Characterization and Cytotoxicity of West Java Coffee Extracts, Chlorogenic Acid, Caffeine on MDA-MB-231, MCF-7 Cell Lines, and Their Impact on MYC and AXIN2 Wnt Pathway Gene Expression

Background: Coffee bean extracts have been widely investigated for their potential anticancer properties, particularly due to bioactive compounds such as chlorogenic acid and caffeine. Breast cancer development involves complex genetic and signaling alterations, including dysregulation of the Wnt/β-catenin pathway. Purpose: To determine the phytochemical composition and quantify caffeine and chlorogenic acid in West Java coffee bean extracts. The study assessed their effects on the viability of MDA-MB-231 and MCF-7 breast cancer cells, and examined impacts on the Wnt pathway, focusing on MYC and AXIN2 expression. Methods: Phytochemical screening and HPLC analysis are used to measure chlorogenic acid and caffeine in green and roasted coffee extracts. Cytotoxic activity and IC 5 0 values in MDA-MB-231 and MCF-7 breast cancer cells were assessed with the WST-8 assay. Gene expression of MYC and AXIN2 was analyzed by q-RT-PCR to assess modulation of the Wnt pathway. Cytotoxic selectivity was tested in HEK293 cells. Flow cytometry analyzes apoptosis and the cell cycle. Molecular mechanisms were explored using docking, 200-ns molecular dynamics simulations, and MM-PBSA binding free energy calculations targeting Tankyrase-1 and Estrogen Receptor Alpha. Results: Roasting and extraction methods affected phytochemicals, with higher temperatures reducing chlorogenic acid levels. Coffee extracts showed cytotoxicity against MDA-MB-231 (IC 5 0 258.4– 637 μg/mL) and MCF-7 (IC 5 0 190.7– 686 μg/mL) cells, and minimal toxicity to HEK293 cells—Green Arabica and Robusta extracts, via maceration, notably downregulated MYC and slightly reduced AXIN2 . Flow cytometry indicated increased late apoptosis and cell-cycle arrest. Docking analysis found that chlorogenic acid binds more strongly to Tankyrase-1 than ERα. MD and MM-PBSA confirmed stable, energetically favorable binding to Tankyrase-1 complex. Conclusion: Coffee bean extracts, especially chlorogenic acid–rich green coffee, show selective antiproliferative effects in breast cancer cells and may act through Wnt signaling rather than estrogen receptors. More in vivo and mechanistic studies are needed to confirm their potential as complementary or preventive anticancer agents. Keywords: breast cancer, chlorogenic acid, Wnt signaling pathway, Tankyrase-1 inhibition, molecular simulation, apoptosis