SARS-CoV-2 new variants: Characteristic features and impact on the efficacy of different vaccines

Khan, Abbas; Khan, Taimoor; Ali, Shughla; Aftab, Summiya; Wang, Yanjing; Wang, Qiankun; Khan, Mazhar; Suleman, Muhammad; Ali, Shahid; Wang, Heng; Ali, Syed Shujait; Wei, Dong‐Qing; Mohammad, Anwar

doi:10.1016/j.biopha.2021.112176

Cited by 62 publications

(55 citation statements)

References 142 publications

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“….617, the total binding energy was reported to be −37.69 kcal/mol. The current findings strongly corroborate with the previous findings, where higher infectivity was associated with the higher total binding energy induced by mutations in the RBD in different variants [12,15,17]. From the preceding, the three variants B.1.1.7, P.1, and B.1.351 exhibit stronger affinity toward GRP78 and thus may increase their infectivity more robustly than others.…”

Section: Estimation Of Free Energysupporting

confidence: 91%

“…These different VOCs, B.1.1.7, B.1.351, B.1618, R.1, B.1.617, and P.1, carry numerous RBD domain-specific mutations on the spike protein, including N501Y, E484K, L452R, and K417N/T [12,14,15]. Stronger binding of the RBD-ACE2 complex due to these mutations is also linked with higher infectivity of SARS-CoV-2 variants [13,17]. Several studies have focused on examining viral RBD-host ACE2 receptor interactions, but other interacting receptors need further investigation.…”

Section: Structural Modeling and Analysismentioning

confidence: 99%

“…It is vital to understand the proteome of SARS-CoV-2 to develop therapeutics-related and proteomics-based methods against COVID-19. Recently, researchers have used several approaches, including determining the evolutionary relationship, developing vaccines, identifying the mutational landscape, and developing novel therapeutics to better challenge SARS-CoV-2 associated health concerns [17]. These treatments include activating a boosted immune response to fight against pathogens or hindering pathogen-receptor interactions from blocking viral attachment and entry into the host cell [18].…”

Section: Introductionmentioning

confidence: 99%

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Structural-Dynamics and Binding Analysis of RBD from SARS-CoV-2 Variants of Concern (VOCs) and GRP78 Receptor Revealed Basis for Higher Infectivity

et al. 2021

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Glucose-regulated protein 78 (GRP78) might be a receptor for SARS-CoV-2 to bind and enter the host cell. Recently reported mutations in the spike glycoprotein unique to the receptor-binding domain (RBD) of different variants might increase the binding and pathogenesis. However, it is still not known how these mutations affect the binding of RBD to GRP78. The current study provides a structural basis for the binding of GRP78 to the different variants, i.e., B.1.1.7, B.1.351, B.1.617, and P.1 (spike RBD), of SARS-CoV-2 using a biomolecular simulation approach. Docking results showed that the new variants bound stronger than the wild-type, which was further confirmed through the free energy calculation results. All-atom simulation confirmed structural stability, which was consistent with previous results by following the global stability trend. We concluded that the increased binding affinity of the B.1.1.7, B.1.351, and P.1 variants was due to a variation in the bonding network that helped the virus induce a higher infectivity and disease severity. Consequently, we reported that the aforementioned new variants use GRP78 as an alternate receptor to enhance their seriousness.

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Section: Estimation Of Free Energysupporting

confidence: 91%

Section: Structural Modeling and Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Structural-Dynamics and Binding Analysis of RBD from SARS-CoV-2 Variants of Concern (VOCs) and GRP78 Receptor Revealed Basis for Higher Infectivity

et al. 2021

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“…The circulation of new variants poses a threat to prophylactic measures that are now available against SARS-CoV-2. Although there is evidence that current vaccine strategies are able to elicit an effective immune response against the variants of interest and variants of concern of SARS-CoV-2 described until now, non-pharmaceutical control measures must remain as continuous public policies to avoid the spread of variants that can potentially cause new waves of COVID-19 [ 44 ]. Crowding, particularly the crowding that occurred within the first year of COVID-19 in Brazil, rapidly changed COVID-19 reports.…”

Section: Discussionmentioning

confidence: 99%

National Holidays and Social Mobility Behaviors: Alternatives for Forecasting COVID-19 Deaths in Brazil

Aragão

Santos

Gonçalves

2021

IJERPH

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In this paper, we investigate the influence of holidays and community mobility on the transmission rate and death count of COVID-19 in Brazil. We identify national holidays and hallmark holidays to assess their effect on disease reports of confirmed cases and deaths. First, we use a one-variate model with the number of infected people as input data to forecast the number of deaths. This simple model is compared with a more robust deep learning multi-variate model that uses mobility and transmission rates (R0, Re) from a SEIRD model as input data. A principal components model of community mobility, generated by the principal component analysis (PCA) method, is added to improve the input features for the multi-variate model. The deep learning model architecture is an LSTM stacked layer combined with a dense layer to regress daily deaths caused by COVID-19. The multi-variate model incremented with engineered input features can enhance the forecast performance by up to 18.99% compared to the standard one-variate data-driven model.

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“…Although this process is believed to be the vital step for the activation of the S protein, the associated protease is still not identified [ 34 ]. For this reason, inhibiting the ACE2–RBD complex is essential to stop the spread of virulence instigated by SARS-CoV-2 [ 35 ].…”

Section: Introductionmentioning

confidence: 99%

Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches

Muhseen

Kadhim

Yahiya

et al. 2021

Biology

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Recently, a new variant, B.1620, with mutations (S477N-E484K) in the spike protein’s receptor-binding domain (RBD) has been reported in Europe. In order to design therapeutic strategies suitable for B.1.620, further studies are required. A detailed investigation of the structural features and variations caused by these substitutions, that is, a molecular level investigation, is essential to uncover the role of these changes. To determine whether and how the binding affinity of ACE2–RBD is affected, we used protein–protein docking and all-atom simulation approaches. Our analysis revealed that B.1.620 binds more strongly than the wild type and alters the hydrogen bonding network. The docking score for the wild type was reported to be −122.6 +/− 0.7 kcal/mol, while for B.1.620, the docking score was −124.9 +/− 3.8 kcal/mol. A comparative binding investigation showed that the wild-type complex has 11 hydrogen bonds and one salt bridge, while the B.1.620 complex has 14 hydrogen bonds and one salt bridge, among which most of the interactions are preserved between the wild type and B.1.620. A dynamic analysis of the two complexes revealed stable dynamics, which corroborated the global stability trend, compactness, and flexibility of the three essential loops, providing a better conformational optimization opportunity and binding. Furthermore, binding free energy revealed that the wild type had a total binding energy of −51.14 kcal/mol, while for B.1.628, the total binding energy was −68.25 kcal/mol. The current findings based on protein complex modeling and bio-simulation methods revealed the atomic features of the B.1.620 variant harboring S477N and E484K mutations in the RBD and the basis for infectivity. In conclusion, the current study presents distinguishing features of B.1.620, which can be used to design structure-based drugs against the B.1.620 variant.

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SARS-CoV-2 new variants: Characteristic features and impact on the efficacy of different vaccines

Cited by 62 publications

References 142 publications

Structural-Dynamics and Binding Analysis of RBD from SARS-CoV-2 Variants of Concern (VOCs) and GRP78 Receptor Revealed Basis for Higher Infectivity

Structural-Dynamics and Binding Analysis of RBD from SARS-CoV-2 Variants of Concern (VOCs) and GRP78 Receptor Revealed Basis for Higher Infectivity

National Holidays and Social Mobility Behaviors: Alternatives for Forecasting COVID-19 Deaths in Brazil

Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches

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