Literature DB >> 30003207

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

James B McAlpine1, Shao-Nong Chen1, Andrei Kutateladze2, John B MacMillan3, Giovanni Appendino4, Andersson Barison5, Mehdi A Beniddir6, Maique W Biavatti7, Stefan Bluml8, Asmaa Boufridi9, Mark S Butler10, Robert J Capon10, Young H Choi11, David Coppage3, Phillip Crews3, Michael T Crimmins12, Marie Csete13, Pradeep Dewapriya10, Joseph M Egan14, Mary J Garson15, Grégory Genta-Jouve16, William H Gerwick17, Harald Gross18, Mary Kay Harper19, Precilia Hermanto20, James M Hook20, Luke Hunter20, Damien Jeannerat21, Nai-Yun Ji22, Tyler A Johnson3, David G I Kingston23, Hiroyuki Koshino24, Hsiau-Wei Lee3, Guy Lewin6, Jie Li25, Roger G Linington14, Miaomiao Liu9, Kerry L McPhail26, Tadeusz F Molinski27, Bradley S Moore17, Joo-Won Nam27, Ram P Neupane27, Matthias Niemitz27, Jean-Marc Nuzillard27, Nicholas H Oberlies27, Fernanda M M Ocampos5, Guohui Pan27, Ronald J Quinn9, D Sai Reddy2, Jean-Hugues Renault27, José Rivera-Chávez27, Wolfgang Robien27, Carla M Saunders27, Thomas J Schmidt27, Christoph Seger27, Ben Shen27, Christoph Steinbeck27, Hermann Stuppner27, Sonja Sturm27, Orazio Taglialatela-Scafati27, Dean J Tantillo27, Robert Verpoorte11, Bin-Gui Wang28, Craig M Williams15, Philip G Williams27, Julien Wist27, Jian-Min Yue27, Chen Zhang27, Zhengren Xu27, Charlotte Simmler1, David C Lankin1, Jonathan Bisson1, Guido F Pauli1.   

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.

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Year:  2018        PMID: 30003207      PMCID: PMC6350634          DOI: 10.1039/c7np00064b

Source DB:  PubMed          Journal:  Nat Prod Rep        ISSN: 0265-0568            Impact factor:   13.423


  267 in total

1.  Dereplication of microbial natural products by LC-DAD-TOFMS.

Authors:  Kristian F Nielsen; Maria Månsson; Christian Rank; Jens Christian Frisvad; Thomas O Larsen
Journal:  J Nat Prod       Date:  2011-10-25       Impact factor: 4.050

2.  MRC's proposal to change the submission procedure for the future submission of assignment papers.

Authors: 
Journal:  Magn Reson Chem       Date:  2017-08-30       Impact factor: 2.447

Review 3.  Long-range (1)H-(15)N heteronuclear shift correlation at natural abundance.

Authors:  G E Martin; C E Hadden
Journal:  J Nat Prod       Date:  2000-04       Impact factor: 4.050

4.  Secondary metabolites by chemical screening: II. Amycins A and B two novel niphimycin analogs isolated from a high producer strain of elaiophylin and nigericin.

Authors:  S Grabley; P Hammann; W Raether; J Wink; A Zeeck
Journal:  J Antibiot (Tokyo)       Date:  1990-06       Impact factor: 2.649

5.  Unified synthesis of quinone sesquiterpenes based on a radical decarboxylation and quinone addition reaction.

Authors:  Taotao Ling; Erwan Poupon; Erik J Rueden; Sun H Kim; Emmanuel A Theodorakis
Journal:  J Am Chem Soc       Date:  2002-10-16       Impact factor: 15.419

Review 6.  Applications of Fluorine in Medicinal Chemistry.

Authors:  Eric P Gillis; Kyle J Eastman; Matthew D Hill; David J Donnelly; Nicholas A Meanwell
Journal:  J Med Chem       Date:  2015-07-22       Impact factor: 7.446

7.  Structure Revision of an Acorane Sesquiterpene Cordycepol A.

Authors:  D Sai Reddy; Andrei G Kutateladze
Journal:  Org Lett       Date:  2016-09-09       Impact factor: 6.005

8.  The correct structure of aquatolide-experimental validation of a theoretically-predicted structural revision.

Authors:  Michael W Lodewyk; Cristian Soldi; Paul B Jones; Marilyn M Olmstead; Juan Rita; Jared T Shaw; Dean J Tantillo
Journal:  J Am Chem Soc       Date:  2012-11-05       Impact factor: 15.419

9.  Coibamide A, a natural lariat depsipeptide, inhibits VEGFA/VEGFR2 expression and suppresses tumor growth in glioblastoma xenografts.

Authors:  Jeffrey D Serrill; Xuemei Wan; Andrew M Hau; Hyo Sang Jang; Daniel J Coleman; Arup K Indra; Adam W G Alani; Kerry L McPhail; Jane E Ishmael
Journal:  Invest New Drugs       Date:  2015-11-12       Impact factor: 3.850

Review 10.  Data standards can boost metabolomics research, and if there is a will, there is a way.

Authors:  Philippe Rocca-Serra; Reza M Salek; Masanori Arita; Elon Correa; Saravanan Dayalan; Alejandra Gonzalez-Beltran; Tim Ebbels; Royston Goodacre; Janna Hastings; Kenneth Haug; Albert Koulman; Macha Nikolski; Matej Oresic; Susanna-Assunta Sansone; Daniel Schober; James Smith; Christoph Steinbeck; Mark R Viant; Steffen Neumann
Journal:  Metabolomics       Date:  2015-11-17       Impact factor: 4.290

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  25 in total

1.  Tri- and Tetrameric Proanthocyanidins with Dentin Bioactivities from Pinus massoniana.

Authors:  Bin Zhou; Yvette Alania; Mariana Reis; Rasika S Phansalkar; Joo-Won Nam; James B McAlpine; Shao-Nong Chen; Ana K Bedran-Russo; Guido F Pauli
Journal:  J Org Chem       Date:  2020-06-17       Impact factor: 4.354

2.  Classification of Flavonoid Metabolomes via Data Mining and Quantification of Hydroxyl NMR Signals.

Authors:  Yang Yu; Guido F Pauli; Lingyi Huang; Li-She Gan; Richard B van Breemen; Dianpeng Li; James B McAlpine; David C Lankin; Shao-Nong Chen
Journal:  Anal Chem       Date:  2020-03-26       Impact factor: 6.986

Review 3.  Making the collective knowledge of chemistry open and machine actionable.

Authors:  Kevin Maik Jablonka; Luc Patiny; Berend Smit
Journal:  Nat Chem       Date:  2022-04-04       Impact factor: 24.427

Review 4.  The Essential Medicinal Chemistry of Cannabidiol (CBD).

Authors:  Kathryn M Nelson; Jonathan Bisson; Gurpreet Singh; James G Graham; Shao-Nong Chen; J Brent Friesen; Jayme L Dahlin; Matthias Niemitz; Michael A Walters; Guido F Pauli
Journal:  J Med Chem       Date:  2020-09-10       Impact factor: 7.446

5.  A Convolutional Neural Network-Based Approach for the Rapid Annotation of Molecularly Diverse Natural Products.

Authors:  Raphael Reher; Hyun Woo Kim; Chen Zhang; Huanru Henry Mao; Mingxun Wang; Louis-Félix Nothias; Andres Mauricio Caraballo-Rodriguez; Evgenia Glukhov; Bahar Teke; Tiago Leao; Kelsey L Alexander; Brendan M Duggan; Ezra L Van Everbroeck; Pieter C Dorrestein; Garrison W Cottrell; William H Gerwick
Journal:  J Am Chem Soc       Date:  2020-02-21       Impact factor: 15.419

Review 6.  Ethnobotany and the Role of Plant Natural Products in Antibiotic Drug Discovery.

Authors:  Gina Porras; François Chassagne; James T Lyles; Lewis Marquez; Micah Dettweiler; Akram M Salam; Tharanga Samarakoon; Sarah Shabih; Darya Raschid Farrokhi; Cassandra L Quave
Journal:  Chem Rev       Date:  2020-11-09       Impact factor: 60.622

Review 7.  Quantum mechanical NMR full spin analysis in pharmaceutical identity testing and quality control.

Authors:  Prabhakar S Achanta; Birgit U Jaki; James B McAlpine; J Brent Friesen; Matthias Niemitz; Shao-Nong Chen; Guido F Pauli
Journal:  J Pharm Biomed Anal       Date:  2020-09-08       Impact factor: 3.935

Review 8.  Microbial natural product databases: moving forward in the multi-omics era.

Authors:  Jeffrey A van Santen; Satria A Kautsar; Marnix H Medema; Roger G Linington
Journal:  Nat Prod Rep       Date:  2020-08-28       Impact factor: 13.423

9.  Development of an NMR-Based Platform for the Direct Structural Annotation of Complex Natural Products Mixtures.

Authors:  Joseph M Egan; Jeffrey A van Santen; Dennis Y Liu; Roger G Linington
Journal:  J Nat Prod       Date:  2021-03-22       Impact factor: 4.050

10.  Pharmaceutical analysis by NMR can accommodate strict impurity thresholds: The case of choline.

Authors:  Prabhakar S Achanta; Matthias Niemitz; J Brent Friesen; Fatkhulla K Tadjimukhamedov; Anton Bzhelyansky; Gabriel I Giancaspro; Shao-Nong Chen; Guido F Pauli
Journal:  J Pharm Biomed Anal       Date:  2022-03-05       Impact factor: 3.935

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