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Opperman M, Mason S, van der Westhuizen J, Loots DT, du Preez I. Urinary drug metabolite profiling of tuberculosis treatment failure using proton nuclear magnetic resonance. J Pharm Biomed Anal 2024; 248:116297. [PMID: 38906071 DOI: 10.1016/j.jpba.2024.116297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/03/2024] [Accepted: 06/07/2024] [Indexed: 06/23/2024]
Abstract
The underlying cause of tuberculosis (TB) treatment failure is still largely unknown. A 1H NMR approach was applied to identify and quantify a subset of TB drugs and drug metabolites: ethambutol (EMB), acetyl isoniazid (AcINH), isonicotinic acid, pyrazinamide (PZA), pyrazinoic acid and 5-hydroxy-pyrazinoic acid, from the urine of TB patients. Samples were collected before, during (weeks one, two and four) and after standardised TB treatment. The median concentrations of the EMB and PZA metabolites were comparable between the samples from patients with eventually cured and failed treatment outcomes. The INH metabolites showed comparatively elevated concentrations in the treatment failure patients during and after treatment. Variation in INH metabolite concentrations couldn't be associated with the varying acetylator genotypes, and it is therefore suggested that treatment failure is influenced more so by other conditions, such as environmental factors, or individual variation in other INH metabolic pathways.
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Affiliation(s)
- Monique Opperman
- Human Metabolomics, North-West University (Potchefstroom Campus), Private Bag x6001, Box 269, Potchefstroom 2531, South Africa
| | - Shayne Mason
- Human Metabolomics, North-West University (Potchefstroom Campus), Private Bag x6001, Box 269, Potchefstroom 2531, South Africa
| | - Jessica van der Westhuizen
- Human Metabolomics, North-West University (Potchefstroom Campus), Private Bag x6001, Box 269, Potchefstroom 2531, South Africa
| | - Du Toit Loots
- Human Metabolomics, North-West University (Potchefstroom Campus), Private Bag x6001, Box 269, Potchefstroom 2531, South Africa
| | - Ilse du Preez
- Human Metabolomics, North-West University (Potchefstroom Campus), Private Bag x6001, Box 269, Potchefstroom 2531, South Africa.
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Parihar R, Shukla R, Baishya B, Kalita J, Haldar R, Misra UK. NMR based CSF metabolomics in tuberculous meningitis: correlation with clinical and MRI findings. Metab Brain Dis 2022; 37:773-785. [PMID: 35029797 DOI: 10.1007/s11011-021-00860-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/23/2021] [Indexed: 10/19/2022]
Abstract
We report the potential role of 1H Nuclear Magnetic Resonance (NMR) based metabolomics in tuberculous meningitis (TBM). We also correlate the significant metabolites with clinical-radiological parameters. Forty-three patients with TBM were included, and their severity of meningitis was graded as stages I to III, and patients with positive Mycobacterium tuberculosis or its nucleic acid was considered as definite TBM. 1H NMR-based metabolomic study was performed on (CSF) samples, and the significant metabolites compared to healthy controls were identified. Outcome at three months was defined as death, poor and good based on the modified Rankin Scale. These metabolites were compared between definite and probable groups of TBM, and also correlated with MRI findings. About 11 metabolites were found to be significant for distinguishing TBM from the controls. In TBM, lactate, glutamate, alanine, arginine, 2-hydroxyisobutyrate, formate, and cis-aconitate were upregulated, and glucose, fructose, glutamine, and myo-inositol were downregulated compared to the controls. For differentiating TBM from the controls, the AUC of the ROC curve generated using these significant metabolites was 0.99, with a 95% confidence interval from 0.96 to 1, demonstrating that these metabolites were able to classify cases with good sensitivity and specificity. Lactate concentration in CSF correlated with hemoglobin, CSF glucose, and infarction. The outcome did not correlate with metabolomics parameters. NMR-based CSF metabolomics have a potential role in differentiating TBM from the controls.
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Affiliation(s)
- Rashmi Parihar
- Centre of Biomedical Research, Lucknow, Uttar Pradesh, 226014, India
- Department of Bioinformatics, Dr. A. P. J. Abdul Kalam Technical University, Lucknow, India
| | - Ruchi Shukla
- Department of Neurology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India
| | - Bikash Baishya
- Centre of Biomedical Research, Lucknow, Uttar Pradesh, 226014, India.
| | - Jayantee Kalita
- Department of Neurology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India.
| | - Rudrashish Haldar
- Department of Anaesthesiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Usha Kant Misra
- Department of Neurology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India
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Emwas AH, Szczepski K, Poulson BG, Chandra K, McKay RT, Dhahri M, Alahmari F, Jaremko L, Lachowicz JI, Jaremko M. NMR as a "Gold Standard" Method in Drug Design and Discovery. Molecules 2020; 25:E4597. [PMID: 33050240 PMCID: PMC7594251 DOI: 10.3390/molecules25204597] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
Studying disease models at the molecular level is vital for drug development in order to improve treatment and prevent a wide range of human pathologies. Microbial infections are still a major challenge because pathogens rapidly and continually evolve developing drug resistance. Cancer cells also change genetically, and current therapeutic techniques may be (or may become) ineffective in many cases. The pathology of many neurological diseases remains an enigma, and the exact etiology and underlying mechanisms are still largely unknown. Viral infections spread and develop much more quickly than does the corresponding research needed to prevent and combat these infections; the present and most relevant outbreak of SARS-CoV-2, which originated in Wuhan, China, illustrates the critical and immediate need to improve drug design and development techniques. Modern day drug discovery is a time-consuming, expensive process. Each new drug takes in excess of 10 years to develop and costs on average more than a billion US dollars. This demonstrates the need of a complete redesign or novel strategies. Nuclear Magnetic Resonance (NMR) has played a critical role in drug discovery ever since its introduction several decades ago. In just three decades, NMR has become a "gold standard" platform technology in medical and pharmacology studies. In this review, we present the major applications of NMR spectroscopy in medical drug discovery and development. The basic concepts, theories, and applications of the most commonly used NMR techniques are presented. We also summarize the advantages and limitations of the primary NMR methods in drug development.
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Affiliation(s)
- Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Kacper Szczepski
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Benjamin Gabriel Poulson
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Kousik Chandra
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Ryan T. McKay
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2W2, Canada;
| | - Manel Dhahri
- Biology Department, Faculty of Science, Taibah University, Yanbu El-Bahr 46423, Saudi Arabia;
| | - Fatimah Alahmari
- Nanomedicine Department, Institute for Research and Medical, Consultations (IRMC), Imam Abdulrahman Bin Faisal University (IAU), Dammam 31441, Saudi Arabia;
| | - Lukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Joanna Izabela Lachowicz
- Department of Medical Sciences and Public Health, Università di Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy
| | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
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van Zyl CDW, Loots DT, Solomons R, van Reenen M, Mason S. Metabolic characterization of tuberculous meningitis in a South African paediatric population using 1H NMR metabolomics. J Infect 2020; 81:743-752. [PMID: 32712206 DOI: 10.1016/j.jinf.2020.06.078] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/23/2020] [Accepted: 06/27/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVE To better characterize the cerebrospinal fluid (CSF) metabolic profile of tuberculous meningitis (TBM) cases using a South African paediatric cohort. METHODS 1H NMR metabolomics was used to analyse the CSF of a South African paediatric cohort. Univariate and multivariate statistical analyses were performed to compare a homogeneous control group with a well-defined TBM group. RESULTS Twenty metabolites were identified to discriminate TBM cases from controls. As expected, reduced glucose and elevated lactate were the dominating discriminators. A closer investigation of the CSF metabolic profile yielded 18 metabolites of statistical significance. Ten metabolites (acetate, alanine, choline, citrate, creatinine, isoleucine, lysine, myo-inositol, pyruvate and valine) overlapped with two other prior investigations. Eight metabolites (2-hydroxybutyrate, carnitine, creatine, creatine phosphate, glutamate, glutamine, guanidinoacetate and proline) were unique to our paediatric TBM cohort. CONCLUSIONS Through strict exclusion criteria, quality control checks and data filtering, eight unique CSF metabolites associated with TBM were identified for the first time and linked to: uncontrolled glucose metabolism, upregulated proline and creatine metabolism, detoxification and disrupted glutamate-glutamine cycle in the TBM samples. Associated with oxidative stress and chronic neuroinflammation, our findings collectively imply destabilization, and hence increased permeability, of the blood-brain barrier in the TBM cases.
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Affiliation(s)
- Christiaan De Wet van Zyl
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom 2531, South Africa
| | - Du Toit Loots
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom 2531, South Africa
| | - Regan Solomons
- Department of Pediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Mari van Reenen
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom 2531, South Africa
| | - Shayne Mason
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom 2531, South Africa.
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Albrecht B, Voronina E, Schipke C, Peters O, Parr MK, Díaz-Hernández MD, Schlörer NE. Pursuing Experimental Reproducibility: An Efficient Protocol for the Preparation of Cerebrospinal Fluid Samples for NMR-based Metabolomics and Analysis of Sample Degradation. Metabolites 2020; 10:metabo10060251. [PMID: 32560109 PMCID: PMC7345835 DOI: 10.3390/metabo10060251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/03/2020] [Accepted: 06/11/2020] [Indexed: 12/14/2022] Open
Abstract
NMR-based metabolomics investigations of human biofluids offer great potential to uncover new biomarkers. In contrast to protocols for sample collection and biobanking, procedures for sample preparation prior to NMR measurements are still heterogeneous, thus compromising the comparability of the resulting data. Herein, we present results of an investigation of the handling of cerebrospinal fluid (CSF) samples for NMR metabolomics research. Origins of commonly observed problems when conducting NMR experiments on this type of sample are addressed, and suitable experimental conditions in terms of sample preparation and pH control are discussed. Sample stability was assessed by monitoring the degradation of CSF samples by NMR, hereby identifying metabolite candidates, which are potentially affected by sample storage. A protocol was devised yielding consistent spectroscopic data as well as achieving overall sample stability for robust analysis. We present easy to adopt standard operating procedures with the aim to establish a shared sample handling strategy that facilitates and promotes inter-laboratory comparison, and the analysis of sample degradation provides new insights into sample stability.
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Affiliation(s)
- Benjamin Albrecht
- Department of Chemistry, Universität zu Köln, Greinstr.4, 50939 Köln, Germany; (B.A.); (E.V.)
| | - Elena Voronina
- Department of Chemistry, Universität zu Köln, Greinstr.4, 50939 Köln, Germany; (B.A.); (E.V.)
| | - Carola Schipke
- Charité– Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Experimental & Clinical Research Center (ECRC), Lindenberger Weg 80, 13125 Berlin, Germany;
| | - Oliver Peters
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany;
| | - Maria Kristina Parr
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2-4, 14195 Berlin, Germany;
| | - M. Dolores Díaz-Hernández
- Department of Chemistry, Universität zu Köln, Greinstr.4, 50939 Köln, Germany; (B.A.); (E.V.)
- Correspondence: (M.D.D.-H.); (N.E.S.); Tel.: +49-221-470-3081 (N.E.S.)
| | - Nils E. Schlörer
- Department of Chemistry, Universität zu Köln, Greinstr.4, 50939 Köln, Germany; (B.A.); (E.V.)
- Correspondence: (M.D.D.-H.); (N.E.S.); Tel.: +49-221-470-3081 (N.E.S.)
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Lu J, Wang P, Wang Q, Wang Y, Jiang M. Validated ¹H and 13C Nuclear Magnetic Resonance Methods for the Quantitative Determination of Glycerol in Drug Injections. Molecules 2018; 23:molecules23051177. [PMID: 29762466 PMCID: PMC6099996 DOI: 10.3390/molecules23051177] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/05/2018] [Accepted: 05/07/2018] [Indexed: 11/16/2022] Open
Abstract
In the current study, we employed high-resolution proton and carbon nuclear magnetic resonance spectroscopy (¹H and 13C NMR) for quantitative analysis of glycerol in drug injections without any complex pre-treatment or derivatization on samples. The established methods were validated with good specificity, linearity, accuracy, precision, stability, and repeatability. Our results revealed that the contents of glycerol were convenient to calculate directly via the integration ratios of peak areas with an internal standard in ¹H NMR spectra, while the integration of peak heights were proper for 13C NMR in combination with an external calibration of glycerol. The developed methods were both successfully applied in drug injections. Quantitative NMR methods showed an extensive prospect for glycerol determination in various liquid samples.
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Affiliation(s)
- Jiaxi Lu
- Institute of Traditional Chinese Medicine Research, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China.
| | - Pengli Wang
- Institute of Traditional Chinese Medicine Research, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China.
| | - Qiuying Wang
- Institute of Traditional Chinese Medicine Research, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China.
| | - Yanan Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100006, China.
| | - Miaomiao Jiang
- Institute of Traditional Chinese Medicine Research, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China.
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