Molecular recognition of VEGF₁₆₅ by DNA aptamers: insights from an integrated computational framework

Vascular endothelial growth factor 165 (VEGF₁₆₅) is a homodimeric angiogenic protein composed of a receptor-binding domain (RBD) and a heparin-binding domain (HBD) connected by a flexible linker. The absence of a complete experimental structure of full-length VEGF₁₆₅ has limited atomic-level understanding of its recognition by DNA aptamers. In this work, we reconstructed the full-length VEGF₁₆₅ structure. Accelerated molecular dynamics simulations were employed to generate a representative conformational ensemble for ensemble docking, followed by molecular dynamics simulations and MM/GBSA calculations to characterize the binding mechanisms, structural dynamics, and binding enthalpies of four anti-VEGF₁₆₅ DNA aptamers (del4, del5, SL₁₂, and SL₂-B). The calculations revealed that all four aptamers predominantly bind to the HBD while forming limited secondary interactions with the RBD. Among the investigated aptamers, del5 and SL₂-B exhibited the most favorable average binding enthalpies. The predicted binding enthalpy of SL₂-B is consistent with its experimentally reported high binding affinity, supporting the computational predictions. The study also provides structural models of the interactions between the truncated aptamers del4 and del5 and VEGF₁₆₅, for which direct experimental binding data are currently unavailable. The favorable predicted binding enthalpy of del5 identifies it as a promising candidate for future experimental validation. These findings provide molecular-level insights into VEGF₁₆₅-aptamer recognition and offer a structural basis for the rational design and optimization of anti-VEGF₁₆₅ DNA aptamers.