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.