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Year : 2022  |  Volume : 1  |  Issue : 1  |  Page : 54-62

In silico screening and characterization of novel natural peptides as spike protein inhibitors of novel coronavirus (severe acute respiratory syndrome coronavirus 2)

Department of Biotechnology, School of Biotechnology, Gangadhar Meher University, Sambalpur, Odisha, India

Correspondence Address:
Raghunath Satpathy
School of Biotechnology, Gangadhar Meher University, Amruta Vihar, Sambalpur, Odisha
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/jpdtsm.jpdtsm_7_22

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BACKGROUND: The present work is a computational approach to discover the novel peptides that can interact and inhibit the action of spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). MATERIALS AND METHODS: A total of 193 numbers probable naturally occurring antiviral peptides were retrieved from the antimicrobial database. The three-dimensional structure of all the peptides was predicted by the Chimera tool followed by energy minimization. Similarly, the spike protein of SARS-CoV-2 chain A (PDB ID 6VBY) structure was obtained from the Protein Data Bank (PDB) and used as the receptor. RESULTS: Protein–protein docking was performed for all the peptides followed by some screening criteria that resulted in three numbers of potential peptides such as CAP11 binds to a receptor-binding domain (RBD), mytilin B to S1/S2 cleavage regions, and mBD-1 as N-terminal-binding domain of spike protein. Further screening and evaluation of solubility and the toxic properties of the peptides it was obtained that the peptide molecules CAP11 and mytilin B are nontoxic. Further, the RBD-binding nature of CAP11 peptide was evaluated comparatively by taking the human ACE2 protein and RBD region of the wild-type SARS-CoV-2, triple mutant, South African mutant (B.1.351), by using molecular docking followed by interface analysis. It was predicted that the CAP11 peptide was able to bind perfectly with the RBD domain of both wild type and triple mutant one but not to the South African mutant.

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