Theoretical Approach: Noble Metal Nanoparticles for Combating the Omicron Variant of SARS-CoV-2

Abstract

Nanoparticles-based viral treatment has expressed an outstanding potency against most viral streams such as SARS-CoV-2, and influenza. Metallic nanoparticles, especially gold and silver, have gained considerable interest and have been extensively manipulated and tested as proposed antiviral agents, owing to their outstanding characteristics, such as their interesting biocompatibility. In our study, we focus on using uncapped ultra-small Gold (AuNP) and Silver (AgNP) nanoparticles of 1.5 nm radius to test their potency against receptor-binding domain (RBD) of the spike protein binding to the angiotensin converting enzyme-2 (ACE2). To explore protein dynamics and the effect of AuNP and AgNP on the RBD-ACE2 binding, a molecular dynamics (MD) simulation was employed. It was found that AuNP has been able to destabilize the bonding between RBD and ACE2, and has caused conformational changes in the RBD domain, while maintaining the ACE2 conformation and structure, compared to the NP-free system. This indicates that AuNP is safe to be used for targeting the omicron variant and hindering it from invading the host cell. While, even if AgNP was able to denature the viral RBD, it affected the host cell receptor ACE2 structure and conformation and helped in increasing their binding compared to the NP-free system. This was confirmed through the free energy of binding calculation including the interaction entropy contribution of the three systems.

Keywords

• Omicron variant
• Spike RBD nanoparticles
• Molecular dynamics
• Binding free energy

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