UNIVERSITY OF CALIFORNIA, SAN DIEGO Chemical Study of Secondary Metabolites from Selected Strains of the Actinomycete Clade MAR 4 A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Oceanography by Ana Paula Domingues de Mello Espindola Committee in charge: William Fenical, Chair Bianca Brahamsha William Gerwick Bradley Moore Emmanuel Theodorakis 2008 Copyright Ana Paula Domingues de Mello Espindola, 2008 All rights reserved. The dissertation of Ana Paula Domingues de Mello Espindola is approved, and is acceptable in quality and form for publication on microfilm: _____________________________________________ _____________________________________________ _____________________________________________ _____________________________________________ _____________________________________________ _____________________________________________ Chair University of California, San Diego 2008 iii TABLE OF CONTENTS Signature page .............................................................................................................. iii Table of Contents ......................................................................................................... iv List of Figures .............................................................................................................. vii List of Schemes ............................................................................................................. x List of Tables ................................................................................................................ xi List of Abbreviations ................................................................................................... xii Acknowledgements .................................................................................................... xiii Vita and Publications ................................................................................................... xv Abstract ....................................................................................................................... xvi I. Introduction to the thesis research: History and roles of natural products ................. 1 I.1. History of natural products as a science ............................................................. 1 I.1.1. Secondary metabolites from plants .............................................................. 2 I.1.2. The “Golden Age” – Secondary metabolites from microorganisms ............ 9 I.1.3. A new frontier – Marine natural products .................................................. 15 I.2. History of natural products chemistry methodology ........................................ 25 I.3. Rise and fall of natural products chemistry ...................................................... 30 I.4. A new source of natural products ..................................................................... 34 I.5. Marine Actinomycetes as a source of natural products ................................... 36 I.5.1. MAR 4 group ............................................................................................... 38 I.6. Importance of the study of secondary metabolites ........................................... 42 I.7. Thesis ................................................................................................................. 44 I.8. References .......................................................................................................... 45 II. Review of terpenoids and meroterpenoids in actinomycetes .................................. 55 iv II.1.1. Terpenoids ................................................................................................... 55 II.1.2. Meroterpenoids ........................................................................................... 59 II.2. Terpenoids in actinomycetes ............................................................................ 60 II.2.1. Meroterpenoids in actinomycetes ............................................................... 63 II.3. Importance of terpenoid production by actinomycetes ..................................... 74 II.4. References ......................................................................................................... 75 III. Nitropyrrolins A-C, farnesyl- -nitropyrroles from an undescribed marine derived actinomycete. ............................................................................................ 81 III.1. Introduction ..................................................................................................... 81 III.2. Results and discussion ..................................................................................... 82 III.3. Experimental section ....................................................................................... 89 III.3.1. General experimental procedures .............................................................. 89 III.3.2. The marine actinomycete (CNQ 509) ....................................................... 89 III.3.3. Compound isolation ................................................................................... 90 III.4. References ....................................................................................................... 97 IV. Marinophenazines A and B from a marine derived actinomycete ...................... 100 IV.1. Introduction ................................................................................................... 100 IV.2. Results and discussion ................................................................................... 103 IV.3. Experimental section ..................................................................................... 106 IV.3.1. General experimental procedures ............................................................ 106 IV.3.2. The marine actinomycete (CNQ 509) ..................................................... 107 IV.3.3. Compound isolation ................................................................................ 107 IV.4. References ..................................................................................................... 111 V. Streptoquinone, a new napthoquinone meroterpenoid from the marine derived actinomycete CNQ 509 .......................................................................... 113 V.1. Introduction .................................................................................................... 113 v V.2. Results and discussion .................................................................................... 115 V.3. Experimental section ...................................................................................... 119 V.3.1. General experimental procedures ............................................................. 119 V.3.2. The marine actinomycete CNQ 509 ......................................................... 119 V.3.3. Compound isolation .................................................................................. 120 V.4. References ...................................................................................................... 122 VI. Active secondary metabolites in a chemoprevention assay from the new marine derived actinomycete, clade MAR 4 (CNR 925)……………… ............ 124 VI.1. Chemoprevention .......................................................................................... 124 V.1.1. Cancer ....................................................................................................... 125 V.1.2. Cancer chemoprevention .......................................................................... 128 VI.2. NF-κB ............................................................................................................ 129 VI.3. Results and discussion ................................................................................... 131 VI.3.1. QSAR studies .......................................................................................... 134 VI.4. Experimental section ..................................................................................... 138 VI.4.1. General experimental procedures ............................................................ 139 VI.4.2. The marine actinomycete CNR 925 ........................................................ 139 VI.4.3. Compound isolation ................................................................................ 140 VI.5. References ..................................................................................................... 142 VII. Conclusion .......................................................................................................... 145 Appendix NMR spectra of the nitropyrrolins NMR spectra of the marinophenazines NMR spectra of Streptoquinone NMR spectra of naphthomarine vi LIST OF FIGURES Chapter I Figure - I.2.1 - Acid-base reaction of caffeine and an acid aqueous solution resulting in change of solubility ..................................................................... 27 Figure - I.5.1 - Example of compounds produced by the three Salinispora species ... 37 Figure - I.5.2 - Phylogenetic diversity from cultured marine actinomycetes .............. 38 Figure - I.5.3 - Phylogenetic tree of MAR 4 strains .................................................... 40 Figure - I.5.4 - Approximate number of compounds produced by actinomycete families ........................................................................................................... 41 Chapter II Figure - II.1.1 – Terpenoid classes .............................................................................