Molecular dynamics analysis of HbA1c-binding aptamer selectivity and stability for aptasensor development

Chronic hyperglycemia from insulin dysfunction underlies diabetes mellitus (DM), a widespread metabolic disease. Glycated hemoglobin (HbA1c) is a clinically relevant biomarker for long-term glucose control and is commonly used in the diagnosis and monitoring of DM. Aptamer-based biosensors (aptasensors) offer an alternative diagnostic strategy with high specificity, thermal stability, and suitability for miniaturized, rapid, and low-cost point-of-care diagnostic devices. This study investigates the binding interaction and selectivity of HbA1c-binding aptamer using molecular docking and molecular dynamics (MD) simulations, and binding free energy calculations. Comparative analyses were performed against nontargets structurally related to HbA1c, including hemoglobin (Hb), glycated human serum albumin (GHSA), human serum albumin (HSA), and glucose. Docking predicted a favorable interaction between the aptamer and HbA1c, further supported by MD simulations indicating stable complex formation through root mean square deviation, root mean square fluctuation, and hydrogen bonding analysis. Binding free energy calculations using the Molecular Mechanics Poisson–Boltzmann Surface Area method yielded the most negative ΔGtotal for HbA1c (−165.63 kcal/mol), compared to Hb (−4.09), GHSA (−7.68), and HSA (0.37), demonstrating higher affinity toward the target. These findings highlight the aptamer’s molecular recognition capability for HbA1c and provide a computational basis for its integration into aptasensor platforms, supporting the development of accurate and user-friendly diagnostic tools for diabetes monitoring in both clinical laboratories and point-of-care settings.