Computational Selectivity Analysis of Aptamer toward Oxidized Low-Density Lipoprotein

High target selectivity is a crucial factor in aptamer performance and practical applicability. The selectivity of four DNA aptamers (AP07, AP11, AP25, and AP29) toward oxidized low-density lipoprotein (oxLDL) was examined through computational prediction and experimental validation. Molecular dynamics simulations, combined with molecular mechanics generalized Born surface area (MM/GBSA) analysis, were employed to evaluate binding preferences against apolipoprotein (apo) B100 (apoB100) of native low-density lipoprotein (LDL), oxidized apoB100 of oxLDL, apoA1 of high-density lipoprotein (HDL), apoC1/apoE of very-low-density lipoprotein (VLDL), and albumin. Among the candidates, AP11 revealed the strongest predicted affinity and selectivity toward oxidized apoB100, exhibiting the lowest binding free energies of −344.52 ± 18.37 kcal/mol. Experimental validation using an aptamer-based electrochemical assay confirmed the computational predictions, with AP11 displaying high selectivity for the entire oxLDL and cross-reactivity below 6% toward LDL, HDL, VLDL, and albumin. Structural analysis indicated that AP11 preserves key conformational motifs upon complex formation, contributing to the oxLDL–aptamer interaction. This integrated computational–experimental framework provides a robust strategy for evaluating and optimizing aptamer selectivity toward complex biomolecular targets.