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Nishizaki Y, Sugimoto N, Miura T, Asakura K, Suematsu T, Korhonen SP, Lehtivarjo J, Niemitz M, Pauli GF. Quantum Mechanical Quantitative Nuclear Magnetic Resonance Enables Digital Reference Standards at All Magnetic Fields and Enhances qNMR Sustainability. Anal Chem 2024; 96:9790-9798. [PMID: 38829167 PMCID: PMC11190874 DOI: 10.1021/acs.analchem.3c05267] [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] [Received: 11/21/2023] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024]
Abstract
Quantum mechanics (QM)-driven 1H iterative functionalized spin analysis produces HifSA profiles, which encode the complete 1H spin parameters ("nuclear genotype") of analytes of interest. HifSA profiles enable the establishment of digital reference standards (dRS) that are portable, FAIR (findable - accessible - interoperable - reusable), and fit for the purpose of quantitative 1H NMR (qHNMR) analysis at any magnetic field. This approach enhances the sustainability of analytical standards. Moreover, the analyte-specific complete chemical shift and J-coupling information in HifSA-based dRS enable computational quantitation of substances in mixtures via QM-total-line-shape fitting (QM-qHNMR). We present the proof of concept for HifSA-based dRS by resolving the highly overlapping NMR resonances in the experimental spectra ("nuclear phenotypes") of the diastereomeric mixture of (2RS, 4RS)- and (2RS, 4SR)-difenoconazole (DFZ), a widely used antifouling food additive. The underlying 1H spin parameters are highly conserved in various solvents, are robust against variation in measurement temperature, and work across a wide range of magnetic fields. QM-qHNMR analysis of DFZ samples at 80, 400, 600, and 800 MHz showed high congruence with metrological reference values. Furthermore, this study introduces QM-qHNMR combined with chiral shift reagents for the analysis of all four DFZ stereoisomers: (2R, 4R)-, (2S, 4S)-, (2R, 4S)-, and (2S, 4R)-DFZ to perform chiral qHNMR measurements.
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Affiliation(s)
- Yuzo Nishizaki
- National
Institute of Health Sciences, Kawasaki, Kanagawa 210-9501, Japan
| | - Naoki Sugimoto
- National
Institute of Health Sciences, Kawasaki, Kanagawa 210-9501, Japan
| | - Toru Miura
- FUJIFILM
Wako Pure Chemical Corporation, Kawagoe, Saitama 350-1101, Japan
| | | | | | | | | | | | - Guido F. Pauli
- University
of Illinois Chicago, Chicago, Illinois 60612, United States
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2
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Procopio N, Bonicelli A. From flesh to bones: Multi-omics approaches in forensic science. Proteomics 2024; 24:e2200335. [PMID: 38683823 DOI: 10.1002/pmic.202200335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 05/02/2024]
Abstract
Recent advancements in omics techniques have revolutionised the study of biological systems, enabling the generation of high-throughput biomolecular data. These innovations have found diverse applications, ranging from personalised medicine to forensic sciences. While the investigation of multiple aspects of cells, tissues or entire organisms through the integration of various omics approaches (such as genomics, epigenomics, metagenomics, transcriptomics, proteomics and metabolomics) has already been established in fields like biomedicine and cancer biology, its full potential in forensic sciences remains only partially explored. In this review, we have presented a comprehensive overview of state-of-the-art analytical platforms employed in omics research, with specific emphasis on their application in the forensic field for the identification of the cadaver and the cause of death. Moreover, we have conducted a critical analysis of the computational integration of omics approaches, and highlighted the latest advancements in employing multi-omics techniques for forensic investigations.
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Affiliation(s)
- Noemi Procopio
- Research Centre for Field Archaeology and Experimental Taphonomy, School of Law and Policing, University of Central Lancashire, Preston, UK
| | - Andrea Bonicelli
- Research Centre for Field Archaeology and Experimental Taphonomy, School of Law and Policing, University of Central Lancashire, Preston, UK
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3
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Douwenga S, van Olst B, Boeren S, Luo Y, Lai X, Teusink B, Vervoort J, Kleerebezem M, Bachmann H. The hierarchy of sugar catabolization in Lactococcus cremoris. Microbiol Spectr 2023; 11:e0224823. [PMID: 37888986 PMCID: PMC10715065 DOI: 10.1128/spectrum.02248-23] [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: 05/29/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE The availability of nutrients to microorganisms varies considerably between different environments, and changes can occur rapidly. As a general rule, a fast growth rate-typically growth on glucose-is associated with the repression of other carbohydrate utilization genes, but it is not clear to what extent catabolite repression is exerted by other sugars. We investigated the hierarchy of sugar utilization after substrate transitions in Lactococcus cremoris. For this, we determined the proteome and carbohydrate utilization capacity after growth on different sugars. The results show that the preparedness of cells for the utilization of "slower" sugars is not strictly determined by the growth rate. The data point to individual proteins relevant for various sugar transitions and suggest that the evolutionary history of the organism might be responsible for deviations from a strictly growth rate-related sugar catabolization hierarchy.
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Affiliation(s)
- Sieze Douwenga
- TI Food and Nutrition, Wageningen, the Netherlands
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Berdien van Olst
- TI Food and Nutrition, Wageningen, the Netherlands
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Sjef Boeren
- TI Food and Nutrition, Wageningen, the Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Yanzhang Luo
- MAGNEtic resonance research FacilitY (MAGNEFY), Wageningen University & Research, Wageningen, the Netherlands
| | - Xin Lai
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Bas Teusink
- TI Food and Nutrition, Wageningen, the Netherlands
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jacques Vervoort
- TI Food and Nutrition, Wageningen, the Netherlands
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Michiel Kleerebezem
- TI Food and Nutrition, Wageningen, the Netherlands
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, the Netherlands
| | - Herwig Bachmann
- TI Food and Nutrition, Wageningen, the Netherlands
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Microbiology Department, NIZO Food Research, Ede, the Netherlands
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4
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The Pleiotropic Effects of Carbohydrate-Mediated Growth Rate Modifications in Bifidobacterium longum NCC 2705. Microorganisms 2023; 11:microorganisms11030588. [PMID: 36985162 PMCID: PMC10059941 DOI: 10.3390/microorganisms11030588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Bifidobacteria are saccharolytic bacteria that are able to metabolize a relatively large range of carbohydrates through their unique central carbon metabolism known as the “bifid-shunt”. Carbohydrates have been shown to modulate the growth rate of bifidobacteria, but unlike for other genera (e.g., E. coli or L. lactis), the impact it may have on the overall physiology of the bacteria has not been studied in detail to date. Using glucose and galactose as model substrates in Bifidobacterium longum NCC 2705, we established that the strain displayed fast and slow growth rates on those carbohydrates, respectively. We show that these differential growth conditions are accompanied by global transcriptional changes and adjustments of central carbon fluxes. In addition, when grown on galactose, NCC 2705 cells were significantly smaller, exhibited an expanded capacity to import and metabolized different sugars and displayed an increased acid-stress resistance, a phenotypic signature associated with generalized fitness. We predict that part of the observed adaptation is regulated by the previously described bifidobacterial global transcriptional regulator AraQ, which we propose to reflect a catabolite-repression-like response in B. longum. With this manuscript, we demonstrate that not only growth rate but also various physiological characteristics of B. longum NCC 2705 are responsive to the carbon source used for growth, which is relevant in the context of its lifestyle in the human infant gut where galactose-containing oligosaccharides are prominent.
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Tang Y, Friesen JB, Lankin DC, McAlpine JB, Nikolić D, Chen SN, Pauli GF. Geraniol-Derived Monoterpenoid Glucosides from Rhodiola rosea: Resolving Structures by QM-HifSA Methodology. JOURNAL OF NATURAL PRODUCTS 2023; 86:256-263. [PMID: 36744762 PMCID: PMC10404350 DOI: 10.1021/acs.jnatprod.2c00836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Monoterpenoids are integral to the chemical composition of the widely used adaptogenic dietary supplement Rhodiola rosea. The present study expands the chemical space and stereochemical information about these taxon-specific constituents from the isolation and characterization of five geraniol-derived glucosides, 1-5. While 1 and 2 exhibited almost identical NMR spectra and shared the same 2D structure ascribed to the 4-hydroxygeraniolglucoside previously described as rosiridin, the NMR-based Mosher ester method revealed the enantiomeric nature of their aglycone moieties. This marks the first report of enantiomeric aglycones among geraniol derivatives. These findings also resolve the long-standing dispute regarding the absolute configuration of rosiridin and congeneric C-4 hydroxylated geraniols and may help explain incongruent bioactivity reports of R. rosea extract. Moreover, the three previously undescribed geranioloids 3-5 were fully characterized by extensive spectroscopic analysis. Quantum mechanics-driven 1H iterative functionalized spin analysis (QM-HifSA) was performed for all isolates and provides detailed NMR spin parameters, with adequate decimal place precision, which enable the distinction of such close congeners exhibiting near identical NMR spectra with high specificity. The outcomes also reinforce the importance of reporting chemical shifts and coupling constants with adequate decimal place precision as a means of achieving specificity and reproducibility in structural analysis.
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Affiliation(s)
- Yu Tang
- UIC Center for Botanical Dietary Supplements Research, Pharmacognosy Institute, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - J Brent Friesen
- Center for Natural Product Technologies (CENAPT), Pharmacognosy Institute, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Physical Sciences Department, Rosary College of Arts and Sciences, Dominican University, River Forest, Illinois 60305, United States
| | - David C Lankin
- UIC Center for Botanical Dietary Supplements Research, Pharmacognosy Institute, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - James B McAlpine
- UIC Center for Botanical Dietary Supplements Research, Pharmacognosy Institute, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Dejan Nikolić
- UIC Center for Botanical Dietary Supplements Research, Pharmacognosy Institute, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Shao-Nong Chen
- UIC Center for Botanical Dietary Supplements Research and Center for Natural Product Technologies (CENAPT), Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Guido F Pauli
- UIC Center for Botanical Dietary Supplements Research and Center for Natural Product Technologies (CENAPT), Pharmacognosy Institute and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
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6
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Draper SL, McCarney ER. Benchtop nuclear magnetic resonance spectroscopy in forensic chemistry. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:106-129. [PMID: 34286862 DOI: 10.1002/mrc.5197] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/21/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique well known for its ability to elucidate structures and analyse mixtures and its quantitative nature. However, the cost and maintenance of high field NMR instruments prevent its widespread use by forensic chemists. The introduction of benchtop NMR spectrometers to the market operating at 40-80 MHz have a small footprint, are easy to use and cost much less than high field instruments, which makes them well suited to meet the needs of forensic chemists. These modern low field spectrometers are often capable of running multiple nuclei including 1 H, 13 C, 19 F and 31 P; 2D NMR experiments and advanced experiments such as solvent suppression and diffusion-ordered spectroscopy (DOSY) are possible. This has resulted in a number of publications in the area of forensic chemistry using benchtop NMR spectroscopy in the last 5 years that was previously missing from the literature. This mini review summarises this research including examples of benchtop NMR being used to identify and quantify compounds relevant to forensics and some advanced methods that may be used to overcome some of the limitations of these instruments for forensic analysis. Further validation and automation are likely required for widespread uptake of benchtop NMR in industry; however, it has been demonstrated as a useful complement to other analytical techniques commonplace of forensic laboratories.
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Affiliation(s)
- Sarah L Draper
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
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7
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Kil YS, Nam JW. Quantum-Mechanical Driven 1H Iterative Full Spin Analysis Addresses Complex Peak Patterns of Choline Sulfate. ACS OMEGA 2022; 7:42607-42612. [PMID: 36440115 PMCID: PMC9685754 DOI: 10.1021/acsomega.2c06092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Choline and choline esters are essential nutrients in biological systems for carrying out normal functions, such as the modulation of neurotransmission and the formation and maintenance of cell membranes. Choline sulfate is reportedly involved in the defense mechanism of accumulating sulfur resources against sulfur deficiency. Contrary to expectations, a full assignment of the 1H NMR spectrum of choline sulfate has not been reported. The present study pioneered a full assignment by quantum-mechanical driven 1H iterative full spin analysis. The complex peak patterns were analyzed in terms of heteronuclear and non-first-order coupling. The 1H-14N coupling constants, including two-bond coupling, which can be neglected, were accurately determined by iterative optimization. Non-first-order splitting has been described to be due to the presence of magnetically non-equivalent geminal protons. Moreover, in the comparison of the methylene proton resonance patterns of choline sulfate with choline and choline phosphate, the differences in the geminal and vicinal coupling constants were further examined through spectral simulation excluding the heteronuclear coupling. The precise spectral interpretation provided in this study is expected to contribute to future 1H NMR-based qualitative or quantitative studies of choline sulfate-containing sources.
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8
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Kil YS, Baral A, Jeong BS, Laatikainen P, Liu Y, Han AR, Hong MJ, Kim JB, Choi H, Park PH, Nam JW. Combining NMR and MS to Describe Pyrrole-2-Carbaldehydes in Wheat Bran of Radiation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:13002-13014. [PMID: 36167496 DOI: 10.1021/acs.jafc.2c04771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) are indispensable analytical tools to provide chemical fingerprints in metabolomics studies. The present study evaluated radiation breeding wheat lines for chemical changes by non-targeted NMR-based metabolomics analysis of bran extracts. Multivariate analysis following spectral binning suggested pyrrole-2-carbaldehydes as chemical markers of four mutant lines with distinct NMR fingerprints in a δH range of 9.28-9.40 ppm. Further NMR and MS data analysis, along with chromatographic fractionation and synthetic preparation, aimed at structure identification of marker metabolites and identified five pyrrole-2-carbaldehydes. Quantum-mechanical driven 1H iterative full spin analysis (QM-HiFSA) on synthetic pyrrole-2-carbaldehydes provided a precise description of complex peak patterns. Biological evaluation of pyrrole-2-carbaldehydes was performed with nine synthetic products, and six compounds showed hepatoprotective effects via modulation of reactive oxygen species production. Given that three out of five identified in wheat bran of radiation were described for hepatoprotective activity, the value of radiation mutation to greatly enhance pyrrole-2-carbaldehyde production was supported.
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Affiliation(s)
- Yun-Seo Kil
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, South Korea
| | - Ananda Baral
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, South Korea
| | - Byeong-Seon Jeong
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, South Korea
| | | | - Yang Liu
- Product Quality & Analytical Method Department, United States Pharmacopeial Convention, Rockville, Maryland 20852, United States
| | - Ah-Reum Han
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do 56212, South Korea
| | - Min-Jeong Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do 56212, South Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do 56212, South Korea
| | - Hyukjae Choi
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, South Korea
| | - Pil-Hoon Park
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, South Korea
| | - Joo-Won Nam
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, South Korea
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9
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Jing SX, Reis M, Alania Y, McAlpine JB, Chen SN, Bedran-Russo AK, Pauli GF. B-type Proanthocyanidins with Dentin Biomodification Activity from Cocoa ( Theobroma cacao). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12456-12468. [PMID: 36134876 PMCID: PMC9547875 DOI: 10.1021/acs.jafc.2c04288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
To enable translational studies, a scalable preparative isolation scheme was developed for underivatized cocoa (Theobroma cacao) proanthocyanidins (PACs), affording six all-B-type oligomeric PACs, including a new tetramer 4. Their structures, including absolute configuration, were unambiguously established by comprehensive spectroscopic and chemical methods. Evaluation of the PACs' dentin biomodification properties employed dynamic mechanical and infrared spectroscopic analyses in dentin bioassay models. PAC treatment enhanced the biomechanical strength of dentin by 5- to 15-fold compared to untreated dentin. Among the PAC agents, the pentamer, cinnamtannin A3 (6), led to the highest complex modulus value of 131 MPa, whereas the "branched" tetramer, 4, showed the lowest, yet still significant bioactivity. This study of specifically singly linked medium-length oligomeric PACs indicates that the linkage site is paramount in determining the potency of these PACs as dentin biomodifiers.
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Affiliation(s)
- Shu-Xi Jing
- Pharmacognosy Institute and Department of Pharmaceutical
Science, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612,
USA
| | - Mariana Reis
- Department of General Dental Sciences, School of Dentistry,
Marquette University, Milwaukee, WI 53233, USA
| | - Yvette Alania
- Department of General Dental Sciences, School of Dentistry,
Marquette University, Milwaukee, WI 53233, USA
| | - James B. McAlpine
- Pharmacognosy Institute and Department of Pharmaceutical
Science, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612,
USA
| | - Shao-Nong Chen
- Pharmacognosy Institute and Department of Pharmaceutical
Science, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612,
USA
| | - Ana K. Bedran-Russo
- Department of General Dental Sciences, School of Dentistry,
Marquette University, Milwaukee, WI 53233, USA
| | - Guido F. Pauli
- Pharmacognosy Institute and Department of Pharmaceutical
Science, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612,
USA
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10
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Moco S. Studying Metabolism by NMR-Based Metabolomics. Front Mol Biosci 2022; 9:882487. [PMID: 35573745 PMCID: PMC9094115 DOI: 10.3389/fmolb.2022.882487] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/24/2022] [Indexed: 12/12/2022] Open
Abstract
During the past few decades, the direct analysis of metabolic intermediates in biological samples has greatly improved the understanding of metabolic processes. The most used technologies for these advances have been mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. NMR is traditionally used to elucidate molecular structures and has now been extended to the analysis of complex mixtures, as biological samples: NMR-based metabolomics. There are however other areas of small molecule biochemistry for which NMR is equally powerful. These include the quantification of metabolites (qNMR); the use of stable isotope tracers to determine the metabolic fate of drugs or nutrients, unravelling of new metabolic pathways, and flux through pathways; and metabolite-protein interactions for understanding metabolic regulation and pharmacological effects. Computational tools and resources for automating analysis of spectra and extracting meaningful biochemical information has developed in tandem and contributes to a more detailed understanding of systems biochemistry. In this review, we highlight the contribution of NMR in small molecule biochemistry, specifically in metabolic studies by reviewing the state-of-the-art methodologies of NMR spectroscopy and future directions.
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Achanta PS, Niemitz M, Friesen JB, Tadjimukhamedov FK, Bzhelyansky A, Giancaspro GI, Chen SN, Pauli GF. Pharmaceutical analysis by NMR can accommodate strict impurity thresholds: The case of choline. J Pharm Biomed Anal 2022; 214:114709. [PMID: 35339885 DOI: 10.1016/j.jpba.2022.114709] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/23/2022] [Accepted: 03/03/2022] [Indexed: 11/19/2022]
Abstract
The ICH guidelines recommend reporting thresholds for regular impurities in drug substances at the level of 0.05% or 0.03% (w/w) depending on the maximum daily intake. Therefore, any instrumental method of analysis applicable to the impurity analysis should be able to detect and quantify the analytes at those levels. This investigation was designed to verify the suitability of 1H NMR spectroscopy for the detection of impurities, as a first step in the process before attempting quantification. In order to minimize demand on equipment, this study employed a 400 MHz instrument for structural confirmation and signal assignments of choline (1) and O-(2-hydroxyethyl)choline (2), a known impurity. The limit of detection (LOD) of 2 in 10 mg of 1 was established as 0.01% on a 400 MHz instrument and 2% on a 60 MHz (benchtop) NMR spectrometer. Thus, impurities for which quantification is required are readily detected at 400 MHz or above. These results are in contrast to the widespread belief that 1H NMR sensitivity is insufficient for pharmaceutical impurity analysis. The choice of solvent was recognized as a critical parameter for 1H NMR LOD analysis. Furthermore, publicly available NMR raw data (HMDB) proved to be valuable for unveiling the otherwise cryptic information hidden in complex signal patterns via 1H NMR iterative Full Spin Analysis. Finally, the study uncovered the less noticed, yet characteristic, 14N-1H coupling in the -N+(CH3)3 groups, adding strong arguments for the Raw NMR Data Initiative. Collectively, the data prove that the analytical capabilities of high-field NMR easily fulfill the ICH requirements for detection of impurity in the presence of an actual substance of interest which makes it a step closer to achieving regulatory standards.
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Affiliation(s)
- Prabhakar S Achanta
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA; Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA
| | - Matthias Niemitz
- NMR Solutions Limited, Tulliportinkatu 3 A 8, 70100 Kuopio, Finland
| | - J Brent Friesen
- Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA; Center for Natural Product Technologies (CENAPT), College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA; Physical Sciences Department, Rosary College of Arts and Sciences, Dominican University, 7900 West Division Street, River Forest, IL 60305, USA
| | | | - Anton Bzhelyansky
- The United States Pharmacopeial Convention, 12601 Twinbrook Pkwy, Rockville, MD 20852, USA
| | - Gabriel I Giancaspro
- The United States Pharmacopeial Convention, 12601 Twinbrook Pkwy, Rockville, MD 20852, USA
| | - Shao-Nong Chen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA; Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA; Center for Natural Product Technologies (CENAPT), College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA
| | - Guido F Pauli
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA; Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA; Center for Natural Product Technologies (CENAPT), College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA.
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12
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Zhao J, Wang M, Saroja SG, Khan IA. NMR technique and methodology in botanical health product analysis and quality control. J Pharm Biomed Anal 2022; 207:114376. [PMID: 34656935 DOI: 10.1016/j.jpba.2021.114376] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022]
Abstract
Botanicals have played an important role in maintaining human health and well-being throughout history. During the past few decades in particular, the use of botanical health products has gained more popularity. Whereas, quality, safety and efficacy concerns have continuously been critical issues due to the intrinsic chemical complexity of botanicals. Chemical analytical technologies play an imperative role in addressing these issues. Nuclear magnetic resonance (NMR) spectroscopy has proven to be a powerful and useful tool for the investigation of botanical health products. In this review, NMR techniques and methodologies that have been successfully applied to the research and development of botanical health products in all stages, from plants to products, are discussed and summarized. Furthermore, applications of NMR together with other analytical techniques in a variety of domains of botanical health products investigation, such as plant species differentiation, adulteration detection, and bio-activity evaluation, are discussed and illustrated with typical examples. This article provides an overview of the potential uses of NMR techniques and methodologies in an attempt to further promote their recognition and utilization in the field of botanical health products analysis and quality control.
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Affiliation(s)
- Jianping Zhao
- National Center for Natural Products Research (NCNPR), School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Mei Wang
- Natural Products Utilization Research Unit, Agricultural Research Service, US Department of Agriculture, University, MS 38677, USA
| | - Seethapathy G Saroja
- National Center for Natural Products Research (NCNPR), School of Pharmacy, University of Mississippi, University, MS 38677, USA
| | - Ikhlas A Khan
- National Center for Natural Products Research (NCNPR), School of Pharmacy, University of Mississippi, University, MS 38677, USA; Division of Pharmacognosy, Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
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13
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Huang Z, Chen MS, Woroch CP, Markland TE, Kanan MW. A framework for automated structure elucidation from routine NMR spectra. Chem Sci 2021; 12:15329-15338. [PMID: 34976353 PMCID: PMC8635205 DOI: 10.1039/d1sc04105c] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/08/2021] [Indexed: 12/25/2022] Open
Abstract
Methods to automate structure elucidation that can be applied broadly across chemical structure space have the potential to greatly accelerate chemical discovery. NMR spectroscopy is the most widely used and arguably the most powerful method for elucidating structures of organic molecules. Here we introduce a machine learning (ML) framework that provides a quantitative probabilistic ranking of the most likely structural connectivity of an unknown compound when given routine, experimental one dimensional 1H and/or 13C NMR spectra. In particular, our ML-based algorithm takes input NMR spectra and (i) predicts the presence of specific substructures out of hundreds of substructures it has learned to identify; (ii) annotates the spectrum to label peaks with predicted substructures; and (iii) uses the substructures to construct candidate constitutional isomers and assign to them a probabilistic ranking. Using experimental spectra and molecular formulae for molecules containing up to 10 non-hydrogen atoms, the correct constitutional isomer was the highest-ranking prediction made by our model in 67.4% of the cases and one of the top-ten predictions in 95.8% of the cases. This advance will aid in solving the structure of unknown compounds, and thus further the development of automated structure elucidation tools that could enable the creation of fully autonomous reaction discovery platforms. A machine learning model and graph generator were able to accurately predict for the presence of nearly 1000 substructures and the connectivity of small organic molecules from experimental 1D NMR data.![]()
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Affiliation(s)
- Zhaorui Huang
- Department of Chemistry, Stanford University Stanford CA 94305 USA
| | - Michael S Chen
- Department of Chemistry, Stanford University Stanford CA 94305 USA
| | | | | | - Matthew W Kanan
- Department of Chemistry, Stanford University Stanford CA 94305 USA
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14
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Achanta PS, Chen SN, Pauli GF. Plain 1 H nuclear magnetic resonance analysis streamlines the quality control of antiviral favipiravir and congeneric World Health Organization essential medicines. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:746-751. [PMID: 33742475 DOI: 10.1002/mrc.5154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/07/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Favipiravir is an established antiviral that is currently being assessed as an investigational drug for the treatment of COVID-19. Favipiravir is strikingly similar to two molecules that the World Health Organization (WHO) lists as essential medicines, which also consist of a six-membered aromatic N-heterocycle bearing a carboxamide function: the anti-tuberculosis agent, pyrazinamide, and nicotinamide, also known as vitamin B3 . We demonstrate the utility of 1 H nuclear magnetic resonance (NMR) profiling, an emerging pharmacopoeial tool, for the highly specific identification, selective differentiation of congeners, and subsequent detection of drug falsification or adulteration of these medicines. The straightforward comparison of basic 1-D 1 H NMR spectra, obtained with benchtop or advanced NMR instruments alike, offers a rapid identity assay and works independently of physical reference materials. This approach accelerates and advances pharmaceutical quality control measures under situations of increased drug demand and altered economy, such as during a pandemic.
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Affiliation(s)
- Prabhakar S Achanta
- WHO Collaborating Center for Traditional Medicine, Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS) and Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Shao-Nong Chen
- WHO Collaborating Center for Traditional Medicine, Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS) and Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
- Institute for Tuberculosis Research (ITR), College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Guido F Pauli
- WHO Collaborating Center for Traditional Medicine, Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS) and Pharmacognosy Institute, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
- Institute for Tuberculosis Research (ITR), College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
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15
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Bhavaraju S, Taylor D, Niemitz M, Lankin DC, Bzhelyansky A, Giancaspro GI, Liu Y, Pauli GF. NMR-Based Quantum Mechanical Analysis Builds Trust and Orthogonality in Structural Analysis: The Case of a Bisdesmosidic Triglycoside as Withania somnifera Aerial Parts Marker. JOURNAL OF NATURAL PRODUCTS 2021; 84:836-845. [PMID: 33625215 PMCID: PMC8049857 DOI: 10.1021/acs.jnatprod.0c01131] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The present study demonstrates the relationship between conventional and quantum mechanical (QM) NMR spectroscopic analyses, shown here to assist in building a convincingly orthogonal platform for the solution and documentation of demanding structures. Kaempferol-3-O-robinoside-7-O-glucoside, a bisdesmosidic flavonol triglycoside and botanical marker for the aerial parts of Withania somnifera, served as an exemplary case. As demonstrated, QM-based 1H iterative full spin analysis (HiFSA) advances the understanding of both individual nuclear resonance spin patterns and the entire 1H NMR spectrum of a molecule and establishes structurally determinant, numerical HiFSA profiles. The combination of HiFSA with regular 1D 1H NMR spectra allows for simplified yet specific identification tests via comparison of high-quality experimental with QM-calculated spectra. HiFSA accounts for all features encountered in 1H NMR spectra: nonlinear high-order effects, complex multiplets, and their usually overlapped signals. As HiFSA replicates spectrum patterns from field-independent parameters with high accuracy, this methodology can be ported to low-field NMR instruments (40-100 MHz). With its reliance on experimental NMR evidence, the QM approach builds up confidence in structural characterization and potentially reduces identity analyses to simple 1D 1H NMR experiments. This approach may lead to efficient implementation of conclusive identification tests in pharmacopeial and regulatory analyses: from simple organics to complex natural products.
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Affiliation(s)
- Sitaram Bhavaraju
- United States Pharmacopeial Convention, Rockville, Maryland 20852, United States
| | - David Taylor
- United States Pharmacopeial Convention, Rockville, Maryland 20852, United States
| | | | - David C Lankin
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Anton Bzhelyansky
- United States Pharmacopeial Convention, Rockville, Maryland 20852, United States
| | - Gabriel I Giancaspro
- United States Pharmacopeial Convention, Rockville, Maryland 20852, United States
| | - Yang Liu
- United States Pharmacopeial Convention, Rockville, Maryland 20852, United States
| | - Guido F Pauli
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
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