Aim: Antibiotics treat various diseases by targeting microorganisms by killing them or reducing their multiplication rate. New Delhi Metallo-beta-lactamase-1 (NDM-1) is produced by bacteria possessing the resistance gene blaNDM-1, the enzyme that makes bacteria resistant to beta-lactams. Bacteriophages, especially Lactococcus, have shown their ability to break down lactams. Hence, the current study computationally evaluated the binding potential of Lactococcus bacteriophages with NDM using Molecular docking and dynamics.
Methods: Modelling of NDM I-TASSER for Main tail protein gp19 OS=Lactococcus phage LL-H or Lactobacillus delbrueckii subsp. lactis after downloading from UNIPROT ID- Q38344. Cluspro tool helps in Understanding cellular function and organization with protein-protein interactions. MD simulations(19) typically compute atom movements over time. Simulations were used to predict the ligand binding status in the physiological environment.
Results: The best binding affinity score was found -1040.6 Kcal/mol compared to other docking scores. MD simulations show in RMSD values for target remains within 1.0 Angstrom, which is acceptable. The ligand-protein fit to receptor protein RMSD values of 2.752 fluctuates within 1.5 Angstrom after equilibration.
Conclusions: Lactococcus bacteriophages showed a strong affinity to the NDM. Hence, this hypothesis, supported by evidence from a computational approach, will solve this life-threatening superbug problem.
Keywords: Lactococcus; bacteriophage; oral biology; oral microflora; protein.
© The Author(s) 2023.