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Thesis Format

Alternative Format

Degree

Master of Science

Program

Chemistry

Supervisor

Hudson, Robert H.E.

Abstract

Positive sense RNA (ribonucleic acid) viruses (+ssRNA) are the known causative agents of diseases throughout history. These includes Hepatitis C Virus (HCV), SARS-CoV, and recently SARS-CoV-2. RNA dependent RNA polymerase (RdRp), a critical enzyme in the life cycle of the virus, can be targeted by using nucleotide antivirals thus causing inhibition. Novel ribonucleotides antiviral agents that possess nucleobase modifications and a 5′-phosphoramidate prodrug moiety, referred to as a ProTide, have been synthesized. The ribonucleoside analogues were constructed by CuI catalyzed azide-alkyne cycloaddition chemistry (CuAAC), also referred to as ‘click’ chemistry. The synthetic route utilized 5-ethynylpyrimidines and azidoribofuranoses as CuI ‘click’ chemistry substrates. Once the nucleosides were appropriately protected, they were phosphorylated with a synthesized phosphoramidate reagent. The final ProTides was screened against SARS-CoV-2 for their inhibition of RdRp along with the evaluation of cytotoxicity showing low inhibition and no cytotoxicity.

Summary for Lay Audience

A common type of infectious virus that affects humans is known as positive sense viruses. These types of viruses enter a host cell and hijack the cell’s translational machinery to synthesize viral proteins that assemble into new viral particles (virions). This repeating process is costly to the cell’s health which ultimately causes cell death. Hepatitis C virus (HCV), West Nile virus and recently SARS-CoV-2 are amongst the viruses that cause severe symptoms which can lead to death of the infected individual. Antiviral targeting must be done at a crucial stage in the viral life cycle. The stage where viral RNA (ribonucleic acid) is replicated is referred to as transcription. This process is important since it is where the virus reproduces copies of its RNA for new virions. Inhibiting this with an antiviral can cause mutations within the viral proteome producing nonviable virions. In this study, novel antivirals were designed, specifically ribonucleotide (the building blocks of RNA) antivirals. To understand how these antivirals would interact with RdRp (RNA dependent RNA polymerase), the enzyme facilitating transcription, molecular docking simulations were performed. Ribonucleotides contain three components: ribofuranose sugar, a nucleobase, and a phosphate group. To induce antiviral activity, the nucleobases of these antivirals were modified. Nucleobases dictate the genetic code (A, C, G, U), straying away from these nucleobases can cause transcription to stop. The modified nucleobases were prepared using a variety of organic synthesis techniques. Then the modified nucleobases were attached to the ribofuranose using a synthetic technique called copper ‘click’ chemistry. The phosphate component itself was modified to a phosphoramidate, forming a ProTide (Prodrug NucleoTide). Prodrugs are a type of drug that are administered in an inactive form and are activated by body enzyme which is a common method in medicinal chemistry to aid in improving potency. Once these ProTides were synthesized, they were screened against SARS-CoV-2 learning that these antivirals were slightly inhibiting RdRp but not as well as was hoped; however, they did not show any cytotoxic effects. The next step is to screen the antivirals against other viral species.

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