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As the global healthcare landscape shifts toward "green" pharmacology, plant-based research has evolved from traditional ethnobotany into a sophisticated discipline of drug discovery. Medicinal plants represent complex chemical libraries, synthesized by nature to produce secondary metabolites such as alkaloids, flavonoids, terpenoids, and phenolic acids. This review provides a comprehensive analysis of the transition from crude plant extracts to isolated bioactive compounds, evaluating the evolution of green extraction technologies (such as ultrasound-assisted and supercritical fluid extraction) over conventional methods to maximize yield and purity. We further examine the multifaceted biological profiles of these metabolites, specifically their mechanistic roles in neutralizing oxidative stress, modulating inflammatory pathways, and inhibiting oncogenic signalling. Despite their therapeutic potential, the clinical translation of phytochemicals is often hindered by poor aqueous solubility, rapid metabolism, and significant batch-to-batch variability. To address these limitations, this paper discusses the integration of "Omics" technologies and in silico molecular docking, which allow for the high-throughput screening of plant-ligand interactions. By bridging the gap between traditional wisdom and computational biology, this review highlights how biotechnological advancements and standardized regulatory frameworks are essential for the sustainable and scalable development of the next generation of plant-derived therapeutics.