Biofunctional Metabolites and Structures
Main Emphasis
In the Research Group of Biofunctional Metabolites and Structures we aim at the discovery, isolation and structure-function characterization of novel metabolites and structures of bacterial or environmental origin that are critical for understanding the mechanism beyond the chronic lung diseases as well as their therapies.
Non-targeted identification of Metabolites
Using bioassay-guided non-targeted metabolomics based on LC-MS and GC-MS techniques coupled with feature-based molecular networking (FBMN) through GNPS, SIRIUS and Cytoscape we are engaged in projects aimed at the identification of novel bioactive metabolites from microbial and environmental sources (pollen, house dust mite, soil, water). Such identified metabolites can serve as a tool to understand the mechanism of the disease (basic research) or be applied as biomarkers or even therapeutics (translational science).
The LC-HRMS-based non-targeted identification of bioactive metabolites produced by non-typeable Haemophilus influenzae (NTHi) is one of our leading projects in the field of non-targeted metabolomics. The medical relevance of this project lies in the fact that NTHi is a pathogenic inhabitant of the lung microbiome of asthmatics. Its pathogenesis is still poorly understood. We hypothesize in our work that primary and secondary metabolites produced by NTHi contribute to its pathogenesis and / or persistence in asthma.
Targeted identification of Metabolites and Structures
Microbial dysbiosis leads to differential production and secretion of metabolites. Therefore, it is of high relevance to understand the changes in the production of certain metabolites involved in the disease, such as butyrate and propionate, prototypical molecules of microbial origin with anti-inflammatory and immunomodulatory properties in the periphery especially along the gut-lung axis.
Our Research Group provides the expertise in the analysis of stool, serum and urine samples performing qualitative and quantitative measurements of metabolites of interest by GC-MS and LC-MS.
Isolation and structure elucidation
Importantly, we are not only interested in elucidating the descriptive compositional data of novel metabolites and structures but also in their deep functional characterization. This is only possible after a previous isolation, purification and structural elucidation of the target compounds.
For the isolation and structure elucidation we extract compounds using organic solvents of appropriate polarity. Precipitation and removal of proteins as well as demineralization are considered depending on the sample type. The extract is further downstream fractionated by solid phase extraction (SPE) or column chromatography (normal phase, reversed-phase or size-exclusion). High-performance liquid chromatography (HPLC) is used to isolate and purify the unknown or target metabolites from the fractions of interest. In the HPLC system, normal-phase and reversed-phase columns are used depending on the polarity of the compound of interest. Advanced analytical techniques such as high-performance LC-MS, GC-MS and NMR spectroscopy (1D and 2D) are used to determine the structure of biofunctional and/or unknown metabolites.
- DZL4-AA 2.2D Duda
Our Research Group of Biofunctional Metabolites and Structures has a strong expertise in the isolation and purification protocols of various microbial and environmental samples, along with the chemical and structural characterization of the obtained compounds. We also have experience in different bioassays to test the activity of the obtained molecules. During our research, we use the following techniques and methods:
Wet chemistry
- Extraction
- Ultracentrifugation
Chromatography
- High performance liquid chromatography (HPLC)
- High performance -thin layer chromatography (TLC, HPTLC)
- Hydrophobic-interaction chromatography
- Gel permeation chromatography
- Affinity chromatography
- High performance-anion exchange chromatography (AEC, HPAEC)
Analytical chemistry
- Gas chromatography (GC)
- Gas chromatography- mass spectrometry (GC-MS, qualitatively and quantitatively)
- Liquid chromatography- mass spectrometry (UHPLC-ESI-TOF-MS)
- Mass spectrometry (ESI-MS)
- Nuclear Magnetic Resonance (NMR)
Bioassays cell cultures
- screening of the biological activity in human Hodgkin lymphoma (KM-H2), human pro-monocytic U-937 cell line and in murine dendritic cell line JAWSII
- ELISA
- Flow cytometry (MACSQuant 16)
Microbiology
- bacteria cultivation at the level of S2 laboratory
Biochemistry techniques
- Western blot
- Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS- PAGE)
2023
Di Lorenzo, F, Nicolardi, S, Marchetti, R, Vanacore, A, Gallucci, N, Duda, K, Nieto Fabregat, F, Nguyen, HNA, Gully, D, Saenz, J, Giraud, E, Paduano, L, Molinaro, A, D'Errico, G & Silipo, A 2023, 'Expanding Knowledge of Methylotrophic Capacity: Structure and Properties of the Rough-Type Lipopolysaccharide from Methylobacterium extorquens and Its Role on Membrane Resistance to Methanol', JACS Au, Jg. 3, Nr. 3, S. 929-942. https://doi.org/10.1021/jacsau.3c00025
2022
Apangu, GP, Gonzalez Roldan, N, Adams-Groom, B, Satchwell, J, Pashley, CH, Werner, M, Kryza, M, Szymanowski, M, Malkiewicz, M, Bruffaerts, N, Hoebeke, L, Grinn-Gofron, A, Grewling, L, Oliver, G, Sindt, C, Kloster, M & Ambelas Skjoth, C 2022, 'Sentinel-2 satellite and HYSPLIT model suggest that local cereal harvesting substantially contribute to peak Alternaria spore concentrations', Agricultural and Forest Meteorology, Jg. 326, S. 109156. https://doi.org/10.1016/j.agrformet.2022.109156
Di Lorenzo, F, Duda, KA, Lanzetta, R, Silipo, A, De Castro, C & Molinaro, A 2022, 'A Journey from Structure to Function of Bacterial Lipopolysaccharides', Chemical reviews, Jg. 122, Nr. 20, S. 15767-15821. https://doi.org/10.1021/acs.chemrev.0c01321
Head
Scientific staff
Alumni
- Dr. Nestor Gonzalez Roldan
Technical staff
