Computational screening of natural compounds from Salvia plebeia R. Br. for inhibition of SARS-CoV-2 main protease

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Research Articles | Published:

Print ISSN : 0970-4078.
Online ISSN : 2229-4473.
Pub Email:
Doi: 10.1007/s42535-021-00304-z
First Page: 345
Last Page: 359
Views: 479

Keywords: Main protease, Salvia plebeia R. Br., Rutin, Plebeiosides B, ADMET, PASS, Molecular docking, Molecular dynamic simulation


The novel Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) has emerged to be the reason behind the COVID-19 pandemic. It was discovered in Wuhan, China and then began spreading around the world, impacting the health of millions. Efforts for treatment have been hampered as there are no antiviral drugs that are effective against this virus. In the present study, we have explored the phytochemical constituents of Salvia plebeia R. Br., in terms of its binding affinity by targeting COVID-19 main protease (Mpro) using computational analysis. Molecular docking analysis was performed using PyRx software. The ADMET and drug-likeness properties of the top 10 compounds showing binding affinity greater than or equal to − 8.0 kcal/mol were analysed using pkCSM and DruLiTo, respectively. Based on the docking studies, it was confirmed that Rutin and Plebeiosides B were the most potent inhibitors of the main protease of SARS-CoV-2 with the best binding affinities of − 9.1 kcal/mol and − 8.9 kcal/mol, respectively. Further, the two compounds were analysed by studying their biological activity using the PASS webserver. Molecular dynamics simulation analysis was performed for the selected protein–ligand complexes to confirm their stability at 300 ns. MM-PBSA provided the basis for analyzing the affinity of the phytochemicals towards Mpro by calculating the binding energy, and secondary structure analysis indicated the stability of protease structure when it is bound to Rutin and Plebeiosides B. Altogether, the study identifies Rutin and Plebeiosides B to be potent Mpro inhibitors of SARS-CoV-2.

Graphic abstract

Main protease, 
                        Salvia plebeia R. Br., Rutin, Plebeiosides B, ADMET, PASS, Molecular docking, Molecular dynamic simulation

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Author Information

Zackria Afraa Aqeel
Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, India

Pattabiraman Ramya
Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, India

Murthy T. P. Krishna
Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, India
Kumar S. Birendra
Department of Biotechnology, M S Ramaiah Institute of Technology, Bengaluru, India

Mathew Blessy Baby
Department of Biotechnology, Dayananda Sagar College of Engineering, Bengaluru, India

Biju Vinai George
Department of Computer Science and Engineering, Christ (Deemed-to-be University), Bengaluru, India