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

Author

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, Jeannerat, Damien, Ji, Nai-Yun, Johnson, Tyler A, Kingston, David GI, Koshino, Hiroyuki, Lee, Hsiau-Wei, Lewin, Guy, Li, Jie, Linington, Roger G, Liu, Miaomiao, McPhail, Kerry L, Molinski, Tadeusz F, Moore, Bradley S, Nam, Joo-Won, Neupane, Ram P, Niemitz, Matthias, Nuzillard, Jean-Marc, Oberlies, Nicholas H, Ocampos, Fernanda MM, Pan, Guohui, Quinn, Ronald J, Reddy, D Sai, Renault, Jean-Hugues, 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, Xu, Zhengren, Simmler, Charlotte, Lankin, David C, Bisson, Jonathan, and Pauli, Guido F

Subjects
Biological Products, Magnetic Resonance Spectroscopy, Reproducibility of Results, Molecular Conformation, Generic health relevance, Organic Chemistry, Chemical Sciences, Biological Sciences, Medical and Health Sciences
Abstract

Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.

Published
2019

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

Author

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, Jeannerat, Damien, Ji, Nai-Yun, Johnson, Tyler A, Kingston, David GI, Koshino, Hiroyuki, Lee, Hsiau-Wei, Lewin, Guy, Li, Jie, Linington, Roger G, Liu, Miaomiao, McPhail, Kerry L, Molinski, Tadeusz F, Moore, Bradley S, Nam, Joo-Won, Neupane, Ram P, Niemitz, Matthias, Nuzillard, Jean-Marc, Oberlies, Nicholas H, Ocampos, Fernanda MM, Pan, Guohui, Quinn, Ronald J, Reddy, D Sai, Renault, Jean-Hugues, 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, Xu, Zhengren, Simmler, Charlotte, Lankin, David C, Bisson, Jonathan, and Pauli, Guido F

Subjects
Organic Chemistry, Chemical Sciences, Clinical Research, Biological Sciences, Medical and Health Sciences, Medicinal and biomolecular chemistry, Traditional, complementary and integrative medicine
Abstract

Correction for 'The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research' by James B. McAlpine et al., Nat. Prod. Rep., 2018, DOI: .

Published
2019

3. Further Probing the Properties of a Unique Sponge-derived Alkaloid Through the Isolation of a New (−)-(5E)‑(8R)‑(14Z)‑Mycothiazole Analogue.

Author

Gerke, Joe A., Odron, Sofia F., Kim, Juri, Dutta, Naibedya, Clarke, Jacqueline G., Media, Joseph, Coppage, David A., Oorloff, Maria, Alcala, Athena, Garcia, Gilberto, Kang, Marissa E.F., Gerke, Cy L., Peterson, Jacob C., Morris, Joseph D., Higuchi-Sanabria, Ryo, Valeriote, Frederick A., Crews, Phillip, and Johnson, Tyler A.

Published
2024
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4. Application of the DP4 Probability Method to Flexible Cyclic Peptides with Multiple Independent Stereocenters: The True Structure of Cyclocinamide A

Author

Cooper, Jason K, Li, Kelin, Aubé, Jeffrey, Coppage, David A, and Konopelski, Joseph P

Subjects
Organic Chemistry, Chemical Sciences, Computers, Molecular, Glycine, Molecular Structure, Peptides, Cyclic, Probability, Pyrroles, Stereoisomerism, Chemical sciences
Abstract

A DP4 protocol has been successfully utilized to establish the true structure of the natural product cyclocinamide A, a flexible cyclic peptide with four isolated stereocenters. Benchmarking the necessary level of theory required to successfully predict the NMR spectra of three previously synthesized isomers of cyclocinamide A led to the prediction of the natural stereochemistry as 4 S, 7 R, 11 R, 14 S, which has been confirmed by total synthesis.

Published
2018

5. Re-evaluation of the Fijianolide/Laulimalide Chemotype Suggests an Alternate Mechanism of Action for C-15/C-20 Analogs

Author

Morris, Joseph D., primary, Takahashi-Ruiz, Leila, additional, Persi, Lauren N., additional, Summers, Jonathan C., additional, McCauley, Erin P., additional, Chan, Peter Y. W., additional, Amberchan, Gabriella, additional, Lizama-Chamu, Itzel, additional, Coppage, David A., additional, Crews, Phillip, additional, Risinger, April L., additional, and Johnson, Tyler A., additional

Published
2022
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6. Reinvestigation of Mycothiazole Reveals the Penta-2,4-dien-1-ol Residue Imparts Picomolar Potency and 8S Configuration

Author

Johnson, Tyler A., primary, Morris, Joseph D., additional, Coppage, David A., additional, Cook, Colon V., additional, Persi, Lauren N., additional, Ogarrio, Marcos A., additional, Garcia, Taylor C., additional, McIntosh, Nicole L., additional, McCauley, Erin P., additional, Media, Joseph, additional, Maheshwari, Mani, additional, Valeriote, Frederick A., additional, Shaw, Jiajiu, additional, and Crews, Phillip, additional

Published
2020
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9. Evaluating Nitrogen-Containing Biosynthetic Products Produced by Saltwater Culturing of Several California Littoral Zone Gram-Negative Bacteria

Author

Lorig-Roach, Nicholas, Still, Patrick C., Coppage, David, Compton, Jennifer E., Crews, Mitchell S., Navarro, Gabriel, Tenney, Karen, and Crews, Phillip

Abstract

The biosynthetic potential of marine-sediment-derived Gram-negative bacteria is poorly understood. Sampling of California near-shore marine environments afforded isolation of numerous Gram-negative bacteria in the Proteobacteria and Bacteriodetes phyla, which were grown in the laboratory to provide extracts whose metabolites were identified by comparative analyses of LC-mass spectrometry and MSndata. Overall, we developed an assemblage of seven bacterial strains grown in five different media types designed to coax out unique secondary metabolite production as a function of varying culture conditions. The changes in metabolite production patterns were tracked using the GNPS MS2fragmentation pattern analysis tool. A variety of nitrogen-rich metabolites were visualized from the different strains grown in different media, and strikingly, all of the strains examined produced the same new, proton-atom-deficient compound, 1-methyl-4-methylthio-β-carboline (1), C13H12N2S. Scale-up liquid culture of Achromobacter spanius(order: Burkholderiales; class: Betaproteobacteria) provided material for the final structure elucidation. The methods successfully combined in this work should stimulate future studies of molecules from marine-derived Gram-negative bacteria.

Published
2024
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17. Diazinon(R): Chronic Toxicity to, and Brain Acetylcholinesterase Inhibition in, the Sheepshead Minnow, Cyprinodon variegatus

Author

Goodman, Larry R., Hansen, David J., Coppage, David L., Moore, James C., and Matthews, Edward

Abstract

We investigated the toxicity of Diazinon to sheepshead minnows continuously exposed in flow-through toxicity tests. In the 96-hour acute test, a measured concentration of 1,400/ µg/liter was lethal to 50% of the juvenile test animals. In the partial life-cycle test, we also investigated uptake of Diazinon by sheepshead minnows and effect of Diazinon on brain acetylcholinesterase (AChE) activity. Average measured concentrations in the partial life-cycle test were nondetectable (control), 0.47, 0.98, 1.8, 3.5, and 6.5 µg of Diazinon per liter of seawater. Although the number of eggs spawned by continuously exposed fish was significantly reduced (a = 0.05) in all concentrations, no concentration tested significantly affected parental survival or fertility of eggs, nor were survival and growth of progeny affected in a subsequent 28-day test. Fish exposed to 0.47 µg/liter spawned 22.6 eggs/female-day, or 69% of control production (32.8 eggs/female-day). The number of eggs spawned by fish exposed to 6.5, 3.5, 1.8, and 0.98 µg/liter Diazinon was similar (14.9–17.9 eggs/female-day), averaging 45–55% of production by control fish. Egg production by fish that had been previously exposed to 3.5 µg/liter did not change significantly following deputation for 23 to 31 days. AChE activity varied inversely with exposure concentration, fish in the highest concentration (6.5 µg/liter) averaging 71% inhibition. The concentration of Diazinon measured in adult fish exposed to 1.8, 3.5, and 6.5 µg/liter averaged 169 times the concentration measured in the water. Diazinon was not consistently detected (<0.05 mg/kg) in fish exposed to 0.98 and 0.47 µg/liter. The maximum acceptable toxicant concentration (MATC) for sheepshead minnows continuously exposed to Diazinon, based on reduced fecundity, is <0.47 µg/liter; the application factor (MATC ÷ 96-hour median lethal concentration) is <0.0003.

Published
1979
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25. 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
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26. Further Probing the Properties of a Unique Sponge-derived Alkaloid Through the Isolation of a New (-)-(5 E )-(8 R )-(14 Z )-Mycothiazole Analogue.

Author

Gerke JA, Odron SF, Kim J, Dutta N, Clarke JG, Media J, Coppage DA, Oorloff M, Alcala A, Garcia G, Kang MEF, Gerke CL, Peterson JC, Morris JD, Higuchi-Sanabria R, Valeriote FA, Crews P, and Johnson TA

Subjects
Animals, Molecular Structure, Humans, Mice, Stereoisomerism, Caenorhabditis elegans drug effects, Hep G2 Cells, Drug Screening Assays, Antitumor, Antineoplastic Agents pharmacology, Antineoplastic Agents chemistry, Antineoplastic Agents isolation & purification, Alkaloids chemistry, Alkaloids pharmacology, Alkaloids isolation & purification, Porifera chemistry, Thiazoles pharmacology, Thiazoles chemistry
Abstract

Scale-up isolation of (+)-(5 Z )-(8 S )-(14 Z )-mycothiazole ( 1 ) from Vanuatu specimens of C. mycofijiensis to semisynthesize (+)-(5 Z )-(8 S )-8- O -acetyl-(14 Z )-mycothiazole ( 2 ) revealed a new diastereomer, (-)-(5 E )-(8 R )-(14 Z )-mycothiazole ( 4 ). The structure of 4 was determined using HRMS, NMR, and comparing optical rotation to (-)-(5 Z )-(8 R )-(14 Z )-mycothiazole ( 3 ) and 2 . The maximum tolerated dose of 2 in mice was 0.1 mg/kg. The IC 50 of 4 in PANC-1 and HepG2 cancer cell lines was 111.6 and 115.0 nM. Evaluation of 4 in C. elegans showed similar oxygen consumption compared to 1 - 2 , and all compounds significantly increased the lifespan. The Z orientation at Δ 5,6 is crucial for picomolar cytotoxicity but not for mitochondrial inhibition.

Published
2024
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27. Reinvestigation of Mycothiazole Reveals the Penta-2,4-dien-1-ol Residue Imparts Picomolar Potency and 8 S Configuration.

Author

Johnson TA, Morris JD, Coppage DA, Cook CV, Persi LN, Ogarrio MA, Garcia TC, McIntosh NL, McCauley EP, Media J, Maheshwari M, Valeriote FA, Shaw J, and Crews P

Abstract

Reinvestigation of mycothiazole ( 1 ) revealed picomolar potency (IC 50 = 0.00016, 0.00027, 0.00035 μM) against pancreatic, (PANC-1), liver (HepG2), and colon (HCT-116) tumor cell lines. Reevaluation of 1 provided [α] D data indicating Vanuatu specimens of C. mycofijiensis contain the 8 S enantiomer of 1 and not the 8 R configuration previously reported. Semisynthesis provided 8- O -acetylmycothiazole ( 2 ), 8-oxomycothiazole ( 8 ), mycothiazole nitrosobenzene derivatives (MND1, MND2: 9a , 9b ), and MND3 ( 10 ) with IC 50 = 0.00129, >1.0, >1.0, >1.0, >1.0 μM, respectively, against PANC-1 cell lines. These results highlight the significance of the penta-2,4-dien-1-ol residue as a key structural feature of 1 required for its cytotoxicty against tumor cell lines., Competing Interests: The authors declare no competing financial interest., (Copyright © 2020 American Chemical Society.)

Published
2020
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