An Insight Based on Computational Analysis of the Interaction between the Receptor-Binding Domain of the Omicron Variants and Human Angiotensin-Converting Enzyme 2

Çeli̇k, İsmail; Abdellattif, Magda H.; Tallei, Trina Ekawati

doi:10.3390/biology11050797

Cited by 11 publications

(6 citation statements)

References 66 publications

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“…This aligns with the findings of an experimental investigation through protein binding assay using Microscale thermophoresis (MST), which revealed that the Omicron variant exhibits a five-fold greater affinity compared to the wild type [18]. Furthermore, this is in agreement with other computational studies which suggested that the Omicron variant binds to ACE2 more strongly than the wild type [50][51][52]. BA.2.75 and BA.4.6_N658S were found to be the most and the least stable variants, respectively.…”

Section: Discussionsupporting

confidence: 91%

Comparative Computational Analysis of Spike Protein Structural Stability in SARS-CoV-2 Omicron Subvariants

Balupuri,

Kim,

Choi

et al. 2023

IJMS

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The continuous emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with multiple spike (S) protein mutations pose serious threats to current coronavirus disease 2019 (COVID-19) therapies. A comprehensive understanding of the structural stability of SARS-CoV-2 variants is vital for the development of effective therapeutic strategies as it can offer valuable insights into their potential impact on viral infectivity. S protein mediates a virus’ attachment to host cells by binding to angiotensin-converting enzyme 2 (ACE2) through its receptor-binding domain (RBD), and mutations in this protein can affect its stability and binding affinity. We analyzed S protein structural stability in various Omicron subvariants computationally. Notably, the S protein sequences analyzed in this work were obtained directly from our own sample collection. We evaluated the binding free energy between S protein and ACE2 in several complex forms. Additionally, we measured distances between the RBD of each chain in S protein to analyze conformational changes. Unlike most of the prior studies, we analyzed full-length S protein–ACE2 complexes instead of only RBD–ACE2 complexes. Omicron subvariants including BA.1, BA.2, BA.2.12.1, BA.4/BA.5, BA.2.75, BA.2.75_K147E, BA.4.6 and BA.4.6_N658S showed enhanced stability compared to wild type, potentially due to distinct S protein mutations. Among them, BA.2.75 and BA.4.6_N658S exhibited the highest and lowest level of stability, respectively.

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Section: Discussionsupporting

confidence: 91%

Comparative Computational Analysis of Spike Protein Structural Stability in SARS-CoV-2 Omicron Subvariants

Balupuri,

Kim,

Choi

et al. 2023

IJMS

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“…The significant number of mutations in the newly emerged, highly transmissible Omicron variants of SARS‐CoV‐2 has aroused concern. The exceptional capacity of the more than 50 mutations overall to avoid antibodies may considerably compromise the existing immunisation effort 1,2 . About 30 of these are mutations in the spike protein 3 .…”

Section: Introductionmentioning

confidence: 99%

“…The exceptional capacity of the more than 50 mutations overall to avoid antibodies may considerably compromise the existing immunisation effort. 1,2 About 30 of these are mutations in the spike protein. 3 The Omicron variant has been shown to improve its transmissibility and ability to evade the immune system, 4 but there are also reports that it reduces hospitalisation rates and causes milder symptoms, such as in vaccinated individuals.…”

mentioning

confidence: 99%

Update on the omicron sub‐variants BA.4 and BA.5

Tallei

Alhumaid

AlMusa

et al. 2022

Reviews in Medical Virology

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Several nations have recently begun to relax their public health protocols, particularly regarding the use of face masks when engaging in outdoor activities. This is because there has been a general trend towards fewer cases of coronavirus disease 2019 (COVID‐19). However, new Omicron sub‐variants (designated BA.4 and BA.5) have recently emerged. These two subvariants are thought to be the cause of an increase in COVID‐19 cases in South Africa, the United States, and Europe. They have also begun to spread throughout Asia. They evolved from the Omicron lineage with characteristics that make them even more contagious and which allow them to circumvent immunity from a previous infection or vaccination. This article reviews a number of scientific considerations about these new variants, including their apparently reduced clinical severity.

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“…In this study, binding affinity analysis allows for determining suitable ligands within the oocyte and sporozoite stage of Plasmodium that could bind to a specific region within FecA (Table 1). With a negative-valued binding affinity, it indicates a thermodynamically favorable ligand-receptor interaction that has a strong affinity binding to the protein, and a stable complex that can induce further signaling cascade [60].…”

Section: Resultsmentioning

confidence: 99%

Preliminary in silico study of a novel paratransgenic weapon against malaria

Sun,

Candra,

Pramanda

et al. 2024

ijobas

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Malaria is an infectious disease caused by Plasmodium spp., a protist whose infection is spread by Anopheles mosquito as a vector. A potential method to counter the infection is through paratransgenesis, a promising genetic control approach. This study proposed a new approach by using a transgene carried in a modified Ti plasmid hosted in Asaia bacterium to carry out two purposes: sensing the presence of Plasmodium protein biomarkers and transferring the toxin transgene to the parasite upon detection, thereby killing it without harming the Asaia carrier. The biosensor mechanism was created by repurposing a TonB dependent iron-uptake transport pathway to transcribe the vir genes of Agrobacterium tumefaciens that facilitate the gene transfer. The aim of this in silico project was to serve as a preliminary study on the likelihood of success of the aforementioned biosensor mechanism. This study utilized Alphafold and RCSB (Research Collaboratory for Structural Bioinformatic Protein Data Bank). As for the research tools: PyMOL, ClusPro website, and PRODIGY (PROtein binDIng enerGY prediction) server was used for data preparation, protein-protein docking and binding affinity analysis respectively. The results were assessed with t-test to analyze the significance of the binding affinity, in comparison to other studies that employed similar methods. The result showed Plasmodium protein GGCS (Gamma-glutamylcysteine synthetase) having the highest binding affinity with FecA (Fe(3+) dicitrate transport protein A). The preliminary data suggested that introducing the toxin transgene may be possible through vir gene transcription from the TonB pathway.

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An Insight Based on Computational Analysis of the Interaction between the Receptor-Binding Domain of the Omicron Variants and Human Angiotensin-Converting Enzyme 2

Cited by 11 publications

References 66 publications

Comparative Computational Analysis of Spike Protein Structural Stability in SARS-CoV-2 Omicron Subvariants

Comparative Computational Analysis of Spike Protein Structural Stability in SARS-CoV-2 Omicron Subvariants

Update on the omicron sub‐variants BA.4 and BA.5

Preliminary in silico study of a novel paratransgenic weapon against malaria

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