Molecular Mechanisms of Functional Foods Revealed by Artificial Intelligence and Systems Biology

Abstract

Based on their various bioactive compounds, including polyphenol, flavonoids, carotenoids, dietary fibres, probiotics, and omega-3 fatty acids, functional foods have proven to be an effective way to promote health and to reduce the risk of chronic diseases. Numerous studies have shown their beneficial effects, but the complexity of the molecular mechanisms responsible for such activities continues to be poorly understood because of the intricacies of gene/protein/metabolite/signaling pathway/gut microbiome interactions. In recent years, the use of artificial intelligence (AI) and systems biology has revolutionized functional food research by facilitating the systematic analysis of complex multidimensional biological information and by helping identify molecular targets, the molecular signatures of the disease under investigation, and regulatory networks. The advancement of machine learning, deep learning, network pharmacology, molecular docking, and multi-omics integration has sped up the identification of bioactive molecules, the prediction of food–target interactions, the pathway enrichment analysis, and the interpretation of the mechanisms underlying the biological responses. These computational tools can also contribute to precision nutrition, by combining individual genomic, metabolomic, and microbiome data to create tailored nutrition plans. However, data quality, model interpretation and understanding, standardization of multi-omics data, clinical validation, and regulatory acceptance remain obstacles to wider translation into healthcare practice. The review aims to summarise the molecular mechanisms that underlie the biological effects of functional foods and to emphasise the emerging contributions of AI and systems biology to understanding these mechanisms. In addition, this work addresses challenges and opportunities at the intersection of computational intelligence and nutrition and highlights new technologies and future opportunities in this field to facilitate the discovery of functional foods and the field of precision nutrition. The synergy of AI, systems biology and functional food research will create a strong foundation for evidence-based dietary interventions and future generation preventive health.