Fragment-Based Discovery of Inhibitors of the Bacterial DnaG-SSB Interaction

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-termi...

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Main Authors:	Zorik Chilingaryan, Stephen J. Headey, Allen T. Y. Lo, Zhi-Qiang Xu, Gottfried Otting, Nicholas E. Dixon, Martin J. Scanlon, Aaron J. Oakley
Format:	Article
Language:	English
Published:	MDPI AG 2018-02-01
Series:	Antibiotics
Subjects:	antibacterial agents fragment-based screening primase protein–protein interactions SSB
Online Access:	http://www.mdpi.com/2079-6382/7/1/14

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spelling	doaj-9c5e2099c6f7403fa551c8523a04181d2020-11-24T23:20:08ZengMDPI AGAntibiotics2079-63822018-02-01711410.3390/antibiotics7010014antibiotics7010014Fragment-Based Discovery of Inhibitors of the Bacterial DnaG-SSB InteractionZorik Chilingaryan0Stephen J. Headey1Allen T. Y. Lo2Zhi-Qiang Xu3Gottfried Otting4Nicholas E. Dixon5Martin J. Scanlon6Aaron J. Oakley7Molecular Horizons and School of Chemistry, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, AustraliaMonash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, AustraliaMolecular Horizons and School of Chemistry, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, AustraliaMolecular Horizons and School of Chemistry, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, AustraliaResearch School of Chemistry, Australian National University, Canberra, ACT 2601, AustraliaMolecular Horizons and School of Chemistry, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, AustraliaMonash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, AustraliaMolecular Horizons and School of Chemistry, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, AustraliaIn 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 using 15N–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.http://www.mdpi.com/2079-6382/7/1/14antibacterial agentsfragment-based screeningprimaseprotein–protein interactionsSSB
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Zorik Chilingaryan Stephen J. Headey Allen T. Y. Lo Zhi-Qiang Xu Gottfried Otting Nicholas E. Dixon Martin J. Scanlon Aaron J. Oakley
spellingShingle	Zorik Chilingaryan Stephen J. Headey Allen T. Y. Lo Zhi-Qiang Xu Gottfried Otting Nicholas E. Dixon Martin J. Scanlon Aaron J. Oakley Fragment-Based Discovery of Inhibitors of the Bacterial DnaG-SSB Interaction Antibiotics antibacterial agents fragment-based screening primase protein–protein interactions SSB
author_facet	Zorik Chilingaryan Stephen J. Headey Allen T. Y. Lo Zhi-Qiang Xu Gottfried Otting Nicholas E. Dixon Martin J. Scanlon Aaron J. Oakley
author_sort	Zorik Chilingaryan
title	Fragment-Based Discovery of Inhibitors of the Bacterial DnaG-SSB Interaction
title_short	Fragment-Based Discovery of Inhibitors of the Bacterial DnaG-SSB Interaction
title_full	Fragment-Based Discovery of Inhibitors of the Bacterial DnaG-SSB Interaction
title_fullStr	Fragment-Based Discovery of Inhibitors of the Bacterial DnaG-SSB Interaction
title_full_unstemmed	Fragment-Based Discovery of Inhibitors of the Bacterial DnaG-SSB Interaction
title_sort	fragment-based discovery of inhibitors of the bacterial dnag-ssb interaction
publisher	MDPI AG
series	Antibiotics
issn	2079-6382
publishDate	2018-02-01
description	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 using 15N–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.
topic	antibacterial agents fragment-based screening primase protein–protein interactions SSB
url	http://www.mdpi.com/2079-6382/7/1/14
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Fragment-Based Discovery of Inhibitors of the Bacterial DnaG-SSB Interaction

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