Targeting decaprenylphosphoryl-β-D-ribose 2'-epimerase for Innovative Drug Development Against Mycobacterium Tuberculosis Drug-Resistant Strains

Abstract

Tuberculosis (TB) remains a global health challenge with the emergence of drug-resistant Mycobacterium tuberculosis variants, necessitating innovative drug molecules. One potential target is the cell wall synthesis enzyme decaprenylphosphoryl-β-D-ribose 2'-epimerase (DprE1), crucial for virulence and survival. This study employed virtual screening of 111 Protein Data Bank (PDB) database molecules known for their inhibitory biological activity against DprE1 with known IC50 values. Six compounds, PubChem ID: 390820, 86287492, 155294899, 155522922, 162651615, and 162665075, exhibited promising attributes as drug candidates and validated against clinical trial inhibitors BTZ043, TBA-7371, PBTZ169, and OPC-167832. Concurrently, this research focused on DprE1 mutation effects using molecular dynamic simulations. Among the 10 mutations tested, C387N significantly influenced protein behavior, leading to structural alterations observed through root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), and solvent-accessible surface area (SASA) analysis. Ligand 2 (ID: 390820) emerged as a promising candidate through ligand-based pharmacophore analysis, displaying enhanced binding compared with reference inhibitors. Molecular dynamic simulations highlighted ligand 2's interaction with the C387N mutation, reducing fluctuations, augmenting hydrogen bonding, and influencing solvent accessibility. These collective findings emphasize ligand 2's efficacy, particularly against severe mutations, in enhancing protein-ligand complex stability. Integrated computational and pharmacophore methodologies offer valuable insights into drug candidates and their interactions within intricate protein environments. This research lays a strategic foundation for targeted interventions against drug-resistant TB, highlighting ligand 2's potential for advanced drug development strategies.

Keywords: 3D pharmacophore; DprE1; Mycobacterium tuberculosis; resistance; virtual screening.

Figure 1.

The workflow used in this study.

Figure 2.

Prediction results of mutational effects on DprE1 stability and flexibility.

Figure 3.

Pharmacophoric map generation: (A and B) The map generated with and without aligned ligand; (C) the distance between each feature in the map; and (D) the best ligand found with the pharmacophore query search with RMSD close to zero.

Figure 4.

Three-dimensional visualization of the interaction between the potential ligand (ID: 390820) and the DprE1 protein, with the residues in green and the ligand in light blue.

Figure 5.

Protein-ligand molecular dynamic analysis for the DprE1 protein, the WT version with reference ligand complex and the 5 mutant deleterious models with reference ligand complexes: WT—reference ligand (light blue), C387G—reference ligand (orange), C387N—reference ligand (green), G17C—reference ligand (dark blue), G61A—reference ligand (yellow), and Y314C—reference ligand (red): (A) RMSD analysis calculated for 100 ns; (B) RMSF of each complex as a function of residue number; (C) radius of gyration of protein-ligand complexes calculated during simulations expressed in pico-second; and (D) the SASA analysis calculated for the complexes for 100 000 ps.

Figure 6.

Molecular dynamic analysis of the best ligand found in affinity ratio and screening of the pharmacophore model, complexed with the WT version of the protein and the most severe mutation found C387N: (A) RMSD analysis calculated for 100 ns in nm of the 4 complexes: WT—reference molecule (light blue), WT—potential molecule (pink), C387N—reference molecule (green), and C387N—potential molecule (purple); (B) RMSF of each complex as a function of the number of residues; (C) the radius of gyration in nm of protein-ligand complexes calculated during simulations expressed in pico-seconds; (D) SASA analysis calculated for the complexes for 100 000 ps; and (E) number of hydrogen bonds calculated for each complex.