In-silico drug repurposing and molecular dynamics puzzled out potential SARS-CoV-2 main protease inhibitors

Abstract

Herein, the DrugBank database which contains 10,036 approved and investigational drugs was explored deeply for potential drugs that target SARS-CoV-2 main protease (M^pro). Filtration process of the database was conducted using three levels of accuracy for molecular docking calculations. The top 35 drugs with docking scores > −11.0 kcal/mol were then subjected to 10 ns molecular dynamics (MD) simulations followed by molecular mechanics–generalized Born surface area (MM-GBSA) binding energy calculations. The results showed that DB02388 and Cobicistat (DB09065) exhibited potential binding affinities towards M^pro over 100 ns MD simulations, with binding energy values of −49.67 and −46.60 kcal/mol, respectively. Binding energy and structural analyses demonstrated the higher stability of DB02388 over Cobicistat. The potency of DB02388 and Cobicistat is attributed to their abilities to form several hydrogen bonds with the essential amino acids inside the active site of M^pro. Compared to DB02388 and Cobicistat, Darunavir showed a much lower binding affinity of −34.83 kcal/mol. The present study highlights the potentiality of DB02388 and Cobicistat as anti-COVID-19 drugs for clinical trials.

Communicated by Ramaswamy H. Sarma.

Graphical Abstract

Keywords:

• COVID-19
• SARS-CoV-2 main protease
• drug repurposing
• in-silico drug discovery
• molecular dynamics

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

The computational work was completed with resources supported by the Science and Technology Development Fund, STDF, Egypt, Grants No. 5480 & 7972.