In Silico Investigation of TATA-Binding Protein as a Therapeutic Target for Chagas Disease: Insights into FDA Drug Repositioning

Abstract

Background: Parasitic diseases, particularly Chagas disease caused by Trypanosoma cruzi, primarily affect developing countries but are now spreading to wealthier nations due to changing migration patterns. With approximately 8 to 9 million cases annually and a rise in drug resistance and side effects, there is an urgent need for new therapeutic approaches. Objectives: This study aimed to identify potential pharmacological compounds to target the TATA Binding Protein (TBP) of T. cruzi. Methods: Over eleven thousand FDA-approved pharmacological compounds were analyzed using in silico methods, including homology modeling, molecular docking, and molecular dynamics simulations. In addition, in vitro assays were conducted to assess the trypanocidal activity of promising candidates against T. cruzi epimastigotes and their selectivity toward macrophage J774.2. Results: Two compounds, DB00890 and DB07635, emerged as promising candidates, demonstrating significant potential against T. cruzi TBP. Compound DB00890 had trypanocidal activity against T. cruzi epimastigotes, with IC₅₀ values of 70.4 µM (SI 2.84) and 37.3 µM (SI 5.36) for the NINOA and A1 strains, respectively. Conclusions: Our findings suggest DB00890 is a promising candidate for the development of new agents against Chagas disease, with the potential for targeted therapies that minimize side effects. These results provide a strong foundation for further research into novel treatments for parasitic diseases caused by T. cruzi.

Keywords: FDA; TBP; Trypanosoma cruzi; drug repositioning; in silico; in vitro.

Figure 1

Illustrates eukaryotic TBPs, highlighting the 14 amino acid residues forming the NC2 motif. Residues conserved for HsTBP are marked in green, while non-conserved residues are depicted in black. In the lower-right corner, the WebLogo diagram shows the degree of residue preservation across the 14 amino acids forming the NC2 region. The purple box shows the TBPs from animals; note that the NC2 motif is entirely conserved. The green box shows the TBPs from organisms in the Fungi kingdom; note the presence of amino acid residues that differ from those in human TBP. Finally, the red box displays the TBPs from T. cruzi and the related protist, Leishmania mexicana; note the significant number of changes in the residues that make up the NC2 motif and that several residues are buried within the protein structure.

Figure 2

Possible ligand-binding sites. (A) Results of blind docking experiments. (B) Potentially druggable sites identified by the DoGSiteScorer Binding Site server. For T. cruzi, the second-most promising druggable site is presented, indicated by its drug score. The NC2 site is also mentioned in the literature as a potential therapeutic target for parasites, including protozoa such as Plasmodium falciparum and Entamoeba histolytica.

Figure 3

The binding profile of the ten leading compounds shows higher selectivity for TcTBP than for HsTBP. On the x-axis, the percentage of interactions of each amino acid residue with the ligand is shown. At the same time, on the y-axis, the interacting compound is displayed along with its binding free energy.

Figure 4

Illustrates the interactions between amino acid residues of the NC2 motif and various ligands. The ten compounds with the highest selectivity index for TcTBP in comparison to HsTBP are displayed.

Figure 5

RMSD plot for TcTBP apo-protein and in complex with FDA-approved compounds DB00890 and DB07635.

Figure 6

RMSF graphs for TcTBP apo-protein and FDA-approved DB00890 and DB07635. Secondary structure elements of HsTBP are annotated with red arrows (β-sheets), green sinusoidal lines (α-helices), and gray lines (unstructured regions).

Figure 7

Gyration radius graphs for TcTBP apo-protein and in complex with potential inhibitors DB00890 and DB07635.

Figure 8

Graphs derived from the molecular dynamics analysis of HsTBP: (A) RMSD profiles for the apo form and complexes with FDA-approved compounds DB00890 and DB07635. (B) RMSF profiles for the apo form and ligand-bound states; secondary structure elements of HsTBP are annotated with red arrows (β-sheets), green sinusoidal lines (α-helices), and gray lines (unstructured regions). (C) Radius of gyration plots for the apo-protein and its complexes with DB00890 and DB07635.