In Silico  Development of EGFRvIII-Targeted Aptamer for Fluorescence Imaging of Glioma

The most prevalent and deadly type of malignant brain tumor is glioma. It has been established that one of the most significant indicators of overall survival, progression-free survival, and neurological prognosis is the extent of resection. Maximum safe resection therefore becomes crucial. Thus, there is an urgent need for a method that can identify the tumor’s border in order to achieve maximal safe excision while safeguarding the healthy brain tissues. Recently, a nanoprobe tagged with quantum dots (QDs) has been designed to specifically bind to tumor cells through aptamers. These aptamers attach to the overexpressed EGFRvIII (epidermal growth factor receptor variation) in glioma cells. Our theory is that these aptamers’ strong binding and high activity are caused by their ability to bind to the receptor’s active site, which allows them to inhibit the receptor’s function. In the present study, we have investigated how these aptamers interact with EGFRvIII receptors using molecular docking simulations. Additionally, we employed artificial intelligence (AI) techniques such as graph neural networks (GNN) and machine learning (ML) to corroborate our findings and elucidate the workings of aptamers. Our findings indicate that the aptamer binds firmly to the receptor’s active site. In order to improve the current aptamers, we have also executed changes in the aptamer sequences. As a result, we discovered that E-M4 created binds to the protein’s active site. In conclusion, the current study will contribute to the development of aptamers targeted at glioma detection and treatments, as well as to our understanding of the binding mechanism of these aptamers to the EGFRvIII receptor.

Keywords: EGDRvIII, Quantum Dots, Glioma, EGFR