The Design, Synthesis, and Biological Evaluation of Novel Prodrugs and Antiviral Agents for HIV and Other Chronic Viral Infections Open Access

Giesler, Kyle (Fall 2017)

Permanent URL: https://etd.library.emory.edu/concern/etds/sf268508b?locale=en
Published

Abstract

Drug delivery is a critical challenge that must be overcome to achieve therapeutic efficacy in vivo. Many drug discovery programs fail to identify targets with desirable absorption, distribution, metabolic, and excretion (ADME) profiles which severely limits their clinical prospect. The conjugation of a prodrug to a pharmacologically active agent provides an opportunity to overcome these limitations and significantly alter the pharmacological profile of the parent. With respect to nucleoside analogues, a large repertoire of prodrugs exists to improve their biological availability, however, many of these prodrugs generate toxic byproducts, experience inefficient cleavage, or are subject to premature degradation prior to delivery of the target. Herein, we have designed and synthesized novel lipid prodrugs for nucleoside analogues that significantly improve the antiviral activity of the parent, are stable in human plasma for 24 h and have the potential to achieve enhanced tissue distribution in vivo. Further, we prepared a series of promising acyclic nucleoside analogues for the treatment of chronic HIV-1 and are actively in the process of targeting other HIV proteins, particularly negative factor (Nef), to combat resistance and introduce novel therapies to market. 

Table of Contents

List of Illustrations

             Figures

             Tables

             Schemes

             List of Abbreviations

Chapter 1: Novel Lipid Prodrugs of Tenofovir: Design, Synthesis, and Biological Evaluation

1.1     Introduction 2

1.1.1     Nucleoside Analogues as Antiviral Drugs 4

1.1.2     Phosphorylation is Required for Metabolic Activation of NAs 5

1.1.3     Kinase Bypass Strategies: Phosphonates 8

1.1.4     Tenofovir and the Use of Prodrugs 9

1.1.5     Tenofovir Alafenamide (TAF) 11

1.1.6     CMX157 12

1.2    The Design of Novel Lipid TFV Conjugates 13

1.3    Synthesis of 1st Gen TFV Disulfide Conjugates 15

1.4    Biological Evaluation of 1st Gen TFV Disulfide Prodrug Conjugates 17

1.5    Stability Studies for our 1st Generation Conjugates 20

1.6    Probing the Mechanism of Cleavage 21

1.7    Second Generation Disulfide Conjugates 23

1.8    Revisiting Our 1st Generation Conjugates 26

1.9    What is the Disulfide Advantage? 28

1.10   Conclusions 30

1.11   Experimental Details 31

1.11.1    Anti-HIV Assay 31

1.11.2    Anti-HBV Assay 32

1.11.3    Cytotoxicity Studies 33

1.11.4    Stability Studies 33

1.11.5    Kinetic Studies 34

1.11.6    Chemical Synthesis and General Procedures 35

1.11.7    Synthesis and Characterization of Lipids 37

1.11.8    Synthesis and Characterization of TFV Conjugates 46

1.12   References 71

Chapter 2: Synthesis and Evaluation of Other Disulfide Prodrug Conjugates

2.1    Introduction 83

2.2    Synthesis of Phosphate Disulfide Conjugates 84

2.2.1     Preparation of Phosphoramidite Coupling Reagents 85

2.2.2     Lipid Conjugates of Nucleoside Analogue 2.1 86

2.2.3     Lipid Conjugates of Emtricitabine (FTC) 88

2.2.4     Lipid Conjugates of Nucleoside Analogue 2.2 89

2.2.5     Lipid Conjugates of AFV  90

2.3    Biological Evaluation of Phosphate Lipid Prodrugs 90

2.4    Experimental Details 92

2.4.1     Anti-HIV Assay 92

2.4.2     Anti-HBV Assay 93

2.4.3     Anti-HCV Assay 94

2.4.4     Cytotoxicity Studies 95

2.4.5     Chemical Synthesis and General Procedures 95

2.4.6     Crystallographic Data 108

2.5    References 110

Chapter 3: A Green and Expeditious Synthesis of Acyclic Thioaminal Nucleoside Analogues from Purine and Pyrimidine Hemiaminals

3.1    Introduction 112

3.2    Synthesis and Substrate Scope 112

3.3    Biological Evaluation 117

3.4    The Pursuit for More Interesting Analogues 118

3.5    Conclusions 120

3.6    Experimental Details 121

3.6.1     Anti-HIV Assay 121

3.6.2     Anti-HBV Assay 122

3.6.3     Anti-HSV Assay 123

3.6.4     Cytotoxicity Studies 123

3.6.5     Chemical Synthesis and General Procedures 123

3.7    Crystallographic Data 140

3.8    References 148

Chapter 4: Towards the Design and Synthesis of Novel HIV-1 Nef Inhibitors

4.1    Introduction 150

4.1.1     Structure of HIV-1 Nef 152

4.1.2     Nef and HIV-1 Pathogenesis 152

4.1.3     Mechanistic Details of Nef-Mediated MHC-I Down-regulation 153

4.2    HTVS Efforts to Identify Novel Nef Inhibitors 156

4.3    In Silico Design of Novel α-Helical Mimetics 159

4.4    Retrosynthetic Analysis of Compound 4.4 161

4.4.1     Synthesis of the R1, R2, and R3 Fragments 161

4.4.2     Towards the Synthesis of Compound 4.4 163

4.5    Conclusions 164

4.6    Experimental Details 165

4.6.1     Computational Analysis 165

4.6.2     Chemical Synthesis 168

4.6.3     Crystallographic Data 181

4.7    References 186

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