This study on the structure–activity relationship of polymyxin B, a cyclic peptide antibiotic, used sixteen synthetic polymyxin B
3 analogs including alanine scanning analogs to elucidate the contribution of the side chains to antimicrobial activity and lipopolysaccharide (LPS) binding. Of these analogs, [Ala
5]-polymyxin B
3 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-Ala
6]-, [
L-Phe
6]-, [Ala
7]-, and [Gly
7]-polymyxin B
3 analogs retained potent antimicrobial activity, indicating that neither the reduction of hydrophobic character of the
D-Phe
6-Leu
7 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 Dab
5 being the most significant.
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