Identification of Novel Inhibitors of <i>Escherichia coli</i> DNA Ligase (LigA)
Present in all organisms, DNA ligases catalyse the formation of a phosphodiester bond between a 3′ hydroxyl and a 5′ phosphate, a reaction that is essential for maintaining genome integrity during replication and repair. Eubacterial DNA ligases use NAD<sup>+</sup> as a cofactor and posse...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-04-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/26/9/2508 |
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| author | Arqam Alomari Robert Gowland Callum Southwood Jak Barrow Zoe Bentley Jashel Calvin-Nelson Alice Kaminski Matthew LeFevre Anastasia J. Callaghan Helen A. Vincent Darren M. Gowers |
| author_facet | Arqam Alomari Robert Gowland Callum Southwood Jak Barrow Zoe Bentley Jashel Calvin-Nelson Alice Kaminski Matthew LeFevre Anastasia J. Callaghan Helen A. Vincent Darren M. Gowers |
| author_sort | Arqam Alomari |
| collection | DOAJ |
| description | Present in all organisms, DNA ligases catalyse the formation of a phosphodiester bond between a 3′ hydroxyl and a 5′ phosphate, a reaction that is essential for maintaining genome integrity during replication and repair. Eubacterial DNA ligases use NAD<sup>+</sup> as a cofactor and possess low sequence and structural homology relative to eukaryotic DNA ligases which use ATP as a cofactor. These key differences enable specific targeting of bacterial DNA ligases as an antibacterial strategy. In this study, four small molecule accessible sites within functionally important regions of <i>Escherichia coli</i> ligase (EC-LigA) were identified using <i>in silico</i> methods. Molecular docking was then used to screen for small molecules predicted to bind to these sites. Eight candidate inhibitors were then screened for inhibitory activity in an <i>in vitro</i> ligase assay. Five of these (geneticin, chlorhexidine, glutathione (reduced), imidazolidinyl urea and 2-(aminomethyl)imidazole) showed dose-dependent inhibition of EC-LigA with half maximal inhibitory concentrations (IC<sub>50</sub>) in the micromolar to millimolar range (11–2600 µM). Two (geneticin and chlorhexidine) were predicted to bind to a region of EC-LigA that has not been directly investigated previously, raising the possibility that there may be amino acids within this region that are important for EC-LigA activity or that the function of essential residues proximal to this region are impacted by inhibitor interactions with this region. We anticipate that the identified small molecule binding sites and inhibitors could be pursued as part of an antibacterial strategy targeting bacterial DNA ligases. |
| first_indexed | 2024-03-10T11:59:08Z |
| format | Article |
| id | doaj.art-9fc2d848c44846f09d6952ec3d521ea7 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T11:59:08Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-9fc2d848c44846f09d6952ec3d521ea72023-11-21T17:05:46ZengMDPI AGMolecules1420-30492021-04-01269250810.3390/molecules26092508Identification of Novel Inhibitors of <i>Escherichia coli</i> DNA Ligase (LigA)Arqam Alomari0Robert Gowland1Callum Southwood2Jak Barrow3Zoe Bentley4Jashel Calvin-Nelson5Alice Kaminski6Matthew LeFevre7Anastasia J. Callaghan8Helen A. Vincent9Darren M. Gowers10School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UKSchool of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UKSchool of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UKSchool of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UKSchool of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UKSchool of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UKSchool of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UKSchool of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UKSchool of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UKSchool of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UKSchool of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UKPresent in all organisms, DNA ligases catalyse the formation of a phosphodiester bond between a 3′ hydroxyl and a 5′ phosphate, a reaction that is essential for maintaining genome integrity during replication and repair. Eubacterial DNA ligases use NAD<sup>+</sup> as a cofactor and possess low sequence and structural homology relative to eukaryotic DNA ligases which use ATP as a cofactor. These key differences enable specific targeting of bacterial DNA ligases as an antibacterial strategy. In this study, four small molecule accessible sites within functionally important regions of <i>Escherichia coli</i> ligase (EC-LigA) were identified using <i>in silico</i> methods. Molecular docking was then used to screen for small molecules predicted to bind to these sites. Eight candidate inhibitors were then screened for inhibitory activity in an <i>in vitro</i> ligase assay. Five of these (geneticin, chlorhexidine, glutathione (reduced), imidazolidinyl urea and 2-(aminomethyl)imidazole) showed dose-dependent inhibition of EC-LigA with half maximal inhibitory concentrations (IC<sub>50</sub>) in the micromolar to millimolar range (11–2600 µM). Two (geneticin and chlorhexidine) were predicted to bind to a region of EC-LigA that has not been directly investigated previously, raising the possibility that there may be amino acids within this region that are important for EC-LigA activity or that the function of essential residues proximal to this region are impacted by inhibitor interactions with this region. We anticipate that the identified small molecule binding sites and inhibitors could be pursued as part of an antibacterial strategy targeting bacterial DNA ligases.https://www.mdpi.com/1420-3049/26/9/2508antibacterial targetchemical inhibitorsDNA ligasemolecular dockingNAD<sup>+</sup>-dependent |
| spellingShingle | Arqam Alomari Robert Gowland Callum Southwood Jak Barrow Zoe Bentley Jashel Calvin-Nelson Alice Kaminski Matthew LeFevre Anastasia J. Callaghan Helen A. Vincent Darren M. Gowers Identification of Novel Inhibitors of <i>Escherichia coli</i> DNA Ligase (LigA) Molecules antibacterial target chemical inhibitors DNA ligase molecular docking NAD<sup>+</sup>-dependent |
| title | Identification of Novel Inhibitors of <i>Escherichia coli</i> DNA Ligase (LigA) |
| title_full | Identification of Novel Inhibitors of <i>Escherichia coli</i> DNA Ligase (LigA) |
| title_fullStr | Identification of Novel Inhibitors of <i>Escherichia coli</i> DNA Ligase (LigA) |
| title_full_unstemmed | Identification of Novel Inhibitors of <i>Escherichia coli</i> DNA Ligase (LigA) |
| title_short | Identification of Novel Inhibitors of <i>Escherichia coli</i> DNA Ligase (LigA) |
| title_sort | identification of novel inhibitors of i escherichia coli i dna ligase liga |
| topic | antibacterial target chemical inhibitors DNA ligase molecular docking NAD<sup>+</sup>-dependent |
| url | https://www.mdpi.com/1420-3049/26/9/2508 |
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