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Targeting Undruggable Protein Interactions with DNA Aptamers: Inhibition of the Interaction Between Yersinia Outer
Oğuz Gök1, Özge Uğurlu2, Canan Özyurt3
1Department of Biochemistry, Faculty of Science, Ege University, 35100 Izmir, Türkiye.
Abstract:
The plague, caused by Yersinia pestis, has resulted in significant mortality over the past century. Despite advances in antimicrobial therapy, plague remains a re-emerging infectious disease with ongoing outbreaks and increasing concerns regarding antimicrobial resistance. Today, plague cases are still being reported, and the loss of effectiveness of treatment methods remains a major challenge. Therefore, effective treatment strategies are needed. In this study, we aimed to develop aptamers specific to Yersinia outer protein M (YopM), a key immunosuppressive protein that is essential for virulence. Our goal was to develop an aptamer that binds to YopM and inhibits its interaction with the human DEAD-box helicase 3 (DDX3) protein. YopM-DDX3 protein interaction was targeted because of its key role in nucleocytoplasmic shuttling of YopM. To achieve this, we developed the YopM16 aptamer using magnetic bead-based (Systematic Evolution of Ligands by Exponential Enrichment) (SELEX). The selected YopM16 aptamer exhibited a half-maximal inhibitory concentration(IC50) value of 103.3 ± 2 nM and effectively inhibited the interaction between YopM and DDX3. The inhibitory effect of the aptamer on protein interaction was confirmed using a pull-down assay and colorimetric test. Given that protein-protein interaction surfaces are considered undruggable, YopM16 is a promising inhibitor with the potential to serve as a molecular tool to investigate the virulence mechanism of YopM, as well as a novel antibacterial agent upon validation of its inhibition in cellular models.
Insights
Researchers developed a novel aptamer, YopM16, to inhibit Yersinia pestis virulence. This aptamer targets the YopM-DDX3 interaction, offering a potential new strategy against plague and antimicrobial resistance.
Area of Science:
- Microbiology and Infectious Diseases
- Biotechnology and Drug Discovery
- Molecular Biology
Background:
- Plague, caused by Yersinia pestis, remains a significant global health threat with increasing antimicrobial resistance.
- Current treatment strategies face challenges due to the re-emerging nature of the disease and evolving resistance patterns.
- Targeting key virulence factors like YopM is crucial for developing novel therapeutic approaches.
Purpose of the Study:
- To develop aptamers specifically targeting Yersinia outer protein M (YopM), a critical immunosuppressive virulence factor.
- To inhibit the YopM-DDX3 protein interaction, which is essential for YopM's nucleocytoplasmic shuttling and virulence.
- To create a potential molecular tool and therapeutic agent against Yersinia pestis infections.
Main Methods:
- Systematic Evolution of Ligands by Exponential Enrichment (SELEX) using magnetic beads to select aptamers.
- Development and characterization of the YopM16 aptamer.
- Validation of aptamer efficacy using pull-down assays and colorimetric tests to confirm inhibition of YopM-DDX3 interaction.
Main Results:
- The YopM16 aptamer was successfully developed and selected.
- YopM16 demonstrated significant inhibition of the YopM-DDX3 protein interaction with an IC50 of 103.3 ± 2 nM.
- The aptamer's inhibitory effect on protein-protein interaction was experimentally confirmed.
Conclusions:
- The YopM16 aptamer effectively inhibits the YopM-DDX3 interaction, a key virulence mechanism of Yersinia pestis.
- This aptamer represents a promising novel inhibitor for 'undruggable' protein-protein interaction targets.
- YopM16 holds potential as a molecular probe for studying YopM virulence and as a future antibacterial agent.
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