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In Silico Identification of Multi-target Anti-SARS-CoV-2 Peptides from Quinoa Seed Proteins

Authors
  • Wong, Fai-Chu1, 1
  • Ong, Joe-Hui1
  • Kumar, D. Thirumal2
  • Chai, Tsun-Thai1, 1
  • 1 Universiti Tunku Abdul Rahman,
  • 2 Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, 602 105 Tamil Nadu India
Type
Published Article
Journal
International Journal of Peptide Research and Therapeutics
Publisher
Springer-Verlag
Publication Date
Apr 09, 2021
Pages
1–11
Identifiers
DOI: 10.1007/s10989-021-10214-y
PMID: 33867899
PMCID: PMC8034280
Source
PubMed Central
Keywords
Disciplines
  • Article
License
Unknown

Abstract

Peptides are promising antagonists against severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). To expedite drug discovery, a computational approach is widely employed for the initial screening of anti-SARS-CoV-2 candidates. This study aimed to investigate the potential of peptides from quinoa seed proteins as multi-target antagonists against SARS-CoV-2 spike glycoprotein receptor-binding domain, main protease, and papain-like protease. Five quinoa proteins were hydrolyzed in silico by papain and subtilisin. Among the 1465 peptides generated, seven could interact stably with the key binding residues and catalytic residues of the viral targets, mainly via hydrogen bonds and hydrophobic interactions. The seven peptides were comparable or superior to previously reported anti-SARS-CoV-2 peptides based on docking scores. Key residues in the seven peptides contributing to binding to viral targets were determined by computational alanine scanning. The seven peptides were predicted in silico to be non-toxic and non-allergenic. The peptides ranged between 546.66 and 3974.87 g/mol in molecular mass, besides exhibiting basic and cationic properties (isoelectric points: 8.26–12.10; net charges: 0.1–4.0). Among the seven peptides, VEDKGMMHQQRMMEKAMNIPRMCGTMQRKCRMS was found to bind the largest number of key residues on the targets. In conclusion, seven putative non-toxic, non-allergenic, multi-target anti-SARS-CoV-2 peptides were identified from quinoa seed proteins. The in vitro and in vivo efficacies of the seven peptides against SARS-CoV-2 deserve attention in future bench-top testing. Supplementary Information The online version contains supplementary material available at 10.1007/s10989-021-10214-y.

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