Tracking the interaction between single-wall carbon nanotube and SARS-Cov-2 spike glycoprotein: A molecular dynamics simulations study

Abstract

COVID-19, a newly discovered type of coronavirus, is the cause of the pandemic infection that was first reported in Wuhan, China, in December 2019. One of the most critical problems in this regard is to identify innovative drugs that may reduce or manage this global health concern. Nanoparticles have shown a pivotal role in drug delivery systems in recent decades. The surface of nanoparticles could be covered by a layer composed of different biomolecules (e.g., proteins and macromolecules) following the incubation with a biological fluid. This protein-rich layer is called “Protein Corona.” In this study, an all-atom molecular dynamics simulation was used for investigating the monomeric B domain of the spike glycoprotein due to its role in the accessibility of the spike glycoprotein to single-wall carbon nanotubes (SWCNTs). The interaction energy values between the carbon nanotube and B domain of the viral spike glycoprotein were evaluated. The obtained results, based on Lennard-Jones potentials, demonstrated that SWCNTs had an affinity to the B domain of the S1 subunit in the spike glycoprotein. The adsorption of SWCNTs on the B domain surface led to a significant change in solvent-accessible surface, internal hydrogen bonds, and finally in the tertiary structure, which could provide a reasonable method to impede the interaction between the angiotensin-converting enzyme II and SARS-CoV-2 spike glycoprotein. A decrease in the mean square displacement of the B domain was shown after the adsorption of SWCNTs as a result of increasing the hydrophobic-hydrophilic properties of the B domain. The arrangement of SWCNTs on the B domain surface and their interaction using the 2-acetamido-2-deoxy-β-D-glucopyranose group (988, 991, and 992) demonstrated that a change in the affinity of the S1 subunit could be used as a barrier to viral replication. The analysis of the SWCNT-B domain complex indicated that the presence of SWCNTs is able to cause alterations in the S1 subunit of the spike protein, and these nanotubes could be employed for further in-vitro and in-vivo antiviral studies. Also, SWCNTs are able to be utilized in drug delivery systems.

Carbon fullerene and nanotube are probable binders to multiple targets of SARS-CoV-2: Insights from computational modeling and molecular dynamic simulation studies

“…Therefore, it is evident that the carbon nanoparticles employed in this study exhibited better binding energy towards the prioritized SARS-CoV-2 targets. There are several studies recently published on the binding potential of carbon-based nanomaterials towards viruses and helps in the detection of viral pathogens or as antiviral agents to viral pandemics including COVID19 ( Reina et al, 2020 ; Shao et al, 2021 ; Serrano-Aroca et al, 2021 ; Jomhori et al, 2021 ; Riley and Narayan, 2021 ).…”

Investigation of the binding and dynamic features of A.30 variant revealed higher binding of RBD for hACE2 and escapes the neutralizing antibody: A molecular simulation approach

“…It has a wide range of applications i.e. used to estimate the binding energy for proteins in different studies including SARS-CoV-2 and neurological disorders [ [38] , [39] , [40] , [41] , [42] , [43] ].…”

E2UbcH5B-derived peptide ligands target HECT E3-E2 binding site and block the Ub-dependent SARS-CoV-2 egression: A computational study

“…All MD trajectories were analyzed using UCSF Chimera, PyMol ( http://www.pymol.org ) and GROMACS. GROMACS modules such as g_rmsd, g_rmsf, g_hbond, g_energy, g_gyrate, and g_sasa were utilized to analyze the stability and behavior of each system [ [53] , [54] , [55] ].…”