A New Aminoglycoside Antibiotic Effective Against NpmA-Expressing Escherichia coli

Abstract

Dissertation Advisor: Professor Andrew G. Myers Matthew Peszko

A New Aminoglycoside Antibiotic Effective Against NpmA-Expressing Escherichia coli

Abstract

Aminoglycoside antibiotics (AGAs) are pseudo-oligosaccharide natural products that have provided effective treatments for life-threatening bacterial infections for over seventy years. Decades of clinical use has resulted in the widespread proliferation of aminoglycoside resistance genes which, when coupled with longstanding toxicity challenges, limits the utility of aminoglycosides in a clinical setting. While the most common mechanism of resistance to AGAs comes in the form of aminoglycoside modifying enzymes (AMEs), ribosomal RNA methyltransferases (RMTs) that directly modify the AGA binding site are increasingly concerning as they frequently coincide on mobile genetic elements containing resistance genes to other antibiotic classes. In 2003, a novel plasmid-mediated aminoglycoside resistance methyltransferase (NpmA) was identified in a clinical isolate of Escherichia coli that provides extensive resistance to the entire class of AGAs. As of starting this research, no AGA is reported to overcome this resistance mechanism. This dissertation presents synthetic advancements and exploratory studies towards next-generation aminoglycoside antibiotics seeking to overcome RMT mechanisms of resistance. In chapter 1, I discuss AGAs as a natural product class and their history. I review mechanisms of action, the basis for antibacterial activity, as well as the biosynthetic origins. I additionally discuss the basis for mammalian toxicity to AGAs and for bacterial resistance, and modern strategies for circumventing both. In chapter 2, I provide a history of semisynthetic modifications to aminoglycosides. With particular focus on modifications that have translated to clinical efficacy and overcoming resistance, I review the most promising changes to the aminoglycoside scaffold in designing next-generation AGA therapeutics. In chapter 3, I present my efforts to prepare fully synthetic 2-deoxystreptamine (2-DOS) as a protected component for an improved synthesis of next-generation AGAs. I describe a key design strategy hinging on intramolecular aldol reaction to establish contiguous equatorial stereocenters during the cyclohexane annulation. Several approaches were examined to access the desired aldolization intermediate to no avail: a tandem addition to a γ,δ-epoxyenone, a stereoselective union between a functionalized organometallic nucleophile and an optically active cyanohydrin, and a linear approach utilizing Vince’s lactam as a readily differentiated chiral pool building block. Previous syntheses are also discussed. In chapter 4, I describe the design and synthesis of C5’-modified AGAs to counter NpmA resistance. Two synthetic strategies are explored: a partially synthetic strategy featuring the union of a synthetic ring I glycosyl donor with a semisynthetic ring II-IV acceptor, and a semisynthetic strategy providing access to a diversifiable C6’-carboxylic acid. Key transformations include a diastereoselective Corey-Bakshi-Shibata reduction of a glutamate-derived aryl ketone to directly yield a C5-aryl lactol, the glycosylation between a C5-phenyl deoxyglycoside donor and pseudotrisaccharide glycosyl acceptors, and the decarboxylative elimination of an aminoglycoside β-hydroxy acid to yield a 4’-deoxypentenoside. Synthetic pitfalls are simultaneously discussed as potential avenues for future AGA semisynthesis endeavors. With this chemistry, novel AGAs were prepared and evaluated against NpmA-expressing bacteria. For chapter 5, as part of an unrelated research project, I present the mechanism proposed for the transformation of cyclopentanone to a dienoic acid and reveal it to be in error. I show that carbon 11 derives not from dimethylsulfoxide as proposed, but from dichloromethane present in the “quenching” solution. The intermediacy of an α-chloromethyl ketone and its subsequent fragmentation in the presence of hydroxide ion is supported by additional experiments, and by extensive literature precedent.