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Nazarski RB. On the Use of Deuterated Organic Solvents without TMS to Report 1H/ 13C NMR Spectral Data of Organic Compounds: Current State of the Method, Its Pitfalls and Benefits, and Related Issues. Molecules 2023; 28:molecules28114369. [PMID: 37298845 DOI: 10.3390/molecules28114369] [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: 04/29/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
The quite popular, simple but imperfect method of referencing NMR spectra to residual 1H and 13C signals of TMS-free deuterated organic solvents (referred to as Method A) is critically discussed for six commonly used NMR solvents with respect to their δH and δC values that exist in the literature. Taking into account the most reliable data, it was possible to recommend 'best' δX values for such secondary internal standards. The position of these reference points on the δ scale strongly depends on the concentration and type of analyte under study and the solvent medium used. For some solvents, chemically induced shifts (CISs) of residual 1H lines were considered, also taking into account the formation of 1:1 molecular complexes (for CDCl3). Typical potential errors that can occur as a result of improper application of Method A are considered in detail. An overview of all found δX values adopted by users of this method revealed a discrepancy of up to 1.9 ppm in δC reported for CDCl3, most likely caused by the CIS mentioned above. The drawbacks of Method A are discussed in relation to the classical use of an internal standard (Method B), two 'instrumental' schemes in which Method A is often implicitly applied, that is, the default Method C using 2H lock frequencies and Method D based on Ξ values, recommended by the IUPAC but only occasionally used for 1H/13C spectra, and external referencing (Method E). Analysis of current needs and opportunities for NMR spectrometers led to the conclusion that, for the most accurate application of Method A, it is necessary to (a) use dilute solutions in a single NMR solvent and (b) to report δX data applied for the reference 1H/13C signals to the nearest 0.001/0.01 ppm to ensure the precise characterization of new synthesized or isolated organic systems, especially those with complex or unexpected structures. However, the use of TMS in Method B is strongly recommended in all such cases.
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Affiliation(s)
- Ryszard B Nazarski
- Theoretical and Structural Chemistry Group, Department of Physical Chemistry, Faculty of Chemistry, University of Lodz, 163/165 Pomorska, 90-236 Łódź, Poland
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Gaudêncio SP, Bayram E, Lukić Bilela L, Cueto M, Díaz-Marrero AR, Haznedaroglu BZ, Jimenez C, Mandalakis M, Pereira F, Reyes F, Tasdemir D. Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation. Mar Drugs 2023; 21:md21050308. [PMID: 37233502 DOI: 10.3390/md21050308] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuration of metabolites with stereogenic centers. This review comprehensively focuses on recent technological and instrumental advances, highlighting the development of methods that alleviate these obstacles, paving the way for accelerating NP discovery towards biotechnological applications. Herein, we emphasize the most innovative high-throughput tools and methods for advancing bioactivity screening, NP chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, and three-dimensional NP structure elucidation.
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Affiliation(s)
- Susana P Gaudêncio
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Engin Bayram
- Institute of Environmental Sciences, Room HKC-202, Hisar Campus, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Lada Lukić Bilela
- Department of Biology, Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina
| | - Mercedes Cueto
- Instituto de Productos Naturales y Agrobiología-CSIC, 38206 La Laguna, Spain
| | - Ana R Díaz-Marrero
- Instituto de Productos Naturales y Agrobiología-CSIC, 38206 La Laguna, Spain
- Instituto Universitario de Bio-Orgánica (IUBO), Universidad de La Laguna, 38206 La Laguna, Spain
| | - Berat Z Haznedaroglu
- Institute of Environmental Sciences, Room HKC-202, Hisar Campus, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Carlos Jimenez
- CICA- Centro Interdisciplinar de Química e Bioloxía, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain
| | - Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, HCMR Thalassocosmos, 71500 Gournes, Crete, Greece
| | - Florbela Pereira
- LAQV, REQUIMTE, Chemistry Department, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Fernando Reyes
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Armilla, Spain
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
- Faculty of Mathematics and Natural Science, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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3
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Judge MT, Ebbels TMD. Problems, principles and progress in computational annotation of NMR metabolomics data. Metabolomics 2022; 18:102. [PMID: 36469142 PMCID: PMC9722819 DOI: 10.1007/s11306-022-01962-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/18/2022] [Indexed: 12/08/2022]
Abstract
BACKGROUND Compound identification remains a critical bottleneck in the process of exploiting Nuclear Magnetic Resonance (NMR) metabolomics data, especially for 1H 1-dimensional (1H 1D) data. As databases of reference compound spectra have grown, workflows have evolved to rely heavily on their search functions to facilitate this process by generating lists of potential metabolites found in complex mixture data, facilitating annotation and identification. However, approaches for validating and communicating annotations are most often guided by expert knowledge, and therefore are highly variable despite repeated efforts to align practices and define community standards. AIM OF REVIEW This review is aimed at broadening the application of automated annotation tools by discussing the key ideas of spectral matching and beginning to describe a set of terms to classify this information, thus advancing standards for communicating annotation confidence. Additionally, we hope that this review will facilitate the growing collaboration between chemical data scientists, software developers and the NMR metabolomics community aiding development of long-term software solutions. KEY SCIENTIFIC CONCEPTS OF REVIEW We begin with a brief discussion of the typical untargeted NMR identification workflow. We differentiate between annotation (hypothesis generation, filtering), and identification (hypothesis testing, verification), and note the utility of different NMR data features for annotation. We then touch on three parts of annotation: (1) generation of queries, (2) matching queries to reference data, and (3) scoring and confidence estimation of potential matches for verification. In doing so, we highlight existing approaches to automated and semi-automated annotation from the perspective of the structural information they utilize, as well as how this information can be represented computationally.
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Affiliation(s)
- Michael T Judge
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, 131 Sir Alexander Fleming Building, South Kensington Campus, London, UK
| | - Timothy M D Ebbels
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, 131 Sir Alexander Fleming Building, South Kensington Campus, London, UK.
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New Techniques of Structure Elucidation for Sesquiterpenes. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2021; 114:253-311. [PMID: 33792862 DOI: 10.1007/978-3-030-59444-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The most significant new techniques that have been used in the twenty-first century for the structure elucidation of sesquiterpenes and some derivatives are reviewed in this chapter. A distinctive feature of these methodologies is the combination of accurate experimental measurements with theoretical data obtained by molecular modeling calculations that allow to visualize, understand, and quantify many structural characteristics. This has been the case for NMR spectroscopy, which has expanded its potential for solving complex structural problems by means of comparison with quantum mechanical molecular models. Ab initio and density functional theory calculations of chemical shifts, coupling constants, and residual chemical shift anisotropies have played important roles in the solution of many structures of sesquiterpenes. The assignments of their absolute configurations by evaluation of calculated and experimental chiroptical properties as electronic and vibrational circular dichroism are also reviewed. This chapter also includes the use of X-ray diffraction analysis with emphasis on calculations of the Flack and Hooft parameters, which are applicable to all molecules that crystallize in non-centrosymmetric space groups. The accurate molecular models of sesquiterpenes, validated by concordance with their experimental properties, are nowadays essential for the interpretation of the effects of these natural products on biological systems.
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Czernek J, Brus J. A Volumetric Analysis of the 1H NMR Chemical Shielding in Supramolecular Systems. Int J Mol Sci 2021; 22:3333. [PMID: 33805147 PMCID: PMC8036968 DOI: 10.3390/ijms22073333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 11/16/2022] Open
Abstract
The liquid state NMR chemical shift of protons is a parameter frequently used to characterize host-guest complexes. Its theoretical counterpart, that is, the 1H NMR chemical shielding affected by the solvent (1H CS), may provide important insights into spatial arrangements of supramolecular systems, and it can also be reliably obtained for challenging cases of an aggregation of aromatic and antiaromatic molecules in solution. This computational analysis is performed for the complex of coronene and an antiaromatic model compound in acetonitrile by employing the GIAO-B3LYP-PCM approach combined with a saturated basis set. Predicted 1H CS values are used to generate volumetric data, whose properties are thoroughly investigated. The 1H CS isosurface, corresponding to a value of the proton chemical shift taken from a previous experimental study, is described. The presence of the 1H CS isosurface should be taken into account in deriving structural information about supramolecular hosts and their encapsulation of small molecules.
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Affiliation(s)
- Jiří Czernek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square #2, 16206 Prague, Czech Republic
| | - Jiří Brus
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square #2, 16206 Prague, Czech Republic
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6
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Quantum mechanical NMR full spin analysis in pharmaceutical identity testing and quality control. J Pharm Biomed Anal 2020; 192:113601. [PMID: 33049645 DOI: 10.1016/j.jpba.2020.113601] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 02/03/2023]
Abstract
Issues related to pharmaceutical quality are arising at an alarming rate. Pharmaceutical quality concerns both the Active Pharmaceutical Ingredients (APIs) and the Finished Drug Product/ Formulation. Recently, there has been a significant increase in the number of reports of harmful impurities in marketed drug formulations. Impurities range from solvents, reactants, adulterants, and catalysts to synthetic byproducts. Quality concerns in commercial preparations may also arise due to shelf life stability. Furthermore, a number of falsified and substandard drug cases have been reported. Most of the techniques which are currently in place can, at best, detect the impurities, but cannot identify them unless they are already known and can be compared to a standard. On the other hand, 1H NMR spectroscopy detects all the hydrogen containing species, typically provides information to elucidate structures partially or even completely, and through its absolute quantitative capabilities even can detect the presence hydrogen-free species indirectly. The structural properties that produce 1H NMR signals as characteristic representations of a given molecule are the chemical shifts (δ in ppm) and coupling constants (J in Hz). Along with the line widths (ω1/2 in Hz), these parameters are bound to both the molecule and the NMR experimental conditions by quantum mechanical (QM) principles. This means that the 1H NMR spectra of APIs can be precisely calculated and compared to the experimental data. This review explains how 1H NMR spectroscopy coupled with Full Spin Analysis can contribute towards the quality control of pharmaceuticals by improving structural dereplication and achieving simultaneous quantification of both APIs and their contaminants.
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Tang Y, Friesen JB, Lankin DC, McAlpine JB, Nikolić D, Niemitz M, Seigler DS, Graham J, Chen SN, Pauli GF. Quantum Mechanics-Based Structure Analysis of Cyclic Monoterpene Glycosides from Rhodiola rosea. JOURNAL OF NATURAL PRODUCTS 2020; 83:1950-1959. [PMID: 32463230 PMCID: PMC7384765 DOI: 10.1021/acs.jnatprod.0c00212] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
NMR- and MS-guided metabolomic mining for new phytoconstituents from a widely used dietary supplement, Rhodiola rosea, yielded two new (+)-myrtenol glycosides, 1 and 2, and two new cuminol glycosides, 3 and 4, along with three known analogues, 5-7. The structures of the new compounds were determined by extensive spectroscopic data analysis. Quantum mechanics-driven 1H iterative full spin analysis (QM-HiFSA) decoded the spatial arrangement of the methyl groups in 1 and 2, as well as other features not recognizable by conventional methods, including higher order spin-coupling effects. Expanding applied HiFSA methodology to monoterpene glycosides advances the toolbox for stereochemical assignments, facilitates their structural dereplication, and provides a more definitive reference point for future phytochemical and biological studies of R. rosea as a resilience botanical. Application of a new NMR data analysis software package, CT, for QM-based iteration of NMR spectra is also discussed.
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Affiliation(s)
- Yu Tang
- UIC/NIH Center for Botanical Dietary Supplements Research, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, United States
| | - J. Brent Friesen
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS) and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, United States
- Physical Sciences Department, Rosary College of Arts and Sciences, Dominican University, River Forest, IL 60305, United States
| | - David C. Lankin
- UIC/NIH Center for Botanical Dietary Supplements Research, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, United States
| | - James B. McAlpine
- UIC/NIH Center for Botanical Dietary Supplements Research, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, United States
| | - Dejan Nikolić
- UIC/NIH Center for Botanical Dietary Supplements Research, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, United States
| | | | - David S. Seigler
- Department of Plant Biology, University of Illinois at Urbana Champaign, Urbana Champaign, IL 61801, United States
| | - James Graham
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS) and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, United States
| | - Shao-Nong Chen
- UIC/NIH Center for Botanical Dietary Supplements Research, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, United States
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS) and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, United States
| | - Guido F. Pauli
- UIC/NIH Center for Botanical Dietary Supplements Research, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, United States
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS) and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, United States
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Zanardi MM, Marcarino MO, Sarotti AM. Redefining the Impact of Boltzmann Analysis in the Stereochemical Assignment of Polar and Flexible Molecules by NMR Calculations. Org Lett 2019; 22:52-56. [DOI: 10.1021/acs.orglett.9b03866] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- María M. Zanardi
- Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, S2002QEO Rosario, Argentina
| | - Maribel O. Marcarino
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - Ariel M. Sarotti
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
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9
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Phansalkar RS, Nam JW, Leme AA, Gan LS, Zhou B, McAlpine JB, Chen SN, Bedran-Russo AK, Pauli GF. Proanthocyanidin Dimers and Trimers from Vitis vinifera Provide Diverse Structural Motifs for the Evaluation of Dentin Biomodification. JOURNAL OF NATURAL PRODUCTS 2019; 82:2387-2399. [PMID: 31433178 PMCID: PMC6899061 DOI: 10.1021/acs.jnatprod.8b00953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Aimed at exploring the dentin biomodification potential of proanthocyanidins (PACs) for the development of dental biomaterials, this study reports the phytochemical and dental evaluation of nine B-type PACs from grape seed extract (GSE). Out of seven isolated dimers (1-7), four new compounds (2, 3, 5, and 6) involved relatively rare ent-catechin or ent-epicatechin monomeric flavan-3-ol units. Low-temperature NMR analyses conducted along with phloroglucinolysis and electronic circular dichroism enabled unequivocal structural characterization and stereochemical assignment. Additionally, one known (8) and one new (9) B-type trimer were characterized. Differential 13C NMR chemical shifts (Δδ) were used to determine the absolute configuration of 9, relative to the dimers 1 and 2 as the possible constituent subunits. Compared to the dimers, the trimers showed superior dentin biomodification properties. The dimers, 1-7, exhibited pronounced differences in their collagenase inhibitory activity, while enhancing dentin stiffness comparably. This suggests that PAC structural features such as the degree of polymerization, relative and absolute configuration have a differential influence on enhancement of dentin biomechanical and biostability. As mechanical enhancement to dentin and resistance to proteolytic biodegradation are both essential properties functional and stable dentin substrate, the structurally closely related PACs suggest a new metric, the dentin biomodification potential (DBMP) that may rationalize both properties.
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Affiliation(s)
- Rasika S. Phansalkar
- Department of Medicinal Chemistry and Pharmacognosy, and Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), University of Illinois at Chicago, College of Pharmacy, Chicago, Illinois 60612, United States
| | - Joo-Won Nam
- Department of Medicinal Chemistry and Pharmacognosy, and Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), University of Illinois at Chicago, College of Pharmacy, Chicago, Illinois 60612, United States
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
| | - Ariene A. Leme
- Department of Restorative Dentistry, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Li-She Gan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 31005, China
| | - Bin Zhou
- Department of Medicinal Chemistry and Pharmacognosy, and Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), University of Illinois at Chicago, College of Pharmacy, Chicago, Illinois 60612, United States
| | - James B. McAlpine
- Department of Medicinal Chemistry and Pharmacognosy, and Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), University of Illinois at Chicago, College of Pharmacy, Chicago, Illinois 60612, United States
| | - Shao-Nong Chen
- Department of Medicinal Chemistry and Pharmacognosy, and Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), University of Illinois at Chicago, College of Pharmacy, Chicago, Illinois 60612, United States
| | - Ana K. Bedran-Russo
- Department of Restorative Dentistry, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Guido F. Pauli
- Department of Medicinal Chemistry and Pharmacognosy, and Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), University of Illinois at Chicago, College of Pharmacy, Chicago, Illinois 60612, United States
- Corresponding Author: Tel: +1 (312) 355-1949. Fax: +1 (312) 355-2693.
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Kutateladze AG, Holt T, Reddy DS. Natural Products Containing the Oxetane and Related Moieties Present Additional Challenges for Structure Elucidation: A DU8+ Computational Case Study. J Org Chem 2019; 84:7575-7586. [DOI: 10.1021/acs.joc.9b01005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Andrei G. Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Tina Holt
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - D. Sai Reddy
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
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McAlpine JB, Chen SN, Kutateladze A, MacMillan JB, Appendino G, Barison A, Beniddir MA, Biavatti MW, Bluml S, Boufridi A, Butler MS, Capon RJ, Choi YH, Coppage D, Crews P, Crimmins MT, Csete M, Dewapriya P, Egan JM, Garson MJ, Genta-Jouve G, Gerwick WH, Gross H, Harper MK, Hermanto P, Hook JM, Hunter L, Jeannerat D, Ji NY, Johnson TA, Kingston DGI, Koshino H, Lee HW, Lewin G, Li J, Linington RG, Liu M, McPhail KL, Molinski TF, Moore BS, Nam JW, Neupane RP, Niemitz M, Nuzillard JM, Oberlies NH, Ocampos FMM, Pan G, Quinn RJ, Reddy DS, Renault JH, Rivera-Chávez J, Robien W, Saunders CM, Schmidt TJ, Seger C, Shen B, Steinbeck C, Stuppner H, Sturm S, Taglialatela-Scafati O, Tantillo DJ, Verpoorte R, Wang BG, Williams CM, Williams PG, Wist J, Yue JM, Zhang C, Xu Z, Simmler C, Lankin DC, Bisson J, Pauli GF. The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research. Nat Prod Rep 2019; 36:35-107. [PMID: 30003207 PMCID: PMC6350634 DOI: 10.1039/c7np00064b] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Indexed: 12/20/2022]
Abstract
Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.
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Affiliation(s)
- James B McAlpine
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - Shao-Nong Chen
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - Andrei Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - John B MacMillan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Giovanni Appendino
- Dipartimento di Scienze Chimiche, Alimentari, Farmaceutiche e Farmacologiche, Universita` del Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
| | | | - Mehdi A Beniddir
- Équipe "Pharmacognosie-Chimie des Substances Naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Maique W Biavatti
- Department of Pharmaceutical Sciences, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Stefan Bluml
- University of Southern California, Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Asmaa Boufridi
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Mark S Butler
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Robert J Capon
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Young H Choi
- Division of Pharmacognosy, Section Metabolomics, Institute of Biology, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - David Coppage
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Michael T Crimmins
- Kenan and Caudill Laboratories of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marie Csete
- University of Southern California, Huntington Medical Research Institutes, 99 N. El Molino Ave., Pasadena, CA 91101, USA
| | - Pradeep Dewapriya
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Joseph M Egan
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Mary J Garson
- School of Chemistry and Molecular Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Grégory Genta-Jouve
- C-TAC, UMR 8638 CNRS, Faculté de Pharmacie de Paris, Paris-Descartes University, Sorbonne, Paris Cité, 4, Aveue de l'Observatoire, 75006 Paris, France
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA 92093, USA and Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Eberhard Karls University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Mary Kay Harper
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Precilia Hermanto
- NMR Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - James M Hook
- NMR Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Luke Hunter
- NMR Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Damien Jeannerat
- University of Geneva, Department of Organic Chemistry, 30 quai E. Ansermet, CH 1211 Geneva 4, Switzerland
| | - Nai-Yun Ji
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road 17, Yantai 264003, People's Republic of China
| | - Tyler A Johnson
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - David G I Kingston
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Hiroyuki Koshino
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Guy Lewin
- Équipe "Pharmacognosie-Chimie des Substances Naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Jie Li
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA
| | - Tadeusz F Molinski
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Bradley S Moore
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA 92093, USA and Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Joo-Won Nam
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Ram P Neupane
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Matthias Niemitz
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Jean-Marc Nuzillard
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Nicholas H Oberlies
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | | | - Guohui Pan
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - D Sai Reddy
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Jean-Hugues Renault
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - José Rivera-Chávez
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Wolfgang Robien
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Carla M Saunders
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Thomas J Schmidt
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Christoph Seger
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Ben Shen
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Christoph Steinbeck
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Hermann Stuppner
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Sonja Sturm
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Orazio Taglialatela-Scafati
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Dean J Tantillo
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Robert Verpoorte
- Division of Pharmacognosy, Section Metabolomics, Institute of Biology, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Bin-Gui Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road 17, Yantai 264003, People's Republic of China and Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Craig M Williams
- School of Chemistry and Molecular Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Philip G Williams
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Julien Wist
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Jian-Min Yue
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Chen Zhang
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Zhengren Xu
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Charlotte Simmler
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - David C Lankin
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - Jonathan Bisson
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - Guido F Pauli
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
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12
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Tantillo DJ. Questions in natural products synthesis research that can (and cannot) be answered using computational chemistry. Chem Soc Rev 2018; 47:7845-7850. [PMID: 29900461 PMCID: PMC6205925 DOI: 10.1039/c8cs00298c] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Questions of relevance to those working in the field of natural products synthesis that can be answered, at least in part, using computational chemistry approaches are described. Illustrative examples are provided, as are descriptions of limitations.
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Affiliation(s)
- Dean J Tantillo
- Department of Chemistry, University of California - Davis, Davis, CA 95616, USA.
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13
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Kutateladze AG, Kuznetsov DM, Beloglazkina AA, Holt T. Addressing the Challenges of Structure Elucidation in Natural Products Possessing the Oxirane Moiety. J Org Chem 2018; 83:8341-8352. [DOI: 10.1021/acs.joc.8b01027] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Andrei G. Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Dmitry M. Kuznetsov
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | | | - Tina Holt
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
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14
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Patiny L, Zasso M, Kostro D, Bernal A, Castillo AM, Bolaños A, Asencio MA, Pellet N, Todd M, Schloerer N, Kuhn S, Holmes E, Javor S, Wist J. The C6H6 NMR repository: An integral solution to control the flow of your data from the magnet to the public. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:520-528. [PMID: 28981966 DOI: 10.1002/mrc.4669] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/21/2017] [Accepted: 09/27/2017] [Indexed: 05/12/2023]
Abstract
NMR is a mature technique that is well established and adopted in a wide range of research facilities from laboratories to hospitals. This accounts for large amounts of valuable experimental data that may be readily exported into a standard and open format. Yet the publication of these data faces an important issue: Raw data are not made available; instead, the information is slimed down into a string of characters (the list of peaks). Although historical limitations of technology explain this practice, it is not acceptable in the era of Internet. The idea of modernizing the strategy for sharing NMR data is not new, and some repositories exist, but sharing raw data is still not an established practice. Here, we present a powerful toolbox built on recent technologies that runs inside the browser and provides a means to store, share, analyse, and interact with original NMR data. Stored spectra can be streamlined into the publication pipeline, to improve the revision process for instance. The set of tools is still basic but is intended to be extended. The project is open source under the Massachusetts Institute of Technology (MIT) licence.
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Affiliation(s)
- Luc Patiny
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Michaël Zasso
- Institut de Police Scientifique, Ecole des Sciences Criminelles, University of Lausanne, Lausanne, CH-1015, Switzerland
| | - Daniel Kostro
- Institut de Police Scientifique, Ecole des Sciences Criminelles, University of Lausanne, Lausanne, CH-1015, Switzerland
| | - Andrés Bernal
- Departamento de Ciencias Básicas y Modelado, Universidad Jorge Tadeo Lozano, Bogotá, Colombia
| | - Andrés M Castillo
- Escuela de Ingeniería de Sistemas y Computación, Universidad del Valle, Cali, Valle, Colombia
| | | | - Miguel A Asencio
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Norman Pellet
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Matthew Todd
- School of Chemistry, The University of Sydney, Sydney, 2006, NSW, Australia
| | - Nils Schloerer
- Department of Chemistry, University of Cologne, Köln, Germany
| | - Stefan Kuhn
- Department of Chemistry, University of Cologne, Köln, Germany
| | - Elaine Holmes
- Division of Computational and Systems Medicine, Imperial College, London, UK
| | - Sacha Javor
- Department of Chemistry and Biochemistry, University of Bern, Bern, 3012, Switzerland
| | - Julien Wist
- Chemistry Department, Universidad del Valle, Cali, Valle, Colombia
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15
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Patiny L, Bolaños A, Castillo AM, Bernal A, Wist J. Teaching NMR spectra analysis with nmr.cheminfo.org. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:529-534. [PMID: 29582456 DOI: 10.1002/mrc.4733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
Teaching spectra analysis and structure elucidation requires students to get trained on real problems. This involves solving exercises of increasing complexity and when necessary using computational tools. Although desktop software packages exist for this purpose, nmr.cheminfo.org platform offers students an online alternative. It provides a set of exercises and tools to help solving them. Only a small number of exercises are currently available, but contributors are invited to submit new ones and suggest new types of problems.
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Affiliation(s)
- Luc Patiny
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH, -1015, Switzerland
| | - Alejandro Bolaños
- Chemistry Department, Universidad del Valle, A.A. 25360, Cali, Valle, Colombia
| | - Andrés M Castillo
- Computer and Systems Engineering School, Universidad del Valle, A.A. 25360, Cali, Valle, Colombia
| | - Andrés Bernal
- Departamento de Ciencias Básicas, Universidad Jorge Tadeo Lozano, Bogotá, Colombia
| | - Julien Wist
- Chemistry Department, Universidad del Valle, A.A. 25360, Cali, Valle, Colombia
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16
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Ibrahim N, Allart-Simon I, De Nicola GR, Iori R, Renault JH, Rollin P, Nuzillard JM. Advanced NMR-Based Structural Investigation of Glucosinolates and Desulfoglucosinolates. JOURNAL OF NATURAL PRODUCTS 2018; 81:323-334. [PMID: 29431450 DOI: 10.1021/acs.jnatprod.7b00776] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Glucosinolates (GLs) constitute a class of plant secondary metabolites that are characteristic of the order Brassicales. They each contain a common hydrophilic moiety connected to a mostly hydrophobic side chain whose constitution is the most frequent structural variant. Their transformations by myrosinases lead to intensively studied and highly reactive compounds of biological relevancy. In other respects, the enzymatic desulfation of GLs produces derivatives (DS-GLs) that are useful for GL analysis. A collection of 31 compounds, GLs and DS-GLs, representing 17 different side chains was established in order to report accurate descriptions of the molecules' 1H-, 13C-, and 15N-NMR parameters. The descriptions of the 1H-NMR spectra were achieved using the PERCH software, which accurately analyzed the complex coupling patterns that arose from strongly coupled nuclei. The chemical shift assignments were supported by 2D COSY, HSQC, and HMBC spectra. The impact of desulfation and the influence of the nature of the side chains on the chemical shift values are discussed. The results of the spectroscopic analysis and the 3D chemical-structure models of the studied molecules were grouped in structure-and-data-format (SDF) files. The NMR parameters were also collected in a simple text file, a spreadsheet file, and a relational database.
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Affiliation(s)
- Nada Ibrahim
- Institut de Chimie Moléculaire de Reims, UMR 7312, SFR CAP'SANTE, Université de Reims Champagne-Ardenne and CNRS , F-51687 Reims, France
| | - Ingrid Allart-Simon
- Institut de Chimie Moléculaire de Reims, UMR 7312, SFR CAP'SANTE, Université de Reims Champagne-Ardenne and CNRS , F-51687 Reims, France
| | - Gina R De Nicola
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Agricoltura e Ambiente (CREA-AA) , Via di Corticella 133, 40128 Bologna, Italy
| | - Renato Iori
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Agricoltura e Ambiente (CREA-AA) , Via di Corticella 133, 40128 Bologna, Italy
| | - Jean-Hugues Renault
- Institut de Chimie Moléculaire de Reims, UMR 7312, SFR CAP'SANTE, Université de Reims Champagne-Ardenne and CNRS , F-51687 Reims, France
| | - Patrick Rollin
- Institut de Chimie Organique et Analytique, UMR 7311, Université d'Orléans and CNRS , BP 6759, F-45067 Orléans, France
| | - Jean-Marc Nuzillard
- Institut de Chimie Moléculaire de Reims, UMR 7312, SFR CAP'SANTE, Université de Reims Champagne-Ardenne and CNRS , F-51687 Reims, France
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17
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Li F, Zhang Z, Zhang G, Che Q, Zhu T, Gu Q, Li D. Determination of Taichunamide H and Structural Revision of Taichunamide A. Org Lett 2018; 20:1138-1141. [PMID: 29400467 DOI: 10.1021/acs.orglett.8b00061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new indole alkaloid, named taichunamide H (1), was obtained from cultures of the fungus Aspergillus versicolor. With observation of a carbon resonance with a chemical shift of 190.4 ppm, generally thought to be a carbonyl, the structure of 1 was initially proposed to be a diastereomer of taichunamide A that contains a unique spiro-azetidine moiety. Further analysis of compound 1 using X-ray diffraction showed that the spiro-azetidine moiety should be revised as a fused-imine-containing pyrrole ring, with the resonance at 190.4 ppm assigned as an imine carbon. Accordingly, the structure of taichunamide A was also revised.
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Affiliation(s)
- Feng Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , Qingdao 266003, P. R. China
| | - Zhenzhen Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , Qingdao 266003, P. R. China
| | - Guojian Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , Qingdao 266003, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology , Qingdao, 266237, P. R. China
| | - Qian Che
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , Qingdao 266003, P. R. China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , Qingdao 266003, P. R. China
| | - Qianqun Gu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , Qingdao 266003, P. R. China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , Qingdao 266003, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology , Qingdao, 266237, P. R. China
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18
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Sarotti AM. Structural revision of two unusual rhamnofolane diterpenes, curcusones I and J, by means of DFT calculations of NMR shifts and coupling constants. Org Biomol Chem 2018; 16:944-950. [DOI: 10.1039/c7ob02916k] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The structures of two unusual rhamnofolane diterpenes, curcusones I and J, have been revised using quantum calculations of NMR shifts.
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Affiliation(s)
- Ariel M. Sarotti
- Instituto de Química Rosario (CONICET)
- Facultad de Ciencias Bioquímicas y Farmacéuticas
- Universidad Nacional de Rosario
- Rosario 2000
- Argentina
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19
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Gao W, McAlpine JB, Choules MP, Napolitano JG, Lankin DC, Simmler C, Ho NA, Lee H, Suh JW, Burton IW, Cho S, Franzblau SG, Chen SN, Pauli GF. Structural Sequencing of Oligopeptides Aided by 1H Iterative Full-Spin Analysis. JOURNAL OF NATURAL PRODUCTS 2017; 80:2630-2643. [PMID: 29035048 DOI: 10.1021/acs.jnatprod.7b00207] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This report describes an approach using 1H NMR iterative full-spin analysis (HiFSA) to extract definitive structural information on unknown peptides from 1D 1H NMR data. By comparing the experimental data and HiFSA fingerprint of a known analogue, it is possible to isolate the characteristic 1H subspectrum of the different amino acids and, thus, elucidate the structure of the peptide. To illustrate this methodology, a comprehensive analysis of five new anti-Mycobacterium tuberculosis peptides (2-6), all analogues of ecumicin (1), was carried out. The method was validated by demonstrating congruence of the HiFSA-based structures with all available data, including MS and 2D NMR. The highly reproducible HiFSA fingerprints of the new ∼1600 amu peptides were generated in this process. Besides oligo-peptides, the HiFSA sequencing approach could be extended to all oligomeric compounds consisting of chains of monomers lacking H-H spin-spin coupling across the moieties. HiFSA sequencing is capable of differentiating complex oligomers that exhibit minor structural differences such as shifted hydoxyl or methyl groups. Because it employs the basic and most sensitive 1D 1H NMR experiment, HiFSA sequencing enables the exploration of peptide analogues up to at least 2000 amu, even with basic contemporary spectrometers and when only sub-milligram amounts of isolates are available.
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Affiliation(s)
- Wei Gao
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - James B McAlpine
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - Mary P Choules
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - José G Napolitano
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Center for Natural Product Technologies, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - David C Lankin
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Center for Natural Product Technologies, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - Charlotte Simmler
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Center for Natural Product Technologies, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - Ngoc Anh Ho
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University , Yongin, Gyeonggi-do 17458, South Korea
| | - Hanki Lee
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University , Yongin, Gyeonggi-do 17458, South Korea
| | - Joo-Won Suh
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University , Yongin, Gyeonggi-do 17458, South Korea
- Division of Biosciences and Bioinformatics, Myongji University , Yongin, Gyeonggi-do 17458, South Korea
| | - Ian W Burton
- Institute for Aquatic and Crop Resource Development, National Research Council , Halifax, Nova Scotia B3H 3Z1, Canada
| | - Sanghyun Cho
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - Shao-Nong Chen
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Center for Natural Product Technologies, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - Guido F Pauli
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Center for Natural Product Technologies, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
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Kutateladze AG, Kuznetsov DM. Triquinanes and Related Sesquiterpenes Revisited Computationally: Structure Corrections of Hirsutanols B and D, Hirsutenol E, Cucumin B, Antrodins C–E, Chondroterpenes A and H, Chondrosterins C and E, Dichrocephone A, and Pethybrene. J Org Chem 2017; 82:10795-10802. [DOI: 10.1021/acs.joc.7b02018] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Andrei G. Kutateladze
- Department of Chemistry and
Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Dmitry M. Kuznetsov
- Department of Chemistry and
Biochemistry, University of Denver, Denver, Colorado 80208, United States
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21
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Nikolić D. CASMI 2016: A manual approach for dereplication of natural products using tandem mass spectrometry. PHYTOCHEMISTRY LETTERS 2017; 21:292-296. [PMID: 28966697 PMCID: PMC5613954 DOI: 10.1016/j.phytol.2017.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The Critical Assessment of Small Molecule Identification (CASMI) contest is an initiative designed as an unbiased test of manual and automated strategies for the identification of small molecules from raw mass spectrometric data. In this contest, the participants are provided a set of high resolution MS and MS/MS data and asked to identify the unknown structure. CASMI 2016 is the fourth round of this contest in which the author participated in Category 1: Best Identification of Natural Products using a manual approach. The provided high resolution mass spectrometric data were interpreted manually using a combination of fragment and neutral loss analysis, literature consultation, manual database searches, deductive logic and experience. Out of 18 challenges, the author submitted correct structures as lead candidates for 14 challenges and 2nd ranked candidate for four challenges and was declared the winner of this category Pitfalls and challenges encountered during data interpretation are discussed.
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Affiliation(s)
- Dejan Nikolić
- UIC/NIH Center for Botanical Dietary Supplements Research, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois College of Pharmacy, 833 S. Wood St. M/C 781, Chicago, IL 60612
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22
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Melchor-Martínez EM, Silva-Mares DA, Torres-López E, Waksman-Minsky N, Pauli GF, Chen SN, Niemitz M, Sánchez-Castellanos M, Toscano A, Cuevas G, Rivas-Galindo VM. Stereochemistry of a Second Riolozane and Other Diterpenoids from Jatropha dioica. JOURNAL OF NATURAL PRODUCTS 2017; 80:2252-2262. [PMID: 28771358 PMCID: PMC5714812 DOI: 10.1021/acs.jnatprod.7b00193] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The dichloromethane extract of the roots of Jatropha dioica afforded riolozatrione (1) and a C-6 epimer of riolozatrione, 6-epi-riolozatrione (2), as a new structure and only the second reported riolozane diterpenoid. The two known diterpenoids jatrophatrione (3) and citlalitrione (4) were also isolated and characterized. Both epimers 1 and 2 are genuine plant constituents, with 2 likely being the biosynthesis precursor of 1 due to the tendency for the quantitative transformation of 2 into 1 under base catalysis. The structural characterization and distinction of the stereoisomers utilized 1H iterative full-spin analysis, yielding complete J-correlation maps that were represented as quantum interaction and linkage tables. The absolute configuration of compounds 1-4 was established by means of vibrational circular dichroism and via X-ray diffraction analysis for 1, 2, and 4. Additionally, the cytotoxic and antiherpetic in vitro activities of the isolates were evaluated.
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Affiliation(s)
- Elda M. Melchor-Martínez
- Facultad de Medicina, Universidad Autónoma de Nuevo León, Avenida Madero y Aguirre Pequeno, Col. Mitras Centro s/n, Monterrey, N.L., C.P. 64460, México
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, C. P. 04510, México
| | - David A. Silva-Mares
- Facultad de Medicina, Universidad Autónoma de Nuevo León, Avenida Madero y Aguirre Pequeno, Col. Mitras Centro s/n, Monterrey, N.L., C.P. 64460, México
| | - Ernesto Torres-López
- Facultad de Medicina, Universidad Autónoma de Nuevo León, Avenida Madero y Aguirre Pequeno, Col. Mitras Centro s/n, Monterrey, N.L., C.P. 64460, México
| | - Noemí Waksman-Minsky
- Facultad de Medicina, Universidad Autónoma de Nuevo León, Avenida Madero y Aguirre Pequeno, Col. Mitras Centro s/n, Monterrey, N.L., C.P. 64460, México
| | - Guido F. Pauli
- Center for Natural Product Technologies (CENAPT), Department of Medicinal Chemistry and Pharmacognosy, and Institute for Tuberculosis Research; College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Shao-Nong Chen
- Center for Natural Product Technologies (CENAPT), Department of Medicinal Chemistry and Pharmacognosy, and Institute for Tuberculosis Research; College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | | | - Mariano Sánchez-Castellanos
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, C. P. 04510, México
| | - Alfredo Toscano
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, C. P. 04510, México
| | - Gabriel Cuevas
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, C. P. 04510, México
| | - Verónica M. Rivas-Galindo
- Facultad de Medicina, Universidad Autónoma de Nuevo León, Avenida Madero y Aguirre Pequeno, Col. Mitras Centro s/n, Monterrey, N.L., C.P. 64460, México
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23
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Polavarapu PL, Covington CL, Raghavan V. To Avoid Chasing Incorrect Chemical Structures of Chiral Compounds: Raman Optical Activity and Vibrational Circular Dichroism Spectroscopies. Chemphyschem 2017; 18:2459-2465. [DOI: 10.1002/cphc.201700764] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Prasad L. Polavarapu
- Department of Chemistry Vanderbilt University 7330 Stevenson Center Nashville TN 37235 USA
| | - Cody L. Covington
- Department of Chemistry Vanderbilt University 7330 Stevenson Center Nashville TN 37235 USA
| | - Vijay Raghavan
- Department of Chemistry Vanderbilt University 7330 Stevenson Center Nashville TN 37235 USA
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24
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AbouZid SF, Ahmed HS, Moawad AS, Owis AI, Chen SN, Nachtergael A, McAlpine JB, Brent Friesen J, Pauli GF. Chemotaxonomic and biosynthetic relationships between flavonolignans produced by Silybum marianum populations. Fitoterapia 2017; 119:175-184. [PMID: 28392269 PMCID: PMC5532885 DOI: 10.1016/j.fitote.2017.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 03/28/2017] [Accepted: 04/04/2017] [Indexed: 11/29/2022]
Abstract
Flavonolignans constitute an important class of plant secondary metabolites formed by oxidative coupling of one flavonoid and one phenylpropanoid moiety. The standardized flavonolignan-rich extract prepared from the fruits of Silybum marianum is known as silymarin and has long been used medicinally, prominently as an antihepatotoxic and as a chemopreventive agent. Principal component analysis of the variation in flavonolignan content in S. marianum samples collected from different locations in Egypt revealed biosynthetic relationships between the flavonolignans. Silybin A, silybin B, and silychristin are positively correlated as are silydianin, isosilychristin, and isosilybin B. The detection of silyamandin in the extracts of S. marianum correlates with isosilychristin and silydianin content. The positive correlation between silydianin, isosilychristin, and silyamandin was demonstrated using quantitative 1H nuclear magnetic resonance spectroscopy (qHNMR). These correlations can be interpreted as evidence for the involvement of a flavonoid radical in the biosynthesis of the flavonolignans in S. marianum. The predominance of silybins A & B over isosilybin A & B in the silybin-rich samples is discussed in light of the relative stabilities of their respective radical flavonoid biosynthetic intermediates.
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Affiliation(s)
- Sameh F AbouZid
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62111, Egypt.
| | - Hayam S Ahmed
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62111, Egypt
| | - Abeer S Moawad
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62111, Egypt
| | - Asmaa I Owis
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62111, Egypt
| | - Shao-Nong Chen
- UIC/NIH Center for Botanical Dietary Supplements Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., M/C 781, Chicago, IL 60612, United States; Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., M/C 781, Chicago, IL 60612, United States
| | - Amandine Nachtergael
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., M/C 781, Chicago, IL 60612, United States
| | - James B McAlpine
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., M/C 781, Chicago, IL 60612, United States
| | - J Brent Friesen
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., M/C 781, Chicago, IL 60612, United States; Physical Sciences Department, Rosary College of Arts and Sciences, Dominican University, 7900 West Division Street, River Forest, IL 60305, United States
| | - Guido F Pauli
- UIC/NIH Center for Botanical Dietary Supplements Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., M/C 781, Chicago, IL 60612, United States; Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., M/C 781, Chicago, IL 60612, United States
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25
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Kutateladze AG, Reddy DS. High-Throughput in Silico Structure Validation and Revision of Halogenated Natural Products Is Enabled by Parametric Corrections to DFT-Computed 13C NMR Chemical Shifts and Spin-Spin Coupling Constants. J Org Chem 2017; 82:3368-3381. [PMID: 28339201 DOI: 10.1021/acs.joc.7b00188] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Halogenated natural products constitute diverse and promising feedstock for molecular pharmaceuticals. However, their solution-structure elucidation by NMR presents several challenges, including the lack of fast methods to compute 13C chemical shifts for carbons bearing heavy atoms. We show that parametric corrections to DFT-computed chemical shifts in conjunction with rff-computed spin-spin coupling constants allow for fast and reliable screening of a large number of reported halogenated natural products, resulting in expedient structure validation or revision. In this paper, we examine more than 100 structures of halogenated terpenoids and other natural products with the new parametric approach and demonstrate that the accuracy of the combined method is sufficient to identify misassignments and suggest revisions in most cases (16 structures are revised). As the 1D 1H and 13C NMR data are ubiquitous and most routinely used in solution structure elucidation, this fast and efficient two-criterion method (nuclear spin-spin coupling and 13C chemical shifts) which we term DU8+ is recommended as the first essential step in structure assignment and validation.
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Affiliation(s)
- Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
| | - D Sai Reddy
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
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26
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Wist J. Complex mixtures by NMR and complex NMR for mixtures: experimental and publication challenges. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:22-28. [PMID: 27668407 DOI: 10.1002/mrc.4533] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/14/2016] [Accepted: 09/22/2016] [Indexed: 06/06/2023]
Abstract
Untargeted strategies have changed the rules of the game in complex mixture analysis, introducing an amazing potential for medical and biological applications that is just starting to be tapped. But with great power come great challenges; although untargeted mixture analysis opens the road for many exciting possibilities, the road is still full of perils. On the one hand, this article highlights some of the difficulties that need to be sorted for mixture analysis by NMR to fulfill its potential, along with insight on how they may be managed. Highlighted key points include the need for 'computer friendly' solutions for sharing data, experimental design and algorithm to facilitate the steady growth of knowledge and modeling ability in the field, and the need for large-scale studies to improve confidence in newly identified biomarkers. On the other hand, the second part of this article presents some breakthroughs in NMR experiments that, when combined, may modify the landscape of mixture analysis. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Julien Wist
- Chemistry Department, Universidad del Valle, Cali, Colombia
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27
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Jeannerat D. Human- and computer-accessible 2D correlation data for a more reliable structure determination of organic compounds. Future roles of researchers, software developers, spectrometer managers, journal editors, reviewers, publisher and database managers toward artificial-intelligence analysis of NMR spectra. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:7-14. [PMID: 27642110 DOI: 10.1002/mrc.4527] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 05/12/2023]
Abstract
The introduction of a universal data format to report the correlation data of 2D NMR spectra such as COSY, HSQC and HMBC spectra will have a large impact on the reliability of structure determination of small organic molecules. These lists of assigned cross peaks will bridge signals found in NMR 1D and 2D spectra and the assigned chemical structure. The record could be very compact, human and computer readable so that it can be included in the supplementary material of publications and easily transferred into databases of scientific literature and chemical compounds. The records will allow authors, reviewers and future users to test the consistency and, in favorable situations, the uniqueness of the assignment of the correlation data to the associated chemical structures. Ideally, the data format of the correlation data should include direct links to the NMR spectra to make it possible to validate their reliability and allow direct comparison of spectra. In order to take the full benefits of their potential, the correlation data and the NMR spectra should therefore follow any manuscript in the review process and be stored in open-access database after publication. Keeping all NMR spectra, correlation data and assigned structures together at all time will allow the future development of validation tools increasing the reliability of past and future NMR data. This will facilitate the development of artificial intelligence analysis of NMR spectra by providing a source of data than can be used efficiently because they have been validated or can be validated by future users. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Damien Jeannerat
- Department of Organic Chemistry, University of Geneva, Geneva 4, Switzerland
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28
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Oguadinma P, Bilodeau F, LaPlante SR. NMR strategies to support medicinal chemistry workflows for primary structure determination. Bioorg Med Chem Lett 2017; 27:242-247. [DOI: 10.1016/j.bmcl.2016.11.066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/21/2016] [Accepted: 11/22/2016] [Indexed: 02/03/2023]
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29
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Buevich AV, Elyashberg ME. Synergistic Combination of CASE Algorithms and DFT Chemical Shift Predictions: A Powerful Approach for Structure Elucidation, Verification, and Revision. JOURNAL OF NATURAL PRODUCTS 2016; 79:3105-3116. [PMID: 28006916 DOI: 10.1021/acs.jnatprod.6b00799] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Structure elucidation of complex natural products and new organic compounds remains a challenging problem. To support this endeavor, CASE (computer-assisted structure elucidation) expert systems were developed. These systems are capable of generating a set of all possible structures consistent with an ensemble of 2D NMR data followed by selection of the most probable structure on the basis of empirical NMR chemical shift prediction. However, in some cases, empirical chemical shift prediction is incapable of distinguishing the correct structure. Herein, we demonstrate for the first time that the combination of CASE and density functional theory (DFT) methods for NMR chemical shift prediction allows the determination of the correct structure even in difficult situations. An expert system, ACD/Structure Elucidator, was used for the CASE analysis. This approach has been tested on three challenging natural products: aquatolide, coniothyrione, and chiral epoxyroussoenone. This work has demonstrated that the proposed synergistic approach is an unbiased, reliable, and very efficient structure verification and de novo structure elucidation method that can be applied to difficult structural problems when other experimental methods would be difficult or impossible to use.
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Affiliation(s)
- Alexei V Buevich
- Department of Discovery and Preclinical Sciences, Process Research and Development, NMR Structure Elucidation, Merck & Co., Inc. , Kenilworth, New Jersey 07033, United States
| | - Mikhail E Elyashberg
- Advanced Chemistry Development (ACD/Laboratories) , Akademik Bakulev Street 6, 117513 Moscow, Russian Federation
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30
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Grimblat N, Kaufman TS, Sarotti AM. Computational Chemistry Driven Solution to Rubriflordilactone B. Org Lett 2016; 18:6420-6423. [DOI: 10.1021/acs.orglett.6b03318] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicolás Grimblat
- Instituto de Química
Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas
y Farmacéuticas, Universidad Nacional de Rosario, Suipacha
531 (S2002LRK) Rosario S2002LRK, Argentina
| | - Teodoro S. Kaufman
- Instituto de Química
Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas
y Farmacéuticas, Universidad Nacional de Rosario, Suipacha
531 (S2002LRK) Rosario S2002LRK, Argentina
| | - Ariel M. Sarotti
- Instituto de Química
Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas
y Farmacéuticas, Universidad Nacional de Rosario, Suipacha
531 (S2002LRK) Rosario S2002LRK, Argentina
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31
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Rakshith D, Santosh P, Pradeep TP, Gurudatt DM, Baker S, Yashavantha Rao HC, Pasha A, Satish S. Application of Bioassay-Guided Fractionation Coupled with a Molecular Approach for the Dereplication of Antimicrobial Metabolites. Chromatographia 2016. [DOI: 10.1007/s10337-016-3188-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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32
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Reddy DS, Kutateladze AG. Structure Revision of an Acorane Sesquiterpene Cordycepol A. Org Lett 2016; 18:4860-4863. [DOI: 10.1021/acs.orglett.6b02341] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D. Sai Reddy
- Department of Chemistry and
Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Andrei G. Kutateladze
- Department of Chemistry and
Biochemistry, University of Denver, Denver, Colorado 80208, United States
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33
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Bisson J, Simmler C, Chen SN, Friesen JB, Lankin DC, McAlpine JB, Pauli GF. Dissemination of original NMR data enhances reproducibility and integrity in chemical research. Nat Prod Rep 2016; 33:1028-33. [PMID: 27197893 PMCID: PMC5001890 DOI: 10.1039/c6np00022c] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The notion of data transparency is gaining a strong awareness among the scientific community. The availability of raw data is actually regarded as a fundamental way to advance science by promoting both integrity and reproducibility of research outcomes. Particularly, in the field of natural product and chemical research, NMR spectroscopy is a fundamental tool for structural elucidation and quantification (qNMR). As such, the accessibility of original NMR data, i.e., Free Induction Decays (FIDs), fosters transparency in chemical research and optimizes both peer review and reproducibility of reports by offering the fundamental tools to perform efficient structural verification. Although original NMR data are known to contain a wealth of information, they are rarely accessible along with published data. This viewpoint discusses the relevance of the availability of original NMR data as part of good research practices not only to promote structural correctness, but also to enhance traceability and reproducibility of both chemical and biological results.
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Affiliation(s)
- Jonathan Bisson
- Center for Natural Product Technologies (CENAPT), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, USA.
| | - Charlotte Simmler
- Center for Natural Product Technologies (CENAPT), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, USA.
| | - Shao-Nong Chen
- Center for Natural Product Technologies (CENAPT), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, USA.
| | - J Brent Friesen
- Center for Natural Product Technologies (CENAPT), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, USA.
| | - David C Lankin
- Center for Natural Product Technologies (CENAPT), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, USA.
| | - James B McAlpine
- Center for Natural Product Technologies (CENAPT), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, USA.
| | - Guido F Pauli
- Center for Natural Product Technologies (CENAPT), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, USA.
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