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Related Experiment Video

Updated: Feb 28, 2026

Engineering Antiviral Agents via Surface Plasmon Resonance
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Innovative Peptide Therapeutics for SARS-CoV-2: Design, Docking, and Functional Analysis.

Samaneh Karimkhanilouei1, Saeid Ghorbian2, Sanaz Mahmazi3

  • 1Department of Biology, Ah.C., Islamic Azad University, Ahar, Iran.

Iranian Journal of Pharmaceutical Research : IJPR
|February 27, 2026
PubMed
Summary

Novel peptide analogs were designed to combat SARS-CoV-2 variants, targeting conserved viral proteins like the Spike (S) protein. Computational methods identified potent peptide candidates, offering a promising avenue for developing new antiviral therapies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Keywords:
Inhibitory PeptideMolecular DockingMolecular Dynamics SimulationPeptide DesignSARS-CoV-2

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A Fluorogenic Peptide Cleavage Assay to Screen for Proteolytic Activity: Applications for coronavirus spike protein activation
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Area of Science:

  • Computational drug discovery
  • Structural biology
  • Bioinformatics

Background:

  • Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants necessitate rapid development of novel therapeutics.
  • Peptide-based drugs present high specificity and low toxicity, ideal for targeting conserved viral proteins.

Purpose of the Study:

  • To design and evaluate novel peptide analogs targeting key SARS-CoV-2 proteins: Spike (S), RNA-dependent RNA polymerase (RdRp), and nucleocapsid (N).
  • To utilize an integrated computational approach combining structural biology, molecular docking, and molecular dynamics (MD) simulations.

Main Methods:

  • Dataset preparation of anti-SARS-CoV-2 peptides from DRAVP database and literature.
  • Screening and design of analogous peptides using AVPPred and lead peptide information.
  • Molecular docking via nCoVDock2 server and 100 ns explicit solvent MD simulations for top-ranked complexes.

Main Results:

  • Designed peptide W showed superior inhibition of S protein (-303.41 a.u.) compared to EK1 lead peptide.
  • Peptide A5 demonstrated effective inhibition of RdRp protein (-187.36 a.u.) compared to lead peptide 5.
  • Peptide A7 exhibited strong inhibition of N protein (-317.69 a.u.), outperforming Plectasin. MD simulations confirmed stability for W and A5 complexes.

Conclusions:

  • Bioinformatics-driven design of engineered peptides offers a promising strategy for SARS-CoV-2 peptide-based therapies.
  • This approach holds potential for developing therapeutic methods against other viral diseases.
  • Computational findings provide a foundation for future in vitro and in vivo validation studies.