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Human pathogens from the Caliciviridae and Hepeviridae families impose a significant health and economic burden on our global society. Despite the substantial toll caused by viruses such as human norovirus, human sapovirus and hepatitis E virus (HEV), we currently have no specific antivirals available to combat these pathogens. The current therapies prescribed for chronic HEV infection are poorly tolerated and can result in treatment failure. Similarly, despite a significant body of research into identifying antivirals and vaccines for controlling human norovirus infections, none have achieved clinical approval. Safe and effective antivirals would be beneficial for the treatment of chronic norovirus and HEV infections and for prophylactic applications during outbreak and epidemic situations. The viral RNA-dependent RNA polymerase (RdRp) is a highly-conserved enzyme that is essential for viral replication and represents a prime antiviral target. Using in vitro polymerase activity assays and viral and replicon cell culture systems, this study describes the identification of broad-spectrum antivirals for further development against calicivirus pathogens and HEV. This study includes the first report of a class of hepatitis C virus (HCV) non-nucleoside inhibitors (NNIs) with cross-family antiviral activity, that demonstrated broad-spectrum inhibition of several calicivirus RdRps. A highly-conserved NNI binding pocket common to RdRps across the Caliciviridae was also identified, which represents a prime target for de novo antiviral design. A novel chemical scaffold is described with low micromolar activity against the human norovirus RdRp, that also demonstrated broad-spectrum activity against RdRps from across three Caliciviridae genera. Finally, an examination of antivirals previously developed against other viruses revealed three compounds with potent antiviral activity against replication of the HEV genotype 1 replicon, demonstrating that repurposing antivirals could provide an accelerated platform for HEV antiviral discovery. In conclusion, this thesis identified several broad-spectrum antivirals for further development against human pathogens such as HEV and norovirus, and a highly-conserved binding pocket for targeted norovirus antiviral design.

Abstract: The Stevens [1,2]-rearrangement of onium ylides has been employed as a valuable synthetic method to construct new C-C bonds. Oxonium ylides are reactive intermediates that undergo facile Stevens rearrangement under mild conditions. In the last several decades, the Stevens rearrangement of oxonium ylides has been extensively employed in synthesis of important core structures, heterocycles and natural products. Despite significant synthetic applications of the Stevens [1,2]-rearrangement, its mechanism has remained ambiguous. Different mechanistic pathways including the presence of either radical or zwitterionic intermediates have been proposed based on the product distribution or CIDNP spectroscopy. However, these mechanistic studies have mostly been performed on ammonium ylides. In Chapter 1, I will describe the Stevens rearrangement of cyclic oxonium ylides and its application in synthetic chemistry. I will also discuss mechanistic studies that have been performed on the Stevens rearrangement of the onium ylides since its discovery. It is known that cyclic oxonium ylides can undergo ring contraction via endocyclic [1,2]-shift. In Chapter 2, I demonstrate the ability of the cyclopropylcarbinyl migrating group to generate cyclobutanones through a [1,2]-shift. The generality of the cylocpropylcarbinyl migration will be demonstrated in this chapter. I will also discuss the importance of strained four membered rings in natural products and synthetic chemistry. [1,2]-Migration of the cyclopropylmethyl group provides more strained structures possessing both cyclobutanone and intact cyclopropane moieties. The presence of the intact cyclopropane in the structure of the cyclobutanones resulting from the Stevens rearrangement, delivers an important message related to the reactive intermediates involved in the reaction mechanism. A fast cyclopropane ring opening is expected in the case of radical intermediates. In Chapter 3, the nature of the reactive intermediates will be described, employing ultrafast radical clocks as differentiation tools to determine the nature of the actual intermediates present during the Stevens rearrangement. The last chapter will describe the design and synthesis of broad-spectrum antivirals which inhibit viral entry. Inspired by the antiviral activity of the epigallocatechin gallate (EGCG), an extracted catechin from green tea, against a large group of unrelated viruses, we designed and synthesized a library of molecules possessing polyphenolic moieties which have been known to be the active site in the EGCG viral inhibition. The effect of the central scaffolds as well as the importance of the functional groups and the number of the polyphenolic structures will be discussed.