Metabolic mechanism

Clarifying the metabolic mechanisms underlying disease is essential for effective treatment, as diseases arise from complex interactions among genetic, environmental, and metabolic factors. Metabolomics has become a key tool for elucidating these mechanisms by identifying disease-related metabolic disruptions and therapeutic targets. Numerous studies demonstrate its utility in revealing how drugs and bioactive compounds exert therapeutic effects, such as breviscapine in Alzheimer’s disease through phospholipid metabolism regulation, polysaccharides in glucose and memory disorders via amino acid and carbohydrate metabolism, aloe emodin in hyperlipidemia by correcting metabolic disturbances, and methotrexate in arthritis through modulation of inflammatory metabolic networks. Metabolomics has also enabled the identification of disease-specific biomarkers and metabolic signatures in conditions including bladder cancer, Clostridium difficile–associated diarrhea, allergic asthma, hypertension, and cardiac fibrosis. Overall, disease reflects a disruption of normal metabolic homeostasis, and metabolomics provides a powerful systems-level approach to understand these imbalances. Continued investigation of metabolic mechanisms, accounting for individual variability and environmental influences, is critical for advancing precision medicine and improving therapeutic strategies.

Drug Efficacy and Screening Using Metabolomics

Metabolomics has emerged as a powerful tool for drug efficacy evaluation and screening, particularly in bridging traditional Chinese medicine (TCM) and Western medicine. Owing to its holistic and systems-level perspective, metabolomics aligns well with TCM theory and provides modern scientific methods to study drug actions, mechanisms, compatibility, and metabolic effects. Its application in TCM research has expanded rapidly, covering single-herb studies focused on pharmacological effects, toxicity, and metabolic mechanisms, as well as compound formulations that emphasize compatibility rules and integrated metabolic pathways.

In TCM research, metabolomics has been successfully used to identify active compounds, differentiate treatment processes, and elucidate mechanisms of action. Studies have identified bioactive anticancer, anti-inflammatory, neuroprotective, and anti-allergic compounds by linking therapeutic effects to specific metabolic pathways such as amino acid, lipid, glycerophospholipid, and energy metabolism. These findings provide scientific validation for traditional formulations and support the global recognition of TCM.

Metabolomics also plays a crucial role in Western drug research, particularly in understanding metabolic mechanisms, efficacy, and safety. MS-based metabolomics supports drug screening, quality control, and impurity analysis, and is widely applied in animal model validation and clinical evaluation. Importantly, metabolomics enables comprehensive assessment of drug-induced toxicity, especially hepatotoxicity and nephrotoxicity, by identifying disrupted metabolic pathways and potential toxicity biomarkers.

Overall, metabolomics provides an integrated platform for evaluating drug efficacy, screening active compounds, and assessing toxicity for both traditional and modern medicines. By revealing system-wide metabolic responses, it supports safer drug development, mechanism-based therapy optimization, and advances in precision and integrative medicine.

Nutritional Metabolomics

Nutritional metabolomics applies metabolomics approaches to systematically study the interactions between diet and organismal metabolism under both healthy and disease conditions. It provides insights into how nutrients, food composition, environmental factors, and biological stress influence metabolic pathways and overall health.

Studies using NMR and MS-based platforms have demonstrated that the metabolic profiles of fruits and vegetables are affected by factors such as geographic origin, cultivation conditions, and abiotic stress, including heavy metals and storage environments. Metabolomics has been used to characterize nutrient composition, secondary metabolites, and bioactive compounds in foods such as cucumbers, kale, plums, ginger, strawberries, kiwi leaves, coffee, bread, wine, and various agricultural products. These analyses help identify metabolite variations linked to nutritional quality, food processing, and storage conditions.

Beyond plant-based foods, metabolomics has also been applied to animal-derived and functional foods. Research has shown that compounds such as royal jelly proteins can influence memory-related metabolic pathways, while differences in metabolic profiles have been observed in foods like black and white sesame. Metabolomics is further used to assess malnutrition, evaluate dietary interventions, and study metabolic responses to food consumption, such as the effects of orange juice on lipid metabolism.

Overall, nutritional metabolomics plays a critical role in addressing global challenges of both undernutrition and overnutrition. By revealing how personalized diets influence metabolic pathways, this approach supports the development of targeted nutritional strategies to prevent and manage chronic metabolic diseases such as diabetes, hypertension, and obesity, thereby contributing to improved public health outcomes.

Agronomy and Plant Biology

Mass spectrometry–based metabolomics is increasingly applied in agronomy and plant biology to understand plant growth, metabolism, and responses to environmental and nutritional stress. By profiling metabolic changes, metabolomics provides valuable insights into how plants adapt to variations in essential elements, nutrient availability, and abiotic stresses.

Studies have shown that metabolomics can elucidate plant responses to excess or deficiency of key elements such as molybdenum, sulfur, magnesium, and nitrogen, revealing tissue-specific metabolic adjustments and identifying metabolites involved in metal chelation, carbon–nitrogen balance, and stress tolerance. This information supports improved fertilizer management, enhanced crop yield, and better grain quality. Metabolomics has also been applied to monitor herbicide residues in crops, contributing to food safety and sustainable agricultural practices.

Beyond crop production, metabolomics is widely used to investigate plant and microbial metabolism under drought stress, nutrient supplementation, and controlled growth conditions. It has been applied to study metabolic regulation in cyanobacteria, drought-induced changes in vegetables, and quality-related metabolic pathways in economically important plants such as tea. Overall, the integration of metabolomics with agronomy and plant biology is becoming increasingly important for crop improvement, stress resistance, disease diagnosis, and agricultural productivity, opening new directions for both metabolomics research and sustainable agriculture.