Identification of potential corticosteroid binding sites on the SARS CoV-2 main protease Mpro — in silico docking study
Authors: Khmil N. V. , Shestopalova A. V. , Kolesnikov V. G. , Boiechko-Nemovcha A. O. 
Published: February 2025

Background: Currently, an increase in the number of new cases of Covid-19 caused by the severe acute respiratory syndrome virus (SARS-CoV-2) is recorded in Ukraine and the world. SARS-CoV-2 provokes exacerbation of chronic diseases and activates inflammatory and allergic reactions. A severe course of Covid-19 increases the duration of hospitalization and the mortality rate among the population. Pathogenetic therapy is carried out with systemic corticosteroids, which suppress the cytokine storm by mitigating the SARS-CoV-2-induced systemic inflammatory response and inhibit SARS-CoV-2 main protease Mpro, a key component of viral replication.

Objectives: The aim of this study is to identify the potential corticosteroid binding sites on SARS CoV-2 main protease Mpro based on the analysis of the energetic and topological characteristics of the complexes as well as to investigate the inhibitory activity of selected corticosteroids against Mpro.

Material and Methods: The crystal structure of Mpro (ID: 6LU7 from Protein Data Bank) (www.rcsb.org) was chosen as a docking target. Molecular docking methods (AutoDock Tools 1.5.7, AutoDock Vina 1.1.2) were used to gain insight into the binding affinity Mpro with systemic corticosteroids such as dexamethasone (DEX), prednisone (PRED), prednisolone (PNL), methylprednisolone (Medrol), triamcinolone (TAC), and hydrocortisone (HCT). Visualization of docking results was done in PyMol 2.5. The protein-ligand interaction profiler (PLIP) and the LigPlot+ web tool were used to identify non-covalent interactions between Mpro and ligands (https://plip-tool.biotec.tu-dresden.de).

Results: In silico docking study demonstrated that all selected corticosteroids bound with amino acid residues of II and III domains of Mpro with binding energy in the range -7.8…-6.6 kcal/mol. The high binding affinity is found for dexamethasone-Mpro (-7.8 kcal/mol); for prednisone, prednisolone, methylprednisolone, triamcinolone, and hydrocortisone the binding energies were -7.4, -7.0, -7.5, -7.6 and -6.6 kcal/mol, respectively. It was shown that hydrogen bonds and hydrophobic interactions were involved in the formation of ligand-protein complexes mainly through residues such as Arg131, Lys137, Thr199, Asp289, Leu272, Leu286, Leu287, Tyr239, and Gly275, which formed the catalytic and distal sites for ligand binding. The inhibition constant of corticosteroids has ranged from 1.90 × 10-6 to 14.4 × 10-6 M.

Conclusion: Our results showed that the favorable binding sites for dexamethasone, prednisone, methylprednisolone, and triamcinolone are located in the catalytic site of domain II and the distal site of domain III of SARS-CoV-2 main protease Mpro with high binding affinities confirming the stability of the complexes. The low inhibition constants values for dexamethasone, prednisone, methylprednisolone, and triamcinolone further confirm the effectiveness of the selected corticosteroids as inhibitors of Mpro activity. Based on the binding energy as well as inhibition constants values dexamethasone, prednisone, methylprednisolone, and triamcinolone were identified as potential inhibitors for Mpro.