Design of Novel Human Microbiome-Derived Peptides for Inhibition of Oxa-48 Carbapenemase: An In-Silico and In-Vitro Approach Publisher Pubmed



S Sadeghi SOLMAZ ; Ma Faramarzi Mohammad ALI ; M Siroosi MARYAM
Source: Microbial Pathogenesis Published:2025

Abstract

Drug-resistant bacteria have become a global healthcare challenge, especially due to their acquisition of resistance to last-resort antibiotics. OXA-48 carbapenemase is one of the notorious enzymes that inactivates carbapenems through hydrolysis. The emergence of OXA-48 and OXA-48-like carbapenemases is a significant concern as they are responsible for many outbreaks of hospital-acquired infections in various countries, with limited treatment options available. Thus, targeting this enzyme and inhibiting its activity can be an attractive therapeutic strategy. In this study, a rational computer-aided approach was applied to design effective inhibitory peptides against OXA-48 carbapenemase. The primary library was constructed based on peptides derived from the Human Antimicrobial Peptide (HAMP) database. The binding of peptides to the enzyme was investigated through molecular docking studies using ClusPro. After each screening step, numerous targeted amino acid substitutions were performed to enhance the affinity and physicochemical properties of the selected peptides. The final selected peptides, in complex with the enzyme, were subjected to 200 ns molecular dynamics (MD) simulations using the GROMACS package, and MM/PBSA analysis was conducted to evaluate the binding free energy of the enzyme-peptide complexes. Finally, the inhibitory effects of the designed peptides were also computationally assessed on OXA-48-like carbapenemases. Homology modeling was used to generate 3D structures of the enzymes whose structures were not solved experimentally. Results indicated that the two final selected peptides effectively interacted with the important residues of OXA-48 carbapenemase and spatially blocked its active site. These peptides also demonstrated high binding affinity to the most common OXA-48-like carbapenemases in silico. In vitro studies on the efficacy of one of the designed peptides, M104, demonstrated that this peptide enhanced the activity of meropenem against a meropenem-resistant, clinical Klebsiella pneumoniae strain harboring the gene blaOXA48 by reducing its minimum inhibitory concentration (MIC) by 4-fold. In an era where effective inhibitors against OXA-48 carbapenemase are limited, present study addressed this urgent need by rationally designed novel peptides. © 2025 Elsevier B.V., All rights reserved.