Docking-based virtual screening and identification of potential COVID-19 main protease inhibitors from brown algae

Abstract

COVID-19 (SARS-CoV-2) is a viral disease that causes acute respiratory syndrome, which has increased the morbidity and mortality rate throughout the world. World Health Organization has declared this COVID-19 outbreak as pandemic and classified health emergency throughout the world. In the recent past, outbreaks of SARS and MERS have shown the interspecies transmission potential of coronaviruses and limitations of already prescribed drugs to overcome this global public health issue. Therefore, there is a dire need to identify a new regimen of targeted drugs from natural compounds having anti-COVID19 potential. This study aimed at screening 1018 brown algal natural compounds (many of them previously reported to have immunomodulatory effects) having probable anti-COVID19 potentials. The source compounds were extracted from MarinLit, a database dedicated to marine natural products and screened against COVID-19 main protease. The top seven compounds were further analysed, and their interactions with the active site were visualized. This study will further warrant screening the potent compounds against the virus in-vitro conditions.

Keywords: Covid-19; Docking-based VS; Seaweed; Structure-based virtual screening.

Fig. 1

(a,b): (Left) Modelled mode of binding of compounds 7,2′'-bieckol and 7-Hydroxyeckol hepta-acetate in Covid-19 main protease (PDB ID = 5R82) active site. (Right) Close-up view of 3-D interaction plot of compounds 7,2′'-bieckol and 7-Hydroxyeckol generated by Discovery Studio Visualizer into the binding site of Covid-19 main protease (PDB ID = 5R82).

Fig. 2

(a,b): (Left) Modelled mode of binding of compounds 5-hydroxy-cystofuranoquinol and Sargaquinoic acid in Covid-19 main protease (PDB ID = 5R82) active site. (Right) Close-up view of 3-D interaction plot of compounds 5-hydroxy-cystofuranoquinol and Sargaquinoic acid generated by Discovery Studio Visualizer into the binding site of Covid-19 main protease (PDB ID = 5R82).

Fig. 3

(a–c): (Left) Modelled mode of binding of compounds Triacetoxy-18-hydroxy-2,7-dolabelladiene, Fallahydroquinone and Methoxybifurcarenone in Covid-19 main protease (PDB ID = 5R82) active site. (Right) Close-up view of 3-D interaction plot of compounds Triacetoxy-18-hydroxy-2,7-dolabelladiene, Fallahydroquinone and Methoxy- bifurcarenone generated by Discovery Studio Visualizer into the binding site of Covid-19 main protease (PDB ID = 5R82).