As links between genotype and phenotype, small-molecule metabolites are attractive biomarkers for disease diagnosis, prognosis, classification, drug screening and treatment, insight into understanding disease pathology and identifying potential targets. Metabolomics technology is crucial for discovering targets of small-molecule metabolites involved in disease phenotype. Mass spectrometry-based metabolomics has implemented in applications in various fields including target discovery, explanation of disease mechanisms and compound screening. It is used to analyze the physiological or pathological states of the organism by investigating the changes in endogenous small-molecule metabolites and associated metabolism from complex metabolic pathways in biological samples. The present review provides a critical update of high-throughput functional metabolomics techniques and diverse applications, and recommends the use of mass spectrometry-based metabolomics for discovering small-molecule metabolite signatures that provide valuable insights into metabolic targets. We also recommend using mass spectrometry-based metabolomics as a powerful tool for identifying and understanding metabolic patterns, metabolic targets and for efficacy evaluation of herbal medicine.

Diabetic nephropathy (DN) exhibits profound spatial metabolic heterogeneity across kidney regions, yet how compartmentalized pathways drive disease progression remains poorly defined. A deeper understanding of the organizational spatial environment and metabolic pathways of diabetic kidney damage will provide new insights to develop new therapies. By integrating high-resolution spatial multi-omics and single-cell transcriptomics, we mapped region-specific metabolic dysregulation in diabetic kidneys, identifying glutathione metabolism, pentose phosphate, and glycolytic pathways as zonally disrupted in cortical and medullary regions. Spatial metabolomics revealed distinct anatomical clustering of ten clinically associated metabolites, while spatial proteomic profiling uncovered sixty-four region-enriched proteins linked to these pathways. Specifically, depending on anatomic location, spatial protein signatures across multiple regions of diabetic mouse kidneys were enriched in each segmentation, respectively. Cross-species integration identified GPX3 as a fibroblast-enriched biomarker strongly correlated with kidney dysfunction and closely related to clinical indicators. Notably, astragaloside IV (ASIV) treatment reversed spatial metabolic perturbations in diabetic mice, restoring glutathione and glycolytic pathway activity in a compartment-specific manner. Single-cell analyses identified five cell types—endothelial cells, fibroblasts, epithelial cells, macrophages and neutrophils—and further revealed fibroblasts as key contributors to regulatory effects via GPX3 overexpression. Importantly, the higher expression of Gpx3 in fibroblasts compared to other cell types, Gpx3 (AUC = 0.995), was further validated, demonstrating the high sensitivity and specificity for DN patients. This multimodal atlas establishes the spatially resolved metabolic blueprint of DN, bridging molecular zoning with anatomical localization of renal tissue to unveil actionable therapeutic targets for metabolic disorders in kidney disease.

Background: Diabetic kidney disease (DKD) is a major cause of end-stage renal disease. Although metformin is widely prescribed, the mechanisms underlying its renoprotective effects remain incompletely understood. Methods: We integrated multi-omics approaches—including network pharmacology, phosphoproteomics, and targeted metabolomics—in both db/db mice (male) and human patients. Analyses were performed on blood and kidney tissue from mice and paired blood/urine samples from DKD patients to identify conserved therapeutic targets and metabolic pathways. Results: Metformin treatment improves glycemic control and renal function (reduced creatinine and urea nitrogen) in DKD mice. Network pharmacology and phosphoproteomic analyses reveal metformin’s engagement with the MAPK pathway, specifically through MAPK1 and MAPK3. Targeted metabolomics identifies four carbohydrate metabolites (mannitol, D-arabitol, D-mannose, and D-xylose) associated with DKD risk in humans. Cross-species validation in mice supports D-Xylose as a potential key biomarker for metformin’s therapeutic effects in DKD, with proximal tubule bicarbonate reclamation and alanine, aspartate and glutamate metabolism as key metabolic pathways. Conclusions: Metformin alleviates DKD through multi-modal mechanisms, modulating the MAPK signaling pathway and carbohydrate metabolites—notably D-xylose. As far as we are aware, these findings provide new mechanistic insights and suggest potential biomarker-driven strategies for DKD management.

Bacteriophage phi29 utilizes a motor to translocate genomic DNA into a preformed procapsid. The motor contains six pRNAs, an enzyme and one 12-subunit connector with a central channel for DNA transportation. A 20-residue peptide containing a His-tag was fused to the N-terminus of the connector protein gp10. This fusion neither interfered with procapsid assembly nor affected the morphology of the prolate-shaped procapsid. However, the pRNA binding and virion assembly activity were greatly reduced. Such decreased functions can be switched back on by the removal of the tag via protease cleavage, supporting the previous finding that the N-terminus of gp10 is essential for the pRNA binding. The DNA-packaging efficiency with dimeric pRNA was more seriously affected by the extension than with monomeric pRNA. It is speculated that the fusion of the tag generated physical hindrance to pRNA binding, with greater influence for the dimers than the monomers due to their size. These results reveal a potential to turn off and turn on the motor by attaching or removing, respectively, a component to outer part of the motor, and offers an approach for the inhibition of viral replication by using a drug or a small peptide targeted to motor components.

Diabetic nephropathy (DN), the leading cause of end-stage renal disease, lacks effective therapies due to an incomplete understanding of its cell-type-specific pathogenesis. Here, through an integrative multi-omics approach, we have decoded the molecular architecture of DN, identify novel therapeutic targets, and validates a promising intervention. Single-cell RNA sequencing of human diabetic kidneys reveals the podocyte as the central cellular nexus of DN, exhibiting specific dysregulation in ferroptosis and glycerophospholipid metabolism, and possessing superior diagnostic potential. High-resolution analysis of podocyte heterogeneity identifies ferroptosis as a key driver of glomerular injury, centered on the dysregulated genes MAPK14/SLC7A11/GPX4. We further demonstrated that astragaloside IV (ASIV) exerts potential protective effects by specifically targeting the ferroptosis pathway, reversing the diabetic transcriptional landscape and preserving podocyte integrity. Spatial metabolomics uncovers profound anatomical compartmentalization of metabolic dysregulation in the renal cortex and medulla, which is effectively regulated by ASIV. Integrated transcriptomic and metabolomic profiling in vitro definitively establishes ferroptosis inhibition as the core mechanism of ASIV-mediated podocyte protection. Finally, clinical metabolomic profiling identifies urinary metabolic intermediates of glycerophospholipid metabolism as highly sensitive and specific non-invasive biomarkers for its diagnosis. Our study delineates a fundamental research framework for DN, from basic mechanism to targeted therapy and precision diagnostics.