Given the significant challenges that viruses pose to public health, the development of effective antiviral therapies remains a key priority in biomedical research and pharmaceutical development. In this paper, novel nanostructures aimed at advancing viral therapies are designed and examined using molecular dynamics simulations. These nanostructures, consisting of DNA origami, heparin, and spermidine-based linkers, were designed and simulated as six complexes. The simulations demonstrate that these complexes exhibit substantial stability and strong intermolecular interactions. The calculated energies for intermolecular interactions between the DNA origami, linker, and heparin indicate strong interactions. Electrostatic energies ranged from −36.1 ± 1.8 to −77.1 ± 6.7 kJ/mol, and van der Waals energies ranged from −56.5 ± 2.3 to −92.3 ± 8.8 kJ/mol. This paper introduces complexes formed through noncovalent interactions that can be tailored for various antiviral purposes. The results suggest that these complexes could serve as a foundation for the development of novel antiviral drugs and offer a promising approach to counter emerging viral threats. Moreover, these nanostructures may also be utilized in targeted drug delivery, gene therapy, tissue engineering, cellular surface engineering, disease diagnosis and anticoagulation.

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