Investigations into Metal-Binding Groups to Probe the DNA Repair Nuclease SNM1A
Citation:
Dürr, Eva-Maria, Investigations into Metal-Binding Groups to Probe the DNA Repair Nuclease SNM1A, Trinity College Dublin.School of Chemistry, 2021Download Item:
Abstract:
SNM1A is a nuclease that is implicated in DNA interstrand crosslink repair and as such is of importance to regular cellular function. However, little is known about its roles, regulation, interaction partners or posttranslational modifications. Research into the function of SNM1A is complicated by its low expression levels, and because overexpression in mammalian cells leads to cytotoxicity. In addition, there is redundancy among repair pathways.
Activity-based protein profiling is a promising approach to further the knowledge about this enzyme. As the active site of SNM1A contains a metal centre, the design of activity-based probes (ABPs) requires the incorporation of metal-binding groups into an oligonucleotide scaffold. To identify suitable metal-binding groups for such probes, insights from metal-binding groups in medicinal chemistry and phosphate bioisosteres were combined. Modified nucleosides, dinucleosides and oligonucleotides were designed and synthesised. These compounds were evaluated for binding to SNM1A to identify the most potent metal-binding groups.
Within this work, results of the synthesis and screening of a series of nucleosides with 5'-modifications are described. Hydroxamic acid modifications emerged as the most potent group, and the positioning of the group relative to the nucleoside core affected the binding strength.
The impact of an oligonucleotide scaffold on the binding affinity was also investigated. Using some of the previously evaluated modifications, the results highlighted the significant interaction between the oligonucleotide scaffold and the enzyme. Squaramide-functionalised oligonucleotides were found to weakly bind to SNM1A, despite the corresponding nucleosides having no activity. A novel synthetic strategy to install these modifications was developed as part of this work.
Finally, the synthesis and testing of a family of malonate-derived nucleosides are described. An alternative strategy to install hydroxamic acid groups was explored, as well as different positioning relative to the nucleoside core. The strongest inhibitor was a 5'-modified nucleoside containing a hydroxamic acid group. Additionally, dinucleosides were synthesised and evaluated with promising results.
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Trinity College Dublin (TCD)
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APPROVED
Author: Dürr, Eva-Maria
Advisor:
McGouran, JoannaPublisher:
Trinity College Dublin. School of Chemistry. Discipline of ChemistryType of material:
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Full text availableKeywords:
chemical biology, modified nucleoside, nuclease, SNM1A, DNA repairMetadata
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