Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations

Abstract

The recent outbreak of novel “coronavirus disease 2019” (COVID-19) has spread rapidly worldwide, causing a global pandemic. In the present work, we have elucidated the mechanism of binding of two inhibitors, namely α-ketoamide and Z31792168, to SARS-CoV-2 main protease (M^pro or 3CL^pro) by using all-atom molecular dynamics simulations and free energy calculations. We calculated the total binding free energy (ΔG_bind) of both inhibitors and further decomposed ΔG_bind into various forces governing the complex formation using the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method. Our calculations reveal that α-ketoamide is more potent (ΔG_bind= − 9.05 kcal/mol) compared to Z31792168 (ΔG_bind= − 3.25 kcal/mol) against COVID-19 3CL^pro. The increase in ΔG_bind for α-ketoamide relative to Z31792168 arises due to an increase in the favorable electrostatic and van der Waals interactions between the inhibitor and 3CL^pro. Further, we have identified important residues controlling the 3CL^pro-ligand binding from per-residue based decomposition of the binding free energy. Finally, we have compared ΔG_bind of these two inhibitors with the anti-HIV retroviral drugs, such as lopinavir and darunavir. It is observed that α-ketoamide is more potent compared to lopinavir and darunavir. In the case of lopinavir, a decrease in van der Waals interactions is responsible for the lower binding affinity compared to α-ketoamide. On the other hand, in the case of darunavir, a decrease in the favorable intermolecular electrostatic and van der Waals interactions contributes to lower affinity compared to α-ketoamide. Our study might help in designing rational anti-coronaviral drugs targeting the SARS-CoV-2 main protease.

Communicated by Ramaswamy H. Sarma

Keywords:

• COVID-19
• SARS-CoV-2 3CLpro
• Molecular Dynamics
• MM-PBSA
• binding free energy

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was partially supported by the Department of Biotechnology, Govt. of India (grant number BT/RLF/Re-entry/40/2014, DBT-Ramalingaswami Re-entry Fellowship), and Department of Science and Technology (DST), Govt. of India (grant number ECR/2017/000010). MFS would like to thank DST, Govt. of India, for providing with the INSPIRE Fellowship (DST/INSPIRE Fellowship/2017/IF170145).