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Combating the Rise of Antimicrobial Resistance: Permeation and Efflux Multiparameter Optimization and a Divergent Total Synthesis of Streptothricin F

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Combating the Rise of Antimicrobial Resistance: Permeation and Efflux Multiparameter Optimization and a Divergent Total Synthesis of Streptothricin F Combating the Rise of Antimicrobial Resistance: Permeation and Efflux Multiparameter Optimization and A Divergent Total Synthesis of Streptothricin F by Matthew G. Dowgiallo B.S. in Chemistry, Le Moyne College A dissertation submitted to The Faculty of the College of Science of Northeastern University in partial fulfillment of the requirements for the degree of Doctor of Philosophy July 31st, 2020 Dissertation directed by Roman Manetsch Associate Professor of Chemistry and Chemical Biology & Pharmaceutical Sciences 1 Dedication To my mother, Eileen Boron Haley, my stepfather Thomas Haley (June 19, 1942-May 26, 2020), my father Glenn Dowgiallo, my stepmother Chery Johnson Dowgiallo, my sister Meghan Dowgiallo, my nephew Grant Dowgiallo, my grandparents Walter and Toni Dowgiallo and my wonderful bride-to-be, Mallory Munro for your love and support. Thank you for bringing joy to my life and always providing me with a source of optimism. 2 Acknowledgements I am extremely appreciative to my mentor and friend, Dr. Roman Manetsch for providing me with the opportunity to pursue my dream to synthesize a complex natural product. The tremendous guidance and trust I received from Roman throughout the years have provided me with the confidence to excel inside and outside of the laboratory setting. Roman has provided me with numerous opportunities to present and learn from prestigious symposiums in the Northeast and across the country, for which I am incredibly grateful. Thank you so much Roman for demonstrating great patience and wisdom in guiding me towards the scientist I have become today. To my committee members, thank you for your unwavering support and critical supervision. Dr. Michael Pollastri, watching you take initiative and provide consistency as our department has changed over the past years has been inspirational. Your willingness to lead and dedication to research in the face of great adversity are lessons I plan to carry into my professional career. Dr. George O’Doherty, thank you for challenging me to not settle for complacency in my research efforts. I have often enjoyed your insightful criticism across the many meetings and talks at Northeastern and beyond, and you have taught me to be a more meticulous researcher. Dr. James Kirby, thank you for believing in the long-ignored activity among the streptothricins and trusting our group with the awesome synthetic challenges accompanying the compound class. To current and former members of the Roman Family, thank you for always listening to my roadblocks throughout synthetic endeavors as well as balancing all the joys of living in the lab together. To Dr. Cynthia Lichorowic and Dr. Iredia Iyamu, thank you for your careful instruction and persistence while I transitioned to my new home in the Manetsch Lab. Thank you to Dr. Fabian Brockmeyer for demonstrating a relentless work ethic and entertaining me with your celebrations while watching Werder Bremen soccer. To Dr. Abdul Shaik, thank you for sharing invaluable 3 laboratory techniques and good lessons in relational dynamics. Thank you, Dr. Prakash Parvatkar, for bringing a fun tradition of singing among the group and cultivating a culture of appreciation for everyone. Thank you, Dr. Chungsik Kim, for encouraging me to have confidence in myself and pursue curiosity in my studies as well as setting an example towards building a wonderful, loving family. Alicia Wager, thank you for reminding me of the excitement and challenges that come with being a first-year graduate student. Thank you, Lili Huang for your kind conversations and the amusement that accompanies our mutual appreciation of cute dogs and cats. Ami Asakawa, thank you for taking the time to explain biology questions associated with my project as well as your precious connections to computer savvy friends and family. Brandon Miller, your enthusiasm and determination to achieve were essential to the vitality of the streptothricin project. I am so grateful for your leadership and willingness to take on responsibility both within the scope of the project and across countless lab duties. Thank you to Minte Kassu, your contributions to the streptothricin project towards investigating the synthesis of β-lysine were vital and completion of the total synthesis and would not have been possible without your strong work ethic. To my dear friend David Zhao, I am so appreciative to have studied alongside you throughout this process. You have been a role model for me in holding yourself responsible for delivering the best quality of work in both your teaching and laboratory results. Thank you to our collaborators with Beth Israel Deaconess Medical Center / Harvard Medical School Dr. Kenneth P. Smith and Dr. Lucius Chiaraviglio for your patience while we pursued the synthesis and isolation of streptothricins as well as your rapid response when compounds were ready. A special thank you to Frank Fronczek from LSU for the crystal support throughout the course of synthesizing streptothricin F intermediates. To our collaborators Dr. Jeffery N. Agar and Dr. Daniel P. Donnelly, thank you for giving me the opportunity to become a 4 part of the groundbreaking work from your lab. To Sue Abbatiello, thank you for your help in obtaining HRMS data while managing your myriad of projects. To the NMR staff at Northeastern, I am incredibly appreciative for your mentorship and assistance. Brian D’Amico, thank you for enforcing the NMR scheduling policies and ensuring accessibility was fair to all users. Jason Guo, thank you for transforming the NMR facility into a safe, modern space for the university and especially for assisting with final data collection. To Dr. Roger Kautz (July 24, 1958-May 27, 2017), thank you so much for your thought-provoking conversation and kindness while teaching me the secrets of Varian. I am so lucky to have studied within the nurturing, stimulating atmosphere you provided to rising graduate students. To my peers, thank you for your guidance and friendship from the beginning. Dr. Andrew Spaulding, you were the first face I met when coming to Northeastern for recruitment weekend, and I am so grateful that I got to learn from you during our time in the Aggen group. Thank you for providing me with advice to become the best version of myself both inside and outside of this world. Dr. Westley Tear, thank you for keeping me accountable for staying active, at least in the early days, as well as your camaraderie throughout the course of our research journey I would like to thank undergraduate researchers Fabiola Caban Bravo, Loren Po, Andrew Fetigan, Clarissa Santori and Gian-Marco Rossi for helping me explore areas of my projects with fresh, new perspectives and providing me with extra sets of hands. To my teammates on the ultimate frisbee field both with the Huskies and Nerd Alert, thank you for providing me with a healthy distraction from my work. The peace of mind I have received from chasing plastic has undoubtedly contributed towards my well-being over the last 6 years. To my roommates Dave Reppucci, Allie Hung and Calvin Marie, thank you for a loving, relaxing and entertaining home life in Camberville. 5 Abstract of Dissertation The emergence of antimicrobial resistance is a constant threat in the scientific community. As multidrug resistant organisms approach pan-resistance, Carbapenem-resistant Enterobacteriaceae (CRE), Acinetobacter baumannii, and Pseudomonas aeruginosa have been categorized as top antimicrobial resistance threats by the Center for Disease Control and Prevention along with the World Health Organization. Unfortunately, the rate of antimicrobial drug discovery and development has drastically slowed since the 1950s with only three new classes of antimicrobials approved by the Food and Drug Administration in the past two decades. Our research efforts aim to combat the rise of antibiotic resistance through two unique strategies: enhancing the clinical utility of a safe and effective medicine towards extensively resistant organisms as well as tuning the selectivity of a highly potent antimicrobial through the development of a novel total synthesis designed to enable rapid analogue generation. Chapter 2 of this dissertation explores the use of potentiators to strengthen the activity of meropenem, a commonly administered carbapenem antibiotic, against CRE. We performed a high- throughput screen (HTS) of possible adjunctives to identify a hit series exhibiting synergistic activity alongside meropenem. HTS downselection featured a cheminformatics approach where prioritization of compounds targeted physicochemical properties optimized for Gram-negative bacterial cell penetration and avoidance of extracellular efflux. Chapter 3 of this dissertation describes a diversity-oriented total synthesis of streptothricin F (ST-F), an aminoglycoside-like natural product with broad-spectrum antimicrobial activity. Through a divergent total synthesis, ST-F was synthesized over 35 total steps and 0.0040% overall yield. We hope to derivatize ST-F to tune its selectivity and maintain or even improve its excellent antimicrobial effect, while widening its therapeutic window through an enhanced safety profile. 6 Table of Contents Dedication .............................................................................................................................................. 2 Acknowledgements ................................................................................................................................ 3 Abstract of Dissertation ........................................................................................................................
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