Synthesis of 2'-Fluoro-2',3'-Dideoxynucleosides as Inhibitors of Hepatitis C Virus RNA-Dependent RNA Polymerase; Synthesis of Cyclobutyl Phosphonate and Phosphoramidate Prodrugs for Inhibition of HIV Reverse Transcriptase Open Access

Neuman, Annette Welty (2013)

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Part I of this dissertation describes the synthesis and biological activity of novel 2'-fluoro-2',3'-dideoxynucleoside analogs. These analogs were synthesized via lactone fluorination with NFSI, followed by nucleobase coupling under Vorbrüggen or SN2 conditions. These compounds were inactive in cell-based assays. While this result may indicate that the corresponding nucleoside triphosphates are not effective inhibitors of the viral polymerases, it may also be the case that the nucleosides are not converted to the triphosphates due to a lack of recognition by cellular kinases. Therefore, nucleoside triphosphates were evaluated in cell-free assays, revealing a clear structure-activity relationship. These results indicate that while a 2'-fluoro substituent is an effective isostere for the 2'-hydroxy moiety, removal of the 3'-hydroxy group leads to loss of activity against viral polymerases.

Part II of this dissertation describes efforts toward the synthesis of cyclobutyl nucleoside phosphonate and phosphonamidate prodrugs. The nucleoside analogs were synthesized via formal [3+1] cycloaddition of protected 1,3-dibromo-2-propanol and methyl methylthiomethyl sulfoxide and subsequent nucleobase coupling under SN2 conditions. Various conditions were screened for preparation of the lipophilic phosphonate prodrug. This compound was ultimately prepared via phosphonodichloridate activation. Purification was attempted via several methods but proved unsuccessful. The phosphonamidate prodrug was prepared by a one-pot procedure. This compound was not able to be purified.

Table of Contents

Table of Contents

Part I: Synthesis of 2'-Fluoro-2',3'-Dideoxynucleosides as Inhibitors of Hepatitis C Virus RNA-Dependent RNA Polymerase

1.1 Statement of Purpose 1

1.2 Introduction 3

1.2.1 Hepatitis C Virus 3

1.2.2 RNA Viruses 4

1.2.3 Life Cycle of HCV 5

1.2.4 FDA-Approved Anti-HCV Treatments 8

1.2.5 RNA-Dependent RNA Polymerase 11

1.2.6 Nucleoside Analogs in Antiviral Therapy 14

1.2.7 Mechanisms of Resistance 18

1.3 Background 19

1.3.1 Obligate and Non-Obligate Chain Terminators 19

1.3.2 Fluorinated Nucleoside Analogs 21

1.3.3 Nucleoside Analogs Containing Non-natural Purine Bases 32

1.3.4 Nucleobase Coupling Methods 34

1.3.5 N7 vs. N9 Regioselectivity 40

1.3.6 Phosphoramidate Prodrugs 41

1.3.7 Synthesis and Antiviral Activity of 2'-Fluoro-2',3'-Dideoxynucleosides 45

1.4 Results and Discussion 48

1.4.1 Synthesis of 2-Fluoro-2',3'-Dideoxycytidine 48

1.4.2 Synthesis of 7-Deaza-2'-Fluoro-2',3'-Dideoxyguanosine 50

1.4.3 Synthesis of 2'-Fluoro-2',3'-Dideoxyguanosine 57

1.4.4 Biological Activity of Synthesized Compounds 63

1.5 Conclusion 69

1.6 Experimental 70

1.7 References 130

Part II: Synthesis of Cyclobutyl Phosphonate and Phosphoramidate Prodrugs for Inhibition of HIV Reverse Transcriptase

2.1 Statement of Purpose 142 2.2 Introduction 144

2.2.1 Current Status of the HIV/AIDS Pandemic 144

2.2.2 The HIV Replication Cycle 145

2.2.3 FDA-Approved Antiretroviral Drugs 148

2.2.4 HIV Reverse Transcriptase 153

2.2.5 RTI Mechanism of Action 155

2.2.6 Mechanisms of HIV Resistance to NRTIs 157

2.2.7 Oxathiolane Nucleoside Analogs 158

2.2.8 Phosphorylation of Nucleoside Analogs 159

2.3 Background 161

2.3.1 Carbocyclic Oxetanocins as Nucleoside Analogs 161

2.3.2 Synthesis of Cyclobutyl Nucleoside Analogs 161

2.3.3 Coupling of Nucleobases with Cyclobutyl Sugar Analogs 163

2.3.4 Nucleoside Phosphonates as Prodrugs 165

2.3.5 Synthesis of Nucleoside Phosphonate Prodrugs 168

2.3.6 Synthesis of Nucleoside Phosphonamidate Prodrugs 172

2.3.7 Synthesis and Anti-HIV Activity of Cyclobutyl Nucleoside Analogs and Prodrugs 173

2.4 Results and Discussion 178

2.4.1 Synthesis of Cyclobutyl Adenine Phosphonate Analogs 178

2.4.2 Synthesis of Cyclobutyl Adenine Phosphonamidate Analogs 185

2.5 Conclusion 186 2.6 Experimental 187 2.7 References 208 Appendix I 214

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