Background/Objectives: Hepatocellular carcinoma (HCC) is the most prevalent primary liver tumor and is often diagnosed at advanced stages with very poor therapeutic response, leading to high mortality. Thus, new therapeutic strategies and biomarkers are urgently needed. We previously showed that the combination of loratadine, raloxifene, and sorafenib exerts synergistic cytotoxicity on HCC cells. Here, we explored potential molecular mechanisms underlying the anticancer effects of this combination using multiomics analyses. Methods: We performed proteomic analyses based on mass spectrometry, transcriptomic analyses using the Clariom D Plus human microarray (Affymetrix), and metabolomic analyses based on nuclear magnetic resonance to investigate the profile changes induced by the drug combination in HuH7 cells. Bioinformatic analyses were applied to associate the omics changes with biological functions, molecular interactions, and clinical relevance in terms of patient survival. Results: We identified several molecules whose expression changed in response to treatment across the three omics profiles analyzed. Some of them were found to be involved in hallmarks of cancer, including sustained proliferation, evasion of growth suppressors, and resistance to cell death. Integrated multi-omics analyses revealed that the drug combination suppresses critical oncogenic drivers (C7orf50, NUP188, and HS2ST1) and that the mitotic cell cycle process, DNA synthesis and cholesterol biosynthesis are the primary pathways affected. Protein–protein interaction analysis revealed five key hubs (KIF2C, PCNA, TRIP13, NDC80, and RPA3), whose expression in HCC is associated with poor clinical prognosis. Conclusions: The combined treatment rewired molecular networks involved in HCC progression. These findings identify clinically relevant molecular targets associated with poor prognosis and provide mechanistic insights into the synergistic anticancer activity of this drug combination.

Hepatocellular carcinoma (HCC) remains a major global health burden. We have recently demonstrated the synergistic cytotoxicity elicited by the combination of loratadine, raloxifene, and sorafenib in liver cancer cells. In this study, we investigated the potential mechanistic basis of this novel multi-drug regimen by identifying candidate protein targets of the three drugs. Potential protein targets of each drug were identified using the Drug Affinity Responsive Target Stability (DARTS) assay in protein extracts from the HCC cell line HuH7, and molecular docking was performed to predict binding modes and explore the structural feasibility of these drug–target interactions. Bioinformatics analyses were conducted to predict biological functions, molecular interactions, and clinical relevance. We identified 147 potential candidate DARTS-stabilized proteins for loratadine, 191 for sorafenib, and 157 for raloxifene; a proportion of these candidate proteins maintained a statistically significant association with overall survival in HCC patients: 20.14% for loratadine, 22.93% for raloxifene, and 24.47% for sorafenib. Cross-referencing with public databases confirmed several previously documented targets—complementing our experimental approach—while revealing numerous previously unreported target candidates. Docking analyses predicted favorable binding interactions between the drugs and several proteins, such as the putative complex between loratadine and N-glycanase 1 (NGLY1), whose expression correlates with reduced overall survival in HCC patients. Functional enrichment analysis showed that several targets are involved in hallmarks of cancer. Clinically relevant candidate targets of loratadine, raloxifene, and sorafenib were identified. However, as these candidate protein targets were identified exclusively in HuH7 cells, they may not fully generalize across all HCC models without further validation. Nevertheless, our results suggest that loratadine, raloxifene and sorafenib modulate key pathways involved in tumorigenesis. These findings strengthen the use of this combination as a promising therapeutic strategy for HCC and provide new opportunities for the identification of novel targets, prognostic markers, and molecular vulnerabilities suitable for pharmacological intervention in HCC and other malignancies and diseases.