In silico Screening of Cyanobacterial and Food Bioactive Compounds to Predict Potential Inhibitors of COVID-19 Main protease (Mpro), Papain-like protease (PLpro) and RNA-dependent RNA polymerase (RdRp)


As novel corona virus (COVID-19) infections has spread throughout the world, world health organization (WHO) has announced COVID-19 as a pandemic infection. Henceforth investigators are conducting extensive research to find possible therapeutic agents against COVID-19. Main protease (Mpro) and papain-like protease (PLpro) that plays an essential role in processing the polyproteins that are translated from the 2019-nCoV RNA and RNA-dependent RNA polymerase (RdRp) that catalyzes the replication of RNA from RNA template becomes as a potential targets for in silico screening of effective therapeutic compounds to COVID-19. In this study we screened binding affinity of cyanobacterial and food bioactive compounds against 2019-nCoV Mpro, PLpro and RdRp using structure-based molecular docking approach. The results showed that cyanobacterial compounds - 7-Deoxy-Desulfo-Cylindrospermopsin, Calothrixins, Eucapsitrione, Tjipanazoles, Ambiguines, Tolyporphyrins, Phycobilins, Microcyclamides, spumigins, cryptophycins and food bioactive compounds – Geraldone, Asarin, Garbanzole, 1-Acetoxy-8-Hydroxy-1,4,4a,9a-Tetrahydroanthraquinone, Sesamolin, Gallocatechin gallate, Quercitrin, Maximol A, Scutellarien, Isoxanthohumol, Gallocatechin gallate, Quercitrin, Maximol A, Scutellarien, Isoxanthohumol, Seasominol, Citracridione I, Anonaine and Momilactone A as potential binders to the selected SARS-CoV-2 receptors with good dock scores and binding pose. Though, further in vitro and/or in vivo research is required to validate the docking results.

Version notes

In the previous version, we screened only 16 bioactive compounds against SARS-CoV-2 Mpro and RdRp. In the updated version, detected and quantified compounds (3751) food bioactive compounds were selected from FooDB (largest food database globally with 70,962 natural compounds), and cyanobacterial compounds from CyanoMetDB (n = 2124) were considered for this study. Further, the compounds were shortlisted to 414 food bioactives and 610 cyanobioactives based on molecular weight (> 600 g/mol food bioactives, (> 700g/mol cyanobioactives removed), hydrogen acceptor or donator capacity (< 2), and parent compounds. Then, we screened shortlisted compounds against SARS-CoV-2 Mpro, PLpro and RdRp.