In silico virtual screening, characterization, docking and molecular dynamics studies of crucial SARS-CoV-2 proteins

Abstract

The ongoing pandemic COVID-19 (COrona Virus Immuno Deficiency-2019) which is caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome–CoronaVirus-2) has emerged as a pandemic with 400,000 plus deaths till date. We do not have any drug or vaccine available for the inhibition of this deadly virus. The expedition for searching a potential drug or vaccine against COVID-19 will be of massive potential and favor. This study is focused on finding an effective natural origin compound which can put a check on the activity of this virus. We chose important proteins from the SARS-CoV-2 genome such as NSP4, NSP15 and RdRp along-with the human ACE2 receptor which is the first point of contact with the virus. Virtual screening and followed up molecular docking resulted in Baicalin and Limonin as the final lead molecules. 200 ns of MD simulation for each protein-ligand complex provides the insights that Baicalin has a potential to target NSP4, NSP15 and RdRp proteins. Limonin which is largely used in traditional Indian medicine system is found to inhibit the human ACE2 receptor (making it inefficient in binding to the receptor binding domain of SARS-CoV-2). Our studies propose Baicalin and Limonin in combination to be studied in vitro and in vivo against COVID-19.

Communicated by Ramaswamy H. Sarma

Keywords:

• COVID-19
• SARS-CoV-2
• molecular docking
• virtual screening
• molecular dynamics simulation

Disclosure statement

The authors declare no conflict of interest.

Additional information

Funding

This article has been supported by Ministry of Health (MOH), Saudi Arabia under grant No. 928 and ethical approval letter with reference number (20-#928E-20.04.2020).