Modeling of non-covalent complexes of the cell-penetrating peptide CADY and its siRNA cargo

CADY is a cell-penetrating peptide spontaneously making non-covalent complexes with short interfering RNAs (siRNAs) in water. Neither the structure of CADY nor that of the complexes is
resolved. We have calculated and analyzed 3D models of CADY and of the non-covalent CADY–siRNA complexes in order to understand their formation and stabilization. Data from the ab initio
calculations and molecular dynamics support that, in agreement with the experimental data, CADY is a polymorphic peptide partly helical. We calculated and compared several complexes with
peptide/siRNA ratios of up to 40. The initial binding of CADYs is essentially due to the electrostatic interactions of the arginines with siRNA phosphates. Due to a repetitive arginine motif
(XLWR(K)), CADYs can adopt multiple positions at the siRNA surface. Nevertheless, several complex properties are common: an average of 14 ± 1 CADYs is required to saturate a siRNA. The
40 CADYs/siRNA that is the optimal ratio for vector stability always corresponds to two layers of CADYs per siRNA and the peptide cage is stabilized by hydrophobic CADY–CADY contacts.
The analysis demonstrates that the hydrophobicity, the positive charges and the polymorphism of CADY are mandatory to make stable the CADY–siRNA complexes.