Molecular dynamic study of SARS-CoV-2 with various S protein mutations and their effect on thermodynamic properties

Abdalla, Mohnad; Eltayb, Wafa Ali; El‐Arabey, Amr Ahmed; Singh, Kamal; Jiang, Xinyi

doi:10.1016/j.compbiomed.2021.105025

Cited by 52 publications

(21 citation statements)

References 20 publications

(24 reference statements)

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“…The trajectory file generated from the production run was analyzed for RMSD, RMSF, hydrogen bonds, salt bridges, and free energy of binding using Desmond, VMD, and PyMOL. 34…”

Section: Methodsmentioning

confidence: 99%

Astaxanthin targets IL-6 and alleviates the LPS-induced adverse inflammatory response of macrophages

Wu,

Bashir,

Shao

et al. 2024

Food Funct.

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“…The trajectory file generated from the production run was analyzed for RMSD, RMSF, hydrogen bonds, salt bridges, and free energy of binding using Desmond, VMD, and PyMOL. 34…”

Section: Methodsmentioning

confidence: 99%

Astaxanthin targets IL-6 and alleviates the LPS-induced adverse inflammatory response of macrophages

Wu,

Bashir,

Shao

et al. 2024

Food Funct.

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“…As for temperature, MD simulations at different temperatures suggested S protein had a stronger binding at a low temperature . Abdalla et al investigated the effects of mutations on S protein stability and solubility through MD simulations in a 100 ns period . Inhibitor and antibody binding to ACE2 was studied by MD simulations. − One of the studies suggested that the SARS-CoV-2 S protein can interact with a nicotinic acetylcholine receptors (nAChRs) inhibitor .…”

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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“…[21] Vaccine Spike Protein S13, L18, T20, P26, D80, D138, W152, R190, D215, C241, R246, P323, K417, L452, S477, E484, N501, A570, D614, A626, H655, P681, A701, T716, S982, T1027, D1118, and V1176 [22] K417, G446, Y449, Y453, L455, F456, Q474, A475, G476, S477, T478, E484, G485, F486, N487, Y489, Q493, Y495, G496, Q498, T500, N501, G502, and Y505 [23] S366, N370, S371, F377, K378, D389, V401, A411, P412, G416, D420, Y421, I434, L452, Y453, R454, L455, K458, S459, I472, A475, G476, S477, T478, G485, F486, and Y505…”

Section: Binding Of Key Residues Refmentioning

confidence: 99%

FAKHRAVAC and BBIBP-CorV vaccine seeds’ binding to angiotensin-converting enzyme 2: A comparative molecular dynamics study

Setareh,

Rad,

Meghdadi

et al. 2023

Preprint

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Background: Safety and efficacy of the SARS-CoV-2 inactivated vaccines have been question since the emergence of SARS-CoV-2 variants of concern (VOCs). Using residue fluctuations and statistically comparing RMSF values, have escalated the understanding of the binding dynamics of the viral proteins to their receptors and here in this study, we compared the interaction between inactivated spike proteins (representing FAKHRAVAC and BBIBP-CorV vaccines seed) and the human Angiotensin-Converting Enzyme 2 (hACE2) receptor. Methodology: Through 100 set of accelerated 1 ns comparative molecular dynamics simulations, we analyze the binding dynamics and energy components of these interactions and compared residue backbone fluctuations using entropy and statistics including KL-Divergence and KS-test. Principal Findings: Our results reveal that FAKHRAVAC and Sinopharm exhibit similar binding dynamics and affinity to hACE2. Further examination of residue-wise fluctuations highlights the common behavior of binding key residues and mutation sites between the two vaccines. However, subtle differences in residue fluctuations, especially at critical sites like Q24, Y435, L455, S477, Y505, and F486, raise the possibility of distinct efficacy profiles. Conclusion: These variations may influence vaccine immunogenicity and safety in response to evolving SARS-CoV-2 variants. The study underscores the importance of considering residue-wise fluctuations for understanding vaccine-pathogen interactions and their implications for vaccine design.

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Molecular dynamic study of SARS-CoV-2 with various S protein mutations and their effect on thermodynamic properties

Cited by 52 publications

References 20 publications

Astaxanthin targets IL-6 and alleviates the LPS-induced adverse inflammatory response of macrophages

Astaxanthin targets IL-6 and alleviates the LPS-induced adverse inflammatory response of macrophages

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

FAKHRAVAC and BBIBP-CorV vaccine seeds’ binding to angiotensin-converting enzyme 2: A comparative molecular dynamics study

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