New Drug Development for Known and Emerging Viruses E-Book

• Herausgeber: Wiley-VCH GmbH
• Kategorie: Wissenschaft und neue Technologien
• Serie: Methods and Principles in Medicinal Chemistry
• Sprache: Englisch

Seitenzahl: 1076

Veröffentlichungsjahr: 2021

Beschreibung

Discusses how to fight Ebola, SARS Corona, and other known or emerging human viruses by building on the successes in antiviral therapy of the past decades

Written by leading medicinal chemists from academia and industry, this book discusses the entire field of antiviral drug discovery and development from a medicinal chemistry perspective, focusing on antiviral drugs, targets, and viral disease mechanisms. It provides an outlook on emerging pathogens such as Ebola, Zika, West Nile, Lassa, and includes a chapter on SARS Coronoavirus-2 causing the present pandemic.

New Drug Development for Known and Emerging Viruses describes the discovery and development process for antiviral agents for different classes of viruses and targets based on the experiences from the nine human viruses for which approved drugs are on the market (HIV, HCV, Influenza, RSV, HBV, HPV, HCMV, HSV, and VZV). It covers the properties and potential of 20 classes of currently approved antivirals, including combination drugs, and looks at novel antiviral strategies against emerging viruses.

• Covers the entire field of antiviral drug discovery and development
• Addresses the need for antiviral drugs to combat major health threats such as Ebola, Zika, West Nile, and SARS Coronavirus-2
• Summarizes the successes of the past 15 years in developing ground-breaking medicines against 9 major human viruses, both from the medicinal chemistry and the pharmacological angle
• Discusses practical and strategic challenges in the drug discovery and development process, including screening technologies, latency, and toxicity issues

New Developments in Antiviral Drugs is an important book for medicinal chemists, pharmaceutical chemists, virologists, and epidemiologists, and will be of great interest to those in the ;pharmaceutical industry and public health agencies.

Leseprobe

Table of Contents

Cover

Title Page

Copyright

Preface

In Memoriam: Farah Elawar

Introduction

References

1 HIV—Disease Overview, Targets for Therapy and Open Issues

1.1 HIV—Disease Overview

1.2 Targets for Antiretroviral Therapy

1.3 Currently Open Issues in HIV/AIDS Research

References

2 Curing Hepatitis C with Direct-Acting Antiviral Therapy

2.1 Introduction

2.2 Tools to Enable Drug Discovery

2.3 Drug Discovery Targets

2.4 NS5B Polymerase Inhibitors

2.5 HCV NS3/4A Protease Inhibitors

2.6 HCV NS5A Inhibitors

2.7 The Evolution of DAA Combination Therapies

2.8 Conclusion

Acknowledgment

References

3 Antiviral Drugs Against Influenza Virus

3.1 The Influenza Virus

3.2 The Pathogenesis of Influenza

3.3 Influenza Drugs and Targets

3.4 Adamantanes and Derivatives

3.5 Neuraminidase Inhibitors

3.6 Polymerase-Inhibitors

3.7 Monoclonal Antibodies

3.8 Host-Targeting Candidates

References

4 Respiratory Syncytial Virus Immunoreactivity, Vaccine Development, and Therapeutics

4.1 Introduction

4.2 RSV Longevity, Immune Evasion, and the Role of IgA

4.3 The Impact of Immunoprophylaxis on the Health Burden of Respiratory Syncytial Virus

4.4 Distinct RSV Symptoms

4.5 History of RSV and Vaccine Development

4.6 New Developments in RSV Vaccine Development

4.7 Antivirals and Therapeutic Antibodies

4.8 Therapeutics for Treating Active RSV Infections (Table 4.1)

4.9 Drug Targets

4.10 Conclusions

References

5 Herpes Simplex Viruses

5.1 Introduction

5.2 Overview of the Viral Replication Cycle

5.3 Treatment of HSV Infections

5.4 Approved Anti-HSV Drugs

5.5 Anti-HSV Drugs in Advanced Development or Recently Entering the Market

5.6 HSV Resistance to Antiviral Drugs

5.7 HSV and Alzheimer's Disease

5.8 Conclusion

References

6 Antiviral Strategies Against the Human Cytomegalo Virus

6.1 The Need for Novel Drugs against CMV and Attempts of the Past

6.2 The Strategy for the Discovery of Letermovir

6.3 The Link between Preclinical Models and Clinical Efficacy

6.4 Clinical Experience

6.5 Other Potential Indications for Letermovir

6.6 Conclusions

References

7 Antiviral Targeting of the Complex Epstein Barr Virus Life Cycle

7.1 Disease Overview

7.2 Antiviral Strategies

7.3 Open Issues

Acknowledgements

References

8 Kaposi's Sarcoma-associated Herpesvirus—Antiviral Treatment

8.1 Introduction to Kaposi's Sarcoma-associated Herpesvirus (KSHV)

8.2 Epidemiological Considerations

8.3 Disease Overview

8.4 Antiviral Strategies

8.5 New Antiviral Strategies Against KSHV in Preclinical Development

References

9 Direct-Acting Antivirals for the Treatment of Chronic Hepatitis B Virus (HBV) Infection

9.1 Nucleos(t)ide Analog Reverse Transcriptase Inhibitors

9.2 HBV Entry Inhibitors

9.3 HBV Capsid Assembly Modulators (CAMs)

9.4 Concluding Remarks

References

10 Hepatitis E Virus—Current Developments in Antiviral Strategies

10.1 Introduction

10.2 Genetic Diversity and Molecular Virology of HEV

10.3 Clinical Course of HEV Infections

10.4 HEV Therapy

10.5 Development of Novel Antivirals Against HEV

10.6 Prevention of Infection and Vaccination Strategies

10.7 Conclusions

References

11 Antiviral Therapy of Adenovirus Infections

11.1 Human Adenovirus

11.2 Adenovirus in Human Stem Cell Transplantation

11.3 Ocular Adenovirus Infections

11.4 Drug Targets for Direct Acting Antivirals

11.5 Conclusion

References

12 ssDNA-Viruses: Human Parvovirus Infection

12.1 Introduction

12.2 Classification

12.3 Molecular Biology

12.4 Parvovirus Replication

12.5 Diseases Associated with Parvovirus Infection

12.6 Antiviral Chemotherapy of Parvovirus B19-infection

12.7 Therapeutic Options and Recommendations

References

13 Antiviral Targets and Strategies to Treat and Prevent Human Norovirus Infections

13.1 Introduction

13.2 Antiviral Targets

13.3 Vaccine Development

13.4 Conclusion and Perspectives

References

14 Antiviral Strategies Against (Non-polio) Picornaviruses

14.1 Classification and Clinical Impact

14.2 The Enterovirus Replication Cycle

14.3 Prevention

14.4 Antiviral Strategies Against Enteroviruses

14.5 Conclusions

References

15 Novel Antiviral Strategies Against Emerging Arbovirus Infections

15.1 Introduction

15.2 Intervention Strategies

15.3 Genome Organization and Viral Replication Cycle

15.4 Targets For Antiviral Therapy

15.5 Direct-acting Antivirals (DAAs)

15.6 RNA-dependent RNA Polymerase Inhibitors

15.7 Protease/Helicase Inhibitors

15.8 Envelope Protein Inhibitors

15.9 Capsid Protein Inhibitors

15.10 NS4B Inhibitors

15.11 Methyltransferase Inhibitors

15.12 Inhibitors with Nonspecific Action

15.13 Host Targeting Antivirals

15.14 Host Cell Nucleoside Biosynthesis Inhibitors

15.15 Host Cell Lipid Biosynthesis Inhibitors

15.16 Host Kinase Inhibitors

15.17 Protein Metabolism Inhibitors

15.18 Endocytosis and Membrane Fusion Inhibitors

15.19 Conclusion and Future Perspectives

References

16 Current Therapies for Biosafety Level 4 Pathogens

16.1 Introduction

16.2 Filoviruses

16.3 Henipaviruses

16.4 Arenaviruses

16.5 Bunyaviruses

16.6 Considerations for the Development of Treatment Strategies Against Viral Hemorrhagic Fever Viruses

References

Note

17 A Focus on Severe Acute Respiratory Syndrome (SARS) Coronavirus (SARS-CoVs) 1 and 2

17.1 Overview on Coronavirus (CoV)

17.2 Licensed and Clinical Investigational Drugs Against CoVs

17.3 Medicinal Chemistry Approaches Toward the Identification of New Drugs

17.4 Conclusions

References

Index

End User License Agreement

List of Tables

Chapter 1

Table 1.1 Explains the mode of action for available cART options, according ...

Table 1.2 Illustrates chemical formula details and CAS registry numbers for ...

Chapter 2

Table 2.1 Nucleoside HCV NS5B polymerase inhibitors.

Table 2.2 Nucleotide inhibitors of HCV NS5B polymerase.

Table 2.3 Non-nucleoside HCV NS5B polymerase thumb domain inhibitors.

Table 2.4 Non-nucleoside NS5B thumb domain inhibitors.

Table 2.5 Non-nucleoside HCV NS5B polymerase palm domain inhibitors.

Table 2.6 Non-nucleoside NS5B polymerase palm domain inhibitors.

Table 2.7 HCV NS3/4 protease acyclic reversible inhibitors.

Table 2.8 HCV NS3/4 protease covalent binding inhibitors.

Table 2.9 HCV NS3/4 protease macrocyclic reversible binding inhibitors.

Table 2.10 HCV NS3/4 protease P2–P4 macrocyclic reversible binding inhibito...

Table 2.11 First-generation HCV NS5A inhibitors.

Table 2.12 Second-generation HCV NS5A inhibitors.

Chapter 3

Table 3.1 Current licensed drugs against influenza.

Chapter 4

Table 4.1 Antiviral compounds against RSV.

Chapter 6

Table 6.1 Sensitivities of different CMV laboratory strains to Letermovir an...

Table 6.2 Comparison of the effect of increasing CMV viral load on EC

50

.

Table 6.3

In vivo

antiviral activity of letermovir in a mouse xenota...

Table 6.4 CMV prophylaxis by letermovir in patients with hematopoietic stem ...

Table 6.5 Potential indications for treating CMV infection outside transplan...

Chapter 8

Table 8.1 Directly acting antivirals (DAA) with activity against KSHV.

Table 8.2 Compounds or biologicals directed at cellular targets and with act...

Chapter 9

Table 9.1 Classification and mode of action of nucleos(t)ide analogs approve...

Table 9.2 Effect of amino acid substitutions in the CAM binding pocket on CA...

Table 9.3 Capsid assembly modulators in clinical development.

Chapter 10

Table 10.1 Compounds tested for anti-HEV effect and discussed in this chapt...

Chapter 11

Table 11.1 Human diseases caused by adenoviruses.

Table 11.2 HAdV antiviral agents in clinical development.

Chapter 14

Table 14.1 Classification and clinical manifestations of human enteroviruses...

Chapter 15

Table 15.1 Antiviral drugs and vaccines for emerging arboviruses.

Table 15.2 Selected direct-acting antivirals for different arboviral viral p...

Table 15.3 Overview of different classes of host-targeting antivirals.

Table 15.4 Chemical names and formula of selected potential antiviral drugs...

Chapter 16

Table 16.1 Overview of small molecules tested against filovirus infection.

Table 16.2 Overview of small molecules tested against henipavirus infection.

Table 16.3 Overview of small molecules tested against infection with BSL4 ar...

Table 16.4 Overview of small molecules tested against infection with CCHFV.

Chapter 17

Table 17.1 Phases of COVID-19 disease.

List of Illustrations

Chapter 1

Figure 1.1 Shows the course of both most important measurable surrogate mark...

Figure 1.2 Shows the viral replication cycle for HIV in the human target cel...

Chapter 2

Figure 2.1 HCV Genome organization. The open reading frame (ORF) codes for a...

Figure 2.2 HCV NS5B RdRp crystal structure with palm, finger, and thumb doma...

Figure 2.3 Nucleoside HCV NS5B inhibitors.

Figure 2.4 Nucleotide HCV NS5B polymerase inhibitors.

Figure 2.5 Non-nucleoside HCV NS5B polymerase thumb domain inhibitors.

Figure 2.6 Non-nucleoside HCV NS5B polymerase thumb domain inhibitors.

Figure 2.7 Non-nucleoside HCV NS5B polymerase palm domain inhibitors.

Figure 2.8 Non-nucleoside HCV NS5B polymerase palm domain inhibitors.

Figure 2.9 Crystal structure of the protease domain of the HCV NS3/4A protea...

Figure 2.10 HCV NS3/4A protease inhibitor early leads that derived from subs...

Figure 2.11 HCV NS3/4A protease acyclic reversible binding inhibitors.

Figure 2.12 HCV NS3/4A protease covalent binding inhibitors.

Figure 2.13 HCV NS3/4A protease macrocyclic reversible binding inhibitors.

Figure 2.14 HCV NS3/4A protease P2–P4 macrocyclic reversible binding inhibit...

Figure 2.15 Crystal structure of HCV NS5A with potential binding residues hi...

Figure 2.16 Early NS5A protein inhibitor screening leads.

Figure 2.17 First-generation HCV NS5A inhibitors.

Figure 2.18 Second-generation NS5A inhibitors.

Chapter 3

Figure 3.1 Mechanism of acute inflammation induction after influenza virus i...

Figure 3.2 Structure of amantadine and rimantadine.

Figure 3.3 Structure of DANA.

Figure 3.4 Structure of the oseltamivir phosphate (prodrug) and oseltamivir ...

Figure 3.5 Chemical structure of zanamivir.

Figure 3.6 Chemical structure of peramivir.

Figure 3.7 Chemical structures of laninamivir (active metabolite) and lanina...

Figure 3.8 Chemical structures of baloxavir marboxil (prodrug) and its activ...

Figure 3.9 Chemical structure of favipiravir and its active form.

Figure 3.10 Chemical structure of pimodivir.

Figure 3.11 Chemical structures of nitazoxanide and its active metabolite ti...

Figure 3.12 Chemical structure of LASAG.

Chapter 4

Figure 4.1 Transmission electron microscopy of RSV from tissue culture. (a a...

Figure 4.2 The RSV life cycle. The RSV life cycle and where potential RSV in...

Figure 4.3 The principal neutralizing determinants of RSV-F fusion glycoprot...

Figure 4.4 Factors that prevent and help clear RSV infection from the airway...

Chapter 5

Figure 5.1 Schematic overview of the HSV replication cycle highlighting step...

Figure 5.2 Chemical structures of anti-HSV drugs.

Chapter 6

Figure 6.1 Small molecular weight inhibitors of the human cytomegalo virus. ...

Figure 6.2 Mode of action of the terminase and terminase inhibitors of CMV. ...

Figure 6.3

In vivo

antiviral activity of letermovir in a mouse xenotransplan...

Figure 6.4 Successful treatment of a lung-transplanted patient with resistan...

Figure 6.5 Organ disease before and after treatment with letermovir. Chest X...

Figure 6.6 CMV prophylaxis by letermovir in patients with hematopoietic stem...

Figure 6.7 Prophylaxis by letermovir against CMV reactivation in CMV-seropos...

Figure 6.8 MSD phase 3 study: time to clinically significant HCMV infection ...

Figure 6.9 MSD phase 3 study: all-cause mortality through week 24 post-trans...

Figure 6.10 Letermovir phase 3 study (MSD): time to engraftment through week...

Figure 6.11 Resistance loci in UL 56 (Source: Courtesy of J. Strizki, MSD)....

Figure 6.12 pUL56 variants observed in subjects with clinically significant ...

Chapter 7

Figure 7.1 Both latent and early lytic EBV infection contribute to virus-ass...

Figure 7.2 Therapeutic interventions against EBV-associated malignancies. (a...

Figure 7.3 Therapeutic interventions against EBV-associated immunopathologie...

Chapter 8

Figure 8.1 Expression of KSHV LANA in a KS biopsy. (a) Immunohistochemistry ...

Figure 8.2 Schematic diagram of the KSHV genome and its latent origin of rep...

Chapter 9

Figure 9.1 Chemical structures of NAs approved for HBV therapy. Adefovir and...

Figure 9.2 HBV core protein assembly domain. (a) Cp149 monomer viewed from t...

Figure 9.3 Structures of different CAMs. Antiviral activity data (EC

50

s) wer...

Figure 9.4 Crystal structure of a HAP molecule binding at the Cp dimer-dimer...

Chapter 10

Figure 10.1 Hepatitis E virus genome organization. Upon entering host cells,...

Figure 10.2 Summary of the discussed anti-HEV compounds. The depicted molecu...

Chapter 11

Figure 11.1 Chemical structures of antiviral drugs used for therapy of HAdV ...

Figure 11.2 Adenovirus replication cycle. (a) Attachment, entry, uncoating: ...

Chapter 12

Figure 12.1 Schematic structure and composition of a parvovirus particle....

Figure 12.2 Genome, transcription and translation map of parvovirus B19. The...

Chapter 13

Figure 13.1 The norovirus genome.

Figure 13.2 Targeting the various steps of the replication of human noroviru...

Figure 13.3 The chemical structure of (a) Guanidinium chloride, (b) Hippuris...

Figure 13.4 The chemical structure of (a) CMX521, (b) 2’-

C

-Methylcytidine, (...

Figure 13.5 The chemical structure of (a) Compound 54, (b) NAF2, (c) Suramin...

Figure 13.6 The chemical structure of (a) Resiquimod (R-848), (b) Vesatolimo...

Chapter 14

Figure 14.1 Enterovirus structure. (a) Schematic structure of an enterovirus...

Figure 14.2 The enterovirus life cycle and strategies for its inhibition. Af...

Figure 14.3 Structural formulae of molecules targeting the entry stages of t...

Figure 14.4 Structural formulae of molecules targeting the post-entry stages...

Chapter 15

Figure 15.1 Schematic representation of the flavivirus (left) and CHIKV geno...

Figure 15.2 Schematic representation of the replication cycle and polyprotei...

Chapter 17

Figure 17.1 (a) Genomic structure of SARS-CoV-2 and comparison with respect ...

Figure 17.2 Remdesivir and its antiviral activity against SARS-CoVs and MERS...

Figure 17.3 Chemical structures of the prodrug Molnupiravir and parent compo...

Figure 17.4 Structure and biological activity of Galidesivir.

Figure 17.5 SARS-CoVs 3CLpro inhibitors: PF-00835231 with biological activit...

Figure 17.6 Architecture of SARS-CoV-2 nsp12. (a) Schematic diagram outlinin...

Figure 17.7 Structure of SARS-CoV-2 replicating RdRp–RNA complex (PDB ID: 6Y...

Figure 17.8 Binding mode of Remdesivir into the SARS-CoV-2 nsp12 active site...

Figure 17.9 (a) The X-ray structure of SARS-CoV-2 3CL

pro

(PDB ID: 6Y2G), sel...

Figure 17.10 Chloromethylketone peptide 2 and Rupintrivir as starting point ...

Figure 17.11 Schematic representation of the main features of covalent rever...

Figure 17.12 Compounds 3–6 reported as SARS-CoV-1 3CL

pro

inhibitors;

a

Figure 17.13 Compounds 7–12 with their biological activities;

a

antivir...

Figure 17.14 Co-crystallographic pose of compounds PF-00835231, 4, 7, 9, 10,...

Figure 17.15 (a) Boceprevir and its biological activity against SARS-CoV-2.

Figure 17.16 Structure of the SARS-CoV-2 S protein in its pre-fusion conform...

Figure 17.17 Structural details of the interface between SARS-CoV-1 (pink, P...

Figure 17.18 The 6-HB fusion core structures of SARS-CoV-1 and SARS-CoV-2. (...

Figure 17.19 The interactions of the broad-spectrum peptide inhibitor EK1 wi...

Figure 17.20 Amino acid sequences of EK-1 and its lipopeptide derivatives.

Figure 17.21 SARS-CoV-2 HR2-derived peptides.

Guide

Cover

Table of Contents

Title Page

Copyright

Preface

In Memoriam: Farah Elawar

Introduction

Begin Reading

Index

End User License Agreement

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Methods and Principles in Medicinal Chemistry

Edited byR. Mannhold, H. Buschmann, J. Holenz

Editorial BoardG. Folkers, H. Kubinyi, H. Timmermann, H. van de Waterbeemd, J. Bondo Hansen

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New Drug Development for Known and Emerging Viruses

Edited byHelga Rübsamen-Schaeff and Helmut Buschmann

Volume Editor

Prof. Dr. Helga Rübsamen-Schaeff

Altestadt 240213 DüsseldorfGermany

Dr. Helmut Buschmann

Sperberweg 1552076 AachenGermany

Series Editors

Prof. Dr. Raimund Mannhold

Rosenweg 7

40489 Düsseldorf

Germany

Dr. Helmut Buschmann

Sperberweg 15

52076 Aachen

Germany

Dr. Jörg Holenz

GRT Therapeutics

Grunenthal Boston Pain Innovation Hub

1 Broadway, Cambridge MA 02142

United States

Cover Image© Erhan Ergin / Fotolia.com for the symbols used in the margin.

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Preface

The area of Medicinal Chemistry aimed at fighting viral diseases has seen enormous progress in recent decades, making this updated reference from Helga Rübsamen-Schaeff and her team of expert authors more than overdue, after Eric De Clercq published last in this series back in 2010.

Many important, novel antiviral drugs have reached patients in recent years, making diseases such as AIDS or Hepatitis C manageable today, while only some years back, their diagnosis had been comparable to a death sentence. While we, the series editors, write this preface, our world is in the midst of a global pandemic caused by SARS CoV-2 (COVID-19), and promising, novel small molecule-based antiviral medicines have reached the clinical stage in record time, complementing vaccine and drug repurposing efforts to manage a global health crisis.

This impressive evolution is the result of the fascinating and relentless efforts of creative expert drug hunters, not accepting the status quo and pushing the boundaries of Medicinal Chemistry to combat the fascinating, yet often lethal efficiency of small fragments of viral RNA or DNA. Their success stories will be told in this fascinating book by Helga and her fellow authors, along with a thorough background review of all relevant viral biology and clinical pathology for the most important viral diseases. The reader will learn about cutting-edge drug discovery strategies to successfully develop antiviral agents, ranging from the use on non-classic elements, selective and kinetically controlled inhibition of viral enzymes, other viral proteins, and even of their RNA or capsids, often supported by the intelligent use of structure-enabled Medicinal Chemistry design.

The first two chapters focus on the science leading to the breakthrough in treating patients with HIV and Hepatitis C, followed by comprehensive overviews on Research and Development, and market entry for drugs against important viruses such as Influenza Virus, Respiratory Syncytial Virus, Herpes Simplex Virus, Human Cytomegalo Virus, Epstein Barr Virus, Kaposi's Sarcoma-associated Herpesvirus, Hepatitis B Virus, and Hepatitis E Virus (Chapters 3–10). Chapters 11–15 focus on Adeno-, Parvo-, Noro-, Picorna-, and Arboviruses RnD, respectively. Finally, a chapter on Biosafety Level 4 Pathogen Therapies and one on SARS CoV-2 virus conclude the reference book.

The combination of background, strategic insights, and applied case studies makes this volume a must read for every scientist involved in antiviral RnD, but also for the wider Medicinal Chemist and drug hunter community, interested in broadening expertise and skillsets.

Helga Rübsamen-Schaeff led Bayer's Virology Research functions from 1994 until 2001 and Bayer's whole Infectious Diseases Research from 2001 to 2006, when she became founder CEO of AiCuris, a German biotech company dedicated to delivering innovative antiviral and antibacterial drugs to patients. Helga has received numerous awards in her career, e.g. recently the Loeffler-Frosch-Medal of the German Society for Virology. Together with her research teams, she has delivered several important medicines and drug candidates, such as recently Letermovir against the cytomegalovirus. For the work on Letermovir, she received the Innovation Award of Northrhine-Westphalia and the Price for Technology and Innovation by the German President of State in 2018. She is member of the National Academy of Sciences, Leopoldina.

The editors would like to thank Helga and all contributing authors for what we believe to be the most complete and up-to-date reference book for antiviral research and development.

Boston, Aachen, and Düsseldorf Jörg Holenz

July 2021 Helmut Buschmann

Raimund Mannhold

In Memoriam: Farah Elawar

On the day we received the proof pages for Chapter 4 of this book, we were shocked and deeply saddened to learn about the tragic passing of Farah Elawar. Farah is the lead author of our contribution: Respiratory Syncytial Virus Immunoreactivity, Vaccine Development, and Therapeutics. She was in the final stages of her Ph.D. studies on the diversity and drug resistance of Respiratory Syncytial Virus in the community, in the Department of Medical Microbiology and Immunology at the University of Alberta. From the beginning of her studies with the Marchant laboratory, she impressed all of us with her enthusiasm and everlasting energy. She was always three steps ahead of her supervisor with the results of her experiments. It was almost as though she could read minds. With this ability, she provided the leadership to conceptualize, write, and finalize this book chapter. With her warm personality, she has made so many friends and has given us so many joyous moments. Farah will be dearly missed and always remembered.

David Marchant and Matthias Gotte

Introduction

More than 60 years ago, in 1959, the first antiviral drug to be licensed was described by Prusoff [1]. It was marketed for the topical treatment of herpes simplex virus infections of the eye. In 1972, Ribavirin was described as a broad-spectrum antiviral agent [2]; however, it had significant side-effects. In contrast, Acyclovir, discovered in 1977, was very well tolerated [3, 4] and became the gold standard for treating infections caused by herpes viruses.

With the discovery of HIV in 1983 as the virus causing AIDS [5], a very active era of search for anti-HIV drugs began. In 1985, the antiviral activity of an existing drug, AZT (zidovudine, a polymerase inhibitor) was first described against HIV [6]. While up to that time, all drugs, with the exception of ribavirin, to which multiple modes of action are being ascribed, were inhibitors of viral polymerases (in case of AZT, the reverse transcriptase), the following years witnessed a very active search for drugs inhibiting other targets of HIV like the protease, fusion, or integrase or non-nucleosidic inhibitors of HIV reverse transcriptase as novel drug classes [7]. Finally, about 24 years after HIV had first been discovered, by combining drugs with different modes of action, the HIV-infection, which had been a death sentence, became a treatable, although chronic disease allowing patients to live a nearly normal lifespan. Likewise, for Hepatitis C (HCV), the discovery of the virus led to a worldwide search for specific antiviral drugs targeting its polymerase, protease, or NS5A. In this case, combining drugs with different modes of action even allowed to cure the chronic HCV infection in the vast majority of patients, 25 years after HCV had first been described. These unprecedented and major achievements against two of the most dangerous small RNA viruses demonstrate the enormous power of academic and industrial research, when combined and targeted toward a specific virus. They are described in the first two chapters of the book. Obviously, while HCV infections can now be cured this goal is still to be reached for HIV and many approaches are being pursued.

The next two chapters deal with two RNA viruses, which also pose significant health problems: Influenza and the Respiratory Syncytial Virus and describe the existing high medical need for therapies in these indications, as well as starting points for novel therapeutic options.

Chapters 5–8 deal with large DNA viruses like Herpes Simplex, Cytomegalovirus, Epstein–Barr Virus, and the Human Herpes Virus 8, all widespread and implicated in a number of severe or fatal conditions. The successful development of novel generations of drugs against Herpes Simplex and Cytomegalovirus using novel targets for attacking these viruses will be described (Chapters 5 and 6). The next chapters highlight potential targets and strategies to be addressed in the search of therapeutics against the Epstein–Barr Virus or the Human Herpes Virus 8 (Chapters 7 and 8).

Chapter 9 describes antiviral efforts against a small DNA virus, Hepatitis B, which causes significant morbidity and mortality worldwide, especially in Asia, and against which strategies for a cure are being sought as well. Here, inhibitors against the viral capsid could be one potential avenue.

The following chapters address small DNA viruses (Hepatitis E, Adeno, and Parvo) and RNA viruses (Noro, Picorna), followed by chapters on emerging viruses like arbovirus infections and biosafety 4 level viruses like EBOLA.

Outbreaks of HIV, SARS-1 Coronavirus, MERS Coronavirus, EBOLA, and Zika clearly have indicated that the globalized world has become very vulnerable to epidemics of often zoonotic viruses infecting humans and spreading quickly due to the strong and multiple connections in to-day’s world. While containment of several outbreaks or eventually treatment (HIV) and even cure (HCV) has been possible in the past, we are now facing an unprecedented outbreak of SARS CoV-2 causing the disease COVID-19. Infections with the virus were first documented in 2019, and the next two years saw a rapid spread leading to a pandemic with millions of cases worldwide and 5 million deaths by the fall of 2021. Efficient transmission by air makes containment of SARS CoV-2 particularly difficult and resulted in very significant economical downturns worldwide. SARS-CoV-2 causes severe respiratory symptoms, but also pathological inflammation and multi-organ-dysfunction, including the acute respiratory distress symptom, cardiovascular events, coagulopathies, nephropathy, and neurological symptoms [8–11]. While several highly active vaccines have meanwhile been discovered and vaccination campaigns are pushed worldwide, there is still a great need for highly potent and well-tolerated direct acting antiviral agents. We will give medicinal chemists insights into targets and strategies for the discovery of these urgently needed therapies against SARS-Cov-2 in the final chapter of this book.

Most of this book will deal with small molecular weight drugs and their targets, but where appropriate and potentially also the better strategy, immune modulators or immune therapies will be discussed as well.

References

1

  Prusoff, W.H. (1959). Synthesis and biological activities of iodo deoxyuridine, an analog of thymidine.

Biochimica and Biophysica Acta

, 32: 295–296.

2

  Sidwell, R.W. Huffmann, J.H., Kahare, G.P., Allen, L.B., Witkowski, J.T. and Robins, R.K. (1972). Broad-spectrum antiviral activity of virazole: 1-ß-D-ribofuranosyl-1,2,4-triazole-3-carboxamide.

Science

177: 705–706.

3

  Elion, G.B., Furman, P.A., Fyfe, J.A., de Miranda, P., Beauchamp, L., and Schaeffer, H.J. (1977). Selectivity of action of an antiherpetic agent, 9-(2-hydroxyethoxymethyl)guanine.

Proceedings of the National Academy of Sciences of the United States of America

, 74: 5716–5720.

4

   Schaeffer, H.J., Beauchamp, L., de Miranda, P., Elion, G.B., Bauer, D.J., and Collins, P. (1978). 9-(2-Hydroxyethoxymethyl) guanine activity against viruses of the herpes group.

Nature

272: 583–585.

5

  Barré-Sinoussi, F., Chermann, J.C., Rey, F., Nugeyre, M. T., Chamaret, S., Gruest, J., Dauguet, C., Axler-Blin, C., Vézinet-Brun, F., Rouzioux, C., Rozenbaum, W., Montagnier, L. (1983). Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS).

Science

220(4599): 868–71, doi: 10.1126/science.6189183

6

  Mitsuya, H., Weinhold, K.J., Furman, P.A., St. Clair, M.H., Lehrman, S.N., Gallo, R.C., Bolognesi, D., Barry, D.W. and Broder, S. (1985). 30-Azido-30-deoxythymidine (BW A509U): an antiviral agent that inhibits the infectivity and cytopathic effect of human T lymphotropic virus type III/lymphadenopathy-associated virus in vitro.

Proceedings of the National Academy of Sciences of the United States of America

, 82: 7096–7100.

7

  De Clercq, E. (2010). Outlook of the antiviral drug era, now more than 50 years after description of the first antiviral drug, in

Antiviral Drug Strategies

(De Clercq, E. Ed.), Wiley-VCH, Weinheim, Page 1.

8

  Zhou, P., Yang, X.L., Wang, X.G., Hu, B., Zhang, L., Zhang, W., Si, H.R., Zhu, Y., Li, B., Huang, C.L., Hui-Chen, H.-D, Chen, J., Luo, Y., Guo, H., Jiang, R.-D., Liu, M.-Q., Chen, Y., Shen, X.-R., Wang, X., Zheng, X.-S., Zhao, K., Chen, Q.-J., Deng, F., Liu, L.-L., Yan, B., Zhan, F.-X., Wang, Y.-Y., Xiao, G.-F. and Shi, Z.-L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin.

Nature

579: 270–273.

9

  Helms, J., Kremer, S., Merdji, H., Clere-Jehl, R., Schenck, M., Kummerlen, C., Collange, O., Boulay, C., Fafi-Kremer, S., Ohana, M. and Anheim, M. (2020). Neurologic Features in Severe SARS-CoV-2 Infection.

New England Journal of Medicine

382: 2268–2270.

10

 Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., Niu, P., Zhan, F., Ma, X., Wang, D., Xu, W., Wu, G., Gao, G.F., and Tan, W. for the China Novel Coronavirus Investigating and Research Team. (2020). A novel coronavirus from patients with pneumonia in China, 2019.

New England Journal of Medicine

382: 727–733.

11

 Gupta, A., Madhavan, M.V., Sehgal, K., Nair, N., Mahajan, S., Sehravat, T.S., Bikdeli, B., Ahluvalia, N., Ausiello, J.C., Wan, E.Y., Freedberg, D.E., Kirtane, A.J., Parikh, S.A., Maurer, M.S. Nordvig, A.S., Accili, D., Bathon, J.M., Mohan, S., Bauer, K.A., Leon, M.B., Krumholz, H.M., Uriel, N., Mehra, M.R., Elkind, M.S.V., Stone, G.W., Schwartz, A., Ho, D.D., Bilezikian, J.P. and Landry, D.W. (2020). Extrapulmonary manifestations of COVID-19.

Nature Medicine

, 26: 1017–1032.

1HIV—Disease Overview, Targets for Therapy and Open Issues

Christoph Stephan

Internal Medicine & Infectious Diseases, Medical Center/Infectious Diseases Unit, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany

Nearly 40 years have passed since the first patients were discovered to have the previously unknown “acquired immunodeficiency syndrome” (AIDS) [1] and 38 years, since the causative virus was discovered [2]. The time since, has been characterized by a dynamically evolving body of epidemiological and basic science that is unique in medical history. Preliminary result is the development of antiretroviral treatments and social medicine progress, accompanied and catalyzed by the predominantly affected risk groups' emancipation, with reintegration into the society.

1.1 HIV—Disease Overview

There has not been a significant change in the natural history of HIV-infection; however, today in industrialized countries, disease manifestation in the form of AIDS can only be observed in undiagnosed, late presenting patients, who already show manifestations of immunological deterioration. Figure 1.1 demonstrates the course of the disease, according to the two most important measurable surrogate markers—CD4-cell count and HIV-RNA (viral load).

After initial HIV transmission, the retrovirus spreads throughout the human body and infects potentially all CD4-receptor positive cells. Consequently, during the first weeks of infection, there is a substantial fall in CD4-positive T-lymphocyte count and a rise in viral load—up to a turning point. Thereafter, CD4-cells rise again and viral load decreases, due to regain of a partial immunological control. At this time, anti-HIV antibodies can be found in plasma, and the patient will now respond positively to serological HIV-tests. Elimination of HIV, however, will not occur due to the rapid variation of viral surface receptors which may hide infected cells from the immune system and lead to divergent virus populations, including in a single patient [3, 4, 5, 6]. This continuous change of HIV stems from proofreading failures which lead to the evolution of many HIV quasispecies. Another reason for the inability to eliminate HIV is the infection of durable reservoir and “archive” cells, e.g. edaphic CD4-receptor-positive macrophage and monocyte cells, leading to the chronic phase of the infection. For approximately 3–10 years, the patient will experience a relatively stable period, marked by individually solid CD4-cell count- and HIV-RNA viral load- “setpoints” [7]. However, after months or years, an immunological exhaustion will occur. Then, the CD4-cell count is substantially decreasing and viral load is rising again. The result may be AIDS, as defined by the emergence of at least one of 26 opportunistic infections and/or tumors, including pneumocystis pneumonia, cerebral toxoplasmosis, tuberculosis, cytomegalovirus retinitis, Kaposi's sarcoma, or B-cell non-Hodgkin lymphoma.

Figure 1.1 Shows the course of both most important measurable surrogate markers from blood count, i.e. CD4-cell count and HIV-RNA (viral load), during untreated HIV infection.

1.2 Targets for Antiretroviral Therapy

The replication of the retrovirus in the human host cell is well described and offers targeted treatment options, in order to prevent viral replication. Figure 1.2 shows the passage of HIV through the human host CD4-receptor positive T-cell. Antiretroviral drugs are able to address specific points in the HIV replication cycle and used in combination antiretroviral therapy (cART) aims to completely suppress HIV-1 replication long term. This will give the immune system a chance to recover and overcome opportunistic infections and tumors and/or to avoid significant deterioration from the beginning, when applied early after infection.

During the retrovirus replication in the human cell, specific cART-drug classes offer to interfere with different therapeutic intervention targets (see Table 1.1, presently favored drugs are printed in bold and Figure 1.2). Such interventions comprise: inhibition of first contact of HIV with the CD4-positive cell (attachment), the cell entry, intracellular reverse transcriptase-enzyme and -activity, DNA-integration, virus assembling by proteases, and virus maturation; the latter leaves immature, noninfectious virus particles. The chemical structures of the different HIV drugs can be found in Table 1.2.

Figure 1.2 Shows the viral replication cycle for HIV in the human target cell, i.e. the CD4-receptor positive cell, and six treatment targets for antiretroviral therapy classes (for numbers in red, see Table 1.1/row 1).

Table 1.1 Explains the mode of action for available cART options, according to the target area in HIV cell passage (for numbers: see Figure 1.2).

No. (

Fig-ure 1.2

)

Drug class: inhibitor of…

Generic names of available cART-drugs

Mode of action: inhibition of the…

Formula

CAS registry number

1

Attachment

Fostemsavir

a

HIV-binding site gp120, used by HIV for first contact with CD4-receptor

C

25

H

26

N

7

O

8

P

864953-29-7

Ibalizumab (TNX-355)

Human CD4-receptor binding site for HIV (whole antibody)

n/a

680188-33-4

2

Entry-/fusion

Enfuvirtid (T20)

HIV-gp41-fusion protein (36 amino acids-containing polypeptide)

C

204

H

301

N

51

O

64

159519-65-0

Maraviroc (MVC)

Human CCR5-coreceptor

C

29

H

41

F

2

N

5

O

376348-65-1

3

Nucleosidal reverse transcriptase (NRTI)

Zidovudin (AZT)

Thymidin-analogue

Nucleobase replacement during RNA–DNA-transcription as faulty chip, leading to early chain termination

C

10

H

13

N

5

O

4

30516-87-1

Lamivudin (3TC)

b

Cytidin-analogue

C

8

H

11

N

3

O

3

S

134678-17-4

Emtricitabine (FTC)

b

C

8

H

10

FN

3

O

3

S

143491-57-0

Tenofovir (TAF/TDF)

b

Adenosine-analogue

C

9

H

14

N

5

O

4

P

147127-20-6

Abacavir (ABC)

b

Gunaosine-analogue

C

14

H

18

N

6

O

136470-78-5

4

Non-nucleosidal reverse transcriptase (NNRTI)

Efavirenz (EFV)

Reverse transcriptase-enzyme binding site

C

14

H

9

ClF

3

NO

2

154598-52-4

Nevirapine (NVP)

C

15

H

14

N

4

O

129618-40-2

Rilpivirine (RPV)

b

C

22

H

18

N

6

500287-72-9

Doravirin (DOR)

b

? >

C

17

H

11

ClF

3

N

5

O

3

1338225-97-0

5

Integrase strand transfer (INSTI)

Raltegravir (RGV)

Viral DNA integration in human host DNA, in cell nucleus

C

20

H

21

FN

6

O

5

518048-05-0

Elvitegravir (EVG)

C

23

H

23

ClFNO

5

697761-98-1

Dolutegravir (DGT)

b

C

20

H

19

F

2

N

3

O

5

1051375-16-6

Bictegravir (BTG)

b

C

21

H

18

F

3

N

3

O

5

1611493-60-7

Cabotegravir

a

C

19

H

17

F

2

N

3

O

5

1051375-10-0

6

Protease (PI)

Darunavir (DRV)

b

gag-pol-polyprotein cleavage

C

27

H

37

N

3

O

7

S

206361-99-1

Atazanavir (ATV)

C

38

H

52

N

6

O

7

198904-31-3

Lopinavir (LPV)

C

37

H

48

N

4

O

5

192725-17-0

7

Maturation/capsid

Lenacapavir

a

Extracellular capsid arrangement

a

C

39

H

32

ClF

10

N

7

O

5

S

2

2189684-44-2

GSK3640254

a

Last protease cleavage event: CA-p24/SP1

a

n/a

n/a

a) In clinical study development—also refer to public study registry online-resource, available at: https://www.clinicaltrials.gov.

b) Modern, recommended first-line combination antiretroviral therapy components: printed in bold. For treatment guidelines from the European AIDS Clinical Society (EACS), version 10, from November 2019, please refer to online-resource, available at: https://www.eacsociety.org/files/2019_guidelines-10.0_final.pdf.

Table 1.2 Illustrates chemical formula details and CAS registry numbers for available cART-drugs.

Drug class: inhibitor of…

Generic drug name/chemical formula/CAS registry no./graphic structure formula

Generic drug name/chemical formula/CAS registry no./graphic structure formula

Attachment

Fostemsavir

a

C

25

H

26

N

7

O

8

P 864953-29-7

Ibalizumab (TNX-355) n/a 680188-33-4 n/a—chemical formula not yet published, the drug is a humanized mouse whole antibody

Entry-/fusion

Enfuvirtid (T20) C

204

H

301

N

51

O

64

159519-65-0

Maraviroc (MVC) C

29

H

41

F

2

N

5

O 376348-65-1

Nucleosidal reverse transcriptase (NRTI)

Zidovudin (AZT) Thymidin-analogue C

10

H

13

N

5

O

4

30516-87-1

Lamivudin (3TC) Cytidine-analogue C

8

H

11

N

3

O

3

S 134678-17-4

Emtricitabine (FTC) Cytidine-analogue C

8

H

10

FN

3

O

3

S 143491-57-0

Tenofovir (TAF/TDF) Adenosine-analogue C

9

H

14

N

5

O

4

P 147127-20-6 As tenofovir alafenamid (TAF)

Abacavir (ABC) Guanosine-analogue C

14

H

18

N

6

O 136470-78-5

Non-nucleosidal reverse transcriptase (NNRTI)

Efavirenz (EFV) C

14

H

9

ClF

3

NO

2

154598-52-4

Nevirapine (NVP) C

15

H

14

N

4

O 129618-40-2

Rilpivirine (RPV) C

22

H

18

N

6

500287-72-9

Doravirin (DOR) C

17

H

11

ClF

3

N

5

O

3

1338225-97-0

Integrase strand transfer (INSTI)

Raltegravir (RGV) C

20

H

21

FN

6

O

5

518048-05-0

Elvitegravir (EVG) C

23

H

23

ClFNO

5

697761-98-1

Dolutegravir (DGT) C

20

H

19

F

2

N

3

O

5

1051375-16-6

Bictegravir (BTG) C

21

H

18

F

3

N

3

O

5

1611493-60-7

Cabotegravir

a

C

19

H

17

F

2

N

3

O

5

1051375-10-0

Protease (PI)

Darunavir (DRV) C

27

H

37

N

3

O

7

S 206361-99-1

Atazanavir (ATV) C

38

H

52

N

6

O

7

198904-31-3

Lopinavir (LPV) C

37

H

48

N

4

O

5

192725-17-0

Maturation/capsid

GS-6207

a

Chemical formula not yet published, CAS registry-no. not yet allocated (as of search on 30 December 2019)

GSK3640254

a

Source: WIKIPEDIA, the free encyclopedia, as accessed online on 30 December 2019, please also see https://en.wikipedia.org.

a) In clinical study development—refer to public study registry online-resource, available at: https://www.clinicaltrials.gov.

1.3 Currently Open Issues in HIV/AIDS Research

Important milestones in cART development have been achieved in the recent decades as standard of care: complete virus suppression, side-effect- and drug-interaction control, and convenience in taking antiretroviral regimens. Recently observed trends in HIV-treatment include the development of long-acting cART drugs, which are administered alternatively, e.g. injected every eight weeks, or once even less frequently implanted periodically.

When in July 2015 the first results from the START-study (Strategic Timing of Antiretroviral Treatment) were published, the benefit from modern cART for patients with early HIV-infection was evident for the first time [8]. Subsequently, antiretroviral therapy guidelines have changed worldwide and recommend cART for everybody with an HIV-infection, independent from the individual clinical category and CD4-cell count. Thereafter, the global focus of interest was to establish programs that could allow every infected person access to cART. Therefore, the United Nations Program on HIV/AIDS (UNAIDS) have established the 90–90–90-targets, in order to end AIDS as a disease and to control HIV transmissions on a society level [9]. Data on beneficial effects of programs, which lowered the barriers to cART, i.e. linked to HIV transmission control, were published before [10]. Moreover, the exciting confirmation of the SWISS STATEMENT hypothesis (Undetectable HIV leads to zero transmissions) [11] was a major step forward to realize antiretroviral treatment as most effective prevention [12] in the absence of a protective vaccine.

Another major open issue is cure from HIV/AIDS. Albeit individual cases of cure from HIV have been reported [13, 14], e.g. by stem cell transplantation from donors with the rare, intrinsic HIV-resistance due to homozygous CCR5-Δ32/Δ32-gene mutations, stem cell transplantation will hardly be feasible for many patients, as this is associated with substantial risks. Alternative therapeutic procedures using the CRISPR-CASP-technique have been tried, but still require further developments [15]. Beyond stem cell manipulation and/or transplantation, the efforts to induce broadly neutralizing antibodies (BNAPs) remain a second scientific approach to achieve at least “functional cure” from HIV [16].

References

1

  CDC (1981). Pneumocystis pneumonia—Los Angeles.

MMWR

30: 250–252.

2

  Barré-Sinoussi, F., Chermann, J.C., Rey, F. et al. (1983). Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS).

Science

220 (4599): 868–871.

3

  Rübsamen-Waigmann, H., Becker, W.B., Helm, E.B. et al. (1986). Isolation of variants of lymphocytopathic retroviruses from the peripheral blood and cerebrospinal fluid of patients with ARC or AIDS.

J. Med. Virol.

19: 335–344.

4

  von Briesen, H., Becker, W.B., Henco, K. et al. (1987). Isolation frequency and growth properties of HIV-variants: multiple simultaneous variants in a patient demonstrated by molecular cloning.

J. Med. Virol.

23: 51–66.

5

   Schwartz, S., Fenyo, E.-M., Felber, B.K., and George, N. (1989). Pavlakis rapidly and slowly replicating human immunodeficiency virus type-1 isolates can be distinguished according to target-cell tropism in T-cell and monocyte cell-lines.

Proceedings of the National Academy of Sciences

, October 1989. doi:

https://doi.org/10.1073/pnas.86.18.7200

.

Source

: PubMed.

6

  Asjö, B., Albert, J., Karlson, A. et al. (1986).

Lancet

ii: 660–662. Tersmette, M., Lange, I.M.A., de Goede, R.E.Y. et al. (1989).

Lancet

i: 983–985.

7

  O'Brien, T.R., Rosenberg, P.S., Yellin, F., and Goedert, J.J. (1998). Longitudinal HIV-1 RNA levels in a cohort of homosexual men.

J. Acquir. Immune Defic. Syndr. Hum. Retrovirol.

18 (2): 155–161.

8

  INSIGHT START Study Group, Lundgren, J.D., Babiker, A.G. et al. (2015). Initiation of antiretroviral terapy in early asymptomatic HIV infection.

N. Engl. J. Med.

373 (9): 795–807.

9

  WHO (2017).

UNAIDS documents: ending AIDS: progress towards the 90–90–90 targets

, published 20 July 2017.

https://www.unaids.org/sites/default/files/media_asset/Global_AIDS_update_2017_en.pdf

.

10

 Nosyk, B., Min, J., Lima, V.D. et al. (2013). HIV-1 disease progression during highly active antiretroviral therapy: an application using population-level data in British Columbia: 1996–2011.

J. Acquir. Immune Defic. Syndr.

63 (5): 653–659.

11

 Vernazza, P., Hirschel, B., Bernasconi, E., and Flepp, M. (2008). HIV-infizierte Menschen ohne andere STD sind unter wirksamer antiretroviraler Therapie sexuell nicht infektiös.

Bull. Med. Suisses

89: 165–169.

12

 Cohen, M.S., Chen, Y.Q., McCauley, M. et al. (2011). Prevention of HIV-1 infection with early antiretroviral therapy.

N. Engl. J. Med.

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2Curing Hepatitis C with Direct-Acting Antiviral Therapy

Michael J. Sofia

Arbutus Biopharma, Inc., Warminster, PA, USA

2.1 Introduction

Viral hepatitis is an inflammation of the liver that progressively leads to liver cirrhosis and eventually liver cancer. Every third person on the planet shows evidence of infection with viral hepatitis and some 500 million individuals are chronically infected. It is the leading cause of liver cancer worldwide and accounts for more than 80% of liver transplants globally. While mortality rates are dropping for many other infectious diseases, there has been an increase in mortality for those individuals diagnosed with chronic viral hepatitis [1].

It was not until the 1960s and 1970s that through a series of epidemiological studies and the work of several laboratories the hepatitis B virus (HBV) was discovered and linked to the occurrence of liver cancer. The development of a diagnostic test and ultimately of a vaccine dramatically reduced the incidence of HBV infection in the western world even though a cure remained far off on the horizon [2]. However, it turns out that HBV was not the only culprit that caused a chronic viral hepatitis that led to liver cancer. A mysterious non-A non-B hepatitis (NANBH) was identified by Harvey Alter and coworkers as a transfusion-associated hepatitis [2]. However, it was not until 1989 and the work of Michael Houghton and coworkers that the hepatitis C virus (HCV) was ultimately identified and its genome was mapped (Figure 2.1) [3, 4]. This work led to a diagnostic test that would allow for the screening of the donated blood supply and virtually eliminate acquiring HCV from blood transfusions [5]. Even with this breakthrough, acquisition of HCV infection via injection drug use and other means of contact with infected blood continued to propagate the disease such that the worldwide prevalence remained significant at approximately 75 million individuals. Because the development of a vaccine was and still is elusive and no cure was available, the spread of HCV continued and those who were infected had little hope that their future would be better.

In 1991, the first approved therapy for treating HCV was the cytokine interferon-α (IFN). First administered three times weekly, this therapy produced very low cure rates that came along with significant side effects such as anemia, neurological complications, and flu-like symptoms. The introduction of the nucleoside ribavirin (RBV), a nonspecific antiviral agent, led to improved cure rates but also added to the side-effect profile of this combination. The advent of pegylated-IFN (PEG-IFN) in combination with RBV, further improved cure rates and reduced the frequency of administration. However, cure rates remained modest and the serious side effects persisted [6].

Figure 2.1 HCV Genome organization. The open reading frame (ORF) codes for a ~3000 amino acid precursor polyprotein that lies between the 3′ and 5′ nontranslated region (NTR). The NS2/3 protease and NS3/4A protease are involved in the polyprotein processing.

Although IFN-containing regimens did provide a modest cure rate, the side effects were sufficiently severe that many patients could not complete the 48-week regimen. It became an aspirational objective to eliminate IFN from drug regimens that cured HCV, but in the early 2000s, it was not obvious how to accomplish this objective. In addition, there were six different viral genotypes (GT) known for HCV and the virus was shown to have a very high mutation rate because of the poor proof-reading function of the viral polymerase. These other factors complicated the outlook and increased the complexity of the task because the most desirable cure therapy would have the characteristics of being pangenotypic, with a high barrier to the formation of resistant virus and IFN-free.

2.2 Tools to Enable Drug Discovery

With the genome of the HCV virus fully delineated, the field was now ready to attempt to identify agents that could impact the virus directly with direct-acting antivirals (DAAs) and see if DAAs could deliver on some of the objectives. Early progress was slow because drug hunters were using surrogate systems such as bovine virus diarrhea virus (BVDV) as a way to evaluate potential drug candidates. Therefore, a new tool needed to be developed, a cell-based assay that drug discovery scientist could use to screen for inhibitors targeting the nonstructural proteins essential for the HCV virus to replicate itself. This was eventually achieved with the development of the HCV replicon cell system pioneered by Bartenschlager and coworkers [7]. By eliminating the gene sequence for the structural proteins, this noninfectious cell system allowed for screening of inhibitors of viral replication against the druggable nonstructural proteins. It also provided a convenient way to assess drug resistance. Eventually, the JFH-1 cell line was developed and provided a way to assess drug candidates in a real infectious system [7].

Another challenge that hampered the discovery of curative therapies was the availability of an accessible and cost-effective animal model. Because of the narrow host tropism, the chimpanzee was the only animal model available for testing new therapeutic agents, but the cost, availability, and ethical concerns limited its use and therefore limited the impact on the discovery and development of new drugs. Although other animal models were eventually developed, their impact was not significant in the scheme of HCV drug discovery.

2.3 Drug Discovery Targets

HCV is a positive-sense single-stranded RNA virus whose genome is approximately 9.6 kb in length. The genome encodes over 3000 amino acids which after polyprotein processing produces three structural proteins and seven nonstructural proteins. The mapping of the HCV virus genome by Houghton and coworkers provided an initial list of viral targets against which drug discovery efforts could be launched (Figure 2.1) [8]. Several of the seven viral nonstructural proteins were considered druggable targets. They included the NS3/4A protease and NS5B viral polymerase around which most of the early drug discovery work focused. Subsequently, efforts targeting the NS4B and NS5A proteins began to emerge with significant focus on agents that bind to NS5A.

In addition to directly targeting the HCV nonstructural proteins, a number of efforts were initiated to target host-related targets that had effects on viral replication or on host immune responses. These targets included cyclophilins, MiR122, and interferon-γ [9–11]. Although targeting these nonviral targets did produce clinical agents that led to reductions in HCV viral load in early clinical trials, it was the work on the DAAs targeting NS3/4A protease, NS5A and NS5B polymerase that ultimately, in various combinations, produced the highly efficacious, safe, and short duration curative interferon-free therapies. The very rapid and successful development of DAA combination therapies made it difficult for host targeting agents to be competitive, especially since they would also have had to be combined with a DAA and could not stand alone.

2.4 NS5B Polymerase Inhibitors

2.4.1 Nucleoside and Nucleotide Inhibitors of NS5B Polymerase

The HCV NS5B RNA-dependent RNA polymerase (RdRp) is responsible for two RNA polymerization steps that are necessary for replicating the viral genome. The RdRp uses the HCV genomic RNA as a template from which the complementary negative RNA strand intermediate is generated and then this negative RNA strand becomes a template for the synthesis of a positive RNA strand [8]. The HCV NS5B polymerase is well conserved across all GTs and contains characteristics common among known viral RdRps [12]. It maintains the characteristic finger, palm, and thumb domains and contains the Asp, Gly, and Asp catalytic triad at the active site with the requirement of needing two divalent metal ions to initiate polymerization (Figure 2.2) [15].

Figure 2.2 HCV NS5B RdRp crystal structure with palm, finger, and thumb domains designated. PDB code 1C2P (1.9Å) [13, 14].

To target the HCV NS5B polymerase, two distinct approaches were pursued. These included the investigation of nucleosides and nucleotides as alternate substrates and the pursuit of non-nucleoside small-molecule allosteric modulators that bind to either the palm or thumb domains of NS5B [16].

The development of nucleos(t)ide inhibitors largely revolved around 2′-α-fluoro-2′-C-methyl and 2′-α-hydroxy-2′-C-methyl substitution on the furanose ring system of the nucleos(t)ide (Figures 2.3 and 2.4, Tables 2.1 and 2.2) [16]. The 2′-methyl substitution was shown to be important for anti-HCV activity. Particularly in combination with the 2′-α-F substitution, 2′-C-methyl substitution induced a level of selectivity for HCV versus other viruses and human polymerases. Also, it was demonstrated that the 2′-α-F substitution provided a profound benefit as it related to specificity for HCV and safety profile. Some of the early 2′-hydroxyl nucleosides having an adenosine or cytosine base, MK-0608 and NM-283 (valopicitabine), suffered from adverse safety observations either in preclinical testing or in human clinical studies resulting in termination of their further development (Figure 2.3 and Table 2.1) [17–19, 48–50]. This is in contrast to the early fluorinated cytosine nucleosides PSI-6130 and its prodrug RG7128 which were not hampered by safety concerns but were ultimately not taken forward in development because of efficacy and other development challenges (Figure 2.3 and Table 2.1). However, it was the study with RG7128 that first demonstrated clinical efficacy in GT 1, 2 and 3 HCV patients, thus establishing the possibility for development of a pangenotypic DAA HCV cure strategy [51].

Resistance was not a significant issue with the 2′-methyl-2′-F or 2′-methyl-2′-OH nucleosides. The S282T amino acid substitution that conferred resistance to these nucleosides was shown not to be a pre-existing variant and was also shown to be quite unfit [20, 52–54].

Figure 2.3 Nucleoside HCV NS5B inhibitors.