Computational studies on the design of NCI natural products as inhibitors to SARS-CoV-2 main protease

Abstract

The pandemic coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 5 million deaths globally. Currently there are no effective drugs available to treat COVID-19. The viral protease replication can be blocked by the inhibition of main protease that is encoded in polyprotein 1a and is therefore a potential protein target for drug discovery. We have carried out virtual screening of NCI natural compounds followed by molecular docking in order to identify hit molecules as probable SARS-CoV-2 main protease inhibitors. The molecular dynamics (MD) simulations of apo form in complex with N3, α-ketoamide and NCI natural products was used to validate the screened compounds. The MD simulations trajectories were analyzed using normal mode analysis and principal component analysis revealing dynamical nature of the protein. These findings aid in understanding the binding of natural products and molecular mechanisms of SARS-CoV-2 main protease inhibition.

Communicated by Ramaswamy H. Sarma

Keywords:

• Severe acute respiratory syndrome coronavirus 2 main protease
• molecular docking
• molecular dynamics simulations
• NCI natural products
• normal mode analysis
• mechanical stiffness
• principal component analysis

Acknowledgements

The authors thanks DST-PURSE and UGC UPE2 for funding, and CMSD for computational facilities.

Disclosure statement

The authors declare no competing interests.

Additional information

Funding

LD thanks University of Hyderabad, UGC for the non-NET fellowship.