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Citation
Tags
HERO ID
8726614
Reference Type
Journal Article
Title
In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations
Author(s)
Khan, A; Umbreen, S; Hameed, A; Fatima, R; Zahoor, U; Babar, Z; Waseem, M; Hussain, Z; Rizwan, M; Zaman, N; Ali, S; Suleman, M; Shah, A; Ali, L; Ali, SS; Wei, DQ
Year
2021
Is Peer Reviewed?
Yes
Journal
Interdisciplinary Sciences: Computational Life Sciences
ISSN:
1913-2751
Volume
13
Issue
3
Page Numbers
521-534
Language
English
PMID
34324157
DOI
10.1007/s12539-021-00447-2
Web of Science Id
WOS:000679237900001
Abstract
The prolific spread of COVID-19 caused by a novel coronavirus (SARS-CoV-2) from its epicenter in Wuhan, China, to every nook and cranny of the world after December 2019, jeopardize the prevailing health system in the world and has raised serious concerns about human safety. Multi-directional efforts are made to design small molecule inhibitors, and vaccines and many other therapeutic options are practiced, but their final therapeutic potential is still to be tested. Using the old drug or vaccine or peptides could aid this process to avoid such long experimental procedures. Hence, here, we have repurposed a small peptide (ATLQAIAS) from the previous study, which reported the inhibitory effects of this peptide. We used in silico mutagenesis approach to design more peptides from the native wild peptide, which revealed that substitutions (T2W, T2Y, L3R, and A5W) could increase the binding affinity of the peptide towards the 3CLpro. Furthermore, using MD simulation and free energy calculation confirmed its dynamics stability and stronger binding affinities. Per-residue energy decomposition analysis revealed that the specified substitution significantly increased the binding affinity at the residue level. Our wide-ranging analyses of binding affinities disclosed that our designed peptide owns the potential to hinder the SARS-CoV-2 and will reduce the progression of SARS-CoV-2-borne pneumonia. Our research strongly suggests the experimental and clinical validation of these peptides to curtail the recent corona outbreak.
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