Exploration of date palm (Phoenix dactylifera) bioactivity as anti-SARS-CoV-2: in silico study

Abstract

The COVID-19 pandemic has highlighted the need for innovation and the development of antiviral agents. One plant with potential antiviral properties is the date palm (Phoenix dactylifera). However, research on the antiviral activity of dates against SARS-CoV-2 is limited. This study aims to assess the antiviral potential of compounds found in date palm fruit using a molecular docking method. Specifically, we compare these compounds to the antiviral drugs ritonavir and nirmatrelvir in their ability to inhibit SARS-CoV-2 proteins. The molecular docking analysis was conducted using various tools and software, including Autodock Vina, DS Visualizer, Autodock Tools, Python, and Marvin Sketch. The results of the study indicate that compounds such as apigenin, diosmetin, and luteolin have strong potential as antiviral agents. The binding affinity of apigenin in date fruit with various SARS-CoV-2 proteins is as follows: -7.6 kcal/mol for 3CL-Pro, -8.7 kcal/mol for Nsp3, -5.7 kcal/mol for PD-ACE-2, and -7.0 kcal/mol for RBD-S. Diosmetin exhibits similar binding affinities with these proteins: -6.7 kcal/mol, -8.5 kcal/mol, -5.6 kcal/mol, and -7.2 kcal/mol, respectively. Luteolin also shows strong binding affinities: -7.9 kcal/mol, -8.6 kcal/mol, -5.7 kcal/mol, and -7.3 kcal/mol. In comparison, nirmatrelvir achieved docking scores of -7.2 kcal/mol, -7.5 kcal/mol, -5.1 kcal/mol, and -6.3 kcal/mol with the same proteins, while ritonavir scored -7.0 kcal/mol, -8.2 kcal/mol, -5.6 kcal/mol, and -6.7 kcal/mol, respectively. Apigenin, diosmetin, and luteolin demonstrate stronger potential than nirmatrelvir and ritonavir, as evidenced by their lower docking scores when compared to these drugs.