Proposing a fungal metabolite-flaviolin as a potential inhibitor of 3CL^pro of novel coronavirus SARS-CoV-2 identified using docking and molecular dynamics

Abstract

The novel SARS-CoV-2 is the etiological agent causing the Coronavirus disease 2019 (COVID-19), which continues to become an inevitable pandemic outbreak. Over a short span of time, the structures of therapeutic target proteins for SARS-CoV-2 were identified based on the homology modelled structure of similar virus, SARS-CoV that transmitted rapidly in 2003. Since the outset of the disease, the research community has been looking for a potential drug lead. Out of all the known resolved structures related to SARS-CoV-2; 3-chymotrypsin (3 C) like protease (3CL^pro) is considered as an attractive anti-viral drug compound on the grounds of its role in viral replication and probable non-interactive competency to bind to any viral host protein. To the best of our knowledge, till date only one compound has been identified and tested in-vitro as a potent inhibitor of 3CL^pro protein, addressed as N3 (PubChem Compound CID: 6323191) and is known to bind irreversibly to 3CL^pro suppressing its activity. Using computational approach, we intend to identify a probable natural fungal metabolite to interact and inhibit 3CL^pro. Here after performing docking and molecular dynamics of various small molecules derived as a secondary metabolite from fungi, we propose Flaviolin as potent inhibitor of 3CL^pro of novel Coronavirus SARS-CoV-2.

Communicated by Ramaswamy H. Sarma

Graphical Abstract

Keywords:

• 3-chymotrypsin like protease (3CLpro
• )
• SARS-CoV-2 novel corona virus
• Fungal metabolites
• docking
• Molecular dynamics

Acknowledgements

Authors are thankful to Gujarat University for providing necessary facilities to perform experiments.

Authors approval

All authors have seen and approved the manuscript.

Disclosure statement

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Compliance with ethical standards

This article does not contain any studies with human participants or animals performed by any of the authors.