Synthesis, molecular docking, and binding Gibbs free energy calculation of β-nitrostyrene derivatives: Potential inhibitors of SARS-CoV-2 3CL protease

Abstract

The outbreak of novel coronavirus disease 2019 (COVID-19), caused by the novel coronavirus (SARS-CoV-2), has had a significant impact on human health and the economic development. SARS-CoV-2 3CL protease (3CLpro) is highly conserved and plays a key role in mediating the transcription of virus replication. It is an ideal target for the design and screening of anti-coronavirus drugs. In this work, seven β-nitrostyrene derivatives were synthesized by Henry reaction and β-dehydration reaction, and their inhibitory effects on SARS-CoV-2 3CL protease were identified by enzyme activity inhibition assay in vitro. Among them, 4-nitro-β-nitrostyrene (compound a) showed the lowest IC₅₀ values of 0.7297 µM. To investigate the key groups that determine the activity of β-nitrostyrene derivatives and their interaction mode with the receptor, the molecular docking using the CDOCKER protocol in Discovery Studio 2016 was performed. The results showed that the hydrogen bonds between β-NO₂ and receptor GLY-143 and the π-π stacking between the aryl ring of the ligand and the imidazole ring of receptor HIS-41 significantly contributed to the ligand activity. Furthermore, the ligand-receptor absolute binding Gibbs free energies were calculated using the Binding Affinity Tool (BAT.py) to verify its correlation with the activity of β-nitrostyrene 3CLpro inhibitors as a scoring function. The higher correlation(r²=0.6) indicates that the absolute binding Gibbs free energy based on molecular dynamics can be used to predict the activity of new β-nitrostyrene 3CLpro inhibitors. These results provide valuable insights for the functional group-based design, structure optimization and the discovery of high accuracy activity prediction means of anti-COVID-19 lead compounds.

Keywords: 3CLpro inhibitor; Binding Gibbs free energies; Molecular docking; Receptor-ligand interaction; SARS-CoV-2; β-nitrostyrene derivatives.

Graphical abstract

Fig. 1

FTIR spectroscopy of compound a-g.

Fig. 2

Dose-response curves for IC₅₀ determination of compounds a-g were generated by nonlinear regression and are shown in pictures A-G, respectively.

Fig. 3

Binding modes between ligands and 3CL protease. Picture A-G show interactions between β-nitrostyrene derivatives and protein amino acids in 3D mode and distance between two atoms in unit Å. Picture I-VII show interactions between β-nitrostyrene derivatives and protein amino acids in 2D mode by DS 2016. Picture H show the results of docking the ligand H69 to the original structure of the complex (PDB ID:7RN4) for retrospective studies. The result of molecular docking is indicated in cyans, and the pose of H69 in the original crystal structure is indicated by magenta.

Fig. 3

Binding modes between ligands and 3CL protease. Picture A-G show interactions between β-nitrostyrene derivatives and protein amino acids in 3D mode and distance between two atoms in unit Å. Picture I-VII show interactions between β-nitrostyrene derivatives and protein amino acids in 2D mode by DS 2016. Picture H show the results of docking the ligand H69 to the original structure of the complex (PDB ID:7RN4) for retrospective studies. The result of molecular docking is indicated in cyans, and the pose of H69 in the original crystal structure is indicated by magenta.

Fig. 3

Binding modes between ligands and 3CL protease. Picture A-G show interactions between β-nitrostyrene derivatives and protein amino acids in 3D mode and distance between two atoms in unit Å. Picture I-VII show interactions between β-nitrostyrene derivatives and protein amino acids in 2D mode by DS 2016. Picture H show the results of docking the ligand H69 to the original structure of the complex (PDB ID:7RN4) for retrospective studies. The result of molecular docking is indicated in cyans, and the pose of H69 in the original crystal structure is indicated by magenta.

Fig. 4

Correlation between the IC₅₀ of seven inhibitors and binding Gibbs free energy. A linear regression shows that lower binding Gibbs free energy correlates with stronger 3CL protease inhibition.

Scheme 1

Synthesis of β-Nitrostyrene derivatives.