Discovery of Spondias mombin flavonoid rutin as a novel DNA methyltransferase 1 inhibitor and potential agent to treat triple negative breast cancer in patients of West African ancestry

Women of West African (WA) ancestry disproportionately experience poor breast cancer outcomes, even when diagnosed with the estrogen receptor (ER)-positive subtype. Recent chromatin accessibility analyses reveal ancestry-specific upregulation of DNA methyltransferase1 (DNMT1), with elevated DNMT1 levels in WA patients correlating with worse survival. Given the traditional use of Spondias mombin in WA populations for breast cancer, and the known epigenetic activity of flavonoids, we investigated the therapeutic potential of its major flavonoid, rutin and sought to delineate a probable mechanism of anticancer action. Seventeen breast cancer-related molecular targets were screened using molecular docking and Molecular Mechanics/Generalized Born Surface Area binding energy calculations. Rutin's binding interactions were analyzed in detail using 2D/3D interaction mapping, hydrogen-bond profiling, and stability metrics. Rutin demonstrated strong potential binding affinity to 10 of 17 breast cancer targets, with the most favorable interaction observed with DNMT1, surpassing those with HER2, mTOR, AKT1, and EGFR. Docking analyses identified multiple stabilizing hydrogen-bond interactions within the DNMT1 catalytic pocket, suggesting direct inhibition of enzymatic activity. Rutin also engaged key regulators of proliferation (CDK4, Cyclin D1), angiogenesis (VEGF-A), and DNA repair (BRCA1/2), indicating a multi-targeted anticancer profile. The strong DNMT1binding supports a mechanism in which rutin may relieve methylation-dependent silencing of tumor suppressor genes, whose reduced expression associates with poor survival, particularly among patients of WA ancestry. Colony-forming assays reveal that rutin exhibits potent antiproliferative activity in breast cancer cells, particularly those derived from patients of WA ancestry. Quantitative PCR analyses show that rutin inhibits DNMT1 gene expression in cells derived from patients of WA ancestry. Our in-silico findings identify rutin as a high-affinity DNMT1inhibitor with multi-pathway anticancer potential, supporting a role for flavonoid-mediated epigenetic reprogramming in reducing breast cancer disparities. Our in vitro findings suggest that rutin inhibits DNMT1 to ultimately suppress TNBC cell proliferation. These results justify further mechanistic validation in ancestry-derived breast cancer models and support the development of S. mombin -derived flavonoids as low-toxicity, ancestry-relevant therapeutic candidates.