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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: 7] [Impact Index Per Article: 1.8] [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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Tzvetkova P, Sternberg U, Gloge T, Navarro-Vázquez A, Luy B. Configuration determination by residual dipolar couplings: accessing the full conformational space by molecular dynamics with tensorial constraints. Chem Sci 2019; 10:8774-8791. [PMID: 31803450 PMCID: PMC6849632 DOI: 10.1039/c9sc01084j] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/19/2019] [Indexed: 12/27/2022] Open
Abstract
Residual dipolar couplings (RDCs) and other residual anisotropic NMR parameters provide valuable structural information of high quality and quantity, bringing detailed structural models of flexible molecules in solution in reach. The corresponding data interpretation so far is directly or indirectly based on the concept of a molecular alignment tensor, which, however, is ill-defined for flexible molecules. The concept is typically applied to a single or a small set of lowest energy structures, ignoring the effect of vibrational averaging. Here, we introduce an entirely different approach based on time averaged molecular dynamics with dipolar couplings as tensorial orientational restraints that can be used to solve structural problems in molecules of any size without the need of introducing an explicit molecular alignment tensor into the computation. RDC restraints are represented by their full 3D interaction tensor in the laboratory frame, for which pseudo forces are calculated using a secular dipolar Hamiltonian as the target. The resulting rotational averaging of each individual tensorial restraint leads to structural ensembles that best fulfil the experimental data. Using one-bond RDCs, the approach has been implemented in the force field procedures of the program COSMOS and extensively tested. A concise theoretical introduction, including the special treatment of force fields for stable and fast MD simulations, as well as applications regarding configurational analyses of small to medium-sized organic molecules with different degrees of flexibility, is given. The observed results are discussed in detail.
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Affiliation(s)
- Pavleta Tzvetkova
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
| | - Ulrich Sternberg
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
| | - Thomas Gloge
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
| | - Armando Navarro-Vázquez
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
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Zong W, Li GW, Cao JM, Lei X, Hu ML, Sun H, Griesinger C, Tan RX. An Alignment Medium for Measuring Residual Dipolar Couplings in Pure DMSO: Liquid Crystals from Graphene Oxide Grafted with Polymer Brushes. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511435] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wen Zong
- College of Chemistry & Materials Engineering; Wenzhou University; Wenzhou 325035 P.R. China
| | - Gao-Wei Li
- Institute of Functional Biomolecules; State Key Laboratory of Pharmaceutical Biotechnology; Nanjing University; Nanjing 210093 P.R. China
| | - Jiang-Ming Cao
- Institute of Functional Biomolecules; State Key Laboratory of Pharmaceutical Biotechnology; Nanjing University; Nanjing 210093 P.R. China
| | - Xinxiang Lei
- College of Chemistry & Materials Engineering; Wenzhou University; Wenzhou 325035 P.R. China
| | - Mao-Lin Hu
- College of Chemistry & Materials Engineering; Wenzhou University; Wenzhou 325035 P.R. China
| | - Han Sun
- Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology; Max Planck Institute for Biophysical Chemistry; 37077 Göttingen Germany
| | - Ren Xiang Tan
- Institute of Functional Biomolecules; State Key Laboratory of Pharmaceutical Biotechnology; Nanjing University; Nanjing 210093 P.R. China
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Zong W, Li GW, Cao JM, Lei X, Hu ML, Sun H, Griesinger C, Tan RX. An Alignment Medium for Measuring Residual Dipolar Couplings in Pure DMSO: Liquid Crystals from Graphene Oxide Grafted with Polymer Brushes. Angew Chem Int Ed Engl 2016; 55:3690-3. [DOI: 10.1002/anie.201511435] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Wen Zong
- College of Chemistry & Materials Engineering; Wenzhou University; Wenzhou 325035 P.R. China
| | - Gao-Wei Li
- Institute of Functional Biomolecules; State Key Laboratory of Pharmaceutical Biotechnology; Nanjing University; Nanjing 210093 P.R. China
| | - Jiang-Ming Cao
- Institute of Functional Biomolecules; State Key Laboratory of Pharmaceutical Biotechnology; Nanjing University; Nanjing 210093 P.R. China
| | - Xinxiang Lei
- College of Chemistry & Materials Engineering; Wenzhou University; Wenzhou 325035 P.R. China
| | - Mao-Lin Hu
- College of Chemistry & Materials Engineering; Wenzhou University; Wenzhou 325035 P.R. China
| | - Han Sun
- Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology; Max Planck Institute for Biophysical Chemistry; 37077 Göttingen Germany
| | - Ren Xiang Tan
- Institute of Functional Biomolecules; State Key Laboratory of Pharmaceutical Biotechnology; Nanjing University; Nanjing 210093 P.R. China
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Liu LY, Sun H, Griesinger C, Liu JK. The Use of a Combination of RDC and Chiroptical Spectroscopy for Determination of the Absolute Configuration of Fusariumin A from the Fungus Fusarium sp. NATURAL PRODUCTS AND BIOPROSPECTING 2016; 6:41-8. [PMID: 26791752 PMCID: PMC4749523 DOI: 10.1007/s13659-015-0084-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 12/21/2015] [Indexed: 05/28/2023]
Abstract
A new alkylpyrrole derivative, fusariumin A (1), was isolated from the culture broth of the fungus Fusarium sp. The absolute configuration of fuasiumin A has been established as (2'R,3'R) using a combination of RDC (residual dipolar coupling)-based NMR and DFT-supported chiroptical spectroscopy. It is worth to note that in this study without the aid of the RDC analysis, an unambiguous determination of configuration and conformation was not feasible due to the excessive conformational possibilities of this open-chain compound.
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Affiliation(s)
- Liang-Yan Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Han Sun
- Department of NMR-based Structural Biology, Max-Planck-Institute of Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
- Leibniz-Institut für Molekulare Pharmakologie, 13125, Berlin, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max-Planck-Institute of Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Ji-Kai Liu
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, 430074, China.
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Reinscheid F, Reinscheid U. Stereochemical analysis of (+)-limonene using theoretical and experimental NMR and chiroptical data. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.10.061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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7
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Trigo-Mouriño P, de la Fuente MC, Gil RR, Sánchez-Pedregal VM, Navarro-Vázquez A. Conformational Analysis of the Anti-obesity Drug Lorcaserin in Water: How To Take Advantage of Long-Range Residual Dipolar Couplings. Chemistry 2013; 19:14989-97. [DOI: 10.1002/chem.201202509] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 06/28/2013] [Indexed: 11/07/2022]
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Schmidts V, Fredersdorf M, Lübken T, Porzel A, Arnold N, Wessjohann L, Thiele CM. RDC-based determination of the relative configuration of the fungicidal cyclopentenone 4,6-diacetylhygrophorone A12. JOURNAL OF NATURAL PRODUCTS 2013; 76:839-844. [PMID: 23659349 DOI: 10.1021/np300728b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The hygrophorones, a class of cyclopentenones isolated from fruiting bodies of the genus Hygrophorus (basidiomycetes), show promising antifungal activity. While the constitution of 4,6-diacetylhygrophorone A(12) (3) and the relative configuration of the stereogenic centers in the cyclopentenone ring were elucidated using standard NMR and MS techniques, the relative configuration of the exocyclic stereogenic center could not be assigned. By introducing a sample of 3 into an alignment medium and measuring anisotropic NMR parameters, namely, residual dipolar couplings, we were able to unambiguously determine the relative configuration of all three stereogenic centers in 4,6-diacetylhygrophorone A(12) simultaneously by fitting several structure proposals to the experimental data.
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Affiliation(s)
- Volker Schmidts
- Clemens Schöpf Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Petersenstraße 22, Darmstadt, Germany
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Müller M, Orben CM, Schützenmeister N, Schmidt M, Leonov A, Reinscheid UM, Dittrich B, Griesinger C. The absolute configuration of (+)- and (-)-erythro-mefloquine. Angew Chem Int Ed Engl 2013; 52:6047-9. [PMID: 23616269 DOI: 10.1002/anie.201300258] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Indexed: 11/05/2022]
Abstract
The controversy over the absolute configuration of (+)-erythro-mefloquine, the less psychosis-causing enantiomer of the anti-malarial drug Lariam, has been resolved by Mosher ester crystallization. The configuration determined previously by physical methods is correct, whereas the configuration determined by three enantioselective syntheses is wrong.
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Affiliation(s)
- Michael Müller
- Max-Planck-Institut für Biophysikalische Chemie, Department of NMR-Based Structural Biology, Am Fassberg 11, 37077 Göttingen, Germany
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11
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Chiral Derivatizing Agents, Macrocycles, Metal Complexes, and Liquid Crystals for Enantiomer Differentiation in NMR Spectroscopy. Top Curr Chem (Cham) 2013; 341:1-68. [DOI: 10.1007/128_2013_433] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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12
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Schmidt M, Sun H, Leonov A, Griesinger C, Reinscheid UM. Chiral discrimination of amines by anisotropic NMR parameters using chiral polyacrylamide-based gels. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50 Suppl 1:S38-S44. [PMID: 23280659 DOI: 10.1002/mrc.3886] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Revised: 09/01/2012] [Accepted: 09/14/2012] [Indexed: 05/28/2023]
Abstract
A new chiral alignment medium for dimethyl sulfoxide, methanol, and water as solvents was developed. Because both enantiomers of the gel are available, it is possible to enantiodiscriminate natural products such as strychnine HCl that naturally occurs as single enantiomer. With the two methods of achieving anisotropy, namely stretching and confinement, the degree of alignment can be adjusted, and the director changed from horizontal to vertical. This increases the applicability. Three compounds were enantiodiscriminated on the basis of residual dipolar coupling data: mefloquine HCl, strychnine HCl, and menthylamine HCl.
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Affiliation(s)
- Manuel Schmidt
- Max Planck Institute for Biophysical Chemistry, NMR II, 37077 Göttingen, Germany
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13
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Meyer NC, Krupp A, Schmidts V, Thiele CM, Reggelin M. Polyacetylenes as Enantiodifferentiating Alignment Media. Angew Chem Int Ed Engl 2012; 51:8334-8. [DOI: 10.1002/anie.201201891] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 06/22/2012] [Indexed: 11/05/2022]
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14
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Meyer NC, Krupp A, Schmidts V, Thiele CM, Reggelin M. Polyacetylenes as Enantiodifferentiating Alignment Media. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201891] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Whitson EL, Sun H, Thomas CL, Henrich CJ, Sayers TJ, McMahon JB, Griesinger C, McKee TC. Synergistic TRAIL sensitizers from Barleria alluaudii and Diospyros maritima. JOURNAL OF NATURAL PRODUCTS 2012; 75:394-9. [PMID: 22313254 PMCID: PMC3311710 DOI: 10.1021/np200805z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Barleria alluaudii and Diospyros maritima were both investigated as part of an ongoing search for synergistic TRAIL (tumor necrosis factor-α-related apoptosis-inducing ligand) sensitizers. As a result of this study, two naphthoquinone epoxides, 2,3-epoxy-2,3-dihydrolapachol (1) and 2,3-epoxy-2,3-dihydro-8-hydroxylapachol (2), both not previously isolated from natural sources, and the known 2-methylanthraquinone (3) were identified from B. alluaudii. Time-dependent density functional theory (TD-DFT) calculations of electronic circular dichroism (ECD) spectra were utilized to establish the absolute configuration of 1 and 2. Additionally, five known naphthoquinone derivatives, maritinone (4), elliptinone (5), plumbagin (6), (+)-cis-isoshinanolone (7), and ethylidene-6,6'-biplumbagin (8), were isolated from D. maritima. Compounds 1, 2, and 4-6 showed varying levels of synergy with TRAIL. Maritinone (4) and elliptinone (5) showed the highest synergistic effect, with more than a 3-fold increase in activity observed with TRAIL than with compound alone.
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Affiliation(s)
- Emily L. Whitson
- Molecular Targets Laboratory, Molecular Discovery Program, Center for Cancer Research, NCI-Frederick, Frederick, Maryland 21702, United States
| | - Han Sun
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Cheryl L. Thomas
- Molecular Targets Laboratory, Molecular Discovery Program, Center for Cancer Research, NCI-Frederick, Frederick, Maryland 21702, United States
| | - Curtis J. Henrich
- Molecular Targets Laboratory, Molecular Discovery Program, Center for Cancer Research, NCI-Frederick, Frederick, Maryland 21702, United States
- SAIC-Frederick, Inc., Frederick, Maryland 21702, United States
| | - Thomas J. Sayers
- SAIC-Frederick, Inc., Frederick, Maryland 21702, United States
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, NCI-Frederick, Frederick, Maryland 21702, United States
| | - James B. McMahon
- Molecular Targets Laboratory, Molecular Discovery Program, Center for Cancer Research, NCI-Frederick, Frederick, Maryland 21702, United States
| | - Christian Griesinger
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Tawnya C. McKee
- Molecular Targets Laboratory, Molecular Discovery Program, Center for Cancer Research, NCI-Frederick, Frederick, Maryland 21702, United States
- Corresponding Author: Tel: (301) 846-1943. Fax: (301) 846-6851.
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Ge HM, Sun H, Jiang N, Qin YH, Dou H, Yan T, Hou YY, Griesinger C, Tan RX. Relative and Absolute Configuration of Vatiparol (1 mg): A Novel Anti-inflammatory Polyphenol. Chemistry 2012; 18:5213-21. [DOI: 10.1002/chem.201104078] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Indexed: 12/21/2022]
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17
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Schmidt M, Sun H, Rogne P, Scriba GKE, Griesinger C, Kuhn LT, Reinscheid UM. Determining the Absolute Configuration of (+)-Mefloquine HCl, the Side-Effect-Reducing Enantiomer of the Antimalaria Drug Lariam. J Am Chem Soc 2012; 134:3080-3. [DOI: 10.1021/ja209050k] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manuel Schmidt
- Department of NMR-Based Structural
Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Han Sun
- Department of NMR-Based Structural
Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Per Rogne
- European Neuroscience Institute Göttingen (ENI-G), Grisebachstraße
5, 37077 Göttingen, Germany
- DFG Research Center Molecular Physiology of the Brain (CMPB) and Cluster
of Excellence 171 “Microscopy at the Nanometer
Range”, Göttingen, Germany
| | - Gerhard K. E. Scriba
- Department of Pharmaceutical
Chemistry, University of Jena, Philosophenweg
14, 07743 Jena, Germany
| | - Christian Griesinger
- Department of NMR-Based Structural
Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Lars T. Kuhn
- European Neuroscience Institute Göttingen (ENI-G), Grisebachstraße
5, 37077 Göttingen, Germany
- DFG Research Center Molecular Physiology of the Brain (CMPB) and Cluster
of Excellence 171 “Microscopy at the Nanometer
Range”, Göttingen, Germany
| | - Uwe M. Reinscheid
- Department of NMR-Based Structural
Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Pérez-Balado C, Sun H, Griesinger C, de Lera ÁR, Navarro-Vázquez A. Residual Dipolar Coupling Enhanced NMR Spectroscopy and Chiroptics: A Powerful Combination for the Complete Elucidation of Symmetrical Small Molecules. Chemistry 2011; 17:11983-6. [DOI: 10.1002/chem.201101385] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Indexed: 11/08/2022]
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Kramer M, Kleinpeter E. A conformational study of N-acetyl glucosamine derivatives utilizing residual dipolar couplings. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 212:174-185. [PMID: 21802325 DOI: 10.1016/j.jmr.2011.06.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 06/22/2011] [Accepted: 06/25/2011] [Indexed: 05/31/2023]
Abstract
The conformational analyses of six non-rigid N-acetyl glucosamine (NAG) derivatives employing residual dipolar couplings (RDCs) and NOEs together with molecular dynamics (MD) simulations are presented. Due to internal dynamics we had to consider different conformer ratios existing in solution. The good quality of the correlation between theoretically and experimentally obtained RDCs show the correctness of the calculated conformers even if the ratios derived from the MD simulations do not exactly meet the experimental data. If possible, the results were compared to former published data and commented.
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Affiliation(s)
- Markus Kramer
- University of Potsdam, Department of Chemistry, Karl-Liebknecht-Str. 24-25, 14476 Potsdam/Golm, Germany
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Sun H, Reinscheid UM, Whitson EL, d'Auvergne EJ, Ireland CM, Navarro-Vázquez A, Griesinger C. Challenge of large-scale motion for residual dipolar coupling based analysis of configuration: the case of fibrosterol sulfate A. J Am Chem Soc 2011; 133:14629-36. [PMID: 21776994 DOI: 10.1021/ja205295q] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Fibrosterol sulfate A is a polysulfated bis-steroid with an atypical side chain. Due to the flexibility of the linker, large-scale motions that change dramatically the shape of the entire molecule are expected. Such motions pose major challenges to the structure elucidation and the correct determination of configuration. In this study, we will describe the determination of the relative configuration of fibrosterol sulfate A through a residual dipolar coupling based multiple alignment tensor analysis complemented by molecular dynamics. For completeness, we applied also the single tensor approach which is unreliable due to the large-scale motions and compare the results.
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Affiliation(s)
- Han Sun
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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