SARS-CoV-2 external structures interacting with nanospheres using docking and molecular dynamics

• Published in: Journal of biomolecular structure & dynamics Vol. 42; no. 19; pp. 9892 - 9907
• Main Authors: Martins da Silva, Anderson Yuri, Arouche, Tiago da Silva, Siqueira, Marcelo Ricardo Souza, Ramalho, Teodorico Castro, de Faria, Lenio Jose Guerreiro, Gester, Rodrigo do Monte, Carvalho Junior, Raul Nunes de, Santana de Oliveira, Mozaniel, Neto, Antonio Maia de Jesus Chaves
• Format: Journal Article
• Language: English
• Published: England Taylor & Francis 02.12.2024
• Subjects: adsorption; Binding Sites; Catalytic Domain; COVID-19 - virology; Humans; Ligands; molecular docking; Molecular Docking Simulation; molecular dynamics; Molecular Dynamics Simulation; nanofiltering; nanospheres; Nanospheres - chemistry; Protein Binding; SARS-CoV-2; SARS-CoV-2 - chemistry; Thermodynamics; SARS-CoV-2; adsorption; molecular docking; molecular dynamics; nanospheres; nanofiltering
• ISSN: 0739-1102; 1538-0254; 1538-0254
• DOI: 10.1080/07391102.2023.2252930

Coronavirus is caused by the SARS-CoV-2 virus has shown rapid proliferation and scarcity of treatments with proven effectiveness. In this way, we simulated the hospitalization of carbon nanospheres, with external active sites of the SARS-CoV-2 virus (M-Pro, S-Gly and E-Pro), which can be adsorbed or inactivated when interacting with the nanospheres. The computational procedures performed in this work were developed with the SwissDock server for molecular docking and the GROMACS software for molecular dynamics, making it possible to extract relevant data on affinity energy, distance between molecules, free Gibbs energy and mean square deviation of atomic positions, surface area accessible to solvents. Molecular docking indicates that all ligands have an affinity for the receptor's active sites. The nanospheres interact favorably with all proteins, showing promising results, especially C60, which presented the best affinity energy and RMSD values ​​for all protein macromolecules investigated. The C60 with E-Pro exhibited the highest affinity energy of −9.361 kcal/mol, demonstrating stability in both molecular docking and molecular dynamics simulations. Our RMSD calculations indicated that the nanospheres remained predominantly stable, fluctuating within a range of 2 to 3 Å. Additionally, the analysis of other structures yielded promising results that hold potential for application in other proteases. Communicated by Ramaswamy H. Sarma