SARS-CoV-2 Omicron Subvariants Do Not Differ Much in Binding Affinity to Human ACE2: A Molecular Dynamics Study.

Publication date: Apr 02, 2024

The emergence of the variant of concern Omicron (B. 1.1. 529) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exacerbates the COVID-19 pandemic due to its high contagious ability. Studies have shown that the Omicron binds human ACE2 more strongly than the wild type. The prevalence of Omicron in new cases of COVID-19 promotes novel lineages with improved receptor binding affinity and immune evasion. To shed light on this open problem, in this work, we investigated the binding free energy of the receptor binding domain of the Omicron lineages BA. 2, BA. 2.3. 20, BA. 3, BA4/BA5, BA. 2.75, BA. 2.75. 2, BA. 4.6, XBB. 1, XBB. 1.5, BJ. 1, BN. 1, BQ. 1.1, and CH. 1.1 to human ACE2 using all-atom molecular dynamics simulation and the molecular mechanics Poisson-Boltzmann surface area method. The results show that these lineages have increased binding affinity compared to the BA. 1 lineage, and BA. 2.75 and BA. 2.75. 2 subvariants bind ACE2 more strongly than others. However, in general, the binding affinities of the Omicron lineages do not differ significantly from each other. The electrostatic force dominates over the van der Waals force in the interaction between Omicron lineages and human cells. Based on our results, we argue that viral evolution does not further improve the affinity of SARS-CoV-2 for ACE2 but may increase immune evasion.

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Concepts Keywords
Coronavirus Ace2
Free Affinity
Molecular Ba
Pandemic Binding
Cov
Covid
Differ
Dynamics
Immune
Lineages
Molecular
Omicron
Receptor
Sars
Subvariants

Semantics

Type Source Name
disease VO Severe acute respiratory syndrome coronavirus 2
disease MESH COVID-19 pandemic
disease MESH Long Covid
disease IDO history
disease MESH viral infection
disease IDO host
disease VO vaccine
drug DRUGBANK Angiotensin II
disease VO efficiency
disease IDO infectivity
disease IDO virulence
disease MESH infection
disease MESH dissociation
disease IDO algorithm
drug DRUGBANK Water
disease IDO site
disease VO time
disease VO population
drug DRUGBANK Sodium Tetradecyl Sulfate
disease MESH Severe acute respiratory syndrome
drug DRUGBANK Guanosine
drug DRUGBANK (S)-Des-Me-Ampa
disease VO Glycoprotein
disease VO organization
disease MESH Pneumonia
drug DRUGBANK Carboxyamidotriazole
disease VO efficient
disease VO volume
drug DRUGBANK Isoxaflutole

Original Article

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