AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides

Abstract

Acinetobacter baumannii has emerged as a prominent nosocomial pathogen, exhibiting a progressive rise in resistance to therapeutic interventions. This rise in resistance calls for alternative strategies. Here, we propose an alternative yet specialized resource on antimicrobial peptides (AMPs) against A. baumannii. Database 'AbAMPdb' is the manually curated collection of 300 entries containing the 250 experimental AMP sequences and 50 corresponding synthetic or mutated AMP sequences. The mutated sequences were modified with reported amino acid substitutions intended for decreasing the toxicity and increasing the antimicrobial potency. AbAMPdb also provides 3D models of all 300 AMPs, comprising 250 natural and 50 synthetic or mutated AMPs. Moreover, the database offers docked complexes comprising 5000 AMPs and their corresponding A. baumannii target proteins. These complexes, accessible in Protein Data Bank format, enable the 2D visualization of the interacting amino acid residues. We are confident that this comprehensive resource furnishes vital information concerning AMPs, encompassing their docking interactions with virulence factors and antibiotic resistance proteins of A. baumannii. To enhance clinical relevance, the characterized AMPs could undergo further investigation both in vitro and in vivo. Database URL: https://abampdb.mgbio.tech/.

Figure 1.

Methodology overview. The database development included four steps; screening of AMPS, evaluation of AMPs, homology modelling and target protein selection to dock with each AMP and integration of all the data into AbAMPdb.

Figure 2.

Web interface displaying the AbAMPdb.

Figure 3.

Architecture of AbAMPdb. The main architecture of the database depicting all types of data integration in the database.

Figure 4.

3D modelled structures of AMPs. 3D modelling of natural AMP and synthetic AMP.

Figure 5.

Docking of experimental AMP and synthetic AMP with pathogenic proteins of A. baumannii reveals top 6 AMPs that has low binding energies.

Figure 6.

Overall statistics and findings.