PhD Scientific Days 2026

Poster Session 2.C - Molecular Medicine

Analysis of GbpC-aptamer binding using an AI-based approach

Name of the presenter

Harkai, Ákos

Institute/workplace of the presenter

Institute of Biochemistry and Molecular Biology

Authors

Ákos Harkai¹
1: Institute of Biochemistry and Molecular Biology

Text of the abstract

The application of artificial intelligence, which has developed spectacularly in recent years, has now gained ground in molecular biology research. With its help, we can analyse the interaction of molecules that have never been studied in a cost-effective and user-friendly way, in silico. The DNA aptamer selected by our research group for the Streptococcus mutans GbpC cell surface protein has proven to be effective in inhibiting bacterial biofilm formation [1], but the exact binding site of the aptamer and the structure of their complex have not yet been investigated.
Our goal is, on the one hand, to determine the structural regions involved in the binding of the original A39 aptamer to protein, on the other hand, to identify aptamer derivatives that exhibit more favourable binding parameters.
The structure of the aptamers and their complexes with the target molecule were examined using the AlphaFold Server online application. Their evaluation was based on the server's accuracy indicators (pLDDT, ipTM, pTM). The predictions obtained during the analysis and the A39-derivatives were visualized using the PyMOL program.
Based on our results, the cytosine-rich region in the random region of the GbpC-specific A39 aptamer binds to the substrate-binding pocket of GbpC with good reliability (90>pLDDT>70). During the analysis of A39-derivatives, we identified aptamer variants that improve the accuracy parameters characterizing the predictions compared to the original A39-GbpC complex (ipTM= 0.72, pTM=0.77) and bind to the protein with greater accuracy (pLDDT>90).
In conclusion, AlphaFold 3 is suitable for examining the spatial structure of aptamer-protein complexes and predicting the potential binding regions of aptamers. With our approach, a functional aptamer can be further optimized post-SELEX. Our future goal is to validate our theoretical results with microscale thermophoresis and cryo-electron microscopy.
„Supported by the 2025-2.1.1-EKÖP-2025-00014 University Research Scholarship Programme of the Ministry for Culture and Innovation from the source of the National Research, Development and Innovation Fund.”
[1] Harkai et al. (2025) Int J Biol Macromol 288, 138579, 12p