In this work, we investigated the potential of aptamers as diabetes diagnostic agents by studying their interactions with the biomarker clusterin protein, which is implicated in cellular stress and inflammation associated with diabetes. This aptamer can bind to the β cells and could be used in the β cell mass for the early detection of Type 1 diabetes. We found particular binding sites on clusterin where aptamers produced stable complexes characterized by numerous hydrogen bonds and salt bridges. Our results show that aptamers can specifically target and bind to clusterin, indicating its potential use in the early detection and tracking of problems associated with diabetes. The accuracy and effectiveness of aptamer-based diagnostics were demonstrated by applying graph neural networks (GNNs), which improved the identification of druggable locations on the protein. The research highlights the potential of aptamers in developing tailored treatments and diagnostic instruments for diabetes, opening the door to more precise and efficient treatment. To combine the clusterin protein with other biomarkers for better diagnostic and predictive potential, future studies should concentrate on standardizing measurement techniques and carrying out extensive validation studies.