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May 9, 2026Future Foods0 citationsOpen Access

Computational exploration of New Delhi Metallo-β-lactamase 1 (NDM-1) inhibitory peptides derived from Lacticaseibacillus paracasei HM-1 fermented camel milk

ASAnamika Singh PYPei-Gee Yap CGChee‐Yuen Gan

Key Points

The study investigates the antimicrobial activity of peptides derived from Lacticaseibacillus paracasei HM-1 fermented camel milk against multidrug-resistant bacteria.
Fermentation of camel milk with Lacticaseibacillus paracasei HM-1 to produce antimicrobial peptides.
LC–MS/MS analysis for peptide identification and bioactivity assessment.
Molecular docking and MD simulations to evaluate peptide–NDM-1 interactions.
Fermented camel milk peptides inhibited MDR Bacillus cereus (20.0 ± 1.0 mm), Staphylococcus aureus (12.0 ± 0.7 mm), Escherichia coli (14.0 ± 0.5 mm), and Salmonella Typhimurium (20.0 ± 0.6 mm).
Lead peptide AAQNLLACGVALGALR demonstrated the highest binding affinity to NDM-1, indicating potential as an effective antimicrobial agent.

Abstract

• Camel milk fermented with L. paracasei HM-1 yielded potent antimicrobial peptides. • Fermentates showed strong activity against MDR B. cereus, S. Typhimurium, E. coli , and S. aureus . • LC–MS/MS identified >2000 peptides; 46 showed high predicted bioactivity scores. • Multiple peptides (e.g., AAQNLLACGVALGALR) strongly interacted with NDM-1 active sites. • Docking and MD simulations revealed stable peptide–NDM-1 binding and inhibitory potential. • Lead peptide AAQNLLACGVALGALR displayed highest affinity and stable multi-residue interactions. Silent pandemic of antimicrobial resistance (AMR) necessitates exploring natural antibiotic alternatives like antimicrobial peptides (AMPs). In a similar quest, present study investigated the antimicrobial potential of AMPs derived from Lacticaseibacillus paracasei HM1 fermented camel milk (FCM) proteins against multi drug resistant Bacillus cereus (BC), Staphylococcus aureus (SA), Escherichia coli (EC), and Salmonella Typhimurium (ST). Antibacterial assays suggested potent antibacterial activity of FCM-AMPs against BC (20.0±1.0mm), SA (12.0±0.7mm), EC (14.0±0.5mm), and ST (20.0±0.6mm). Further, identification, and in silico analysis of these AMPs revealed that peptides CCFSSCAMR, KCCFSSCAMR, AAQNLLACGVALGALR, FLPPLQPAVMVPFLQPK, and LLPAPPLLR showed potent interaction and binding with β-lactamase giving insights into their antimicrobial mechanisms. The research findings indicate FCM derived AMPs as potent antibacterial agents targeting both cell membrane and antibiotic degrading enzymes. Going ahead, further validation, safety assessment, and clinical trials will be essential to develop these peptides into effective antimicrobial therapies against AMR pathogens.

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