Proposition of a new allosteric binding site for potential SARS-CoV-2 3CL protease inhibitors by utilizing molecular dynamics simulations and ensemble docking

Abstract

The SARS-CoV-2 3CL protease (3CLpro) shows a high similarity with 3CL proteases of other beta-coronaviruses, such as SARS and MERS. It is the main enzyme involved in generating various non-structural proteins that are important for viral replication and is one of the most important proteins responsible for SARS-CoV-2 virulence. In this study, we have conducted an ensemble docking of molecules from the DrugBank database using both the crystallographic structure of the SARS-CoV-2 3CLpro, as well as five conformations obtained after performing a cluster analysis of a 300 ns molecular dynamics (MD) simulation. This procedure elucidated the inappropriateness of the active site for non-covalent inhibitors, but it has also shown that there exists an additional, more favorable, allosteric binding site, which could be a better target for non-covalent inhibitors, as it could prevent dimerization and activation of SARS-CoV-2 3CLpro. Two such examples are radotinib and nilotinib, tyrosine kinase inhibitors already in use for treatment of leukemia and which binding to the newly found allosteric binding site was also confirmed using MD simulations.

Communicated by Ramaswamy H. Sarma

Graphical Abstract

Keywords:

• 3CL protease
• molecular dynamics
• SARS-CoV-2
• radotinib
• nilotinib

Acknowledgements

The authors also acknowledge University of Zagreb, University Computing Centre (SRCE) for granting computational time on the Isabella cluster.

Disclosure statement

The authors declare no conflict of interest.

Additional information

Funding

This study was funded by RFBR, DST, CNPq, SAMRC, project number 20-53-80002.