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Designing Anti-Microbial Peptides Against Major β-Lactamase Enzymes in Clinically Important Gram-Negative Bacterial
Soumya Basu1,2, Sahil Mandar Joshi2, Sudha Ramaiah3
1Medical and Biological Computing Laboratory, School of Bio-Sciences and Technology (SBST), Vellore Institute of Technology, Vellore, 632014, India.
Abstract:
Anti-microbial resistance (AMR) creating healthcare concerns worldwide requires ardent exploration of therapeutic alternatives. Although anti-microbial peptides (AMP) are popular for broad-spectrum activity, recent evidence of increasing resistance to membrane-acting AMPs by ESKAPE pathogens has compelled us to design novel AMPs as therapeutic candidates. A library of 60 AMPs comprising natural AMPs and their mutants was constructed through in-silico methods. After physico-chemical property evaluations, each peptide in the library was subjected to flexible molecular docking against four major β-lactamases in Gram-negative ESKAPE pathogens. Among the potent AMP mutants, a Lactoferricin B-Mutant (M4) possessed uniformly high affinity with SHV1, OXA48, NDM1, and AmpC having energies -842.0Kcal/mol, -774.8Kcal/mol, -1103.3Kcal/mol, and -858.8Kcal/mol respectively. Coarse-grained clustering and flexibility analysis further accounted for the residue-level stable configurations of the protein-peptide complexes with high affinity. Highest affinity of Lactoferricin B_M4 was found with NDM1 due to H-bonds, salt-bridges, and hydrophobic interactions with the metallo-β-lactamase domain including crucial active-site residue Asp124. Molecular dynamics simulation further confirmed the stability of Lactoferricin B_M4-NDM1 complex having low residue-level root-mean square deviations (RMSD), atomic-level fluctuations, and radius of gyration (Rg). The study encourages experimental validations and similar methods to identify potential AMPs against drug-resistant pathogens.
Insights
Novel antimicrobial peptides (AMPs) were designed to combat antimicrobial resistance (AMR). A specific mutant, Lactoferricin B-Mutant (M4), showed high affinity for key bacterial enzymes, offering a promising therapeutic alternative.
Area of Science:
- Biochemistry
- Computational Biology
- Drug Discovery
Background:
- Antimicrobial resistance (AMR) is a global health crisis necessitating new therapeutic strategies.
- Existing membrane-acting antimicrobial peptides (AMPs) face increasing resistance from ESKAPE pathogens.
- Novel AMP design is crucial to overcome drug resistance in critical bacterial infections.
Purpose of the Study:
- To design and evaluate novel antimicrobial peptides (AMPs) as potential therapeutics against drug-resistant pathogens.
- To identify AMP candidates with high binding affinity to key resistance enzymes in Gram-negative bacteria.
- To computationally assess the stability and interaction mechanisms of promising AMP-enzyme complexes.
Main Methods:
- In-silico construction of a library of 60 natural AMPs and mutants.
- Physico-chemical property evaluation and flexible molecular docking against four major β-lactamases (SHV1, OXA48, NDM1, AmpC).
- Coarse-grained clustering, flexibility analysis, and molecular dynamics simulations to confirm complex stability and interactions.
Main Results:
- A Lactoferricin B-Mutant (M4) demonstrated high binding affinity across all tested β-lactamases, particularly NDM1 (-1103.3 Kcal/mol).
- Molecular dynamics simulations confirmed the stable interaction of Lactoferricin B_M4 with NDM1, involving hydrogen bonds, salt bridges, and hydrophobic interactions.
- Analysis revealed specific interactions with the NDM1 active site, including residue Asp124, highlighting a potential mechanism of action.
Conclusions:
- Lactoferricin B-Mutant (M4) is a promising candidate for combating antimicrobial resistance due to its strong binding affinity and stable interactions with key bacterial enzymes.
- Computational methods, including molecular docking and dynamics simulations, are effective for identifying novel AMPs against drug-resistant pathogens.
- The findings support further experimental validation of Lactoferricin B_M4 as a potential therapeutic agent against ESKAPE pathogens.
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