ArticleFrontiers in pharmacology2022
Design of novel disturbing peptides against ACE2 SARS-CoV-2 spike-binding region by computational approaches.
Article in Frontiers in pharmacology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- In silico analysis of PERK interactions with engineered alpha lactalbumin peptides using molecular dynamics simulations.Scientific reports · 2026Article
- Molecular dynamics insights into the interactions of biocompatible synthetic polymer composites with carbon-based nanoparticle derivatives: a comparative study of PLGA and PCL interactions with GO/rGO.Journal of computer-aided molecular design · 2025Article
- Structure-guided design and cloning of peptide inhibitors targeting CDK9/cyclin T1 protein-protein interaction.Frontiers in pharmacology · 2024Article
- Designing peptides predicted to bind to the omicron variant better than ACE2 via computational protein design and molecular dynamics.PloS one · 2023Article
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Authors and funding
3 authors.
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Abstract
The SARS-CoV-2, the virus which is responsible for COVID-19 disease, employs its spike protein to recognize its receptor, angiotensin-converting enzyme 2 (ACE2), and subsequently enters the host cell. In this process, the receptor-binding domain (RBD) of the spike has an interface with the α1-helix of the peptidase domain (PD) of ACE2. This study focuses on the disruption of the protein-protein interaction (PPI) of RBD-ACE2. Among the residues in the template (which was extracted from the ACE2), those with unfavorable energies were selected for substitution by mutagenesis. As a result, a library of 140 peptide candidates was constructed and the binding affinity of each candidate was evaluated by molecular docking and molecular dynamics simulations against the α1-helix of ACE2. Finally, the most potent peptides P23 (GFNNYFPHQSYGFMPTNGVGY), P28 (GFNQYFPHQSYGFPPTNGVGY), and P31 (GFNRYFPHQSYGFCPTNGVGY) were selected and their dynamic behaviors were studied. The results showed peptide inhibitors increased the radius, surface accessible area, and overall mobility of residues of the protein. However, no significant alteration was seen in the key residues in the active site. Meanwhile, they can be proposed as promising agents against COVID-19 by suppressing the viral attachment and curbing the infection at its early stage. The designed peptides showed potency against beta, gamma, delta, and omicron variants of SARS-CoV-2.
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