Contribution of Each Amino Acid Residue in Polymyxin B3 to Antimicrobial and Lipopolysaccharide Binding Activity

This study on the structure–activity relationship of polymyxin B, a cyclic peptide antibiotic, used sixteen synthetic polymyxin B3 analogs including alanine scanning analogs to elucidate the contribution of the side chains to antimicrobial activity and lipopolysaccharide (LPS) binding. Of these analogs, [Ala5]-polymyxin B3 showed greatly reduced antimicrobial activity against Escherichia coli (E. coli), Salmonella Typhimurium (S. Typhimurium) and Pseudomonas aeruginosa (P. aeruginosa) with MIC values of 4—16 nmol/ml, suggesting that the Dab (α,γ-diaminobutyric acid) residue at position 5 is the most important residue contributing to bactericidal activity. The antibacterial contribution of Dab when located within the lactam ring (positions 5, 8 and 9) was greater than when located outside the ring (positions 1 and 3). [D-Ala6]-, [L-Phe6]-, [Ala7]-, and [Gly7]-polymyxin B3 analogs retained potent antimicrobial activity, indicating that neither the reduction of hydrophobic character of the D-Phe6-Leu7 region nor the D-configuration at position 6 is indispensable for antimicrobial activity. LPS binding studies showed that decreased hydrophobicity of the lactam ring had little effect, but the Nγ-amino function of the Dab residues at position 1, 3, 5, 8 and 9 greatly affected LPS binding, with the contribution of Dab5 being the most significant.