Possibility of HIV-1 protease inhibitors-clinical trial drugs as repurposed drugs for SARS-CoV-2 main protease: a molecular docking, molecular dynamics and binding free energy simulation study

Abstract

Initially, the SARS-CoV-2 virus was emerged from Wuhan, China and rapidly spreading across the world and urges the scientific community to develop antiviral therapeutic agents. Among several strategies, drug repurposing will help to react immediately to overcome the COVID-19 pandemic. In the present study, we have chosen two clinical trial drugs against HIV-1 protease namely, TMB607 and TMC310911 to use as the inhibitors of SARS-CoV-2 main protease (M^pro) enzyme. To make use of these two inhibitors as the repurposed drugs for COVID-19, it is essential to know the molecular basis of the binding mechanism of these two molecules with the SARS-CoV-2 M^pro. To understand the binding mechanism, we have performed molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations against the SARS-CoV-2 M^pro. The docking results indicate that both molecules form intermolecular interactions with the active site amino acids of M^pro enzyme. However, during the MD simulations, TMB607 forms strong interaction with the key amino acids of M^pro, and remains intact. The RMSD and RMSF values of both complexes were stable throughout the MD simulations. The MM-GBSA binding free energy values of both complexes are −43.7 and −34.9 kcal/mol, respectively. This in silico study proves that the TMB607 molecule binds strongly with the SARS-CoV-2 M^pro enzyme and it may be suitable for the drug repurposing of COVID-19 and further drug designing.

Communicated by Ramaswamy H. Sarma

Keywords:

• SARS-COV-2M^pro
• HIV-1 protease clinical trial drugs
• drug repurposing
• molecular docking
• molecular dynamics
• binding free energy

Acknowledgements

The authors thank the Computer Centre, Periyar University, Salem to perform the computational work in the High Performance Cluster (HPC) Computer.

Disclosure statement

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