Discovery of a New Class of Thiazolidin-4-one-Based Inhibitors of Human Dihydroorotate Dehydrogenase: Biological Activity Evaluation, Molecular Docking, and Molecular Dynamics

Abstract

The continuous outbreak of various viruses reminds us to prepare broad-spectrum antiviral drugs. Human dihydroorotate dehydrogenase (hDHODH) inhibitor exhibits broad-spectrum antiviral effects. In order to explore the novel type of human dihydroorotate dehydrogenase inhibitor (hDHODHi), we have optimized, designed, and synthesized 17 compounds and conducted biological activity evaluation, molecular docking, and molecular dynamics studies. The results of biological activity evaluation showed that compounds 10 and 16 exhibited submicromolar inhibitory activity, with IC₅₀ values of 0.188 ± 0.004 and 0.593 ± 0.012 μM, respectively. Molecular docking studies showed that compounds 10 and 16 were in good agreement with the hDHODH activity pocket and interacted well with amino acid residues. Compared to the cocrystallized structure of the brequinar analogue complex, inhibitors 10 and 16 increased their direct interaction with Ala55. In addition, molecular dynamics studies showed that inhibitors 10 and 16 have strong affinity for proteins, and their complexes are stable, which confirms the significant inhibitory effect of inhibitors 10 and 16 on hDHODH in vitro. Through analysis, it was found that the carboxyl group and para introduced fluorine atoms in R ¹, as well as the naphthalene in R ², are key factors in improving activity. This conclusion provides help for further research into hDHODH inhibitors in the future. This study has promoted the significance of the development of broad-spectrum antiviral drugs.

Figure 1

Picture “a” shows the binding modes of compound 10 with hDHODH. HDHODH (PDB ID: 1D3G) is shown as a transparent blue-white cartoon. The critical residues are presented as cyan lines. Arg136, Gln47, and Ala55 are displayed as green sticks. Compound 10 is colored salmon. Hydrogen bonds are shown as black dashed lines. Picture “b” shows the binding modes of compound 16 with hDHODH. HDHODH (PDB ID: 1D3G) is shown as a transparent blue-white cartoon. The critical residues are presented as slate lines. Arg136, Gln47, and Ala55 are displayed as green sticks. Compound 2 is colored cyan. Hydrogen bonds are shown as black dashed lines. We used PyMOL to analyze protein–ligand interactions and visualize the binding modes.

Figure 2

Picture “a” shows the binding modes of all compounds with hDHODH. HDHODH (PDB ID: 1D3G) is shown as a transparent blue-white cartoon. The critical residues are presented as slate lines. Arg136, Gln47, and Ala55 are displayed as cyan sticks. Compound 10 is colored salmon. Compound 16 is colored green. Other compounds are colored yellow. Hydrogen bonds are shown as black dashed lines. Picture “b” shows the binding modes of all compounds with hDHODH. HDHODH (PDB ID: 1D3G) is shown as a transparent pale cyan surface. Compound 10 is colored salmon. Compound 16 is colored green. Other compounds are colored yellow. We used PyMOL to analyze protein–ligand interactions and visualize the binding modes.

Figure 3

Time evolution RMSD of the protein C-α atom over 100 ns for hDHODH bound to compound 10 (a) and compound 16 (b).

Figure 4

Time evolution RMSF of each residue of the protein C-α atom over 100 ns for hDHODH bound to compound 10 (a) and compound 16 (b).

Figure 5

Structural representation of alterations occurring during the binding of compound 10 (a) and compound 16 (b), solvent accessible surface area of hDHODH.