A Computational Study of the Interaction of Amphiphilic α-Helical Cell-Penetrating Peptides with Heparan Sulfate

Recent studies have suggested that extracellular glycosaminoglycans (GAGs), such as heparan sulfate (HS), can bind cell-penetrating peptides (CPPs) and cluster during CPP binding, thereby affecting the efficiency of a wide range of CPPs. Recently, we experimentally investigated the HS interactions of four peptides, which were chosen from our amphiphilic alpha-helical CPP library and had only one or two amino acid(s) differences (Arg/Glu and Ala/Phe). Here, we describe the computational methods and molecular dynamics (MD) simulations used to reveal the detailed binding and clustering mechanisms of these four peptides with HS. The order of the HS-binding affinities and HS-clustering abilities of the four CPPs, which were obtained from the binding free energies calculated in our MD simulations, almost agreed with our previous experimental data. Using free energy decomposition analyses, Arg-containing peptides were found to contribute more electrostatic energy to the binding enthalpy in comparison with Glu-containing peptides, whereas Phe-containing peptides benefited more from nonelectrostatic energy in comparison with Ala-containing peptides. Furthermore, although electrostatic interactions were revealed as the initial driving force in HS CPP binding, nonelectrostatic interactions might be more favorable during the HS CPP clustering process because of their tolerance to local charge mismatch. Consequently, CPPs that adopt a nonelectrostatic-dominant HS-binding mechanism could be internalized by cells more efficiently. Therefore, the present study provides important insights into the design of useful CPPs.