1
|
Abdel-Shafy EA, Melak T, MacIntyre DA, Zadra G, Zerbini LF, Piazza S, Cacciatore S. MetChem: a new pipeline to explore structural similarity across metabolite modules. BIOINFORMATICS ADVANCES 2023; 3:vbad053. [PMID: 37424942 PMCID: PMC10322652 DOI: 10.1093/bioadv/vbad053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/28/2023] [Accepted: 04/19/2023] [Indexed: 07/11/2023]
Abstract
Summary Computational analysis and interpretation of metabolomic profiling data remains a major challenge in translational research. Exploring metabolic biomarkers and dysregulated metabolic pathways associated with a patient phenotype could offer new opportunities for targeted therapeutic intervention. Metabolite clustering based on structural similarity has the potential to uncover common underpinnings of biological processes. To address this need, we have developed the MetChem package. MetChem is a quick and simple tool that allows to classify metabolites in structurally related modules, thus revealing their functional information. Availabilityand implementation MetChem is freely available from the R archive CRAN (http://cran.r-project.org). The software is distributed under the GNU General Public License (version 3 or later).
Collapse
Affiliation(s)
| | | | - David A MacIntyre
- March of Dimes Prematurity Research Centre, Imperial College London, London SW7 2AZ, UK
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Giorgia Zadra
- Institute of Molecular Genetics, National Research Council, Pavia 27100, Italy
| | - Luiz F Zerbini
- Cancer Genomics, International Centre for Genetic Engineering and Biotechnology, Cape Town 7925, South Africa
| | - Silvano Piazza
- Computation Biology, International Centre for Genetic Engineering and Biotechnology, Trieste 34149, Italy
| | | |
Collapse
|
2
|
Stężycka O, Frańska M, Beszterda-Buszczak M. Exploring Glycosylated Soy Isoflavones Affinities toward G-tetrads as Studied by Survival Yield Method. Chemphyschem 2023; 24:e202300056. [PMID: 36861944 DOI: 10.1002/cphc.202300056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/17/2023] [Indexed: 03/03/2023]
Abstract
Taking soy-based food supplements for menopausal symptoms by women may reduce the risk of cancer. Therefore, the interaction between nucleic acids (or their constituents) and ingredients of the supplements, e. g., isoflavone glucosides, on the molecular level, has been of interest with respect to cancer therapy. In this work, the interaction between isoflavone glucosides and G-tetrads, namely [4G+Na]+ ions (G stands for guanosine or deoxyguanosine), were analyzed by using electrospray ionization-collision induced dissociation-mass spectrometry (ESI-CID-MS) and survival yields method. The strength of isoflavone glucosides-[4G+Na]+ interaction in the gas phase was determined from Ecom50 - the energy required to fragment 50 % of selected precursor ions. Glycitin-[4G+Na]+ interaction was found to be the strongest, and the interaction between isoflavone glucosides and guanosine tetrad was established to be stronger than that between isoflavone glucosides and deoxyguanosine tetrad.
Collapse
Affiliation(s)
- Olga Stężycka
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Magdalena Frańska
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Monika Beszterda-Buszczak
- Poznań University of Life Sciences, Department of Food Biochemistry and Analysis, Mazowiecka 48, 60-623, Poznań, Poland
| |
Collapse
|
3
|
Using targeted metabolomics to elucidate the indole auxin network in plants. Methods Enzymol 2022; 676:239-278. [DOI: 10.1016/bs.mie.2022.07.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
4
|
Brunmair J, Gotsmy M, Niederstaetter L, Neuditschko B, Bileck A, Slany A, Feuerstein ML, Langbauer C, Janker L, Zanghellini J, Meier-Menches SM, Gerner C. Finger sweat analysis enables short interval metabolic biomonitoring in humans. Nat Commun 2021; 12:5993. [PMID: 34645808 PMCID: PMC8514494 DOI: 10.1038/s41467-021-26245-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 09/22/2021] [Indexed: 01/28/2023] Open
Abstract
Metabolic biomonitoring in humans is typically based on the sampling of blood, plasma or urine. Although established in the clinical routine, these sampling procedures are often associated with a variety of compliance issues, which are impeding time-course studies. Here, we show that the metabolic profiling of the minute amounts of sweat sampled from fingertips addresses this challenge. Sweat sampling from fingertips is non-invasive, robust and can be accomplished repeatedly by untrained personnel. The sweat matrix represents a rich source for metabolic phenotyping. We confirm the feasibility of short interval sampling of sweat from the fingertips in time-course studies involving the consumption of coffee or the ingestion of a caffeine capsule after a fasting interval, in which we successfully monitor all known caffeine metabolites as well as endogenous metabolic responses. Fluctuations in the rate of sweat production are accounted for by mathematical modelling to reveal individual rates of caffeine uptake, metabolism and clearance. To conclude, metabotyping using sweat from fingertips combined with mathematical network modelling shows promise for broad applications in precision medicine by enabling the assessment of dynamic metabolic patterns, which may overcome the limitations of purely compositional biomarkers.
Collapse
Affiliation(s)
- Julia Brunmair
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Mathias Gotsmy
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Laura Niederstaetter
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Benjamin Neuditschko
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Andrea Bileck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University and Medical University of Vienna, Vienna, Austria
| | - Astrid Slany
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Max Lennart Feuerstein
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Clemens Langbauer
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Lukas Janker
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University and Medical University of Vienna, Vienna, Austria
| | - Jürgen Zanghellini
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Samuel M Meier-Menches
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University and Medical University of Vienna, Vienna, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
- Joint Metabolome Facility, University and Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
5
|
Karunaratne E, Hill DW, Pracht P, Gascón JA, Grimme S, Grant DF. High-Throughput Non-targeted Chemical Structure Identification Using Gas-Phase Infrared Spectra. Anal Chem 2021; 93:10688-10696. [PMID: 34288660 PMCID: PMC8404482 DOI: 10.1021/acs.analchem.1c02244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The high-throughput identification of unknown metabolites in biological samples remains challenging. Most current non-targeted metabolomics studies rely on mass spectrometry, followed by computational methods that rank thousands of candidate structures based on how closely their predicted mass spectra match the experimental mass spectrum of an unknown. We reasoned that the infrared (IR) spectra could be used in an analogous manner and could add orthologous structure discrimination; however, this has never been evaluated on large data sets. Here, we present results of a high-throughput computational method for predicting IR spectra of candidate compounds obtained from the PubChem database. Predicted spectra were ranked based on their similarity to gas-phase experimental IR spectra of test compounds obtained from the NIST. Our computational workflow (IRdentify) consists of a fast semiempirical quantum mechanical method for initial IR spectra prediction, ranking, and triaging, followed by a final IR spectra prediction and ranking using density functional theory. This approach resulted in the correct identification of 47% of 258 test compounds. On average, there were 2152 candidate structures evaluated for each test compound, giving a total of approximately 555,200 candidate structures evaluated. We discuss several variables that influenced the identification accuracy and then demonstrate the potential application of this approach in three areas: (1) combining IR and mass spectra rankings into a single composite rank score, (2) identifying the precursor and fragment ions using cryogenic ion vibrational spectroscopy, and (3) the incorporation of a trimethylsilyl derivatization step to extend the method compatibility to less-volatile compounds. Overall, our results suggest that matching computational with experimental IR spectra is a potentially powerful orthogonal option for adding significant high-throughput chemical structure discrimination when used with other non-targeted chemical structure identification methods.
Collapse
Affiliation(s)
- Erandika Karunaratne
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Dennis W Hill
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Philipp Pracht
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - José A Gascón
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - David F Grant
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| |
Collapse
|
6
|
Chitranshi N, Dheer Y, Kumar S, Graham SL, Gupta V. Molecular docking, dynamics, and pharmacology studies on bexarotene as an agonist of ligand-activated transcription factors, retinoid X receptors. J Cell Biochem 2019; 120:11745-11760. [PMID: 30746761 DOI: 10.1002/jcb.28455] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/05/2018] [Accepted: 12/06/2018] [Indexed: 01/24/2023]
Abstract
Retinoid X receptors (RXRs) belong to the nuclear receptor superfamily, and upon ligand activation, these receptors control gene transcription via either homodimerization with themselves or heterodimerization with the partner-nuclear receptor. The protective effects of RXRs and RXR agonists have been reported in several neurodegenerative diseases, including in the retina. This study was aimed to prioritize compounds from natural and synthetic origin retinoids as potential RXR agonists by molecular docking and molecular dynamic simulation strategies. The docking studies indicated bexarotene as a lead compound that can activate various RXR receptor isoforms (α, β, and γ) and has a strong binding affinity to the receptor protein than retinoic acid, which is known as a natural endogenous RXR agonist. Dynamic simulation studies confirmed that the hydrogen bonding and hydrophobic interactions were highly stable in all the three isoforms of the RXR-bexarotene complex. To further validate the significance of the RXR receptor in neurons, in vitro pharmacological treatment of neuronal SH-SY5Y cells with bexarotene was performed. In vitro data from SH-SY5Y cells confirmed that bexarotene activated RXR-simulated neurite outgrowth significantly. We conclude that bexarotene could be potentially used as an exogenous activator of RXRs and emerge as a good drug target for several neurodegenerative disorders.
Collapse
Affiliation(s)
- Nitin Chitranshi
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales
| | - Yogita Dheer
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales
| | - Sanjay Kumar
- Bioinformatics Centre, Biotech Park, Jankipuram, Lucknow, Uttar Pradesh, India
| | - Stuart L Graham
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales
- Save Sight Institute, Sydney University, Sydney, New South Wales, Australia
| | - Vivek Gupta
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales
| |
Collapse
|
7
|
Carneiro G, Radcenco AL, Evaristo J, Monnerat G. Novel strategies for clinical investigation and biomarker discovery: a guide to applied metabolomics. Horm Mol Biol Clin Investig 2019; 38:/j/hmbci.ahead-of-print/hmbci-2018-0045/hmbci-2018-0045.xml. [PMID: 30653466 DOI: 10.1515/hmbci-2018-0045] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/13/2018] [Indexed: 01/16/2023]
Abstract
Metabolomics is an emerging technology that is increasing both in basic science and in human applications, providing a physiological snapshot. It has been highlighted as one of the most wide ranging and reliable tools for the investigation of physiological status, the discovery of new biomarkers and the analysis of metabolic pathways. Metabolomics uses innovative mass spectrometry (MS) allied to chromatography or nuclear magnetic resonance (NMR). The recent advances in bioinformatics, databases and statistics, have provided a unique perception of metabolites interaction and the dynamics of metabolic pathways at a system level. In this context, several studies have applied metabolomics in physiology- and disease-related works. The application of metabolomics includes, physiological and metabolic evaluation/monitoring, individual response to different exercise, nutritional interventions, pathological processes, responses to pharmacological interventions, biomarker discovery and monitoring for distinct aspects, such as: physiological capacity, fatigue/recovery and aging among other applications. For metabolomic analyses, despite huge improvements in the field, several complex methodological steps must be taken into consideration. In this regard, the present article aims to summarize the novel aspects of metabolomics and provide a guide for metabolomics for professionals related to physiologist and medical applications.
Collapse
Affiliation(s)
- Gabriel Carneiro
- Proteomics Laboratoy, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andres Lopez Radcenco
- Departamento de Química del Litoral, CENUR Litoral Norte, Universidad de la República, Montevideo, Uruguay
| | - Joseph Evaristo
- Proteomics Laboratoy, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gustavo Monnerat
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, IBCCF-UFRJ, Av. Carlos Chagas Filho 373 - CCS - Bloco G, Rio de Janeiro 21941-902, Brazil, Phone/Fax: +55 21 25626555
| |
Collapse
|
8
|
Dossin E, Martin E, Diana P, Castellon A, Monge A, Pospisil P, Bentley M, Guy PA. Prediction Models of Retention Indices for Increased Confidence in Structural Elucidation during Complex Matrix Analysis: Application to Gas Chromatography Coupled with High-Resolution Mass Spectrometry. Anal Chem 2016; 88:7539-47. [DOI: 10.1021/acs.analchem.6b00868] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Eric Dossin
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland
| | - Elyette Martin
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland
| | - Pierrick Diana
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland
| | - Antonio Castellon
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland
| | - Aurelien Monge
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland
| | - Pavel Pospisil
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland
| | - Mark Bentley
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland
| | - Philippe A. Guy
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland
| |
Collapse
|
9
|
Hamdalla MA, Rajasekaran S, Grant DF, Măndoiu II. Metabolic pathway predictions for metabolomics: a molecular structure matching approach. J Chem Inf Model 2015; 55:709-18. [PMID: 25668446 DOI: 10.1021/ci500517v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Metabolic pathways are composed of a series of chemical reactions occurring within a cell. In each pathway, enzymes catalyze the conversion of substrates into structurally similar products. Thus, structural similarity provides a potential means for mapping newly identified biochemical compounds to known metabolic pathways. In this paper, we present TrackSM, a cheminformatics tool designed to associate a chemical compound to a known metabolic pathway based on molecular structure matching techniques. Validation experiments show that TrackSM is capable of associating 93% of tested structures to their correct KEGG pathway class and 88% to their correct individual KEGG pathway. This suggests that TrackSM may be a valuable tool to aid in associating previously unknown small molecules to known biochemical pathways and improve our ability to link metabolomics, proteomic, and genomic data sets. TrackSM is freely available at http://metabolomics.pharm.uconn.edu/?q=Software.html .
Collapse
Affiliation(s)
- Mai A Hamdalla
- ‡Computer Science Department, Helwan University, Cairo, Egypt
| | | | | | | |
Collapse
|
10
|
Menikarachchi LC, Hill DW, Hamdalla MA, Mandoiu II, Grant DF. In silico enzymatic synthesis of a 400,000 compound biochemical database for nontargeted metabolomics. J Chem Inf Model 2013; 53:2483-92. [PMID: 23991755 DOI: 10.1021/ci400368v] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Current methods of structure identification in mass-spectrometry-based nontargeted metabolomics rely on matching experimentally determined features of an unknown compound to those of candidate compounds contained in biochemical databases. A major limitation of this approach is the relatively small number of compounds currently included in these databases. If the correct structure is not present in a database, it cannot be identified, and if it cannot be identified, it cannot be included in a database. Thus, there is an urgent need to augment metabolomics databases with rationally designed biochemical structures using alternative means. Here we present the In Vivo/In Silico Metabolites Database (IIMDB), a database of in silico enzymatically synthesized metabolites, to partially address this problem. The database, which is available at http://metabolomics.pharm.uconn.edu/iimdb/, includes ~23,000 known compounds (mammalian metabolites, drugs, secondary plant metabolites, and glycerophospholipids) collected from existing biochemical databases plus more than 400,000 computationally generated human phase-I and phase-II metabolites of these known compounds. IIMDB features a user-friendly web interface and a programmer-friendly RESTful web service. Ninety-five percent of the computationally generated metabolites in IIMDB were not found in any existing database. However, 21,640 were identical to compounds already listed in PubChem, HMDB, KEGG, or HumanCyc. Furthermore, the vast majority of these in silico metabolites were scored as biological using BioSM, a software program that identifies biochemical structures in chemical structure space. These results suggest that in silico biochemical synthesis represents a viable approach for significantly augmenting biochemical databases for nontargeted metabolomics applications.
Collapse
Affiliation(s)
- Lochana C Menikarachchi
- Department of Pharmaceutical Sciences, University of Connecticut , 69 North Eagleville Road, Storrs, Connecticut 06269, United States
| | | | | | | | | |
Collapse
|