1
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Sager E, Tzvetkova P, Lingel A, Gossert AD, Luy B. Hydrogen bond formation may enhance RDC-based discrimination of enantiomers. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:639-647. [PMID: 38785031 DOI: 10.1002/mrc.5448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 05/25/2024]
Abstract
The distinction of enantiomers based on residual anisotropic parameters obtained by alignment in chiral poly-γ-benzyl-L-glutamate (PBLG) is among the strongest in high-resolution NMR spectroscopy. However, large variations in enantiodifferentiation among different solutes are frequently observed. One hypothesis is that the formation of hydrogen bonds between solute and PBLG is important for the distinction of enantiomers. With a small set of three almost spherical enantiomeric pairs, for which 1DCH residual dipolar couplings are measured, we address this issue in a systematic way: borneol contains a single functional group that can act as a hydrogen bond donor, camphor has a single group that may act as a hydrogen bond acceptor, and quinuclidinol can act as both hydrogen bond donor and acceptor. The results are unambiguous: although camphor shows low enantiodifferentiation with PBLG and alignment that can be predicted well by the purely steric TRAMITE approach, the distinction of enantiomers for the other enantiomeric pairs is significantly higher with alignment properties that must involve a specific interaction in addition to steric alignment.
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Affiliation(s)
- Emine Sager
- Institute of Organic Chemistry and Institute for Biological Interfaces 4-Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Novartis Biomedical Research, Basel, Switzerland
| | - Pavleta Tzvetkova
- Institute of Organic Chemistry and Institute for Biological Interfaces 4-Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | | | | | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4-Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
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2
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Anklin C, Gil RR. Full configurational and conformational analysis of artemisinin by one-bond carbon-carbon residual dipolar couplings at natural abundance. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:599-604. [PMID: 38558418 DOI: 10.1002/mrc.5443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/04/2024]
Abstract
Configurational and conformational analysis of the biologically relevant natural product artemisinin was conducted using carbon-carbon residual dipolar couplings (1DCC RDCs) at natural abundance. These RDCs were measured through the 2D-INADEQUATE NMR experiment using a sample aligned in a compressed poly (methyl methacrylate) (PMMA) gel swollen in CDCl3. Singular value decomposition (SVD) fitting analysis of all carbon-carbon bonds, 1DCC RDCs, in relation to the full configuration/conformational space (32 diastereoisomers) of artemisinin, unambiguously identified the correct configuration of artemisinin.
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Affiliation(s)
- Clemens Anklin
- Bruker BioSpin Corporation, Billerica, Massachusetts, USA
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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3
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Silva Elipe MV, Ndukwe IE, Murray JI. Cryogen-free 400-MHz nuclear magnetic resonance spectrometer as a versatile tool for pharmaceutical process analytical technology. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:512-534. [PMID: 38369696 DOI: 10.1002/mrc.5434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/20/2024]
Abstract
The discovery of new ceramic materials containing Ba-La-Cu oxides in 1986 that exhibited superconducting properties at high temperatures in the range of 35 K or higher, recognized with the Nobel Prize in Physics in 1987, opened a new world of opportunities for nuclear magnetic resonance (NMRs) and magnetic resonance imaging (MRIs) to move away from liquid cryogens. This discovery expands the application of high temperature superconducting (HTS) materials to fields beyond the chemical and medical industries, including electrical power grids, energy, and aerospace. The prototype 400-MHz cryofree HTS NMR spectrometer installed at Amgen's chemistry laboratory has been vital for a variety of applications such as structure analysis, reaction monitoring, and CASE-3D studies with RDCs. The spectrometer has been integrated with Amgen's chemistry and analytical workflows, providing pipeline project support in tandem with other Kinetic Analysis Platform technologies. The 400-MHz cryofree HTS NMR spectrometer, as the name implies, does not require liquid cryogens refills and has smaller footprint that facilitates installation into a chemistry laboratory fume hood, sharing the hood with a process chemistry reactor. Our evaluation of its performance for structural analysis with CASE-3D protocol and for reaction monitoring of Amgen's pipeline chemistry was successful. We envision that the HTS magnets would become part of the standard NMR and MRI spectrometers in the future. We believe that while the technology is being developed, there is room for all magnet options, including HTS, low temperature superconducting (LTS) magnets, and low field benchtop NMRs with permanent magnets, where utilization will be dependent on application type and costs.
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Affiliation(s)
| | - Ikenna Edward Ndukwe
- Department of Attribute Sciences, Process Development, Amgen Inc., Thousand Oaks, California, USA
| | - James I Murray
- Pivotal and Commercial Drug Substance Technologies, Process Development, Amgen Inc., Thousand Oaks, California, USA
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4
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Passaglia L, Zanardi MM, Sarotti AM. Study of heavy atom influence on poly-halogenated compounds using DP4/MM-DP4+/DP4+: insights and trends. Org Biomol Chem 2024; 22:2435-2442. [PMID: 38416037 DOI: 10.1039/d3ob02077k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy complemented by density functional theory (DFT) calculations is a crucial tool for structural elucidation. Nevertheless, the precision of NMR predictions is influenced by the 'heavy atom effect', wherein heavy atoms affect the shielding values of neighboring light atoms (HALA effect). Standard practice in the field involves removing the conflicting signals. However, in the case of polyhalogenated molecules, this is challenging due to the significant amount of information that ends up being lost. In this study the HALA is thoroughly investigated in the context of three leading probability methods: DP4, MM-DP4+, and DP4+. The results show that DP4+ is more sensitive to C-Cl or C-Br signals, which is a consequence of the longer bond lengths computed with DFT. Removing conflicting signals is highly effective in DP4+, but has an uncertain outcome in methods based on molecular mechanics geometries, such as DP4 and MM-DP4+. A detailed investigation of the effect of bond distance on the corresponding chemical shifts has also been conducted.
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Affiliation(s)
- Lucas Passaglia
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina.
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, S2002QEO Rosario, Argentina
| | - María M Zanardi
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, S2002QEO Rosario, Argentina
| | - Ariel M Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina.
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5
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Doro-Goldsmith E, Song Q, Li XL, Li XM, Hu XY, Li HL, Liu HR, Wang BG, Sun H. Absolute Configuration of 12 S-Deoxynortryptoquivaline from Ascidian-Derived Fungus Aspergillus clavatus Determined by Anisotropic NMR and Chiroptical Spectroscopy. JOURNAL OF NATURAL PRODUCTS 2024; 87:381-387. [PMID: 38289330 PMCID: PMC10897928 DOI: 10.1021/acs.jnatprod.3c01157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/24/2024]
Abstract
Tryptoquivalines are highly toxic metabolites initially isolated from the fungus Aspergillus clavatus. The relative and absolute configuration of tryptoquivaline derivates was primarily established by comparison of the chemical shifts, NOE data, and ECD calculations. A de novo determination of the complete relative configuration using NMR spectroscopy was challenging due to multiple spatially separated stereocenters, including one nonprotonated carbon. In this study, we isolated a new tryptoquivaline derivative, 12S-deoxynortryptoquivaline (1), from the marine ascidian-derived fungus Aspergillus clavatus AS-107. The correct assignment of the relative configuration of 1 was accomplished using anisotropic NMR spectroscopy, while the absolute configuration was determined by comparing calculated and experimental ECD spectra. This case study highlights the effectiveness of anisotropic NMR parameters over isotropic NMR parameters in determining the relative configuration of complex natural products without the need for crystallization.
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Affiliation(s)
- Elisa Doro-Goldsmith
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, Berlin 13125, Germany
- School
of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Qi Song
- CAS
and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China
| | - Xiao-Lu Li
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, Berlin 13125, Germany
| | - Xiao-Ming Li
- CAS
and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China
| | - Xue-Yi Hu
- CAS
and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China
| | - Hong-Lei Li
- CAS
and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China
| | - Hao-Ran Liu
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, Berlin 13125, Germany
- Institute
of Chemistry, Technische Universität
Berlin, Straße des
17. Juni 135, Berlin 10623, Germany
| | - Bin-Gui Wang
- CAS
and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China
- University
of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Han Sun
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, Berlin 13125, Germany
- Institute
of Chemistry, Technische Universität
Berlin, Straße des
17. Juni 135, Berlin 10623, Germany
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6
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Silva Elipe MV, Ndukwe IE, Navarro-Vázquez A. Anisotropic NMR data acquisition with a prototype 400 MHz cryogen-free NMR spectrometer. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:530-543. [PMID: 37530063 DOI: 10.1002/mrc.5380] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023]
Abstract
High-temperature superconducting (HTS) materials have recently been incorporated into the construction of HTS cryogen-free magnets for nuclear magnetic resonance (NMR) spectroscopy. These HTS NMR spectrometers do not require liquid cryogens, thereby providing significant cost savings and facilitating easy integration into chemistry laboratories. However, the optimal performance of these HTS magnets against standard cryogen NMR magnets must be evaluated, especially with demanding modern NMR applications such as NMR in anisotropic media. The stability of the HTS magnets over time and their performance with complex pulse sequence experiments are the main unknown factors of this new technology. In this study, we evaluate the utility of our prototype 400 MHz cryogen-free power-driven HTS NMR spectrometer, installed in the fumehood of a chemistry laboratory, for stereochemical analysis of three commercial natural products (artemisinin, artemether, and dihydroartemisinin) via measurement of anisotropic NMR data, in particular, residual dipolar couplings. The accuracy of measurement of the anisotropic NMR data with the HTS magnet spectrometer is evaluated through the CASE-3D fitting protocol, as implemented in the Mestrenova-StereoFitter software program.
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Affiliation(s)
| | | | - Armando Navarro-Vázquez
- Departmento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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7
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da Silva Oliveira L, Crnkovic CM, de Amorim MR, Navarro-Vázquez A, Paz TA, Freire VF, Takaki M, Venâncio T, Ferreira AG, de Freitas Saito R, Chammas R, Berlinck RGS. Phomactinine, the First Nitrogen-Bearing Phomactin, Produced by Biatriospora sp. CBMAI 1333. JOURNAL OF NATURAL PRODUCTS 2023; 86:2065-2072. [PMID: 37490470 DOI: 10.1021/acs.jnatprod.3c00383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Metabolomics analyses and improvement of growth conditions were applied toward diversification of phomactin terpenoids by the fungus Biatriospora sp. CBMAI 1333. Visualization of molecular networking results on Gephi assisted the observation of phomactin diversification and guided the isolation of new phomactin variants by applying a modified version of chemometrics based on a fractional factorial design. Consequentially, the first nitrogen-bearing phomactin, phomactinine (1), with a new rearranged carbon skeleton, was isolated and identified. The strategy combining metabolomics and chemometrics can be extended to include bioassay potency, structure novelty, and metabolic diversification connected or not to genomic analyses.
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Affiliation(s)
- Leandro da Silva Oliveira
- Instituto de Química de São Carlos, Universidade de São Paulo, C.P. 780, CEP 13560-970, São Carlos, SP Brazil
| | - Camila M Crnkovic
- Instituto de Química de São Carlos, Universidade de São Paulo, C.P. 780, CEP 13560-970, São Carlos, SP Brazil
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, CEP 05508-000, São Paulo, SP Brazil
| | - Marcelo R de Amorim
- Instituto de Química de São Carlos, Universidade de São Paulo, C.P. 780, CEP 13560-970, São Carlos, SP Brazil
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco Cidade Universitária CEP, 50.740-540 Recife, PE Brazil
| | - Tiago A Paz
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, CEP 14040-903, Ribeirão Preto, SP Brazil
| | - Vitor F Freire
- Instituto de Química de São Carlos, Universidade de São Paulo, C.P. 780, CEP 13560-970, São Carlos, SP Brazil
| | - Mirelle Takaki
- Instituto de Química de São Carlos, Universidade de São Paulo, C.P. 780, CEP 13560-970, São Carlos, SP Brazil
| | - Tiago Venâncio
- Departamento de Química, Universidade Federal de São Carlos, CEP 13565-905, São Carlos, SP Brazil
| | - Antonio G Ferreira
- Departamento de Química, Universidade Federal de São Carlos, CEP 13565-905, São Carlos, SP Brazil
| | - Renata de Freitas Saito
- Centro de Investigação Translacional em Oncologia, Instituto do Câncer do Estado de São Paulo, Faculdade de Medicina, Universidade de São Paulo, Avenida Dr. Arnaldo, 251 - Cerqueira César, 01246-000, São Paulo, SP Brazil
| | - Roger Chammas
- Centro de Investigação Translacional em Oncologia, Instituto do Câncer do Estado de São Paulo, Faculdade de Medicina, Universidade de São Paulo, Avenida Dr. Arnaldo, 251 - Cerqueira César, 01246-000, São Paulo, SP Brazil
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, C.P. 780, CEP 13560-970, São Carlos, SP Brazil
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8
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Dandawate M, Choudhury R, Krishna GR, Reddy DS. Total Synthesis and Absolute Configuration Determination of the α-Glycosidase Inhibitor (3 S,4 R)-6-Acetyl-3-hydroxy-2,2-dimethylchroman-4-yl ( Z)-2-Methylbut-2-enoate from Ageratina grandifolia. JOURNAL OF NATURAL PRODUCTS 2023. [PMID: 37316456 DOI: 10.1021/acs.jnatprod.3c00236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Herein, we report the first total synthesis of α-glycosidase inhibitor (3R, 4S)-6-acetyl-3-hydroxy-2,2-dimethylchroman-4-yl (Z)-2-methylbut-2-enoate as well as its enantiomer. Our synthesis confirms the chromane structure separately proposed by Navarro-Vazquez and Mata, on the basis of DFT computations. Furthermore, our synthesis allowed us to determine the absolute configuration of the natural compound as (3S, 4R) and not (3R, 4S).
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Affiliation(s)
- Monica Dandawate
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Rahul Choudhury
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Gamidi Rama Krishna
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - D Srinivasa Reddy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
- CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
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9
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Wieske LHE, Peintner S, Erdélyi M. Ensemble determination by NMR data deconvolution. Nat Rev Chem 2023:10.1038/s41570-023-00494-x. [PMID: 37169885 DOI: 10.1038/s41570-023-00494-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2023] [Indexed: 05/13/2023]
Abstract
Nuclear magnetic resonance (NMR) is the spectroscopic technique of choice for determining molecular conformations in solution at atomic resolution. As solution NMR spectra are rich in structural and dynamic information, the way in which the data should be acquired and handled to deliver accurate ensembles is not trivial. This Review provides a guide to the NMR experiment selection and parametrization process, the generation of viable theoretical conformer pools and the deconvolution of time-averaged NMR data into a conformer ensemble that accurately represents a flexible molecule in solution. In addition to reviewing the key elements of solution ensemble determination of flexible mid-sized molecules, the feasibility and pitfalls of data deconvolution are discussed with a comparison of the performance of representative algorithms.
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Affiliation(s)
| | - Stefan Peintner
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Máté Erdélyi
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden.
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10
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Thompson AA, Harbut MB, Kung PP, Karpowich NK, Branson JD, Grant JC, Hagan D, Pascual HA, Bai G, Zavareh RB, Coate HR, Collins BC, Côte M, Gelin CF, Damm-Ganamet KL, Gholami H, Huff AR, Limon L, Lumb KJ, Mak PA, Nakafuku KM, Price EV, Shih AY, Tootoonchi M, Vellore NA, Wang J, Wei N, Ziff J, Berger SB, Edwards JP, Gardet A, Sun S, Towne JE, Venable JD, Shi Z, Venkatesan H, Rives ML, Sharma S, Shireman BT, Allen SJ. Identification of small-molecule protein-protein interaction inhibitors for NKG2D. Proc Natl Acad Sci U S A 2023; 120:e2216342120. [PMID: 37098070 PMCID: PMC10160951 DOI: 10.1073/pnas.2216342120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 03/10/2023] [Indexed: 04/26/2023] Open
Abstract
NKG2D (natural-killer group 2, member D) is a homodimeric transmembrane receptor that plays an important role in NK, γδ+, and CD8+ T cell-mediated immune responses to environmental stressors such as viral or bacterial infections and oxidative stress. However, aberrant NKG2D signaling has also been associated with chronic inflammatory and autoimmune diseases, and as such NKG2D is thought to be an attractive target for immune intervention. Here, we describe a comprehensive small-molecule hit identification strategy and two distinct series of protein-protein interaction inhibitors of NKG2D. Although the hits are chemically distinct, they share a unique allosteric mechanism of disrupting ligand binding by accessing a cryptic pocket and causing the two monomers of the NKG2D dimer to open apart and twist relative to one another. Leveraging a suite of biochemical and cell-based assays coupled with structure-based drug design, we established tractable structure-activity relationships with one of the chemical series and successfully improved both the potency and physicochemical properties. Together, we demonstrate that it is possible, albeit challenging, to disrupt the interaction between NKG2D and multiple protein ligands with a single molecule through allosteric modulation of the NKG2D receptor dimer/ligand interface.
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Affiliation(s)
- Aaron A. Thompson
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Michael B. Harbut
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - Pei-Pei Kung
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Nathan K. Karpowich
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - Jeffrey D. Branson
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - Joanna C. Grant
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Deborah Hagan
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - Heather A. Pascual
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Guoyun Bai
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | | | - Heather R. Coate
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Bernard C. Collins
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Marjorie Côte
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Christine F. Gelin
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | | | - Hadi Gholami
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Adam R. Huff
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - Luis Limon
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Kevin J. Lumb
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - Puiying A. Mak
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Kohki M. Nakafuku
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Edmund V. Price
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - Amy Y. Shih
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Mandana Tootoonchi
- Discovery Immunology, Janssen Research & Development, San Diego, CA92121
| | - Nadeem A. Vellore
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Jocelyn Wang
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Na Wei
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Jeannie Ziff
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Scott B. Berger
- Discovery Immunology, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - James P. Edwards
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Agnès Gardet
- Discovery Immunology, Janssen Research & Development, San Diego, CA92121
| | - Siquan Sun
- Discovery Immunology, Janssen Research & Development, San Diego, CA92121
| | - Jennifer E. Towne
- Discovery Immunology, Janssen Research & Development, San Diego, CA92121
| | | | - Zhicai Shi
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | | | - Marie-Laure Rives
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Sujata Sharma
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - Brock T. Shireman
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Samantha J. Allen
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
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11
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Guerrero De León E, Sánchez-Martínez H, Morán-Pinzón JA, Del Olmo Fernández E, López-Pérez JL. Computational Structural Revision of Elaeophorbate and Other Triterpenoids with the Help of NAPROC-13. A New Strategy for Structural Revision of Natural Products. JOURNAL OF NATURAL PRODUCTS 2023; 86:897-908. [PMID: 36881492 DOI: 10.1021/acs.jnatprod.2c01135] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A considerable number of natural products have been published in recent years with misassigned structure, even though they had been correctly elucidated in the past. The availability of databases containing revised structures can prevent the amplification of errors in structural elucidation. NAPROC-13, a dereplication tool based on the 13C chemical shift, has been used to search for substances that, possessing the same chemical shifts, have been described with different structures. The correct structure of these different structural proposals is verified by computational chemistry. This paper reports the structural revision of nine triterpenoids following this methodology.
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Affiliation(s)
- Estela Guerrero De León
- CIPFAR, Departamento de Farmacología, Facultad de Medicina, Universidad de Panamá, Avenue Octavio Mendez Pereira, Panama City 0824, Panama
| | - Hugo Sánchez-Martínez
- CIPFAR, Departamento de Farmacología, Facultad de Medicina, Universidad de Panamá, Avenue Octavio Mendez Pereira, Panama City 0824, Panama
| | - Juan A Morán-Pinzón
- CIPFAR, Departamento de Farmacología, Facultad de Medicina, Universidad de Panamá, Avenue Octavio Mendez Pereira, Panama City 0824, Panama
| | - Esther Del Olmo Fernández
- Departamento de Ciencias Farmacéuticas, Área de Química Farmacéutica, Facultad de Farmacia, CIETUS, IBSAL, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
| | - José L López-Pérez
- CIPFAR, Departamento de Farmacología, Facultad de Medicina, Universidad de Panamá, Avenue Octavio Mendez Pereira, Panama City 0824, Panama
- Departamento de Ciencias Farmacéuticas, Área de Química Farmacéutica, Facultad de Farmacia, CIETUS, IBSAL, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
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12
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Gouilleux B, Moussallieh FM, Lesot P. Anisotropic 1 H STD-NMR Spectroscopy: Exploration of Enantiomer-Polypeptide Interactions in Chiral Oriented Environments. Chemphyschem 2023; 24:e202200508. [PMID: 36196851 DOI: 10.1002/cphc.202200508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/01/2022] [Indexed: 11/07/2022]
Abstract
We explore and report for the first time the use of 1 H saturation transfer difference NMR experiments (STD-NMR) in weakly aligning chiral anisotropic media to identify the hydrogen sites of enantiomers of small chiral molecules interacting with the side-chain of poly-γ-benzyl-l-glutamate (PBLG), a helically chiral polypeptide polymer. The first experimental results obtained on three model mono-stereogenic compounds outcomes are highly promising and demonstrate the possibility to track down possible differences of spatial position of enantiomers at the vicinity of the polymer side-chain. Anisotropic STD experiments appear to be well suited for rapid screening of chiral analytes that bind favorably to orienting polymeric systems, while providing new insights into the mechanism of enantio-discrimination without resorting to the time-consuming determination of molecular order parameters.
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Affiliation(s)
- Boris Gouilleux
- Université Paris-Saclay, UFR d'Orsay, RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Bât. 410, 15, rue du Doyen Georges Poitou, 91405, Orsay cedex, France
| | - Francois-Marie Moussallieh
- Université Paris-Saclay, UFR d'Orsay, RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Bât. 410, 15, rue du Doyen Georges Poitou, 91405, Orsay cedex, France
| | - Philippe Lesot
- Université Paris-Saclay, UFR d'Orsay, RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Bât. 410, 15, rue du Doyen Georges Poitou, 91405, Orsay cedex, France.,Centre National de la Recherche Scientifique (CNRS), 3, rue Michel Ange, 75016, Paris, France
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13
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Stereochemical investigation of flexible macrocyclic cembranes depending on residual dipolar couplings method. Tetrahedron 2023. [DOI: 10.1016/j.tet.2023.133301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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14
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McCalpin SD, Fu R, Ravula T, Wu G, Ramamoorthy A. Magnetically aligned nanodiscs enable direct measurement of 17O residual quadrupolar coupling for small molecules. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 346:107341. [PMID: 36473327 DOI: 10.1016/j.jmr.2022.107341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
The use of 17O in NMR spectroscopy for structural studies has been limited due to its low natural abundance, low gyromagnetic ratio, and quadrupolar relaxation. Previous solution 17O work has primarily focused on studies of liquids where the 17O quadrupolar coupling is averaged to zero by isotropic molecular tumbling, and therefore has ignored the structural information contained in this parameter. Here, we use magnetically aligned polymer nanodiscs as an alignment medium to measure residual quadrupolar couplings (RQCs) for 17O-labelled benzoic acid in the aqueous phase. We show that increasing the magnetic field strength improves spectral sensitivity and resolution and that each satellite peak of the expected pentet pattern resolves clearly at 18.8 T. We observed no significant dependence of the RQC magnitudes on the magnetic field strength. However, changing the orientation of the alignment medium alters the RQC by a consistent factor, suggesting that 17O RQCs measured in this way can provide reliable orientational information for elucidations of molecular structures.
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Affiliation(s)
- Samuel D McCalpin
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Thirupathi Ravula
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gang Wu
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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15
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Epimeric Mixture Analysis and Absolute Configuration Determination Using an Integrated Spectroscopic and Computational Approach-A Case Study of Two Epimers of 6-Hydroxyhippeastidine. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010214. [PMID: 36615407 PMCID: PMC9822407 DOI: 10.3390/molecules28010214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/26/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Structural elucidation has always been challenging, and misassignment remains a stringent issue in the field of natural products. The growing interest in discovering unknown, complex natural structures accompanies the increasing awareness concerning misassignments in the community. The combination of various spectroscopic methods with molecular modeling has gained popularity in recent years. In this work, we demonstrated, for the first time, its power to fully elucidate the 2-dimensional and 3-dimensional structures of two epimers in an epimeric mixture of 6-hydroxyhippeastidine. DFT calculation of chemical shifts was first performed to assist the assignment of planar structures. Furthermore, relative and absolute configurations were established by three different ways of computer-assisted structure elucidation (CASE) coupled with ORD/ECD/VCD spectroscopies. In addition, the significant added value of OR/ORD computations to relative and absolute configuration determination was also revealed. Remarkably, the differentiation of two enantiomeric scaffolds (crinine and haemanthamine) was accomplished via OR/ORD calculations with cross-validation by ECD and VCD.
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16
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Cuadrado C, Daranas AH, Sarotti AM. May the Force (Field) Be with You: On the Importance of Conformational Searches in the Prediction of NMR Chemical Shifts. Mar Drugs 2022; 20:699. [PMID: 36355022 PMCID: PMC9694776 DOI: 10.3390/md20110699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/29/2022] [Accepted: 11/04/2022] [Indexed: 09/21/2023] Open
Abstract
NMR data prediction is increasingly important in structure elucidation. The impact of force field selection was assessed, along with geometry and energy cutoffs. Based on the conclusions, we propose a new approach named mix-J-DP4, which provides a remarkable increase in the confidence level of complex stereochemical assignments-100% in our molecular test set-with a very modest increment in computational cost.
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Affiliation(s)
- Cristina Cuadrado
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), 38206 La Laguna, Tenerife, Spain
| | - Antonio Hernández Daranas
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), 38206 La Laguna, Tenerife, Spain
| | - Ariel M. Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
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17
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Liu Y, Ndukwe IE, Reibarkh M, Martin GE, Williamson RT. Prediction of anisotropic NMR data without knowledge of alignment medium structure by surface decomposition. Phys Chem Chem Phys 2022; 24:20164-20182. [PMID: 35996986 DOI: 10.1039/d2cp02621j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Prediction of anisotropic NMR data directly from solute-medium interaction is of significant theoretical and practical interest, particularly for structure elucidation, configurational analysis and conformational studies of complex organic molecules and natural products. Current prediction methods require an explicit structural model of the alignment medium: a requirement either impossible or impractical on a scale necessary for small organic molecules. Here we formulate a comprehensive mathematical framework for a parametrization protocol that deconvolutes an arbitrary surface of the medium into several simple local landscapes that are distributed over the medium's surface by specific orientational order parameters. The shapes and order parameters of these local landscapes are determined via fitting that maximizes the congruence between experimentally determined anisotropic NMR measurables and their predicted counterparts, thus avoiding the need for an a priori knowledge of the global medium morphology. This method achieves substantial improvements in the accuracy of predicted anisotropic NMR values compared to current methods, as demonstrated herein with sixteen natural products. Furthermore, because this formalism extracts structural commonalities of the medium by combining anisotropic NMR data from different compounds, its robustness and accuracy are expected to improve as more experimental data become available for further re-optimization of fitting parameters.
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Affiliation(s)
- Yizhou Liu
- Analytical Research and Development, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, CT, 06340, USA.
| | - Ikenna E Ndukwe
- Analytical Research and Development, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - Mikhail Reibarkh
- Analytical Research and Development, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - Gary E Martin
- Analytical Research and Development, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - R Thomas Williamson
- Analytical Research and Development, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
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18
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Immel S, Köck M, Reggelin M. NMR-Based Configurational Assignments of Natural Products: How Floating Chirality Distance Geometry Calculations Simplify Gambling with 2 N-1 Diastereomers. JOURNAL OF NATURAL PRODUCTS 2022; 85:1837-1849. [PMID: 35820115 DOI: 10.1021/acs.jnatprod.2c00427] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Using NMR data, the assignment of the correct 3D configuration and conformation to unknown natural products is of pivotal importance in pharmaceutical and medicinal chemistry. In this report, we quantify the probability of configurational assignments to judge the quality of structural elucidations using Bayesian inference in combination with floating-chirality distance geometry simulations. Based on reference-free NOE/ROE data, residual dipolar couplings (RDCs), and residual quadrupolar couplings (RQCs) in various combinations, we demonstrate how the relative configurations of three natural compounds, namely, jatrohemiketal (1), artemisinin (2), and Taxol (3), can be unambiguously established without the necessity to carry out time-consuming DFT-based configurational and conformational analyses. Our results quantitatively describe how reliably molecular geometries can be inferred from experimental NMR data, thereby unequivocally unveiling remaining assignment ambiguities. The methodology presented here will dramatically reduce the risk of incorrect structural assignments based on the overinterpretation of incomplete data and DFT-based structure models in chemistry.
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Affiliation(s)
- Stefan Immel
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Matthias Köck
- Alfred-Wegener-Institut für Polar- und Meeresforschung in der Helmholtz-Gemeinschaft, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Michael Reggelin
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
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19
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Li XL, Ru T, Navarro-Vázquez A, Lindemann P, Nazaré M, Li XW, Guo YW, Sun H. Weizhouochrones: Gorgonian-Derived Symmetric Dimers and Their Structure Elucidation Using Anisotropic NMR Combined with DP4+ Probability and CASE-3D. JOURNAL OF NATURAL PRODUCTS 2022; 85:1730-1737. [PMID: 35792821 DOI: 10.1021/acs.jnatprod.2c00257] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Natural product dimers have intriguing structural features and often have remarkable pharmacological activities. We report here two uncommon marine gorgonian-derived symmetric dimers, weizhouochrones A (1) and B (2), with indenone-derived monomers, that were isolated from the coral Anthogorgia ochracea collected from the South China Sea. These dimers are difficult targets for structure elucidation that solely relies upon conventional NMR data such as NOEs and J-couplings. Here, to explore the application of emerging methods on the structure elucidation of challenging molecules, we explored a number of different anisotropic and computational NMR approaches. The measurements of anisotropic NMR parameters of weizhouochrone A, including residual dipolar couplings (RDCs) and residual chemical shift anisotropy (RCSA), allowed us to successfully determine the planar structure and its relative configuration. This result was corroborated by a computational NMR analysis based on DP4+ probability and computer-assisted 3D structure elucidation (CASE-3D).
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Affiliation(s)
- Xiao-Lu Li
- Group of Structural Chemistry and Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Tong Ru
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| | - Peter Lindemann
- Group of Medicinal Chemistry, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Marc Nazaré
- Group of Medicinal Chemistry, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Xu-Wen Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Yue-Wei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Han Sun
- Institute of Chemistry, Technical University of Berlin, Berlin 10623, Germany
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20
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Fuentes-Monteverde JCC, Nath N, Forero AM, Balboa EM, Navarro-Vázquez A, Griesinger C, Jiménez C, Rodríguez J. Connection of Isolated Stereoclusters by Combining 13C-RCSA, RDC, and J-Based Configurational Analyses and Structural Revision of a Tetraprenyltoluquinol Chromane Meroterpenoid from Sargassum muticum. Mar Drugs 2022; 20:462. [PMID: 35877755 PMCID: PMC9319238 DOI: 10.3390/md20070462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/06/2022] [Accepted: 07/15/2022] [Indexed: 12/10/2022] Open
Abstract
The seaweed Sargassum muticum, collected on the southern coast of Galicia, yielded a tetraprenyltoluquinol chromane meroditerpene compound known as 1b, whose structure is revised. The relative configuration of 1b was determined by J-based configurational methodology combined with an iJ/DP4 statistical analysis and further confirmed by measuring two anisotropic properties: carbon residual chemical shift anisotropies (13C-RCSAs) and one-bond 1H-13C residual dipolar couplings (1DCH-RDCs). The absolute configuration of 1b was deduced by ECD/OR/TD-DFT methods and established as 3R,7S,11R.
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Affiliation(s)
- Juan Carlos C. Fuentes-Monteverde
- Departamento de Química e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain; (J.C.C.F.-M.); (A.M.F.)
- NMR Based Structural Biology, MPI for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Nilamoni Nath
- Department of Chemistry, Gauhati University, Gopinath Bardoloi Nagar, Guwahati 781014, India;
| | - Abel M. Forero
- Departamento de Química e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain; (J.C.C.F.-M.); (A.M.F.)
| | - Elena M. Balboa
- Department of Chemical Engineering, Faculty of Science, Campus Ourense, University of Vigo, As Lagoas s/n, 32004 Ourense, Spain;
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, CCEN, Universidade Federal de Pernambuco, Cidade Universitária, Recife 50740-550, Brazil;
| | - Christian Griesinger
- NMR Based Structural Biology, MPI for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Carlos Jiménez
- Departamento de Química e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain; (J.C.C.F.-M.); (A.M.F.)
| | - Jaime Rodríguez
- Departamento de Química e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain; (J.C.C.F.-M.); (A.M.F.)
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21
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Elyashberg M, Novitskiy IM, Bates RW, Kutateladze AG, Williams CM. Reassignment of Improbable Natural Products Identified through Chemical Principle Screening. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mikhail Elyashberg
- Advanced Chemistry Development Inc. (ACD/Labs) Toronto ON, M5C 1B5 Canada
| | - Ivan M. Novitskiy
- Department of Chemistry and Biochemistry University of Denver Denver CO 80208 United States
| | - Roderick W. Bates
- Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371
| | - Andrei G. Kutateladze
- Department of Chemistry and Biochemistry University of Denver Denver CO 80208 United States
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences University of Queensland Brisbane 4072 Queensland Australia
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22
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Yu G, Wang G, Duan M, Jiang B, Zhang X, Li C, He L, Liu M. Self-Assembled Oligopeptide (FK) 4 as a Chiral Alignment Medium for the Anisotropic NMR Analysis of Organic Compounds. ACS APPLIED MATERIALS & INTERFACES 2022; 14:29223-29229. [PMID: 35712808 DOI: 10.1021/acsami.2c05506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Anisotropic NMR parameters have been proven to be powerful for the structural elucidation of organic molecules. Herein, we present an alignment medium based on the self-assembled (FK)4 oligopeptide, showing excellent properties in measurements of anisotropic NMR parameters in both D2O and CD3OD. The preparation of the (FK)4-based alignment medium is simple and rapid. The low viscosity of the anisotropic phase makes it easy to be transferred to the NMR tube. The alignment of the oligopeptide is fast, stable, and homogeneous, with weak background signals, permitting the acquirement of high-quality NMR spectra. The performance of this alignment medium in residual dipolar coupling measurements and diastereomer discriminations is demonstrated by analyzing several different analytes. The enantiodiscrimination property of the (FK)4 oligopeptide is revealed by the difference of residual chemical shift anisotropy of the two enantiomers in the 1D 13C spectrum, granting its potential use for the quantification and identification of enantiomers of small molecules.
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Affiliation(s)
- Gangjin Yu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guan Wang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mojie Duan
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Jiang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xu Zhang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lichun He
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Optics Valley Laboratory, Hubei 430074, China
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23
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Tsai YH, Amichetti M, Zanardi MM, Grimson R, Daranas AH, Sarotti AM. ML- J-DP4: An Integrated Quantum Mechanics-Machine Learning Approach for Ultrafast NMR Structural Elucidation. Org Lett 2022; 24:7487-7491. [PMID: 35508069 DOI: 10.1021/acs.orglett.2c01251] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A new tool, ML-J-DP4, provides an efficient and accurate method for determining the most likely structure of complex molecules within minutes using standard computational resources. The workflow involves combining fast Karplus-type J calculations with NMR chemical shifts predictions at the cheapest HF/STO-3G level enhanced using machine learning (ML), all embedded in the J-DP4 formalism. Our ML provides accurate predictions, which compare favorably alongside with other ML methods.
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Affiliation(s)
- Yi-Hsuan Tsai
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
| | - Milagros Amichetti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
| | - María Marta Zanardi
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, S2002QEO Rosario, Argentina
| | - Rafael Grimson
- Instituto de Investigación e Ingeniería Ambiental (IIIA), Universidad Nacional de San Martín (UNSAM) y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires 1650, Argentina
| | - Antonio Hernandez Daranas
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), La Laguna, 38206 Tenerife, Spain
| | - Ariel M Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
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24
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Sternberg U, Farès C. Statistical evaluation of simulated NMR data of flexible molecules. Phys Chem Chem Phys 2022; 24:9608-9618. [PMID: 35403649 DOI: 10.1039/d2cp00330a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new probability score-named χ-probability-is introduced for evaluating the fit of mixed NMR datasets to calculate molecular model ensembles, in order to answer challenging structural questions such as the determination of stereochemical configurations. Similar to the DP4 parameter, the χ-probability is based on Bayes theorem and expresses the probability that an experimental NMR dataset fits to a given individual within a finite set of candidate structures or configurations. Here, the χ-probability is applied to single out the correct configuration in four example cases, with increasing complexity and conformational mobility. The NMR data (which include RDCs, NOE distances and 3J couplings) are calculated from MDOC (Molecular Dynamics with Orientational Constraints) trajectories and are investigated against experimentally measured data. It is demonstrated that this approach singles out the correct stereochemical configuration with probabilities more than 98%, even for highly mobile molecules. In more demanding cases, a decisive χ-probability test requires that the datasets include high-quality NOE distances in addition to RDC values.
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Affiliation(s)
- Ulrich Sternberg
- Research Partner of Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. .,COSMOS-Software, Jena, Germany
| | - Christophe Farès
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, 45470 Mülheim an der Ruhr, Germany.
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25
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Immel S, Köck M, Reggelin M. Bayesian Inference Applied to NMR-Based Configurational Assignments by Floating Chirality Distance Geometry Calculations. J Am Chem Soc 2022; 144:6830-6838. [PMID: 35412312 DOI: 10.1021/jacs.2c00813] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using NMR data, the assignment of the correct 3D configuration and conformation to unknown natural products is of pivotal importance in pharmaceutical and medicinal chemistry. In this report, we quantify the quality and probability of structural elucidations using Bayesian inference in combination with floating chirality distance geometry simulations. Here, we will discuss the configurational analysis of three complex natural products including isopinocampheol (1), plakilactone H (2), and iodocallophycoic acid A (3) using NMR restraints of various types and in different combinations (residual dipolar couplings (RDCs) and NOE-derived distances). Our results quantitatively demonstrate how reliably molecular geometries can be inferred from experimental NMR data, unequivocally unveiling remaining assignment ambiguities. The methodology presented here can dramatically reduce the risk of incorrect structural assignments based on the overinterpretation of incomplete data in chemistry.
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Affiliation(s)
- Stefan Immel
- Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Matthias Köck
- Alfred-Wegener-Institut für Polar- and Meeresforschung in der Helmholtz-Gemeinschaft, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Michael Reggelin
- Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
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Pinto BN, Moura GA, Demuner AJ, Alvarenga ES. Structural elucidation of a novel pyrrolizidine alkaloid isolated from Crotalaria retusa L. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
Detection and characterisation of very weak, non-covalent interactions in solution is inherently challenging. Low affinity, short complex lifetime and a constant battle against entropy brings even the most sensitive spectroscopic methods to their knees. Herein we introduce a strategy for the accurate experimental description of weak chemical forces in solution. Its scope is demonstrated by the detailed geometric and thermodynamic characterisation of the weak halogen bond of a non-fluorinated aryl iodide and an ether oxygen (0.6 kJ mol-1 ). Our approach makes use of the entropic advantage of studying a weak force intramolecularly, embedded into a cooperatively folding system, and of the combined use of NOE- and RDC-based ensemble analyses to accurately describe the orientation of the donor and acceptor sites. Thermodynamic constants (ΔG, ΔH and ΔS), describing the specific interaction, were derived from variable temperature chemical shift analysis. We present a methodology for the experimental investigation of remarkably weak halogen bonds and other related weak forces in solution, paving the way for their improved understanding and strategic use in chemistry and biology.
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Affiliation(s)
- Stefan Peintner
- Department of Chemistry – BMCUppsala UniversitySE-75123UppsalaSweden
| | - Máté Erdélyi
- Department of Chemistry – BMCUppsala UniversitySE-75123UppsalaSweden
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Wesp S, Wolf K, Immel S, Reggelin M. Poly(arylisocyanides) as Versatile, Enantiodiscriminating Alignment Media for Small Molecules. Chempluschem 2022; 87:e202100507. [PMID: 35072980 DOI: 10.1002/cplu.202100507] [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: 11/17/2021] [Revised: 01/02/2022] [Indexed: 11/08/2022]
Abstract
Lyotropic liquid crystalline (LLC) phases of amino acid derived polyarylisocyanides were employed as chiral alignment media for the measurement of residual dipolar couplings (RDCs) of small chiral organic molecules. Anisotropic samples in CDCl3 displayed quadrupolar splittings of the deuterium signal in the range of several hundreds of Hertz. The LLC phases showed excellent orienting properties for a broad range of analytes bearing various functional groups. The precise extraction of RDCs in the range of up to ±40 Hertz from F2-coupled HSQC spectra was possible. Additionally, the chiral environment offers the opportunity for diastereomorphous interactions with the enantiomers of chiral analytes leading to two different sets of RDCs. This differential order effect was particularly pronounced with ketones and alcohols.
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Affiliation(s)
- Svenja Wesp
- Technische Universität Darmstadt, Clemens Schöpf Institut für Organische Chemie und Biochemie, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
| | - Kai Wolf
- Technische Universität Darmstadt, Clemens Schöpf Institut für Organische Chemie und Biochemie, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
| | - Stefan Immel
- Technische Universität Darmstadt, Clemens Schöpf Institut für Organische Chemie und Biochemie, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
| | - Michael Reggelin
- Technische Universität Darmstadt, Clemens Schöpf Institut für Organische Chemie und Biochemie, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
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29
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Aroulanda C, Lesot P. Molecular enantiodiscrimination by NMR spectroscopy in chiral oriented systems: Concept, tools, and applications. Chirality 2021; 34:182-244. [PMID: 34936130 DOI: 10.1002/chir.23386] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/20/2021] [Accepted: 10/15/2021] [Indexed: 11/06/2022]
Abstract
The study of enantiodiscriminations in relation to various facets of enantiomorphism (chirality/prochirality) and/or molecular symmetry is an exciting area of modern organic chemistry and an ongoing challenge for nuclear magnetic resonance (NMR) spectroscopists who have developed many useful analytical approaches to solve stereochemical problems. Among them, the anisotropic NMR using chiral aligning solvents has provided a set of new and original tools by making accessible all intramolecular, order-dependent NMR interactions (anisotropic interactions), such as residual chemical shift anisotropy (RCSA), residual dipolar coupling (RDC), and residual quadrupolar coupling (RQC) for spin I > 1/2, while preserving high spectral resolution. The force of NMR in enantiopure, oriented solvents lies on its ability to orient differently in average on the NMR timescale enantiomers of chiral molecules and enantiotopic elements of prochiral ones, leading distinct NMR spectra or signals to be detected. In this compendium mainly written for all chemists playing with (pro)chirality, we overview various key aspects of NMR in weakly aligning chiral solvents as the lyotropic liquid crystals (LLCs), in particular those developed in France to study (pro)chiral compounds in relation with chemists needs: study of enantiopurity of mixture, stereochemistry, natural isotopic fractionation, as well as molecular conformation and configuration. Key representative examples covering the diversity of enantiomorphism concept, and the main and most recent applications illustrating the analytical potential of this NMR in polypeptide-based chiral liquid crystals (CLCs) are examined. The latest analytical strategy developed to determine in-solution conformational distribution of flexibles solutes using NMR in polypeptide-based aligned solvents is also proposed.
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Affiliation(s)
- Christie Aroulanda
- RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Université Paris-Saclay, Orsay cedex, France
| | - Philippe Lesot
- RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Université Paris-Saclay, Orsay cedex, France
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Immel S, Köck M, Reggelin M. NMR-Based Configurational Assignments of Natural Products: Gibbs Sampling and Bayesian Inference Using Floating Chirality Distance Geometry Calculations. Mar Drugs 2021; 20:14. [PMID: 35049868 PMCID: PMC8781118 DOI: 10.3390/md20010014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/12/2021] [Accepted: 12/20/2021] [Indexed: 02/07/2023] Open
Abstract
Floating chirality restrained distance geometry (fc-rDG) calculations are used to directly evolve structures from NMR data such as NOE-derived intramolecular distances or anisotropic residual dipolar couplings (RDCs). In contrast to evaluating pre-calculated structures against NMR restraints, multiple configurations (diastereomers) and conformations are generated automatically within the experimental limits. In this report, we show that the "unphysical" rDG pseudo energies defined from NMR violations bear statistical significance, which allows assigning probabilities to configurational assignments made that are fully compatible with the method of Bayesian inference. These "diastereomeric differentiabilities" then even become almost independent of the actual values of the force constants used to model the restraints originating from NOE or RDC data.
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Affiliation(s)
- Stefan Immel
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Matthias Köck
- Alfred-Wegener-Institut für Polar-und Meeresforschung in der Helmholtz-Gemeinschaft, Am Handelshafen 12, 27570 Bremerhaven, Germany;
| | - Michael Reggelin
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
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Moreira LMG, Junker J. Sampling CASE Application for the Quality Control of Published Natural Product Structures. Molecules 2021; 26:molecules26247543. [PMID: 34946623 PMCID: PMC8708086 DOI: 10.3390/molecules26247543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 09/06/2021] [Accepted: 10/19/2021] [Indexed: 12/03/2022] Open
Abstract
Structure elucidation with NMR correlation data is dicey, as there is no way to tell how ambiguous the data set is and how reliably it will define a constitution. Many different software tools for computer assisted structure elucidation (CASE) have become available over the past decades, all of which could ensure a better quality of the elucidation process, but their use is still not common. Since 2011, WebCocon has integrated the possibility to generate theoretical NMR correlation data, starting from an existing structural proposal, allowing this theoretical data then to be used for CASE. Now, WebCocon can also read the recently presented NMReDATA format, allowing for uncomplicated access to CASE with experimental data. With these capabilities, WebCocon presents itself as an easily accessible Web-Tool for the quality control of proposed new natural products. Results of this application to several molecules from literature are shown and demonstrate how CASE can contribute to improve the reliability of Structure elucidation with NMR correlation data.
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Farley KA, Koos MRM, Che Y, Horst R, Limberakis C, Bellenger J, Lira R, Gil-Silva LF, Gil RR. Cross-Linked Poly-4-Acrylomorpholine: A Flexible and Reversibly Compressible Aligning Gel for Anisotropic NMR Analysis of Peptides and Small Molecules in Water. Angew Chem Int Ed Engl 2021; 60:26314-26319. [PMID: 34609778 DOI: 10.1002/anie.202106794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 11/07/2022]
Abstract
Determination of the solution conformation of both small organic molecules and peptides in water remains a substantial hurdle in using NMR solution conformations to guide drug design due to the lack of easy to use alignment media. Herein we report the design of a flexible compressible chemically cross-linked poly-4-acrylomorpholine gel that can be used for the alignment of both small molecules and cyclic peptides in water. To test the new gel, residual dipolar couplings (RDCs) and J-coupling constants were used in the configurational analysis of strychnine hydrochloride, a molecule that has been studied extensively in organic solvents as well as a small cyclic peptide that is known to form an α-helix in water. The conformational ensembles for each molecule with the best fit to the data are reported. Identification of minor conformers in water that cannot easily be determined by conventional NOE measurements will facilitate the use of RDC experiments in structure-based drug design.
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Affiliation(s)
- Kathleen A Farley
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Martin R M Koos
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Ye Che
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Reto Horst
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Chris Limberakis
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Justin Bellenger
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Ricardo Lira
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | | | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
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Farley KA, Koos MRM, Che Y, Horst R, Limberakis C, Bellenger J, Lira R, Gil‐Silva LF, Gil RR. Cross‐Linked Poly‐4‐Acrylomorpholine: A Flexible and Reversibly Compressible Aligning Gel for Anisotropic NMR Analysis of Peptides and Small Molecules in Water. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Martin R. M. Koos
- Department of Chemistry Carnegie Mellon University 4400 Fifth Avenue Pittsburgh PA 15213 USA
| | - Ye Che
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Reto Horst
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Chris Limberakis
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Justin Bellenger
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Ricardo Lira
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | | | - Roberto R. Gil
- Department of Chemistry Carnegie Mellon University 4400 Fifth Avenue Pittsburgh PA 15213 USA
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Navarro-Vázquez A. Computational Structural Revision of a 4-Hydroxy-3-(1'-angeloyloxy-2',3'-epoxy-3'-methyl)butylacetophenone Compound from Ageratina grandifolia. JOURNAL OF NATURAL PRODUCTS 2021; 84:2043-2047. [PMID: 34192466 DOI: 10.1021/acs.jnatprod.1c00398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The structure of the reported compound 4-hydroxy-3-((S)-1'-angeloyloxy-(R)-2',3'-epoxy-3'-methyl)butylacetophenone (1), isolated from Ageratina grandifolia, has been revised through the use of DFT computational predictions. Re-examination of the reported experimental and DFT computed chemical shifts has led to the proposal of a chromane skeleton rather than the original epoxide derivative. Empirical predictions of the 13C and 1H NMR shifts showed a much better fit for the chromane structure than for the epoxide. The relative configuration of the molecule was established using CASE-3D methodology on the basis of new DFT chemical shielding and J-coupling predictions, allowing the proposal of a new rel-2,2-dimethyl-3R-hydroxy-4S-(1-angeloyloxy)chromane structure (2) for the isolated compound. However, DFT prediction of the optical rotation for the CASE-3D selected configuration/conformations did not provide a conclusive answer for the absolute configuration.
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Affiliation(s)
- Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Avenida Professor Moraes Rego, 1235, Cidade Universitária, 50670-901, Recife, PE, Brazil
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Elyashberg M, Argyropoulos D. Computer Assisted Structure Elucidation (CASE): Current and future perspectives. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:669-690. [PMID: 33197069 DOI: 10.1002/mrc.5115] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/31/2020] [Accepted: 11/08/2020] [Indexed: 06/11/2023]
Abstract
The first efforts for the development of methods for Computer-Assisted Structure Elucidation (CASE) were published more than 50 years ago. CASE expert systems based on one-dimensional (1D) and two-dimensional (2D) Nuclear Magnetic Resonance (NMR) data have matured considerably by now. The structures of a great number of complex natural products have been elucidated and/or revised using such programs. In this article, we discuss the most likely directions in which CASE will evolve. We act on the premise that a synergistic interaction exists between CASE, new NMR experiments, and methods of computational chemistry, which are continuously being improved. The new developments in NMR experiments (long-range correlation experiments, pure-shift methods, coupling constants measurement and prediction, residual dipolar couplings [RDCs]), and residual chemical shift anisotropies [RCSAs], evolution of density functional theory (DFT), and machine learning algorithms will have an influence on CASE systems and vice versa. This is true also for new techniques for chemical analysis (Atomic Force Microscopy [AFM], "crystalline sponge" X-ray analysis, and micro-Electron Diffraction [micro-ED]), which will be used in combination with expert systems. We foresee that CASE will be utilized widely and become a routine tool for NMR spectroscopists and analysts in academic and industrial laboratories. We believe that the "golden age" of CASE is still in the future.
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Pérez-Vásquez A, Padilla-Mayne S, Martínez AL, Calderón JS, Macías-Rubalcava ML, Torres-Colín R, Rangel-Grimaldo M, Mata R. Antinociceptive Activity of Compounds from the Aqueous Extract of Melampodium divaricatum. Chem Biodivers 2021; 18:e2100369. [PMID: 34138517 DOI: 10.1002/cbdv.202100369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/17/2021] [Indexed: 01/05/2023]
Abstract
A decoction prepared from the aerial parts of Melampodium divaricatum showed antinociceptive and antihyperalgesic responses when tested in the formalin model in mice. From the CH2 Cl2 fraction of the decoction, two non-previously reported secondary metabolites, 3-O-β-D-glucopyranosyl-16α-hydroxy-ent-kaurane (1) and melampodiamide (2) [(2'R*,4'Z)-2'-hydroxy-N-[(2S*,3S*,4R*)-1,3,4-trihydroxyoctadec-2-yl]tetracos-4-enamide] were separated and characterized by spectroscopic, spectrometric, and computational techniques. The flavonoids isoquercitrin and hyperoside, which possessed noted antinociceptive properties, were obtained from the active AcOEt fraction of the decoction. The chemical composition of the essential oil of the plant was also analyzed by gas chromatography-mass spectrometry. The major constituents were (E)-caryophyllene, germacrene D, β-elemene, δ-elemene, γ-patchoulene, and 7-epi-α-selinene. Headspace solid-phase microextraction analysis detected (E)-caryophyllene as the main volatile compound of the plant.
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Affiliation(s)
- Araceli Pérez-Vásquez
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Sofía Padilla-Mayne
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Ana Laura Martínez
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - José S Calderón
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | | | - Rafael Torres-Colín
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Manuel Rangel-Grimaldo
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Rachel Mata
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
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Zanardi MM, Sarotti AM. Sensitivity Analysis of DP4+ with the Probability Distribution Terms: Development of a Universal and Customizable Method. J Org Chem 2021; 86:8544-8548. [DOI: 10.1021/acs.joc.1c00987] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- María Marta Zanardi
- Instituto de Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, S2002QEO Rosario, Argentina
| | - Ariel M. Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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38
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The advances of characterization and evaluation methods for the compatibility and assembly structure stability of food soft matter. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.04.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Köck M, Reggelin M, Immel S. Model-Free Approach for the Configurational Analysis of Marine Natural Products. Mar Drugs 2021; 19:md19060283. [PMID: 34063741 PMCID: PMC8223791 DOI: 10.3390/md19060283] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 12/17/2022] Open
Abstract
The NMR-based configurational analysis of complex marine natural products is still not a routine task. Different NMR parameters are used for the assignment of the relative configuration: NOE/ROE, homo- and heteronuclear J couplings as well as anisotropic parameters. The combined distance geometry (DG) and distance bounds driven dynamics (DDD) method allows a model-free approach for the determination of the relative configuration that is invariant to the choice of an initial starting structure and does not rely on comparisons with (DFT) calculated structures. Here, we will discuss the configurational analysis of five complex marine natural products or synthetic derivatives thereof: the cis-palau’amine derivatives 1a and 1b, tetrabromostyloguanidine (1c), plakilactone H (2), and manzamine A (3). The certainty of configurational assignments is evaluated in view of the accuracy of the NOE/ROE data available. These case studies will show the prospective breadth of application of the DG/DDD method.
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Affiliation(s)
- Matthias Köck
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Correspondence: (M.K.); (S.I.)
| | - Michael Reggelin
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany;
| | - Stefan Immel
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany;
- Correspondence: (M.K.); (S.I.)
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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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Krupp A, Noll M, Reggelin M. Valine derived poly (acetylenes) as versatile chiral lyotropic liquid crystalline alignment media for RDC-based structure elucidations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:577-586. [PMID: 32012341 DOI: 10.1002/mrc.5003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/22/2020] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
Anisotropic samples of lyotropic liquid crystalline (LLC) phases of valine derived polyaryl acetylenes were employed as chiral alignment media for the measurement of residual dipolar couplings (RDCs) of 12 small, chiral, organic molecules. The quadrupolar splitting of the deuterium signal of CDCl3 can be adjusted by temperature and concentration changes from 0 to 350 Hz. The LLC phases showed excellent orienting properties for all analytes bearing various functional groups. The precise extraction of RDCs in the range of up to ±30 Hz from F2-coupled HSQC spectra was possible. Additionally, the chiral environment led to diastereomorphous interactions with the enantiomers of chiral analytes leading to two different sets of RDCs. This differential order effect was particularly pronounced with H-bond donors like alcohols and 2° amines.
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Affiliation(s)
- Alexis Krupp
- Clemens Schöpf Institut for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
- Nitrochemie Aschau GmbH, Aschau am Inn, Germany
| | - Markus Noll
- Clemens Schöpf Institut for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Michael Reggelin
- Clemens Schöpf Institut for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
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de Melo Sousa CM, Giordani RB, de Almeida WAM, Griesinger C, Gil RR, Navarro-Vázquez A, Hallwass F. Effect of the solvent on the conformation of monocrotaline as determined by isotropic and anisotropic NMR parameters. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:561-568. [PMID: 31715029 DOI: 10.1002/mrc.4968] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/25/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
The conformation in solution of monocrotaline, a pyrrolizidine alkaloid presenting an eleven-membered macrocyclic diester ring, has been investigated using a combination of isotropic and anisotropic nuclear magnetic resonance parameters measured in four solvents of different polarity (D2 O, DMSO-d6 , CDCl3 , and C6 D6 ). Anisotropic nuclear magnetic resonance parameters were measured in different alignment media, based on their compatibility with the solvent of interest: cromoglycate liquid crystal solution was used for D2 O, whereas a poly (methyl methacrylate) polymer gel was chosen for CDCl3 and C6 D6 , and a poly (hydroxyethyl methacrylate) gel for DMSO-d6 . Whereas the pyrrolizidine ring shows an E6 exo-puckered conformation in all of the solvents, the macrocyclic eleven-membered ring adopts different populations of syn-parallel and anti-parallel relative orientation of the carbonyl groups according to the polarity of the solvent.
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Affiliation(s)
- Cleyton Marcos de Melo Sousa
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
- Instituto Federal de Pernambuco, Caruaru, Pernambuco, Brazil
| | - Raquel Brandt Giordani
- Laboratório de Farmacognosia, Departamento de Farmácia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | - Christian Griesinger
- Abteilung für NMR-basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Fernando Hallwass
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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43
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Navarro-Vázquez A. A DFT/machine-learning hybrid method for the prediction of 3 J HCCH couplings. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:414-422. [PMID: 32808318 DOI: 10.1002/mrc.5087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 08/09/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
A machine learning model for the prediction of vicinal proton-proton couplings has been developed based on a hybrid representation that includes geometrical and electronic parameters derived from natural bond orbital (NBO) analysis of low-level BLYP/STO-3G computations. The model can predict 3 JHH couplings with accuracy comparable or better than the well-known Altona equation, and it can provide sensible 3 JHH predictions in systems not well handled by the Altona equation such as epoxide or cyclopropane rings.
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Affiliation(s)
- Armando Navarro-Vázquez
- Departamento de Química Fundamental, CCEN, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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44
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Reggelin M, Immel S. Configurational Analysis by Residual Dipolar Couplings: Critical Assessment of "Structural Noise" from Thermal Vibrations. Angew Chem Int Ed Engl 2021; 60:3412-3416. [PMID: 33137233 PMCID: PMC7898695 DOI: 10.1002/anie.202011081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Indexed: 12/11/2022]
Abstract
The certainty of configurational assignments of natural products based on anisotropic NMR parameters, such as residual dipolar couplings (RDCs), must be amended by estimates on structural noise emerging from thermal vibrations. We show that vibrational analysis significantly affects the error margins with which RDCs can be back-calculated from molecular models, and the implications of thermal motions on the differentiability of diastereomers are derived.
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Affiliation(s)
- Michael Reggelin
- Technische Universität DarmstadtClemens Schöpf Institut für Organische Chemie und BiochemieAlarich-Weiss-Strasse 464287DarmstadtGermany
| | - Stefan Immel
- Technische Universität DarmstadtClemens Schöpf Institut für Organische Chemie und BiochemieAlarich-Weiss-Strasse 464287DarmstadtGermany
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45
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Reggelin M, Immel S. Configurational Analysis by Residual Dipolar Couplings: Critical Assessment of “Structural Noise” from Thermal Vibrations. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Michael Reggelin
- Technische Universität Darmstadt Clemens Schöpf Institut für Organische Chemie und Biochemie Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Stefan Immel
- Technische Universität Darmstadt Clemens Schöpf Institut für Organische Chemie und Biochemie Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
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46
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Abstract
Halogens cause pronounced and systematic effects on the 13C NMR chemical shift (δ13C) of an adjacent carbon nucleus, usually leading to a decrease in the values across the halogen series. Although this normal halogen dependence (NHD) is known in organic and inorganic compounds containing the carbon atom in its neutral and cationic forms, information about carbanions is scarce. To understand how δ13C changes in molecules with different charges, the shielding mechanisms of CHX3, CX3+, and CX3- (X = Cl, Br, or I) systems are investigated via density functional theory calculations and further analyzed by decomposition into contributions of natural localized molecular orbitals. An inverse halogen dependence (IHD) is determined for the anion series as a result of the negative spin-orbit contribution instead of scalar paramagnetic effects. The presence of a carbon nonbonding orbital in anions allows magnetic couplings that generate a deshielding effect on the nucleus and contradicts the classical association between δ13C and atomic charge.
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Affiliation(s)
- Renan V Viesser
- Institute of Chemistry, University of Campinas - UNICAMP, P.O. Box 6154, 13083-970, Campinas, São Paulo, Brazil.
| | - Cláudio F Tormena
- Institute of Chemistry, University of Campinas - UNICAMP, P.O. Box 6154, 13083-970, Campinas, São Paulo, Brazil.
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47
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Monroe AZ, Gordon WH, Wood JS, Martin GE, Morgan JB, Williamson RT. Structural revision of a Wnt/β-catenin modulator and confirmation of cannabielsoin constitution and configuration. Chem Commun (Camb) 2021; 57:5658-5661. [DOI: 10.1039/d1cc01971f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this report, we revise the structure for a previously reported synthetic product proposed to be the 1R,2S-cannabidiol epoxide and reassign it as cannabielsoin using anisotropic NMR and synthetic chemistry methods.
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Affiliation(s)
- Angelina Z. Monroe
- Department of Chemistry & Biochemistry
- University of North Carolina Wilmington
- Wilmington
- USA
| | - William H. Gordon
- Department of Chemistry & Biochemistry
- University of North Carolina Wilmington
- Wilmington
- USA
| | - Jared S. Wood
- Department of Chemistry & Biochemistry
- University of North Carolina Wilmington
- Wilmington
- USA
| | - Gary E. Martin
- Department of Chemistry
- Seton Hall University
- South Orange
- USA
| | - Jeremy B. Morgan
- Department of Chemistry & Biochemistry
- University of North Carolina Wilmington
- Wilmington
- USA
| | - R. Thomas Williamson
- Department of Chemistry & Biochemistry
- University of North Carolina Wilmington
- Wilmington
- USA
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48
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Daranas AH, Sarotti AM. Are Computational Methods Useful for Structure Elucidation of Large and Flexible Molecules? Belizentrin as a Case Study. Org Lett 2020; 23:503-507. [PMID: 33382270 DOI: 10.1021/acs.orglett.0c04016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Quantum mechanical NMR methods are progressively becoming decisive in structure elucidation. However, problems arise using low-level calculations for complex molecules, whereas methods using higher levels of theory are not practical for large molecules. This report outlines a synergistic effort employing computationally inexpensive quantum mechanical NMR calculations with conformer selection incorporating 3JHH values as a way to solve the structure of large, complex, and highly flexible molecules using readily available computational resources with belizentrin as a case study.
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Affiliation(s)
- Antonio Hernández Daranas
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), La Laguna 38206, Tenerife, Spain
| | - Ariel M Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
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49
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Recchia MJJ, Cohen RD, Liu Y, Sherer EC, Harper JK, Martin GE, Williamson RT. "One-Shot" Measurement of Residual Chemical Shift Anisotropy Using Poly-γ-benzyl-l-glutamate as an Alignment Medium. Org Lett 2020; 22:8850-8854. [PMID: 33140974 DOI: 10.1021/acs.orglett.0c03225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A method for the measurement of residual chemical shift anisotropy in one experiment using a biphasic isotropic/anisotropic lyotropic liquid crystalline medium based on poly-γ-benzyl-l-glutamate as the alignment medium is presented. This approach is demonstrated on the model compound strychnine and neotricone, a depsidone natural product with a questionable structural assignment based on comparison with the closely related excelsione and in-depth density functional theory calculations.
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Affiliation(s)
- Michael J J Recchia
- Department of Chemistry & Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28409, United States
| | - Ryan D Cohen
- Analytical Research & Development, Merck & Company Inc., Rahway, New Jersey 07065, United States
| | - Yizhou Liu
- Analytical Research & Development, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Edward C Sherer
- Analytical Research & Development, Merck & Company Inc., Rahway, New Jersey 07065, United States
| | - James K Harper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Gary E Martin
- Department of Chemistry, Seton Hall University, South Orange, New Jersey 07079, United States
| | - R Thomas Williamson
- Department of Chemistry & Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28409, United States
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50
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Sager E, Tzvetkova P, Gossert AD, Piechon P, Luy B. Determination of Configuration and Conformation of a Reserpine Derivative with Seven Stereogenic Centers Using Molecular Dynamics with RDC-Derived Tensorial Constraints*. Chemistry 2020; 26:14435-14444. [PMID: 32744785 PMCID: PMC7702126 DOI: 10.1002/chem.202002642] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/22/2020] [Indexed: 11/11/2022]
Abstract
NMR-based determination of the configuration of complex molecules containing many stereocenters is often not possible using traditional NOE data and coupling patterns. Making use of residual dipolar couplings (RDCs), we were able to determine the relative configuration of a natural product containing seven stereocenters, including a chiral amine lacking direct RDC data. To identify the correct relative configuration out of 32 possible ones, experimental RDCs were used in three different approaches for data interpretation: by fitting experimental data based singular value decomposition (SVD) using a single alignment tensor and either (i) a single conformer or (ii) multiple conformers, or alternatively (iii) using molecular dynamics simulations with tensorial orientational constraints (MDOC). Even though in all three approaches one and the same configuration could be selected and clear discrimination between possible configurations was achieved, the experimental data was not fully satisfied by the methods based on single tensor approaches. While these two approaches are faster, only MDOC is able to fully reproduce experimental results, as the obtained conformational ensemble adequately covers the conformational space necessary to describe the molecule with inherent flexibility.
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Affiliation(s)
- Emine Sager
- Institut für Organische ChemieKarlsruher Institut für Technologie (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
- Novartis Pharma AGNovartis Institutes for Biomedical Research4002BaselSwitzerland
| | - Pavleta Tzvetkova
- Institut für Biologische Grenzflächen 4—Magnetische ResonanzKarlsruher Institut für Technologie (KIT)Postfach 364076021KarlsruheGermany
| | - Alvar D. Gossert
- Novartis Pharma AGNovartis Institutes for Biomedical Research4002BaselSwitzerland
- Institut für Molekularbiologie und BiophysikETH Zürich8093ZürichSwitzerland
| | - Philippe Piechon
- Novartis Pharma AGNovartis Institutes for Biomedical Research4002BaselSwitzerland
| | - Burkhard Luy
- Institut für Organische ChemieKarlsruher Institut für Technologie (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
- Institut für Biologische Grenzflächen 4—Magnetische ResonanzKarlsruher Institut für Technologie (KIT)Postfach 364076021KarlsruheGermany
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