Abstract
The coronavirus disease-19 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is rampant in the world and is a serious threat to global health. The SARS-CoV-2 RNA has been detected in various environmental media, which speeds up the pace of the virus becoming a global biological pollutant. Because many engineered nanomaterials (ENMs) are capable of inducing anti-microbial activity, ENMs provide excellent solutions to overcome the virus pandemic, for instance by application as protective coatings, biosensors, or nano-agents. To tackle some mechanistic issues related to the impact of ENMs on SARS-CoV-2, we investigated the molecular interactions between carbon nanoparticles (CNPs) and a SARS-CoV-2 RNA fragment (i.e., a model molecule of frameshift stimulation element from the SARS-CoV-2 RNA genome) using molecular mechanics simulations. The interaction affinity between the CNPs and the SARS-CoV-2 RNA fragment increased in the order of fullerenes < graphenes < carbon nanotubes. Furthermore, we developed quantitative structure–activity relationship (QSAR) models to describe the interactions of 17 different types of CNPs from three dimensions with the SARS-CoV-2 RNA fragment. The QSAR models on the interaction energies of CNPs with the SARS-CoV-2 RNA fragment show high goodness-of-fit and robustness. Molecular weight, surface area, and the sum of degrees of every carbon atom were found to be the primary structural descriptors of CNPs determining the interactions. Our research not only offers a theoretical insight into the adsorption/separation and inactivation of SARS-CoV-2, but also allows to design novel ENMs which act efficiently on the genetic material RNA of SARS-CoV-2. This contributes to minimizing the challenge of time-consuming and labor-intensive virus experiments under high risk of infection, whilst meeting our precautionary demand for options to handle any new versions of the coronavirus that might emerge in the future.
Highlights
The outbreak of a new coronavirus which has lasted for more than a year, has brought great disaster to human beings (Diffenbaugh et al, 2020; Slot et al, 2020; Snape and Viner, 2020)
To search for the best geometry with various forms of energy for each complex of the carbon nanoparticles (CNPs) with the syndrome coronavirus (SARS)-CoV-2 RNA fragment, a classical annealing simulation was per forming with the Materials Studio software package (Ver. 8.0)
In order to reveal the mechanisms of the interactions of CNPs with the SARS-CoV-2 RNA fragment, the Eint derived from the total potential energies, the ‘van der Waals’ energies, and electrostatic energies are summarized in Fig. 3 and Table S1 (Supplementary Material)
Summary
The outbreak of a new coronavirus which has lasted for more than a year, has brought great disaster to human beings (Diffenbaugh et al, 2020; Slot et al, 2020; Snape and Viner, 2020). In response to the virus pandemic, nanoscience and nanotechnology are offering opportunities and challenges (Fig. 1) Viruses such as the avian influenza virus (H5N1), the severe acute respiratory syndrome coronavirus (SARS), the swine influenza virus (H1N1), and the Middle East respiratory syndrome coronavirus Engineered nanomaterials (ENMs) have such special properties due to the small size and relative large surface to volume ratio, which is in part why ENMs have been widely used for a variety of biomedical applications. In this respect there is a growing need for design of ENMs that are highly specific and efficiently taken up into target cells. Un derstanding the interaction mechanisms between ENMs and macro molecules that are part of SARS-CoV-2 is an important foundation for the application of ENMs versus COVID-19
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