Abstract: Neferine effectively protected HEK293/hACE2 and HuH7 cell lines from infection by different coronaviruses pseudovirus particles (SARS-CoV-2, SARS-CoV-2 [D614G, N501Y/D614G, 501Y.V1, 501Y.V2, 501Y.V3 variants], SARS-CoV, MERS-CoV) in vitro, with median effect concentration (EC50 ) of 0.13-0.41 muM.
Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics.
Discussion: Recently, the United Kingdom has reported that a large proportion of new cases in South East England belonged to a new single phylogenetic cluster defined by multiple spike protein mutations (deletions 69-70 and 144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H).
Discussion: Whereas mutations emerging within the receptor binding domain such as N501Y and N440K might have a direct impact on ACE2 binding, our work further supports the idea that distant variations affecting RBD dynamics, such as D614G, must also be monitor
Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations.
Abstract: However, the introduction of lineage B.1.1.7 (UK variant/S_N501Y) and S_E484K mutation in lineage B.1.1.25 in a few sequences reported in late December 2020 is of particular concern.
Result: Notably, two potential mutations, E484K (B.1.1.25) and N501Y (B.1.1.7-UK Variant/GRY clade), at the receptor-binding domain (RBD) were determined in this analysis: E484K occurred in two strains sampled on 19 December 2020 from the capital city Dhaka (EPI_ISL_890188 and EPI_ISL_774976), whereas N501Y was found in three strains collected on 31 December 2020
Discussion: However, the introduction of lineage B.1.1.7/GRY (UK variant/S_N501Y mutation) in late December 2020 in Bangladesh was of particular concern.
Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide.
Introduction: Specifically, we show that N501Y in RBD introduces additional stabilizing interactions with Y41 and K353 of ACE2, which can contribute to enhanced infectivity of the new variants that carry N501Y.
Introduction: Using our simulated interactions as foundation, we evaluate the effect of N501Y, a recent mutation that accounts for the majority of new infections in South East England.
Discussion: As an example of application, we have used the simulations as guide to evaluate how the novel N501Y mutation may modulate the affinity between virus and host (Figure 3).
Discussion: Specifically, our analysis suggests that N501Y leads to additional stabilizing interactions (i.e., with Y41 and K353 of host ACE2, see Figure 3b) that can facilitate virus binding.
The Spike of Concern-The Novel Variants of SARS-CoV-2.
Introduction: A ten-fold affinity gain is brought about by the N501Y mutation as Y501 interacts through a strong, aromatic stacking interaction with Y41 and forms two new hydrogen bonds with D38 and K353 in hAce2.
Introduction: Allosteric key positions, like E484 or N501, possess sufficient structural freedom to accommodate new residues without significant affinity loss (sometimes even affinity gains, i.e., N501Y) while changing the surface of the binding site such that neutralising antibodies fail to bind.
Introduction: For example, a high in-host evolution rate was found over a period of 70 days in a cancer patient, and the spontaneous appearance of the RBD mutations E484K and N501Y were observed 75 days and 128 days post-diagnosis in a patient suffering from the PMID: 34074219
2021
mAbs
Introduction: An N501Y variant of SARS-CoV-2 (B.1.1.7, 20I/501Y.V1) that first emerged in the United Kingdom is now spreading to the rest of the world, and it appears to be much more contagious than the original virus.
Introduction: However, this same N501Y mutation is also found in a variant (B.1.351, 20 H/501Y.V2) with mutations of K417N, E484K, and N501Y from South Africa and a variant (P1, 20 J/501Y.V3) with K417T, E484K, and N501Y from Brazil with additional mutations within the RBD.
Introduction: We found that this N501Y single mutation confers an ~10-fold increase in affinity between RBD a
Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters.
Discussion: Currently, besides the D614G variant, several mutations within the receptor binding domains (RBD) of the S protein have attracted most scientists' attention due to their increased frequency in certain countries, including S477N (Australia and some Central European), N439K (UK and European), and N501Y (part of th
Epitope-specific antibody responses differentiate COVID-19 outcomes and variants of concern.
Discussion: All 3 VOCs harbor an N501Y mutation within S-RBD, while the B.1.351 and P.1 variants contain 2 additional RBD changes, K417N/T and E484K.
Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2.
PMID: 34086459
2021
The journal of physical chemistry letters
Abstract: Lastly, the energetics of emerging SARS-CoV-2 mutations were studied, showing that the affinity of the RBD for ACE2 is increased by N501Y and E484K mutations but is slightly decreased by K417N.
Introduction: Among a number of mutations, one common to both is N501Y, which has now also been observed in a Brazilian variant (lineage P.1).
Introduction: In contrast, two of the widespread mutations found in several strains, N501Y and E484K, greatly enhanced binding to ACE2, by -4.5 and -1.3 kcal/mol, respectively.
Introduction: Recent mutations of SARS-CoV-2 have increased infectivity, and many of them are believed to facilitate binding to ACE2.- Therefore, it is imperative to understand the mechanisms behind enhanced binding
SARS_CoV_2 mutation literature information.
PMID: 
2021
Journal of medical virology
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