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Devi G, Gorki V, Walter NS, Sivangula S, Sobhia ME, Jachak S, Puri R, Kaur S. Exploring the efficacy of ethnomedicinal plants of Himalayan region against the malaria parasite. JOURNAL OF ETHNOPHARMACOLOGY 2024; 321:117394. [PMID: 37967777 DOI: 10.1016/j.jep.2023.117394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/28/2023] [Accepted: 11/04/2023] [Indexed: 11/17/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Plasmodium falciparum multi-drug resistant (MDR) strains are a great challenge to global health care. This predicament implies the urgent need to discover novel antimalarial drugs candidate from alternative natural sources. The Himalaya constitute a rich repository of medicinal plants which have been used traditionally in the folklore medicine since ages and having no scientific evidence for their activity. Crambe kotschyana Boiss. and Eremurus himalaicus Baker are used for their antipyretic and hepatoprotective properties in Kinnaur district of Himachal Pradesh, India. AIM OF THE STUDY This study would investigate the antiplasmodial efficacy of C. kotschyana and E. himalaicus extracts, their fractions and active components using in vitro, in vivo and in silico approaches to provide a scientific insight into their activity. METHODS The methanol extracts of C. kotschyana (CKME) and E. himalaicus (EHME) were prepared by maceration followed by fractionation using ethyl acetate. The isolation of flavonoid glycosides isorhamnetin-3, 7-di-O-glucoside from C. kotschyana and luteolin-6-C-glucoside (isoorientin) from E. himalaicus was carried out by antiplasmodial activity-guided isolation. In vitro antimalarial activity was assessed by WHO method while in vitro cytotoxicity was ascertained employing the MTT assay. Molecular docking and molecular dynamics simulation were performed using the Glide module of Schrödinger Software and Gromacs-2022 software package respectively. In vivo curative activity was assessed by Ryley and Peters method. RESULTS The methanol extracts of both the plants illustrated the best antiplasmodial activity followed by the ethyl acetate fractions. Iso-orientin (IC50 6.49 μg/ml) and Isorhamnetin-3,7-di-O-glucoside (IC50 9.22 μg/ml) illustrated considerable in vitro activity even against P. falciparum resistant strain. Extracts/fractions as well as the isolated compounds were found to be non-toxic with CC50 > 640 μg/ml. Molecular docking studies were performed with these 2 O-glucosides against four malaria targets to understand the binding pose of these molecules and the results suggested that these molecules have selectivity for lactate dehydrogenase enzyme. CKME and EHME exhibited curative activity in vivo along with increase in Mean Survival Time of mice. CONCLUSION The research delineated the scientific evidence that both the therapeutic herbs possessed antimalarial activity and notably, bioactive compounds responsible to exhibit the antimalarial activity have been isolated, identified and characterized. Further studies are underway to assess the antiplasmodial efficacy of isolated compounds alone and in combination with standard antimalarials.
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Affiliation(s)
- Geeta Devi
- Ethnobotany and Medicinal Plant Laboratory, Department of Botany, Panjab University, Chandigarh, 160014, India.
| | - Varun Gorki
- Parasitology Laboratory, Department of Zoology, Panjab University, Chandigarh, 160014, India
| | - Neha Sylvia Walter
- Parasitology Laboratory, Department of Zoology, Panjab University, Chandigarh, 160014, India
| | - Srikanth Sivangula
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S. A. S Nagar, Punjab, India
| | - M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S. A. S Nagar, Punjab, India
| | - Sanjay Jachak
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, 160062, India
| | - Richa Puri
- Ethnobotany and Medicinal Plant Laboratory, Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Sukhbir Kaur
- Parasitology Laboratory, Department of Zoology, Panjab University, Chandigarh, 160014, India.
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Takamura H, Hattori K, Ohashi T, Otsu T, Kadota I. Relative stereochemical determination of the C61-C83 fragment of symbiodinolide using a stereodivergent synthetic approach. Org Biomol Chem 2023; 21:8837-8848. [PMID: 37791452 DOI: 10.1039/d3ob01420g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Structural determination is required in the use of marine natural products to create novel drugs and drug leads in medicinal chemistry. Symbiodinolide, which is a polyol marine natural product with a molecular weight of 2860, increases the intracellular Ca2+ concentration and exhibits inhibitory activity against cyclooxygenase-1. Seventy percent of the structure of symbiodinolide has been stereochemically clarified. Herein, we report the elucidation of the relative configuration of the C61-C83 fragment, which is among the remaining thirty percent, using a stereodivergent synthetic strategy. We first assigned the relative configuration of the C61-C74 fragment. Two candidate diastereomers of the C61-C74 fragment were synthesized, and their NMR data were compared with those of the natural product, revealing the relative stereochemistry of this component. We then narrowed down the candidate compounds for the C69-C83 fragment from 16 possible diastereomers by analyzing the NMR data of the natural product, and we thus selected eight candidate diastereomers. Stereodivergent synthesis of the candidates for this fragment and comparison of the NMR data of the natural product and the eight synthetic products resulted in the relative stereostructural clarification of the C69-C83 fragment. These individually determined relative stereochemistries of the C61-C74 and C69-C83 fragments were connected via the common C69-C73 tetrahydropyran moiety of the fragments. Finally, the relative configuration of the C61-C83 fragment of symbiodinolide was determined. The stereodivergent synthetic approach used in this study can be extended to the stereochemical determination of other fragments of symbiodinolide.
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Affiliation(s)
- Hiroyoshi Takamura
- Department of Chemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan.
| | - Kosuke Hattori
- Department of Chemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan.
| | - Takumi Ohashi
- Department of Chemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan.
| | - Taichi Otsu
- Department of Chemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan.
| | - Isao Kadota
- Department of Chemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan.
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Wang Y, Fan A, Cohen RD, Dal Poggetto G, Huang Z, Yang H, Martin GE, Sherer EC, Reibarkh M, Wang X. Unequivocal identification of two-bond heteronuclear correlations in natural products at nanomole scale by i-HMBC. Nat Commun 2023; 14:1842. [PMID: 37012241 PMCID: PMC10070429 DOI: 10.1038/s41467-023-37289-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/09/2023] [Indexed: 04/05/2023] Open
Abstract
HMBC is an essential NMR experiment for determining multiple bond heteronuclear correlations in small to medium-sized organic molecules, including natural products, yet its major limitation is the inability to differentiate two-bond from longer-range correlations. There have been several attempts to address this issue, but all reported approaches suffer various drawbacks, such as restricted utility and poor sensitivity. Here we present a sensitive and universal methodology to identify two-bond HMBC correlations using isotope shifts, referred to as i-HMBC (isotope shift detection HMBC). Experimental utility was demonstrated at the sub-milligram / nanomole scale with only a few hours of acquisition time required for structure elucidation of several complex proton-deficient natural products, which could not be fully elucidated by conventional 2D NMR experiments. Because i-HMBC overcomes the key limitation of HMBC without significant reduction in sensitivity or performance, i-HMBC can be used as a complement to HMBC when unambiguous identifications of two-bond correlations are needed.
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Affiliation(s)
- Yunyi Wang
- Analytical Research & Development, Merck & Co. Inc, Rahway, NJ, 07065, USA
| | - Aili Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Ryan D Cohen
- Analytical Research & Development, Merck & Co. Inc, Rahway, NJ, 07065, USA
| | | | - Zheng Huang
- Process Research & Development, Merck & Co. Inc, Rahway, NJ, 07065, USA
| | - Haifeng Yang
- Process Research & Development, Merck & Co. Inc, Rahway, NJ, 07065, USA
| | - Gary E Martin
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ, 07079, USA
| | - Edward C Sherer
- Analytical Research & Development, Merck & Co. Inc, Rahway, NJ, 07065, USA
| | - Mikhail Reibarkh
- Analytical Research & Development, Merck & Co. Inc, Rahway, NJ, 07065, USA.
| | - Xiao Wang
- Analytical Research & Development, Merck & Co. Inc, Rahway, NJ, 07065, USA.
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4
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Approaches to Configuration Determinations of Flexible Marine Natural Products: Advances and Prospects. Mar Drugs 2022; 20:md20050333. [PMID: 35621984 PMCID: PMC9143581 DOI: 10.3390/md20050333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/07/2023] Open
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, 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.
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Tarazona G, Fernández R, Pérez M, Millán RE, Jiménez C, Rodríguez J, Cuevas C. Enigmazole C: A Cytotoxic Macrocyclic Lactone and Its Ring-Opened Derivatives from a New Species of Homophymia Sponge. JOURNAL OF NATURAL PRODUCTS 2022; 85:1059-1066. [PMID: 35234467 PMCID: PMC9040057 DOI: 10.1021/acs.jnatprod.1c01179] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Indexed: 06/14/2023]
Abstract
A new macrolide, enigmazole C (1), and two additional analogues, enigmazoles E (2) and D (3), were obtained from a new species of the Homophymia genus as part of an ongoing discovery program at PharmaMar to study cytotoxic substances from marine sources. The structures were fully characterized by cumulative analyses of NMR, IR, and MS spectra, along with density functional theory computational calculations. All three of the new compounds feature an unusual 2,3-dihydro-4H-pyran-4-one moiety, but only enigmazoles C (1) and D (3) showed cytotoxic activity in the micromolar range against A-549 (lung), HT-29 (colon), MDA-MB-231 (breast), and PSN-1 (pancreas) tumor cells.
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Affiliation(s)
- Guillermo Tarazona
- R&D, PharmaMar, Avenida De los Reyes, 1, Pol. Ind. La Mina-Norte, 28770-Colmenar Viejo, Madrid, Spain
| | - Rogelio Fernández
- R&D, PharmaMar, Avenida De los Reyes, 1, Pol. Ind. La Mina-Norte, 28770-Colmenar Viejo, Madrid, Spain
| | - Marta Pérez
- R&D, PharmaMar, Avenida De los Reyes, 1, Pol. Ind. La Mina-Norte, 28770-Colmenar Viejo, Madrid, Spain
| | - Ramón E. Millán
- Departmento
de Química, Facultad de Ciencias and Centro de Investigacions
Científicas Avanzadas (CICA), Universidade
de A Coruña, 15071 A Coruña, Spain
| | - Carlos Jiménez
- Departmento
de Química, Facultad de Ciencias and Centro de Investigacions
Científicas Avanzadas (CICA), Universidade
de A Coruña, 15071 A Coruña, Spain
| | - Jaime Rodríguez
- Departmento
de Química, Facultad de Ciencias and Centro de Investigacions
Científicas Avanzadas (CICA), Universidade
de A Coruña, 15071 A Coruña, Spain
| | - Carmen Cuevas
- R&D, PharmaMar, Avenida De los Reyes, 1, Pol. Ind. La Mina-Norte, 28770-Colmenar Viejo, Madrid, Spain
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6
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Segraves NL, Koenig SG, Stults J, Ma S, DiPasquale AG, Robinson SJ, Russell DJ. Challenges in the structure determination of a dimeric impurity found during development of GDC-0326. J Pharm Biomed Anal 2022; 213:114627. [DOI: 10.1016/j.jpba.2022.114627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022]
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7
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Górecki M, Frelek J. Towards seeking the right chiroptical tool to assign the stereochemistry of bioactive compounds: Effectiveness, challenges, and perspectives. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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8
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Pultar F, Hansen ME, Wolfrum S, Böselt L, Fróis-Martins R, Bloch S, Kravina AG, Pehlivanoglu D, Schäffer C, LeibundGut-Landmann S, Riniker S, Carreira EM. Mutanobactin D from the Human Microbiome: Total Synthesis, Configurational Assignment, and Biological Evaluation. J Am Chem Soc 2021; 143:10389-10402. [PMID: 34212720 DOI: 10.1021/jacs.1c04825] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mutanobactin D is a non-ribosomal, cyclic peptide isolated from Streptococcus mutans and shows activity reducing yeast-to-hyphae transition as well as biofilm formation of the pathogenic yeast Candida albicans. We report the first total synthesis of this natural product, which relies on enantioselective, zinc-mediated 1,3-dipolar cycloaddition and a sequence of cascading reactions, providing the key lipidated γ-amino acid found in mutanobactin D. The synthesis enables configurational assignment, determination of the dominant solution-state structure, and studies to assess the stability of the lipopeptide substructure found in the natural product. The information stored in the fingerprint region of the IR spectra in combination with quantum chemical calculations proved key to distinguishing between epimers of the α-substituted β-keto amide. Synthetic mutanobactin D drives discovery and analysis of its effect on growth of other members of the human oral consortium. Our results showcase how total synthesis is central for elucidating the complex network of interspecies communications of human colonizers.
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Affiliation(s)
- Felix Pultar
- Laboratorium für Organische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Moritz E Hansen
- Laboratorium für Organische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Susanne Wolfrum
- Laboratorium für Organische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Lennard Böselt
- Laboratorium für Physikalische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Ricardo Fróis-Martins
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 266a, 8057 Zürich, Switzerland.,Institute of Experimental Immunology, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Susanne Bloch
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, Muthgasse 11, 1190 Vienna, Austria
| | - Alberto G Kravina
- Laboratorium für Organische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Deren Pehlivanoglu
- Laboratorium für Organische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Christina Schäffer
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, Muthgasse 11, 1190 Vienna, Austria
| | - Salomé LeibundGut-Landmann
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 266a, 8057 Zürich, Switzerland.,Institute of Experimental Immunology, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Erick M Carreira
- Laboratorium für Organische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
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9
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Sidebottom PJ. Crews' rule-Still useful but often misquoted. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:752-753. [PMID: 33728662 DOI: 10.1002/mrc.5153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 03/07/2021] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Philip J Sidebottom
- Jealott's Hill International Research Centre, Syngenta, Bracknell, Berkshire, UK
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10
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Nazarski RB. Summary of DFT calculations coupled with current statistical and/or artificial neural network (ANN) methods to assist experimental NMR data in identifying diastereomeric structures. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2020.152548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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11
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Burns DC, Reynolds WF. Minimizing the risk of deducing wrong natural product structures from NMR data. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:500-533. [PMID: 33855734 DOI: 10.1002/mrc.4933] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 06/12/2023]
Abstract
There continues to be a disturbing number of natural products reported in the literature whose structures are incorrect. At least in part, this reflects the fact that many natural product chemists have limited formal nuclear magnetic resonance training. Gaps in training and lack of awareness regarding the challenges and ambiguities associated with two-dimensional nuclear magnetic resonance data interpretation can easily lead to errors in structure elucidation. The purpose of this tutorial is to point out some of these issues, highlight the kinds of errors that have been made and provide specific advice on how to avoid these missteps such that the risk of reporting a wrong structure is minimized.
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Affiliation(s)
- Darcy C Burns
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - William F Reynolds
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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Sestile S, Richardson D, Toomey R, Cool LG, Harper JK. NMR structural characterization from one-bond 13 C 13 C couplings: Complete assignment of a hydrogen-poor depsidone. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:23-33. [PMID: 32687644 DOI: 10.1002/mrc.5077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/20/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
The connectivity, conformation, tautomeric form, and dynamics of a new depsidone (perisalazinic acid) were characterized using one-bond 13 C13 C NMR scalar couplings (1 JCC ) obtained from the INADEQUATE experiment. Characterization of perisalazinic acid using more conventional NMR techniques is problematic due to the extremely limited number of CH protons present. In the present study, 81 candidate structures were considered and a best fit structure was selected by comparing computed 1 JCC values for each candidate to 15 experimental values. Of the six flexible moieties in perisalazinic acid, three are adequately represented by a single orientation stabilized by intramolecular hydrogen bonding. The three remaining groups are present as mixtures of conformers with two sites consisting of a pair of conformations and another disordered over six orientations. This study demonstrates the feasibility of complete three-dimensional structural characterization of an unknown using only theoretical and experimental 1 JCC values.
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Affiliation(s)
- Shannon Sestile
- Department of Chemistry, University of Central Florida, Orlando, FL, USA
| | - David Richardson
- Department of Chemistry, University of Central Florida, Orlando, FL, USA
| | - Ryan Toomey
- Department of Chemistry, Utah Valley University, Orem, UT, USA
| | - Laurence G Cool
- Agricultural Research Service, United States Department of Agriculture, Albany, CA, USA
| | - James K Harper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
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13
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Fuwa H. Structure determination, correction, and disproof of marine macrolide natural products by chemical synthesis. Org Chem Front 2021. [DOI: 10.1039/d1qo00481f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Integration of chemical synthesis, NMR spectroscopy, and various analytical means is key to success in the structure elucidation of stereochemically complex marine macrolide natural products.
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Affiliation(s)
- Haruhiko Fuwa
- Department of Applied Chemistry
- Faculty of Science and Engineering
- Chuo University
- Tokyo 112-8551
- Japan
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14
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Zatout R, Masi M, Sangermano F, Vurro M, Zonno MC, Santoro E, Calabrò V, Superchi S, Evidente A. Drophiobiolins A and B, Bioactive Ophiobolan Sestertepenoids Produced by Dreschslera gigantea. JOURNAL OF NATURAL PRODUCTS 2020; 83:3387-3396. [PMID: 33074690 DOI: 10.1021/acs.jnatprod.0c00836] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Two new bioactive ophiobolan sestertepenoids, named drophiobiolins A and B (1 and 2) were isolated from Drechslera gigantea, a fungus proposed as a mycoherbicide for biocontrol of Digitaria sanguinalis. They were isolated together with ophiobolin A, the main metabolite, 6-epi-ophiobolin A, 3-anhydro-6-epi-ophiobolin A, and ophiobolin I. Drophiobolins A and B were characterized by NMR, HRESIMS, and chemical methods as 7-hydroxy-7-(6-hydroxy-6-methylheptan-2-yl)-1,9a-dimethyl-3-oxo-3,3a,6,6a,7,8,9,9a,10,10a-decahydrodicyclopenta [a,d][8]annulene-4-carbaldehyde and 6-(hydroxymethyl)-3',9,10a-trimethyl-5'-(2-methylprop-1-en-1-yl)-3a,4,4',5',10,10a-hexahydro-1H,3'H-spiro[dicyclopenta[a,d] [8]annulene-3,2'-furan]-5,7(2H,9aH)-dione. The relative configuration of drophiobolins A and B, which did not afford crystals suitable for X-ray analysis, was determined by NOESY experiments, while the absolute configuration was assigned by comparison of their experimental and TDDFT calculated electronic circular dichroism (ECD) spectra. The phytotoxic activity of drophiobolins A and B was tested by leaf-puncture assay on cultivated (Lycopersicon esculentum L.), as well as on host (Digitaria sanguinalis L.) and nonhost (Chenopodium album L.) weed plants, compared to that of ophiobolin A. Both of the newly identified ophiobolins showed significant phytotoxicity. Drophiobolins A and B exhibited cytotoxicity against Hela B cells with an IC50 value of 10 μM. However, they had a lesser or no effect against Hacat, H1299, and A431 cells when compared to that of ophiobolin A.
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Affiliation(s)
- Roukia Zatout
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, Via Cintia 4, 80126 Napoli, Italy
- Laboratoire de Mycologie, de Biotechnologie et de l'Activité Microbienne (LaMyBAM), Département de Biologie Appliquée, Université des Frères Mentouri, Constantine1, BP, 325 Route de Aïn El Bey, 25017 Constantine, Algeria
| | - Marco Masi
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, Via Cintia 4, 80126 Napoli, Italy
| | - Felicia Sangermano
- Dipartimento di Biologia, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, Via Cintia 4, 80126 Napoli, Italy
| | - Maurizio Vurro
- Istituto di Scienze delle Produzioni Alimentari, CNR, Via Amendola 122/O, 70126 Bari, Italy
| | - Maria Chiara Zonno
- Istituto di Scienze delle Produzioni Alimentari, CNR, Via Amendola 122/O, 70126 Bari, Italy
| | - Ernesto Santoro
- Dipartimento di Scienze, Università della Basilicata, Via dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Viola Calabrò
- Dipartimento di Biologia, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, Via Cintia 4, 80126 Napoli, Italy
| | - Stefano Superchi
- Dipartimento di Scienze, Università della Basilicata, Via dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Antonio Evidente
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, Via Cintia 4, 80126 Napoli, Italy
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Kato S, Mizukami D, Sugai T, Tsuda M, Fuwa H. Total synthesis and complete configurational assignment of amphirionin-2. Chem Sci 2020; 12:872-879. [PMID: 34163854 PMCID: PMC8179035 DOI: 10.1039/d0sc06021f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022] Open
Abstract
Amphirionin-2 is a linear polyketide metabolite that exhibits potent and selective cytotoxic activity against certain human cancer cell lines. We disclose herein the first total synthesis of amphirionin-2 and determination of its absolute configuration. Our synthesis featured an extensive use of cobalt-catalyzed Mukaiyama-type cyclization of γ-hydroxy olefins for stereoselective formation of all the tetrahydrofuran rings found in the natural product, and a late-stage Stille-type coupling for convergent assembly of the entire carbon backbone. Four candidate diastereomers of amphirionin-2 were synthesized in a unified, convergent manner, and their spectroscopic/chromatographic properties were compared with those of the authentic material. The present study culminated in the reassignment of the C5/C7 relative configuration, assignment of the C12/C18 relative configuration, and determination of the absolute configuration of amphirionin-2.
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Affiliation(s)
- Shota Kato
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
| | - Daichi Mizukami
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
| | - Tomoya Sugai
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
| | - Masashi Tsuda
- Center for Advanced Marine Core Research and Department of Agriculture and Marine Science, Kochi University Nankoku Kochi 783-8502 Japan
| | - Haruhiko Fuwa
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
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16
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Ndukwe IE, Wang X, Lam NYS, Ermanis K, Alexander KL, Bertin MJ, Martin GE, Muir G, Paterson I, Britton R, Goodman JM, Helfrich EJN, Piel J, Gerwick WH, Williamson RT. Synergism of anisotropic and computational NMR methods reveals the likely configuration of phormidolide A. Chem Commun (Camb) 2020; 56:7565-7568. [PMID: 32520016 PMCID: PMC7436192 DOI: 10.1039/d0cc03055d] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Characterization of the complex molecular scaffold of the marine polyketide natural product phormidolide A represents a challenge that has persisted for nearly two decades. In light of discordant results arising from recent synthetic and biosynthetic reports, a rigorous study of the configuration of phormidolide A was necessary. This report outlines a synergistic effort employing computational and anisotropic NMR investigation, that provided orthogonal confirmation of the reassigned side chain, as well as supporting a further correction of the C7 stereocenter.
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Affiliation(s)
- Ikenna E Ndukwe
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Xiao Wang
- Analytical Research & Development, Merck & Co. Inc, Rahway, NJ, USA
| | - Nelson Y S Lam
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Kristaps Ermanis
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Kelsey L Alexander
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA and Department of Chemistry, University of California, San Diego, CA, USA
| | - Matthew J Bertin
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI, USA
| | - Gary E Martin
- Department of Chemistry, Seton Hall University, South Orange, NJ, USA
| | - Garrett Muir
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Ian Paterson
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Robert Britton
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | | | - Eric J N Helfrich
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
| | - William H Gerwick
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - R Thomas Williamson
- Department of Chemistry & Biochemistry, University of North Carolina Wilmington, Wilmington, NC, USA.
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17
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Masi M, Pannacci E, Santoro E, Zermane N, Superchi S, Evidente A. Stoechanones A and B, Phytotoxic Copaane Sesquiterpenoids Isolated from Lavandula stoechas with Potential Herbicidal Activity against Amaranthus retroflexus. JOURNAL OF NATURAL PRODUCTS 2020; 83:1658-1665. [PMID: 32383878 DOI: 10.1021/acs.jnatprod.0c00182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
From the organic extract of Lavandula stoechas, a Mediterranean native plant species, two new phytotoxic copaane sesquiterpenoids were isolated and named stoechanones A and B (1 and 2). They were obtained together with the methyl esters of caffeic and p-coumaric acids and the flavonoid apigenin (3-5, respectively). The structures of stoechanones A and B were determined by spectroscopic (essentially 1D and 2D 1H and 13C NMR and HRESIMS) and chemical methods, and they were characterized as 9,10-dihydroxy-8-isopropyl-1,5-dimethyltricyclo[4.4.0.02.7]dec-4-en-3-one and its 9-O-acetyl derivative. Their relative configurations were assigned by NOESY experiments, and the absolute configurations by comparison of the experimental and DFT-computed ECD spectra. When assayed through Petri dish bioassays, both stoechanones A and B showed phytotoxic effects against seed germination and seedling growth of Amaranthus retroflexus, strongly inhibiting seed germination percentage and radicle and hypocotyl lengths of seedlings. Owing to the herbicidal activity toward A. retroflexus, these two new tricyclic sesquiterpenoids could be proposed and developed as natural bioherbicides in order to increase the control of this problematic weed in the future.
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Affiliation(s)
- Marco Masi
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Napoli, Italy
| | - Euro Pannacci
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy
| | - Ernesto Santoro
- Dipartimento di Scienze, Università della Basilicata, Via dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Nadjia Zermane
- Faculty of Sciences, University of Algiers, 2 Didouche Mourad Street, 16002 Algiers, Algeria
| | - Stefano Superchi
- Dipartimento di Scienze, Università della Basilicata, Via dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Antonio Evidente
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Napoli, Italy
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18
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Santoro E, Vergura S, Scafato P, Belviso S, Masi M, Evidente A, Superchi S. Absolute Configuration Assignment to Chiral Natural Products by Biphenyl Chiroptical Probes: The Case of the Phytotoxins Colletochlorin A and Agropyrenol. JOURNAL OF NATURAL PRODUCTS 2020; 83:1061-1068. [PMID: 32091903 PMCID: PMC7997626 DOI: 10.1021/acs.jnatprod.9b01068] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The application of flexible biphenyls as chiroptical probes for the absolute configuration assignment to chiral natural products is described. The method is straightforward and reliable and can be applied to conformationally mobile and ECD silent compounds, not treatable by computational analysis of chiroptical data. By this approach, the (6'R) absolute configuration of the phytotoxin colletochlorin A (1) was confirmed, while the absolute configuration of the phytotoxin agropyrenol (2), previously assigned by the NMR Mosher method, was revised and assigned as (3'S,4'S). Moreover, with the biphenyl method the configurational assignment can be obtained simply by the sign of a diagnostic Cotton effect at 250 nm in the ECD spectrum, thus allowing application without the need of advanced knowledge of chiroptical spectroscopy and computational protocols.
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Affiliation(s)
- Ernesto Santoro
- Department
of Sciences, University of Basilicata, Viale dell’Ateneo Lucano
10, 85100 Potenza, Italy
| | - Stefania Vergura
- Department
of Sciences, University of Basilicata, Viale dell’Ateneo Lucano
10, 85100 Potenza, Italy
| | - Patrizia Scafato
- Department
of Sciences, University of Basilicata, Viale dell’Ateneo Lucano
10, 85100 Potenza, Italy
| | - Sandra Belviso
- Department
of Sciences, University of Basilicata, Viale dell’Ateneo Lucano
10, 85100 Potenza, Italy
| | - Marco Masi
- Department
of Chemical Sciences, University of Naples
Federico II, Complesso Universitario Monte San’Angelo, Via Cintia 4, 80126 Napoli, Italy
| | - Antonio Evidente
- Department
of Chemical Sciences, University of Naples
Federico II, Complesso Universitario Monte San’Angelo, Via Cintia 4, 80126 Napoli, Italy
| | - Stefano Superchi
- Department
of Sciences, University of Basilicata, Viale dell’Ateneo Lucano
10, 85100 Potenza, Italy
- Tel: +39-0971-20-6098. Fax: +39-0971-20-5678.
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19
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Burns AS, Dooley C, Carlson PR, Ziller JW, Rychnovsky SD. Relative and Absolute Structure Assignments of Alkenes Using Crystalline Osmate Derivatives for X-ray Analysis. Org Lett 2019; 21:10125-10129. [DOI: 10.1021/acs.orglett.9b04133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Alexander S. Burns
- Department of Chemistry, University of California at Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Charles Dooley
- Department of Chemistry, University of California at Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Paul R. Carlson
- Department of Chemistry, University of California at Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Joseph W. Ziller
- Department of Chemistry, University of California at Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Scott D. Rychnovsky
- Department of Chemistry, University of California at Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
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20
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Bracegirdle J, Robertson LP, Hume PA, Page MJ, Sharrock AV, Ackerley DF, Carroll AR, Keyzers RA. Lamellarin Sulfates from the Pacific Tunicate Didemnum ternerratum. JOURNAL OF NATURAL PRODUCTS 2019; 82:2000-2008. [PMID: 31306000 DOI: 10.1021/acs.jnatprod.9b00493] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Six new lamellarin sulfates (1-6) were isolated from the methanolic extract of the Pacific tunicate Didemnum ternerratum, collected from the Kingdom of Tonga. Mass spectrometric molecular networking through the GNPS platform was used to target the isolation of 1-6. Planar structures were elucidated through a combination of NMR and MS experiments. Through comparison of experimental and calculated ECD spectra, the absolute configurations of atropisomers 2-5 were determined, with their energetic barriers to racemization also determined computationally. The cytotoxicity of the compounds was tested against the human colon carcinoma cell line HCT-116, where lamellarin D-8-sulfate (5) exhibited moderate activity with an IC50 of 9.7 μM.
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Affiliation(s)
| | - Luke P Robertson
- Environmental Futures Research Institute , Griffith University , Southport 4222 , Gold Coast , Australia
- Griffith Institute for Drug Discovery , Griffith University , Nathan 4111 , Brisbane , Australia
| | | | - Michael J Page
- National Institute of Water & Atmospheric Research (NIWA) , P.O. Box 893, Nelson , New Zealand
| | | | | | - Anthony R Carroll
- Environmental Futures Research Institute , Griffith University , Southport 4222 , Gold Coast , Australia
- Griffith Institute for Drug Discovery , Griffith University , Nathan 4111 , Brisbane , Australia
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21
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Grauso L, Teta R, Esposito G, Menna M, Mangoni A. Computational prediction of chiroptical properties in structure elucidation of natural products. Nat Prod Rep 2019; 36:1005-1030. [PMID: 31166350 DOI: 10.1039/c9np00018f] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Covering: up to 2019This review covers the current status of the quantum mechanical prediction of chiroptical properties, such as electronic CD and optical rotation, as needed for stereochemical assignments in new natural products. The reliability of the prediction of chiroptical properties is steadily increasing, with a parallel decrease in the required computational resources. Now, quantum mechanical calculations for a medium-sized natural product can be reliably performed by natural product chemists on a mainstream PC. This review is aimed to guide natural product chemists through the numerous steps involved in such calculations. Through a concise, but comprehensive, discussion of the current computational practice, enriched by a few illustrative examples, this review provides readers with the theoretical background and practical knowledge needed to select the most appropriate parameters for performing the calculations, to anticipate possible problems, and to critically evaluate the reliability of their computational results. Common reasons for mistakes are also discussed; in particular, the importance of the correct evaluation of conformational ensembles of flexible molecules (an aspect often overlooked in current research) is stressed.
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Affiliation(s)
- Laura Grauso
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici (NA), Italy
| | - Roberta Teta
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Germana Esposito
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Marialuisa Menna
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Alfonso Mangoni
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy.
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22
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Sakamoto K, Hakamata A, Iwasaki A, Suenaga K, Tsuda M, Fuwa H. Total Synthesis, Stereochemical Revision, and Biological Assessment of Iriomoteolide-2a. Chemistry 2019; 25:8528-8542. [PMID: 30882926 DOI: 10.1002/chem.201900813] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/13/2019] [Indexed: 01/14/2023]
Abstract
Iriomoteolide-2a is a marine macrolide metabolite isolated from a cultured broth of the benthic dinoflagellate Amphidinium sp. HYA024 strain. This naturally occurring substance was reported to show remarkable cytotoxic activity against human cancer cell lines HeLa and DG-75 and in vivo antitumor activity against murine leukemia P388 cell line. Herein, the total synthesis, stereochemical revision, and biological assessment of iriomoteolide-2a are reported in detail. Total synthesis of the proposed structure 1 of iriomoteolide-2a featured a late-stage convergent assembly of three components by a Suzuki-Miyaura coupling, an esterification, and a ring-closing metathesis. However, the NMR data of synthetic 1 were not identical to those of the natural product. Careful analysis of the NMR data of the authentic material and synthesis/NMR analysis of appropriately designed model compounds led to consideration of four possible stereoisomers 2-5 as candidates for the correct structure. Accordingly, total syntheses of 2-5 were achieved by taking advantage of the convergent strategy, and comparison of the NMR spectra of synthetic 2-5 with those of the natural product led to the conclusion that 5 shows the correct relative configuration of iriomoteolide-2a. The absolute configuration of this natural product was finally established through chiral HPLC analysis of synthetic 5/ent-5 with the authentic sample. The antiproliferative activity of the synthetic compounds was assessed against HeLa and A549 cells to show that, in contrast to expectation, synthetic 5 and ent-5 were only marginally active in these cell lines. This work clearly underscores the vital role of total synthesis in the establishment of the structure and biological activity of natural products.
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Affiliation(s)
- Keita Sakamoto
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan.,Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Akihiro Hakamata
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Arihiro Iwasaki
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Kiyotake Suenaga
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Masashi Tsuda
- Center for Advanced Marine Core Research and Department of, Agriculture and Marine Science, Kochi University, Nankoku, Kochi, 783-8502, Japan
| | - Haruhiko Fuwa
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
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23
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Chhetri BK, Lavoie S, Sweeney-Jones AM, Kubanek J. Recent trends in the structural revision of natural products. Nat Prod Rep 2019; 35:514-531. [PMID: 29623331 DOI: 10.1039/c8np00011e] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: 2012 to 2017 This article reviews recent reports on the structural revision of natural products. Through a critical assessment of the original and revised published structures, the article addresses why each structure was targeted for revision, discusses the techniques and key discrepancies that led to the proposal of the revised structure, and offers measures that may have been taken during the original structure determination to prevent error. With the revised structures in hand, weaknesses of original proposals are assessed, providing a better understanding on the logic behind structure determination.
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Affiliation(s)
- Bhuwan Khatri Chhetri
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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24
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Duong TH, Beniddir MA, Boustie J, Nguyen KPP, Chavasiri W, Bernadat G, Le Pogam P. DP4-Assisted Structure Elucidation of Isodemethylchodatin, a New Norlichexanthone Derivative Meager in H-Atoms, from the Lichen Parmotrema tsavoense. Molecules 2019; 24:molecules24081527. [PMID: 31003403 PMCID: PMC6515090 DOI: 10.3390/molecules24081527] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/14/2019] [Accepted: 04/15/2019] [Indexed: 11/16/2022] Open
Abstract
A phytochemical investigation of the foliose lichen Parmotrema tsavoense (Krog and Swinscow) Krog and Swinscow (Parmeliaceae) resulted in the isolation of a new trichlorinated xanthone, isodemethylchodatin. The structure elucidation of this new norlichexanthone derivative proved tricky owing to proton deficiency, and to the lack of NMR data of closely related analogues. The structure of this compound was determined based on an integrated interpretation of 13C-NMR chemical shifts, MS spectra, and DP4-based computational chemistry was also performed to provide an independent and unambiguous validation of the determined structure. Isodemethylchodatin represents the first chlorinated lichexanthone/norlichexanthone derivative bearing a methoxy group at C-5.
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Affiliation(s)
- Thuc-Huy Duong
- Department for Management of Science and Technology Development, Ton Duc Thang University, Ho Chi Minh City 748355, Vietnam.
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 748355, Vietnam.
| | - Mehdi A Beniddir
- Équipe "Pharmacognosie⁻Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 Rue Jean-Baptiste Clément, 92290 Châtenay-Malabry, France.
| | - Joël Boustie
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)⁻UMR 6226, Univ Rennes, F-35000 Rennes, France.
| | - Kim-Phi-Phung Nguyen
- Department of Organic Chemistry, University of Science, National University⁻Ho Chi Minh City, 227 Nguyen Van Cu Str., Dist. 5, Ho Chi Minh City 748355, Vietnam.
| | - Warinthorn Chavasiri
- Natural Products Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Rd., Patumwan, Bangkok 10330, Thailand.
| | - Guillaume Bernadat
- Équipe "Pharmacognosie⁻Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 Rue Jean-Baptiste Clément, 92290 Châtenay-Malabry, France.
| | - Pierre Le Pogam
- Équipe "Pharmacognosie⁻Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 Rue Jean-Baptiste Clément, 92290 Châtenay-Malabry, France.
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25
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Menna M, Imperatore C, Mangoni A, Della Sala G, Taglialatela-Scafati O. Challenges in the configuration assignment of natural products. A case-selective perspective. Nat Prod Rep 2019; 36:476-489. [DOI: 10.1039/c8np00053k] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
An overview by a case study approach on the currently available methods for the configurational analysis of natural products.
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Affiliation(s)
- Marialuisa Menna
- Department of Pharmacy
- University of Naples Federico II
- 80131 Napoli
- Italy
| | | | - Alfonso Mangoni
- Department of Pharmacy
- University of Naples Federico II
- 80131 Napoli
- Italy
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26
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Burns DC, Mazzola EP, Reynolds WF. The role of computer-assisted structure elucidation (CASE) programs in the structure elucidation of complex natural products. Nat Prod Rep 2019; 36:919-933. [DOI: 10.1039/c9np00007k] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Computer-assisted structure elucidation can help to determine the structures of complex natural products while minimizing the risk of structure errors.
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Affiliation(s)
- Darcy C. Burns
- Department of Chemistry
- University of Toronto
- Toronto
- Canada
| | - Eugene P. Mazzola
- Department of Chemistry & Biochemistry
- University of Maryland
- College Park
- USA
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27
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McAlpine JB, Chen SN, Kutateladze A, MacMillan JB, Appendino G, Barison A, Beniddir MA, Biavatti MW, Bluml S, Boufridi A, Butler MS, Capon RJ, Choi YH, Coppage D, Crews P, Crimmins MT, Csete M, Dewapriya P, Egan JM, Garson MJ, Genta-Jouve G, Gerwick WH, Gross H, Harper MK, Hermanto P, Hook JM, Hunter L, Jeannerat D, Ji NY, Johnson TA, Kingston DGI, Koshino H, Lee HW, Lewin G, Li J, Linington RG, Liu M, McPhail KL, Molinski TF, Moore BS, Nam JW, Neupane RP, Niemitz M, Nuzillard JM, Oberlies NH, Ocampos FMM, Pan G, Quinn RJ, Reddy DS, Renault JH, Rivera-Chávez J, Robien W, Saunders CM, Schmidt TJ, Seger C, Shen B, Steinbeck C, Stuppner H, Sturm S, Taglialatela-Scafati O, Tantillo DJ, Verpoorte R, Wang BG, Williams CM, Williams PG, Wist J, Yue JM, Zhang C, Xu Z, Simmler C, Lankin DC, Bisson J, Pauli GF. The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research. Nat Prod Rep 2019; 36:35-107. [PMID: 30003207 PMCID: PMC6350634 DOI: 10.1039/c7np00064b] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Indexed: 12/20/2022]
Abstract
Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.
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Affiliation(s)
- James B McAlpine
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - Shao-Nong Chen
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - Andrei Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - John B MacMillan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Giovanni Appendino
- Dipartimento di Scienze Chimiche, Alimentari, Farmaceutiche e Farmacologiche, Universita` del Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
| | | | - Mehdi A Beniddir
- Équipe "Pharmacognosie-Chimie des Substances Naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Maique W Biavatti
- Department of Pharmaceutical Sciences, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Stefan Bluml
- University of Southern California, Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Asmaa Boufridi
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Mark S Butler
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Robert J Capon
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Young H Choi
- Division of Pharmacognosy, Section Metabolomics, Institute of Biology, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - David Coppage
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Michael T Crimmins
- Kenan and Caudill Laboratories of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marie Csete
- University of Southern California, Huntington Medical Research Institutes, 99 N. El Molino Ave., Pasadena, CA 91101, USA
| | - Pradeep Dewapriya
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Joseph M Egan
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Mary J Garson
- School of Chemistry and Molecular Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Grégory Genta-Jouve
- C-TAC, UMR 8638 CNRS, Faculté de Pharmacie de Paris, Paris-Descartes University, Sorbonne, Paris Cité, 4, Aveue de l'Observatoire, 75006 Paris, France
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA 92093, USA and Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Eberhard Karls University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Mary Kay Harper
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Precilia Hermanto
- NMR Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - James M Hook
- NMR Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Luke Hunter
- NMR Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Damien Jeannerat
- University of Geneva, Department of Organic Chemistry, 30 quai E. Ansermet, CH 1211 Geneva 4, Switzerland
| | - Nai-Yun Ji
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road 17, Yantai 264003, People's Republic of China
| | - Tyler A Johnson
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - David G I Kingston
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Hiroyuki Koshino
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Guy Lewin
- Équipe "Pharmacognosie-Chimie des Substances Naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Jie Li
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA
| | - Tadeusz F Molinski
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Bradley S Moore
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA 92093, USA and Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Joo-Won Nam
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Ram P Neupane
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Matthias Niemitz
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Jean-Marc Nuzillard
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Nicholas H Oberlies
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | | | - Guohui Pan
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - D Sai Reddy
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Jean-Hugues Renault
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - José Rivera-Chávez
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Wolfgang Robien
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Carla M Saunders
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Thomas J Schmidt
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Christoph Seger
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Ben Shen
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Christoph Steinbeck
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Hermann Stuppner
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Sonja Sturm
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Orazio Taglialatela-Scafati
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Dean J Tantillo
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Robert Verpoorte
- Division of Pharmacognosy, Section Metabolomics, Institute of Biology, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Bin-Gui Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road 17, Yantai 264003, People's Republic of China and Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Craig M Williams
- School of Chemistry and Molecular Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Philip G Williams
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Julien Wist
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Jian-Min Yue
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Chen Zhang
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Zhengren Xu
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Charlotte Simmler
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - David C Lankin
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - Jonathan Bisson
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - Guido F Pauli
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
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Takamura H. Synthetic Approach toward the Structural Elucidation of Symbiodinolide: Stereodivergent Synthesis and Stereostructural Revision of the C79-C104 Fragment. J SYN ORG CHEM JPN 2018. [DOI: 10.5059/yukigoseikyokaishi.76.474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Shubina LK, Makarieva TN, Guzii AG, Denisenko VA, Popov RS, Dmitrenok PS, Stonik VA. Absolute Configuration of the Cytotoxic Marine Alkaloid Monanchocidin A. JOURNAL OF NATURAL PRODUCTS 2018; 81:1113-1115. [PMID: 29553737 DOI: 10.1021/acs.jnatprod.8b00105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The absolute configuration of the cytotoxic guanidine alkaloid monanchocidin A with 11 stereogenic centers from the marine sponge Monanchora pulchra was determined as 5 R, 8 S, 10 S, 13 R, 14 S, 15 R, 19 R, 23 R, 37 S, 42 S, 43 R after extensive reductive degradation and conversion of the resulting alcohols to MTPA derivatives.
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Affiliation(s)
- Larisa K Shubina
- G. B. Elyakov Pacific Institute of Bioorganic Chemistry , Far-Eastern Branch of the Russian Academy of Sciences , Prospect 100-let Vladivostoku 159 , Vladivostok 690022 , Russian Federation
| | - Tatyana N Makarieva
- G. B. Elyakov Pacific Institute of Bioorganic Chemistry , Far-Eastern Branch of the Russian Academy of Sciences , Prospect 100-let Vladivostoku 159 , Vladivostok 690022 , Russian Federation
| | - Alla G Guzii
- G. B. Elyakov Pacific Institute of Bioorganic Chemistry , Far-Eastern Branch of the Russian Academy of Sciences , Prospect 100-let Vladivostoku 159 , Vladivostok 690022 , Russian Federation
| | - Vladimir A Denisenko
- G. B. Elyakov Pacific Institute of Bioorganic Chemistry , Far-Eastern Branch of the Russian Academy of Sciences , Prospect 100-let Vladivostoku 159 , Vladivostok 690022 , Russian Federation
| | - Roman S Popov
- G. B. Elyakov Pacific Institute of Bioorganic Chemistry , Far-Eastern Branch of the Russian Academy of Sciences , Prospect 100-let Vladivostoku 159 , Vladivostok 690022 , Russian Federation
| | - Pavel S Dmitrenok
- G. B. Elyakov Pacific Institute of Bioorganic Chemistry , Far-Eastern Branch of the Russian Academy of Sciences , Prospect 100-let Vladivostoku 159 , Vladivostok 690022 , Russian Federation
| | - Valentin A Stonik
- G. B. Elyakov Pacific Institute of Bioorganic Chemistry , Far-Eastern Branch of the Russian Academy of Sciences , Prospect 100-let Vladivostoku 159 , Vladivostok 690022 , Russian Federation
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30
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Liu Y, Saurí J, Mevers E, Peczuh MW, Hiemstra H, Clardy J, Martin GE, Williamson RT. Unequivocal determination of complex molecular structures using anisotropic NMR measurements. Science 2017; 356:356/6333/eaam5349. [PMID: 28385960 DOI: 10.1126/science.aam5349] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/16/2017] [Indexed: 11/02/2022]
Abstract
Assignment of complex molecular structures from nuclear magnetic resonance (NMR) data can be prone to interpretational mistakes. Residual dipolar couplings and residual chemical shift anisotropy provide a spatial view of the relative orientations between bonds and chemical shielding tensors, respectively, regardless of separation. Consequently, these data constitute a reliable reporter of global structural validity. Anisotropic NMR parameters can be used to evaluate investigators' structure proposals or structures generated by computer-assisted structure elucidation. Application of the method to several complex structure assignment problems shows promising results that signal a potential paradigm shift from conventional NMR data interpretation, which may be of particular utility for compounds not amenable to x-ray crystallography.
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Affiliation(s)
- Yizhou Liu
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Josep Saurí
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Emily Mevers
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Mark W Peczuh
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Unit 3060, Storrs, CT 06269, USA
| | - Henk Hiemstra
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Gary E Martin
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, NJ 07065, USA.
| | - R Thomas Williamson
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, NJ 07065, USA.
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31
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Ferrocene derivatives of liquid chiral molecules allow assignment of absolute configuration by X-ray crystallography. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.tetasy.2017.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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32
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Lorig-Roach N, Still PC, Coppage D, Compton JE, Crews MS, Navarro G, Tenney K, Crews P. Evaluating Nitrogen-Containing Biosynthetic Products Produced by Saltwater Culturing of Several California Littoral Zone Gram-Negative Bacteria. JOURNAL OF NATURAL PRODUCTS 2017; 80:2304-2310. [PMID: 28777571 PMCID: PMC5687060 DOI: 10.1021/acs.jnatprod.7b00302] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The biosynthetic potential of marine-sediment-derived Gram-negative bacteria is poorly understood. Sampling of California near-shore marine environments afforded isolation of numerous Gram-negative bacteria in the Proteobacteria and Bacteriodetes phyla, which were grown in the laboratory to provide extracts whose metabolites were identified by comparative analyses of LC-mass spectrometry and MSn data. Overall, we developed an assemblage of seven bacterial strains grown in five different media types designed to coax out unique secondary metabolite production as a function of varying culture conditions. The changes in metabolite production patterns were tracked using the GNPS MS2 fragmentation pattern analysis tool. A variety of nitrogen-rich metabolites were visualized from the different strains grown in different media, and strikingly, all of the strains examined produced the same new, proton-atom-deficient compound, 1-methyl-4-methylthio-β-carboline (1), C13H12N2S. Scale-up liquid culture of Achromobacter spanius (order: Burkholderiales; class: Betaproteobacteria) provided material for the final structure elucidation. The methods successfully combined in this work should stimulate future studies of molecules from marine-derived Gram-negative bacteria.
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Affiliation(s)
- Nicholas Lorig-Roach
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Patrick C. Still
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - David Coppage
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Jennifer E. Compton
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Mitchell S. Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Gabriel Navarro
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Karen Tenney
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Phillip Crews
- Corresponding Author Tel (P. Crews): (831) 459-2603. Fax: (831) 459-2935.
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33
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Luciano P, Imperatore C, Senese M, Aiello A, Casertano M, Guo YW, Menna M. Assignment of the Absolute Configuration of Phosphoeleganin via Synthesis of Model Compounds. JOURNAL OF NATURAL PRODUCTS 2017; 80:2118-2123. [PMID: 28699746 DOI: 10.1021/acs.jnatprod.7b00397] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The full absolute configuration assignment of phosphoeleganin (1), a recently discovered marine-derived phosphorylated polyketide with protein tyrosine phosphatase 1B inhibitory activity, was achieved. It was based on the synthesis of model diasteroisomeric compounds of the C-8-C-12 segment portion of phosphoeleganin, chiral derivatization methods, and application of the universal NMR database concept.
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Affiliation(s)
- Paolo Luciano
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , Via D. Montesano, 49, I-80131 Napoli, Italy
| | - Concetta Imperatore
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , Via D. Montesano, 49, I-80131 Napoli, Italy
| | - Maria Senese
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , Via D. Montesano, 49, I-80131 Napoli, Italy
| | - Anna Aiello
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , Via D. Montesano, 49, I-80131 Napoli, Italy
| | - Marcello Casertano
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , Via D. Montesano, 49, I-80131 Napoli, Italy
| | - Yue-W Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Zu Chong Zhi Road 555, Shanghai 201203, People's Republic of China
| | - Marialuisa Menna
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , Via D. Montesano, 49, I-80131 Napoli, Italy
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Abstract
Covering: July 2012 to June 2015. Previous review: Nat. Prod. Rep., 2013, 30, 869-915The structurally diverse imidazole-, oxazole-, and thiazole-containing secondary metabolites are widely distributed in terrestrial and marine environments, and exhibit extensive pharmacological activities. In this review the latest progress involving the isolation, biological activities, and chemical and biogenetic synthesis studies on these natural products has been summarized.
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Affiliation(s)
- Zhong Jin
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China. and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
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Martucci H, Campit SE, Gee SR, Bray WM, Gokey T, Cada AK, Yen TY, Minoura K, Guliaev AB, Lokey RS, Amagata T. Naphthablins B and C, Meroterpenoids Identified from the Marine Sediment-Derived Streptomyces sp. CP26-58 Using HeLa Cell-Based Cytological Profiling. JOURNAL OF NATURAL PRODUCTS 2017; 80:684-691. [PMID: 28128950 DOI: 10.1021/acs.jnatprod.6b00996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
HeLa cell-based cytological profiling (CP) was applied to an extract library of marine sediment-derived actinomycetes to discover new cytotoxic secondary metabolites. Among the hit strains, Streptomyces sp. CP26-58 was selected for further investigation to identify its cytotoxic metabolites. CP revealed that the known ionophore tetronasin (1) was responsible for the cytotoxic effect found in the extract. Furthermore, three naphthoquinone meroterpenoids, naphthablin A (2) and two new derivatives designated as naphthablins B (3) and C (4), were isolated from other cytotoxic fractions. The structures of the new compounds were elucidated based on analysis of their HRESIMS and comprehensive NMR data. The absolute configurations of the new compounds were deduced by simulating ECD spectra and calculating potential energies for the model compounds using density function theory (DFT) calculations. Compound 1 showed a significant cytotoxic effect against HeLa cells with an IC50 value of 0.23 μM, and CP successfully clustered 1 with calcium ionophores.
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Affiliation(s)
- Hana Martucci
- Department of Chemistry and Biochemistry, San Francisco State University , 1600 Holloway Avenue, San Francisco, California 94132, United States
| | - Scott E Campit
- Department of Chemistry and Biochemistry, San Francisco State University , 1600 Holloway Avenue, San Francisco, California 94132, United States
| | - Stephanie R Gee
- Department of Chemistry and Biochemistry, San Francisco State University , 1600 Holloway Avenue, San Francisco, California 94132, United States
| | - Walter M Bray
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California, 95064, United States
| | - Trevor Gokey
- Department of Chemistry and Biochemistry, San Francisco State University , 1600 Holloway Avenue, San Francisco, California 94132, United States
| | - A King Cada
- Department of Chemistry and Biochemistry, San Francisco State University , 1600 Holloway Avenue, San Francisco, California 94132, United States
| | - Ten-Yang Yen
- Department of Chemistry and Biochemistry, San Francisco State University , 1600 Holloway Avenue, San Francisco, California 94132, United States
| | - Katsuhiko Minoura
- Osaka University of Pharmaceutical Sciences , 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Anton B Guliaev
- Department of Chemistry and Biochemistry, San Francisco State University , 1600 Holloway Avenue, San Francisco, California 94132, United States
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California, 95064, United States
| | - Taro Amagata
- Department of Chemistry and Biochemistry, San Francisco State University , 1600 Holloway Avenue, San Francisco, California 94132, United States
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Saurí J, Parella T, Williamson RT, Martin GE. Improving the performance of J-modulated ADEQUATE experiments through homonuclear decoupling and non-uniform sampling. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:191-197. [PMID: 26332452 DOI: 10.1002/mrc.4322] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/17/2015] [Accepted: 07/27/2015] [Indexed: 06/05/2023]
Abstract
Homonuclear 13 C-13 C couplings at natural abundance can be measured using the J-modulated Adequate DoublE QUAntumTransfer Experiment (ADEQUATE) experiment. To somewhat ameliorate F1 digitization requirements, a scaling factor was incorporated into the original pulse sequence. Non-uniform sampling provides an obvious avenue to further facilitate the acquisition of 1 JCC and n JCC homonuclear coupling constant data. We introduce homonuclear decoupling (HD) analogous to that described for the 1,1-HD-ADEQUATE and 1,n-HD-ADEQUATE experiments and evaluate the combination of non-uniform sampling and HD on the acquisition of both 1 JCC and n JCC homonuclear 13 C-13 C coupling constants using ibuprofen as a model compound. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Josep Saurí
- Process and Analytical Chemistry, NMR Structure Elucidation, Merck Research Laboratories, Rahway, NJ, 07065, USA
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, 08193, Bellaterra (Barcelona), Catalonia, Spain
| | - R Thomas Williamson
- Process and Analytical Chemistry, NMR Structure Elucidation, Merck Research Laboratories, Rahway, NJ, 07065, USA
| | - Gary E Martin
- Process and Analytical Chemistry, NMR Structure Elucidation, Merck Research Laboratories, Rahway, NJ, 07065, USA
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37
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Guo YA, Zhao M, Xu Z, Ye T. Total Synthesis and Stereochemical Assignment of Actinoranone. Chemistry 2017; 23:3572-3576. [DOI: 10.1002/chem.201700476] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Yi-an Guo
- Key Laboratory of Chemical Genomics; Engineering Laboratory for Chiral Drug Synthesis; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Xili, Nanshan District Shenzhen 518055 China
| | - Meng Zhao
- Key Laboratory of Chemical Genomics; Engineering Laboratory for Chiral Drug Synthesis; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Xili, Nanshan District Shenzhen 518055 China
| | - Zhengshuang Xu
- Key Laboratory of Chemical Genomics; Engineering Laboratory for Chiral Drug Synthesis; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Xili, Nanshan District Shenzhen 518055 China
| | - Tao Ye
- Key Laboratory of Chemical Genomics; Engineering Laboratory for Chiral Drug Synthesis; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Xili, Nanshan District Shenzhen 518055 China
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38
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Buevich AV, Elyashberg ME. Synergistic Combination of CASE Algorithms and DFT Chemical Shift Predictions: A Powerful Approach for Structure Elucidation, Verification, and Revision. JOURNAL OF NATURAL PRODUCTS 2016; 79:3105-3116. [PMID: 28006916 DOI: 10.1021/acs.jnatprod.6b00799] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Structure elucidation of complex natural products and new organic compounds remains a challenging problem. To support this endeavor, CASE (computer-assisted structure elucidation) expert systems were developed. These systems are capable of generating a set of all possible structures consistent with an ensemble of 2D NMR data followed by selection of the most probable structure on the basis of empirical NMR chemical shift prediction. However, in some cases, empirical chemical shift prediction is incapable of distinguishing the correct structure. Herein, we demonstrate for the first time that the combination of CASE and density functional theory (DFT) methods for NMR chemical shift prediction allows the determination of the correct structure even in difficult situations. An expert system, ACD/Structure Elucidator, was used for the CASE analysis. This approach has been tested on three challenging natural products: aquatolide, coniothyrione, and chiral epoxyroussoenone. This work has demonstrated that the proposed synergistic approach is an unbiased, reliable, and very efficient structure verification and de novo structure elucidation method that can be applied to difficult structural problems when other experimental methods would be difficult or impossible to use.
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Affiliation(s)
- Alexei V Buevich
- Department of Discovery and Preclinical Sciences, Process Research and Development, NMR Structure Elucidation, Merck & Co., Inc. , Kenilworth, New Jersey 07033, United States
| | - Mikhail E Elyashberg
- Advanced Chemistry Development (ACD/Laboratories) , Akademik Bakulev Street 6, 117513 Moscow, Russian Federation
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Tan C, Liu Z, Chen S, Huang X, Cui H, Long Y, Lu Y, She Z. Antioxidative Polyketones from the Mangrove-Derived Fungus Ascomycota sp. SK2YWS-L. Sci Rep 2016; 6:36609. [PMID: 27811993 PMCID: PMC5095669 DOI: 10.1038/srep36609] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/17/2016] [Indexed: 01/25/2023] Open
Abstract
Three novel 2,3-diaryl indone derivatives, ascomindones A−C (1−3), and two new isobenzofuran derivatives, ascomfurans A (4) and B (5), together with four know compounds (6−9) were isolated from the culture of a mangrove-derived fungus Ascomycota sp. SK2YWS-L. Their structures were elucidated on the interpretation of spectroscopic data. 1 and 4 were further constructed by analysis of X-ray diffraction. Antioxidant properties based on 2,2-diphenyl-1-picrylhydrazyl (DPPH), hydroxyl radical scavenging activities and the ferric reducing ability power (FRAP) of the new compounds were assayed. All of them exhibited significant effects, of which 1 showed more potent activity than ascorbic acid in scavenging DPPH radical with IC50 value of 18.1 μM.
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Affiliation(s)
- Chunbin Tan
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Zhaoming Liu
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Senhua Chen
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Xishan Huang
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Hui Cui
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Yuhua Long
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China.,School of Chemistry and Environment, South China Normal University, 348 West Outer Ring Road, Guangzhou 510006, China
| | - Yongjun Lu
- School of Life Sciences and Biomedical Center, Sun Yat-Sen University, Guangzhou 510275, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou 510006, China
| | - Zhigang She
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou 510006, China
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40
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Andernach L, Sandjo LP, Liermann JC, Schlämann R, Richter C, Ferner JP, Schwalbe H, Schüffler A, Thines E, Opatz T. Terphenyl Derivatives from Allantophomopsis lycopodina. JOURNAL OF NATURAL PRODUCTS 2016; 79:2718-2725. [PMID: 27731998 DOI: 10.1021/acs.jnatprod.6b00690] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Three secondary fungal metabolites 1-3 with a benzo[b]naphtho[2,1-d]furan skeleton were isolated from submerged cultures of the ascomycete Allantophomopsis lycopodina. The NMR-based structure elucidation was challenging due to a low H/C ratio of only 0.64 and 0.68, respectively. NMR measurements in two different solvents and the use of NMR experiments such as HSQC-TOCSY and LR-HSQMBC proved to be helpful in this respect. The proposed structures obtained from the comprehensive analysis of the NMR data were verified by comparison of recorded and computed NMR chemical shifts from quantum chemical calculations of several constitutional isomers and were further analyzed with the aid of the DP4 and DP4+ probabilities.
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Affiliation(s)
- Lars Andernach
- Institute of Organic Chemistry, Johannes Gutenberg-University , Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Louis P Sandjo
- Institute of Organic Chemistry, Johannes Gutenberg-University , Duesbergweg 10-14, D-55128 Mainz, Germany
- Departamento de Ciências Farmacêuticas, Centro de Ciências da Saúde, Bloco J/K, Universidade Federal de Santa Catarina , Florianópolis 88040-900, SC, Brazil
| | - Johannes C Liermann
- Institute of Organic Chemistry, Johannes Gutenberg-University , Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Ricardo Schlämann
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH , Erwin-Schrödinger-Straße 56, D-67663 Kaiserslautern, Germany
| | - Christian Richter
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt , Max-von-Laue-Straße 7, D-60438 Frankfurt am Main, Germany
| | - Jan-Peter Ferner
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt , Max-von-Laue-Straße 7, D-60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt , Max-von-Laue-Straße 7, D-60438 Frankfurt am Main, Germany
| | - Anja Schüffler
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH , Erwin-Schrödinger-Straße 56, D-67663 Kaiserslautern, Germany
| | - Eckhard Thines
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH , Erwin-Schrödinger-Straße 56, D-67663 Kaiserslautern, Germany
- Institut für Mikrobiologie und Weinforschung, Johannes Gutenberg-University Mainz , Johann-Joachim-Becherweg 15, 55128 Mainz, Germany
| | - Till Opatz
- Institute of Organic Chemistry, Johannes Gutenberg-University , Duesbergweg 10-14, D-55128 Mainz, Germany
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41
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Gaspar H, Cutignano A, Grauso L, Neng N, Cachatra V, Fontana A, Xavier J, Cerejo M, Vieira H, Santos S. Erylusamides: Novel Atypical Glycolipids from Erylus cf. deficiens. Mar Drugs 2016; 14:md14100179. [PMID: 27727161 PMCID: PMC5082327 DOI: 10.3390/md14100179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/02/2016] [Accepted: 09/15/2016] [Indexed: 11/16/2022] Open
Abstract
Among marine organisms, sponges are the richest sources of pharmacologically-active compounds. Stemming from a previous lead discovery program that gathered a comprehensive library of organic extracts of marine sponges from the off-shore region of Portugal, crude extracts of Erylus cf. deficiens collected in the Gorringe Bank (Atlantic Ocean) were tested in the innovative high throughput screening (HTS) assay for inhibitors of indoleamine 2,3-dioxygenase (IDO) and showed activity. Bioassay guided fractionation of the dichloromethane extract led to the isolation of four new glycolipids, named erylusamide A–D. The structures of the isolated compounds were established by 1D and 2D nuclear magnetic resonance (NMR) spectroscopy, high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) and chemical derivatization. The metabolites shared a pentasaccharide moiety constituted by unusual highly acetylated d-glucose moieties as well as d-xylose and d-galactose. The aglycones were unprecedented long chain dihydroxyketo amides. Erylusamides A, B and D differ in the length of the hydrocarbon chain, while erylusamide C is a structural isomer of erylusamide B.
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Affiliation(s)
- Helena Gaspar
- Centro de Química e Bioquímica (CQB), Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal.
- MARE-Centro de Ciências do Mar e do Ambiente, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal.
| | - Adele Cutignano
- CNR-Istituto di Chimica Biomolecolare, Bio-Organic Chemistry Unit, via Campi Flegrei 34, Pozzuoli (NA) 80078, Italy.
| | - Laura Grauso
- CNR-Istituto di Chimica Biomolecolare, Bio-Organic Chemistry Unit, via Campi Flegrei 34, Pozzuoli (NA) 80078, Italy.
| | - Nuno Neng
- Centro de Química e Bioquímica (CQB), Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal.
| | - Vasco Cachatra
- Centro de Química e Bioquímica (CQB), Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal.
| | - Angelo Fontana
- CNR-Istituto di Chimica Biomolecolare, Bio-Organic Chemistry Unit, via Campi Flegrei 34, Pozzuoli (NA) 80078, Italy.
| | - Joana Xavier
- Department of Biology and Centre for Geobiology, University of Bergen, P.O. Box 7803, Bergen N-5020, Norway.
| | - Marta Cerejo
- Research & Innovation Accelerator, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, Caparica 2829-516, Portugal.
| | - Helena Vieira
- BioISI, Instituto de Biociências e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal.
| | - Susana Santos
- Centro de Química e Bioquímica (CQB), Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal.
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Saurí J, Reibarkh M, Zhang T, Cohen RD, Wang X, Molinski TF, Martin GE, Williamson RT. Band-Selective 2D HSQMBC: A Universal Technique for Detection and Measurement of 35,37Cl Isotope Effects for 13C Nuclei. Org Lett 2016; 18:4786-4789. [DOI: 10.1021/acs.orglett.6b02158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Josep Saurí
- NMR Structure Elucidation, Process Research and Development and ‡Discovery Chemistry, MRL, Merck & Co., Inc., P.O. Box 2000, Rahway, New Jersey 07065, United States
- Department of Chemistry and Biochemistry and ∥Skaggs School of
Pharmacy and Pharmaceutical
Sciences, University of California, San Diego, 9500 Gilman Drive
MC-0358, La Jolla, California 92093, United States
| | - Mikhail Reibarkh
- NMR Structure Elucidation, Process Research and Development and ‡Discovery Chemistry, MRL, Merck & Co., Inc., P.O. Box 2000, Rahway, New Jersey 07065, United States
- Department of Chemistry and Biochemistry and ∥Skaggs School of
Pharmacy and Pharmaceutical
Sciences, University of California, San Diego, 9500 Gilman Drive
MC-0358, La Jolla, California 92093, United States
| | - Ting Zhang
- NMR Structure Elucidation, Process Research and Development and ‡Discovery Chemistry, MRL, Merck & Co., Inc., P.O. Box 2000, Rahway, New Jersey 07065, United States
- Department of Chemistry and Biochemistry and ∥Skaggs School of
Pharmacy and Pharmaceutical
Sciences, University of California, San Diego, 9500 Gilman Drive
MC-0358, La Jolla, California 92093, United States
| | - Ryan D. Cohen
- NMR Structure Elucidation, Process Research and Development and ‡Discovery Chemistry, MRL, Merck & Co., Inc., P.O. Box 2000, Rahway, New Jersey 07065, United States
- Department of Chemistry and Biochemistry and ∥Skaggs School of
Pharmacy and Pharmaceutical
Sciences, University of California, San Diego, 9500 Gilman Drive
MC-0358, La Jolla, California 92093, United States
| | - Xiao Wang
- NMR Structure Elucidation, Process Research and Development and ‡Discovery Chemistry, MRL, Merck & Co., Inc., P.O. Box 2000, Rahway, New Jersey 07065, United States
- Department of Chemistry and Biochemistry and ∥Skaggs School of
Pharmacy and Pharmaceutical
Sciences, University of California, San Diego, 9500 Gilman Drive
MC-0358, La Jolla, California 92093, United States
| | - Tadeusz F. Molinski
- NMR Structure Elucidation, Process Research and Development and ‡Discovery Chemistry, MRL, Merck & Co., Inc., P.O. Box 2000, Rahway, New Jersey 07065, United States
- Department of Chemistry and Biochemistry and ∥Skaggs School of
Pharmacy and Pharmaceutical
Sciences, University of California, San Diego, 9500 Gilman Drive
MC-0358, La Jolla, California 92093, United States
| | - Gary E. Martin
- NMR Structure Elucidation, Process Research and Development and ‡Discovery Chemistry, MRL, Merck & Co., Inc., P.O. Box 2000, Rahway, New Jersey 07065, United States
- Department of Chemistry and Biochemistry and ∥Skaggs School of
Pharmacy and Pharmaceutical
Sciences, University of California, San Diego, 9500 Gilman Drive
MC-0358, La Jolla, California 92093, United States
| | - R. Thomas Williamson
- NMR Structure Elucidation, Process Research and Development and ‡Discovery Chemistry, MRL, Merck & Co., Inc., P.O. Box 2000, Rahway, New Jersey 07065, United States
- Department of Chemistry and Biochemistry and ∥Skaggs School of
Pharmacy and Pharmaceutical
Sciences, University of California, San Diego, 9500 Gilman Drive
MC-0358, La Jolla, California 92093, United States
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43
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Jamison MT, Molinski TF. Jamaicensamide A, a Peptide Containing β-Amino-α-keto and Thiazole-Homologated η-Amino Acid Residues from the Sponge Plakina jamaicensis. JOURNAL OF NATURAL PRODUCTS 2016; 79:2243-2249. [PMID: 27547840 DOI: 10.1021/acs.jnatprod.6b00336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A new cyclic peptide, jamaicensamide A, composed of six amino acids, including a thiazole-homologated amino acid, was isolated from the Bahamian sponge Plakina jamaicensis, along with known compounds bitungolide A and franklinolide A. The structure of the title peptide was solved by integrated analysis of MS, 1D and 2D NMR data, oxidation-hydrolyses to α-amino acids, and their stereodetermination by Marfey's method. The close structural resemblance of Western Atlantic-derived jamaicensamide A to known Western Pacific-derived peptides of lithistid sponges in the genus Theonella and Discodermia suggests a common origin: the symbiotic bacterium Entotheonella sp., a so-called "talented producer" responsible for biosynthesis of most Theonella-associated peptides. Similar natural products from sponges of disparate genera evince the likelihood that these invertebrates harbor the same or a very similar symbiont.
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Affiliation(s)
- Matthew T Jamison
- Department of Chemistry and Biochemistry and ‡Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , 9500 Gilman Dr. MC-0358, La Jolla, California 92093-0358, United States
| | - Tadeusz F Molinski
- Department of Chemistry and Biochemistry and ‡Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , 9500 Gilman Dr. MC-0358, La Jolla, California 92093-0358, United States
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44
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Gaudêncio SP, Pereira F. Dereplication: racing to speed up the natural products discovery process. Nat Prod Rep 2015; 32:779-810. [PMID: 25850681 DOI: 10.1039/c4np00134f] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: 1993-2014 (July)To alleviate the dereplication holdup, which is a major bottleneck in natural products discovery, scientists have been conducting their research efforts to add tools to their "bag of tricks" aiming to achieve faster, more accurate and efficient ways to accelerate the pace of the drug discovery process. Consequently dereplication has become a hot topic presenting a huge publication boom since 2012, blending multidisciplinary fields in new ways that provide important conceptual and/or methodological advances, opening up pioneering research prospects in this field.
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Affiliation(s)
- Susana P Gaudêncio
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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45
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Christmann M, Hu J, Kitamura M, Stoltz B. Tetrahedron reports on organic chemistry. Tetrahedron 2015. [DOI: 10.1016/s0040-4020(15)00744-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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46
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47
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Li K, Chung-Davidson YW, Bussy U, Li W. Recent advances and applications of experimental technologies in marine natural product research. Mar Drugs 2015; 13:2694-713. [PMID: 25939037 PMCID: PMC4446601 DOI: 10.3390/md13052694] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 04/02/2015] [Accepted: 04/14/2015] [Indexed: 11/16/2022] Open
Abstract
Marine natural products are a rich source of novel and biologically active compounds. The number of identified marine natural compounds has grown 20% over the last five years from 2009 to 2013. Several challenges, including sample collection and structure elucidation, have limited the development of this research field. Nonetheless, new approaches, such as sampling strategies for organisms from extreme ocean environments, nanoscale NMR and computational chemistry for structural determination, are now available to overcome the barriers. In this review, we highlight the experimental technology innovations in the field of marine natural products, which in our view will lead to the development of many new drugs in the future.
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Affiliation(s)
- Ke Li
- Department of Fisheries and Wildlife, Michigan State University, Room 13 Natural Resources Building, 480 Wilson Road, East Lansing, MI 48824, USA.
| | - Yu-Wen Chung-Davidson
- Department of Fisheries and Wildlife, Michigan State University, Room 13 Natural Resources Building, 480 Wilson Road, East Lansing, MI 48824, USA.
| | - Ugo Bussy
- Department of Fisheries and Wildlife, Michigan State University, Room 13 Natural Resources Building, 480 Wilson Road, East Lansing, MI 48824, USA.
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, Room 13 Natural Resources Building, 480 Wilson Road, East Lansing, MI 48824, USA.
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48
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Kim H, Yang I, Ryu SY, Won DH, Giri AG, Wang W, Choi H, Chin J, Hahn D, Kim E, Han C, Lee J, Nam SJ, Ho WK, Kang H. Acredinones A and B, voltage-dependent potassium channel inhibitors from the sponge-derived fungus Acremonium sp. F9A015. JOURNAL OF NATURAL PRODUCTS 2015; 78:363-367. [PMID: 25689430 DOI: 10.1021/np5007586] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Two new benzophenones, acredinones A (1) and B (2), were isolated from a marine-sponge-associated Acremonium sp. fungus. Their chemical structures were elucidated on the interpretation of spectroscopic data. The structure of 1 was confirmed by palladium-catalyzed hydrogenation, followed by spectroscopic data analysis. Acredinones A (1) and B (2) inhibited the outward K(+) currents of the insulin secreting cell line INS-1 with IC50 values of 0.59 and 1.0 μM, respectively.
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Affiliation(s)
- Hiyoung Kim
- †Center for Marine Natural Products and Drug Discovery, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 151-747, Korea
| | - Inho Yang
- †Center for Marine Natural Products and Drug Discovery, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 151-747, Korea
| | - Shin-Young Ryu
- ‡National Research Laboratory for Cell Physiology and Department of Physiology, Seoul National University College of Medicine, 28 Yonkeun-Dong, Chongno-Ku, Seoul 110-799, Korea
| | - Dong Hwan Won
- †Center for Marine Natural Products and Drug Discovery, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 151-747, Korea
| | - Awadut G Giri
- †Center for Marine Natural Products and Drug Discovery, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 151-747, Korea
| | - Weihong Wang
- †Center for Marine Natural Products and Drug Discovery, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 151-747, Korea
| | - Hyukjae Choi
- §College of Pharmacy, Yeungnam University, 214-1 Dae-dong, Gyeongsan 712-749, Korea
| | - Jungwook Chin
- †Center for Marine Natural Products and Drug Discovery, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 151-747, Korea
| | - Dongyup Hahn
- †Center for Marine Natural Products and Drug Discovery, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 151-747, Korea
| | - Eunhee Kim
- †Center for Marine Natural Products and Drug Discovery, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 151-747, Korea
| | - Chulkyeong Han
- †Center for Marine Natural Products and Drug Discovery, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 151-747, Korea
| | - Jihye Lee
- †Center for Marine Natural Products and Drug Discovery, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 151-747, Korea
| | - Sang-Jip Nam
- ⊥Department of Chemistry and Nano Science, Global Top 5 Program, Ewha Womans University, Seoul 120-750, Korea
| | - Won-Kyung Ho
- ‡National Research Laboratory for Cell Physiology and Department of Physiology, Seoul National University College of Medicine, 28 Yonkeun-Dong, Chongno-Ku, Seoul 110-799, Korea
| | - Heonjoong Kang
- †Center for Marine Natural Products and Drug Discovery, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 151-747, Korea
- ∥Research Institute of Oceanography, Seoul National University, NS-80, Seoul 151-747, Korea
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49
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Takamura H, Wada H, Ogino M, Kikuchi T, Kadota I, Uemura D. Stereodivergent Synthesis and Relative Stereostructure of the C1–C13 Fragment of Symbiodinolide. J Org Chem 2015; 80:3111-23. [DOI: 10.1021/acs.joc.5b00027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiroyoshi Takamura
- Department
of Chemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan
| | - Hiroko Wada
- Department
of Chemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan
| | - Mao Ogino
- Department
of Chemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan
| | - Takahiro Kikuchi
- Department
of Chemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan
| | - Isao Kadota
- Department
of Chemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan
| | - Daisuke Uemura
- Department
of Chemistry, Faculty of Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka 259-1293, Japan
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50
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Batista Jr. JM, Blanch EW, Bolzani VDS. Recent advances in the use of vibrational chiroptical spectroscopic methods for stereochemical characterization of natural products. Nat Prod Rep 2015; 32:1280-302. [DOI: 10.1039/c5np00027k] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A comprehensive look into application of vibrational optical activity methods for conformational and configurational assignments in natural product molecules over the last 15 years is provided.
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Affiliation(s)
- João M. Batista Jr.
- Department of Chemistry
- Federal University of São Carlos – UFSCar
- São Carlos
- Brazil
| | - Ewan W. Blanch
- School of Applied Sciences
- RMIT University
- Melbourne
- Australia
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