Abstract
Before entering the cell, the SARS-CoV-2 spike glycoprotein receptor-binding domain (RBD) binds to the human angiotensin-converting enzyme 2 (hACE2) receptor. Hence, this RBD is a critical target for the development of antiviral agents. Recent studies have discovered that SARS-CoV-2 variants with mutations in the RBD have spread globally. The purpose of this in silico study was to determine the potential of a fruit bromelain-derived peptide. DYGAVNEVK. to inhibit the entry of various SARS-CoV-2 variants into human cells by targeting the hACE binding site within the RBD. Molecular docking analysis revealed that DYGAVNEVK interacts with several critical RBD binding residues responsible for the adhesion of the RBD to hACE2. Moreover, 100 ns MD simulations revealed stable interactions between DYGAVNEVK and RBD variants derived from the trajectory of root-mean-square deviation (RMSD), radius of gyration (Rg), and root-mean-square fluctuation (RMSF) analysis, as well as free binding energy calculations. Overall, our computational results indicate that DYGAVNEVK warrants further investigation as a candidate for preventing SARS-CoV-2 due to its interaction with the RBD of SARS-CoV-2 variants.
Highlights
As of 21 October 2021, the WHO (World Health Organization) had received reports of 241,886,635 confirmed coronavirus disease 2019 (COVID-19) cases worldwide, with4,919,755 deaths
The Multiple sequence alignment (MSA) results for the receptor-binding domain (RBD) wild type and its variants are presented in Figure 1 and Table 1
These results show the positions of mutations in the RBD of SARS-CoV-2
Summary
As of 21 October 2021, the WHO (World Health Organization) had received reports of 241,886,635 confirmed coronavirus disease 2019 (COVID-19) cases worldwide, with4,919,755 deaths. The Centers for Disease Control and Prevention (CDC) have classified the SARS-CoV-2 variants as variants of interest (VOI), variants of concern (VOC), and variants of high consequence (VOHC). The B.1.1.7 lineage (alpha variant) was first described in the United Kingdom, while the B.1.351 lineage (beta variant) was initially reported in South Africa, and the P.1 lineage (gamma variant) was first reported in Brazil. Each of these three variants contains the N501Y mutation, which converts the amino acid asparagine (N) to tyrosine (Y) in the receptor-binding domain (RBD) subunit
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