Identification of tuna protein-derived peptides as potent SARS-CoV-2 inhibitors via molecular docking and molecular dynamic simulation

•Potency of peptides target to Mpro and ACE2 were investigated by molecular docking.•Gly143 and Gln189 played key roles in the interactions of peptide E-M and Mpro.•The RBD of ACE2 was occupied by peptide E-M to inhibit the activity of SARS-CoV-2.•Peptide E-M may be the potent nutritional supplement...

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Published in:Food chemistry 2021-04, Vol.342, p.128366-128366, Article 128366
Main Authors: Yu, Zhipeng, Kan, Ruotong, Ji, Huizhuo, Wu, Sijia, Zhao, Wenzhu, Shuian, David, Liu, Jingbo, Li, Jianrong
Format: Article
Language:English
Subjects:
ACE2
Animals
Antiviral Agents - chemistry
Antiviral Agents - pharmacology
Binding Sites
COVID-19 - virology
Fish Proteins - chemistry
Humans
Hydrogen Bonding
Molecular docking
Molecular Docking Simulation
Molecular Dynamics Simulation
Mpro
Peptides
Peptides - chemistry
Peptides - pharmacology
Protein Binding
Protein supplementation
SARS-CoV-2 - drug effects
Tuna
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Summary:•Potency of peptides target to Mpro and ACE2 were investigated by molecular docking.•Gly143 and Gln189 played key roles in the interactions of peptide E-M and Mpro.•The RBD of ACE2 was occupied by peptide E-M to inhibit the activity of SARS-CoV-2.•Peptide E-M may be the potent nutritional supplement for COVID-19 patients. The present study aimed to identify potential SARS-CoV-2 inhibitory peptides from tuna protein by virtual screening. The molecular docking was performed to elicit the interaction mechanism between targets (Mpro and ACE2) and peptides. As a result, a potential antiviral peptide EEAGGATAAQIEM (E-M) was identified. Molecular docking analysis revealed that E-M could interact with residues Thr190, Thr25, Thr26, Ala191, Leu50, Met165, Gln189, Glu166, His164, His41, Cys145, Gly143, and Asn119 of Mpro via 11 conventional hydrogen bonds, 9 carbon hydrogen bonds, and one alkyl interaction. The formation of hydrogen bonds between peptide E-M and the residues Gly143 and Gln189 of Mpro may play important roles in inhibiting the activity of Mpro. Besides, E-M could bind with the residues His34, Phe28, Thr27, Ala36, Asp355, Glu37, Gln24, Ser19, Tyr83, and Tyr41 of ACE2. Hydrogen bonds and electrostatic interactions may play vital roles in blocking the receptor ACE2 binding with SARS-CoV-2.
ISSN:0308-8146
1873-7072
DOI:10.1016/j.foodchem.2020.128366