Constant-pH Molecular Dynamics of Cationic Peptide Dendrimers Binding to siRNA

Transfection, the process of delivering genetic material into eukaryotic cells, is crucial in biotechnology and the development of treatments. Naked nucleic acids face challenges such as enzymatic degradation, poor pharmacokinetics, and immunogenicity, which can be mitigated by delivery systems such as liposomes, cationic polymers, and dendrimers that protect and enhance uptake. Peptide dendrimers, in particular, show promise as nucleic acid carriers due to their lower cytotoxicity and immunogenicity, though their mechanisms, efficiency, and optimization remain to be clarified. Here, we characterized the configurational, conformational, and protonation landscapes of different peptide dendrimers in complex with siRNA. We found that nucleic acids modulate dendrimer structure, with electrostatic interactions strengthened at low pH through enhanced protonation of the N-termini. Although experimental data show that the more hydrophobic dendrimer examined displays the highest apparent affinity for siRNA, its reduced number of lysine residues results in weaker overall binding due to diminished charge density. This higher affinity observed is likely linked to increased aggregation propensity. In contrast, the dendrimer sequence with branching residues of inverted chirality, which performs worse, shows the lowest propensity for aggregation. Our work suggests that chirality has only a negligible effect on the dendrimer–siRNA binding modes, and that such differences are subtle, particularly at the monomeric level. Overall, this work provides mechanistic insight into dendrimer–siRNA interactions and outlines potential strategies to refine dendrimer design for improved nucleic acid delivery.