ArticleComputers in biology and medicine2022
Molecular dynamic study of SARS-CoV-2 with various S protein mutations and their effect on thermodynamic properties.
Article in Computers in biology and medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 74 citations in OpenAlex.
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- Molecular dynamics-based computational investigations on the influence of tumor suppressor p53 binding protein against other proteins/peptides.Scientific reports · 2024Article
- Benchmark Investigation of SARS-CoV-2 Mutants' Immune Escape with 2B04 Murine Antibody: A Step Towards Unraveling a Larger Picture.Current issues in molecular biology · 2024Article
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- Evaluation of Potential Furin Protease Inhibitory Properties of Pioglitazone, Rosiglitazone, and Pirfenidone: An In Silico Docking and Molecular Dynamics Simulation Approach.Current issues in molecular biology · 2024Article
- Explainable artificial intelligence-assisted virtual screening and bioinformatics approaches for effective bioactivity prediction of phenolic cyclooxygenase-2 (COX-2) inhibitors using PubChem molecular fingerprints.Molecular diversity · 2024Article
- 6-Octadecenoic and Oleic Acid in Liquid Smoke Rice Husk Showed COVID-19 Inhibitor Properties.Advances in pharmacological and pharmaceutical sciences · 2024Article
- Cytotoxic Evaluation, Molecular Docking, Molecular Dynamics, and ADMET Prediction of Isolupalbigenin Isolated fromOncoTargets and therapy · 2024Article
- Potential Effect of Baobab's Polyphenols as Antihyperlipidemic Agents: In Silico Study.Molecules (Basel, Switzerland) · 2023Article
- Post-COVID-19 effect on biochemical parameters in children: Should we take heed?Saudi journal of biological sciences · 2023Article
- Marine AlgaMarine drugs · 2022Article
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- Computational Study of Asian Propolis Compounds as Potential Anti-Type 2 Diabetes Mellitus Agents by Using Inverse Virtual Screening with the DIA-DB Web Server, Tanimoto Similarity Analysis, and Molecular Dynamic Simulation.Molecules (Basel, Switzerland) · 2022Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Studying the structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein is important to understand the infection process. The S protein is necessary in completing the virus life cycle and is responsible for the appearance of new variants and drug and vaccine resistance. Understanding the structure and dynamics of biological macromolecules is essential for understanding how they function. In this work, we investigated the effects of mutations on S protein stability and solubility through molecular dynamic (MD) simulation in a 100 ns (ns) period. We screened four variants in addition to the wild type (WT). Results show that changes on MD simulation parameters of S protein indicate fluctuations and changes in the conformation, especially in the area between 300 and 600 amino acids (aa). This provides us an image of how the virus protein can reshape itself to adapt to any changes that occur in human angiotensin-converting enzyme 2 or drugs that can target the protein region. Our results also show that the Brazil variant has high fluctuations and unstable folding at some stages compared with other variants.
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