Result: First, the 10 most observed or fast-growing RBD mutations are N501Y, L452R, T478K, E484K, K417T, S477N, N439K, K417N, F490S, and S494P, as shown in Table 1.
Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines.
Result: 4 and Tables 4 and 5 The summary of our superimposition results includes that the following we-named first group of variants; 20A/S.A262S, 20A/S.L452R, 20A/S.N501T, 20A/S.N501Y, 20A/S.P681H, 20A/S.P681R, 20A/S.V1176F, 20A/S.N439K, 20A/S.S98F, 20A/S.L5F, 20A/S.P272L, 20A/S.D1163Y, 20A/S.N439K, 20A/S.S98F, 20A/S.L5F, 20A/S.P272L, 20A/S.D1163Y and 20A/S.G1167V have
Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2).
PMID: 34495817
2021
Journal of biomolecular structure & dynamics
Introduction: A recurrent emergence and significant onward transmission of a mutation in the spike gene which result in loss of H69/V70 has recently been reported to co-occur with the receptor binding motif (RBM) amino acid substitutions N501Y, N439K and Y453F (Kemp et al.,).
Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2.
PMID: 34478710
2021
The Journal of biological chemistry
Result: S1), notably mutations L452R (8.8%), E484K (7.7%), T478K (5.9%), S477N (2.2%), and N439K (1.2%), which are also found in other various VOCs and were shown to either increase infectivity or promote the evasion of antibody responses.
SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern.
PMID: 34468141
2021
Journal of chemical information and modeling
Discu
Discussion: In fact, N439K RBD forms a new interaction with the human ACE2 receptor (hACE2) and has enhanced affinity for hACE2.
Discussion: In particular, the number of residues defining the epitope located in the long RBD loop (residues 417-503, recognized by many protective Abs) is much lower in mutants 501Y.V2.noDelta, B1.1.28, and N439K (see Figures 2 and 3, Table S2).
Discussion: In the case of the mutation N439K, it has been reported that this variant maintains fitness while evading antibodies immunity.
Discussion: The salt bridge at the RBD-hACE2 interface (RBD N439K/hACE2 E329) plausibly adds a strong interaction at the binding interface during viral cell entry.
PMID: 34414185
2021
Frontiers in cell and developmental biology
Table: N439K
Figure: (B) Characteristic dynamic fluctuations of both RBD-REGN10987 and RBD(N439K)-REGN10987 complexes.
Figure: (B) The RMSDs of the backbone atoms of both RBD-hACE2 complexes, the RBD-hACE2 is colored orange and RBD(N439K)-hACE2 is colored blue.
Figure: (C) The RMSFs of Calphaatoms of both RBD-hACE2 complexes, where RBD-hACE2 is colored orange and RBD(
Figure: (C) The binding free energies for SARS-CoV-2 RBM-hACE2 (including wild type and variant N439K), using orange for wild-type and blue for mutant type.
Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies.
Discussion: It has been demonstrated that N439K mutation which has been found in more than 30 countries confer resistance against several neutralizing monoclonal antibodies, including one authorized for emergency use by the FDA.
SARS-CoV-2 receptor-binding mutations and antibody contact sites.
Result: C1317A at 5% and G1558T at 0.9% lead to N439K and A520S mutations, respectively.
Result: Although no significant frequency change has been observed for the N439K mutant, there has been a more than 70-fold increase in the presence of the S477N mutation, suggesting that selection may be playing a role in the propagation of this RBD mutant.
Result: Collectively, 13 mutations found in our GISAID analysis coded for an RB
Discussion: Some of the highest frequency mutations with improved binding to the ACE2 receptor included S477N, N439K, V367F, and N501Y.
Identification of natural compounds as SARS-CoV-2 entry inhibitors by molecular docking-based virtual screening with bio-layer interferometry.
Abstract: The EGCG was further validated with no observable animal toxicity and certain antiviral effect against SARS-CoV-2 pseudovirus mutants (D614G, N501Y, N439K & Y453F).
Introduction: Recently, the D614G and N501Y mutants were discovered in Northern Europe and Africa, whereas N439K is commonly found in over 300 countries.
Result: Notably, the most effective compound EGCG is predicted to bind at P2, which does not harbour any of the mutations D614G, N439K, Y453F, N501Y.
Result: Of note, three mutations on the RBD (N439K,
Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein.
PMID: 34463219
2021
Journal of biomolecular structure & dynamics
Introduction: The top-binding ligands were additionally screened against biologically significant SARS-CoV-2 mutations occurring in the RBD of the S protein such as N501Y, E484K,
Method: Using the same PDB ID, the SARS-CoV-2 variants (N501Y, E484K, K417N/T, A475V, L452R, V483A, F490L, S477N, N439K) were constructed using UCSF chimera platform by editing necessary amino acids of the S protein via the swapaa command which utilizes information from a rotamer library (Shapovalov & Dunbrack,).
SARS_CoV_2 mutation literature information.
PMID: 
2021
ArXiv
Browser Board
Co-occurred Entities
Filtrator
ViMRT