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Shen SM, Appendino G, Guo YW. Pitfalls in the structural elucidation of small molecules. A critical analysis of a decade of structural misassignments of marine natural products. Nat Prod Rep 2022; 39:1803-1832. [PMID: 35770685 DOI: 10.1039/d2np00023g] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: July 2010 to August 2021This article summarizes more than 200 cases of misassigned marine natural products reported between July 2010 and August 2021, sorting out errors according to the structural elements. Based on a comparative analysis of the original and the revised structures, major pitfalls still plaguing the structural elucidation of small molecules were identified, emphasizing the role of total synthesis, crystallography, as well as chemical- and biosynthetic logic to complement spectroscopic data. Distinct "trends" in natural product misassignment are evident between compounds of marine and plant origin, with an overall much lower incidence of "impossible" structures within misassigned marine natural products.
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Affiliation(s)
- Shou-Mao Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. .,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Giovanni Appendino
- Dipartimento di Scienze del Farmaco, Universitá degli Studi del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Yue-Wei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. .,Drug Discovery Shandong Laboratory, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
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Abstract
This review deals with the synthesis of naturally occurring alkaloids containing partially or completely saturated pyrimidine nuclei. The interest in these compounds is associated with their structural diversity, high biological activity and toxicity. The review is divided into four parts, each of which describes a number of synthetic methodologies toward structurally different naturally occurring alkaloids containing saturated cyclic six-membered amidine, guanidine, aminal and urea (thiourea) moieties, respectively. The development of various synthetic strategies for the preparation of these compounds has remarkably increased during the past few decades. This is primarily due to the fact that some of these compounds are isolated only in limited quantities, which makes it practically impossible to study their full structural characteristics and biological activity.
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Guillen PO, Jaramillo KB, Genta-Jouve G, Thomas OP. Marine natural products from zoantharians: bioactivity, biosynthesis, systematics, and ecological roles. Nat Prod Rep 2020; 37:515-540. [DOI: 10.1039/c9np00043g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dazzling marine zoantharians represent a reservoir of chemical diversity that remains to be unveiled. These fragile animals have so far been found to harbour the highly bioactive palytoxins or zoanthamines but also the harmless ecdysteroids or zoanthozanthins.
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Affiliation(s)
- Paul O. Guillen
- Marine Biodiscovery
- School of Chemistry and Ryan Institute
- National University of Ireland Galway (NUI Galway)
- H91 TK33 Galway
- Ireland
| | - Karla B. Jaramillo
- ESPOL Escuela Superior Politécnica del Litoral, ESPOL
- Centro Nacional de Acuacultura e Investigaciones Marinas
- Guayaquil
- Ecuador
- Zoology
| | - Grégory Genta-Jouve
- Muséum National d'Histoire Naturelle
- Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245)
- Sorbonne Universités
- CNRS
- Paris
| | - Olivier P. Thomas
- Marine Biodiscovery
- School of Chemistry and Ryan Institute
- National University of Ireland Galway (NUI Galway)
- H91 TK33 Galway
- Ireland
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Abstract
This review covers the literature published in 2013 for marine natural products (MNPs), with 982 citations (644 for the period January to December 2013) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1163 for 2013), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
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Abstract
Marine indole alkaloids comprise a large and steadily growing group of secondary metabolites. Their diverse biological activities make many compounds of this class attractive starting points for pharmaceutical development. Several marine-derived indoles were found to possess cytotoxic, antineoplastic, antibacterial and antimicrobial activities, in addition to the action on human enzymes and receptors. The newly isolated indole alkaloids of marine origin since the last comprehensive review in 2003 are reported, and biological aspects will be discussed.
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Affiliation(s)
- Natalie Netz
- Institute of Organic Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.
| | - Till Opatz
- Institute of Organic Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.
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Gao C, Yi X, Huang R, Yan F, He B, Chen B. Alkaloids from Corals. Chem Biodivers 2013; 10:1435-47. [DOI: 10.1002/cbdv.201100276] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Indexed: 11/07/2022]
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Schmidt AW, Reddy KR, Knölker HJ. Occurrence, Biogenesis, and Synthesis of Biologically Active Carbazole Alkaloids. Chem Rev 2012; 112:3193-328. [PMID: 22480243 DOI: 10.1021/cr200447s] [Citation(s) in RCA: 899] [Impact Index Per Article: 74.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Arndt W. Schmidt
- Department Chemie, Technische Universität Dresden,
Bergstrasse 66, 01069 Dresden, Germany
| | - Kethiri R. Reddy
- Department Chemie, Technische Universität Dresden,
Bergstrasse 66, 01069 Dresden, Germany
| | - Hans-Joachim Knölker
- Department Chemie, Technische Universität Dresden,
Bergstrasse 66, 01069 Dresden, Germany
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Wagner D, Luck DG, Toonen RJ. The biology and ecology of black corals (Cnidaria: Anthozoa: Hexacorallia: Antipatharia). ADVANCES IN MARINE BIOLOGY 2012; 63:67-132. [PMID: 22877611 DOI: 10.1016/b978-0-12-394282-1.00002-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Antipatharians, commonly known as black corals, are treasured by many cultures for medicinal purposes and to produce jewellery. Despite their economic and cultural importance, very little is known about the basic biology and ecology of black corals because most species inhabit deeper-water environments (>50m) which are logistically challenging to study. There has been a recent increase of studies focusing on antipatharians; however, these have not yet been comprehensively reviewed. This literature review seeks to summarize the available information on the biology and ecology of antipatharians. Although black corals occur throughout all oceans and from subtidal to abyssal depths, they are particularly common in tropical and subtropical regions at depths below 50m. Antipatharians are generally found in areas with hard substrates, low-light and strong currents. Under favourable conditions, some black coral species form dense aggregations to the point of becoming ecologically dominant. Zooplankton appears to be the major component of the diet of black corals, which feed as suspension feeders and use mucus and nematocysts to capture their prey. Previously categorized as azooxanthellate corals, recent research has revealed that many antipatharians appear capable of harbouring symbionts, but unlike other corals, dinoflagellates of the genus Symbiodinium are generally not important to the nutrition of black corals. Antipatharians reproduce through both sexual and asexual processes. In general, polyps and colonies are gonochoric, with fertilization and larval development likely occurring externally; however, to date antipatharian larvae have only been observed for a single species. Antipatharians are generally slow-growing and long-lived organisms with maximum longevities ranging from decades to millennia. Black corals are more abundant with depth, a pattern which has been hypothesized to avoid competition with obligate photosynthetic fauna. Additionally, antipatharians may compete for space by using sweeper tentacles and secondary metabolites. With the exception of a few predators such as gastropods and green sea turtles, antipatharians appear to be little impacted by predation. Like other corals, antipatharians can be habitat engineers of importance to a myriad of associated organisms including arthropods, annelids, echinoderms, mollusks, sponges and cnidarians, several of which are adapted to live exclusively on black corals. Given that most black coral species inhabit remote environments, our understanding of these organisms will depend on our ability to effectively sample and study them. Future collections, particularly in deeper waters (>50m), will be needed to determine whether antipatharian species have limited biogeographical distributions or whether this has simply been an artefact of low sampling efforts away from population centres and taxonomic uncertainties within this group. Additionally, biological and ecological studies require increased sample sizes because most information is currently derived from the examination of only a handful of specimens.
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Affiliation(s)
- Daniel Wagner
- Papahānaumokuākea Marine National Monument, Honolulu, Hawai'i, USA.
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Bai X, Chen Y, Chen W, Lei H, Shi G. Volatile constituents, inorganic elements and primary screening of bioactivity of black coral cigarette holders. Mar Drugs 2011; 9:863-878. [PMID: 21673895 PMCID: PMC3111188 DOI: 10.3390/md9050863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Revised: 05/05/2011] [Accepted: 05/09/2011] [Indexed: 02/05/2023] Open
Abstract
Black corals (BC) have been used for a long time in Chinese medicine, and may have some pharmaceutical functions when used as material for cigarette holders in southeast China. This study is aimed to investigate the bioactivities of volatile constituents in BC and to explore the folklore behind the use of BC cigarette holders (BCCHs). We extracted the volatile constituents of BC by supercritical fluid extraction (SFE) with carbon dioxide (CO₂-SFE), then identified and analyzed the constituents by gas chromatography-mass spectrometry (GC-MS). In total, 15 components were reliably identified in BC and found to be biologically active. These included triethyl phosphate, butylated hydroxytoluene, cedrol, n-hexadecanoic acid, squalene, and cholesterol. Meanwhile 13 inorganic elements (P, Ca, Mg, S, B, Si, Fe, Cu, Zn, Ba, etc.) were determined by inductively coupled plasma spectrometer (ICPS). In the bioactivity tests, the BC extract (BCE) showed a scavenging activity of 2,2-diphenyl-1-picrylhydrazyl free radicals and hydroxyl radicals by phenanthroline-Fe (II) oxidation and moderate inhibition of Gram-positive microorganisms. The antioxidant and antimicrobial activities of BC, which are related to the active chemical composition, may explain the perceived benefit for cigarette smokers who use BCCHs.
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Affiliation(s)
- Xueting Bai
- Department of Pharmacology, Shantou University Medical College, Shantou 515041, China; E-Mails: (X.B.); (Y.C.)
| | - Yicun Chen
- Department of Pharmacology, Shantou University Medical College, Shantou 515041, China; E-Mails: (X.B.); (Y.C.)
| | - Weizhou Chen
- Marine Biology Institute, Shantou University, Shantou 515063, China; E-Mail:
| | - Huaping Lei
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; E-Mail:
| | - Ganggang Shi
- Department of Pharmacology, Shantou University Medical College, Shantou 515041, China; E-Mails: (X.B.); (Y.C.)
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11
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Natural Products Chemistry Research 2009's Progress in China. Chin J Nat Med 2011. [DOI: 10.1016/s1875-5364(11)60011-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Blunt JW, Copp BR, Munro MHG, Northcote PT, Prinsep MR. Marine natural products. Nat Prod Rep 2010; 28:196-268. [PMID: 21152619 DOI: 10.1039/c005001f] [Citation(s) in RCA: 343] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- John W Blunt
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
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Al-Lihaibi SS, Ayyad SEN, Shaher F, Alarif WM. Antibacterial Sphingolipid and Steroids from the Black Coral Antipathes dichotoma. Chem Pharm Bull (Tokyo) 2010; 58:1635-8. [DOI: 10.1248/cpb.58.1635] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | | | - Fekry Shaher
- Department of Marine Chemistry, Faculty of Marine Sciences, King Abdulaziz University
| | - Walied Mohamed Alarif
- Department of Marine Chemistry, Faculty of Marine Sciences, King Abdulaziz University
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