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Doctoral Dissertation Template UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE ADVANCEMENT OF NATURAL PRODUCTS: OPTIMIZATION OF INSTRUMENTATION AND EXAMPLES OF THEIR APPLICATION TO THE ISOLATION OF NEW COMPOUNDS A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By ALLISON OLIVIA MATTES Norman, Oklahoma 2019 ADVANCEMENT OF NATURAL PRODUCTS: OPTIMIZATION OF INSTRUMENTATION AND EXAMPLES OF THEIR APPLICATION TO THE ISOLATION OF NEW COMPOUNDS A DISSERTATION APPROVED FOR THE DEPARTMENT OF CHEMISTRY AND BIOCHEMISTRY BY Dr. Robert Cichewicz, Chair Dr. Bradley Stevenson Dr. Daniel Glatzhofer Dr. Indrajeet Sharma Dr. Zhibo Yang © Copyright by ALLISON OLIVIA MATTES 2019 All Rights Reserved. To friends, family, mentors, and peers. iv Acknowledgements First and foremost, I must acknowledge Dr. Cichewicz for the mentorship and patience of helping me develop my skills. In chapter 3, edits and mentorship was also completed with the aid of Dr. David Russell and Dr. Sarah Robinson while at an internship at Genetech in San Francisco, CA. In chapter 4, the “chemical zoo” team tirelessly worked on all the soil samples to isolate, purify, extract, and sequence each fungus. Most notable of these coming from the work of Sara Helff and Carolyn Le. Jarod King completed all assay work on both the small scale isolation for initial identification as well as the pure compound MICs. In chapter 5, the isolation, purification, and identification of Sphecaloma were completed by the endophyte team led by Dr. Shikha Srivastava and the initial chemical extraction of the fungus, initial isolation of the elsinochromes and the isolation of persephacin A were completed by Dr. Saiket Haldar. Structure elucidation was completed in conjunction with both Dr. Saiket Haldar and Dr. Lin Du. Both in vitro and in vivo assays reported here were completed by Dr. Shikha Srivastava. All NMR data for chapters 4 and 5 was collected using instruments maintained by Dr. Susan Nimmo and her guidance and training on the instruments were essential to this work. v Table of Contents Acknowledgements ........................................................................................................... v List of Tables ................................................................................................................... xi List of Figures ................................................................................................................. xii Abstract ......................................................................................................................... xvii Chapter 1: Introduction ..................................................................................................... 1 1.1 What is a Natural Product? ................................................................................... 1 1.2 Historic Examples of Natural Products and Their Users ...................................... 2 1.2.1 Ancient Times to Renaissance ..................................................................... 2 1.3 Advancements in the 19th-20th Centuries ........................................................ 4 1.3.1 Pitfalls in Extracts to Market ....................................................................... 6 1.3.2 The Debate of Rational Design Versus Natural Products ............................ 7 1.3.3 Prospects for the Future ............................................................................... 8 1.3.4 Summary and Relevance to Dissertation ................................................... 11 Chapter 2: Hypothesis and Chapter Overviews .............................................................. 13 2.1 Introduction ......................................................................................................... 13 2.2 Hypothesis........................................................................................................... 13 2.2 Chapter 3. Applications of 19F Quantitative NMR to Pharmaceutical Analysis 14 2.3 Chapter 4. Asteltoxin G Is a Selective Toxin of Pancreatic Cancer Line Spheroids While Preserving Normal Fibroblasts and Normal Pancreas Spheroids. ..... 14 2.4 Chapter 5. Isolation of Cyclic Peptide ................................................................ 15 2.5 Other Noteworthy Contributions ........................................................................ 16 Chapter 3: Improving Development of Natural Products with 19F NMR ....................... 17 vi 3.1: Abstract .............................................................................................................. 17 3.2: Acknowledgements ............................................................................................ 17 3.3 Introduction ......................................................................................................... 17 3.4 Results and Discussion ....................................................................................... 21 3.4.1 Acquiring Quantitative 19F NMR Spectra - T1 Relaxation ....................... 21 3.4.2 Acquiring Quantitative 19F NMR Spectra - Tip Angle .............................. 22 3.4.3 Acquiring Quantitative 19F NMR Spectra - Acquisition Time .................. 22 3.4.4 Acquiring Quantitative 19F NMR Spectra - Excitation Bandwidth ........... 23 3.4.5 Acquiring Quantitative 19F NMR Spectra - Signal to Noise ...................... 24 3.4.6 Acquiring Quantitative 19F NMR Spectra - Number of Transients ........... 25 3.4.7 Processing Quantitative 19F NMR Spectra - Apodization ......................... 26 3.4.8 Processing Quantitative 19F NMR Spectra - Fourier Number ................... 26 3.4.9 Processing Quantitative 19F NMR Spectra - Data Reduction .................... 28 3.4.10 Processing Quantitative 19F NMR Spectra - Extracting Peak Intensities 28 3.4.11 Conversion of Signal Intensity to Concentration - Internal Standard Versus Absolute Intensity ................................................................................... 29 3.3.12 Implementation of Absolute 19F qNMR Method ..................................... 30 3.4 Conclusions ......................................................................................................... 33 Chapter 4: Isolation of Asteltoxin Derivative ................................................................. 35 4.1 Abstract ............................................................................................................... 35 4.2 Acknowledgements ............................................................................................. 35 4.3 Introduction ......................................................................................................... 36 4.4 Results and Discussion: ...................................................................................... 39 vii 4.4.1 Screenings .................................................................................................. 39 4.4.2 Compound Identification and Structure Elucidation ................................. 40 4.4.3 Pure Compound Assays ............................................................................. 50 4.4.4 Stability of Compounds and Their Activity ............................................... 62 4.5 Conclusion: ......................................................................................................... 63 4.6 Experimental: ...................................................................................................... 64 4.6.1 Small Scale Screening of Soil Samples ..................................................... 64 4.6.2 Large Scale Regrow of Small Scale Hit .................................................... 64 4.6.3 Fungal Isolation and Identification ............................................................ 65 4.6.4 Compound Isolation ................................................................................... 65 4.6.5 Calculation for Absolute Configuration of Asteltoxin G ........................... 66 4.6.7 Monolayer Cytotoxicity and Selectivity Assays ........................................ 66 4.6.8 Spheroid Cytotoxicity and Selectivity Assays ........................................... 67 4.6.9 Compound Degradations Study ................................................................. 67 Chapter 5: Antifungal Cyclic Peptide from Sphaceloma corylii .................................... 67 5.1 Abstract ............................................................................................................... 67 5.2 Acknowledgements ............................................................................................. 68 5.3 Introduction ......................................................................................................... 69 5.4 Results and Discussion ....................................................................................... 71 5.4.1 Selection and Identification of Isolate ....................................................... 71 5.4.2 Compound Isolation and Structure Determination .................................... 72 5.4.3 Media Optimization and Optimized Isolation ............................................ 85 5.4.4 Bioactivity .................................................................................................. 90 viii 5.4.5 Systemicity and Infiltration Studies ........................................................... 92 5.5 Conclusion .......................................................................................................... 95
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