Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study

Khan, Abbas; Hussain, Sarfaraz; Ahmad, Sajjad; Suleman, Muhammad; Bukhari, Imrana; Khan, Taimoor; Rashid, Farooq; Azad, A. K. M.; Waseem, Muhammad; Khan, Wajid; Hussain, Zahid; Khan, Asghar; Ali, Syed Shujait; Qin, Qiyao; Wei, Dong‐Qing

doi:10.1016/j.compbiomed.2021.105163

Cited by 19 publications

(18 citation statements)

References 54 publications

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“…60,61 To explore these aspects of ACE2 biology, most ACE2 PD structural studies focus on screening of inhibitors [62][63][64][65][66][67] and on the energetics of complexing with viral spike proteins. [68][69][70][71][72][73] As the conformational ensemble of proteins are crucial for their biological functions, we investigated how orthosteric and allosteric binding can affect the functional ACE2 PD conformational dynamics using the inhibitor MLN-4760 and S1 RBD fragments from SARS-CoV-1 and SARS-CoV-2.…”

Section: Resultsmentioning

confidence: 99%

Allosteric control of ACE2 peptidase domain dynamics

et al. 2022

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Section: Resultsmentioning

confidence: 99%

Allosteric control of ACE2 peptidase domain dynamics

et al. 2022

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“…The mechanism of tighter binding of the SARS-CoV-2 S-protein was studied by using MD simulations and MM/GBSA or MM/PBSA calculations by Xue et al, Jafary et al, Spinello et al., and Bhattacharyya et al Interestingly, MM/PBSA calculations at different temperatures suggested that the SARS-CoV-2 RBD was more resistant to temperature changes than the SARS-CoV RBD . Researchers ran MM/PBSA calculations and found that some mutations on S protein could facilitate stronger interactions with human ACE2. − …”

Section: Methods and Approachesmentioning

confidence: 99%

Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2

Gao¹,

Wang²,

Chen³

et al. 2022

Chem. Rev.

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Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus–host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein–protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.

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“…In addition, one of the recent structural studies have generated model structures of S-protein to predict the mutations of higher stability [43] . In other studies, the interactions of RBD region with human ACE2 have been investigated to obtain insights into virulence strengths of some of the variants [44] , [45] , [46] . There are previous reports of designing peptides as well as small molecules to target the RBD region, which would potentially inhibit virus entry [47] , [48] , [49] , [50] .…”

Section: Introductionmentioning

confidence: 99%