Emerging SARS-CoV-2 variants: impact on vaccine efficacy and neutralizing antibodies

Sharun, Khan; Tiwari, Ruchi; Dhama, Kuldeep; Emran, Talha Bin; Rabaan, Ali A.; Mutair, Abbas Al

doi:10.1080/21645515.2021.1923350

Cited by 39 publications

(27 citation statements)

References 23 publications

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“…These characteristics affect the effectiveness of vaccines and therapeutics used for treating COVID-19 infection. It is also considered to be responsible for community infection (World Health Organization 2021 ; Sharun et al 2021 ). Moreover, it alters the B.1.525 virion replication inside the host cells (Zhou et al 2021a ).…”

Section: Significance Of D614g In B1525 (Eta) Variantmentioning

confidence: 99%

D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity

Bhattacharya

Chatterjee

Sharma

et al. 2021

Appl Microbiol Biotechnol

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Section: Significance Of D614g In B1525 (Eta) Variantmentioning

confidence: 99%

D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity

Bhattacharya

Chatterjee

Sharma

et al. 2021

Appl Microbiol Biotechnol

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“…Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has had a major impact on human health and socioeconomic status globally [1,2]. SARS-CoV-2 is a single-stranded positive-sense RNA (+ssRNA) with a 29.9 kb genomic length and contains two large ORFs (ORF1a and ORF1b) which encode for 16 non-structural protein (nsp1-16) and structural protein encoding genes [3,4]. Morphologically, the virus consists of four structural proteins, namely spike (S), envelope (E), membrane (M), and nucleocapsid (N), among which the former three are integral membrane proteins and the latter remains complexed with its RNA genome.…”

Section: Introductionmentioning

confidence: 99%

Interactions of the Receptor Binding Domain of SARS-CoV-2 Variants with hACE2: Insights from Molecular Docking Analysis and Molecular Dynamic Simulation

Çeli̇k

Yadav

Düzgün

et al. 2021

Biology

Self Cite

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Since the beginning of the coronavirus 19 (COVID-19) pandemic in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been evolving through the acquisition of genomic mutations, leading to the emergence of multiple variants of concern (VOCs) and variants of interest (VOIs). Currently, four VOCs (Alpha, Beta, Delta, and Gamma) and seven VOIs (Epsilon, Zeta, Eta, Theta, Iota, Kappa, and Lambda) of SARS-CoV-2 have been identified in worldwide circulation. Here, we investigated the interactions of the receptor-binding domain (RBD) of five SARS-CoV-2 variants with the human angiotensin-converting enzyme 2 (hACE2) receptor in host cells, to determine the extent of molecular divergence and the impact of mutation, using protein-protein docking and dynamics simulation approaches. Along with the wild-type (WT) SARS-CoV-2, this study included the Brazilian (BR/lineage P.1/Gamma), Indian (IN/lineage B.1.617/Delta), South African (SA/lineage B.1.351/Beta), United Kingdom (UK/lineage B.1.1.7/Alpha), and United States (US/lineage B.1.429/Epsilon) variants. The protein-protein docking and dynamics simulation studies revealed that these point mutations considerably affected the structural behavior of the spike (S) protein compared to the WT, which also affected the binding of RBD with hACE2 at the respective sites. Additional experimental studies are required to determine whether these effects have an influence on drug–S protein binding and its potential therapeutic effect.

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“…The emergence of mutations in this spike has direct implications for the high rate of viral infection since a conformational change in the RBD has resulted in stronger binding to the ACE2 receptor. Single amino acid substitutions should be monitored because they can have phenotypic consequences [ 47 , 48 ].…”

Section: Resultsmentioning

confidence: 99%

Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach

et al. 2022

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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.

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Emerging SARS-CoV-2 variants: impact on vaccine efficacy and neutralizing antibodies

Cited by 39 publications

References 23 publications

D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity

D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity

Interactions of the Receptor Binding Domain of SARS-CoV-2 Variants with hACE2: Insights from Molecular Docking Analysis and Molecular Dynamic Simulation

Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach

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