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Developing Biocatalytic Processes for the Synthesis of Nitro Compounds

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Developing Biocatalytic Processes for the Synthesis of Nitro Compounds DEVELOPING BIOCATALYTIC PROCESSES FOR THE SYNTHESIS OF NITRO COMPOUNDS By RAN ZUO A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2018 © 2018 Ran Zuo To my mother, my father and my wife ACKNOWLEDGMENTS First, I would like to thank my committee chair, Dr. Yousong Ding, for his support and direction through these five years in graduate school. I appreciate his immense support, guidance and patience throughout my graduate studies. His constant advice and encouragement were a tremendous source of inspiration for me to complete my dissertation. I would also like to extend my appreciation to Dr. Robert Huigens III, Dr. Hendrik Luesch, Dr. Jon Stewart, and Dr. Steven Bruner for graciously agreeing to be members of my dissertation committee. I am grateful for their advice, encouragement and constructive comments on my research over the past several years. I would also like to thank our collaborators: Dr. Rosemary Loria, Dr. Yucheng Zhang and Dr. Jose Huguet-Tapia, for providing Streptomyces strains and lending their expertise in the thaxtomin biosynthesis and extraction; Dr. Steven Bruner and Dr. Matt Burg for the help in the TxtE crystallization; Dr. Robert Huigens III, Ms. Yasmeen Abouelhassan, Dr. Aaron Garrison and Dr. Akash Basak for providing a collection of antimicrobial compounds and guidance in the anti-biofilm assay. I thank them for their support and fruitful discussions. I also thank the former and current staff of the Medicinal Chemistry Department - Ms. Nancy Burgos, Mr. David Jenkins and Ms. Jan Kallman - for their support during my graduate study. I am also grateful to Ms. Laura Faux for providing LC-MS training and troubleshooting. Finally, I must thank the former and current members in the Ding research lab for their assistance and friendship. I thank Dr. Guang Yang for expanding my repertoire of molecular biology, Dr. Yu Sha for the help in the mass spectrum analysis, Mr. Yi Zhang 4 and Mr. Guangde Jiang for the help in the NMR analysis, and Ms. Peilan Zhang for the help in the bioassay. I appreciate the technical expertise that everyone has shared as well as the insightful discussions we had. I hope our friendships continue for the years to come. 5 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ............................................................................................................ 9 LIST OF FIGURES ........................................................................................................ 10 LIST OF ABBREVIATIONS ........................................................................................... 13 ABSTRACT ................................................................................................................... 15 CHAPTER 1 INTRODUCTION TO BIOCATALYSIS.................................................................... 17 Biocatalysis: a Practical Alternative to Traditional Catalysis in Chemical Synthesis ............................................................................................................. 17 Methodology Development in the Engineering of Biocatalysts ............................... 19 Directed Evolution ............................................................................................ 19 Rational Design ................................................................................................ 22 Semi-rational Design ........................................................................................ 23 De novo Design ................................................................................................ 25 Whole-cell Based Biocatalysis ................................................................................ 26 Cytochromes P450 as Biocatalysts ........................................................................ 27 Generalized Catalytic Cycle of P450 ................................................................ 28 Electron Transfer Partners of P450s ................................................................ 29 Development and Applications of P450s as Biocatalysts ................................. 30 Developing Biocatalytic Processes for the Nitration Reaction ................................. 33 Chemical Nitration Methods ............................................................................. 35 Natural Nitration Strategies .............................................................................. 36 Putative Catalytic Cycle of TxtE in Aromatic Nitration ...................................... 38 Research Aims ....................................................................................................... 38 2 CREATION AND BIOCHEMICAL ANALYSIS OF AN ARTIFICIAL SELF- SUFFICIENT CYTOCHROME P450 DIRECTLY NITRATES TRYPTOPHAN* ...... 52 Introduction ............................................................................................................. 52 Results .................................................................................................................... 56 Preparation of Self-sufficient TxtE Variants ...................................................... 56 Catalytic Activity of Fusion Enzymes ................................................................ 57 Biochemical Characterization of TxtE and TxtE-BM3R .................................... 58 Design and Production of Chimeric TxtE-BM3R Variants ................................ 59 Nitration Performance of Chimeric TxtE-BM3R Variants .................................. 61 Conclusion and Discussion ..................................................................................... 63 Methods and Materials............................................................................................ 65 6 General Chemicals, DNA sub-cloning, and Bacterial Strains ........................... 65 Construction of Self-sufficient TxtE Variants .................................................... 66 Construction of TxtE-BM3R Variants ................................................................ 67 Heterologous Expression and Purification of Recombinant Proteins ................ 68 Analytical HPLC Analysis ................................................................................. 68 Biochemical Characterization of Self-sufficient TxtE Variants .......................... 68 Spectral Analysis of Chimeric TxtE-BM3R Variants ......................................... 69 Catalytic Activities of Chimeric TxtE-BM3R Variants ........................................ 70 3 DEVELOPING TXTE AS NITRATION BIOCATALYSTS BY ENGINEERING ITS BINDING POCKET ................................................................................................. 85 Introduction ............................................................................................................. 85 Results .................................................................................................................... 86 Substrate Scope of TxtE and TB14 .................................................................. 86 Structural Characterization of TB14 Catalyzed Tryptophan Analogues Nitration Products .......................................................................................... 89 Structural Characterization of TB14 Catalyzed Styrene-analogues Conversion Products ..................................................................................... 94 Identification of Key Residues for Tailoring TB14 Substrate Scope ................. 95 Preparation and Functional Characterization of TB14 Binding Pocket Mutant Library ............................................................................................... 96 Substrate Scope of TB14 Variants ................................................................... 98 Conclusion and Discussion ..................................................................................... 99 Methods and Materials.......................................................................................... 102 General Chemicals, DNA Sub-cloning, and Bacterial Strains ......................... 102 Large-scale Enzymatic Synthesis of Nitrated Products .................................. 103 Analytical and Semi-preparative HPLC Analysis ............................................ 103 LC-MS and LC-MS/MS Analysis of Nitrated Products .................................... 104 NMR Analysis of Nitrated Tryptophan and Styrene Analogues ...................... 104 Marfey’s Derivatization ................................................................................... 105 4 DEVELOPING E. COLI CELL FACTORIES FOR THE PRODUCTION OF NITRO AROMATICS ............................................................................................ 136 Introduction ........................................................................................................... 136 Results .................................................................................................................. 138 Creation of E. coli Strain for the Whole Cell Nitration Reaction ...................... 138 Optimization of Heterologous Enzyme Expression ......................................... 140 Optimization of Fermentation Conditions ....................................................... 140 Production of Nitrated Tryptophan Analogues by Whole Cell Nitration System .......................................................................................................
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