The Impact of Mutation Sets in Receptor-Binding Domain of SARS-CoV-2 Variants on Stability of the RBD–ACE2 Complex

Peka, Mykyta; Balatsky, Viktor

doi:10.2217/fvl-2022-0152

Cited by 5 publications

(6 citation statements)

References 65 publications

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“…The Q493R and Q498R mutations introduce two new salt bridges, such as E35 and E38, respectively replacing hydrogen bond formation and remodelling the electrostatic interactions with the ACE2 receptor of Wuhan-Hu-1 RBD. S477N leads to the formation of new hydrogen bonds between the asparagine side chain and the ACE2 S19 backbone amine and carbonyl groups (47,49,50). These interactions illustrate that key amino acid sites on the ACE2 receptor are important for viral binding.…”

Section: Discussionmentioning

confidence: 95%

“…It supports protective preventive measures for potential hosts in advance to control future outbreaks and reduce animal infections. The constant mutation of coronavirus increases its ability to bind to the ACE2 receptor as well as resist the immune response (47). For example, N501Y can form a new interaction with the ACE2 receptor Y41, and it is widely present in mutants (48).…”

Section: Discussionmentioning

confidence: 99%

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Analysis the molecular similarity of least common amino acid sites in ACE2 receptor to predict the potential susceptible species for SARS-CoV-2

Hu,

Fan,

Villalan

et al. 2023

Preprint

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This research offers a bioinformatics approach to forecasting both domestic and wild animals' likelihood of being susceptible to SARS-CoV-2 infection. Genomic sequencing can resolve phylogenetic relationships between the virus and the susceptible host. The genome sequence of SARS-CoV-2 is highly interactive with the specific sequence region of the ACE2 receptor of the host species. We further evaluate this concept to identify the most important SARS-CoV-2 binding amino acid sites in the ACE2 receptor sequence through the common similarity of the last common amino acid sites (LCAS) in known susceptible host species. Therefore, the SARS-CoV-2 viral genomic interacting key amino acid region in the ACE2 receptor sequence of known susceptible human host was summarized and compared with other reported known SARS-CoV-2 susceptible host species. We identified the 10 most significant amino acid sites for interaction with SARS-CoV-2 infection from the ACE2 receptor sequence region based on the LCAS similarity pattern in known sensitive SARS-CoV-2 hosts. The most significant 10 LCAS were further compared with ACE2 receptor sequences of unknown species to evaluate the similarity of the last common amino acid pattern (LCAP). We predicted the probability of SARS-CoV-2 infection risk in unknown species through the LCAS similarity pattern. This method can be used as a screening tool to assess the risk of SARS-CoV-2 infection in domestic and wild animals to prevent outbreaks of infection.

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Section: Discussionmentioning

confidence: 95%

Section: Discussionmentioning

confidence: 99%

Analysis the molecular similarity of least common amino acid sites in ACE2 receptor to predict the potential susceptible species for SARS-CoV-2

Hu,

Fan,

Villalan

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…It supports protective preventive measures for potential hosts in advance to control future outbreaks and reduce animal infections. The constant mutation of coronavirus increases its ability to bind to the ACE2 receptor as well as resist the immune response [ 53 ]. For example, N501Y can form a new interaction with the ACE2 receptor Y41, and it is widely present in mutants [ 54 ].…”

Section: Discussionmentioning

confidence: 99%

“…The Q493R and Q498R mutations introduce two new salt bridges, such as E35 and E38, respectively replacing hydrogen bond formation and remodeling the electrostatic interactions with the ACE2 receptor of Wuhan-Hu-1 RBD. S477N leads to the formation of new hydrogen bonds between the asparagine side chain and the ACE2 S19 backbone amine and carbonyl groups [ 53 , 55 , 56 ]. These interactions illustrate that key amino acid sites on the ACE2 receptor are important for viral binding.…”

Section: Discussionmentioning

confidence: 99%

Analysis the molecular similarity of least common amino acid sites in ACE2 receptor to predict the potential susceptible species for SARS-CoV-2

Hu,

Villalan,

Fan

et al. 2024

PLoS ONE

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SARS-CoV-2 infections in animals have been reported globally. However, the understanding of the complete spectrum of animals susceptible to SARS-CoV-2 remains limited. The virus’s dynamic nature and its potential to infect a wide range of animals are crucial considerations for a One Health approach that integrates both human and animal health. This study introduces a bioinformatic approach to predict potential susceptibility to SARS-CoV-2 in both domestic and wild animals. By examining genomic sequencing, we establish phylogenetic relationships between the virus and its potential hosts. We focus on the interaction between the SARS-CoV-2 genome sequence and specific regions of the host species’ ACE2 receptor. We analyzed and compared ACE2 receptor sequences from 29 species known to be infected, selecting 10 least common amino acid sites (LCAS) from key binding domains based on similarity patterns. Our analysis included 49 species across primates, carnivores, rodents, and artiodactyls, revealing complete consistency in the LCAS and identifying them as potentially susceptible. We employed the LCAS similarity pattern to predict the likelihood of SARS-CoV-2 infection in unexamined species. This method serves as a valuable screening tool for assessing infection risks in domestic and wild animals, aiding in the prevention of disease outbreaks.

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“… 38 An in silico study of BA.1, BA.2, BA.3, BA.5, and BA.2.75 subvariants revealed similar behavior. 39 The MM-PBSA method was used to estimate the binding free energy of BA.1 and BA.2 subvariants with ACE2, 40 while the MM-GBSA method was utilized to study the interaction of BA.1, BA.1.1, BA.2, BA.3, BA.4/5, 41 and XBB.1.5 42 with ACE2. Emma et al obtained the free energy of Omicron BA.2 binding with the human cell using a well-tempered extended adaptive biasing force algorithm.…”

Section: Introductionmentioning

confidence: 99%

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

Nguyen,

2024

J. Phys. Chem. B

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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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The Impact of Mutation Sets in Receptor-Binding Domain of SARS-CoV-2 Variants on Stability of the RBD–ACE2 Complex

Cited by 5 publications

References 65 publications

Analysis the molecular similarity of least common amino acid sites in ACE2 receptor to predict the potential susceptible species for SARS-CoV-2

Analysis the molecular similarity of least common amino acid sites in ACE2 receptor to predict the potential susceptible species for SARS-CoV-2

Analysis the molecular similarity of least common amino acid sites in ACE2 receptor to predict the potential susceptible species for SARS-CoV-2

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

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