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,
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.
Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein.
PMID: 34419160
2021
Infectious diseases of poverty
Table: 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 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.
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.
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.,).
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
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.
SARS_CoV_2 mutation literature information.
PMID: 
2021
Antibody therapeutics
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