The Synthesis-Enabled Stereochemical Elucidation of the Marine Natural Products Hemicalide and Phormidolide A A thesis submitted for the degree of Doctor of Philosophy at the University of Cambridge Nelson Y. S. Lam Trinity College Department of Chemistry August 2019 Declaration This thesis is the result of my own work and includes nothing which is the outcome of work done in collaboration except as declared in the Preface and specified in the text. It is not substantially the same as any that I have submitted, or, is being concurrently submitted for a degree or diploma or other qualification at the University of Cambridge or any other University or similar institution except as declared in the Preface and specified in the text. I further state that no substantial part of my thesis has already been submitted, or, is being concurrently submitted for any such degree, diploma or other qualification at the University of Cambridge or any other University or similar institution except as declared in the Preface and specified in the text. It does not exceed the prescribed word limit of 60,000 words, excluding experimental data. _________________________ Nelson Yuen Sum Lam August 2019 Part of the work described in this thesis has been published in the following peer-reviewed articles: Han, B. Y.; Lam, N. Y. S.; MacGregor, C. I.; Goodman, J. M.; Paterson, I. Chem. Commun. 2018, 54, 3247– 3250. Lam, N. Y. S.; Muir, G.; Rao Challa, V.; Britton, R.; Paterson, I. Chem. Commun. 2019, 55, 9717–9720. i ii Acknowledgements If I have seen further than others it is by standing upon the shoulders of giants The work described in this thesis would not have been possible without the abundant support and camaraderie of my mentors, collaborators and friends. I am indebted to Prof. Ian Paterson for the opportunity to be part of a team with decades of world-leading expertise in organic synthesis. His principled perspectives and incredible breadth of knowledge have made for many fantastic discussions that I hope will continue for years to come. I am also grateful for my academic mentors, Profs. Jonathan Goodman, David Spring, Rob Britton (SFU) and Christian Hartinger (Auckland), who have given me their advice over the years. I am fortunate to have worked with a fantastic team of scientists during my PhD. Above all, I am very grateful to Dr. Bing Yuan Han for his guidance and solidarity, and Garrett Muir for his ceaseless enthusiasm in our ongoing project towards phormidolide A. Both were instrumental for the advances we have made towards our projects and their names deserve to be in equal standing alongside mine on the front cover of this thesis. I am particularly grateful for Drs. Bing Yuan Han and Andrew Phillips for taking the time to proofread my thesis. Additionally, none of this research would have been possible without Nic Davies, Naomi Hobbs and Carlos Davies for their excellent technical support, and Dr. Peter Grice, Duncan Howe and Andrew Mason for their fountain of NMR expertise. Moving halfway around the world has been made easier by the wonderful lab environment created by everyone in the Paterson group past and present, as well as the Spring and Phipps groups who share our lab space. These people have all contributed to the dynamic atmosphere that is Lab 122. The four years have been fruitful not just in the pursuit of knowledge, but also in forging lifelong friendships. Through the ups and many downs of PhD life, I am indebted to the support from my fellow lab mates, and my friends near and far: Ruth, Dråkšo, Sarah, Brieuc, Paula, Sofia, Jesse, Mark, Catherine, Micah, Ryan and Anthony to name a few. I have to especially thank Rachel, my fellow PhD companion, with whom over our four years celebrated the joys with food and weathered the storms with more food. Finally, I would like to express my gratitude to the people and organisations who have supported my time in Cambridge through their generous funding: Dr. Nigel Evans, Sir Noel Robinson and the Woolf Fisher Trust, and Eashwar Krishnan, Tzo-Tze Ang and Trinity College. iii iv Abstract The structural complexity and biological activity of marine natural products have made them attractive targets for synthetic chemists. In cases where their relative and/or absolute configuration is unknown, total synthesis becomes a powerful method to enable their structural elucidation, as highlighted in Part I. This thesis discusses synthetic efforts towards two marine natural products, hemicalide (1) and phormidolide A (2), with the end goal of establishing and/or confirming the compound’s full stereochemistry. O HO 23 O OMe O OH OH OMe 1 27 HO 41 18 14 8 COOH OH O OH 24 42 36 31 OH OMe 46 H H Hemicalide (1) O Br O OH OH OH OH OH 33 16 O 29 25 21 OMe 13 O 15 O 1 Phormidolide A (2): Reported structure 7 OH Hemicalide’s low isolation yield from its marine sponge source meant that none of the 21 stereocenters were assigned in the original patent literature. Previous computational and synthetic work by Ardisson and Cossy, as well as the Paterson and Goodman groups, have narrowed down the possibilities for the C1-C15, C16-C25 and C35-C46 fragments to a single diastereomer with reasonable confidence. However, the relative configuration between fragments and the absolute stereochemistry remains unknown. Part II describes the synthesis of the C16-C28 dihydroxylactone fragment, which was used to successfully assemble a diastereomer of the C1-C28 truncate. Comparisons with the alternative configuration synthesised by Han enabled the definitive assignment of the relative configuration between the C1-C15 and the C16-C25 region of hemicalide. These studies also illuminated the nature of the C1 carboxyl group in the natural product. Phormidolide A possesses several fascinating structural motifs. Its terminal bromomethoxydiene (BMD) motif in particular, is unprecedented among natural products. Furthermore, inconclusive stereochemical evidence presented in the literature meant that a synthesis-guided stereochemical evaluation is required. Part III discusses synthetic efforts to the natural product, involving the expedient synthesis of the C18-C23 vinyl iodide and the C25-C33 side chain bearing the unique BMD motif. Towards the end goal of a total synthesis, this chapter also illustrates the evolution of the fragment coupling strategy, which led to the reassignment of seven of the 11 stereocentres present in phormidolide A. v vi Table of Contents Declaration i Acknowledgements iii Abstract v Table of Contents vii Abbreviations xi Nomenclature xiv PART I – INTRODUCTION 1 1.1. Marine Natural Products and their Characterisation 1 1.2. The Role of Synthesis in Correcting Stereochemical Misassignments 2 1.3. Summary 8 PART II – HEMICALIDE 9 2. Introduction 9 2.1. Isolation, 2D structural elucidation and biological activity of hemicalide 9 2.2. Current progress towards the stereochemical assignment of hemicalide 10 2.2.1. Assignment of the C1-C15 polypropionate stereohexad 11 2.2.2. Assignment of the C18-C24 dihydroxylactone 12 2.2.3. Assignment of the remainder of hemicalide: the C25-C46 region 14 2.2.4. Relative configuration between the C1-C15 and C16-C25 region 16 2.3. Previous synthetic work towards hemicalide 19 2.3.1. Synthesis of the C1-C15 region 19 2.3.2. Synthesis of the revised C16-C25 region 22 2.3.3. Synthesis of the C35-C46 region 25 2.3.4. Fragment union studies: Ardisson/Cossy’s synthesis of the full carbon skeleton of hemicalide 28 2.4. Summary 31 3. Results and Discussion 33 vii 3.1. The Paterson approach to hemicalide 33 3.2. Synthesis of the opposite enantiomeric series for the C16-28 fragment 36 3.2.1. Synthesis of the aldol adduct ent-50 36 3.2.2. Synthesis of the dihydroxylactone ent-52 41 3.2.3. Completion of the enantiomeric C16-C28 fragment ent-53 44 3.3. Fragment union, derivatisation of the C1-C28 truncate and NMR comparisons 46 3.3.1. Derivatisation of the C1-C28 fragment for NMR comparison 48 3.3.2. Global silyl deprotection of the C1-C28 truncate 48 3.4. NMR comparisons of the C1-C28 truncates with hemicalide 52 3.4.1. NMR comparisons between the 13,18-syn and 13,18-anti acids 53 3.4.2. NMR comparisons between the 13,18-syn and 13,18-anti salts 55 4. Hemicalide: Conclusions and Future Work 59 4.1. Conclusions 59 4.2. Future work 61 4.2.1. Future work in the C1-C28 fragment 61 4.2.2. Beyond the C1-C28 region: towards the stereochemical elucidation of hemicalide 63 PART III - PHORMIDOLIDE A 67 5. Introduction 67 5.1. Isolation and biological activity of phormidolide A 67 5.2. Structural and stereochemical determination of phormidolide A 68 5.2.1. Relative configuration of C18-C33 region of phormidolide A 69 5.2.2. Relative and absolute configuration of C1-C18 region of phormidolide A 70 5.2.3. The biosynthesis of phormidolide A and its stereochemical implications 72 5.3. Related congeners to phormidolide A: oscillariolide and phormidolides B-D 77 5.4. Previous synthetic efforts towards congeners of phormidolide A 80 viii 5.4.1. Álvarez’s synthesis of the macrolactone region in phormidolides B-D 80 5.4.2. Álvarez’s approach towards the side chain of the phormidolides 83 5.4.3. Attempted endgame for phormidolide C and D as reported by Álvarez 85 5.5. Phormidolide A: a summary 87 6. Results and Discussion 89 6.1. Overview of initial synthetic plan 89 6.2. Synthesis of the C18-C24 fragment 91 6.2.1.