ArticleComputers in biology and medicine2022
SARS-CoV-2 Omicron spike glycoprotein receptor binding domain exhibits super-binder ability with ACE2 but not convalescent monoclonal antibody.
Article in Computers in biology and medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 36 citations in OpenAlex.
- Subtle Changes at the RBD/hACE2 Interface During SARS-CoV-2 Variant Evolution: A Molecular Dynamics Study.Biomolecules · 2025Article
- A Simple Analysis of the Second (Extra) Disulfide Bridge of VMolecules (Basel, Switzerland) · 2024Article
- SARS-CoV-2 Omicron Spike shows strong binding affinity and favourable interaction landscape with the TLR4/MD2 compared to other variants.Journal, genetic engineering & biotechnology · 2024Article
- Benzimidazole compound abrogates SARS-COV-2 receptor-binding domain (RBD)/ACE2 interaction In vitro.Microbial pathogenesis · 2023Article
- Insight into SARS-CoV-2 Omicron variant immune escape possibility and variant independent potential therapeutic opportunities.Heliyon · 2023Review
- Global emerging Omicron variant of SARS-CoV-2: Impacts, challenges and strategies.Journal of infection and public health · 2023Review
- Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2.PloS one · 2023Article
- Pathogen-host adhesion between SARS-CoV-2 spike proteins from different variants and human ACE2 studied at single-molecule and single-cell levels.Emerging microbes & infections · 2022Article
- Lucidenic acid A inhibits the binding of hACE2 receptor with spike protein to prevent SARS-CoV-2 invasion.Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association · 2022Article
- Omicron variant (B.1.1.529) and its sublineages: What do we know so far amid the emergence of recombinant variants of SARS-CoV-2?Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2022Review
- Review
- Structural basis of Omicron immune evasion: A comparative computational study.Computers in biology and medicine · 2022Article
- Article
- SARS-CoV-2 Omicron Variant Binds to Human Cells More Strongly than the Wild Type: Evidence from Molecular Dynamics Simulation.The journal of physical chemistry. B · 2022Article
- Interference of Chaga mushroom terpenoids with the attachment of SARS-CoV-2; in silico perspective.Computers in biology and medicine · 2022Article
- Functional mutations of SARS-CoV-2: implications to viral transmission, pathogenicity and immune escape.Chinese medical journal · 2022Article
- Emerging evidence on Omicron (B.1.1.529) SARS-CoV-2 variant.Journal of medical virology · 2022Review
- Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations.International journal of molecular sciences · 2022Article
- [Strengthening the prevention and treatment of Omicron infection in children].Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics · 2022Article
- In Silico Screening of Bioactive Compounds of Representative Seaweeds to Inhibit SARS-CoV-2 ACE2-Bound Omicron B.1.1.529 Spike Protein Trimer.Marine drugs · 2022Article
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
SARS-CoV-2, the causative virus for COVID-19 has now super-mutated into the Omicron (Om) variant. On its spike (S) glycoprotein alone, more than 30 substitutions have been characterized with 15 within the receptor binding domain (RBD); It therefore calls to question the transmissibility and antibody escapability of Omicron. This study was setup to investigate the Omicron RBD's interaction with ACE2 (host receptor) and a SARS-CoV-2 neutralizing monoclonal antibody (mAb). In-silico mutagenesis was used to generate the Om-RBD in complex with ACE2 or mAb from the wildtype. HDOCK server was used to redock and score the mAbs in Om-RBD bound state relative to the wildtype. Stability of interaction between all complexes were investigated using all-atom molecular dynamics (MD). Analyses of trajectories showed that Om-RBD has evolved into an efficient ACE2 binder, via pi-pi (Om-RBD-Y501/ACE2-Y41) and salt-bridge (Om-RBD-K493/ACE2-Y41) interactions. Conversely, in binding mAb, it has become less efficient (Center of mass distance of RBD from mAb complex, wildtype ≈ 30 Å, Omicron ≈ 41 Å). Disruption of Om-RBD/mAb complex resulted from loose interaction between Om-RBD and the light chain complementarity-determining region residues. Omicron is expected to be better transmissible and less efficiently interacting with neutralizing convalescent mAbs with consequences on transmissibility provided other mutations within the S protein similarly promote cell fusion and viral entry.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.