Monitoring and modelling the glutamine metabolic pathway: a review and future perspectives.

BACKGROUND: Analysis of the glutamine metabolic pathway has taken a special place in metabolomics research in recent years, given its important role in cell biosynthesis and bioenergetics across several disorders, especially in cancer cell survival. The science of metabolomics addresses the intricate intracellular metabolic network by exploring and understanding how cells function and respond to external or internal perturbations to identify potential therapeutic targets. However, despite recent advances in metabolomics, monitoring the kinetics of a metabolic pathway in a living cell in situ, real-time and holistically remains a significant challenge. AIM: This review paper explores the range of analytical approaches for monitoring metabolic pathways, as well as physicochemical modeling techniques, with a focus on glutamine metabolism. We discuss the advantages and disadvantages of each method and explore the potential of label-free Raman microspectroscopy, in conjunction with kinetic modeling, to enable real-time and in situ monitoring of the cellular kinetics of the glutamine metabolic pathway. KEY SCIENTIFIC CONCEPTS: Given its important role in cell metabolism, the ability to monitor and model the glutamine metabolic pathways are highlighted. Novel, label free approaches have the potential to revolutionise metabolic biosensing, laying the foundation for a new paradigm in metabolomics research and addressing the challenges in monitoring metabolic pathways in living cells.

A comparative proteomic approach using metabolic pathways for the identification of potential drug targets against Helicobacter pylori.

BACKGROUND: Helicobacter pylori is the most highlighted pathogen across the globe especially in developing countries. Severe gastric problems like ulcers, cancers are associated with H. pylori and its prevalence is widespread. Evolution in the genome and cross-resistance with different antibiotics are the major reason of its survival and pandemic resistance against current regimens. OBJECTIVES: To prioritize potential drug target against H. pylori by comparing metabolic pathways of its available strains. METHODS: We used various computational tools to extract metabolic sets of all available (61) strains of H. pylori and performed pan genomics and subtractive genomics analysis to prioritize potential drug target. Additionally, the protein interaction and detailed structure-based studies were performed for further characterization of protein. RESULTS: We found 41 strains showing similar set of metabolic pathways. However, 19 strains were found with unique set of metabolic pathways. The metabolic set of these 19 strains revealed 83 unique proteins and BLAST against human proteome further funneled them to 38 non-homologous proteins. The druggability and essentiality testing further converged our findings to a single unique protein as a potential drug target against H. pylori. CONCLUSION: We prioritized one protein-based drug target which upon subject to applied protocol was found as close homolog of the Saccharopine dehydrogenase. Our study has opened further avenues of research regarding the discovery of new drug targets against H. pylori.

A Serum Metabolomic Study on Rats Induced by Polygoni Multiflori Radix and Polygoni Multiflori Radix Preparata by Pattern Recognition and Pathways Analysis.

This study focused on the differential metabolomic effects between water extracts of Polygoni Multiflori Radix and Polygoni Multiflori Radix Preparata in rats. The extracts were subsequently administered for 28 d. Serum biochemical indicators were tested, hematoxylin-eosin staining and immunohistochemistry staining were used to detect histopathological changes in the livers. Ultra-performance LC/quadrupole time-of-flight mass spectrometry was used to detect the changes in endogenous metabolites. Finally, we performed detailed analysis of the changes in metabolic pathways. Hematoxylin-eosin staining and immunohistochemistry staining results indicated that the water extracts of Polygoni Multiflori Radix and Polygoni Multiflori Radix Preparata had mild liver injury effect. Fifty-two differential endogenous biomarkers were confirmed as potential biomarkers between Polygoni Multiflori Radix and Polygoni Multiflori Radix Preparata groups. In the positive ion mode, the biomarkers included 31 Phosphatidyl cholines (PCs), six lysoPCs, and ceramide. In the negative ion mode, 12 biomarkers were confirmed, including glycodeoxycholic acid, chenodeoxycholic acid, and deoxycholic acid, etc. In Hydrophilic Interaction Liquid Chromatography (HILIC) mode, nine biomarkers were confirmed, including niacinamide, L-palmitoylcarnitine, and butyrylcarnitine, etc. Using MetaboAnalyst 4.0, six related metabolic pathways, including taurine and hypotaurine metabolism, sphingolipid metabolism, glycerophospholipid metabolism, nicotinate and nicotinamide metabolism, arginine and proline metabolism, and tryptophan metabolism and primary bile synthesis, were confirmed as the most differential pathways between the Polygoni Multiflori Radix and Polygoni Multiflori Radix Preparata groups.

Usefulness of Amino Acid Profiling in Ovarian Cancer Screening with Special Emphasis on Their Role in Cancerogenesis.

The aim of this study was to quantitate 42 serum-free amino acids, propose the biochemical explanation of their role in tumor development, and identify new ovarian cancer (OC) biomarkers for potential use in OC screening. The additional value of this work is the schematic presentation of the interrelationship between metabolites which were identified as significant for OC development and progression. The liquid chromatography-tandem mass spectrometry technique using highly-selective multiple reaction monitoring mode and labeled internal standards for each analyzed compound was applied. Performed statistical analyses showed that amino acids are potentially useful as OC biomarkers, especially as variables in multi-marker models. For the distinguishing metabolites the following metabolic pathways involved in cancer growth and development were proposed: histidine metabolism; tryptophan metabolism; arginine biosynthesis; arginine and proline metabolism; and alanine, aspartate and glutamine metabolism. The presented research identifies histidine and citrulline as potential new OC biomarkers. Furthermore, it provides evidence that amino acids are involved in metabolic pathways related to tumor growth and play an important role in cancerogenesis.

Metabolomics study on the toxicity of Annona squamosa by ultraperformance liquid-chromatography high-definition mass spectrometry coupled with pattern recognition approach and metabolic pathways analysis.

ETHNOPHARMACOLOGICAL RELEVANCE: Annona squamosa Linn (Annonaceae) is a commonly used and effective traditional Chinese medicine (TCM) especially in the South China. The seeds of Annona squamosa Linn (SAS) have been used as a folk remedy to treat "malignant sores" (cancer) in South of China, but they also have high toxicity on human body. AIM OF THE STUDY: To discover the potential biomarkers in the mice caused by SAS. MATERIALS AND METHODS: We made metabonomics studies on the toxicity of SAS by ultraperformance liquid-chromatography high-definition mass spectrometry coupled with pattern recognition approach and metabolic pathways analysis. RESULTS: The significant difference in metabolic profiles and changes of metabolite biomarkers between the Control group and SAS group were well observed. 11 positive ions and 9 negative ions (P<0.05) were indicated based on UFLC-QTOF-HDMS. The metabolic pathways of SAS group are discussed according to the identified endogenous metabolites, and eight metabolic pathways are identified using Kyoto Encyclopedia of Genes and Genomes (KEGG). CONCLUSIONS: The present study demonstrates that metabonomics analysis could greatly facilitate and provide useful information for the further comprehensive understanding of the pharmacological activity and potential toxicity of SAS in the progress of them being designed to a new anti-tumor medicine.

Serum metabolomics study of lupus nephritis based on ultra high performance liquid chromatography mass spectrometry / 中华风湿病学杂志

Objective The metabolomics methods were applied to discover the serum differences metabolites in patients with lupus nephritis (LN),and to establish the diagnostic model and study the metabolic pathways change due to the interference of LN and explore the pathogenesis of LN.Methods Positive and negative ions mode of ultra high performance liquid chromatography-high resolution mass spectrometry (HPLS-HRMS) were used to analyze the serum samples of 38 LN patients and 35 healthy controls,respectively.Both univariate and multivariate data analysis were performed with SPSS software (V17.0,Chicago,USA) and SIMCA-P+ package (V12.0,Umetrics,Sweden),respectively.A supervised pattern recognition method,orthogonal partial least squares-discriminant analysis (OPLS-DA),was employed to study the metabolomics differences between control group and LN patients group.The metabolic pathways were analyzed by Metabo Analyst 3.0.Results LN patients and healthy controls could be well separated by OPLS-DA model Q2 of 0.583.Eighteen compounds (theophylline,oxidized glutathione,capric acid,norvaline,hippuric acid,sphingosine,sorbitol,cortisol,pyrrole-2-carboxylic acid,deoxycholic acid,tryptamine,5-aminolevulinic acid,glucose 6-phosphate,riboflavin,cortisone,taurine,creatinine,glycerophosphocholine) were initially identified as potential serum metabolic markers to distinguish LN patients from healthy people.Alternated metabolism pathways included citrate metabolism,pyrimidine metabolism and amino acid metabolism.Conclusion Through analysis of the metabolic pathways of different metabolites,the significant impact of LN on citrate metabolism,pyrimidine metabolism and amino acid metabolism pathways are identified.Some of the different metabolites are involved in the process of immunization.These results will benefit the early intervention and treatment of LN and the research of the mechanism of pathogenesis.