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1. The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research

Author

Jie Li, Ben Shen, Orazio Taglialatela-Scafati, Matthias Niemitz, Sonja Sturm, Jian Min Yue, Andrei G. Kutateladze, Craig M. Williams, Nicholas H. Oberlies, Phillip Crews, Jean-Hugues Renault, Hermann Stuppner, John B. MacMillan, David Coppage, Harald Gross, Bin Gui Wang, Hiroyuki Koshino, Shao-Nong Chen, Bradley S. Moore, Carla M. Saunders, Jonathan Bisson, Andersson Barison, Miaomiao Liu, David G. I. Kingston, Young Hae Choi, Dean J. Tantillo, Mary J. Garson, Christoph Seger, Mehdi A. Beniddir, Hsiau Wei Lee, Wolfgang Robien, Zhengren Xu, Maique W. Biavatti, Tadeusz F. Molinski, David C. Lankin, Stefan Bluml, Damien Jeannerat, Philip G. Williams, José Rivera-Chávez, Julien Wist, Grégory Genta-Jouve, Ram P. Neupane, James B. McAlpine, Chen Zhang, Ronald J. Quinn, Joo-Won Nam, William H. Gerwick, Giovanni Appendino, Fernanda Maria Marins Ocampos, Jean-Marc Nuzillard, Joseph M. Egan, Luke Hunter, Marie Csete, Guohui Pan, Robert Verpoorte, Roger G. Linington, Tyler A. Johnson, Precilia Hermanto, Kerry L. McPhail, Mark S. Butler, Guy Lewin, Charlotte Simmler, Guido F. Pauli, Michael T. Crimmins, Mary Kay Harper, Thomas J. Schmidt, Christoph Steinbeck, James M. Hook, Nai Yun Ji, D. Sai Reddy, Asmaa Boufridi, Robert J. Capon, Pradeep Dewapriya, Jeannerat, Damien, Mcalpine, James B, Chen, Shao-Nong, Kutateladze, Andrei, Macmillan, John B, Appendino, Giovanni, Barison, Andersson, Beniddir, Mehdi A, Biavatti, Maique W, Bluml, Stefan, Boufridi, Asmaa, Butler, Mark S, Capon, Robert J, Choi, Young H, Coppage, David, Crews, Phillip, Crimmins, Michael T, Csete, Marie, Dewapriya, Pradeep, Egan, Joseph M, Garson, Mary J, Genta-Jouve, Grégory, Gerwick, William H, Gross, Harald, Harper, Mary Kay, Hermanto, Precilia, Hook, James M, Hunter, Luke, Nai-Yun, Ji, Johnson, Tyler A, Kingston, David G I, Koshino, Hiroyuki, Lee, Hsiau-Wei, Lewin, Guy, Jie, Li, Linington, Roger G, Liu, Miaomiao, Mcphail, Kerry L, Molinski, Tadeusz F, Moore, Bradley S, Nam, Joo-Won, Neupane, Ram P, Niemitz, Matthia, Nuzillard, Jean-Marc, Oberlies, Nicholas H, Ocampos, Fernanda M M, Pan, Guohui, Quinn, Ronald J, Reddy, D Sai, Renault, Jean-Hugue, Rivera-Chávez, José, Robien, Wolfgang, Saunders, Carla M, Schmidt, Thomas J, Seger, Christoph, Shen, Ben, Steinbeck, Christoph, Stuppner, Hermann, Sturm, Sonja, Taglialatela-Scafati, Orazio, Tantillo, Dean J, Verpoorte, Robert, Wang, Bin-Gui, Williams, Craig M, Williams, Philip G, Wist, Julien, Yue, Jian-Min, Zhang, Chen, Zhengren, Xu, Simmler, Charlotte, Lankin, David C, Bisson, Jonathan, Pauli, Guido F, Thallion Pharmaceuticals Inc., Brunel University London [Uxbridge], Dipartimento di Scienze Chimiche, DIPARTIMENTO DI SCIENZE CHIMICHE, Departamento de Química, Universidade Federal do Paraná (UFPR), Molécules bioactives, conception, isolement et synthèse (MBCIS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Equipe C-TAC (UMR 8638), Chimie Organique, Médicinale et Extractive et Toxicologie Expérimentale (COMETE - UMR 8638), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Sorbonne Paris Cité (USPC), University of Tübingen, University of New South Wales [Sydney] (UNSW), Department of organic Chemistry - University of Geneva, University of Geneva [Switzerland], Department of Chemistry and Biochemistry, University of California, University of California [Santa Cruz] (UCSC), University of California-University of California, Center for Marine Biotechnology and Biomedicine, University of California, Institut de Chimie Moléculaire de Reims - UMR 7312 (ICMR), SFR Condorcet, Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Chinese Academy of Sciences [Beijing] (CAS), University of Münster, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, University of Innsbruck, Section Metabolomics (DIVISION OF PHARMACOGNOSY), Universiteit Leiden [Leiden]-Institute of Biology, Institut National de l'Environnement Industriel et des Risques (INERIS), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), and Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
NMR, Natural Products, Raw Data, Reproducibility, Value (ethics), Magnetic Resonance Spectroscopy, Molecular Conformation, [CHIM.INOR]Chemical Sciences/Inorganic chemistry, 010402 general chemistry, Medical and Health Sciences, 01 natural sciences, Biochemistry, Article, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Component (UML), Drug Discovery, Dissemination, Biological Products, Biological studies, 010405 organic chemistry, Organic Chemistry, Reproducibility of Results, Biological Sciences, Transparency (behavior), Data science, Nmr data, 0104 chemical sciences, Chemical Sciences, ddc:540, Generic health relevance, Natural Product Research, Raw data, [CHIM.CHEM]Chemical Sciences/Cheminformatics
Abstract

International audience; With 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.

Published
2019

2. Bicyclic 6-6 Systems: Three Heteroatoms 1:2

Author

Wendy Anne Loughlin and Asmaa Boufridi

Subjects
Pyridazine, chemistry.chemical_compound, chemistry, Bicyclic molecule, Pyrazine, Thiazine, Heteroatom, Organic chemistry, Reactivity (chemistry), Conjugated system, Catalysis
Abstract

The chemistry of 6-6 fused heterocycles containing three heteroatoms arranged 1:2 with no heteroatoms occupying the bridgehead position is reviewed and updated for the period 2006–18. The heterocyclic systems include those with nitrogen, oxygen, sulfur as the heteroatoms and primarily covers pyrido[x,y-z]pyridazine, pyrdimidine, pyrazine rings, along with pyrido-, pyrano-, thiopyrano[x,y-z][1,n]oxazine and thiazine rings. The reactivity, synthetic transformations and methods for their preparation, including fully conjugated and nonconjugated rings, are described. Applications of the heterocycles that have emerged in the decade include, catalytic synthetic approaches, uses in semi-conducting polymers, and significant medicinal chemistry advances (anti-cancer, anti-hypertensive and anti-pain).

Published
2022

3. A Ring-Distortion Strategy from Marine Natural Product Ilimaquinone Leads to Quorum Sensing Modulators

Author

Mehdi A. Beniddir, Blandine Séon-Méniel, Sylvain Petek, Asmaa Boufridi, David Lachkar, Cécile Debitus, Laurent Evanno, Florent Tintillier, Erwan Poupon, Assia Lamali, Karine Leblanc, Grégory Genta-Jouve, Stéphanie Denis, Denis Saulnier, and Jean-Christophe Jullian

Subjects
Natural product, biology, 010405 organic chemistry, Vibrio harveyi, Organic Chemistry, 010402 general chemistry, Ring (chemistry), biology.organism_classification, 01 natural sciences, Chemical space, 0104 chemical sciences, Quinone, chemistry.chemical_compound, Quorum sensing, chemistry, Biochemistry, Ilimaquinone, Moiety, Physical and Theoretical Chemistry
Abstract

We report herein a ring-distortion strategy applied to marine natural substances ilimaquinone and 5-epi-ilimaquinone. A chemically diverse library of molecules was synthesised that included rearrangements of the sesquiterpene moiety and original reorganisations of the quinone ring. Chemoinformatic analyses evaluated the rise of structural diversity and the exploration of chemical space. Some focussed biological activities of this library were also investigated; quorum sensing activity of Vibrio harveyi was envisaged and some of the new compounds were shown to be good quorum sensing inhibitor candidates, whereas others were activators. Toxicities were also evaluated and some products showed micromolar activities against human umbilical vein endothelium, human hepatocellular carcinoma and human lung carcinoma (A549) cells.

Published
2018

4. Evaluation of fermentation conditions triggering increased antibacterial activity from a near-shore marine intertidal environment-associated Streptomyces species

Author

Asmaa Boufridi, Ronald J. Quinn, A.L. English, and D. I. Kurtboke

Subjects
Pigments, 0301 basic medicine, lcsh:Biotechnology, 030106 microbiology, Biomedical Engineering, Marine biodiscovery, Intertidal zone, medicine.disease_cause, Applied Microbiology and Biotechnology, Streptomyces, Article, 03 medical and health sciences, chemistry.chemical_compound, Antibiotics, Structural Biology, lcsh:TP248.13-248.65, Marine streptomycetes, Botany, Genetics, medicine, Food science, lcsh:QH301-705.5, Escherichia coli, biology, biology.organism_classification, Antimicrobial, Bioactive compound, Spore, 030104 developmental biology, lcsh:Biology (General), chemistry, Marine natural products, Fermentation, Fermentation media, Antibacterial activity
Abstract

A near-shore marine intertidal environment-associated Streptomyces isolate (USC-633) from the Sunshine Coast Region of Queensland, Australia, cultivated under a range of chemically defined and complex media to determine optimal parameters resulting in the secretion of diverse array of secondary metabolites with antimicrobial properties against various antibiotic resistant bacteria. Following extraction, fractioning and re-testing of active metabolites resulted in persistent antibacterial activity against Escherichia coli (Migula) (ATCC 13706) and subsequent Nuclear Magnetic Resonance (NMR) analysis of the active fractions confirmed the induction of metabolites different than the ones in fractions which did not display activity against the same bacterial species. Overall findings again confirmed the value of One Strain–Many Compounds (OSMAC) approach that tests a wide range of growth parameters to trigger bioactive compound secretion increasing the likelihood of finding novel therapeutic agents. The isolate was found to be adaptable to both marine and terrestrial conditions corresponding to its original near-shore marine intertidal environment. Wide variations in its morphology, sporulation and diffusible pigment production were observed when different growth media were used.

Published
2017

5. A ring-distortion strategy from marine natural product ilimaquinone leads to quorum sensing modulators

Author

Evanno, Laurent, Lachkar, David, Lamali, Assia, Boufridi, Asmaa, Seon-Meniel, Blandine, Tintillier, Florent, Saulnier, Denis, Denis, Stephanie, Genta-Jouve, Grégory, Jullian, Jean-Christophe, Leblanc, Karine, Beniddir, Mehdi A., Petek, Sylvain, Debitus, Cécile, Poupon, Erwan, Biomolécules : Conception, Isolement, Synthèse (BioCIS), Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-CY Cergy Paris Université (CY), Ecosystèmes Insulaires Océaniens (UMR 241) (EIO), Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD)-Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD), Equipe C-TAC (UMR 8638), Chimie Organique, Médicinale et Extractive et Toxicologie Expérimentale (COMETE - UMR 8638), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and ANR-11-EBIM-0006,POMARE,Invertébrés benthiques de Polynésie, Martinique et Réunion : interactions et évaluation de la chimiodiversité pour un usage durable de la biodiversité(2011)

Subjects
ozonolysis, Ilimaquinone, acid-catalyzed rearrangements, ACL, sesquiterpene quinones, Quinones, diverse compounds, Quorum sensing, vibrio-harveyi, Synthetic methods, unified synthesis, Molecular diversity, radical decarboxylation, quinone addition-reaction, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, sponge dactylospongia-elegans, Ring-distortion, complex
Abstract

WOS:000434220200016; International audience; We report herein a ring-distortion strategy applied to marine natural substances ilimaquinone and 5-epi-ilimaquinone. A chemically diverse library of molecules was synthesised that included rearrangements of the sesquiterpene moiety and original reorganisations of the quinone ring. Chemoinformatic analyses evaluated the rise of structural diversity and the exploration of chemical space. Some focussed biological activities of this library were also investigated; quorum sensing activity of Vibrio harveyi was envisaged and some of the new compounds were shown to be good quorum sensing inhibitor candidates, whereas others were activators. Toxicities were also evaluated and some products showed micromolar activities against human umbilical vein endothelium, human hepatocellular carcinoma and human lung carcinoma (A549) cells.

Published
2018

6. Correction: The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research

Author

Mary J. Garson, Jean-Marc Nuzillard, Ronald J. Quinn, Charlotte Simmler, Roger G. Linington, Tyler A. Johnson, Precilia Hermanto, Robert Verpoorte, Jian-Min Yue, Craig M. Williams, Guy Lewin, Bradley S. Moore, Dean J. Tantillo, Damien Jeannerat, Jie Li, Ram P. Neupane, Christoph Steinbeck, Nicholas H. Oberlies, James M. Hook, Hermann Stuppner, David G. I. Kingston, Giovanni Appendino, Carla M. Saunders, Jean-Hugues Renault, John B. MacMillan, Asmaa Boufridi, Wolfgang Robien, Mark S. Butler, Orazio Taglialatela-Scafati, Matthias Niemitz, Michael T. Crimmins, David C. Lankin, Luke Hunter, Nai Yun Ji, Philip G. Williams, Mehdi A. Beniddir, Robert J. Capon, Stefan Bluml, Pradeep Dewapriya, Maique W. Biavatti, Thomas J. Schmidt, Harald Gross, Julien Wist, Joo-Won Nam, Bin Gui Wang, Miaomiao Liu, Jonathan Bisson, James B. McAlpine, Ben Shen, Chen Zhang, Phillip Crews, Fernanda Maria Marins Ocampos, David Coppage, Grégory Genta-Jouve, Andersson Barison, José Rivera-Chávez, Young Hae Choi, Sonja Sturm, Hiroyuki Koshino, Hsiau-Wei Lee, Guido F. Pauli, Christoph Seger, Joseph M. Egan, D. Sai Reddy, Mary Kay Harper, William H. Gerwick, Marie Csete, Guohui Pan, Kerry L. McPhail, Andrei G. Kutateladze, Shao-Nong Chen, Zhengren Xu, Tadeusz F. Molinski, Thallion Pharmaceuticals Inc., Brunel University London [Uxbridge], Dipartimento di Scienze Chimiche, DIPARTIMENTO DI SCIENZE CHIMICHE, Departamento de Química, Universidade Federal do Paraná (UFPR), Molécules bioactives, conception, isolement et synthèse (MBCIS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Chimie Organique, Médicinale et Extractive et Toxicologie Expérimentale (COMETE - UMR 8638), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), University of Tübingen, University of Maryland [College Park], University of Maryland System, School of Mathematics [Manchester], University of Manchester [Manchester], Department of organic Chemistry - University of Geneva, University of Geneva [Switzerland], University of Michigan [Ann Arbor], University of Michigan System, Institut de Chimie Moléculaire de Reims - UMR 7312 (ICMR), SFR Condorcet, Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Chinese Academy of Sciences [Beijing] (CAS), Hamburg University of Applied Sciences [Hamburg], European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, University of Innsbruck, Section of Metabolomics, Pharmacognosy Department, Institute of Biology, Gorlaeus Laboratories, Universiteit Leiden [Leiden], Institut National de l'Environnement Industriel et des Risques (INERIS), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), and Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Reproducibility, business.industry, Organic Chemistry, Biological Sciences, Medical and Health Sciences, Biochemistry, Nmr data, Transparency (behavior), Chemistry, Clinical Research, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Chemical Sciences, Drug Discovery, Value (economics), Natural Product Research, Process engineering, business, human activities, ComputingMilieux_MISCELLANEOUS, [CHIM.CHEM]Chemical Sciences/Cheminformatics
Abstract

With 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., Covering: up to 2018 With 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.

Published
2019

8. Harnessing the Properties of Natural Products

Author

Asmaa Boufridi and Ronald J. Quinn

Subjects
0301 basic medicine, Pharmacology, Biological Products, 010405 organic chemistry, Nanotechnology, Biology, Toxicology, 01 natural sciences, Natural (archaeology), Chemical space, 0104 chemical sciences, Molecular Weight, Small Molecule Libraries, 03 medical and health sciences, 030104 developmental biology, Drug Discovery, Animals, Humans, Biochemical engineering, Biological sciences, Organism
Abstract

Natural products (NPs) have been used as traditional medicines since antiquity. With more than 1060 estimated compounds with molecular weights less than 500 Da representing chemical space, NPs occupy a very small percentage; however, they are significantly overrepresented in biologically relevant chemical space. The classical approach concentrates on identifying one or more NPs with biological activity from a source organism. There is much more to be learned from NPs than we can discover this narrow view. In this review, we discuss ways to harness the global properties of NPs.

Published
2017

9. An unprecedented blue chromophore found in nature using a 'chemistry first' and molecular networking approach : discovery of dactylocyanines A-H

Author

Natacha Bonneau, David Lachkar, Guanming Chen, Erwan Poupon, Cécile Debitus, Asmaa Boufridi, Sylvain Petek, Mehdi A. Beniddir, Jean-François Gallard, Pascal Retailleau, Laurent Evanno, Biomolécules : Conception, Isolement, Synthèse (BioCIS), Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-CY Cergy Paris Université (CY), Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Molécules bioactives, conception, isolement et synthèse (MBCIS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), ANR-11-EBIM-0006,POMARE,Invertébrés benthiques de Polynésie, Martinique et Réunion : interactions et évaluation de la chimiodiversité pour un usage durable de la biodiversité(2011), Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)

Subjects
Magnetic Resonance Spectroscopy, Stereochemistry, Molecular Conformation, 010402 general chemistry, Crystallography, X-Ray, 01 natural sciences, ilimaquinone, Catalysis, Molecular conformation, marine natural dyes, golgi membranes, Tandem Mass Spectrometry, residue, chromophore, Animals, chromophores, zwitterionic, Chromatography, High Pressure Liquid, Biological Products, molecular networking, cyanines, 010405 organic chemistry, Chemistry, ACL, Organic Chemistry, Solvatochromism, sesquiterpenoid quinones, sulfoxides, Quinones, Dactylospongia metachromia, General Chemistry, Chromophore, Combinatorial chemistry, vesiculation, zwitterions, 0104 chemical sciences, Porifera, Golgi membranes, Ilimaquinone, Molecular networking, nakijiquinones, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, strategy, Sesquiterpenes, marine sponge, Chlortetracycline
Abstract

WOS:000413167100012; International audience; Guided by a "chemistry first" approach using molecular networking, eight new bright-blue colored natural compounds, namely dactylocyanines A-H (3-10), were isolated from the Polynesian marine sponge Dactylospongia metachromia. Starting from ilimaquinone (1), an hemisynthetic phishing probe (2) was prepared for annotating and matching structurally related natural substances in D. metachromia crude extract network. This strategy allowed characterizing for the first time in Nature the blue zwitterionic quinonoid chromophore. The solvatochromic properties of the latter are reported.

Published
2017

10. Ilimaquinone and 5-epi-Ilimaquinone: Beyond a Simple Diastereomeric Ratio, Biosynthetic Considerations from NMR-Based Analysis

Author

Erwan Poupon, Sylvain Petek, David Lachkar, Mehdi A. Beniddir, Cécile Debitus, Dirk Erpenbeck, Asmaa Boufridi, Laurent Evanno, Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS), The Natural History Museum [London] (NHM), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Molécules bioactives, conception, isolement et synthèse (MBCIS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Biomolécules : Conception, Isolement, Synthèse (BioCIS), Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-CY Cergy Paris Université (CY), Department of Earth and Environmental Sciences [München], Ludwig-Maximilians-Universität München (LMU), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Ecosystèmes Insulaires Océaniens (UMR 241) (EIO), Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD)-Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de Recherche pour le Développement (IRD), ANR-11-EBIM-0006,POMARE,Invertébrés benthiques de Polynésie, Martinique et Réunion : interactions et évaluation de la chimiodiversité pour un usage durable de la biodiversité(2011), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Dactylospongia elegans, Stereochemistry, New materials, GOLGI MEMBRANES, ETHYLSMENOQUINONE, 01 natural sciences, 03 medical and health sciences, Computational chemistry, RNASE-H ACTIVITY, INDO-PACIFIC, Biological evaluation, ABSOLUTE STEREOCHEMISTRY, 010405 organic chemistry, Chemistry, ACL, Diastereomer, Dactylospongia metachromia, SELECTIVE INHIBITOR, General Chemistry, Apoptosis induction, RNase H activity, 0104 chemical sciences, SESQUITERPENE QUINONES, MARINE SPONGE METABOLITES, 030104 developmental biology, Ilimaquinone, DACTYLOSPONGIA, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, HUMAN-IMMUNODEFICIENCY
Abstract

00000; International audience; Dactylospongia metachromia and Dactylospongia elegans collected from French Polynesia were studied with a particular focus on the variation of the diastereomeric ratio between ilimaquinone (4) and 5-epi-ilimaquinone (5). More than 100 samples, covering an area of 4100km(2), were studied to try to clarify this intriguing issue. Nuclear magnetic resonance appeared as the non-destructive, straightforward technique of choice for a relative quantitative study. A random distribution, unique at that point in nature, is observed and leads to biosynthetic considerations. Biological evaluation of both compounds was also performed and showed moderate discrepancies in cytotoxicity and apoptosis induction.

Published
2017

11. Biotransformations versus chemical modifications: new cytotoxic analogs of marine sesquiterpene ilimaquinone

Author

Didier Buisson, Laurent Evanno, Cécile Debitus, Sylvain Petek, Mehdi A. Beniddir, Erwan Poupon, Asmaa Boufridi, Biomolécules : Conception, Isolement, Synthèse (BioCIS), Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-CY Cergy Paris Université (CY), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes Insulaires Océaniens (UMR 241) (EIO), Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD)-Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de Recherche pour le Développement (IRD), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), ANR-11-EBIM-0006,POMARE,Invertébrés benthiques de Polynésie, Martinique et Réunion : interactions et évaluation de la chimiodiversité pour un usage durable de la biodiversité(2011), Molécules bioactives, conception, isolement et synthèse (MBCIS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS), Équipe 'Pharmacognosie-Chimie des Substances Naturelles' BioCIS, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), and Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Marine natural substance, Stereochemistry, metabolite, Epoxidation, 010402 general chemistry, Sesquiterpene, 01 natural sciences, Biochemistry, Hydroxylation, chemistry.chemical_compound, Ethanolamine, Biotransformation, fragmentation, Drug Discovery, rnase-h activity, Organic chemistry, ComputingMilieux_MISCELLANEOUS, human-immunodeficiency, protein-transport, illimaquinone, Marine sponge, Mucor plumbeus, Ilimaquinone, biology, [CHIM.ORGA]Chemical Sciences/Organic chemistry, 010405 organic chemistry, Chemistry, ACL, transformation, Organic Chemistry, Biological activity, biology.organism_classification, 0104 chemical sciences, Quinone, selective inhibitor, Mucor circinelloides, mucor-plumbeus, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; Highly biologically active marine sesquiterpene ilimaquinone was selected for chemical modifications. Its biotransformation was investigated using a combinatorial approach as an original way to screen different strains of microorganisms. Mucor circinelloides ATCC 8541 was able to structurally modify ilimaquinone into three different compounds. A stereospecific epoxidation was observed and compared to chemical epoxidation. A hydroxylation of the decalin ring was also observed as well as an unexpected substitution on the quinone ring by ethanolamine. Compounds were evaluated against several cell lines.

Published
2016

12. Biotransformations versus chemical modifications : new cytotoxic analogs of marine sesquiterpene ilimaquinone [plus Supporting information]

Author

Boufridi, A., Petek, Sylvain, Evanno, L., Beniddir, M.A., Debitus, Cécile, Buisson, D., and Poupon, E.

Abstract

Highly biologically active marine sesquiterpene ilimaquinone was selected for chemical modifications. Its biotransformation was investigated using a combinatorial approach as an original way to screen different strains of microorganisms. Mucor circinelloides ATCC 8541 was able to structurally modify ilimaquinone into three different compounds. A stereospecific epoxidation was observed and compared to chemical epoxidation. A hydroxylation of the decalin ring was also observed as well as an unexpected substitution on the quinone ring by ethanolamine. Compounds were evaluated against several cell lines.

Published
2016

13. Turning Metabolomics into Drug Discovery

Author

Ronald J. Quinn and Asmaa Boufridi

Subjects
0301 basic medicine, natural products, Computer science, Drug discovery, General Chemistry, Pharmacology, Drug quality, 03 medical and health sciences, 030104 developmental biology, Metabolomics, Drug delivery, retention time, Metabolome, Biochemical engineering, HPLC, druggability, log P
Abstract

Metabolomics is the "omics" that studies the whole metabolome. It has a wide range of applications, inter alia chemotaxonomy, environmental influences, agriculture, etc. Here we review the application of metabolomics in natural product research. The importance of physicochemical properties to drug delivery are discussed in relation to turning metabolomic studies towards drug discovery. We believe that coupling metabolomic studies with standards of known physicochemical properties in order to calibrate the chromatographic columns can be beneficial in identifying compounds of candidate drug quality.

Published
2016

14. Cover Feature: A Ring-Distortion Strategy from Marine Natural Product Ilimaquinone Leads to Quorum Sensing Modulators (Eur. J. Org. Chem. 20-21/2018)

Author

Grégory Genta-Jouve, Assia Lamali, Sylvain Petek, Laurent Evanno, Asmaa Boufridi, Erwan Poupon, Denis Saulnier, Cécile Debitus, Florent Tintillier, David Lachkar, Blandine Séon-Méniel, Karine Leblanc, Stéphanie Denis, Mehdi A. Beniddir, and Jean-Christophe Jullian

Subjects
Quorum sensing, chemistry.chemical_compound, Natural product, Chemistry, Stereochemistry, Distortion, Organic Chemistry, Ilimaquinone, Cover (algebra), Physical and Theoretical Chemistry, Ring (chemistry)
Published
2018

15. De l’étude d’éponges du genre Dactylospongia aux particularités chimiques des ilimaquinones

Author

Boufridi, Asmaa, Molécules bioactives, conception, isolement et synthèse (MBCIS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Université Paris Sud - Paris XI, and Erwan Poupon

Subjects
Marine sponges, Ilimaquinone, Semi-synthesis, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Biosynthèse, Dactylospongia metachromia, Diastereomeric ratio, Biosynthesis, Isolement, Hémisynthèse, Isolation, Sesquiterpenes quinones, Dactylospongia elegans, Sesquiterpènes quinones, Ratio diastéréoisomérique, Biotransformation, Éponges marines
Abstract

Our team is one of the partners of the international project PoMaRe ("Benthic Invertebrates of Polynesia, Martinique and Reunion"). We worked directly with Dr. Cécile Debitus from the IRD in French Polynesia, her team was in charge of collecting samples of marine sponges in different atolls of the Pacific.In the laboratory, we focused particularly on two abundant species in Polynesia: Dactylospongia metachromia and Dactylospongia elegans. Our job was to isolate their major metabolites: the ilimaquinones and perform various studies around these two epimeric sesquiterpene quinones.The work was organized as follows:- Extraction of ilimaquinones: ilimaquinones were isolated from the sponge Dactylospongia metachromia with a yield > 3%. A study of the variation of their respective percentage in relation with the geography of collection was undertaken, involving more than one hundred samples. This is the first study of this scale to be achieved. The sponge D. elegans was also studied, our results revealed the presence of ilimaquinone but also a nearby structure: isospongiaquinone.- Structural modifications of ilimaquinones:* Chemical modifications: structural changes were studied on ilimaquinones to delimit their reactivity: various analogues have been obtained. Among others, natural substances isospongiaquinone, 5-epi-isospongiaquinone and neomamanuthaquinone have been obtained. In these studies, a new reaction was discovered modifying the quinone surprisingly under oxidizing conditions.* Enzymatic modifications: micro-organisms were used to carry out biotransformations on the skeleton of ilimaquinone, three compounds were obtained. These changes have affected both the decalin and the quinone of our substrate. An original reaction has also been observed for the first time.-Molecular modeling and electrochemistry: a molecular modeling study has allowed us to calculate the energy of formation of ilimaquinones based on biosynthesis assumptions that we can now better understand. Finally an electrochemistry study evaluated the redox properties of these natural molecules with high potential in terms of biological activity.; Notre équipe est l’un des partenaires du projet international PoMaRé (« Invertébrésbenthiques de Polynésie, Martinique et de la Réunion »). Nous travaillons encollaboration directe avec le Dr Cécile Debitus de l’IRD en Polynésie française, sonéquipe étant notamment en charge de collecter des échantillons d’éponges marinesdans différents atolls du Pacifique.Au laboratoire, nous nous sommes intéressés particulièrement à deux espècesabondantes en Polynésie : Dactylospongia metachromia et Dactylospongia elegans.Notre travail a consisté à isoler leurs métabolites spécialisés majoritaires : lesilimaquinones, puis à réaliser diverses études autour de ces deux sesquiterpènesquinoniques épimériques. Le travail s’est organisé de la façon suivante :- Extraction des ilimaquinones : les ilimaquinones ont été isolées de l’éponge Dactylospongia metachromia avec un rendement > 3 %. Une étude de la variation de leur pourcentage respectif par rapport à la géographie de collecte de l’éponge a été entreprise. Impliquant plus d’une centaine d’échantillons, c’est la première fois qu’une étude d’une telle ampleur est réalisée. L’éponge D. elegans a également été étudiée, nos études ont révélé la présence de l’ilimaquinone mais aussi d’une structure proche : l’isospongiaquinone.- Modifications structurales autour des ilimaquinones : Par voie chimique : des modifications ont été étudiées sur les ilimaquinones afin de cerner leur réactivité, divers analogues ont ainsi été obtenus. Entre autres, les substances naturelles isospongiaquinone, 5-epi-isospongiaquinone et néomamanuthaquinone ont pu être hémisynthétisées. Lors de ces études, une nouvelle réaction a été découverte modifiant la quinone de façon surprenante dans des conditions oxydantes. Par voie enzymatique : des micro-organismes ont été utilisés pour réaliser des biotransformations sur le squelette de l’ilimaquinone, trois composés ont été obtenus. Ces modifications ont touché à la fois la décaline et la quinone de notre substrat. Une réaction de fonctionnalisation originale a d’ailleurs pu être observée pour la première fois.- Modélisation moléculaire et électrochimie : une étude de modélisation moléculaire nous a permis de calculer l’énergie de formation des ilimaquinones en nous basant sur les hypothèses de biosynthèse que nous pouvons maintenant mieux appréhender. Finalement une étude d’électrochimie nous a permis d’évaluer les propriétés oxydo-réductrices de ces molécules naturelles à fortes potentialités en termes d’activités biologiques.

Published
2014

16. From the study of sponges of the genus Dactylospongia to chemical peculiarities of ilimaquinones

Author

Boufridi, Asmaa, Molécules bioactives, conception, isolement et synthèse (MBCIS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Université Paris Sud - Paris XI, and Erwan Poupon

Subjects
Marine sponges, Ilimaquinone, Semi-synthesis, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Biosynthèse, Dactylospongia metachromia, Diastereomeric ratio, Biosynthesis, Isolement, Hémisynthèse, Isolation, Sesquiterpenes quinones, Dactylospongia elegans, Sesquiterpènes quinones, Ratio diastéréoisomérique, Biotransformation, Éponges marines
Abstract

Our team is one of the partners of the international project PoMaRe ("Benthic Invertebrates of Polynesia, Martinique and Reunion"). We worked directly with Dr. Cécile Debitus from the IRD in French Polynesia, her team was in charge of collecting samples of marine sponges in different atolls of the Pacific.In the laboratory, we focused particularly on two abundant species in Polynesia: Dactylospongia metachromia and Dactylospongia elegans. Our job was to isolate their major metabolites: the ilimaquinones and perform various studies around these two epimeric sesquiterpene quinones.The work was organized as follows:- Extraction of ilimaquinones: ilimaquinones were isolated from the sponge Dactylospongia metachromia with a yield > 3%. A study of the variation of their respective percentage in relation with the geography of collection was undertaken, involving more than one hundred samples. This is the first study of this scale to be achieved. The sponge D. elegans was also studied, our results revealed the presence of ilimaquinone but also a nearby structure: isospongiaquinone.- Structural modifications of ilimaquinones:* Chemical modifications: structural changes were studied on ilimaquinones to delimit their reactivity: various analogues have been obtained. Among others, natural substances isospongiaquinone, 5-epi-isospongiaquinone and neomamanuthaquinone have been obtained. In these studies, a new reaction was discovered modifying the quinone surprisingly under oxidizing conditions.* Enzymatic modifications: micro-organisms were used to carry out biotransformations on the skeleton of ilimaquinone, three compounds were obtained. These changes have affected both the decalin and the quinone of our substrate. An original reaction has also been observed for the first time.-Molecular modeling and electrochemistry: a molecular modeling study has allowed us to calculate the energy of formation of ilimaquinones based on biosynthesis assumptions that we can now better understand. Finally an electrochemistry study evaluated the redox properties of these natural molecules with high potential in terms of biological activity.; Notre équipe est l’un des partenaires du projet international PoMaRé (« Invertébrésbenthiques de Polynésie, Martinique et de la Réunion »). Nous travaillons encollaboration directe avec le Dr Cécile Debitus de l’IRD en Polynésie française, sonéquipe étant notamment en charge de collecter des échantillons d’éponges marinesdans différents atolls du Pacifique.Au laboratoire, nous nous sommes intéressés particulièrement à deux espècesabondantes en Polynésie : Dactylospongia metachromia et Dactylospongia elegans.Notre travail a consisté à isoler leurs métabolites spécialisés majoritaires : lesilimaquinones, puis à réaliser diverses études autour de ces deux sesquiterpènesquinoniques épimériques. Le travail s’est organisé de la façon suivante :- Extraction des ilimaquinones : les ilimaquinones ont été isolées de l’éponge Dactylospongia metachromia avec un rendement > 3 %. Une étude de la variation de leur pourcentage respectif par rapport à la géographie de collecte de l’éponge a été entreprise. Impliquant plus d’une centaine d’échantillons, c’est la première fois qu’une étude d’une telle ampleur est réalisée. L’éponge D. elegans a également été étudiée, nos études ont révélé la présence de l’ilimaquinone mais aussi d’une structure proche : l’isospongiaquinone.- Modifications structurales autour des ilimaquinones : Par voie chimique : des modifications ont été étudiées sur les ilimaquinones afin de cerner leur réactivité, divers analogues ont ainsi été obtenus. Entre autres, les substances naturelles isospongiaquinone, 5-epi-isospongiaquinone et néomamanuthaquinone ont pu être hémisynthétisées. Lors de ces études, une nouvelle réaction a été découverte modifiant la quinone de façon surprenante dans des conditions oxydantes. Par voie enzymatique : des micro-organismes ont été utilisés pour réaliser des biotransformations sur le squelette de l’ilimaquinone, trois composés ont été obtenus. Ces modifications ont touché à la fois la décaline et la quinone de notre substrat. Une réaction de fonctionnalisation originale a d’ailleurs pu être observée pour la première fois.- Modélisation moléculaire et électrochimie : une étude de modélisation moléculaire nous a permis de calculer l’énergie de formation des ilimaquinones en nous basant sur les hypothèses de biosynthèse que nous pouvons maintenant mieux appréhender. Finalement une étude d’électrochimie nous a permis d’évaluer les propriétés oxydo-réductrices de ces molécules naturelles à fortes potentialités en termes d’activités biologiques.

Published
2014

17. Ilimaquinone and minor metabolites from Polynesian marine sponges: Isolation and ecology

Author

Alexandre Maciuk, Laurent Evanno, Cécile Debitus, Erwan Poupon, and Asmaa Boufridi

Subjects
Pharmacology, Marine sponges, Complementary and alternative medicine, Ecology, Ecology (disciplines), Organic Chemistry, Drug Discovery, Ilimaquinone, Pharmaceutical Science, Molecular Medicine, Biology, Isolation (microbiology), Analytical Chemistry
Published
2012

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