Molecular insight, rational chemical design and computational assessment of thiazole-based DHODH inhibitors: from structural modelling to binding free energy calculations

Dihydroorotate dehydrogenase (DHODH) is a key enzyme in <i>de novo</i> pyrimidine biosynthesis and has emerged as a promising target for cancer, inflammation, and autoimmune diseases. In this study, a series of computational techniques-HQSAR, 3D-QSAR (CoMSIA), molecular docking, molecular dynamics (MD) simulations, and MM/PBSA free energy calculations-were employed to investigate the structure-activity relationships (SAR) of thiazole-based DHODH inhibitors. HQSAR (R²_cv = 0.846; R²_test = 0.700) and CoMSIA (R²cv = 0.742; R²_test = 0.817) models demonstrated strong predictivity. Contour maps highlighted the significance of hydrophobic and electrostatic groups on both fused and aromatic rings for inhibitory activity. Docking studies revealed that LEU46, PRO52, ARG136, TYR356, and THR360 are key residues in ligand binding. MD simulations over 500 ns confirmed M33, P26, and P39 as the most stable complexes, while P44 and P46 showed more flexibility. Binding free energy calculations identified P39 and P46 as potent binders due to favorable van der Waals and electrostatic interactions. M33 and P26 showed moderate affinity and high structural stability, making them promising leads. In contrast, P44 exhibited low stability and binding energy. Overall, this work offers valuable insights into thiazole-based DHODH inhibitor design and guides the development of selective therapeutic candidates.