Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context.
Abstract: By using our pipeline, we built 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for the VoC B.1.1.7-United Kingdom (carrying the mutations of concern/interest N501Y, S494P, E484K at the RBD), P.1-Japan/Brazil (RBD mutations: K417T, E484K, N501Y), B.1.351-South Africa (RBD mutations: K417N, E484K, N501Y), B.1.427/B.1.429-California (RBD mutations: L452R), the B.1.141 (
Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India.
E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody.
PMID: 34915409
2022
International immunopharmacology
Introduction: Later, it was demonstrated that the S494P caused a 3-5 fold decrease in neutralization titer and was reported in many cases in UK, USA, and Mexico.
Introduction: Using a large-scale genomic screening pipeline, my group previously identified two spike mutants, V367F and S494P, with enhanced human ACE2 binding ability.
Table: S494P
Prolonged shedding of infectious viruses with haplotype switches of SARS-CoV-2 in an immunocompromised patient.
PMID: 35430092
2022
Journal of infection and chemotherapy
Abstract: Seven haplotypes were identified and the non-synonymous mutations accumulated in the spike gene which included E484Q and S494P.
Conclusion: From haplotype 4 through haplotype 7, diversity was observed mainly in the S gene, and two of them (E484Q and S494P) were additional mutations in the receptor-binding motif of the receptor-binding domain (RBD).
Review of the mechanisms of SARS-CoV-2 evolution and transmission.
Introduction: A list of vaccine-escape (vaccine-breakthrough) mutations was tabulated in our early work, including S494P, Q493L, K417N, F490S, F486L, R403K, E484K, L452R, K417T, F490L, E484Q, and A475S.
Introduction: Many of these co-mutation sets involve vaccine-escape mutations predicted in our early work: S494P, Q493L, K417N, F490S, F486L, R403K,
Abstract: Irrespective of the geographical region, in the case of the adaptive mutations, N501Y (48.38%) was found to be the dominant mutation followed by L452R (17.52%), T478K (14.31%), E484K (4.69%), S477N (3.29%), K417T (1.64%), N439K (0.7%) and S494P (0.7%).
Method: Some adaptive mutations, namely Y453F, S477N, T478K, E484K, S494P and N501Y, were also found in long-term COVID-19 infections.
Result: During this period,
The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America.
3Introduction: Moreover, we have pointed out that Y449S and Y449H are two vaccine-resistant mutations, and ""Y449S, S494P, K417N,
Introduction: Later on, we have provided a list of most likely vaccine escape RBD mutations with high frequency, including S494P, Q493L, K417N, F490S, F486L, R403K, E484K, L452R, K417T, F490L, E484Q, and A475S.
Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies.
Figure: Change in binding free energy (DeltaDeltaG = DeltaGWILD-TYPE - DeltaGMUTANT) predicted by computational mutagenesis of the S-RBDCoV-2 wild-type residues E484 (A), Q493 (B), S494P (C), V483 (D), F486 (E), Y489 (F), Y449 (G), L452 (H), T470 (I), and F490 (J) for the corresponding S-RBDCoV-2/LY-CoV555 mAb complexes.
Discussion: Spike variants identified in these studies that presented reduced susceptibility to the LY-CoV555 mAb included the following substitutions: E484D/K/Q, F490S, Q493R, and S494P.
Discussion: Remarkably, the spike S494P mutation is a component of the B.1.17 + S494P
Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI).
Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants.
PMID: 34543625
2021
The Journal of biological chemistry
Table: S494P
Figure: Panels A-I show the data for the wild-type RBD, single amino acid mutations K417N, Y453F, S477N, T478I, E484K, S494P, N501Y, and for the triple mutant K417T/
Figure: The single mutants of RBD used in this study were K417N, N439K, Y453F, S477N, T478I, E484K, S494P and N501Y (Alpha variant).
SARS_CoV_2 mutation literature information.
PMID: 
2022
The EPMA journal
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