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Herbs are widely utilized in the Western Ghats region of India to treat liver diseases and viral-like infections. However, such practices lack scientific evidence at the molecular level and may often pose adverse drug reactions. This study intends to identify phytocompounds with druggability and non-toxic profiles with potential activity against hepatitis B virus-induced hepatocellular carcinoma. The details of phytocompounds in traditionally utilized herbs in the Western Ghats region were collated from chemical databases and publications. The druggability and toxicity of these compounds were predicted using MolSoft and ADVERpred, respectively. The probable targets of these phytocompounds were predicted using BindingDB. Moreover, compound-gene set pathways, cellular processes, and functional enrichment analyses were also performed using STRING and KEGG pathway databases. Subsequently, herb–compound–target–disease pathway networks were constructed using Cytoscape. The potential hub protein was virtually screened against the ligand dataset using the POAP pipeline. Finally, molecular dynamics (MD) simulations of the most potential protein–ligand complexes were performed in triplicate using Schrödinger Desmond. Amongst 274 compounds from 16 herbs studied, 36 showed drug-likeness with nontoxic properties and were also predicted to modulate 16 potential targets involved in the pathogenesis of HBV-induced HCC. Among all the molecules screened, flavonoids and diterpenoids from Andrographis paniculata and Thespesia populnea scored the highest edge count via modulating multiple targets and pathways. Moreover, molecular docking and MD simulation (100ns) also inferred that the top-ranking Andrographin and Gossypetin exhibit stable intermolecular interactions with EGFR protein, which was identified as a highly connected hub protein in the constructed network. All these findings are suggestive of identified moieties as potential therapeutics for targeting HBV-associated HCC sans adverse drug reactions. [ABSTRACT FROM AUTHOR]