Mechanisms of the binding of camptothecin derivatives with topoisomerase I: Molecular docking, molecular dynamics simulations, and binding free energy calculations.

contextTopoisomerase 1 (TOP1) is a key anticancer target, and camptothecin (CPT) and its derivatives are typical TOP1 inhibitors. Among them, the 7-aminourea and 7-aminothiourea derivatives of CPT (XSJ07 and XSJ05, respectively) exhibit potent inhibitory activity, yet their binding mechanisms remain unclear. In this study, we investigated the interactions of XSJ05 and XSJ07 with TOP1 to clarify their molecular recognition behavior. Both compounds intercalated into the cleaved-DNA-binding site to form stable TOP1-DNA-ligand ternary complexes. The calculated binding free energies of the XSJ05/TOP1 and XSJ07/TOP1 systems were -58.34 and -51.60 kcal/mol, respectively. These findings provide mechanistic insights into the binding of CPT derivatives to TOP1 and may guide the rational design of novel CPT-based inhibitors.

methodsMolecular docking, molecular dynamics (MD) simulations, and binding free energy calculations were employed to characterize the interactions of XSJ05 and XSJ07 with TOP1. Ligand structures were optimized at the B3LYP/6-311++G(d,p) level, and partial atomic charges were derived using the RESP protocol based on HF/6-31G calculations in Gaussian 16. Docking was performed using AutoDock 4.2 with grid parameters defined from the TPT/TOP1 crystal structure. MD simulations of the ligand-TOP1-DNA ternary complexes were conducted using AMBER24 with the ff19SB force field for TOP1 and DNA, GAFF2 for the ligands, and explicit TIP3P water. Each system was equilibrated and simulated for 500 ns in triplicate. Binding free energies and per-residue energy decompositions were calculated using the MM/GBSA method implemented in AMBER Tools, with analysis performed using the CPPTRAJ module.