Identification and prioritization of phytochemicals from medicinal plants with inhibitory activity against the transpeptidase enzyme of Streptococcus pyogenes

Document Type : Research paper

Authors

1 Department of Plan Production, Agriculture Faculty of Bardsir, Shahid Bahonar University of Kerman, Kerman, Iran.

2 Department of Food Industrial, Agriculture Faculty of Bardsir, Shahid Bahonar University of Kerman, Kerman, Iran.

Abstract

Antibiotic-resistant bacteria, particularly Streptococcus pyogenes, which is responsible for a wide array of diseases, represent a significant public health threat. Natural therapeutic agents derived from medicinal plants, notably essential oils, have garnered interest due to their potential antimicrobial properties. This study investigated the antibacterial activity of secondary metabolites from sixteen medicinal plants against Streptococcus pyogenes through bioinformatics approaches. A comprehensive insilco analysis was conducted on 890 phytochemicals to evaluate their interactions with the bacterial transpeptidase enzyme via molecular docking and molecular dynamics (MD) simulations. The transpeptidase enzyme sequence was subjected to various analytical procedures, including the ProtParam tool, EMBOSS Antigenic program, and VICMpred server. ProtParam analysis revealed that the enzyme has a molecular weight of 23.54 kDa, comprises 206 amino acids, with an isoelectric point (pI) of 6.24, an instability index of 31.21, and an aliphatic index of 83.25. The EMBOSS Antigenic program predicted eleven potential antigenic sites within the enzyme, with scores indicating cellular process involvement (1.1164), molecular information (-1.5058), molecular metabolism (-0.965), and virulence factors (-0.686). Molecular docking results identified that compounds from licorice, barberry, turmeric, plantain, nettle, cinnamon, aloe vera, and thyme exhibited significant binding affinities, with interaction energies ranging from -7.0 to -9.3 kcal/mol. Nineteen phytochemicals, including methoxyhydnocarpine, linalyl acetate, kaempferol, and glycyrrhizic acid, demonstrated high binding affinity and stability. MD simulations further confirmed that the enzyme-ligand complexes maintained considerable stability throughout the simulation duration. Additionally, the investigated molecules displayed favorable total interaction energies, spanning from -4.55507 to -90.562 kcal/mol. Collectively, these findings suggest that the identified natural compounds possess promising antibacterial potential, warranting further experimental validation and drug development efforts.

Keywords

References

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History

  • Receive Date: 25 January 2025
  • Revise Date: 27 May 2025
  • Accept Date: 28 May 2025

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