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SARS-CoV-2 external structures interacting with nanospheres using docking and molecular dynamics
Anderson Yuri Martins da Silva1,2,3, Tiago da Silva Arouche1,2, Marcelo Ricardo Souza Siqueira3
1Laboratory for the Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, Belem, Brazil.
Journal of Biomolecular Structure & Dynamics
|September 15, 2023
Summary
Carbon nanospheres show promise for treating SARS-CoV-2 by interacting with viral proteins. Molecular simulations reveal strong binding affinities, particularly for C60, suggesting potential therapeutic applications.
Area of Science:
- Computational chemistry
- Nanotechnology
- Virology
Background:
- Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has rapidly proliferated, highlighting an urgent need for effective treatments.
- Existing treatments for coronavirus are limited, necessitating novel therapeutic strategies.
Purpose of the Study:
- To computationally investigate the potential of carbon nanospheres as antiviral agents against SARS-CoV-2.
- To simulate the interaction of carbon nanospheres with key SARS-CoV-2 proteins (M-Pro, S-Gly, E-Pro) for adsorption or inactivation.
Main Methods:
- Utilized SwissDock server for molecular docking to assess binding affinities.
- Employed GROMACS software for molecular dynamics simulations to evaluate stability and interactions.
- Analyzed key parameters including affinity energy, Gibbs free energy, and root-mean-square deviation (RMSD).
Main Results:
- Molecular docking revealed favorable interactions between nanospheres and all investigated SARS-CoV-2 proteins.
- C60 nanospheres demonstrated the highest affinity energy (-9.361 kcal/mol) with the E-Pro protein.
- Molecular dynamics simulations confirmed the stability of nanosphere-protein complexes, with RMSD values typically between 2-3 Å.
Conclusions:
- Carbon nanospheres, particularly C60, exhibit significant potential for SARS-CoV-2 inhibition through favorable binding to viral proteins.
- The findings support the development of nanosphere-based therapies for coronavirus and potentially other viral proteases.
