Computational Insights into How Cationic Residue Length Tunes Antibacterial Activity in Ultrashort Histidine-Based Lipopeptides

Ultrashort cationic lipopeptides (USCLs) are promising alternatives to traditional antibiotics due to their rapid, potent, and broad-spectrum activity, even against multidrug-resistant (MDR) bacteria. Here, we explore how cationic side chain length modulates the antibacterial activity of histidine-based USCLs, using amidated myristoylhistidylhistidine (Myr-HH-NH₂) as a template. The middle histidine (His, H) was systematically replaced with arginine (Arg, R), lysine (Lys, K), or its shorter homologues: ornithine (Orn), diaminobutyric acid (Dab), and diaminopropionic acid (Dap) with 3, 2, and 1 methylene units, respectively. Quantum mechanical calculations were performed to assess how this variation in cationic side chain length affects ion pair-π interaction with the membrane lipid palmitoyl oleoylphosphatidylglycerol (POPG). The results suggest that lipopeptides with shorter cationic residues are likely within the optimal window of ion pair-π interactions for potent antibacterial activity. Among the Lys homologues, Orn in Myr-OrnH-NH₂ appears to interact optimally, as evidenced by its potent activity against <i>E. coli</i> ATCC 25922 and <i>S. aureus</i> ATCC 25923. In contrast, interactions that are too weak, as with His⁰ in Myr-HH-NH₂, or relatively too strong, as with Lys in Myr-KH-NH₂, are associated with reduced activity. Based on these findings, Orn could be the optimal cationic residue with the potential to enhance the antibacterial activity of other His-based peptides. Leveraging these insights, two new temporin-SHf derivatives were designed, with C2K-SHf-1 exhibiting potent activity 250 times that of its parent peptide. Beyond their potential to combat AMR, this study provides valuable insights for the design of next-generation USCLs with superior antimicrobial efficacy.