Targeting the Skp2–Cks1 protein–protein interaction: structures, assays, and preclinical inhibitors

Abstract

The Skp2–Cks1 protein–protein interaction (PPI) within the SCF^Skp2 ubiquitin ligase acts as a co-receptor for phosphorylated CDK inhibitors—most prominently p27^Kip1—relieving CDK inhibition and advancing the cell cycle, a dependency accentuated in RB-pathway–defective cancers. Crystallographic and cryo-EM analyses delineate a composite pocket formed by the Skp2 leucine-rich-repeat groove and the phosphate-recognition site of Cks1; Cks1-centered open–closed motions further influence druggability. Using HTRF/TR-FRET and AlphaScreen biochemistry, alongside cell-based target-engagement readouts in some studies, three small-molecule classes have emerged that disrupt this PPI: 1,3-diphenyl-pyrazines and triazolo[1,5-a]pyrimidines (lead E35) with low-micromolar potency, and “Skp2E3LI” compounds with micromolar cellular activity. These agents elevate p27 (and in some reports p21), curb proliferation, and show in-vivo effects in defined models: diphenyl-pyrazines in prostate and gastric xenografts, E35 in gastric xenografts, and Skp2E3LIs in estrogen-driven endometrial hyperplasia. Additional strategies that impinge on the Skp2 axis—such as SKPin-C1 or neddylation blockade—suppress osteosarcoma and small-cell lung cancer models; doxorubicin combinations are synergistic in osteosarcoma, whereas neddylation combinations yield enhanced but not uniformly synergistic activity. Genetic validation comes from a Cks1^N45R knock-in that prevents Skp2–Cks1 binding, stabilizes p27, and phenocopies Skp2 loss without systemic lethality. Key needs include pushing potency into the sub-micromolar range, broad selectivity profiling, and defining long-term safety in proliferative tissues, with biomarker-guided development focused on RB1 loss, SKP2 overexpression, and nuclear p27 depletion. Degrader approaches (PROTACs/molecular glues) remain preclinical. This review synthesizes these advances and outlines priorities for translation.