Fig 1.
Flow chart of the current study.
Table 1.
Molecular docking results showing binding affinities of the small molecules along with control inhibitor (their 2D structures are given in S1 Fig).
Fig 2.
Structural visualization of ligand binding within the TrMD active pocket.
A) Overview of the ligand-bound TrMD dimer showing positioning of all complexes. B) Control complex with the native ligand (magenta) showing partial pocket occupancy. C) Complex-45 (orange) stably situated within the binding site. D) Complex-56 (green) deeply embedded in the active pocket with close contact to key residues. E) Complex-57 (yellow) exhibiting deep insertion into the pocket, suggesting strong binding affinity.
Fig 3.
2D interaction diagram illustrating molecular interactions between TrMD and ligands.
A) Control B) Complex-45 C) Complex-56 and D) Complex-57.
Fig 4.
Comparative molecular dynamics analysis of trmd-ligands complexes.
A) RMSD profiles showing structural stability over 100 ns B) RMSF indicating residue-level flexibility C) RoG depicting overall compactness during the first 25 ns.
Fig 5.
Depicting the hydrophobicity of all the complexes during the simulation time intervals.
Table 2.
Binding energy values (kcal/mol) for filtered hits-TrmD complexes.
Fig 6.
Binding free energy evaluation for complexes of compound-45, compound-56, compound-57, and control through WaterSwap calculations.
Table 3.
Lipinski Rule of five calculated for the selected compounds by SWISS-ADME.
Table 4.
ADMET properties calculated for the selected compounds by SWISS-ADME.