Intrinsic conformational flexibility limits stable small-molecule engagement of SKP2 in breast cancer: an integrated network and molecular dynamics study

Dysregulation of the ubiquitin-proteasome system is a hallmark of breast cancer, yet the identification of selectively targetable E3 ubiquitin ligases remains a significant challenge. Skp2, a key oncogenic E3 ligase, has emerged as a promising therapeutic target; however, the development of effective small-molecule inhibitors has been limited. To systematically investigate this, we analyzed the primate ubiquitin ligome (523 E3 ligases) and constructed a Skp1–Cullin1–F-box (SCF)-restricted interaction network comprising 61 nodes, identifying S-phase kinase-associated protein 2 (SKP2) as a central hub across multiple topological parameters. Consistent with its regulatory importance, SKP2 was found to be overexpressed across breast cancer subtypes, particularly in aggressive molecular classes. A conserved SKP2 binding region was systematically interrogated using integrated molecular docking and molecular dynamics simulations to assess the stability of small-molecule interactions. Although docking indicated favorable binding interactions, dynamic analysis revealed limited binding persistence, with ligand-bound systems exhibiting increased structural deviations relative to the apo state (~ 0.90 to ~ 1.30 nm RMSD), substantial ligand mobility (RMSD up to ~ 5 nm), and progressive sampling of partially displaced or solvent-exposed ligand positions during the simulations. These findings indicate that the evaluated compounds did not maintain stable engagement with the initial SKP2 binding region under the present computational conditions and suggest that both the flexible, surface-exposed nature of the SKP2 interface and ligand-specific instability may contribute to the difficulty of sustained small-molecule binding. Our observations are consistent with reported challenges in targeting SKP2 using small-molecule inhibitors, but do not establish a definitive mechanistic basis for those limitations. Nevertheless, this study provides a computational framework for understanding how SKP2 conformational dynamics may influence ligand engagement and may support the future design of improved SKP2-targeting strategies in breast cancer.