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Forecasting what biological effects an active metabolite compartmentalized in a medicinal plant may have on human health requires intensive research and clinical trials. There are inconsistencies in the application of herbal medicine in the treatment of disease mostly due to the metabolic composition. Different herbal strains, growing media and environmental conditions will alter the metabolite composition of herbal extracts. A modeling approach to identify the genes, enzymes and signaling pathways involved in the biosynthesis of the medicinal plant metabolites could harmonize the process of predicting the metabolite composition. The structural similarity of primary and secondary plant herbal metabolites does not always provide complete assurance of what pharmacological effect they may have on the respective human metabolic system. Many of the medicinal plant metabolites are either unknown or not searchable through current computational resources. In this review, we have discussed that a system based biological approach comparing human and plant metabolic signaling networks that could be additionally productive to ascertain the regulatory and biological processes conferred by a metabolite and their bioactivity pathways in living systems. A combination of a both systems and structural based approaches can generate new models that render a better metabolite composition bioactivity reduction, thereby enhancing the efficacy, safety, and toxicity of herbal medicine processing.

Metabolic similarity of plant and human: implications for efficacy and regulatory compliance of herbal therapies