Search

Your search keyword '"Alexander E. Fox Ramos"' showing total 6 results
Start Over Author "Alexander E. Fox Ramos"
6 results on '"Alexander E. Fox Ramos"'

1. CANPA: Computer-Assisted Natural Products Anticipation

Author

Erwan Poupon, Pierre Champy, Coralie Pavesi, Vincent Dumontet, Grégory Genta-Jouve, Alexander E. Fox Ramos, Mehdi A. Beniddir, Marc Litaudon, Biomolécules : Conception, Isolement, Synthèse (BioCIS), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine, Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Cibles Thérapeutiques et conception de médicaments (CiTCoM - UMR 8038), and Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)

Subjects
Computer science, Molecular Conformation, Computational biology, 010402 general chemistry, 01 natural sciences, Natural (archaeology), Analytical Chemistry, chemistry.chemical_compound, Alkaloids, Tandem Mass Spectrometry, [CHIM]Chemical Sciences, Compound structure, ComputingMilieux_MISCELLANEOUS, Structure (mathematical logic), Biological Products, Natural product, Chemistry, 010401 analytical chemistry, Pipeline (software), Data science, 0104 chemical sciences, Plant Leaves, Workflow, Anticipation (artificial intelligence), Molecular networking, Computer-Aided Design, Alstonia
Abstract

Traditional natural products discovery workflows implying a combination of different targeting strategies including structure- and/or bioactivity-based approaches, afford no information about new compound structure until late in the discovery pipeline. By integrating a MS/MS prediction module and a collaborative library of (bio)chemical transformations, we have developed a new platform, coined MetWork, that is able of anticipating the structural identity of metabolites starting from any identified compound. In our quest to discover new monoterpene indole alkaloids, we demonstrate the utility of the MetWork platform by anticipating the structures of five previously undescribed sarpagine-like N-oxide alkaloids that have been targeted and isolated from the leaves of Alstonia balansae using a molecular networking-based dereplication strategy fueled by computer-generated annotations. This study constitutes the first example of non peptidic molecular networking-based natural product discovery workflow, in which the targeted structures were initially generated, and therefore anticipated by a computer prior to their isolation.

Published
2019
Full Text
View/download PDF

2. Natural products targeting strategies involving molecular networking: different manners, one goal

Author

Mehdi A. Beniddir, Laurent Evanno, Alexander E. Fox Ramos, Erwan Poupon, and Pierre Champy

Subjects
Prioritization, Biological Products, Expediting, 010405 organic chemistry, Computer science, Organic Chemistry, 010402 general chemistry, 01 natural sciences, Biochemistry, Data science, Mass Spectrometry, Natural (archaeology), 0104 chemical sciences, Workflow, Drug Discovery, Molecular networking, Isolation (database systems), Metabolic Networks and Pathways, Pace
Abstract

Covering: up to 2019Landmark advances in bioinformatics tools have recently enhanced the field of natural products research, putting today's natural product chemists in the enviable position of being able to perform the efficient targeting/discovery of previously undescribed molecules by expediting the prioritization of the isolation workflow. Among these advances, MS/MS molecular networking has appeared as a promising approach to dereplicate complex natural product mixtures, leading to a real revolution in the "art of natural product isolation" by accelerating the pace of research of this field. This review illustrates through selected cornerstone studies the new thinking in natural product isolation by drawing a parallel between the different underlying philosophies behind the use of molecular networking in targeting natural products.

Published
2019
Full Text
View/download PDF

3. Molecular Networking Reveals Serpentinine-Related Bisindole Alkaloids from Picralima nitida , a Previously Well-Investigated Species

Author

Karine Leblanc, Elisabeth Mouray, Mehdi A. Beniddir, Charlotte Fox Alcover, Jean-François Gallard, Alexander E. Fox Ramos, Philippe Grellier, Faustin Aka Kabran, Guillaume Bernadat, Erwan Poupon, Pierre Le Pogam, Institut national des sciences de l'Univers (INSU - CNRS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Laboratoire d'océanographie et de biogéochimie (LOB), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-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), Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Équipe 'Pharmacognosie-Chimie des Substances Naturelles' BioCIS, Centre National de la Recherche Scientifique (CNRS), Biomolécules : Conception, Isolement, Synthèse (BioCIS), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine, Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CY Cergy Paris Université (CY), Université Félix Houphouët-Boigny (UFHB), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), and Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
Stereochemistry, MESH: Secologanin Tryptamine Alkaloids, [SDV]Life Sciences [q-bio], Monoterpene, MESH: Molecular Structure, Pharmaceutical Science, 01 natural sciences, Alstonine, Analytical Chemistry, chemistry.chemical_compound, MESH: Apocynaceae, Drug Discovery, [CHIM]Chemical Sciences, MESH: Plasmodium falciparum, ComputingMilieux_MISCELLANEOUS, MESH: Antiparasitic Agents, Pharmacology, Picralima, Indole test, biology, 010405 organic chemistry, Organic Chemistry, biology.organism_classification, 0104 chemical sciences, MESH: Indole Alkaloids, 010404 medicinal & biomolecular chemistry, Monomer, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Complementary and alternative medicine, chemistry, Molecular networking, Molecular Medicine, MESH: Monoterpenes, Derivative (chemistry)
Abstract

International audience; Five new monoterpene indole alkaloids (1-5), including four serpentinine-related bisindoles and one alstonine derivative monomer, have been isolated from the aerial parts of Picralima nitida. Their structures were elucidated by analysis of their HRMS and NMR spectroscopic data, and their absolute configurations were deduced from the comparison of experimental and simulated ECD spectra. In addition, two known compounds (6 and 7), previously undescribed from P. nitida, have also been purified. The compound isolation workflow was guided by a molecular networking-based dereplication strategy. Twenty-three compounds were dereplicated from the EtOH extract of P. nitida and fractions network and were assigned various levels of identification confidence. The antiparasitic activities against Plasmodium falciparum as well as the cytotoxic activity against the MRC-5 cell line were determined for compounds 1-7.

Published
2020
Full Text
View/download PDF

4. Molecular Networking Reveals Serpentinine-Related Bisindole Alkaloids from

Author

Charlotte Fox, Alcover, Guillaume, Bernadat, Faustin A, Kabran, Pierre, Le Pogam, Karine, Leblanc, Alexander E, Fox Ramos, Jean-François, Gallard, Elisabeth, Mouray, Philippe, Grellier, Erwan, Poupon, and Mehdi A, Beniddir

Subjects
Apocynaceae, Antiparasitic Agents, Molecular Structure, Plasmodium falciparum, Monoterpenes, Secologanin Tryptamine Alkaloids, Indole Alkaloids
Abstract

Five new monoterpene indole alkaloids (

Published
2020

5. Collected mass spectrometry data on monoterpene indole alkaloids from natural product chemistry research

Author

Laurent Evanno, Mariia S. Kirillova, Fanny Roussi, Gaëla Cauchie, Pierre Champy, Marc Litaudon, Guy Lewin, Anne-Marie Le Ray, Raphaël Grougnet, Erwan Poupon, Marina Kritsanida, Lengo Mambu, Alexander E. Fox Ramos, Antonio M. Echavarren, Fedor M. Miloserdov, Pascal Richomme-Peniguel, Michel Frederich, Khalijah Awang, Sylvie Michel, Hazrina Hazni, Dimitri Bréard, Pierre Le Pogam, Christelle Lémus, Marion Girardot, Elvis Otogo N’Nang, Michael E. Muratore, Mehdi A. Beniddir, Charlotte Fox Alcover, Thomas Gaslonde, Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Substances d'Origine Naturelle et Analogues Structuraux (SONAS), Université d'Angers (UA), Université de Liège, Synthèse et structure de molécules d'interet pharmacologique (SSMIP), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Microbiologie de l'Eau (MDE), Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-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), PEIRENE (PEIRENE), Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), Université de Limoges (UNILIM)-Université de Limoges (UNILIM), Institut de Recherche en Gestion des Organisations (IRGO), Université de Bordeaux (UB)-Institut d'Administration des Entreprises (IAE) - Bordeaux, Équipe 'Pharmacognosie-Chimie des Substances Naturelles' BioCIS, Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11), Université de Rennes (UR), and Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Statistics and Probability, Data descriptor, Data Descriptor, 010504 meteorology & atmospheric sciences, Monoterpene, Library and Information Sciences, Tandem mass spectrometry, Mass spectrometry, 01 natural sciences, Education, 03 medical and health sciences, chemistry.chemical_compound, Life Science, [CHIM]Chemical Sciences, Metabolomics, Organic chemistry, lcsh:Science, 030304 developmental biology, 0105 earth and related environmental sciences, Indole test, Natural products, 0303 health sciences, Natural product, Indole alkaloid, Accession number (library science), Data acquisition, Computer Science Applications, chemistry, 13. Climate action, lcsh:Q, Statistics, Probability and Uncertainty, Information Systems
Abstract

This Data Descriptor announces the submission to public repositories of the monoterpene indole alkaloid database (MIADB), a cumulative collection of 172 tandem mass spectrometry (MS/MS) spectra from multiple research projects conducted in eight natural product chemistry laboratories since the 1960s. All data have been annotated and organized to promote reuse by the community. Being a unique collection of these complex natural products, these data can be used to guide the dereplication and targeting of new related monoterpene indole alkaloids within complex mixtures when applying computer-based approaches, such as molecular networking. Each spectrum has its own accession number from CCMSLIB00004679916 to CCMSLIB00004680087 on the GNPS. The MIADB is available for download from MetaboLights under the identifier: MTBLS142 (https://www.ebi.ac.uk/metabolights/MTBLS142)., Design Type(s)mass spectrometry data transformation objective • mass spectrometry data analysis objective • data integration objectiveMeasurement Type(s)mass spectrumTechnology Type(s)liquid chromatography-tandem mass spectrometryFactor Type(s)Sample Characteristic(s)Strychnos usambarensis • Picralima nitida • Geissospermum laeve • Pleiocarpa mutica • Alstonia • Callichilia inaequalis • Chimarris cymosa • Mostuea brunonis • Gonioma • Cinchona • Catharanthus roseus • Voacanga grandifolia Machine-accessible metadata file describing the reported data (ISA-Tab format)

Published
2019
Full Text
View/download PDF

6. Revisiting Previously Investigated Plants: A Molecular Networking-Based Study of Geissospermum laeve

Author

Jean-François Gallard, Philippe M. Loiseau, Sébastien Pomel, Alexander E. Fox Ramos, Laurent Evanno, Erwan Poupon, Elisabeth Mouray, Christophe Duplais, Jean-Christophe Jullian, Marc Litaudon, Philippe Grellier, Alexandre Maciuk, Mehdi A. Beniddir, Charlotte Fox Alcover, Guillaume Bernadat, Pierre Champy, Équipe 'Pharmacognosie-Chimie des Substances Naturelles' BioCIS, Centre National de la Recherche Scientifique (CNRS), Institut de Chimie des Substances Naturelles (ICSN), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Molécules bioactives, conception, isolement et synthèse (MBCIS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie et Biochimie des Substances Naturelles, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire de Pharmacognosie (BioCIS), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Laboratoire de chimie et biochimie des substances naturelles, Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Cienciactiva, an initiative of the National Council for Science, Technology and Technological Innovation (CONCYTEC) [239-2015-FONDECYT], French ANR [ANR-15-CE29-0001], Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, food.ingredient, Stereochemistry, Antiparasitic, medicine.drug_class, Monoterpene, Plasmodium falciparum, Pharmaceutical Science, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, 01 natural sciences, Analytical Chemistry, Indole Alkaloids, 03 medical and health sciences, Antimalarials, food, Parasitic Sensitivity Tests, Drug Discovery, Secologanin Tryptamine Alkaloids, medicine, Organic chemistry, Humans, Nuclear Magnetic Resonance, Biomolecular, ComputingMilieux_MISCELLANEOUS, Pharmacology, Indole test, Apocynaceae, biology, Antiparasitic Agents, Molecular Structure, 010405 organic chemistry, Geissospermum, Organic Chemistry, Absolute configuration, biology.organism_classification, Antiparasitic agent, 0104 chemical sciences, French Guiana, Plant Leaves, 030104 developmental biology, Complementary and alternative medicine, Molecular Medicine, Drug Screening Assays, Antitumor, Leishmania donovani
Abstract

International audience; Three new monoterpene indole alkaloids (13) have been isolated from the bark of Geissospermum laeve-, together with the known alkaloids (-)-leuconolam (4), geissolosimine (5), and geissospermine (6). The structures of 1-3 were elucidated by analysis of their HRMS and NMR spectroscopic data. The absolute configuration of geissolaevine (I). was deduced from the comparison of experimental and theoretically calculated ECD spectra. The isolation workflow was guided by a molecular networking-based dereplication strategy using an in-house database of monoterpene indole alkaloids. In addition, five known compounds previously undescribed in the Geissospermum genus were dereplicated from the G. laeve alkaloid extract network and were assigned with various levels of identification confidence. The antiparasitic activities against Plasmodium falciparum and Leishmania donovani as well as the Ortotoxic activity against the MRC-5 cell line were determined for compounds 1-5.

Published
2017
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results