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A strategy to optimize the peptide-based inhibitors against different mutants of the spike protein of SARS-CoV-2

Prerna Priya, Abdul Basit, Pradipta Bandyopadhyay
doi: https://doi.org/10.1101/2022.02.27.482153
Prerna Priya
1Department of Botany, Purnea Mahila College, Purnia, Bihar, India
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  • For correspondence: priya.prerna54@gmail.com
Abdul Basit
2School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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Pradipta Bandyopadhyay
2School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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Abstract

SARS-CoV-2 virus has caused high-priority health concerns at a global level. Vaccines have stalled the proliferation of viruses to some extent. Yet, the emergence of newer, potentially more infectious, and dangerous mutants such as delta and omicron are among the major challenges in finding a more permanent solution for this pandemic. The effectiveness of antivirals Molnupiravir and Paxlovid, authorized for emergency use by the FDA, are yet to be assessed at larger populations. Patients with a high risk of disease progression or hospitalization have received treatment with a combination of antibodies (antibody-cocktail). Most of the mutations leading to the new lineage of SARS-CoV-2 are found in the spike protein of this virus that plays a key role in facilitating host entry. The current study has investigated how to modify a promising peptide-based inhibitor of spike protein, LCB3, against common mutations in the target protein so that it retains its efficacy against the spike protein. LCB3 being a prototype for protein-based inhibitors is an ideal testing system to learn about protein-based inhibitors. Two common mutations N501Y and K417N are considered in this work. Using a structure-based approach that considers free energy decomposition of residues, distance, and the interactions between amino acids, we propose the substitutions of amino acid residues of LCB3 inhibitors. Our binding free energy calculations suggest a possible improvement in the binding affinity of existing inhibitor LCB3 to the mutant forms of the S-protein using simple substitutions at specific positions of the inhibitor. This approach, being general, can be used in different inhibitors and other mutations and help in fighting against SARS-CoV-2.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted February 28, 2022.
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A strategy to optimize the peptide-based inhibitors against different mutants of the spike protein of SARS-CoV-2
Prerna Priya, Abdul Basit, Pradipta Bandyopadhyay
bioRxiv 2022.02.27.482153; doi: https://doi.org/10.1101/2022.02.27.482153
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A strategy to optimize the peptide-based inhibitors against different mutants of the spike protein of SARS-CoV-2
Prerna Priya, Abdul Basit, Pradipta Bandyopadhyay
bioRxiv 2022.02.27.482153; doi: https://doi.org/10.1101/2022.02.27.482153

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