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.
Result: N501Y Replacement Displaces Glutamine 498 from the SARS-CoV-2 ACE2 Interface.
Result: The N501Y Mutation Decreses Electrostatic Binding in B.1.1.7.
Result: The only amino acid exchange localized in the RBD is N501Y, which resides at the RBD-ACE2 interface (Figure S1a).
Result: Thus, we hypothesized that changes in RBD behavior are a direct effect of the N501Y mutation and further analyzed it.
Discus
Discussion: Although MD simulation data on wt S protein RBDACE2 interaction has been reported, data on dynamic changes induced by the N501Y variant found in B.1.1.7 (British), B.1.351 (South African) and P.1 (Brazilian, Japanese) is lacking.
Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2.
Result: Below, we demonstrate how our contact data may be applied to evaluate potential consequences of specific mutations, such as N501Y in the recently prevalent B.1.1.7 lineage that was originally detected in the UK.
Result: For this, we note that N501Y would enable the formation of stabilizing cation- interaction with K353 of ACE2.
Result: For this, we performed in-silico mutagenesis of N501Y in the RBD-ACE2 complex, using the FoldX software.
Result: Hence, a tyrosine (N501Y) side chain that allows for more favorable hydrogen bonds between molecules would further facilitate binding.
Result: In addition, the longer side chain of N501Y (relative to N501) may facilitate the intermolecular hydrogen-bonding between the OH group of PMID: 34071984
2021
Viruses
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 imper
SARS_CoV_2 mutation literature information.
PMID: 
2021
Journal of medical virology
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