Integrated computational and biochemical identification of quinoline-8-arylsulfonamides as disruptors of the Skp2–Cks1 protein–protein interaction

Abstract

Context

The Skp2–Cks1 protein–protein interaction is essential for the recognition and ubiquitination of cell-cycle regulators such as p27 and represents an attractive target for anticancer drug discovery. This study aimed to identify small-molecule disruptors of the Skp2–Cks1 interface from a quinoline-8-arylsulfonamide library using an integrated computational and experimental approach. Comparative MM/PBSA analysis indicated that C2 and C1 produced the greatest predicted weakening of the interface, with ΔΔGₚₚᵢ values of +13.19 and +9.54 kcal/mol, respectively. Conversely, C3 and C4 yielded negative values of −15.21 and −26.47 kcal/mol, consistent with predicted interface stabilization. These computational findings were supported by the biochemical activity ranking: C2 and C1 exhibited the lowest IC₅₀ values, at 1.48 ± 0.13 and 1.87 ± 0.13 µM, respectively, compared with 2.62 ± 0.35 µM for the reference compound NSC689857. C3 and C4 showed substantially weaker activity. These findings identify quinoline-8-arylsulfonamides as a promising chemotype for targeting the Skp2–Cks1 interface and prioritize C2 for further optimization.

Methods

A funnel-based virtual screening strategy was applied to 74 compounds, incorporating diversity and drug-likeness filtering, molecular docking with AutoDock Vina, short molecular dynamics refinement, and MM/PBSA rescoring. Prioritized complexes underwent 1000 ns molecular dynamics simulations, free-energy landscape analysis, quantitative assessment of protein–protein interaction disruption metrics, and in silico ADMET profiling. Comparative MM/PBSA calculations evaluated ligand-induced changes in Skp2–Cks1 interaction energy relative to the apo complex. Biochemical inhibitory activity was assessed using an in vitro homogeneous time-resolved fluorescence (HTRF) assay.