Integrated Network Pharmacology, Molecular Modeling, LC–MS Profiling, and Semisynthetic Approach for the Roots of <i>Rubia tinctorum</i> L. Metabolites in Cancer Treatment

<i>Rubia tinctorum</i> L. is one of the most widely used plants in folk medicine, with many reported pharmacological activities. One of these valuable activities is its anticancer efficacy. The aim of this study is to explore the multilevel mechanisms of <i>R. tinctorum</i> metabolites in cancer treatment using network pharmacology, together with molecular docking and in vitro studies. The network pharmacology analysis enabled us to reveal the hit anticancer <i>R. tinctorum</i> constituents, which were found to be acacetin, alizarin, anthragallol, 2-hydroxyanthraquinone, and xanthopurpurin. The most enriched cancer-linked target genes were PLCG1, BCL2, CYP1B1, NSD2, and ESR2. The pathways that were mostly involved in the anticancer mechanism of <i>R. tinctorum</i> metabolites were found to be metabolic pathways as well as pathways in cancer and apoptosis. Molecular docking of the identified hit anticancer constituents on the active sites of the most enriched genes unveiled that acacetin and alizarin possessed the lowest binding energies on the active sites of NSD2 and BCL2, respectively. While anthragallol showed the most stabilized interaction on the active sites of PLCG1, CYP1B1, and ESR2. Consequently, <i>R. tinctorum</i> extracts were evaluated for their in vitro cytotoxicity on a panel of cancerous cells. Among the tested <i>R. tinctorum</i> extracts, the chloroform extract was the strongest one with an IC₅₀ = 3.987 μg/mL on the MCF-7 breast cancer cell line. Consequently, it was subjected to chromatographic separation and purification to isolate its major components with reported anticancer activity (scopoletin, rubiadin, chrysophanic acid, alizarin, purpurin, nor-damnacanthal, emodin, and rutin). Alizarin and purpurin constituted the main anthraquinones in <i>R. tinctorum</i> <i>.</i> Thus, they were quantified using LC/MS analysis. Moreover, a semisynthetic approach of alizarin toward the enhancement of its anticancer effect on the tested cancer cells was attained. Among the synthesized compounds, 2-methyl alizarin was the most active one with an IC₅₀ = 8.878 μg/mL against the HepG2 cell line. This study provides deep insights into the anticancer mechanisms of <i>R. tinctorum</i> metabolites for the first time using network pharmacology and valorizes their significance as valuable anticancer agents.