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The success story of plant-based medicine has been overlooked during the advent of the modern pharmaceutical industry. Despite the negligence of the multibillion-dollar drug industry, people entirely rely on medicinal plants in some parts of the world. In this study, we have emphasized going back to those traditional medicinal practices to determine their underlying mechanism to move forward on phytochemical-based drug development. We screened Medicinal Plant Database Bangladesh (MPDB2.0) to find traditionally used medicinal plants and their active compounds.Here, mangiferin, extracted from Mangifera indica, has interacted with cell cycle regulator Cyclin-dependent Kinase 4 (CDK4). CDK4 is differentially expressed during Glioblastoma multiforme (GBM), Brain Lower Grade Glioma (LGG), and Sarcoma (SARC). Expression of CDK4 is interlinked to the patients’ survival rate and its consistent expression throughout different stages has provided the advantage to use it as a diagnostic tool and drug target.This study demonstrated that a simple mango tree extracted active compound ‘mangiferin’ may work as a potential anticancer drug, and leveraging the recent advancement of sequencing and gene expression data can accelerate the phytochemical-based drug discovery process.