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Experimental and in silico evaluations of the possible molecular interaction between airborne particulate matter and SARS-CoV-2

TitleExperimental and in silico evaluations of the possible molecular interaction between airborne particulate matter and SARS-CoV-2
Publication TypeArticolo su Rivista peer-reviewed
Year of Publication2023
AuthorsRomeo, Alice, Pellegrini Roberto, Gualtieri Maurizio, Benassi Barbara, Santoro Massimo, Iacovelli Federico, Stracquadanio Milena, Falconi Mattia, Marino Carmela, Zanini Gabriele, and Arcangeli Caterina
JournalScience of The Total Environment
Date PublishedJan-06-2023
KeywordsClassical molecular dynamics simulation, COVID-19 pandemic, PM2.5, SARS-CoV-2

During the early stage of the COVID-19 pandemic (winter 2020), the northern part of Italy has been significantly
affected by viral infection compared to the rest of the country leading the scientific community to hypothesize
that airborne particulate matter (PM) could act as a carrier for the SARS-CoV-2. To address this controversial issue,
we first verified and demonstrated the presence of SARS-CoV-2 RNA genome on PM2.5 samples, collected in
the city of Bologna (Northern Italy) in winter 2021. Then, we employed classical molecular dynamics (MD) simulations
to investigate the possible recognition mechanism(s) between a newly modelled PM2.5 fragment and the
SARS-CoV-2 Spike protein. The potential molecular interaction highlighted by MD simulations suggests that the
glycans covering the upper Spike protein regions would mediate the direct contact with the PM2.5 carbon core
surface, while a cloud of organic and inorganic PM2.5 components surround the glycoprotein with a network of
non-bonded interactions resulting in up to 4769 total contacts. Moreover, a binding free energy of
−207.2±3.9 kcal/mol was calculated for the PM-Spike interface through the MM/GBSA method, and structural
analyses also suggested that PM attachment does not alter the protein conformational dynamics. Although the association
between the PM and SARS-CoV-2 appears plausible, this simulation does not assess whether these established
interactions are sufficiently stable to carry the virus in the atmosphere, or whether the virion retains its
infectiousness after the transport. While these key aspects should be verified by further experimental analyses,
for the first time, this pioneering study gains insights into the molecular interactions between PM and SARS-CoV-
2 Spike protein and will support further research aiming at clarifying the possible relationship between PM abundance
and the airborne diffusion of viruses.

Short TitleScience of The Total Environment
Citation Key11658