Methods in Molecular Biology 1055 Ute Roessner Daniel Anthony Dias Editors Metabolomics Tools for Natural Product Discovery Methods and Protocols M ETHODS IN MOLECULAR BIOLOGY™ Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hat fi eld, Hertfordshire, AL10 9AB, UK For further volumes: http://www.springer.com/series/7651 Metabolomics Tools for Natural Product Discovery Methods and Protocols Edited by Ute Roessner and Daniel Anthony Dias School of Botany, The University of Melbourne, Parkville, Victoria, Australia Editors Ute Roessner Daniel Anthony Dias School of Botany School of Botany The University of Melbourne The University of Melbourne Parkville, Victoria, Australia Parkville , Victoria , Australia ISSN 1064-3745 ISSN 1940-6029 (electronic) ISBN 978-1-62703-576-7 ISBN 978-1-62703-577-4 (eBook) DOI 10.1007/978-1-62703-577-4 Springer New York Heidelberg Dordrecht London Library of Congress Control Number: 2013945168 © Springer Science+Business Media, LLC 2013 This work is subject to copyright. 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Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specifi c statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. ©Photographed by Dr Britta Drevermann, Dandenong Ranges National Park, Tremont, Victoria, Australia (2012) Printed on acid-free paper Humana Press is a brand of Springer Springer is part of Springer Science+Business Media (www.springer.com) Pref ace The inspiration behind this volume of Methods in Molecular Biology: Metabolomics Tools for Natural Product Discoveries is to unite the diverse methodologies and protocols that have developed from classical natural product chemistry now transitioning to modern day metabolomics to identify bioactive secondary metabolites for the purpose of drug discov- ery. Natural product chemistry maybe regarded as an older science with the isolation of many natural products between the 1970s and 1990s mainly due to the advent of improved, highly sensitive separation methods, mass spectrometry, and nuclear magnetic resonance spectroscopy. Therefore, it is worthwhile to summarize recent advancements in current comprehensive analytical platforms and present how metabolomics is now being integrated into this classical fi eld to dereplicate and profi le natural product extracts. The aims of this book are to discuss and in part review, how natural product chemistry is transitioning to metabolomics as a result of the advent of comprehensive analytical plat- forms. Applications for the extraction of selected natural products (secondary metabolites) from less common sources such as bryophytes and hard corals are presented. Various bio- logical assays including anticancer, anti diabetic, antibacterial, and various metabolomic, biomarker, and dereplication strategies are discussed. Comprehensive applications and strategies for gas chromatography-mass spectrometry (GC-MS) (polar metabolite profi l- ing and fatty acid analysis), liquid chromatography-mass spectrometry (LC-MS) (untar- geted profi ling and lipidomics), and nuclear magnetic resonance (NMR) spectroscopy (profi ling) metabolomic-based studies are discussed. Finally, protocols and strategies for the structure elucidation of isolated natural products by NMR, determination of absolute confi gurations, and the discovery, biosynthesis, and engineering of novel enterocin and wailupemycin polyketide analogues and the synthesis of K 1 and K2 melatonin metabolites are presented. Methods in Molecular Biology: Metabolomics Tools for Natural Product Discoveries is tar- geted at chemists, biologists, pharmacologists, students, and researchers in related fi elds to appreciate the current available methodologies and protocols for natural product isolation, biomarker discovery, dereplication, biological assays, and comprehensive metabolomic plat- forms available for high-throughput analyses. Parkville , Victoria, Australia Ute Roessner Daniel Anthony Dias v Contents Preface . v Contributors . ix 1 Bryophytes: Liverworts, Mosses, and Hornworts: Extraction and Isolation Procedures . 1 Yoshinori Asakawa and Agnieszka Ludwiczuk 2 Plant Tissue Extraction for Metabolomics . 21 Ute Roessner and Daniel Anthony Dias 3 Detection of Polar Metabolites Through the Use of Gas Chromatography–Mass Spectrometry . 29 David P. De Souza 4 A Robust GC-MS Method for the Quantitation of Fatty Acids in Biological Systems. 39 Nirupama Samanmalie Jayasinghe and Daniel Anthony Dias 5 A Workflow from Untargeted LC-MS Profiling to Targeted Natural Product Isolation . 57 Damien L. Callahan and Candace E. Elliott 6 Lipidomics: Extraction Protocols for Biological Matrices . 71 Thusitha Wasntha Thilaka Rupasinghe 7 Metabolite Analysis of Biological Fluids and Tissues by Proton Nuclear Magnetic Resonance Spectroscopy . 81 John Robert Sheedy 8 NMR Spectroscopy: Structure Elucidation of Cycloelatanene A: A Natural Product Case Study. 99 Sylvia Urban and Daniel Anthony Dias 9 NMR-Based Metabolomics: A Probe to Utilize Biodiversity . 117 Lúcia P. Santos Pimenta, Hye Kyong Kim, Robert Verpoorte, and Young Hae Choi 10 Extraction Protocol for Nontargeted NMR and LC-MS Metabolomics-Based Analysis of Hard Coral and Their Algal Symbionts. 129 Benjamin R. Gordon, William Leggat, and Cherie A. Motti 11 Determination of Absolute Configuration Using Single Crystal X-Ray Diffraction . 149 Abigail L. Albright and Jonathan M. White 12 Natural Product Chemistry in Action: The Synthesis of Melatonin Metabolites K1 and K2 . 163 Helmut M. Hügel and Oliver A.H. Jones vii viii Contents 13 Discovery, Biosynthesis, and Rational Engineering of Novel Enterocin and Wailupemycin Polyketide Analogues . 171 John A. Kalaitzis 14 Bioassays for Anticancer Activities . 191 Janice McCauley, Ana Zivanovic, and Danielle Skropeta 15 Screening for Antidiabetic Activities . 207 Rima Caccetta and Hani Al Salami 16 Screening for Antibacterial, Antifungal, and Anti quorum Sensing Activity . 219 Elisa J. Hayhoe and Enzo A. Palombo 17 Metabolomics and Dereplication Strategies in Natural Products . 227 Ahmed Fares Tawfike, Christina Viegelmann, and RuAngelie Edrada-Ebel 18 Bridging the Gap: Basic Metabolomics Methods for Natural Product Chemistry . 245 Oliver A.H. Jones and Helmut M. Hügel 19 Strategies in Biomarker Discovery. Peak Annotation by MS and Targeted LC-MS Micro-Fractionation for De Novo Structure Identification by Micro-NMR . 267 Philippe J. Eugster, Gaëtan Glauser, and Jean-Luc Wolfender 20 Statistical Analysis of Metabolomics Data . 291 Alysha M.De Livera, Moshe Olshansky, and Terence P. Speed Index . 309 Contributors HANI AL SALAMI • Curtin Health Innovation Research Institute, School of Pharmacy, Curtin University , Perth , Australia ABIGAIL L. ALBRIGHT • School of Chemistry , The University of Melbourne , Melbourne , Australia ; Bio21 Institute (Molecular Science and Biotechnology Institute) , The University of Melbourne , Melbourne , Australia YOSHINORI ASAKAWA • Faculty of Pharmaceutical Sciences , Tokushima Bunri University , Tokushima , Japan RIMA CACCETTA • School of Pharmacy, Curtin Health Innovation Research Institute, Curtin University , Perth , Australia DAMIEN L. CALLAHAN • Metabolomics Australia, School of Botany , The University of Melbourne , Parkville, VIC , Australia YOUNG HAE CHOI • Natural Products Laboratory, Institute of Biology, Leiden University , Leiden , The Netherlands ALYSHA M. DE LIVERA • Metabolomics Australia, Bio21 Institute (Molecular Science and Biotechnology Institute) , The University of Melbourne , Melbourne , Australia DAVID P. DE SOUZA • Metabolomics Australia, Bio21 Institute (Molecular Science and Biotechnology Institute) , The University of Melbourne , Melbourne , Australia DANIEL ANTHONY DIAS • School of Botany , The University of Melbourne , Parkville, Victoria , Australia RUANGELIE EDRADA-EBEL • Strathclyde Institute of Pharmacy and Biomedical Sciences , University of Strathclyde , Glasgow , UK CANDACE E. ELLIOTT • School of Botany , The University of Melbourne , Melbourne, Australia PHILIPPE J.