Exploring the anticancer potential of pyrimidine derivatives via molecular docking and dynamics

Ovarian cancer (OC) is a highly lethal disease characterized by challenges in early diagnosis and a high mortality rate. Pyrimidine derivatives, known for their active sites and ability to bind effectively with drugs, have shown potential in targeted therapies. This study investigates the bioactive potential of compounds against OC targets 6SGI, 6GUK, and 5N7V using computational approaches. Molecular docking was performed with AutoDock Vina to estimate the binding affinity of the ligands, and GROMACS simulations were used to evaluate receptor stability and conformational changes. Results indicated that compound having CID 135504987 revealed strong binding affinities, particularly for 6SGI (– 8.5 kcal/mol), 6GUK (– 8.3 kcal/mol) and 5N7V (– 7.6 kcal/mol) and Root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), and solvent-accessible surface area (SASA) analyses highlighted the superior stability of the 6GUK complex compared to 5N7V and 6SGI. The 6GUK complex exhibited narrower Rg fluctuations (2.01–2.07 nm) and consistent SASA values (145–160 nm²) throughout the simulation. The study demonstrates that CID 135504987 is a promising bioactive inhibitor, comparable to the chemotherapeutic drug 5-Fluorouracil. These findings emphasize the significance of computational tools like docking and molecular dynamics simulations in accelerating drug discovery, offering a cost-effective approach to designing novel therapeutic agents for ovarian cancer treatment.