Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a significant global health challenge due to the emergence of drug-resistant strains. This study targets Flavin-dependent thymidylate synthase (ThyX), an essential enzyme in the thymidylate biosynthesis pathway crucial for bacterial DNA replication. We utilized advanced computational techniques, including molecular dynamics (MD) simulations and interaction energy analysis, to examine the binding interactions and stability of various thiazole-thiadiazole compounds with Mtb ThyX. Our results, corroborated by experimental validation, demonstrate that ligand binding enhances ThyX protein stability, with compound 5l exhibiting the strongest stabilizing effect. Root mean square fluctuation (RMSF) data indicate a consistent binding mechanism, while radius of gyration (RG) and solvent accessible surface area (SASA) analyses confirm structural stability. Key interactions with conserved residues such as Glu74, Ser105, Tyr44, and Ser100 were highlighted through hydrogen bonding and cluster analysis, underscoring protein-ligand complex stability. Principal component analysis (PCA) suggests an allosteric regulation mechanism within ThyX, driven by ligand binding, which induces conformational changes. Free energy landscape (FEL) analysis shows rapid stabilization in ligand-bound states. Compound 5l stands out due to its favourable pharmacokinetic properties and safety, making it a promising candidate for anti-tuberculosis drug development.
Keywords: MD simulations; Mtb ThyX; Principle component analysis.
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