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In Silico Analysis of Bacteriocins from Lactic Acid Bacteria Against SARS-CoV-2
Ismail Erol1, Seyfullah Enes Kotil2, Ozkan Fidan3
1Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey. ismail.erol@med.bau.edu.tr.
Probiotics and Antimicrobial Proteins
|November 27, 2021
Summary
Bacteriocins like pediocin PA-1 show strong binding to SARS-CoV-2 spike protein variants, offering potential for new COVID-19 treatments. These antimicrobial peptides may inhibit viral entry into human cells.
Area of Science:
- Biochemistry
- Virology
- Microbiology
Background:
- The COVID-19 pandemic, caused by SARS-CoV-2, necessitates novel therapeutic strategies due to the lack of specific biotherapeutics.
- SARS-CoV-2 pathogenesis involves its spike protein binding to the ACE2 receptor on host cells.
Purpose of the Study:
- To compute binding energies between various bacteriocins and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein (wild type and beta variant).
- To identify bacteriocins with high binding affinity for potential use in preventing viral entry.
Main Methods:
- Molecular docking analyses were employed to evaluate binding energies between bacteriocins and the SARS-CoV-2 RBD.
- Molecular dynamics (MD) simulations were conducted to validate the stability of interactions for top-scoring candidates.
Main Results:
- Pediocin PA-1 and salivaricin P exhibited the strongest binding scores (-12 kcal/mol) with the wild-type RBD.
- Pediocin PA-1, salivaricin B, and salivaricin P showed enhanced binding affinity towards double mutants (-13.8, -13.0, and -12.5 kcal/mol, respectively).
- Pediocin PA-1 demonstrated stronger binding to RBD mutants, especially double and triple mutants, while Salivaricin B showed improved affinity against the triple mutant.
Conclusions:
- Pediocin PA-1, salivaricin P, and salivaricin B are promising candidates for inhibiting SARS-CoV-2 (including the beta variant) entry into human cells.
- These bacteriocins, derived from lactic acid bacteria, offer potential alternative strategies for the treatment and prophylaxis of COVID-19.
