Harnessing Natural Product Compounds to Target Dormancy Survival Regulator (DosR) in Latent Tuberculosis Infection (LTBI): An In Silico Strategy Against Dormancy

Abstract

Dormancy occurs when Mycobacterium tuberculosis (Mtb) enters a non-replicating and metabolically inactive state in response to hostile environment. During this state, it is highly resistant to conventional antibiotics, which increase the urgency to develop new potential drugs against dormant bacilli. In view of this, the dormancy survival regulator (DosR) protein is thought to be an essential component that plays a key role in bacterial adaptation to dormancy during hypoxic conditions. Herein, the NP-lib database containing natural product compounds was screened virtually against the binding site of the DosR protein using the MTiopen screen web server. A series of computational analyses were performed, including redocking, intermolecular interaction analysis, and MDS, followed by binding free energy analysis. Through screening, 1000 natural product compounds were obtained with docking energy ranging from -8.5 to -4.1 kcal/mol. The top four lead compounds were then selected for further investigation. On comparative analysis of intermolecular interaction, dynamics simulation and MM/GBSA calculation revealed that M3 docked with the DosR protein (docking score = -8.1 kcal/mol, RMSD = ~7 Å and ΔG Bind = -53.51 kcal/mol) exhibited stronger stability than reference compound Ursolic acid (docking score = -6.2 kcal/mol, RMSD = ~13.5 Å and ΔG Bind = -44.51 kcal/mol). Hence, M3 is recommended for further validation through in vitro and in vivo studies against latent tuberculosis infection.

Keywords: DosR; dormancy; molecular dynamics simulation; structure-based virtual screening; tuberculosis.

Figure 1

Structures of previously identified anti-tuberculosis compounds (a) ZINC34198774 and (b) HC104A, that showed structural similarity with the identified hits (M1–M4).

Figure 2

Structures of the selected natural product compounds: (a) M1, (b) M2, (c) M3, (d) M4, and (e) reference compound (Ursolic acid).

Figure 3

2D and 3D interaction profiles for the protein–ligand docked complexes; (a) DosR-M1, (b) DosR-M2, (c) DosR-M3, (d) DosR-M4, and (e) reference compound DosR-(Ursolic acid). Three-dimensional and 2D structures were generated from Maestro 12.8 version. In the 3D structure, the compound is represented by ball and stick model (pink color), and protein is represented by ribbon in constant green color. In 2D interaction diagram, hydrogen bonds (violet arrows), hydrophobic (green), positive (violet), negative (red), polar (blue), and glycine (creamy white) interactions are presented to be involved in docked complexes.

Figure 4

Root mean square deviation plot for the backbone atoms of DosR protein with selected natural product compounds: (a) DosR-M1, (b) DosR-M2, (c) DosR-M3, (d) DosR-M4, and (e) reference compound DosR-(Ursolic acid), fit on selected target protein were extracted from 200 ns MDS trajectories of different docked complexes.

Figure 5

RMSF plot generated for the DosR protein docked with selected natural product compounds and reference molecule, i.e., (a) M1, (b) M2, (c) M3, (d) M4, and (e) reference compound (Ursolic acid).

Figure 6

RMSF plot generated for the docked natural product compounds and reference molecule, i.e., (a) M1, (b) M2, (c) M3, (d) M4, and (e) reference compound (Ursolic acid), fit in the DosR protein during 200 ns MDS interval.

Figure 7

Protein–ligand interactions mapping (green: hydrogen bonding; grey: hydrophobic interaction; pink: ionic interaction; blue: water bridges) for DosR protein docked with selected natural product compounds, i.e., (a) DosR-M1, (b) DosR-M2, (c) DosR-M3, (d) DosR-M4, and (e) reference compound DosR (Ursolic acid), extracted from 200 ns Molecular dynamic simulations.

Figure 8

A detailed schematic representation of atomic interaction of ligand of natural product compounds and the reference molecule, i.e., (a) M1, (b) M2, (c) M3, (d) M4, and (e) reference compound (Ursolic acid), docked with DosR protein. On the chosen trajectory (0.00 to 200.01 nsec), interactions that occur more than 30.0% of the simulation period are displayed.

Figure 9

Calculated net binding free energy and energy components values for DosR protein complex with selected natural product compounds, i.e., (a) M1, (b) M2, (c) M3, (d) M4, and (e) reference compound (Ursolic acid), snapshots extracted from MDS trajectory.