A proteome-scale reverse screening approach reveals multi-target interactions of anthraquinone derivatives in cancer-related pathways.

Abstract

Cancer is a multifactorial and heterogeneous disease in which single-target therapeutic strategies often fail to achieve sustained efficacy. Anthraquinone derivatives exhibit diverse anticancer activities; however, their comprehensive molecular targets and mechanisms of action remain incompletely characterized. In this study, a proteome-wide reverse virtual screening strategy was applied to identify potential human protein targets of five sugar-free anthraquinone derivatives, including emodin, chrysophanol, aloe-emodin, physcion, and rhein. 67,000 human protein structures were screened using AutoDock Vina, followed by binding energy-based filtering and removal of redundant targets, resulting in 123 non-redundant proteins. Functional annotation and pathway analysis revealed cancer-associated biological processes linked to the identified targets. Comparative pathway analysis identified 64 overlapping pathways, from which 10 key pathways and six core protein targets were prioritized based on multi-ligand convergence. Predicted binding affinities of the retained ligand-target combinations for the prioritized targets ranged from -9.0 to -10.7 kcal/mol, with emodin and chrysophanol showing comparatively stronger binding affinities. LigPlot + analysis characterized hydrogen-bonding and hydrophobic interactions involved in ligand stabilization. Furthermore, 100 ns molecular dynamics simulations showed that 19 of the 27 simulated ligand-protein complexes retained the predicted binding mode, while the remainder underwent partial or complete ligand dissociation, and in silico ADMET analysis indicated acceptable drug-like properties and pharmacokinetic profiles. Overall, this integrative computational framework combines proteome-scale target discovery, pathway prioritization, structural validation, molecular dynamics, and ADMET evaluation to provide a systems-level perspective on the potential multi-target anticancer mechanisms of anthraquinone derivatives and identify candidate targets for future experimental validation.