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Elyashberg M, Tyagarajan S, Mandal M, Buevich AV. Enhancing Efficiency of Natural Product Structure Revision: Leveraging CASE and DFT over Total Synthesis. Molecules 2023; 28:molecules28093796. [PMID: 37175206 PMCID: PMC10180399 DOI: 10.3390/molecules28093796] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Natural products remain one of the major sources of coveted, biologically active compounds. Each isolated compound undergoes biological testing, and its structure is usually established using a set of spectroscopic techniques (NMR, MS, UV-IR, ECD, VCD, etc.). However, the number of erroneously determined structures remains noticeable. Structure revisions are very costly, as they usually require extensive use of spectroscopic data, computational chemistry, and total synthesis. The cost is particularly high when a biologically active compound is resynthesized and the product is inactive because its structure is wrong and remains unknown. In this paper, we propose using Computer-Assisted Structure Elucidation (CASE) and Density Functional Theory (DFT) methods as tools for preventive verification of the originally proposed structure, and elucidation of the correct structure if the original structure is deemed to be incorrect. We examined twelve real cases in which structure revisions of natural products were performed using total synthesis, and we showed that in each of these cases, time-consuming total synthesis could have been avoided if CASE and DFT had been applied. In all described cases, the correct structures were established within minutes of using the originally published NMR and MS data, which were sometimes incomplete or had typos.
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Affiliation(s)
- Mikhail Elyashberg
- Advanced Chemistry Development Inc. (ACD/Labs), Toronto, ON M5C 1B5, Canada
| | | | - Mihir Mandal
- Medicinal Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Alexei V Buevich
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, NJ 07033, USA
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2
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Köse A, Soydaş E, Kara Y. Unique reaction of cyclicimides containing double bond with chlorosulfonyl isocyanate and theoretical computations: Solvent-free reactions. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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3
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Dorn RW, Wall BJ, Ference SB, Norris SR, Lubach JW, Rossini AJ, VanVeller B. Attached Nitrogen Test by 13C- 14N Solid-State NMR Spectroscopy for the Structure Determination of Heterocyclic Isomers. Org Lett 2022; 24:5635-5640. [PMID: 35731042 PMCID: PMC9933616 DOI: 10.1021/acs.orglett.2c01576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Differentiation of heterocyclic isomers by solution 1H, 13C, and 15N NMR spectroscopy is often challenging due to similarities in their spectroscopic signatures. Here, 13C{14N} solid-state NMR spectroscopy experiments are shown to operate as an "attached nitrogen test", where heterocyclic isomers are easy to distinguish based on one-dimensional nitrogen-filtered 13C solid-state NMR. We anticipate that these NMR experiments will facilitate the assignment of heterocyclic isomers during synthesis and natural product discovery.
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Affiliation(s)
- Rick W. Dorn
- Iowa State University, Department of Chemistry, Ames, IA, USA, 50011.,US Department of Energy, Ames Laboratory, Ames, IS, USA, 50011
| | - Brendan J. Wall
- Iowa State University, Department of Chemistry, Ames, IA, USA, 50011
| | - Sarah B. Ference
- Iowa State University, Department of Chemistry, Ames, IA, USA, 50011
| | - Sean R. Norris
- Iowa State University, Department of Chemistry, Ames, IA, USA, 50011
| | | | - Aaron J. Rossini
- Iowa State University, Department of Chemistry, Ames, IA, USA, 50011.,US Department of Energy, Ames Laboratory, Ames, IS, USA, 50011.,Corresponding Author, 515-294-8952 , 515-294-7613
| | - Brett VanVeller
- Iowa State University, Department of Chemistry, Ames, IA, USA, 50011.,Corresponding Author, 515-294-8952 , 515-294-7613
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4
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Osipyan A, Shaabani S, Warmerdam R, Shishkina SV, Boltz H, Dömling A. Automated, Accelerated Nanoscale Synthesis of Iminopyrrolidines. Angew Chem Int Ed Engl 2020; 59:12423-12427. [PMID: 32048418 PMCID: PMC7383484 DOI: 10.1002/anie.202000887] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Indexed: 12/24/2022]
Abstract
Miniaturization and acceleration of synthetic chemistry is an emerging area in pharmaceutical, agrochemical, and materials research and development. Herein, we describe the synthesis of iminopyrrolidine-2-carboxylic acid derivatives using chiral glutamine, oxo components, and isocyanide building blocks in an unprecedented Ugi-3-component reaction. We used I-DOT, a positive-pressure-based low-volume and non-contact dispensing technology to prepare more than 1000 different derivatives in a fully automated fashion. In general, the reaction is stereoselective, proceeds in good yields, and tolerates a wide variety of functional groups. We exemplify a pipeline of fast and efficient nanomole-scale scouting to millimole-scale synthesis for the discovery of a useful novel reaction with great scope.
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Affiliation(s)
- Angelina Osipyan
- Pharmacy Department, Drug Design groupUniversity of GroningenDeusinglaan 19713AVGroningenThe Netherlands
| | - Shabnam Shaabani
- Pharmacy Department, Drug Design groupUniversity of GroningenDeusinglaan 19713AVGroningenThe Netherlands
| | - Robert Warmerdam
- Pharmacy Department, Drug Design groupUniversity of GroningenDeusinglaan 19713AVGroningenThe Netherlands
| | - Svitlana V. Shishkina
- SSI “Institute for Single Crystals,”National Academy of Science of Ukraine60 Lenina Ave.Kharkiv61001Ukraine
| | - Harry Boltz
- Dispendix GmbHHeßbrühlstraße 770565StuttgartGermany
| | - Alexander Dömling
- Pharmacy Department, Drug Design groupUniversity of GroningenDeusinglaan 19713AVGroningenThe Netherlands
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5
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Osipyan A, Shaabani S, Warmerdam R, Shishkina SV, Boltz H, Dömling A. Automated, Accelerated Nanoscale Synthesis of Iminopyrrolidines. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Angelina Osipyan
- Pharmacy Department, Drug Design group University of Groningen Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Shabnam Shaabani
- Pharmacy Department, Drug Design group University of Groningen Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Robert Warmerdam
- Pharmacy Department, Drug Design group University of Groningen Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Svitlana V. Shishkina
- SSI “Institute for Single Crystals,” National Academy of Science of Ukraine 60 Lenina Ave. Kharkiv 61001 Ukraine
| | - Harry Boltz
- Dispendix GmbH Heßbrühlstraße 7 70565 Stuttgart Germany
| | - Alexander Dömling
- Pharmacy Department, Drug Design group University of Groningen Deusinglaan 1 9713 AV Groningen The Netherlands
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Schrey H, Spiteller P. E- and Z-Proxamidines, Unprecedented 1,3-Diazacyclooct-1-ene Alkaloids from Fruiting Bodies of Laccaria proxima. Chemistry 2019; 25:8035-8042. [PMID: 31033066 DOI: 10.1002/chem.201900566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Indexed: 11/07/2022]
Abstract
Fruiting bodies of Laccaria proxima were screened for the presence of new secondary metabolites by means of HPLC-UV and LC-HR-(+)-ESIMS. Thus, two isomeric alkaloids with a highly unusual core structure, E-proxamidine and its Z-isomer, were isolated from Laccaria proxima. The proxamidines consist of an eight-membered heterocyclic ring system with a formamidine unit. The structures were established by 2D NMR spectroscopic methods, HR-(+)-ESIMS, and HR-(+)-ESIMS/MS. The proxamidines are probably biosynthetically derived from tryptophan, dimethylallyl pyrophosphate, and S-adenosylmethionine and the eight-membered ring of the proxamidines is likely to be generated by a rearrangement of the tryptophan sceleton. Metabolic profiling of fruiting bodies of some other Laccaria species revealed that the proxamidines appear in significant amounts only in L. proxima making the compounds suitable as chemotaxonomic markers. E-Proxamidine exhibits herbicidal activity against Lepidium sativum.
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Affiliation(s)
- Hedda Schrey
- Institut für Organische und Analytische Chemie, Universität Bremen, Leobener Straße 7, 28359, Bremen, Germany
| | - Peter Spiteller
- Institut für Organische und Analytische Chemie, Universität Bremen, Leobener Straße 7, 28359, Bremen, Germany
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7
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Köse A, Ünal A, Şahin E, Bozkaya U, Kara Y. An anomalous addition of chlorosulfonyl isocyanate to a carbonyl group: the synthesis of ((3a S,7a R, E)-2-ethyl-3-oxo-2,3,3a,4,7,7a-hexahydro-1 H-isoindol-1-ylidene)sulfamoyl chloride. Beilstein J Org Chem 2019; 15:931-936. [PMID: 31164929 PMCID: PMC6541324 DOI: 10.3762/bjoc.15.89] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 03/15/2019] [Indexed: 11/28/2022] Open
Abstract
In this study, we developed a new addition reaction of chlorosulfonyl isocyanate (CSI), starting from 2-ethyl-3a,4,7,7a-tetrahydro-1H-isoindole-1,3(2H)-dione. The addition reaction of CSI with 2-ethyl-3a,4,7,7a-tetrahydro-1H-isoindole-1,3(2H)-dione resulted in the formation of ylidenesulfamoyl chloride, whose exact configuration was determined by X-ray crystal analysis. We explain the mechanism of product formation supported by theoretical calculations.
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Affiliation(s)
- Aytekin Köse
- Department of Chemistry, Aksaray University, 68100 Aksaray, Turkey
| | - Aslı Ünal
- Department of Chemistry, Hacettepe University, 06800 Ankara, Turkey
| | - Ertan Şahin
- Department of Chemistry, Atatürk University, 25240 Erzurum, Turkey
| | - Uğur Bozkaya
- Department of Chemistry, Hacettepe University, 06800 Ankara, Turkey
| | - Yunus Kara
- Department of Chemistry, Atatürk University, 25240 Erzurum, Turkey
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8
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Bai SM, Ren HM, Zheng GJ, Chen G. Senobtusin, a novel alkaloid with amidine moiety from Senecio obtusatus Wall. ex DC. Nat Prod Res 2017; 31:2450-2453. [DOI: 10.1080/14786419.2017.1309532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Shu-Min Bai
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Hong-Mei Ren
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Guo-Jun Zheng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Guang Chen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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9
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Rodríguez J, Jiménez C, Blanco M, Tarazona G, Fernández R, Cuevas C. Lanesoic Acid: A Cytotoxic Zwitterion from Theonella sp. Org Lett 2016; 18:5832-5835. [PMID: 27802052 DOI: 10.1021/acs.orglett.6b02832] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lanesoic acid (1) was isolated and characterized from Theonella sp. during PharmaMar's ongoing program to study cytotoxic substances from marine sources. Its planar structure, elucidated by spectral analysis (NMR, IR, UV, and MS), possesses an unusual skeleton containing a tetrahydropyrimidine cation that is stabilized as a zwitterion by an internal carboxylate counterion. The stereostructure of 1 was deduced from ROESY-NOESY, J-based configurational analysis (JBCA), and density functional theory (DFT) computational calculations fitted using the recently published DP4+ parameter. Compound 1 was moderately active and selective against pancreas PSN1 cells (IC50 = 8.9 μg/mL) and inactive against colon HT-29, breast MD-MB-23, and NSCLC lung tumor cells.
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Affiliation(s)
- Jaime Rodríguez
- Departamento de Química Fundamental, Facultade de Ciencias e Centro de Investigacións Científicas Avanzadas (CICA) Rua As Carballeiras s/n, Universidade da Coruña , 15071 A Coruña, Spain
| | - Carlos Jiménez
- Departamento de Química Fundamental, Facultade de Ciencias e Centro de Investigacións Científicas Avanzadas (CICA) Rua As Carballeiras s/n, Universidade da Coruña , 15071 A Coruña, Spain
| | - María Blanco
- Departamento de Química Fundamental, Facultade de Ciencias e Centro de Investigacións Científicas Avanzadas (CICA) Rua As Carballeiras s/n, Universidade da Coruña , 15071 A Coruña, Spain
| | - Guillermo Tarazona
- Natural Products Department, PharmaMar S.A., Pol. Ind. La Mina Norte , Avda de los Reyes 1, 28770 Colmenar Viejo, Spain
| | - Rogelio Fernández
- Natural Products Department, PharmaMar S.A., Pol. Ind. La Mina Norte , Avda de los Reyes 1, 28770 Colmenar Viejo, Spain
| | - Carmen Cuevas
- Natural Products Department, PharmaMar S.A., Pol. Ind. La Mina Norte , Avda de los Reyes 1, 28770 Colmenar Viejo, Spain
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10
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Figueroa L, Jiménez C, Rodríguez J, Areche C, Chávez R, Henríquez M, de la Cruz M, Díaz C, Segade Y, Vaca I. 3-Nitroasterric Acid Derivatives from an Antarctic Sponge-Derived Pseudogymnoascus sp. Fungus. JOURNAL OF NATURAL PRODUCTS 2015; 78:919-923. [PMID: 25732560 DOI: 10.1021/np500906k] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Four new nitroasterric acid derivatives, pseudogymnoascins A-C (1-3) and 3-nitroasterric acid (4), along with the two known compounds questin and pyriculamide, were obtained from the cultures of a Pseudogymnoascus sp. fungus isolated from an Antarctic marine sponge belonging to the genus Hymeniacidon. The structures of the new compounds were determined by extensive NMR and MS analyses. These compounds are the first nitro derivatives of the known fungal metabolite asterric acid. Several asterric acid derivatives isolated from other fungal strains have shown antibacterial and antifungal activities. However, the new compounds described in this work were inactive against a panel of bacteria and fungi (MIC > 64 μg/mL).
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Affiliation(s)
- Luis Figueroa
- †Departamento de Química, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Carlos Jiménez
- ‡Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Química Fundamental, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain
| | - Jaime Rodríguez
- ‡Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Química Fundamental, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain
| | - Carlos Areche
- †Departamento de Química, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Renato Chávez
- §Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Alameda 3363, Estación Central, Santiago, Chile
| | - Marlene Henríquez
- †Departamento de Química, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Mercedes de la Cruz
- ⊥Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Caridad Díaz
- ⊥Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Yuri Segade
- ‡Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Química Fundamental, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain
| | - Inmaculada Vaca
- †Departamento de Química, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
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11
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Rodríguez J, Nieto RM, Blanco M, Valeriote FA, Jiménez C, Crews P. Thelepamide: an unprecedented ketide-amino acid from Thelepus crispus, a marine annelid worm. Org Lett 2013; 16:464-7. [PMID: 24359301 DOI: 10.1021/ol403350e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Thelepamide (1) was characterized during a program to study cytotoxic substances from an unusual source, the tidal zone-derived annelid Thelephus crispus. Its structure contains a tetraketide and a tripeptide subunit and possesses striking atom diversity, consisting of 17 carbons and 8 heteroatoms. The relative configurations at four chiral sites were elucidated via ROESY, J-based configurational analysis, and DFT calculations. It was modestly active against leukemia cells (IC50 = 5 μg/mL) and inactive against solid tumor cell lines.
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Affiliation(s)
- Jaime Rodríguez
- Departamento de Química Fundamental, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña , 15071 A Coruña, Spain
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12
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Stereoselective cyanation of 4-formyl and 4-imino-?-lactams: application to the synthesis of polyfunctionalized ?-lactams. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.02.062] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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13
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Synthetic biotechnology to study and engineer ribosomal bottromycin biosynthesis. ACTA ACUST UNITED AC 2012; 19:1278-87. [PMID: 23021914 DOI: 10.1016/j.chembiol.2012.08.013] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 08/03/2012] [Accepted: 08/09/2012] [Indexed: 12/23/2022]
Abstract
Bottromycins represent a promising class of antibiotics binding to the therapeutically unexploited A-site of the bacterial ribosome. By inhibiting translation they are active against clinically important pathogens, such as vancomycin-resistant Enterococci. Structurally, bottromycins are heavily modified peptides exhibiting various unusual biosynthetic features. To set the stage for compound modification and yield optimization, we identified the biosynthetic gene cluster, used synthetic biotechnology approaches to establish and improve heterologous production, and generated analogs by pathway genetic engineering. We unambiguously identified three radical SAM methyltransferase-encoding genes required for various methylations at unactivated carbons yielding tert-butyl valine, methyl-proline, and β-methyl-phenylalanine residues, plus a gene involved in aspartate methyl-ester formation. Evidence for the formation of the exo-thiazole unit and for a macrocyclodehydration mechanism leading to amidine ring formation is provided.
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14
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Suyama TL, Gerwick WH, McPhail KL. Survey of marine natural product structure revisions: a synergy of spectroscopy and chemical synthesis. Bioorg Med Chem 2011; 19:6675-701. [PMID: 21715178 PMCID: PMC3205310 DOI: 10.1016/j.bmc.2011.06.011] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 05/09/2011] [Accepted: 06/02/2011] [Indexed: 11/16/2022]
Abstract
The structural assignment of new natural product molecules supports research in a multitude of disciplines that may lead to new therapeutic agents and or new understanding of disease biology. However, reports of numerous structural revisions, even of recently elucidated natural products, inspired the present survey of techniques used in structural misassignments and subsequent revisions in the context of constitutional or configurational errors. Given the comparatively recent development of marine natural products chemistry, coincident with modern spectroscopy, it is of interest to consider the relative roles of spectroscopy and chemical synthesis in the structure elucidation and revision of those marine natural products that were initially misassigned. Thus, a tabulated review of all marine natural product structural revisions from 2005 to 2010 is organized according to structural motif revised. Misassignments of constitution are more frequent than perhaps anticipated by reliance on HMBC and other advanced NMR experiments, especially when considering the full complement of all natural products. However, these techniques also feature prominently in structural revisions, specifically of marine natural products. Nevertheless, as is the case for revision of relative and absolute configuration, total synthesis is a proven partner for marine, as well as terrestrial, natural products structure elucidation. It also becomes apparent that considerable 'detective work' remains in structure elucidation, in spite of the spectacular advances in spectroscopic techniques.
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Affiliation(s)
- Takashi L. Suyama
- Department of Pharmaceutical Sciences, 203 Pharmacy Building, Oregon State University, Corvallis OR 97331, U.S.A
| | - William H. Gerwick
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla CA 92093-0212, U.S.A
| | - Kerry L. McPhail
- Department of Pharmaceutical Sciences, 203 Pharmacy Building, Oregon State University, Corvallis OR 97331, U.S.A
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15
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Belov VN, Sokolov VV, Zlatopolskiy BD, de Meijere A. A Novel Rearrangement of Cyclic Glutamine Derivatives: Ring Contraction in 3,6-Diamino-2,3,4,5-tetrahydropyridin-2-ones to Yield 5-Iminoproline Amides. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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16
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Unexpected property of ectoine synthase and its application for synthesis of the engineered compatible solute ADPC. Appl Microbiol Biotechnol 2011; 91:113-22. [PMID: 21468713 DOI: 10.1007/s00253-011-3211-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 01/21/2011] [Indexed: 10/18/2022]
Abstract
A new cyclic amino acid was detected in a deletion mutant of the moderately halophilic bacterium Halomonas elongata deficient in ectoine synthesis. Using mass spectroscopy (MS) and nuclear magnetic resonance (NMR) techniques, the substance was identified as 5-amino-3,4-dihydro-2H-pyrrole-2-carboxylate (ADPC). We were able to demonstrate that ADPC is the product of a side reaction of lone ectoine synthase (EC 4.2.1.108), which forms ADPC by cyclic condensation of glutamine. This reaction was shown to be reversible. Subsequently, a number of ectoine derivatives, in particular 4,5-dihydro-2-methylimidazole-4-carboxylate (DHMICA) and homoectoine, were also shown to be cleaved by ectoine synthase, which is classified as a hydro-lyase. This study thus reports for the first time that ectoine synthase accepts more than one substrate and is a reversible enzyme able to catalyze both the intramolecular condensation into and the hydrolytic cleavage of cyclic amino acid derivatives. As ADPC supports growth of bacteria under salt stress conditions and stabilizes enzymes against freeze-thaw denaturation, it displays typical properties of compatible solutes. As ADPC has not yet been described as a natural compound, it is presented here as the first man-made compatible solute created through genetic engineering.
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17
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Espada A, Anta C, Bragado A, Rodríguez J, Jiménez C. An approach to speed up the isolation of hydrophilic metabolites from natural sources at semipreparative level by using a hydrophilic-lipophilic balance/mixed-mode strong cation exchange-high-performance liquid chromatography/mass spectrometry system. J Chromatogr A 2011; 1218:1790-4. [PMID: 21329935 DOI: 10.1016/j.chroma.2011.01.072] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 01/14/2011] [Accepted: 01/23/2011] [Indexed: 11/28/2022]
Abstract
An approach to speed up the isolation of hydrophilic metabolites in complex natural matrixes by using a HLB/MCX-HPLC/MS system based on the retention properties of hydrophilic-lipophilic and cation exchange polymeric cartridges was developed. This methodology was successfully applied to the re-isolation of small water soluble compounds with completely different structures from two different natural extracts such as a dipeptide (vanchrobactin) from a bacterium culture broth and a pyrrolidine bearing a carboxylic acid moiety (clionapyrrolidine A) from a sponge. This method improved not only the efficiency of the isolation methodology but also the isolation time in relation to the existing methods.
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Affiliation(s)
- Alfonso Espada
- Analytical Technologies DCR&T Alcobendas, Lilly S.A., Avenida de la Industria 30, Alcobendas/Madrid, Spain.
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18
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Mitchell RE. Synthesis of amino acid conjugates to 2-imino-3-methylene-5-carboxypyrrolidine and 2-imino-3-methylene-6-carboxypiperidine. Bioorg Med Chem Lett 2010; 20:1910-2. [DOI: 10.1016/j.bmcl.2010.01.128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 01/26/2010] [Accepted: 01/28/2010] [Indexed: 11/27/2022]
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19
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Appel D, Lentzen G. The pyrostatins A and B do not inhibit N-acetyl-beta-D-glucosaminidase. J Enzyme Inhib Med Chem 2010; 24:1106-8. [PMID: 19555187 DOI: 10.1080/14756360802632831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The compounds pyrostatin A and B, isolated from Streptomyces sp. SA-3501 have been reported as N-acetyl-beta-D-glucosaminidase inhibitors with inhibition constants in the micromolar range. Recently, a comparison of NMR spectral data of the pyrostatins has led to a structural revision of the pyrostatins. It was shown that the pyrostatins A and B are identical to the ectoines 5-hydroxectoine and ectoine, respectively. Ectoines are known as compatible osmolytes in many halophilic and stress-tolerant bacteria. We have performed enzymatic experiments demonstrating that neither ectoine nor 5-hydroxyectoine exhibit an inhibitory effect on N-acetyl-beta-D-glucosaminidase. The previously reported inhibition of N-acetyl-beta-D-glucosaminidase by pyrostatins A and B may thus be due to the contamination of the compound preparations with a strong N-acetyl-beta-D-glucosaminidase inhibitor with an inhibition constant (Ki) in the nanomolar range, as has been reported in other Streptomyces species.
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Affiliation(s)
- Daniel Appel
- bitop AG, Stockumer Strasse 28, 58453 Witten, Germany
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Chaves-Fonnegra A, Castellanos L, Zea S, Duque C, Rodríguez J, Jiménez C. Clionapyrrolidine A--a metabolite from the encrusting and excavating sponge Cliona tenuis that kills coral tissue upon contact. J Chem Ecol 2008; 34:1565-74. [PMID: 19023625 DOI: 10.1007/s10886-008-9565-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Revised: 10/27/2008] [Accepted: 11/03/2008] [Indexed: 11/29/2022]
Abstract
The Caribbean encrusting and excavating sponge Cliona tenuis successfully competes for space with reef corals by undermining, killing, and displacing live coral tissue at rates of up to 20 cm per year. The crude extract from this sponge, along with the more polar partitions, kills coral tissue and lowers the photosynthetic potential of coral zooxanthellae. We used a bioassay-guided fractionation of the extract to identify the compound(s) responsible. The crude extract, the aqueous partition, and compound 1, herein named clionapyrrolidine A [(-)-(5S)-2-imino-1-methylpyrrolidine-5-carboxylic acid], when incorporated into gels at close to natural volumetric concentrations, killed coral tissue when brought into forced contact with live coral for periods of 1-4 days. This is the first report of a pure chemical produced by a sponge that kills coral tissue upon direct contact. The results are consistent with the localized coral death that occurs when C. tenuis-colonized coral fragments are thrown forcibly against live coral during storms. However, healed C. tenuis fragments placed directly onto live coral were killed readily by coral defenses, and fragments placed in close proximity to coral did not have any effect on the adjacent coral tissue. Solutions of clionapyrrolidine A in sea water were only slightly toxic against live coral. Hence, the coral death naturally brought about by C. tenuis when undermining live coral does not occur through external release of allelochemicals; below-polyp mechanisms must be explored further. N-acetylhomoagmatine (2), originally isolated from Cliona celata from the Northeastern Atlantic, was also assayed for comparison purposes because of its structural similarity to siphonodictidine, a toxic compound produced by a coral excavating sponge of the genus Aka. The lack of activity of N-acetylhomoagmatine at close to natural concentrations seems to indicate that the guanidine moiety, which is also present in siphonodictidine, is not a sufficiently strong structural motif for activity against corals.
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Affiliation(s)
- Andia Chaves-Fonnegra
- Departamento de Biología y Centro de Estudios en Ciencias del Mar, Universidad Nacional de Colombia, Cerro Punta Betín, AA 10-16, Santa Marta, Colombia
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Sawangwong P, Wattanadilok R, Kijjoa A, Silva AM, Eaton G, Herz W. Secondary metabolites from a marine sponge Cliona patera. BIOCHEM SYST ECOL 2008. [DOI: 10.1016/j.bse.2008.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Blunt JW, Copp BR, Hu WP, Munro MHG, Northcote PT, Prinsep MR. Marine natural products. Nat Prod Rep 2008; 25:35-94. [PMID: 18250897 DOI: 10.1039/b701534h] [Citation(s) in RCA: 284] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review covers the literature published in 2006 for marine natural products, with 758 citations (534 for the period January to December 2006) referring to compounds isolated from marine microorganisms and phytoplankton, green algae, brown algae, red algae, sponges, cnidaria, bryozoans, molluscs, tunicates and echinoderms. The emphasis is on new compounds (779 for 2006), together with their relevant biological activities, source organisms and country of origin. 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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