SARS-CoV-2 Omicron spike glycoprotein receptor binding domain exhibits super-binder ability with ACE2 but not convalescent monoclonal antibody

Omotuyi, Olaposi Idowu; Olubiyi, Olujide O.; Nash, Oyekanmi; Afolabi, Elizabeth; Oyinloye, Babatunji Emmanuel; Fatumo, Segun; Femi-Oyewo, Mbang N.; Bogoro, Suleiman

doi:10.1016/j.compbiomed.2022.105226

Cited by 31 publications

(39 citation statements)

References 33 publications

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“…In the receptor-binding domain (RBD), the crucial mutations G446S, N501Y, G496S, Y505H, Q493R, E484A, T478K, S477N, K417N, G339D, S371L, S373P, S375F, N440K, and Q498R occur in the RBD of omicron B.1.1.529 variant [5][6][7]. The mutated residues Q493R, G496S, and Q498R, in particular, strengthen RBD adherence to the angiotensin-converting enzyme 2 (ACE2) receptor [5,8]. Additionally, the N501Y mutation localizes at RBD, which might help attain higher binding to host cells and result in elevated transmission and infectiousness [9].…”

Section: Introductionmentioning

confidence: 99%

In Silico Screening of Bioactive Compounds of Representative Seaweeds to Inhibit SARS-CoV-2 ACE2-Bound Omicron B.1.1.529 Spike Protein Trimer

et al. 2022

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Omicron is an emerging SARS-CoV-2 variant, evolved from the Indian delta variant B.1.617.2, which is currently infecting worldwide. The spike glycoprotein, an important molecule in the pathogenesis and transmissions of SARS-CoV-2 variants, especially omicron B.1.1.529, shows 37 mutations distributed over the trimeric protein domains. Notably, fifteen of these mutations reside in the receptor-binding domain of the spike glycoprotein, which may alter transmissibility and infectivity. Additionally, the omicron spike evades neutralization more efficiently than the delta spike. Most of the therapeutic antibodies are ineffective against the omicron variant, and double immunization with BioNTech-Pfizer (BNT162b2) might not adequately protect against severe disease induced by omicron B.1.1.529. So far, no efficient antiviral drugs are available against omicron. The present study identified the promising inhibitors from seaweed’s bioactive compounds to inhibit the omicron variant B.1.1.529. We have also compared the seaweed’s compounds with the standard drugs ceftriaxone and cefuroxime, which were suggested as beneficial antiviral drugs in COVID-19 treatment. Our molecular docking analysis revealed that caffeic acid hexoside (−6.4 kcal/mol; RMSD = 2.382 Å) and phloretin (−6.3 kcal/mol; RMSD = 0.061 Å) from Sargassum wightii (S. wightii) showed the inhibitory effect against the crucial residues ASN417, SER496, TYR501, and HIS505, which are supported for the inviolable omicron and angiotensin-converting enzyme II (ACE2) receptor interaction. Cholestan-3-ol, 2-methylene-, (3beta, 5 alpha) (CMBA) (−6.0 kcal/mol; RMSD = 3.074 Å) from Corallina officinalis (C. officinalis) manifested the strong inhibitory effect against the omicron RBD mutated residues LEU452 and ALA484, was magnificently observed as the essential residues in Indian delta variant B.1.617.2 previously. The standard drugs (ceftriaxone and cefuroxime) showed no or less inhibitory effect against RBD of omicron B.1.1.529. The present study also emphasized the pharmacological properties of the considered chemical compounds. The results could be used to develop potent seaweed-based antiviral drugs and/or dietary supplements to treat omicron B.1.1529-infected patients.

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Section: Introductionmentioning

confidence: 99%

In Silico Screening of Bioactive Compounds of Representative Seaweeds to Inhibit SARS-CoV-2 ACE2-Bound Omicron B.1.1.529 Spike Protein Trimer

et al. 2022

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“…Ultimately, when the viral particles have accumulated, some symptoms start to appear, such as destruction in the endothelial barrier, losing the capacity of oxygen diffusion, and in severe cases, the increase in inflammation caused by different cytokines can lead to death [ 10 ]. In addition, many studies have predicted the interaction between different molecules and the RBD of the spike protein [ [11] , [12] , [13] ]. Our main concern is targeting GRP78, accordingly, contradicting the SARS-CoV-2 entry.…”

Section: Introductionmentioning

confidence: 99%

Interference of Chaga mushroom terpenoids with the attachment of SARS-CoV-2; in silico perspective

Elshemey

Elfiky

Ibrahim

et al. 2022

Computers in Biology and Medicine

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“…There are several experimental and computational studies which clearly show the cause of a high transmission of the Omicron variant and its immune evasion [ [28] , [29] , [30] , [31] ]. The increase in the binding of the SARS-CoV-2 receptor ACE2 with the RBD is the main cause of the enhanced transmission of the Omicron variant.…”

Section: Introductionmentioning

confidence: 99%

Structural basis of Omicron immune evasion: A comparative computational study

Contractor

Globisch

Swaroop

et al. 2022

Computers in Biology and Medicine

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SARS-CoV-2 Omicron spike glycoprotein receptor binding domain exhibits super-binder ability with ACE2 but not convalescent monoclonal antibody

Cited by 31 publications

References 33 publications

In Silico Screening of Bioactive Compounds of Representative Seaweeds to Inhibit SARS-CoV-2 ACE2-Bound Omicron B.1.1.529 Spike Protein Trimer

In Silico Screening of Bioactive Compounds of Representative Seaweeds to Inhibit SARS-CoV-2 ACE2-Bound Omicron B.1.1.529 Spike Protein Trimer

Interference of Chaga mushroom terpenoids with the attachment of SARS-CoV-2; in silico perspective

Structural basis of Omicron immune evasion: A comparative computational study

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