1
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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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2
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Venturi L, Bua E, Caputo G, Mileo V. Residual Dipolar Coupling Based Conformational Analysis Allows the Configurational Assessment of Steroids with up to Eight Stereocenters. Chempluschem 2023; 88:e202200391. [PMID: 36811319 DOI: 10.1002/cplu.202200391] [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: 11/07/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023]
Abstract
Residual dipolar couplings (RDCs) induced by anisotropic media have been proved as a powerful tool for the structure elucidation of organic molecules in solution in nuclear magnetic resonance (NMR) based analysis. The value of dipolar couplings to solve complex conformational and configurational problems represents indeed an appealing analytical tool for the pharmaceutical industry particularly focusing on the stereochemistry characterization of NCEs since the early phase of the drug development process. In our work, RDCs were used for the conformational and configurational study of synthetic steroids with multiple stereocenters - prednisone and beclomethasone dipropionate (BDP) -. For both molecules the correct relative configuration was identified among all the possible diastereoisomers (32 and 128 respectively) arising from the compounds stereogenic carbons. Only for prednisone the use of additional experimental data (i. e. rOes) was necessary to resolve the right stereochemical structure.
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Affiliation(s)
- Luca Venturi
- Preclinical Analytics and Early Formulations Department, Chiesi Farmaceutici Spa, Largo Belloli 11/A, 43123, Parma, PR, Italy
| | - Emanuela Bua
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27/A, 43124, Parma, PR, Italy
| | - Giulia Caputo
- Pharmacy Department, University "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini, 66100, Chieti, CH, Italy
| | - Valentina Mileo
- Preclinical Analytics and Early Formulations Department, Chiesi Farmaceutici Spa, Largo Belloli 11/A, 43123, Parma, PR, Italy
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3
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Fadler RE, Al Ouahabi A, Qiao B, Carta V, König NF, Gao X, Zhao W, Zhang Y, Lutz JF, Flood AH. Chain Entropy Beats Hydrogen Bonds to Unfold and Thread Dialcohol Phosphates inside Cyanostar Macrocycles To Form [3]Pseudorotaxanes. J Org Chem 2021; 86:4532-4546. [PMID: 33636075 PMCID: PMC8063573 DOI: 10.1021/acs.joc.0c02887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The recognition of substituted phosphates underpins many processes including DNA binding, enantioselective catalysis, and recently template-directed rotaxane synthesis. Beyond ATP and a few commercial substrates, however, little is known about how substituents effect organophosphate recognition. Here, we examined alcohol substituents and their impact on recognition by cyanostar macrocycles. The organophosphates were disubstituted by alcohols of various chain lengths, dipropanol, dihexanol, and didecanol phosphate, each accessed using modular solid-phases syntheses. Based on the known size-selective binding of phosphates by π-stacked dimers of cyanostars, threaded [3]pseudorotaxanes were anticipated. While seen with butyl substituents, pseudorotaxane formation was disrupted by competitive OH···O- hydrogen bonding between both terminal hydroxyls and the anionic phosphate unit. Crystallography also showed formation of a backfolded propanol conformation resulting in an 8-membered ring and a perched cyanostar assembly. Motivated by established entropic penalties accompanying ring formation, we reinstated [3]pseudorotaxanes by extending the size of the substituent to hexanol and decanol. Chain entropy overcomes the enthalpically favored OH···O- contacts to favor random-coil conformations required for seamless, high-fidelity threading of dihexanol and didecanol phosphates inside cyanostars. These studies highlight how chain length and functional groups on phosphate's substituents can be powerful design tools to regulate binding and control assembly formation during phosphate recognition.
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Affiliation(s)
- Rachel E Fadler
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Abdelaziz Al Ouahabi
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, Strasbourg, 67034, France
| | - Bo Qiao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Veronica Carta
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Niklas F König
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, Strasbourg, 67034, France
| | - Xinfeng Gao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Wei Zhao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Yankai Zhang
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, Strasbourg, 67034, France
| | - Jean-François Lutz
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, Strasbourg, 67034, France
| | - Amar H Flood
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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4
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Conformational Investigations in Flexible Molecules Using Orientational NMR Constraints in Combination with 3J-Couplings and NOE Distances. Molecules 2019; 24:molecules24234417. [PMID: 31816930 PMCID: PMC6930577 DOI: 10.3390/molecules24234417] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/21/2019] [Accepted: 11/26/2019] [Indexed: 12/19/2022] Open
Abstract
The downscaling of NMR tensorial interactions, such as dipolar couplings, from tens of kilohertz to a few hertz in low-order media is the result of dynamics spanning several orders of magnitudes, including vibrational modes (~ns-fs), whole-molecule reorientation (~ns) and higher barrier internal conformational exchange (<ms). In this work, we propose to employ these dynamically averaged interactions to drive an “alignment-tensor-free” molecular dynamic simulation with orientation constraints (MDOC) in order to efficiently access the conformational space sampled by flexible small molecules such as natural products. Key to this approach is the application of tensorial pseudo-force restraints which simultaneously guide the overall reorientation and conformational fluctuations based on defined memory function over the running trajectory. With the molecular mechanics force-field, which includes bond polarization theory (BPT), and complemented with other available NMR parameters such as NOEs and scalar J-couplings, MDOC efficiently arrives at dynamic ensembles that reproduce the entire NMR dataset with exquisite accuracy and theoretically reveal the systems conformational space and equilibrium. The method as well as its potential towards configurational elucidation is presented on diastereomeric pairs of flexible molecules: a small 1,4-diketone 1 with a single rotatable bond as well as a 24-ring macrolide related to the natural product mandelalide A 2.
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5
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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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6
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Di Pietro ME, Sternberg U, Luy B. Molecular Dynamics with Orientational Tensorial Constraints: A New Approach to Probe the Torsional Angle Distributions of Small Rotationally Flexible Molecules. J Phys Chem B 2019; 123:8480-8491. [PMID: 31502838 DOI: 10.1021/acs.jpcb.9b07008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The potential of residual dipolar couplings (RDCs) in conformational studies of small molecules is now widely recognized, but current theoretical approaches for their interpretation have several limitations and there is still the need for a general method to probe the torsional angle distributions applicable to any rotationally flexible molecule. Molecular dynamics simulations with RDC-based orientational tensorial constraints (MDOC), implemented in the software COSMOS, are presented here as a conceptually new strategy. For the cases of the fluorinated anti-inflammatory drug diflunisal and the disaccharide cellobiose, we demonstrate that MDOC simulations with one-bond RDCs as tensorial constraints unveil torsion distributions and allow the determination of relative configuration in the presence of rotational flexibility. The independence of the initial structure or any a priori assumption as well as the possibility to combine different experimental constraints represent features, which make the COSMOS software a promising tool for the investigation of torsional angle distributions of flexible molecules, regardless of their size and degree of freedom.
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Affiliation(s)
- Maria E Di Pietro
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Karlsruhe 76131 , Germany
| | - Ulrich Sternberg
- COSMOS GbR , Jena 07743 , Germany.,Research Partner , Karlsruhe Institute of Technology (KIT) , Karlsruhe 76131 , Germany
| | - Burkhard Luy
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Karlsruhe 76131 , Germany.,Institute for Biological Interfaces 4-Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Eggenstein-Leopoldshafen 76021 , Germany
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7
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Pérez-Victoria I, Oves-Costales D, Lacret R, Martín J, Sánchez-Hidalgo M, Díaz C, Cautain B, Vicente F, Genilloud O, Reyes F. Structure elucidation and biosynthetic gene cluster analysis of caniferolides A–D, new bioactive 36-membered macrolides from the marine-derived Streptomyces caniferus CA-271066. Org Biomol Chem 2019; 17:2954-2971. [DOI: 10.1039/c8ob03115k] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The structures of caniferolides A–D have been determined combining NMR and bioinformatics prediction of the absolute configuration.
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8
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Li GW, Liu H, Qiu F, Wang XJ, Lei XX. Residual Dipolar Couplings in Structure Determination of Natural Products. NATURAL PRODUCTS AND BIOPROSPECTING 2018; 8:279-295. [PMID: 29943349 PMCID: PMC6102172 DOI: 10.1007/s13659-018-0174-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 06/14/2018] [Indexed: 05/16/2023]
Abstract
The determination of natural products stereochemistry remains a formidable task. Residual dipolar couplings (RDCs) induced by anisotropic media are a powerful tool for determination of the stereochemistry of organic molecule in solution. This review will provide a short introduction on RDCs-based methodology for the structural elucidation of natural products. Special attention is given to the current availability of alignment media in organic solvents. The applications of RDCs for structural analysis of some examples of natural products were discussed and summarized. This review provides a short introduction on RDCs-based methodology for the structural elucidation of natural products. Special attention is given to the current availability of alignment media in organic solvents. The applications of RDCs for structural analysis of some examples of natural products were discussed and summarized.
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Affiliation(s)
- Gao-Wei Li
- College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, People's Republic of China
| | - Han Liu
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, 430074, People's Republic of China
| | - Feng Qiu
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, 430074, People's Republic of China
| | - Xiao-Juan Wang
- College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, People's Republic of China
| | - Xin-Xiang Lei
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, 430074, People's Republic of China.
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9
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Determination of the conformational states of strychnine in solution using NMR residual dipolar couplings in a tensor-free approach. Methods 2018; 148:4-8. [PMID: 30036639 DOI: 10.1016/j.ymeth.2018.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/10/2018] [Accepted: 07/17/2018] [Indexed: 12/14/2022] Open
Abstract
Small molecules with rotatable bonds can occupy different conformational states in solution as a consequence of their thermal fluctuations. The accurate determination of the structures of such states, as well as of their statistical weights, has been challenging because of the technical difficulties in extracting information from experimental measurements, which are normally averaged over the conformational space available. Here, to achieve this objective, we present an approach based on a recently proposed tensor-free method for incorporating NMR residual dipolar couplings as structural restraints in replica-averaged molecular dynamics simulations. This approach enables the information provided by the experimental data to be used in the spirit of the maximum entropy principle to determine the structural ensembles of small molecules. Furthermore, in order to enhance the sampling of the conformational space we incorporated the metadynamics method in the simulations. We illustrate the method in the case of strychnine, determining the three major conformational states of this small molecule and their associated occupation probabilities.
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10
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Lakshmi JK, Pattnaik B, Kavitha R, Mallavadhani UV, Jagadeesh B. Conformation of flexibly linked triterpene dimers by using RDC-enhanced NMR spectroscopy. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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11
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Cornilescu G, Ramos Alvarenga RF, Wyche TP, Bugni TS, Gil RR, Cornilescu CC, Westler WM, Markley JL, Schwieters CD. Progressive Stereo Locking (PSL): A Residual Dipolar Coupling Based Force Field Method for Determining the Relative Configuration of Natural Products and Other Small Molecules. ACS Chem Biol 2017; 12:2157-2163. [PMID: 28617580 DOI: 10.1021/acschembio.7b00281] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Establishing the relative configuration of a bioactive natural product represents the most challenging part in determining its structure. Residual dipolar couplings (RDCs) are sensitive probes of the relative spatial orientation of internuclear vectors. We adapted a force field structure calculation methodology to allow free sampling of both R and S configurations of the stereocenters of interest. The algorithm uses a floating alignment tensor in a simulated annealing protocol to identify the conformations and configurations that best fit experimental RDC and distance restraints (from NOE and J-coupling data). A unique configuration (for rigid molecules) or a very small number of configurations (for less rigid molecules) of the structural models having the lowest chiral angle energies and reasonable magnitudes of the alignment tensor are provided as the best predictions of the unknown configuration. For highly flexible molecules, the progressive locking of their stereocenters into their statistically dominant R or S state dramatically reduces the number of possible relative configurations. The result is verified by checking that the same configuration is obtained by initiating the locking from different regions of the molecule. For all molecules tested having known configurations (with conformations ranging from mostly rigid to highly flexible), the method accurately determined the correct configuration.
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Affiliation(s)
| | - René F. Ramos Alvarenga
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Thomas P. Wyche
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Biological
Chemistry and Molecular Pharmacology Department, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Tim S. Bugni
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Roberto R. Gil
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | | | | | | | - Charles D. Schwieters
- Center for
Information Technology, National Institutes of Health, Bethesda, Maryland 20892-5624, United States
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12
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Scheeff S, Menche D. Total syntheses of the archazolids: an emerging class of novel anticancer drugs. Beilstein J Org Chem 2017; 13:1085-1098. [PMID: 28684988 PMCID: PMC5480361 DOI: 10.3762/bjoc.13.108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/09/2017] [Indexed: 12/19/2022] Open
Abstract
V-ATPase has recently emerged as a promising novel anticancer target based on extensive in vitro and in vivo studies with the archazolids, complex polyketide macrolides which present the most potent V-ATPase inhibitors known to date, rendering these macrolides important lead structures for the development of novel anticancer agents. The limited natural supply of these metabolites from their myxobacterial source renders total synthesis of vital importance for the further preclinical development. This review describes in detail the various tactics and strategies employed so far in archazolid syntheses that culminated in three total syntheses and discusses the future synthetic challenges that have to be addressed.
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Affiliation(s)
- Stephan Scheeff
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Dirk Menche
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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13
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França JAA, Navarro-Vázquez A, Lei X, Sun H, Griesinger C, Hallwass F. Complete NMR assignment and conformational analysis of 17-α-ethinylestradiol by using RDCs obtained in grafted graphene oxide. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:297-303. [PMID: 27637176 DOI: 10.1002/mrc.4526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/08/2016] [Accepted: 09/13/2016] [Indexed: 06/06/2023]
Abstract
The 1 H and 13 C NMR spectra of 17-α-ethinylestradiol (EE2), a well-known contraceptive, including diastereotopic methylene groups, were fully assigned with the help of residual dipolar couplings (RDC) measured in the recently developed grafted graphene oxide orienting medium. RDC analysis, which included all 1 DCH couplings and the long-range 2 DCH1 H-C≡13 C coupling, also pointed to the presence of a minor conformation arising from pseudo-rotation of the steroid B ring. Saturation-transfer difference (STD) measurements revealed that the most likely interaction between EE2 and orienting medium occurred on the C and D ring. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- José A A França
- Instituto Federal de Alagoas, Campus Piranhas, Avenida Sergipe, s/n° Xingó, 57460-000, Piranhas, AL, Brazil
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Avenida Professor Moraes Rego, 1235, Cidade Universitária, 50670-901, Recife, PE, Brazil
| | - Xinxiang Lei
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, 430074, PR China
| | - Han Sun
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Robert-Rössle-StraΒe 10, 13125, Berlin, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Fassberg 11, 37077, Göttingen, Germany
| | - Fernando Hallwass
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Avenida Professor Moraes Rego, 1235, Cidade Universitária, 50670-901, Recife, PE, Brazil
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14
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Gölz JP, Bockelmann S, Mayer K, Steinhoff HJ, Wieczorek H, Huss M, Klare JP, Menche D. EPR Studies of V-ATPase with Spin-Labeled Inhibitors DCC and Archazolid: Interaction Dynamics with Proton Translocating Subunit c. ChemMedChem 2015; 11:420-8. [DOI: 10.1002/cmdc.201500500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Jan Philipp Gölz
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Svenja Bockelmann
- Fachbereich Biologie/Chemie; Universität Osnabrück; 49069 Osnabrück Germany
| | - Kerstin Mayer
- Institut für Organische Chemie; Ruprecht-Karls-Universität Heidelberg; INF 270; 69120 Heidelberg Germany
| | | | - Helmut Wieczorek
- Fachbereich Biologie/Chemie; Universität Osnabrück; 49069 Osnabrück Germany
| | - Markus Huss
- Fachbereich Biologie/Chemie; Universität Osnabrück; 49069 Osnabrück Germany
| | - Johann P. Klare
- Fachbereich Physik; Universität Osnabrück; 49069 Osnabrück Germany
| | - Dirk Menche
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Str. 1 53121 Bonn Germany
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15
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Kolmer A, Edwards LJ, Kuprov I, Thiele CM. Conformational analysis of small organic molecules using NOE and RDC data: A discussion of strychnine and α-methylene-γ-butyrolactone. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 261:101-109. [PMID: 26556179 DOI: 10.1016/j.jmr.2015.10.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 10/02/2015] [Accepted: 10/07/2015] [Indexed: 06/05/2023]
Abstract
To understand the properties and/or reactivity of an organic molecule, an understanding of its three-dimensional structure is necessary. Simultaneous determination of configuration and conformation often poses a daunting challenge. Thus, the more information accessible for a given molecule, the better. Additionally to (3)J-couplings, two sources of information, quantitative NOE and more recently also RDCs, are used for conformational analysis by NMR spectroscopy. In this paper, we compare these sources of conformational information in two molecules: the configurationally well-characterized strychnine 1, and the only recently configurationally and conformationally characterized α-methylene-γ-butyrolactone 2. We discuss possible sources of error in the measurement and analysis process, and how to exclude them. By this means, we are able to bolster the previously proposed flexibility for these two molecules.
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Affiliation(s)
- Andreas Kolmer
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 16, 64287 Darmstadt, Germany
| | - Luke J Edwards
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QG, United Kingdom
| | - Ilya Kuprov
- School of Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton, University Road, Southampton SO17 1BJ, United Kingdom
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 16, 64287 Darmstadt, Germany.
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Nath N, d'Auvergne EJ, Griesinger C. Long-Range Residual Dipolar Couplings: A Tool for Determining the Configuration of Small Molecules. Angew Chem Int Ed Engl 2015; 54:12706-10. [PMID: 26359945 DOI: 10.1002/anie.201504432] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/14/2015] [Indexed: 11/07/2022]
Abstract
Together with NOE and J coupling, one-bond residual dipolar coupling (RDC), which reports on the three-dimensional orientation of an internuclear vector in the molecular frame, plays an important role in the conformation and configuration analysis of small molecules in solution by NMR spectroscopy. When the molecule has few C-H bonds, or too many bonds are in parallel, the available RDCs may not be sufficient to obtain the alignment tensor used for structure elucidation. Long-range RDCs that connect nuclei over multiple bonds are normally not parallel to the single bonds and therefore complement one-bond RDCs. Herein we present a method for extracting the long-range RDC of a chosen proton or group of protons to all remotely connected carbon atoms, including non-protonated carbon atoms. Alignment tensors fitted directly to the total long-range couplings (T=J+D) enabled straightforward analysis of both the long-range and one-bond RDCs for strychnine.
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Affiliation(s)
- Nilamoni Nath
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen (Germany)
| | - Edward J d'Auvergne
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen (Germany)
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen (Germany).
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Nath N, d'Auvergne EJ, Griesinger C. Long-Range Residual Dipolar Couplings: A Tool for Determining the Configuration of Small Molecules. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504432] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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18
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Machine learning estimates of natural product conformational energies. PLoS Comput Biol 2014; 10:e1003400. [PMID: 24453952 PMCID: PMC3894151 DOI: 10.1371/journal.pcbi.1003400] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 10/10/2013] [Indexed: 11/19/2022] Open
Abstract
Machine learning has been used for estimation of potential energy surfaces to speed up molecular dynamics simulations of small systems. We demonstrate that this approach is feasible for significantly larger, structurally complex molecules, taking the natural product Archazolid A, a potent inhibitor of vacuolar-type ATPase, from the myxobacterium Archangium gephyra as an example. Our model estimates energies of new conformations by exploiting information from previous calculations via Gaussian process regression. Predictive variance is used to assess whether a conformation is in the interpolation region, allowing a controlled trade-off between prediction accuracy and computational speed-up. For energies of relaxed conformations at the density functional level of theory (implicit solvent, DFT/BLYP-disp3/def2-TZVP), mean absolute errors of less than 1 kcal/mol were achieved. The study demonstrates that predictive machine learning models can be developed for structurally complex, pharmaceutically relevant compounds, potentially enabling considerable speed-ups in simulations of larger molecular structures. Molecular dynamics simulations provide insight into the dynamic behavior of molecules, e.g., into the adopted spatial arrangements of its atoms over time. Methods differ in the approximations they employ, resulting in a trade-off between accuracy and speed that ranges from highly accurate but expensive quantum mechanical calculations to fast but more inaccurate molecular mechanics force fields. Machine learning, a sub-discipline of artificial intelligence, provides algorithms that learn from data, that is, make predictions based on previously seen examples. By starting with a few expensive quantum mechanical calculations, training a machine learning algorithm on them, and then using the resulting model to carry out the molecular dynamics simulation, one can improve the accuracy/speed trade-off. We have developed and applied such a hybrid quantum mechanics/machine learning approach to Archazolid A, a natural product from the myxobacterium Archangium gephyra and a potent inhibitor of vacuolar-type ATPase. By dynamically refining our model over the course of the simulation, we achieve errors of less than 1 kcal/mol while saving over 40% of the quantum mechanical calculations. Our study demonstrates the feasibility of predictive machine learning models for the dynamics of structurally complex, pharmaceutically relevant compounds, potentially enabling considerable speed-ups in simulations of even larger biomolecular structures.
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Kakita VMR, Rachineni K, Bharatam J. Unambiguous determination of conformation and relative configuration of a multiple stereo-centre molecule Rifamycin-S by using scaled residual dipolar couplings: A case study. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.08.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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20
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Parella T, Espinosa JF. Long-range proton-carbon coupling constants: NMR methods and applications. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 73:17-55. [PMID: 23962883 DOI: 10.1016/j.pnmrs.2013.07.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 07/03/2013] [Accepted: 07/03/2013] [Indexed: 06/02/2023]
Abstract
A general review of novel NMR methods to measure heteronuclear long-range proton-carbon coupling constants ((n)JCH; n>1) in small molecules is made. NMR experiments are classified in terms of NMR pulse scheme and cross-peak nature. A discussion about simplicity, general applicability and accuracy for each particular NMR experiment is presented and exemplified. Important aspects such as the sign determination and measurement of very small coupling values involving protonated and non-protonated carbons as well as the complementarity between different experiments are also discussed. Finally, a compilation of applications in structural and conformational analysis of different types of molecules since 2000 is surveyed.
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Affiliation(s)
- Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
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21
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Blundell CD, Packer MJ, Almond A. Quantification of free ligand conformational preferences by NMR and their relationship to the bioactive conformation. Bioorg Med Chem 2013; 21:4976-87. [PMID: 23886813 PMCID: PMC3744816 DOI: 10.1016/j.bmc.2013.06.056] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 06/24/2013] [Indexed: 12/22/2022]
Abstract
Accurate unbound solution 3D-structures of ligands provide unique opportunities for medicinal chemistry and, in particular, a context to understand binding thermodynamics and kinetics. Previous methods of deriving these 3D-structures have had neither the accuracy nor resolution needed for drug design and have not yet realized their potential. Here, we describe and apply a NMR methodology to the aminoglycoside streptomycin that can accurately quantify accessible 3D-space and rank the occupancy of observed conformers to a resolution that enables medicinal chemistry understanding and design. Importantly, it is based upon conventional small molecule NMR techniques and can be performed in physiologically-relevant solvents. The methodology uses multiple datasets, an order of magnitude more experimental data than previous NMR approaches and a dynamic model during refinement, is independent of computational chemistry and avoids the problem of virtual conformations. The refined set of solution 3D-shapes for streptomycin can be grouped into two major families, of which the most populated is almost identical to the 30S ribosomal subunit bioactive shape. We therefore propose that accurate unbound ligand solution conformations may, in some cases, provide a subsidiary route to bioactive shape without crystallography. This experimental technique opens up new opportunities for drug design and more so when complemented with protein co-crystal structures, SAR data and pharmacophore modeling.
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Affiliation(s)
- Charles D Blundell
- C4X Discovery Ltd, Unit 310 Ducie House, Ducie Street, Manchester M1 2JW, UK
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22
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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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Cen-Pacheco F, Rodríguez J, Norte M, Fernández JJ, Hernández Daranas A. Connecting Discrete Stereoclusters by Using DFT and NMR Spectroscopy: The Case of Nivariol. Chemistry 2013; 19:8525-32. [DOI: 10.1002/chem.201204272] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/22/2013] [Indexed: 11/08/2022]
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Giraudeau P, Montag T, Charrier B, Thiele CM. Fast access to residual dipolar couplings by single-scan 2D NMR in oriented media. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50 Suppl 1:S53-S57. [PMID: 22865710 DOI: 10.1002/mrc.3856] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 07/10/2012] [Accepted: 07/10/2012] [Indexed: 06/01/2023]
Abstract
Residual dipolar couplings (RDCs) have revolutionized the structure determination of biomolecular and organic compounds. So far, their measurement has been rather time-consuming, but one might imagine that RDCs can one day also be useful in the investigation of compounds with limited stability or short lifetimes. For such applications, it is indispensable to shorten the experiment time. In this communication, we show the first measurement of RDCs from single-scan two-dimensional NMR. An ultrafast HSQC NMR pulse sequence is presented, which includes several of the recent improvements brought to ultrafast NMR in terms of sensitivity, resolution, and spectral width. Ultrafast spectra are obtained in as little time as 60 s on an organic compound at natural abundance, namely (+)-isopinocampheol. When extracting the RDCs from these ultrafast data, a good agreement with those extracted from conventional spectra (obtained in a much longer time) is observed. These results point out the efficiency of the ultrafast approach, particularly when considering the total experiment duration.
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Affiliation(s)
- Patrick Giraudeau
- CNRS, CEISAM UMR 6230, BP 92208, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes Cedex 03, France.
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25
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Tzvetkova P, Luy B, Simova S. Configuration verification via RDCs on the example of a tetra-substituted pyrrolidine ring. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50 Suppl 1:S92-S101. [PMID: 23280666 DOI: 10.1002/mrc.3902] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 10/12/2012] [Accepted: 10/22/2012] [Indexed: 06/01/2023]
Abstract
The configurational analysis of organic compounds is an important application for high resolution NMR spectroscopy. In the present study, a tetra-substituted pyrrolidine with four chiral carbon atoms is analyzed using classical methods based on (3) J and NOE data in solution and compared and verified with recently introduced alternative approaches via residual dipolar couplings (RDCs) in two weak anisotropic alignment media. The molecule shows sufficient rigidity in the five-membered ring for the configurational characterization with the various techniques. However, the flexibility caused by the many freely rotating bonds potentially poses problems for the interpretation of data. It is shown that RDCs measured in poly-γ-benzyl-l-glutamate and a stretched polydimethylsiloxane gel provide useful information for the distinction of diastereomers, but the success varies with the data interpretation strategy used. Although a general improvement of corresponding correlation factors is observed when limiting data to a subset of dipolar couplings directly connected to the central ring, the distinction power is reduced because of the smaller number of RDCs available for potential model falsification. Singular value decomposition for fitting experimental RDCs is able to distinguish in most cases the correct from incorrect configurations, but the differences in correlation factors can be relatively small. Surprisingly, predicting RDCs using the rod model as implemented in PALES gives best results in distinguishing the eight possible diastereomers. It is also found that the use of proton-phosphorus and carbon-phosphorus RDCs helps with the configurational analysis of the model compound.
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Affiliation(s)
- Pavleta Tzvetkova
- Institute of Organic Chemistry and Institute for Biological Surfaces, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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26
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Persch E, Basile T, Bockelmann S, Huss M, Wieczorek H, Carlomagno T, Menche D. Synthesis and biological evaluation of a water-soluble derivative of the potent V-ATPase inhibitor archazolid. Bioorg Med Chem Lett 2012; 22:7735-8. [DOI: 10.1016/j.bmcl.2012.09.081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 09/19/2012] [Accepted: 09/22/2012] [Indexed: 10/27/2022]
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27
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Navarro-Vázquez A. MSpin-RDC. A program for the use of residual dipolar couplings for structure elucidation of small molecules. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50 Suppl 1:S73-S79. [PMID: 23280663 DOI: 10.1002/mrc.3905] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 10/24/2012] [Accepted: 11/06/2012] [Indexed: 05/28/2023]
Abstract
We developed a new program, MSpin-RDC for the analysis of residual dipolar coupling data. This software, specially designed for small molecule analysis, can directly read many molecular-modeling and popular chemistry file formats and accept RDC values as a simple free-format table. Alignment tensor can then be computed by singular value decomposition, as well as predicted using inertia and gyration tensor-based methodologies. Trial structures are then ranked according to their Cornilescu's quality factor (Q) values. Analysis of multiconformational problems and fitting of RDC data to relative populations can be accomplished using the single-tensor approximation.
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Affiliation(s)
- Armando Navarro-Vázquez
- Departamento de Química Orgánica, Facultade de Química, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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28
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Trigo-Mouriño P, Navarro-Vázquez A, Sánchez-Pedregal VM. Influence of solvent and salt concentration on the alignment properties of acrylamide copolymer gels for the measurement of RDC. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50 Suppl 1:S29-S37. [PMID: 23280658 DOI: 10.1002/mrc.3889] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 09/11/2012] [Accepted: 09/21/2012] [Indexed: 06/01/2023]
Abstract
The dependence of molecular alignment with solvent nature and salt concentration has been investigated for mechanically stretched polyacrylamide copolymer gels. Residual dipolar couplings (RDCs) were recorded for D(2)O, DMSO-d(6), and DMSO-d(6)/D(2)O solutions containing different proportions of the solvents and different sodium chloride concentrations. Alignment tensors were determined by fitting the experimental RDCs to the DFT-computed structure of N-methylcodeinium ion. Analysis of the tensors shows that the degree of alignment decreases with the proportion of DMSO-d(6) as well as with the concentration of sodium chloride, most likely due to enhanced ion-pair aggregation. Furthermore, rotation of the alignment tensor is observed when increasing the salt concentration.
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Affiliation(s)
- Pablo Trigo-Mouriño
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, Universidade de Santiago de Compostela, Campus Vida, 15782, Santiago de Compostela, Spain
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29
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Dreisigacker S, Latek D, Bockelmann S, Huss M, Wieczorek H, Filipek S, Gohlke H, Menche D, Carlomagno T. Understanding the Inhibitory Effect of Highly Potent and Selective Archazolides Binding to the Vacuolar ATPase. J Chem Inf Model 2012; 52:2265-72. [DOI: 10.1021/ci300242d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sandra Dreisigacker
- Structural and Computational Biology Unit, EMBL, Mayerhofstrasse 1, D-69117 Heidelberg, Germany
- Institute of Organic Chemistry, Ruprecht-Karls University Heidelberg, Im Neuenheimer
Feld 270, D-69120 Heidelberg, Germany
| | - Dorota Latek
- Structural and Computational Biology Unit, EMBL, Mayerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Svenja Bockelmann
- Department of Animal Physiology, Faculty of Biology and Chemistry, University of Osnabrück, Barbarastrasse 11, D-49069 Osnabrück, Germany
| | - Markus Huss
- Department of Animal Physiology, Faculty of Biology and Chemistry, University of Osnabrück, Barbarastrasse 11, D-49069 Osnabrück, Germany
| | - Helmut Wieczorek
- Department of Animal Physiology, Faculty of Biology and Chemistry, University of Osnabrück, Barbarastrasse 11, D-49069 Osnabrück, Germany
| | - Slawomir Filipek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Holger Gohlke
- Heinrich-Heine-University Düsseldorf,
Institute of Pharmaceutical and Medicinal Chemistry, Universitätsstrasse
1, D-40225 Düsseldorf, Germany
| | - Dirk Menche
- Institute of Organic Chemistry, Ruprecht-Karls University Heidelberg, Im Neuenheimer
Feld 270, D-69120 Heidelberg, Germany
| | - Teresa Carlomagno
- Structural and Computational Biology Unit, EMBL, Mayerhofstrasse 1, D-69117 Heidelberg, Germany
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Carlomagno T. NMR in natural products: understanding conformation, configuration and receptor interactions. Nat Prod Rep 2012; 29:536-54. [PMID: 22456471 DOI: 10.1039/c2np00098a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to 2011. Natural products are of tremendous importance in both traditional and modern medicine. For medicinal chemistry natural products represent a challenge, as their chemical synthesis and modification are complex processes, which require many, often stereo-selective, synthetic steps. A prerequisite for the design of analogs of natural products, with more accessible synthetic routes, is the availability of their bioactive conformation. Nuclear Magnetic Resonance (NMR) spectroscopy and X-ray crystallography are the two techniques of choice to investigate the structure of natural products. In this review, I describe the most recent advances in NMR to study the conformation of natural products either free in solution or bound to their cellular receptors. In chapter 2, I focus on the use of residual dipolar couplings (RDC). On the basis of a few examples, I discuss the benefit of complementing classical NMR parameters, such as NOEs and scalar couplings, with dipolar couplings to simultaneously determine both the conformation and the relative configuration of natural products in solution. Chapter 3 is dedicated to the study of the structure of natural products in complex with their cellular receptors and is further divided in two sections. In the first section, I describe two solution-state NMR methodologies to investigate the binding mode of low-affinity ligands to macromolecular receptors. The first approach, INPHARMA (Interligand Noes for PHArmacophore Mapping), is based on the observation of interligand NOEs between two small molecules binding competitively to a common receptor. INPHARMA reveals the relative binding mode of the two ligands, thus allowing ligand superimposition. The second approach is based on paramagnetic relaxation enhancement (PRE) of ligand resonances in the presence of a receptor containing a paramagnetic center. In the second section, I focus on solid-state NMR spectroscopy as a tool to access the bioactive conformation of natural products in complex with macromolecular receptors.
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Affiliation(s)
- Teresa Carlomagno
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg
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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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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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Gil RR. Konstitutions-, Konfigurations- und Konformationsanalyse niedermolekularer organischer Verbindungen auf der Grundlage von dipolaren Restkopplungen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101561] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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34
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Gil RR. Constitutional, Configurational, and Conformational Analysis of Small Organic Molecules on the Basis of NMR Residual Dipolar Couplings. Angew Chem Int Ed Engl 2011; 50:7222-4. [DOI: 10.1002/anie.201101561] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Indexed: 11/06/2022]
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Horstmann N, Essig S, Bockelmann S, Wieczorek H, Huss M, Sasse F, Menche D. Archazolid A-15-O-β-D-glucopyranoside and iso-archazolid B: potent V-ATPase inhibitory polyketides from the myxobacteria Cystobacter violaceus and Archangium gephyra. JOURNAL OF NATURAL PRODUCTS 2011; 74:1100-1105. [PMID: 21513292 DOI: 10.1021/np200036v] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Two structurally novel analogues of the macrolides archazolids A and B, archazolid A-15-O-β-D-glucopyranoside (archazolid E, 5) and iso-archazolid B (archazolid F, 6), were isolated from the myxobacterium Cystobacter violaceus and Archangium gephyra, respectively. Macrolactone 5 represents the first 15-O-glycoside of the archazolids. iso-Archazolid B (6) incorporates a C-3 alkene and presents the first constitutional isomer reported for this natural product class. The structures of these polyketides were determined by spectroscopic analysis, in particular by HMBC, HMQC, and ROESY NMR investigations and by chemical degradation. iso-Archazolid B (6) demonstrated extremely high antiproliferative and V-ATPase inhibitory effects, with IC(50) values in the picomolar range, while only moderate activity was observed for glycoside 5. iso-Archazolid B presents the most potent archazolid known.
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Affiliation(s)
- Nicole Horstmann
- Institut für Organische Chemie, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany
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Kummerlöwe G, Grage SL, Thiele CM, Kuprov I, Ulrich AS, Luy B. Variable angle NMR spectroscopy and its application to the measurement of residual chemical shift anisotropy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 209:19-30. [PMID: 21256060 DOI: 10.1016/j.jmr.2010.11.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 11/30/2010] [Accepted: 11/30/2010] [Indexed: 05/30/2023]
Abstract
The successful measurement of anisotropic NMR parameters like residual dipolar couplings (RDCs), residual quadrupolar couplings (RQCs), or residual chemical shift anisotropy (RCSA) involves the partial alignment of solute molecules in an alignment medium. To avoid any influence of the change of environment from the isotropic to the anisotropic sample, the measurement of both datasets with a single sample is highly desirable. Here, we introduce the scaling of alignment for mechanically stretched polymer gels by varying the angle of the director of alignment relative to the static magnetic field, which we call variable angle NMR spectroscopy (VA-NMR). The technique is closely related to variable angle sample spinning NMR spectroscopy (VASS-NMR) of liquid crystalline samples, but due to the mechanical fixation of the director of alignment no sample spinning is necessary. Also, in contrast to VASS-NMR, VA-NMR works for the full range of sample inclinations between 0° and 90°. Isotropic spectra are obtained at the magic angle. As a demonstration of the approach we measure ¹³C-RCSA values for strychnine in a stretched PDMS/CDCl₃ gel and show their usefulness for assignment purposes. In this context special care has been taken with respect to the exact calibration of chemical shift data, for which three approaches have been derived and tested.
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Affiliation(s)
- Grit Kummerlöwe
- Department Chemie, Lehrstuhl Organische Chemie II, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
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37
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Kummerlöwe G, Crone B, Kretschmer M, Kirsch SF, Luy B. Dipolare Restkopplungen als effektives Instrument der Konstitutionsanalyse: die unerwartete Bildung tricyclischer Verbindungen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007305] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Residual Dipolar Couplings as a Powerful Tool for Constitutional Analysis: The Unexpected Formation of Tricyclic Compounds. Angew Chem Int Ed Engl 2011; 50:2643-5. [DOI: 10.1002/anie.201007305] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Indexed: 11/07/2022]
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Andersson H, Demaegdt H, Vauquelin G, Lindeberg G, Karlén A, Hallberg M, Erdélyi M, Hallberg A. Disulfide Cyclized Tripeptide Analogues of Angiotensin IV as Potent and Selective Inhibitors of Insulin-Regulated Aminopeptidase (IRAP). J Med Chem 2010; 53:8059-71. [DOI: 10.1021/jm100793t] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Hanna Andersson
- Department of Medicinal Chemistry, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden
| | - Heidi Demaegdt
- Department of Molecular and Biochemical Pharmacology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Georges Vauquelin
- Department of Molecular and Biochemical Pharmacology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Gunnar Lindeberg
- Department of Medicinal Chemistry, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden
| | - Anders Karlén
- Department of Medicinal Chemistry, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden
| | - Mathias Hallberg
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, SE-751 24 Uppsala, Sweden
| | - Máté Erdélyi
- Department of Chemistry, University of Gothenburg, SE-412 96 Göteborg, Sweden
| | - Anders Hallberg
- Department of Medicinal Chemistry, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden
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Moulin E, Nevado C, Gagnepain J, Kelter G, Fiebig HH, Fürstner A. Synthesis and evaluation of an Iejimalide-archazolid chimera. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.05.043] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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41
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Arnold L, Marx A, Thiele C, Reggelin M. Polyguanidines as Chiral Orienting Media for Organic Compounds. Chemistry 2010; 16:10342-6. [DOI: 10.1002/chem.201000940] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Trigo-Mouriño P, Santamaría-Fernández R, Sánchez-Pedregal VM, Navarro-Vázquez A. Conformational Analysis of an Isoquinolinium Hydrochloride in Water Using Residual Dipolar Couplings. J Org Chem 2010; 75:3101-4. [DOI: 10.1021/jo902502h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pablo Trigo-Mouriño
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Raquel Santamaría-Fernández
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Víctor M. Sánchez-Pedregal
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Marx A, Böttcher B, Thiele C. Enhancing the Orienting Properties of Poly(γ-benzyl-L-glutamate) by means of Additives. Chemistry 2010; 16:1656-63. [DOI: 10.1002/chem.200902287] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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44
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Böttcher B, Schmidts V, Raskatov J, Thiele C. Bestimmung der Konformation des Schlüsselintermediats einer enantioselektiven Palladium-katalysierten allylischen Substitution mithilfe dipolarer Restkopplungen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903649] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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45
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Böttcher B, Schmidts V, Raskatov J, Thiele C. Determination of the Conformation of the Key Intermediate in an Enantioselective Palladium-Catalyzed Allylic Substitution from Residual Dipolar Couplings. Angew Chem Int Ed Engl 2009; 49:205-9. [DOI: 10.1002/anie.200903649] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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46
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Menche D, Hassfeld J, Li J, Mayer K, Rudolph S. Modular Total Synthesis of Archazolid A and B. J Org Chem 2009; 74:7220-9. [DOI: 10.1021/jo901565n] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dirk Menche
- Institut für Organische Chemie, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg
- Helmholtz-Zentrum für Infektionsforschung, Medizinische Chemie, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Jorma Hassfeld
- Helmholtz-Zentrum für Infektionsforschung, Medizinische Chemie, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Jun Li
- Helmholtz-Zentrum für Infektionsforschung, Medizinische Chemie, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Kerstin Mayer
- Institut für Organische Chemie, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg
| | - Sven Rudolph
- Helmholtz-Zentrum für Infektionsforschung, Medizinische Chemie, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
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Marx A, Schmidts V, Thiele CM. How different are diastereomorphous orientations of enantiomers in the liquid crystalline phases of PBLG and PBDG: a case study. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:734-740. [PMID: 19504463 DOI: 10.1002/mrc.2454] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The orientational properties of the two enantiomers of an example compound, namely isopinocampheol [(+)- and (-)-IPC] in the two enantiomers of a liquid crystalline phase, namely Poly-gamma-benzyl-L/D-glutamate (PBLG/PBDG) with the organic cosolvent CDCl(3), were investigated. The interactions can be either enantiomorphous, leading to equal orientations and residual dipolar couplings (RDCs), or diastereomorphous, leading to different orientations and RDCs. The difference between the two diastereomorphous orientations was determined to be rather small (5 degrees in the Euler angle beta). Furthermore, we investigated whether one of the two diastereomorphous interactions is favored.
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Affiliation(s)
- Andreas Marx
- Technische Universität Darmstadt, Clemens Schöpf Institut für Organische Chemie und Biochemie, Petersenstr. 22, 64287 Darmstadt, Germany
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48
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Thiele CM, Maliniak A, Stevensson B. Use of Local Alignment Tensors for the Determination of Relative Configurations in Organic Compounds. J Am Chem Soc 2009; 131:12878-9. [DOI: 10.1021/ja904536b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christina M. Thiele
- Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Petersenstr. 22, D-64287 Darmstadt, Germany, and Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, Sweden
| | - Arnold Maliniak
- Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Petersenstr. 22, D-64287 Darmstadt, Germany, and Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, Sweden
| | - Baltzar Stevensson
- Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Petersenstr. 22, D-64287 Darmstadt, Germany, and Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, Sweden
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Thiele C, Schmidts V, Böttcher B, Louzao I, Berger R, Maliniak A, Stevensson B. On the Treatment of Conformational Flexibility when Using Residual Dipolar Couplings for Structure Determination. Angew Chem Int Ed Engl 2009; 48:6708-12. [DOI: 10.1002/anie.200902398] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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50
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Thiele C, Schmidts V, Böttcher B, Louzao I, Berger R, Maliniak A, Stevensson B. On the Treatment of Conformational Flexibility when Using Residual Dipolar Couplings for Structure Determination. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902398] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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