In silico analysis of immunogenicity and molecular interaction of aromatic plant peptides with SARS-CoV-2

Abstract

SARS-CoV-2 is an RNA coronavirus that causes respiratory infections as the current COVID-19 pandemic. The health systems combat this infection with palliative care; however, there are few specific treatments for this pathogen. This context represents the possibility of searching for alternative treatments, such as using molecules from natural products. Our main objective was the in silico study of aromatic plant peptides and their interaction with specific proteins of SARS-CoV-2 that do not compromise the immune response. Five hundred eighty-three peptides with less than 30 amino acids from Thymus vulgaris L., Cymbopogon citratus, Salvia officinalis, Ocimum basilicum L, and Zingiber officinale were processed. The methodology applied filters according to the highest molecular docking scores to find 20 peptides for each plant species. The peptides show solid molecular interaction of the Spike RBD, S2, and Nsp4 proteins’ active sites, using less than –150 kcal/mol energy. Nsp4 protein exposes the most interaction with all species. 35 and 65% of these peptides were recorded with low activation of the immune response through antigenicity, score below 0.5, and absence of allergenicity. These results indicate the use of plant-derived molecules that can be implemented in consumption to combat the viral replication of SARS-CoV-2.