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Marine Drugs
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Configurational and Conformational Studies on the Structures of Marine Natural...
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Configurational and Conformational Studies on the Structures of Marine Natural Products

A special issue of Marine Drugs (ISSN 1660-3397). This special issue belongs to the section "Structural Studies on Marine Natural Products".

Deadline for manuscript submissions: closed (15 May 2022) | Viewed by 14409

Special Issue Editor

Priv.-Doz. Dr. Matthias Köck

E-Mail Website
Guest Editor
Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
Interests: marine natural products; NMR; structure elucidation; distance geometry; distancebounds driven dynamics; spectrometric

Special Issue Information

Dear Colleague,

The determination of the configuration (relative and absolute) and conformation of natural products is essential to understand their biological interactions and is the basis for their procurement through total synthesis. When crystalline products are unavailable, structural elucidations can be highly difficult, especially when the targets do not lend themselves easily to standard 2D NMR techniques. The configurational analysis of complex natural products by NMR spectroscopy is still a challenging task, although isotropic (NOE/ROE as well as homo- and heteronuclear J couplings) and anisotropic (RDCs, RQCs, and RCSA) NMR parameters, as well as DFT-based calculation of NMR parameters, are now available. Despite numerous attempts, to date, there is so far no standard or even automated protocol for the configurational and conformational assignment of natural products or small organic molecules in general. The natural products literature is still filled with structural misassignments, despite enormous advances in NMR spectroscopy. Computer-aided structure elucidation of natural products is improving but far from completion. This is especially true for the solution of configurational problems, which is not an issue in biomolecular NMR dealing with polymers composed of repetitive units of known absolute configurations.

This Special Issue will focus on NMR methods for the identification of the relative configuration and conformation of marine natural products, including a wide variety of NMR parameters and computational methods for their use.

Priv.-Doz. Dr. Matthias Köck
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Marine Drugs is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • NMR spectroscopy
  • Structure elucidation
  • Configurational analysis
  • NOE/ROE data
  • Anisotropic NMR parameters
  • NMR-based computational methods
  • Distance geometry
  • Density-functional theory
  • Synthesis
  • Structural revision

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Published Papers (4 papers)

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Research

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10 pages, 3628 KiB  
Article
Structure Revision and Protein Tyrosine Phosphatase Inhibitory Activity of Drazepinone
by Fei Cao, Li Pan, Wenbin Gao, Yunfeng Liu, Caijuan Zheng and Yahui Zhang
Mar. Drugs 2021, 19(12), 714; https://doi.org/10.3390/md19120714 - 20 Dec 2021
Cited by 5 | Viewed by 2783
Abstract
From the marine-derived fungus Penicillium sumatrense (Trichocomaceae), a pair of enantiomers [(+)-1 and (−)-1] were isolated with identical 1D NMR data to drazepinone, which was originally reported to have a trisubstituted naphthofuroazepinone skeleton. In this study, we confirmed the structures [...] Read more.
From the marine-derived fungus Penicillium sumatrense (Trichocomaceae), a pair of enantiomers [(+)-1 and (−)-1] were isolated with identical 1D NMR data to drazepinone, which was originally reported to have a trisubstituted naphthofuroazepinone skeleton. In this study, we confirmed the structures of the two enantiomers as drazepinone and revised their structures by detailed analysis of extensive 2D NMR data and a comparison of the calculated 13C chemical shifts, ECD, VCD, and ORD spectra with those of the experiment ones. (+)-1 and (−)-1 were evaluated for their PTP inhibitory activity in vitro. (−)-1 showed selective PTP inhibitory activity against PTP1B and TCPTP with IC50 values of 1.56 and 12.5 μg/mL, respectively. Full article
(This article belongs to the Special Issue Configurational and Conformational Studies on the Structures of Marine Natural Products)
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13 pages, 5445 KiB  
Article
Structure and Absolute Configuration of Phenanthro-perylene Quinone Pigments from the Deep-Sea Crinoid Hypalocrinus naresianus
by Sahithya Phani Babu Vemulapalli, Juan Carlos Fuentes-Monteverde, Niels Karschin, Tatsuo Oji, Christian Griesinger and Klaus Wolkenstein
Mar. Drugs 2021, 19(8), 445; https://doi.org/10.3390/md19080445 - 3 Aug 2021
Cited by 6 | Viewed by 3226
Abstract
Two new water-soluble phenanthroperylene quinones, gymnochrome H (2) and monosulfated gymnochrome A (3), as well as the known compounds gymnochrome A (4) and monosulfated gymnochrome D (5) were isolated from the deep-sea crinoid Hypalocrinus naresianus [...] Read more.
Two new water-soluble phenanthroperylene quinones, gymnochrome H (2) and monosulfated gymnochrome A (3), as well as the known compounds gymnochrome A (4) and monosulfated gymnochrome D (5) were isolated from the deep-sea crinoid Hypalocrinus naresianus, which had been collected in the deep sea of Japan. The structures of the compounds were elucidated by spectroscopic analysis including HRMS, 1D 1H and 13C NMR, and 2D NMR. The absolute configuration was determined by ECD spectroscopy, analysis of J-couplings and ROE contacts, and DFT calculations. The configuration of the axial chirality of all isolated phenanthroperylene quinones (2–5) was determined to be (P). For gymnochrome H (2) and monosulfated gymnochrome A (3), a (2′S,2″R) configuration was determined, whereas for monosulfated gymnochrome D (5) a (2′R,2″R), configuration was determined. Acetylated quinones are unusual among natural products from an echinoderm and gymnochrome H (2) together with the recently reported gymnochrome G (1) represent the first isolated acetylated phenanthroperylene quinones. Full article
(This article belongs to the Special Issue Configurational and Conformational Studies on the Structures of Marine Natural Products)
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15 pages, 3431 KiB  
Article
Model-Free Approach for the Configurational Analysis of Marine Natural Products
by Matthias Köck, Michael Reggelin and Stefan Immel
Mar. Drugs 2021, 19(6), 283; https://doi.org/10.3390/md19060283 - 21 May 2021
Cited by 9 | Viewed by 3834
Abstract
The NMR-based configurational analysis of complex marine natural products is still not a routine task. Different NMR parameters are used for the assignment of the relative configuration: NOE/ROE, homo- and heteronuclear J couplings as well as anisotropic parameters. The combined distance geometry (DG) [...] Read more.
The NMR-based configurational analysis of complex marine natural products is still not a routine task. Different NMR parameters are used for the assignment of the relative configuration: NOE/ROE, homo- and heteronuclear J couplings as well as anisotropic parameters. The combined distance geometry (DG) and distance bounds driven dynamics (DDD) method allows a model-free approach for the determination of the relative configuration that is invariant to the choice of an initial starting structure and does not rely on comparisons with (DFT) calculated structures. Here, we will discuss the configurational analysis of five complex marine natural products or synthetic derivatives thereof: the cis-palau’amine derivatives 1a and 1b, tetrabromostyloguanidine (1c), plakilactone H (2), and manzamine A (3). The certainty of configurational assignments is evaluated in view of the accuracy of the NOE/ROE data available. These case studies will show the prospective breadth of application of the DG/DDD method. Full article
(This article belongs to the Special Issue Configurational and Conformational Studies on the Structures of Marine Natural Products)
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Review

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28 pages, 11828 KiB  
Review
Approaches to Configuration Determinations of Flexible Marine Natural Products: Advances and Prospects
by Zong-Qing Huo, Feng Zhu, Xing-Wang Zhang, Xiao Zhang, Hong-Bao Liang, Jing-Chun Yao, Zhong Liu, Gui-Min Zhang, Qing-Qiang Yao and Guo-Fei Qin
Mar. Drugs 2022, 20(5), 333; https://doi.org/10.3390/md20050333 - 19 May 2022
Cited by 9 | Viewed by 3640
Abstract
Flexible marine natural products (MNPs), such as eribulin and bryostatin, play an important role in the development of modern marine drugs. However, due to the multiple chiral centers and geometrical uncertainty of flexible systems, configuration determinations of flexible MNPs face great challenges, which, [...] Read more.
Flexible marine natural products (MNPs), such as eribulin and bryostatin, play an important role in the development of modern marine drugs. However, due to the multiple chiral centers and geometrical uncertainty of flexible systems, configuration determinations of flexible MNPs face great challenges, which, in turn, have led to obstacles in druggability research. To resolve this issue, the comprehensive use of multiple methods is necessary. Additionally, configuration assignment methods, such as X-ray single-crystal diffraction (crystalline derivatives, crystallization chaperones, and crystalline sponges), NMR-based methods (JBCA and Mosher’s method), circular dichroism-based methods (ECCD and ICD), quantum computational chemistry-based methods (NMR calculations, ECD calculations, and VCD calculations), and chemical transformation-based methods should be summarized. This paper reviews the basic principles, characteristics, and applicability of the methods mentioned above as well as application examples to broaden the research and applications of these methods and to provide a reference for the configuration determinations of flexible MNPs. Full article
(This article belongs to the Special Issue Configurational and Conformational Studies on the Structures of Marine Natural Products)
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