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Becette OB, Marino JP, Brinson RG. Structural Fingerprinting of Antisense Oligonucleotide Therapeutics by Solution NMR Spectroscopy. Pharm Res 2023; 40:1373-1382. [PMID: 36195820 DOI: 10.1007/s11095-022-03403-x] [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: 06/14/2022] [Accepted: 09/21/2022] [Indexed: 10/10/2022]
Abstract
PURPOSE Antisense oligonucleotide (ASO) therapeutics are an emerging class of biopharmaceuticals to treat and prevent diseases, particularly those involving "undruggable" protein targets. Impurities generated throughout the ASO drug manufacturing and formulation pipeline can be detrimental to drug safety and efficacy. Therefore, analytical techniques are needed to rigorously characterize these molecules for quality assurance purposes. METHODS We demonstrate 1D and 2D nuclear magnetic resonance (NMR) spectroscopy methods that can generate high-resolution structural "fingerprints" of ASOs. RESULTS AND CONCLUSIONS 1D 1H and 31P measurements are shown to provide rapid initial assessment of the ASO integrity. In particular, a well-resolved pair of 31P signals arising from the 5´-end of the phosphorodiamidate morpholino oligomer (PMO) are sensitive to complex formation and oligomerization state. 2D 1H-1H, 1H-13C, and 1H-15 N experiments, although less sensitive, are further shown to enable resonance assignment, which will allow the tracking of structural changes at high-resolution during the drug development and manufacturing processes. We further anticipate that the described NMR approaches will be broadly applicable to fully formulated ASO therapeutics, including modalities other than PMOs.
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Affiliation(s)
- Owen B Becette
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland, 20850, USA
| | - John P Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland, 20850, USA
| | - Robert G Brinson
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland, 20850, USA.
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2
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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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3
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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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4
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Ray KK, Verma AR, Gonzalez RL, Kinz-Thompson CD. Inferring the shape of data: a probabilistic framework for analysing experiments in the natural sciences. Proc Math Phys Eng Sci 2022; 478:20220177. [PMID: 37767180 PMCID: PMC10521765 DOI: 10.1098/rspa.2022.0177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 09/26/2022] [Indexed: 09/29/2023] Open
Abstract
A critical step in data analysis for many different types of experiments is the identification of features with theoretically defined shapes in N -dimensional datasets; examples of this process include finding peaks in multi-dimensional molecular spectra or emitters in fluorescence microscopy images. Identifying such features involves determining if the overall shape of the data is consistent with an expected shape; however, it is generally unclear how to quantitatively make this determination. In practice, many analysis methods employ subjective, heuristic approaches, which complicates the validation of any ensuing results-especially as the amount and dimensionality of the data increase. Here, we present a probabilistic solution to this problem by using Bayes' rule to calculate the probability that the data have any one of several potential shapes. This probabilistic approach may be used to objectively compare how well different theories describe a dataset, identify changes between datasets and detect features within data using a corollary method called Bayesian Inference-based Template Search; several proof-of-principle examples are provided. Altogether, this mathematical framework serves as an automated 'engine' capable of computationally executing analysis decisions currently made by visual inspection across the sciences.
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Affiliation(s)
- Korak Kumar Ray
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Anjali R. Verma
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Ruben L. Gonzalez
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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5
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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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7
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Burns DC, Reynolds WF. Minimizing the risk of deducing wrong natural product structures from NMR data. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:500-533. [PMID: 33855734 DOI: 10.1002/mrc.4933] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 06/12/2023]
Abstract
There continues to be a disturbing number of natural products reported in the literature whose structures are incorrect. At least in part, this reflects the fact that many natural product chemists have limited formal nuclear magnetic resonance training. Gaps in training and lack of awareness regarding the challenges and ambiguities associated with two-dimensional nuclear magnetic resonance data interpretation can easily lead to errors in structure elucidation. The purpose of this tutorial is to point out some of these issues, highlight the kinds of errors that have been made and provide specific advice on how to avoid these missteps such that the risk of reporting a wrong structure is minimized.
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Affiliation(s)
- Darcy C Burns
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - William F Reynolds
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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8
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Wu D, Carillo KJ, Shie JJ, Yu SSF, Tzou DLM. Resolving Entangled JH-H-Coupling Patterns for Steroidal Structure Determinations by NMR Spectroscopy. Molecules 2021; 26:molecules26092643. [PMID: 33946512 PMCID: PMC8124291 DOI: 10.3390/molecules26092643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 11/16/2022] Open
Abstract
For decades, high-resolution 1H NMR spectroscopy has been routinely utilized to analyze both naturally occurring steroid hormones and synthetic steroids, which play important roles in regulating physiological functions in humans. Because the 1H signals are inevitably superimposed and entangled with various JH–H splitting patterns, such that the individual 1H chemical shift and associated JH–H coupling identities are hardly resolved. Given this, applications of thess information for elucidating steroidal molecular structures and steroid/ligand interactions at the atomic level were largely restricted. To overcome, we devoted to unraveling the entangled JH–H splitting patterns of two similar steroidal compounds having fully unsaturated protons, i.e., androstanolone and epiandrosterone (denoted as 1 and 2, respectively), in which only hydroxyl and ketone substituents attached to C3 and C17 were interchanged. Here we demonstrated that the JH–H values deduced from 1 and 2 are universal and applicable to other steroids, such as testosterone, 3β, 21-dihydroxygregna-5-en-20-one, prednisolone, and estradiol. On the other hand, the 1H chemical shifts may deviate substantially from sample to sample. In this communication, we propose a simple but novel scheme for resolving the complicate JH–H splitting patterns and 1H chemical shifts, aiming for steroidal structure determinations.
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Affiliation(s)
- Danni Wu
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 11529, Taiwan; (D.W.); (K.J.C.); (J.-J.S.); (S.S.-F.Y.)
| | - Kathleen Joyce Carillo
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 11529, Taiwan; (D.W.); (K.J.C.); (J.-J.S.); (S.S.-F.Y.)
- International Graduate Program, SCST, Academia Sinica, Nankang, Taipei 11529, Taiwan
- The Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu 30013, Taiwan
| | - Jiun-Jie Shie
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 11529, Taiwan; (D.W.); (K.J.C.); (J.-J.S.); (S.S.-F.Y.)
| | - Steve S.-F. Yu
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 11529, Taiwan; (D.W.); (K.J.C.); (J.-J.S.); (S.S.-F.Y.)
| | - Der-Lii M. Tzou
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 11529, Taiwan; (D.W.); (K.J.C.); (J.-J.S.); (S.S.-F.Y.)
- Department of Applied Chemistry, National Chia-Yi University, Chia-Yi 60004, Taiwan
- Correspondence:
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9
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Nam JW, Phansalkar RS, Lankin DC, McAlpine JB, Leme-Kraus AA, Bedran-Russo AK, Chen SN, Pauli GF. Targeting Trimeric and Tetrameric Proanthocyanidins of Cinnamomum verum Bark as Bioactives for Dental Therapies. JOURNAL OF NATURAL PRODUCTS 2020; 83:3287-3297. [PMID: 33151073 PMCID: PMC8041212 DOI: 10.1021/acs.jnatprod.0c00570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The present study elucidated the structures of three A-type tri- and tetrameric proanthocyanidins (PACs) isolated from Cinnamomum verum bark to the level of absolute configuration and determined their dental bioactivity using two therapeutically relevant bioassays. After selecting a PAC oligomer fraction via a biologically diverse bioassay-guided process, in tandem with centrifugal partition chromatography, phytochemical studies led to the isolation of PAC oligomers that represent the main bioactive principles of C. verum: two A-type tetrameric PACs, epicatechin-(2β→O→7,4β→8)-epicatechin-(4β→6)-epicatechin-(2β→O→7,4β→8)-catechin (1) and parameritannin A1 (2), together with a trimer, cinnamtannin B1 (3). Structure determination of the underivatized proanthocyanidins utilized a combination of HRESIMS, ECD, 1D/2D NMR, and 1H iterative full spin analysis data and led to NMR-based evidence for the deduction of absolute configuration in constituent catechin and epicatechin monomeric units.
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Affiliation(s)
- Joo-Won Nam
- Department of Pharmaceutical Sciences, Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), University of Illinois at Chicago, Chicago, IL 60612, United States
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
| | - Rasika S. Phansalkar
- Department of Pharmaceutical Sciences, Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), University of Illinois at Chicago, Chicago, IL 60612, United States
| | - David C. Lankin
- Department of Pharmaceutical Sciences, Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), University of Illinois at Chicago, Chicago, IL 60612, United States
| | - James B. McAlpine
- Department of Pharmaceutical Sciences, Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), University of Illinois at Chicago, Chicago, IL 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, United States
| | - Ariene A. Leme-Kraus
- Department of Restorative Dentistry, College of Dentistry, University of Illinois at Chicago, Chicago, IL 60612, United States
| | - Ana K. Bedran-Russo
- Department of Restorative Dentistry, College of Dentistry, University of Illinois at Chicago, Chicago, IL 60612, United States
- Department of General Dental Sciences, School of Dentistry, Marquette University, Milwaukee, WI 53233, United States
| | - Shao-Nong Chen
- Department of Pharmaceutical Sciences, Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), University of Illinois at Chicago, Chicago, IL 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, United States
| | - Guido F. Pauli
- Department of Pharmaceutical Sciences, Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), University of Illinois at Chicago, Chicago, IL 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, United States
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10
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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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11
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Thapa P, Gu Y, Kil YS, Baek SC, Kim KH, Han AR, Seo EK, Choi H, Chang JH, Nam JW. N-Acetyldopamine derivatives from Periostracum Cicadae and their regulatory activities on Th1 and Th17 cell differentiation. Bioorg Chem 2020; 102:104095. [PMID: 32721777 DOI: 10.1016/j.bioorg.2020.104095] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/04/2020] [Accepted: 07/08/2020] [Indexed: 01/07/2023]
Abstract
Bioassay-guided fractionation of a 90% ethanol extract of Periostracum Cicadae led to the isolation of two new N-acetyldopamine dimers (1a/1b) along with six known dimers (2a/2b, 3a/3b, and 4a/4b) and two monomers (5a/5b); compounds 2a/2b, 4a/4b and 5a/5b were newly isolated from this material. All compounds were isolated as enantiomeric mixtures and each enantiomer was successfully separated by chiral-phase HPLC. The structures including absolute configurations were confirmed by high-resolution electrospray ionization mass spectrometry (HR-ESIMS), 1D/2D nuclear magnetic resonance (NMR) spectroscopy, 1H iterative Full Spin Analysis (HiFSA), and electronic circular dichroism (ECD) spectroscopy. Subsequently, the bioactivities of these isolates were evaluated via CD4+ T cell differentiations, which are critical for immune responses and inflammation. The results revealed that compound 5b was observed to enhance the IFN-γ+ Th1 differentiation, which may have a potential for cancer immunotherapy.
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Affiliation(s)
- Punam Thapa
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Republic of Korea
| | - Ye Gu
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Republic of Korea
| | - Yun-Seo Kil
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Republic of Korea
| | - Su Cheol Baek
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ah-Reum Han
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Eun Kyoung Seo
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Hyukjae Choi
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Republic of Korea
| | - Jae-Hoon Chang
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Republic of Korea.
| | - Joo-Won Nam
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Republic of Korea; Department of Pharmaceutical Sciences, Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, United States.
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12
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Sels D, Dashti H, Mora S, Demler O, Demler E. Quantum approximate Bayesian computation for NMR model inference. NAT MACH INTELL 2020; 2:396-402. [PMID: 33163858 PMCID: PMC7643990 DOI: 10.1038/s42256-020-0198-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 06/02/2020] [Indexed: 12/30/2022]
Abstract
Recent technological advances may lead to the development of small scale quantum computers capable of solving problems that cannot be tackled with classical computers. A limited number of algorithms has been proposed and their relevance to real world problems is a subject of active investigation. Analysis of many-body quantum system is particularly challenging for classical computers due to the exponential scaling of Hilbert space dimension with the number of particles. Hence, solving problems relevant to chemistry and condensed matter physics are expected to be the first successful applications of quantum computers. In this paper, we propose another class of problems from the quantum realm that can be solved efficiently on quantum computers: model inference for nuclear magnetic resonance (NMR) spectroscopy, which is important for biological and medical research. Our results are based on three interconnected studies. Firstly, we use methods from classical machine learning to analyze a dataset of NMR spectra of small molecules. We perform a stochastic neighborhood embedding and identify clusters of spectra, and demonstrate that these clusters are correlated with the covalent structure of the molecules. Secondly, we propose a simple and efficient method, aided by a quantum simulator, to extract the NMR spectrum of any hypothetical molecule described by a parametric Heisenberg model. Thirdly, we propose a simple variational Bayesian inference procedure for extracting Hamiltonian parameters of experimentally relevant NMR spectra.
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Affiliation(s)
- Dries Sels
- Department of Physics, Harvard University, 17 Oxford st., Cambridge, MA 02138, USA
- Theory of quantum and complex systems, Universiteit Antwerpen, B-2610 Antwerpen, Belgium
| | - Hesam Dashti
- Division of Preventive Medicine, Brigham and Womens Hospital, Harvard Medical School, 900 Commonwealth Ave., Boston, MA 02215, USA
| | - Samia Mora
- Division of Preventive Medicine, Brigham and Womens Hospital, Harvard Medical School, 900 Commonwealth Ave., Boston, MA 02215, USA
- Division of Cardiovascular Medicine, Brigham and Womens Hospital, Harvard Medical School, 900 Commonwealth Ave., Boston, MA 02215, USA
| | - Olga Demler
- Division of Preventive Medicine, Brigham and Womens Hospital, Harvard Medical School, 900 Commonwealth Ave., Boston, MA 02215, USA
| | - Eugene Demler
- Department of Physics, Harvard University, 17 Oxford st., Cambridge, MA 02138, USA
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Choules MP, Bisson J, Simmler C, McAlpine JB, Giancaspro G, Bzhelyansky A, Niemitz M, Pauli GF. NMR reveals an undeclared constituent in custom synthetic peptides. J Pharm Biomed Anal 2020; 178:112915. [PMID: 31671336 PMCID: PMC6913887 DOI: 10.1016/j.jpba.2019.112915] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/27/2019] [Accepted: 10/05/2019] [Indexed: 10/25/2022]
Abstract
Whereas generic, LC-based pharmaceutical control quality procedures depend largely on the detection mode and can be particularly 'blind' to certain impurities, NMR is a more versatile and, thus, often more judicious detector. While adulteration presents ever-evolving challenges for the analysis of active pharmaceutical ingredients (APIs) and finished products sold in the worldwide (online) marketplace, research chemicals are usually trusted rather than being considered flawed or even adulterated. This report shows how NMR analysis uncovered the unanticipated presence of substantial amounts of mannitol (20 and 43% w/w) as undeclared constituent in two custom synthetic peptides, DR and DRVYI, that were sourced commercially. Quantitative 1H NMR (qHNMR) readily detected the contaminant, even on a 60 MHz benchtop instrument, and quantified the highly polar and UV-transparent adulterant. Quantum-mechanical 1H iterative Full Spin Analysis (HiFSA) not only achieved unambiguous identification of both the mannitol and the peptides, but also confirmed the quantitative results. The cases show that experimental verification supersedes trust in both pharmaceutical and research QC. They also highlight the promising utility of both established high-field and recently re-evolving low-field benchtop qHNMR. The unanticipated findings remind manufacturers and researchers alike about the advantages of including/performing NMR and qNMR with routine CofA documentation and/or verification of research grade chemicals. Especially when done jointly, this can greatly improve confidence in research and help streamline the pharmaceutical QC toolbox.
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Affiliation(s)
- Mary P Choules
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, 833 S. Wood St., Chicago 60612, IL, USA; Institute for Tuberculosis Research (ITR), University of Illinois College of Pharmacy, 833 S. Wood St., Chicago, 60612 IL, USA
| | - Jonathan Bisson
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, 833 S. Wood St., Chicago 60612, IL, USA; Institute for Tuberculosis Research (ITR), University of Illinois College of Pharmacy, 833 S. Wood St., Chicago, 60612 IL, USA; Center for Natural Product Technologies (CENAPT), University of Illinois College of Pharmacy, 833 S. Wood St., Chicago, 60612, IL, USA
| | - Charlotte Simmler
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, 833 S. Wood St., Chicago 60612, IL, USA; Institute for Tuberculosis Research (ITR), University of Illinois College of Pharmacy, 833 S. Wood St., Chicago, 60612 IL, USA; Center for Natural Product Technologies (CENAPT), University of Illinois College of Pharmacy, 833 S. Wood St., Chicago, 60612, IL, USA
| | - James B McAlpine
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, 833 S. Wood St., Chicago 60612, IL, USA; Institute for Tuberculosis Research (ITR), University of Illinois College of Pharmacy, 833 S. Wood St., Chicago, 60612 IL, USA; Center for Natural Product Technologies (CENAPT), University of Illinois College of Pharmacy, 833 S. Wood St., Chicago, 60612, IL, USA; Program for Collaboration in the Pharmaceutical Sciences (PCRPS), University of Illinois College of Pharmacy, 833 S. Wood St., Chicago, 60612, IL, USA
| | - Gabriel Giancaspro
- The United States Pharmacopeial Convention, 12601 Twinbrook Pkwy., Rockville, 20852, MD, USA
| | - Anton Bzhelyansky
- The United States Pharmacopeial Convention, 12601 Twinbrook Pkwy., Rockville, 20852, MD, USA
| | | | - Guido F Pauli
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, 833 S. Wood St., Chicago 60612, IL, USA; Institute for Tuberculosis Research (ITR), University of Illinois College of Pharmacy, 833 S. Wood St., Chicago, 60612 IL, USA; Center for Natural Product Technologies (CENAPT), University of Illinois College of Pharmacy, 833 S. Wood St., Chicago, 60612, IL, USA; Program for Collaboration in the Pharmaceutical Sciences (PCRPS), University of Illinois College of Pharmacy, 833 S. Wood St., Chicago, 60612, IL, USA.
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14
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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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15
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Choules MP, Bisson J, Gao W, Lankin DC, McAlpine JB, Niemitz M, Jaki BU, Franzblau SG, Pauli GF. Quality Control of Therapeutic Peptides by 1H NMR HiFSA Sequencing. J Org Chem 2019; 84:3055-3073. [PMID: 30793905 DOI: 10.1021/acs.joc.8b02704] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ensuring identity, purity, and reproducibility are equally essential during synthetic chemistry, drug discovery, and for pharmaceutical product safety. Many peptidic APIs are large molecules that require considerable effort for integrity assurance. This study builds on quantum mechanical 1H iterative Full Spin Analysis (HiFSA) to establish NMR peptide sequencing methodology that overcomes the intrinsic limitations of principal compendial methods in identifying small structural changes or minor impurities that affect effectiveness and safety. HiFSA sequencing yields definitive identity and purity information concurrently, allowing for API quality assurance and control (QA/QC). Achieving full peptide analysis via NMR building blocks, the process lends itself to both research and commercial applications as 1D 1H NMR (HNMR) is the most sensitive and basic NMR experiment. The generated HiFSA profiles are independent of instrument or software tools and work at any magnetic field strength. Pairing with absolute or 100% qHNMR enables quantification of mixtures and/or determination of peptide conformer populations. Demonstration of the methodology uses single amino acids (AAs) and peptides of increasing size, including the octapeptide, angiotensin II, and the nonapeptide, oxytocin. The feasibility of HiFSA coupled with automated NMR and qHNMR for use in QC/QA efforts is established through case-based examples and recommended procedures.
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16
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Burns DC, Mazzola EP, Reynolds WF. The role of computer-assisted structure elucidation (CASE) programs in the structure elucidation of complex natural products. Nat Prod Rep 2019; 36:919-933. [DOI: 10.1039/c9np00007k] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Computer-assisted structure elucidation can help to determine the structures of complex natural products while minimizing the risk of structure errors.
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Affiliation(s)
- Darcy C. Burns
- Department of Chemistry
- University of Toronto
- Toronto
- Canada
| | - Eugene P. Mazzola
- Department of Chemistry & Biochemistry
- University of Maryland
- College Park
- USA
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17
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Markley JL, Dashti H, Wedell JR, Westler WM, Eghbalnia HR. Tools for Enhanced NMR-Based Metabolomics Analysis. Methods Mol Biol 2019; 2037:413-427. [PMID: 31463858 PMCID: PMC7995344 DOI: 10.1007/978-1-4939-9690-2_23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Metabolomics is the study of profiles of small molecules in biological fluids, cells, or organs. These profiles can be thought of as the "fingerprints" left behind from chemical processes occurring in biological systems. Because of its potential for groundbreaking applications in disease diagnostics, biomarker discovery, and systems biology, metabolomics has emerged as a rapidly growing area of research. Metabolomics investigations often, but not always, involve the identification and quantification of endogenous and exogenous metabolites in biological samples. Software tools and databases play a crucial role in advancing the rigor, robustness, reproducibility, and validation of these studies. Specifically, the establishment of a robust library of spectral signatures with unique compound descriptors and atom identities plays a key role in profiling studies based on data from nuclear magnetic resonance (NMR) spectroscopy. Here, we discuss developments leading to a rigorous basis for unique identification of compounds, reproducible numbering of atoms, the compact representation of NMR spectra of metabolites and small molecules, tools for improved compound identification, quantification and visualization, and approaches toward the goal of rigorous analysis of metabolomics data.
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Affiliation(s)
- John L Markley
- Department of Biochemistry, University of Wisconsin Madison, Madison, WI, USA.
| | - Hesam Dashti
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jonathan R Wedell
- Department of Biochemistry, University of Wisconsin Madison, Madison, WI, USA
| | - William M Westler
- Department of Biochemistry, University of Wisconsin Madison, Madison, WI, USA
| | - Hamid R Eghbalnia
- Department of Biochemistry, University of Wisconsin Madison, Madison, WI, USA
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18
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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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19
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Pérez-Hernández N, Becerra-Martínez E, Joseph-Nathan P. Complete 1H NMR assignment of cholesteryl benzoate. Steroids 2018; 138:72-81. [PMID: 30033341 DOI: 10.1016/j.steroids.2018.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/25/2018] [Accepted: 06/29/2018] [Indexed: 10/28/2022]
Abstract
The 750 MHz 1H NMR spectrum of cholesteryl benzoate (1b) could be assigned completely, which means all chemical shifts and all coupling constants, including some long-range values, were established. This task was possible by extracting many approximate coupling constant values in the overlapped spectrum region from an HSQC experiment, and using these values in the 1H iterative full spin analysis integrated in the PERCH NMR software. The task was facilitated using our published data for 3β-acetoxypregna-5,16-dien-20-one (3), the assignment data of the sesquiterpene benzoquinone dihydroperezone (2), also performed in the present study, which contains the same carbon atoms chain than cholesterol (1a), and an HSQC study of (25R)-27-deuteriocholesterol (1c) we prepared some 40 years ago. The HSQC values of 1c in combination with the coupling constants of 1b also allowed to completely assigning the spectrum of 1c. The complete assignment of 1b and 1c further provided the opportunity to estimate the hydrogen shifts induced upon benzoylation of cholesterol. Comparison of the experimental vicinal coupling constants of 1b with the values calculated using the Altona software provides an excellent correlation. In addition, a single crystal X-ray diffraction study of 1b provided the molecular conformation in the solid state, which revealed the side chain adopts an extended conformation.
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Affiliation(s)
- Nury Pérez-Hernández
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07320, Mexico
| | - Elvia Becerra-Martínez
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, Mexico City 07738, Mexico
| | - Pedro Joseph-Nathan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, Mexico City 07000, Mexico.
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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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21
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Spin System Modeling of Nuclear Magnetic Resonance Spectra for Applications in Metabolomics and Small Molecule Screening. Anal Chem 2017; 89:12201-12208. [PMID: 29058410 DOI: 10.1021/acs.analchem.7b02884] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The exceptionally rich information content of nuclear magnetic resonance (NMR) spectra is routinely used to identify and characterize molecules and molecular interactions in a wide range of applications, including clinical biomarker discovery, drug discovery, environmental chemistry, and metabolomics. The set of peak positions and intensities from a reference NMR spectrum generally serves as the identifying signature for a compound. Reference spectra normally are collected under specific conditions of pH, temperature, and magnetic field strength, because changes in conditions can distort the identifying signatures of compounds. A spin system matrix that parametrizes chemical shifts and coupling constants among spins provides a much richer feature set for a compound than a spectral signature based on peak positions and intensities. Spin system matrices expand the applicability of NMR spectral libraries beyond the specific conditions under which data were collected. In addition to being able to simulate spectra at any field strength, spin parameters can be adjusted to systematically explore alterations in chemical shift patterns due to variations in other experimental conditions, such as compound concentration, pH, or temperature. We present methodology and software for efficient interactive optimization of spin parameters against experimental 1D-1H NMR spectra of small molecules. We have used the software to generate spin system matrices for a set of key mammalian metabolites and are also using the software to parametrize spectra of small molecules used in NMR-based ligand screening. The software, along with optimized spin system matrix data for a growing number of compounds, is available from http://gissmo.nmrfam.wisc.edu/ .
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22
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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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23
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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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24
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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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25
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Perez-Hernandez N, Gordillo-Roman B, Arrieta-Baez D, Cerda-Garcia-Rojas CM, Joseph-Nathan P. Complete 1 H NMR assignment of cedranolides. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:169-176. [PMID: 26132551 DOI: 10.1002/mrc.4246] [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: 01/09/2015] [Revised: 03/03/2015] [Accepted: 03/17/2015] [Indexed: 06/04/2023]
Abstract
Complete and unambiguous 1 H NMR chemical shift assignment of α-cedrene (2) and cedrol (9), as well as for α-pipitzol (1), isocedrol (10), and the six related compounds 3-8 has been established by iterative full spin analysis using the PERCH NMR software (PERCH Solutions Ltd., Kuopio, Finland). The total sets of coupling constants are described and correlated with the conformational equilibria of the five-membered ring of 1-10, which were calculated using the complete basis set method. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Nury Perez-Hernandez
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, México, D. F., 07320, Mexico
| | - Barbara Gordillo-Roman
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, México, D. F., 07000, Mexico
| | - Daniel Arrieta-Baez
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, México, D. F., 07738, Mexico
| | - Carlos M Cerda-Garcia-Rojas
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, México, D. F., 07000, Mexico
| | - Pedro Joseph-Nathan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, México, D. F., 07000, Mexico
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26
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Gao W, Napolitano JG, Lankin DC, Kim JY, Jin YY, Lee H, Suh JW, Chen SN, Pauli GF. Computer-assisted 1 H NMR analysis of the anti-tuberculosis drug lead ecumicin. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:239-244. [PMID: 27094011 PMCID: PMC5071145 DOI: 10.1002/mrc.4425] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/10/2016] [Indexed: 05/28/2023]
Affiliation(s)
- Wei Gao
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - José G. Napolitano
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - David C. Lankin
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Jin-Yong Kim
- Division of Bioscience and Bioinformatics, College of Natural Science, Myongji University, Cheoin-gu, Yongin, Gyeonggi-Do, 17058, Korea
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin, Gyeonggi-Do, 17058, Korea
| | - Ying-Yu Jin
- Division of Bioscience and Bioinformatics, College of Natural Science, Myongji University, Cheoin-gu, Yongin, Gyeonggi-Do, 17058, Korea
| | - Hanki Lee
- Division of Bioscience and Bioinformatics, College of Natural Science, Myongji University, Cheoin-gu, Yongin, Gyeonggi-Do, 17058, Korea
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin, Gyeonggi-Do, 17058, Korea
| | - Joo-Won Suh
- Division of Bioscience and Bioinformatics, College of Natural Science, Myongji University, Cheoin-gu, Yongin, Gyeonggi-Do, 17058, Korea
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin, Gyeonggi-Do, 17058, Korea
| | - Shao-Nong Chen
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Guido F. Pauli
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
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27
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Bae M, Park SH, Kwon Y, Lee SK, Shin J, Nam JW, Oh DC. QM-HiFSA-Aided Structure Determination of Succinilenes A-D, New Triene Polyols from a Marine-Derived Streptomyces sp. Mar Drugs 2017; 15:E38. [PMID: 28216577 PMCID: PMC5334618 DOI: 10.3390/md15020038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 02/02/2017] [Accepted: 02/08/2017] [Indexed: 02/01/2023] Open
Abstract
Based on profiles of secondary metabolites produced by marine bacteria obtained using LC/MS, succinilenes A-D (1-4), new triene polyols, were discovered from a culture of a Streptomyces strain SAK1, which was collected in the southern area of Jeju Island, Republic of Korea. The gross structures of 1-4 were primarily determined through analysis of NMR spectra. The double bond geometries of the succinilenes, which could not be established from conventional ¹H NMR spectra because of the highly overlapped olefinic signals, were successfully deciphered using the recently developed quantum-mechanics-driven ¹H iterative full spin analysis (QM-HiFSA). Succinilenes A-C (1-3) displayed inhibitory effects against lipopolysaccharide (LPS)-induced nitric oxide (NO) production, indicating their anti-inflammatory significance. These three compounds (1-3) commonly bear a succinic acid moiety, although succinilene D (4), which did not inhibit NO production, does not have this moiety in its structure. The absolute configurations of succinilenes A-D (1-4) were established through J-based configuration analysis, the modified Mosher's method following methanolysis, and CD spectral analysis.
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Affiliation(s)
- Munhyung Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea.
| | - So Hyun Park
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea.
| | - Yun Kwon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea.
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea.
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea.
| | - Joo-Won Nam
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea.
- Department of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA.
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea.
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28
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Nam JW, Phansalkar RS, Lankin DC, McAlpine JB, Leme-Kraus AA, Vidal CMP, Gan LS, Bedran-Russo A, Chen SN, Pauli GF. Absolute Configuration of Native Oligomeric Proanthocyanidins with Dentin Biomodification Potency. J Org Chem 2017; 82:1316-1329. [PMID: 28098463 PMCID: PMC5451120 DOI: 10.1021/acs.joc.6b02161] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The structurally complex oligomeric proanthocyanidins (OPACs) are promising biomimetic agents, capable of strengthening the macromolecular backbone of teeth via intermolecular and intermicrofibrillar cross-linking. This study establishes analytical methods capable of determining the absolute configuration of the catechin-type monomeric units of underivatized OPACs. This preserves the capacity of their biological evaluation, aimed at understanding the inevitably stereospecific interactions between the OPACs and dentin collagen. Guided by dental bioassays (modulus of elasticity, long-term stability), two new trimeric and tetrameric A-type OPACs were discovered as dentin biomodifiers from pine (Pinus massoniana) bark: epicatechin-(2β→O→7,4β→8)-epicatechin-(2β→O→7,4β→8)-catechin (5) and epicatechin-(2β→O→7,4β→8)-epicatechin-(2β→O→7,4β→6)-epicatechin-(2β→O→7,4β→8)-catechin (6), respectively. Combining 1D/2D NMR, HRESIMS, ECD, 1H iterative full spin analysis (HiFSA), and gauge-invariant atomic orbital (GIAO) δ calculations, we demonstrate how 13C NMR chemical shifts (diastereomeric building blocks (A-type dimers)) empower the determination of the absolute configuration of monomeric units in the higher oligomers 5 and 6. Collectively, NMR with ECD reference data elevates the level of structural information achievable for these structurally demanding molecules when degradation analysis is to be avoided. Considering their numerous and deceptively subtle, but 3D impactful, structural variations, this advances the probing of OPAC chemical spaces for species that bind selectively to collagenous and potentially other biologically important biomacromolecules.
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Affiliation(s)
- Joo-Won Nam
- Department of Medicinal Chemistry & Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
| | - Rasika S. Phansalkar
- Department of Medicinal Chemistry & Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - David C. Lankin
- Department of Medicinal Chemistry & Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - James B. McAlpine
- Department of Medicinal Chemistry & Pharmacognosy, 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
| | - Ariene A. Leme-Kraus
- Department of Restorative Dentistry, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Cristina M. P. Vidal
- 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 310058, People’s Republic of China
| | - Ana Bedran-Russo
- Department of Restorative Dentistry, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Shao-Nong Chen
- Department of Medicinal Chemistry & Pharmacognosy, 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
| | - Guido F. Pauli
- Department of Medicinal Chemistry & Pharmacognosy, 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
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29
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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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30
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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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31
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Phelps AM, Chan VS, Napolitano JG, Krabbe SW, Schomaker JM, Shekhar S. Ligand-Controlled Synthesis of Azoles via Ir-Catalyzed Reactions of Sulfoxonium Ylides with 2-Amino Heterocycles. J Org Chem 2016; 81:4158-69. [PMID: 27104299 DOI: 10.1021/acs.joc.6b00497] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An iridium-catalyzed method was developed for the synthesis of imidazo-fused pyrrolopyrazines. The presence or absence of a nitrogenated ligand controlled the outcome of the reaction, leading to simple β-keto amine products in the absence of added ligand and the cyclized 7- and 8-substituted-imidazo[1,2-a]pyrrolo[2,3-e]pyrazine products in the presence of ligand. This catalyst control was conserved across a variety of ylide and amine coupling partners. The substrate was shown to act as a ligand for the iridium catalyst in the absence of other ligands via NMR spectroscopy. Kinetic studies indicated that formation of the Ir-carbene was reversible and the slow step of the reaction. These mechanistic investigations suggest that the β-keto amine products form via an intramolecular carbene N-H insertion, and the imidazopyrrolopyrazines form via an intermolecular carbene N-H insertion.
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Affiliation(s)
- Alicia M Phelps
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | | | | | | | - Jennifer M Schomaker
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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32
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Pauli GF, Niemitz M, Bisson J, Lodewyk MW, Soldi C, Shaw JT, Tantillo DJ, Saya JM, Vos K, Kleinnijenhuis RA, Hiemstra H, Chen SN, McAlpine JB, Lankin DC, Friesen JB. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving. J Org Chem 2016; 81:878-89. [PMID: 26812443 PMCID: PMC4746703 DOI: 10.1021/acs.joc.5b02456] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The revision of the structure of
the sesquiterpene aquatolide from
a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling
NMR data, X-ray crystallography, and the recent confirmation via full
synthesis exemplify that the achievement of “structural correctness”
depends on the completeness of the experimental evidence. Archived
FIDs and newly acquired aquatolide spectra demonstrate that archiving
and rigorous interpretation of 1D 1H NMR data may enhance
the reproducibility of (bio)chemical research and curb the growing
trend of structural misassignments. Despite being the most accessible
NMR experiment, 1D 1H spectra encode a wealth of information
about bonds and molecular geometry that may be fully mined by 1H iterative full spin analysis (HiFSA). Fully characterized
1D 1H spectra are unideterminant for a given structure.
The corresponding FIDs may be readily submitted with publications
and collected in databases. Proton NMR spectra are indispensable for
structural characterization even in conjunction with 2D data. Quantum
interaction and linkage tables (QuILTs) are introduced for a more
intuitive visualization of 1D J-coupling relationships,
NOESY correlations, and heteronuclear experiments. Overall, this study
represents a significant contribution to best practices in NMR-based
structural analysis and dereplication.
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Affiliation(s)
- Guido F Pauli
- Department of Medicinal Chemistry & Pharmacognosy and Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Matthias Niemitz
- PERCH Solutions Limited , Puijonkatu 24B5, 70110 Kuopio, Finland
| | - Jonathan Bisson
- Department of Medicinal Chemistry & Pharmacognosy and Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Michael W Lodewyk
- Physical Science Department, Butte College , Oroville, California 95965, United States
| | - Cristian Soldi
- Department of Chemistry, University of California-Davis , One Shields Avenue, Davis, California 95616, United States.,Federal University of Santa Catarina , Centro de Curitibanos, Rod. Ulysses Gaboardi, Km 3, Curitibanos, SC 89520-000, Brazil
| | - Jared T Shaw
- Department of Chemistry, University of California-Davis , One Shields Avenue, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California-Davis , One Shields Avenue, Davis, California 95616, United States
| | - Jordy M Saya
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Klaas Vos
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Roel A Kleinnijenhuis
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Henk Hiemstra
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Shao-Nong Chen
- Department of Medicinal Chemistry & Pharmacognosy and Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , 833 South Wood Street, Chicago, Illinois 60612, United States
| | - James B McAlpine
- Department of Medicinal Chemistry & Pharmacognosy and Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , 833 South Wood Street, Chicago, Illinois 60612, United States
| | - David C Lankin
- Department of Medicinal Chemistry & Pharmacognosy and Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , 833 South Wood Street, Chicago, Illinois 60612, United States
| | - J Brent Friesen
- Physical Sciences Department, Rosary College of Arts and Sciences, Dominican University , 7900 West Division Street, River Forest, Illinois 60305, United States
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33
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Becerra-Martinez E, Ramírez-Gualito KE, Pérez-Hernández N, Joseph-Nathan P. Total (1)H NMR assignment of 3β-acetoxypregna-5,16-dien-20-one. Steroids 2015; 104:208-13. [PMID: 26476187 DOI: 10.1016/j.steroids.2015.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 09/17/2015] [Accepted: 10/09/2015] [Indexed: 11/15/2022]
Abstract
This work describes the total and unambiguous assignment of the 750 MHz (1)H NMR spectrum of 3β-acetoxypregna-5,16-dien-20-one or 16-DPA (1), the well-known intermediate utilized in the synthesis of biological important commercial steroids. The task was accomplished by extracting the coupling constant values in the overlapped spectrum region by HSQC, and using these values in the (1)H iterative full spin analysis integrated in the PERCH NMR software. Comparison of the experimental vicinal coupling constants of 1 with the values calculated using Altona provides an excellent correlation. The same procedure, when applied to the published data of progesterone (2) and testosterone (3), afforded an acceptable correlation for 2 and a poor correlation for 3. In the last case, this suggested the reassignment of all four vicinal coupling constants for the methylene signals at the C-15 and C-16 positions, demonstrating the utility of this methodology.
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Affiliation(s)
- Elvia Becerra-Martinez
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, México, D.F. 07738, Mexico
| | - Karla E Ramírez-Gualito
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, México, D.F. 07738, Mexico
| | - Nury Pérez-Hernández
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, México, D.F. 07320, Mexico
| | - Pedro Joseph-Nathan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, México, D.F. 07000, Mexico.
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34
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Nam JW, Phansalkar RS, Lankin DC, Bisson J, McAlpine JB, Leme AA, Vidal CMP, Ramirez B, Niemitz M, Bedran-Russo A, Chen SN, Pauli GF. Subtle Chemical Shifts Explain the NMR Fingerprints of Oligomeric Proanthocyanidins with High Dentin Biomodification Potency. J Org Chem 2015. [PMID: 26214362 DOI: 10.1021/acs.joc.5b01082] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The ability of certain oligomeric proanthocyanidins (OPACs) to enhance the biomechanical properties of dentin involves collagen cross-linking of the 1.3-4.5 nm wide space via protein-polyphenol interactions. A systematic interdisciplinary search for the bioactive principles of pine bark has yielded the trimeric PAC, ent-epicatechin-(4β→8)-epicatechin-(2β→O→7,4β→8)-catechin (3), representing the hitherto most potent single chemical entity capable of enhancing dentin stiffness. Building the case from two congeneric PAC dimers, a detailed structural analysis decoded the stereochemistry, spatial arrangement, and chemical properties of three dentin biomodifiers. Quantum-mechanics-driven (1)H iterative full spin analysis (QM-HiFSA) of NMR spectra distinguished previously unrecognized details such as higher order J coupling and provided valuable information about 3D structure. Detection and quantification of H/D-exchange effects by QM-HiFSA identified C-8 and C-6 as (re)active sites, explain preferences in biosynthetic linkage, and suggest their involvement in dentin cross-linking activity. Mapping of these molecular properties underscored the significance of high δ precision in both (1)H and (13)C NMR spectroscopy. Occurring at low- to subppb levels, these newly characterized chemical shift differences in ppb are small but diagnostic measures of dynamic processes inherent to the OPAC pharmacophores and can help augment our understanding of nanometer-scale intermolecular interactions in biomodified dentin macromolecules.
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35
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Napolitano JG, Simmler C, McAlpine JB, Lankin DC, Chen SN, Pauli GF. Digital NMR profiles as building blocks: assembling ¹H fingerprints of steviol glycosides. JOURNAL OF NATURAL PRODUCTS 2015; 78:658-65. [PMID: 25714117 PMCID: PMC4696868 DOI: 10.1021/np5008203] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This report describes a fragment-based approach to the examination of congeneric organic compounds by NMR spectroscopy. The method combines the classic interpretation of 1D- and 2D-NMR data sets with contemporary computer-assisted NMR analysis. Characteristic NMR profiles of key structural motifs were generated by (1)H iterative full spin analysis and then joined together as building blocks to recreate the (1)H NMR spectra of increasingly complex molecules. To illustrate the methodology described, a comprehensive analysis of steviol (1), seven steviol glycosides (2-8) and two structurally related isosteviol compounds (9, 10) was carried out. The study also assessed the potential impact of this method on relevant aspects of natural product research including structural verification, chemical dereplication, and mixture analysis.
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Affiliation(s)
- José G. Napolitano
- Department of Medicinal Chemistry and Pharmacognosy, Institute for Tuberculosis Research, and UIC/NIH Center for Botanical Dietary Supplements Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Charlotte Simmler
- Department of Medicinal Chemistry and Pharmacognosy, Institute for Tuberculosis Research, and UIC/NIH Center for Botanical Dietary Supplements Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - James B. McAlpine
- Department of Medicinal Chemistry and Pharmacognosy, Institute for Tuberculosis Research, and UIC/NIH Center for Botanical Dietary Supplements Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - David C. Lankin
- Department of Medicinal Chemistry and Pharmacognosy, Institute for Tuberculosis Research, and UIC/NIH Center for Botanical Dietary Supplements Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Shao-Nong Chen
- Department of Medicinal Chemistry and Pharmacognosy, Institute for Tuberculosis Research, and UIC/NIH Center for Botanical Dietary Supplements Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Guido F. Pauli
- Department of Medicinal Chemistry and Pharmacognosy, Institute for Tuberculosis Research, and UIC/NIH Center for Botanical Dietary Supplements Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
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36
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Ramos Alvarenga R, Friesen JB, Nikolić D, Simmler C, Napolitano JG, van Breemen R, Lankin D, McAlpine JB, Pauli GF, Chen SN. K-targeted metabolomic analysis extends chemical subtraction to DESIGNER extracts: selective depletion of extracts of hops (Humulus lupulus). JOURNAL OF NATURAL PRODUCTS 2014; 77:2595-604. [PMID: 25437744 PMCID: PMC4280114 DOI: 10.1021/np500376g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Indexed: 05/22/2023]
Abstract
This study introduces a flexible and compound targeted approach to Deplete and Enrich Select Ingredients to Generate Normalized Extract Resources, generating DESIGNER extracts, by means of chemical subtraction or augmentation of metabolites. Targeting metabolites based on their liquid-liquid partition coefficients (K values), K targeting uses countercurrent separation methodology to remove single or multiple compounds from a chemically complex mixture, according to the following equation: DESIGNER extract = total extract ± target compound(s). Expanding the scope of the recently reported depletion of extracts by immunoaffinity or solid phase liquid chromatography, the present approach allows a more flexible, single- or multi-targeted removal of constituents from complex extracts such as botanicals. Chemical subtraction enables both chemical and biological characterization, including detection of synergism/antagonism by both the subtracted targets and the remaining metabolite mixture, as well as definition of the residual complexity of all fractions. The feasibility of the DESIGNER concept is shown by K-targeted subtraction of four bioactive prenylated phenols, isoxanthohumol (1), 8-prenylnaringenin (2), 6-prenylnaringenin (3), and xanthohumol (4), from a standardized hops (Humulus lupulus L.) extract using specific solvent systems. Conversely, adding K-targeted isolates allows enrichment of the original extract and hence provides an augmented DESIGNER material. Multiple countercurrent separation steps were used to purify each of the four compounds, and four DESIGNER extracts with varying depletions were prepared. The DESIGNER approach innovates the characterization of chemically complex extracts through integration of enabling technologies such as countercurrent separation, K-by-bioactivity, the residual complexity concepts, as well as quantitative analysis by (1)H NMR, LC-MS, and HiFSA-based NMR fingerprinting.
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Affiliation(s)
- René
F. Ramos Alvarenga
- UIC/NIH
Center for Botanical Dietary Supplements Research, Department of Medicinal
Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - J. Brent Friesen
- Department
of Physical Sciences, Rosary College of Art and Sciences, Dominican University, River Forest, Illinois 60305, United States
| | - Dejan Nikolić
- UIC/NIH
Center for Botanical Dietary Supplements Research, Department of Medicinal
Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Charlotte Simmler
- UIC/NIH
Center for Botanical Dietary Supplements Research, Department of Medicinal
Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - José G. Napolitano
- UIC/NIH
Center for Botanical Dietary Supplements Research, Department of Medicinal
Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Richard van Breemen
- UIC/NIH
Center for Botanical Dietary Supplements Research, Department of Medicinal
Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - David
C. Lankin
- UIC/NIH
Center for Botanical Dietary Supplements Research, Department of Medicinal
Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - James B. McAlpine
- UIC/NIH
Center for Botanical Dietary Supplements Research, Department of Medicinal
Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Guido F. Pauli
- UIC/NIH
Center for Botanical Dietary Supplements Research, Department of Medicinal
Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- G.F.P.:
E-mail: ; Phone: (312) 355-1949; Fax: (312) 355-2693
| | - Shao-Nong Chen
- UIC/NIH
Center for Botanical Dietary Supplements Research, Department of Medicinal
Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- S.-N.C.: E-mail: ; Phone: (312) 996-7253; Fax: (312) 355-2693
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37
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Pauli GF, Chen SN, Simmler C, Lankin DC, Gödecke T, Jaki BU, Friesen JB, McAlpine JB, Napolitano JG. Importance of purity evaluation and the potential of quantitative ¹H NMR as a purity assay. J Med Chem 2014; 57:9220-31. [PMID: 25295852 PMCID: PMC4255677 DOI: 10.1021/jm500734a] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
In any biomedical and chemical context,
a truthful description of chemical constitution requires coverage
of both structure and purity. This qualification affects all drug
molecules, regardless of development stage (early discovery to approved
drug) and source (natural product or synthetic). Purity assessment
is particularly critical in discovery programs and whenever
chemistry is linked with biological and/or therapeutic outcome. Compared
with chromatography and elemental analysis, quantitative NMR (qNMR)
uses nearly universal detection and provides a versatile and orthogonal
means of purity evaluation. Absolute qNMR with flexible calibration
captures analytes that frequently escape detection (water, sorbents).
Widely accepted structural NMR workflows require minimal or no adjustments
to become practical 1H qNMR (qHNMR) procedures with simultaneous
qualitative and (absolute) quantitative capability. This study reviews
underlying concepts, provides a framework for standard qHNMR purity
assays, and shows how adequate accuracy and precision are achieved
for the intended use of the material.
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Affiliation(s)
- Guido F Pauli
- Department of Medicinal Chemistry and Pharmacognosy and ‡Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , 833 S. Wood Street, Chicago, Illinois 60612, United States
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38
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Alvarez-Cisneros C, Muñoz MA, Suárez-Castillo OR, Pérez-Hernández N, Cerda-García-Rojas CM, Morales-Ríos MS, Joseph-Nathan P. Stereospecific (5) JHortho,OMe couplings in methoxyindoles, methoxycoumarins, and methoxyflavones. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2014; 52:491-499. [PMID: 25042582 DOI: 10.1002/mrc.4103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 06/06/2014] [Accepted: 06/09/2014] [Indexed: 06/03/2023]
Abstract
Long-range coupling constants (5) JHortho,OMe were measured in series of methoxyindoles, methoxycoumarins, and methoxyflavones by the modified J doubling in the frequency domain method. The COSY and NOESY spectra revealed the coupling of the -OMe group with a specific proton at the ortho position and its preferred conformation. Homonuclear (1) H-(1) H couplings were confirmed by irradiation of the -OMe signal. Density functional theory calculations of (5) JHortho,OMe using the modified aug-cc-pVTZ basis set evidenced that the Fermi contact term shows good agreement with the experimental J values. Accurate chemical shift and coupling constant values followed after iterative quantum mechanical spectral analysis using the PERCH software.
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Affiliation(s)
- Celina Alvarez-Cisneros
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, México, D. F., 07000, Mexico
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39
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Pauli GF, Chen SN, Lankin DC, Bisson J, Case RJ, Chadwick LR, Gödecke T, Inui T, Krunic A, Jaki B, McAlpine JB, Mo S, Napolitano JG, Orjala J, Lehtivarjo J, Korhonen SP, Niemitz M. Essential parameters for structural analysis and dereplication by (1)H NMR spectroscopy. JOURNAL OF NATURAL PRODUCTS 2014; 77:1473-87. [PMID: 24895010 PMCID: PMC4076039 DOI: 10.1021/np5002384] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Indexed: 05/12/2023]
Abstract
The present study demonstrates the importance of adequate precision when reporting the δ and J parameters of frequency domain (1)H NMR (HNMR) data. Using a variety of structural classes (terpenoids, phenolics, alkaloids) from different taxa (plants, cyanobacteria), this study develops rationales that explain the importance of enhanced precision in NMR spectroscopic analysis and rationalizes the need for reporting Δδ and ΔJ values at the 0.1-1 ppb and 10 mHz level, respectively. Spectral simulations paired with iteration are shown to be essential tools for complete spectral interpretation, adequate precision, and unambiguous HNMR-driven dereplication and metabolomic analysis. The broader applicability of the recommendation relates to the physicochemical properties of hydrogen ((1)H) and its ubiquity in organic molecules, making HNMR spectra an integral component of structure elucidation and verification. Regardless of origin or molecular weight, the HNMR spectrum of a compound can be very complex and encode a wealth of structural information that is often obscured by limited spectral dispersion and the occurrence of higher order effects. This altogether limits spectral interpretation, confines decoding of the underlying spin parameters, and explains the major challenge associated with the translation of HNMR spectra into tabulated information. On the other hand, the reproducibility of the spectral data set of any (new) chemical entity is essential for its structure elucidation and subsequent dereplication. Handling and documenting HNMR data with adequate precision is critical for establishing unequivocal links between chemical structure, analytical data, metabolomes, and biological activity. Using the full potential of HNMR spectra will facilitate the general reproducibility for future studies of bioactive chemicals, especially of compounds obtained from the diversity of terrestrial and marine organisms.
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Affiliation(s)
- 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
| | - Shao-Nong Chen
- Department
of Medicinal Chemistry and Pharmacognosy, 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
| | - Jonathan Bisson
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Ryan J. Case
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Lucas R. Chadwick
- Bells Brewery, 8938 Krum Avenue, Kalamazoo, Michigan 49009, United States
| | - Tanja Gödecke
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Taichi Inui
- 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
| | - Aleksej Krunic
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Birgit
U. Jaki
- 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
| | - Shunyan Mo
- Department
of Medicinal Chemistry and Pharmacognosy, 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
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Jimmy Orjala
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Juuso Lehtivarjo
- School of Pharmacy, University of Eastern Finland, P.O.
Box 1627, 70211 Kuopio, Finland
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40
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Qiu F, McAlpine JB, Lankin DC, Burton I, Karakach T, Chen SN, Pauli GF. 2D NMR barcoding and differential analysis of complex mixtures for chemical identification: the Actaea triterpenes. Anal Chem 2014; 86:3964-72. [PMID: 24673652 PMCID: PMC4004191 DOI: 10.1021/ac500188j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 03/07/2014] [Indexed: 12/19/2022]
Abstract
The interpretation of NMR spectroscopic information for structure elucidation involves decoding of complex resonance patterns that contain valuable molecular information (δ and J), which is not readily accessible otherwise. We introduce a new concept of 2D-NMR barcoding that uses clusters of fingerprint signals and their spatial relationships in the δ-δ coordinate space to facilitate the chemical identification of complex mixtures. Similar to widely used general barcoding technology, the structural information of individual compounds is encoded as a specifics pattern of their C,H correlation signals. Software-based recognition of these patterns enables the structural identification of the compounds and their discrimination in mixtures. Using the triterpenes from various Actaea (syn. Cimicifuga) species as a test case, heteronuclear multiple-bond correlation (HMBC) barcodes were generated on the basis of their structural subtypes from a statistical investigation of their δH and δC data in the literature. These reference barcodes allowed in silico identification of known triterpenes in enriched fractions obtained from an extract of A. racemosa (black cohosh). After dereplication, a differential analysis of heteronuclear single-quantum correlation (HSQC) spectra even allowed for the discovery of a new triterpene. The 2D barcoding concept has potential application in a natural product discovery project, allowing for the rapid dereplication of known compounds and as a tool in the search for structural novelty within compound classes with established barcodes.
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Affiliation(s)
- Feng Qiu
- Department
of Medicinal Chemistry and Pharmacognosy, 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
| | - David C. Lankin
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Ian Burton
- Institute
for Marine Biosciences, National Research
Council, Halifax, Nova Scotia B3H 3Z1, Canada
| | - Tobias Karakach
- Institute
for Marine Biosciences, National Research
Council, Halifax, Nova Scotia B3H 3Z1, Canada
| | - Shao-Nong Chen
- Department
of Medicinal Chemistry and Pharmacognosy, 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
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