AmBAMP.db: a data repository for natural amphibian derived biofilm active peptides and disulfide engineered peptides

Abstract

Antibiotic resistance remains a critical global public health concern, leading to over 35,000 fatalities annually (as reported by CDC), necessitating urgent intervention. Recently, antimicrobial peptides (AMPs) have emerged as a promising therapeutic candidate to antibiotics due to their broad-spectrum activity. However, their therapeutic application is hindered by intrinsic functional characteristics such as toxicity, hemolytic activity against human erythrocytes, and limited tissue penetration. Addressing these challenges require further optimization. In this study, we aimed to extract peptides possessing optimized anti-biofilm activity against ESKAPE pathogens. Therefore, a peptide library was constructed through database and literature screening as well as through the disulfide-engineering of retrieved peptide sequences through amino acid walking method in the N′→ C′ direction. The library was assessed for functional properties such as cell penetrating potential, hemolytic activity and cytotoxicity using in- silico tools (i.e., CelPPD, DBAASP, ToxinPred etc.). Whereas, physicochemical properties were analyzed with R-peptide package. The 60ns molecular dynamic simulation of prioritized docked complexes was carried out with GROMACS. AmBAMP.db was created using DJango framework. From the initial library of 186 peptides twenty-one AMPs showing efficient functional properties were selected for molecular docking against 24 biofilm-associated targets from ESKAPE pathogens. Among these prioritized AMPs, DMS-PS1 mutant (26m4) exhibited high binding affinity across various targets involved in biofilm formation. The highest affinity (lowest docking score) complexes include 26m4_luxS (E .cloacae), 26m4_pilU (P. aeruginosa), 26m4_bap (A. baumannii), 26m4_Type I FimA (K. pneumoniae), 26m4-agrD (S. aureus), 26m4_srtC (E. faecalis), and 26m4_luxS (E. faecalis) with docking scores -226Kcal/mol, -207Kcal/mol, -175Kcal/mol, -190Kcal/mol, -197Kcal/mol, -228Kcal/mol, and - 202Kcal/mol respectively. Coarse-grained dynamic analysis and intermolecular interaction profiles confirmed stable configurations and strong binding affinities within the peptide-protein complexes. DMS-PS1 mutant (26m4) exhibited highest binding affinity with the phospholipase A1 (pIdA) from A. baumannii, forming five hydrogen bonds within the phospholipase A1 domain (PLA1) of the target protein. MD simulations 2 further validated the stability of the docked complexes, showing low atomic-level fluctuations (RMSF and B-factors per residue), root-mean-square deviations (RMSD), as well as radius of gyration (Rg). The comprehensive physicochemical and functional properties datasets, along with binding affinity profiles, were deposited in the AmBAMP.db for broader accessibility and exploration. In-vitro validation of prioritized peptides from AmBAMP.db holds promise for developing alternative therapeutics against biofilm-associated infections caused by multidrug-resistant ESKAPE pathogens. Additionally, the database can be expanded to include more peptides for broader applications.