Development of chemical probes for intracellular nucleotide delivery, profiling of the metabolic fate(s) of nucleoside monoester phosphoramidates, and a nucleotide mimetic inhibitor of eIF4E

Abstract

Significant progress has been made towards the development of phosphate prodrugs for intracellular delivery of monophosphates. Such efforts led to the successful application of the aryloxy amino acid phosphoramidate (ProTide) strategy for development of sofosbuvir. Although widely successful, several drawbacks of the ProTide strategy limit its utility for delivery of significant levels of nucleotide analogs in tissues other than the liver. In order to broaden the utility of phosphate prodrugs, we have developed pronucleotide strategies that address the inefficiencies of the ProTide system. Chapter 2 describes the design and development of an anchimerically activated pronucleotide strategy, incorporating 2-(methylthio)ethyl and tryptamine as phosphate protecting moieties. The prodrug is activated by a sulfur mediated intramolecular cyclo-de-esterification reaction to yield a monoester phosphoramidate, which gets hydrolyzed by HINT1 to release a monophosphate. In a proof-of-concept application, we applied the pronucleotide strategy towards intracellular delivery of 7-Chlorophenoxyethyl guanosine monophosphate, as a chemical tool for translational control of protein synthesis. Furthermore, in Chapter 3 we provide another proof-of-concept application of the new pronucleotide strategy for intracellular delivery of 2´-C-β-Methyl guanosine monophosphate as an anti-Dengue virus (DENV) agent. In a related project, we sought to profile the protein interacting partners of nucleoside monoester phosphoramidates. Mapping the small molecule-protein interactome of nucleoside monoester phosphoramidates should help us decipher the mode of cellular uptake and identify other metabolizing enzymes of nucleoside monoester phosphoramidates (excluding HINT1). Chapter 4 outlines the design and synthesis of phosphoramidate-based photoaffinity probes as chemical tools for profiling the protein binding partners of nucleoside monoester phosphoramidates. The synthesized probes were utilized for in vitro proteomics studies in whole cell extracts (lysates) and in live cells. Finally, we describe the design and development of a nucleotide mimetic inhibitor of eIF4E in Chapter 5. As a proof-of-concept application, we employed a sulfamido alkyl moiety as a substitute for 5´-phosphate in the design of 5´-mRNA cap analog antagonists of eIF4E. We successfully synthesized a mimetic of 7-Chlorophenoxyethyl guanosine monophosphate and demonstrated that its binding potency to eIF4E is comparable to that of the parent nucleotide, with only a modest loss in binding potency.