance (STD-NMR) and surface plasmon resonance assays identified inhibitors of the primase/SSB-Ct interaction. Hits were shown to bind to the SSB-Ct-binding site using15N–1H HSQC spectra. STD-NMR was used to demonstrate binding of one hit to other SSB-Ct binding partners, confirming the possibility of simultaneous inhibition of multiple protein/SSB interactions. The fragment molecules represent promising scaffolds on which to build to discover new antibacterial compounds.",
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author = "Zorik Chilingaryan and Headey, {Stephen J.} and Lo, {Allen T.Y.} and Xu, {Zhi Qiang} and Gottfried Otting and Dixon, {Nicholas E.} and Scanlon, {Martin J.} and Oakley, {Aaron J.}",
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Chilingaryan, Z, Headey, SJ, Lo, ATY, Xu, ZQ, Otting, G, Dixon, NE, Scanlon, MJ & Oakley, AJ 2018, 'Fragment-based discovery of inhibitors of the bacterial DnaG-SSB interaction', Antibiotics, vol. 7, no. 1, 14, pp. 1-12. https://doi.org/10.3390/antibiotics7010014

Fragment-based discovery of inhibitors of the bacterial DnaG-SSB interaction. / Chilingaryan, Zorik; Headey, Stephen J.; Lo, Allen T.Y.; Xu, Zhi Qiang; Otting, Gottfried; Dixon, Nicholas E.; Scanlon, Martin J.; Oakley, Aaron J.

In: Antibiotics, Vol. 7, No. 1, 14, 01.03.2018, p. 1-12.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Chilingaryan, Zorik

AU - Headey, Stephen J.

AU - Lo, Allen T.Y.

AU - Xu, Zhi Qiang

AU - Otting, Gottfried

AU - Dixon, Nicholas E.

AU - Scanlon, Martin J.

AU - Oakley, Aaron J.

PY - 2018/3/1

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N2 - In bacteria, the DnaG primase is responsible for synthesis of short RNA primers used to initiate chain extension by replicative DNA polymerase(s) during chromosomal replication. Among the proteins with which Escherichia coli DnaG interacts is the single-stranded DNA-binding protein, SSB. The C-terminal hexapeptide motif of SSB (DDDIPF; SSB-Ct) is highly conserved and is known to engage in essential interactions with many proteins in nucleic acid metabolism, including primase. Here, fragment-based screening by saturation-transfer difference nuclear magnetic resonance (STD-NMR) and surface plasmon resonance assays identified inhibitors of the primase/SSB-Ct interaction. Hits were shown to bind to the SSB-Ct-binding site using15N–1H HSQC spectra. STD-NMR was used to demonstrate binding of one hit to other SSB-Ct binding partners, confirming the possibility of simultaneous inhibition of multiple protein/SSB interactions. The fragment molecules represent promising scaffolds on which to build to discover new antibacterial compounds.

AB - In bacteria, the DnaG primase is responsible for synthesis of short RNA primers used to initiate chain extension by replicative DNA polymerase(s) during chromosomal replication. Among the proteins with which Escherichia coli DnaG interacts is the single-stranded DNA-binding protein, SSB. The C-terminal hexapeptide motif of SSB (DDDIPF; SSB-Ct) is highly conserved and is known to engage in essential interactions with many proteins in nucleic acid metabolism, including primase. Here, fragment-based screening by saturation-transfer difference nuclear magnetic resonance (STD-NMR) and surface plasmon resonance assays identified inhibitors of the primase/SSB-Ct interaction. Hits were shown to bind to the SSB-Ct-binding site using15N–1H HSQC spectra. STD-NMR was used to demonstrate binding of one hit to other SSB-Ct binding partners, confirming the possibility of simultaneous inhibition of multiple protein/SSB interactions. The fragment molecules represent promising scaffolds on which to build to discover new antibacterial compounds.

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Chilingaryan Z, Headey SJ, Lo ATY, Xu ZQ, Otting G, Dixon NE et al. Fragment-based discovery of inhibitors of the bacterial DnaG-SSB interaction. Antibiotics. 2018 Mar 1;7(1):1-12. 14. https://doi.org/10.3390/antibiotics7010014