Interactions of Ozone-Functionalized Activated Charcoal with SARS-Cov-2 Proteases Using Molecular Docking and Dynamics

Abstract

The high contamination by the SARS-Cov-2 virus has led to the search for ways to minimize contagion. Masks are used as part of a strategy of measures to suppress transmission and save lives. However, they are not sufficient to provide an adequate level of protection against COVID-19. Activated charcoal has an efficient antibacterial action, adsorption and low cost. Here, the interaction between two molecules of activated carbon was analyzed, interacting with two structures of the SARS-Cov-2, through docking and molecular dynamics using the platforms Autodock Vina 4.2.6, Gaussian 09 and Amber 16. As a result, the complexes from ozone-functionalized coal to viral structures happen mainly through hydrophobic interactions at the binding site of each receptor. The values of the mean square deviations of the two systems formed by ligands/receptors and showed better stability. The results of Gibbs free energy showed a better interaction between proteins and functionalized charcoal, with △Gtotal values of −48.530 and −38.882 kcal/mol. Thus, the set formed by combinations of proteins with functionalized activated carbon tends to more efficiently adsorb the protein components of the coronavirus to the pores of the activated carbon with ozone during filtration.

Molecular Interactions of the Omicron, Kappa, and Delta SARS-CoV-2 Spike Proteins with Quantum Dots of Graphene Oxide

“…RMSD quanti es structural deviations during simulations concerning the initial crystallographic structure, showcasing system stability and balance over time. Free energy calculations, essential for understanding binding a nities and diverse molecular processes [96-99], were estimated using MM/PBGBSA methods [100].…”

Identification of Potential TMPRSS2 Inhibitors for COVID-19 Treatment in Chinese Medicine by Computational Approaches and Surface Plasmon Resonance Technology

“…Top CCDs with the highest LigScore2 values in the active site of TMPS2 after docking were submitted for further verification through MD simulations using the Amber16 software package. Gaussian 09 43 and antechamber program 44 in Amber16 were employed to prepare the GAFF (general Amber force field) parameters 45 for the small molecule CCDs, and TMPS2 was prepared by using the ff14sb field force parameter. 46 The prepared CCDs and TMPS2 were then loaded onto the leap module, and the systems were neutralized with hydrogen atoms and antagonist ions automatically added.…”