Side Chain Length in Lysine and Its Homologues Modulates Noncovalent Interactions in Histidine-Rich Peptides

The versatility of noncovalent interactions enables the engineering of pH-responsive nanostructures of histidine (His)-rich peptides that function as efficient drug delivery systems and potent anti-infective agents. Despite their importance, no prior work has investigated how the side chain length of lysine (Lys) and its homologues affects the formation and strength of these noncovalent interactions in His-rich peptides. Here, we used Drude polarizable molecular dynamics and quantum mechanical calculations to quantify cation-π, π-π, CH-π, and H-bond interactions of His-based peptides in a membrane-mimicking 30% (v/v) trifluoroethanol/water using myristoylated lipopeptide Myr-<i>X</i>-His-NH₂ as a model system. <i>X</i> represents the cationic residue arginine (Arg), Lys, or its shorter homologues ornithine (Orn), diaminobutyric acid (Dab), and diaminopropanoic acid (Dap), containing 3, 4, 3, 2, and 1 methylene units, respectively. We found that the length of the cationic side chain strongly influences both the geometry and energetics of the interactions. Dab, with its optimal two-methylene chain, positions its ammonium group close to the His ring, forming the strongest and most favorable cation-π interactions among the Lys and its homologues. In contrast, Orn, with its suboptimal chain length, forms the weakest intramolecular interactions with His and instead appears to favor interactions with the membrane-mimicking solvent. These results suggest that Dab may be the optimal cationic residue for His-rich cell-penetrating peptides (CPPs), whereas Orn may be better suited for membrane-lytic antimicrobial peptides (AMPs). These structure-interaction relationships identified here can guide the design of next-generation CPPs and AMPs with optimized activity and minimized toxicity.