9XAO | pdb_00009xao

Spatial structure of the antimicrobial peptide Ap9

PDB DOI: https://doi.org/10.2210/pdb9XAO/pdb

Classification: ANTIBIOTIC
Organism(s): Abarenicola pacifica
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-10-22 Released: 2026-06-10
Deposition Author(s): Safronova, V.N., Lushpa, V.A., Panteleev, P.V., Ovchinnikova, T.V., Bocharov, E.V.
Funding Organization(s): Russian Science Foundation

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 10
Selection Criteria: structures with the least restraint violations

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Marine Antimicrobial Peptide as a Promising Alternative to Polymyxin B.

Safronova, V.N., Lushpa, V.A., Shipunova, V.O., Volovik, M.V., Dobrochaeva, K.L., Kruglikov, R.N., Bolosov, I.A., Dashevskii, D.E., Mishin, A.V., Batishchev, O.V., Korobova, O.V., Borzilov, A.I., Slashcheva, G.A., Dyachenko, I.A., Bocharov, E.V., Panteleev, P.V., Ovchinnikova, T.V.

(2026) Mar Drugs 24

PubMed: 42188290 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/md24050154
Primary Citation Related Structures:
9XAO, 9XAP

PubMed Abstract:
The rise in antimicrobial resistance represents a significant challenge to global health. The reason partially lies in an inappropriate use of conventional antibiotics and the subsequent rapid spread of multidrug-resistant pathogen strains. This emergency requires an urgent search for conceptually new antimicrobial agents. A viable alternative to conventional antibiotics is antimicrobial peptides (AMPs), which are ribosomally synthesized molecules with considerable potential as next-generation anti-infectious therapeutics. Previously, we have reported on the β-hairpin peptide Ap9, an analog of abarenicin from the marine polychaeta Abarenicola pacifica , with potent activity against key Gram-negative pathogens. Here, it is shown that Ap9 acts in a manner resembling polymyxin B, namely via interaction with lipopolysaccharide (LPS), and retains its activity against polymyxin-resistant isolates without observed cross-resistance, and causes insignificant damage in cytoplasmic membrane at bactericidal concentrations. NMR spectroscopy reveals that LPS binding induces a conformational rearrangement of Ap9, its dimer formation, and local structural remodeling of the peptide region (residues 8-12) into 3 ₁₀-helix. Bacterial resistance to Ap9 was found to be relatively low with a reduced susceptibility associated with infrequent genetic alterations, such as the mutation in lptD or the deletion in mlaA . Furthermore, Ap9 demonstrates a favorable tolerability, a wider therapeutic window than that of polymyxin B, and a sufficiently long half-life through the systemic use, as well as in vivo efficacy in murine models of Gram-negative infections, including sepsis caused by the mcr-1 -harboring Escherichia coli strain. The obtained results point to Ap9 as a promising candidate for further preclinical studies aimed at development of an alternative to polymyxins.