Computational Repurposing and Experimental Validation of YBX1 Inhibitors in Hepatocellular Carcinoma

Background/Objectives: Hepatocellular carcinoma (HCC) is the most common type of liver cancer worldwide. While early-stage HCC can often be treated with surgical resection, ablation, or liver transplantation, advanced disease typically relies on systemic chemotherapy. Sorafenib is the standard first-line therapy for advanced and unresectable HCC; however, both intrinsic and acquired resistance remain major clinical challenges. The Y-box binding protein-1 (YBX1), a transcription factor implicated in drug resistance across multiple cancers, is highly expressed in HCC and represents a potential therapeutic target. This study aimed to identify novel YBX1 inhibitors using a drug repurposing strategy to overcome sorafenib resistance. Methods: A combined in silico and in vitro approach was employed. The cold shock (DNA-binding) domain of YBX1 was modeled, and a comprehensive library of experimental and FDA-approved compounds from the DrugBank database was screened using multi-layered high-throughput virtual screening (HTVS). Candidate compounds with predicted direct interaction with YBX1 were further evaluated through literature review and experimental validation. Results: Virtual screening identified 22 potential compounds predicted to interact with YBX1. Further literature review and feasibility assessment narrowed the list to six candidates: malonaldehyde, mercaptoethanol, glycine, para-chlorophenol, methoxyamine, and ethanolamine. For further evaluation, glycine (a food supplement with no toxicity) was selected for detailed functional studies and was shown to inhibit YBX1 and downregulate its target genes. Conclusions: These findings support YBX1 as a promising therapeutic target in hepatocellular carcinoma and demonstrate the utility of drug repurposing to rapidly identify candidate inhibitors. Targeting YBX1 may provide a viable strategy for enhancing treatment efficacy and overcoming sorafenib resistance in advanced HCC.