Phosphodiesterases and Their Inhibitors E-Book

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

Seitenzahl: 374

Veröffentlichungsjahr: 2014

Beschreibung

Written by the pioneers of Viagra, the first blockbuster PDE inhibitor drug. Beginning with a review of the first wave of phosphodiesterase (PDE) inhibitors, this book focuses on new and emerging PDE targets and their inhibitors. Drug development options for all major human PDE families are discussed and cover diverse therapeutic fields, such as neurological/psychiatric, cardiovascular/metabolic, pain, and allergy/respiratory diseases. Finally, emerging chemotherapeutic applications of PDE inhibitors against malaria and other tropical diseases are discussed.

Leseprobe

CONTENTS

Cover

Methods and Principles in Medicinal Chemistry

Title Page

Copyright

List of Contributors

Preface

A Personal Foreword

Chapter 1: Introduction

Chapter 2: Toward a New Generation of PDE5 Inhibitors through Advances in Medicinal Chemistry

2.1 Introduction

2.2 The First-Generation Agents

2.3 PDE5 as a Mechanism and Alternative Indications Beyond MED

2.4 A Summary of PDE5 Chemotypes Reported Post-2010

2.5 Second-Generation PDE5 Inhibitors from Pfizer: Pyrazolopyrimidines

2.6 Second-Generation PDE5 Inhibitors from Pfizer: Pyridopyrazinones

2.7 Conclusions

Acknowledgments

References

Chapter 3: PDE4: New Structural Insights into the Regulatory Mechanism and Implications for the Design of Selective Inhibitors

3.1 Introduction

3.2 Isoforms, Domain Organization, and Splice Variants

3.3 Structural Features of the Catalytic Site

3.4 Regulation of PDE4 Activity

3.5 Crystal Structure of Regulatory Domains of PDE4

3.6 UCR2 Interaction and Selectivity

3.7 Conclusions

References

Chapter 4: PDE4: Recent Medicinal Chemistry Strategies to Mitigate Adverse Effects

4.1 Introduction

4.2 Brief Summary of pan-PDE4 Inhibitors

4.3 PDE4 Strategies to Avoid Gastrointestinal Events

4.4 Conclusions

References

Chapter 5: The Function, Enzyme Kinetics, Structural Biology, and Medicinal Chemistry of PDE10A

5.1 Enzymology and Protein Structure

5.2 Papaverine-Related PDE10A Inhibitors

5.3 MP-10/PF-2545920 Class of Inhibitors

5.4 PF-2545920/MP-Inspired Inhibitors

5.5 PF-2545920/Papaverine/Quinazoline Hybrid Series of Inhibitors

5.6 PET Ligand Development

5.7 Summary and Future

References

Chapter 6: The State of the Art in Selective PDE2A Inhibitor Design

6.1 Introduction

6.2 Selective PDE2A Inhibitors

6.3 Methods

6.4 Conclusions

References

Chapter 7: Crystal Structures of Phosphodiesterase 9A and Insight into Inhibitor Discovery

7.1 Introduction

7.2 Subtle Asymmetry of the PDE9 Dimer in the Crystals

7.3 The Structure of the PDE9 Catalytic Domain

7.4 Interaction of Inhibitors with PDE9

7.5 Implication on Inhibitor Selectivity

References

Chapter 8: PDEs as CNS Targets: PDE9 Inhibitors for Cognitive Deficit Diseases

8.1 PDE9A Enzymology and Pharmacology

8.2 Crystal Structures of PDE9A Inhibitors

8.3 Medicinal Chemistry Efforts toward Identifying PDE9A Inhibitors for Treating Cognitive Disorders

8.4 Analysis of CNS Desirability of PDE9A Inhibitors

8.5 Conclusions

References

Chapter 9: Phosphodiesterase 8B

9.1 Introduction

9.2 Identification

9.3 Properties

9.4 Expression and Tissue Distribution

9.5 Functions of PDE8B

9.6 Inhibitors and Potential Therapeutic Uses

References

Chapter 10: Selective New Small-Molecule Inhibitors of Phosphodiesterase 1

10.1 Introduction

10.2 PDE1 Enzymology

10.3 PDE1 Inhibitors

10.4 Conclusion

References

Chapter 11: Recent Advances in the Development of PDE7 Inhibitors

11.1 Introduction

11.2 Historical Development of PDE7 Inhibitors

11.3 Recent Advances in the Discovery of PDE7 Inhibitors for Peripheral Therapeutic Benefit

11.4 Recent Advances in the Discovery of PDE7 Inhibitors for CNS-Related Disorders

11.5 Recent Advances in the Discovery of Dual PDE7 Inhibitors

11.6 Identifying Next-Generation PDE7 Inhibitors

11.7 Summary

References

Chapter 12: Inhibitors of Protozoan Phosphodiesterases as Potential Therapeutic Approaches for Tropical Diseases

12.1 Introduction

12.2 Malaria

12.3 Chagas Disease

12.4 Leishmaniasis

12.5 Human African Trypanosomiasis

12.6 Conclusion

Acknowledgments

References

Index

End User License Agreement

List of Tables

Table 1.1

Table 1.2

Table 6.1

Table 6.2

Table 6.3

Table 6.4

Table 7.1

Table 8.1

Table 9.1

Table 9.2

Table 9.3

Table 10.1

Table 10.2

Table 10.3

Table 10.4

Table 11.1

Table 12.1

Table 12.2

Table 12.3

List of Illustrations

Figure 1.1

Figure 1.2

Figure 2.1

Figure 2.2

Figure 2.3

Figure 2.4

Figure 2.5

Figure 2.6

Figure 2.7

Figure 2.8

Figure 2.9

Figure 2.10

Figure 2.11

Figure 2.12

Figure 2.13

Figure 2.14

Figure 2.15

Figure 2.16

Figure 3.1

Figure 3.2

Figure 3.3

Figure 3.4

Figure 3.5

Figure 3.6

Figure 4.1

Figure 4.2

Figure 4.3

Figure 4.4

Figure 4.5

Figure 4.6

Figure 4.7

Figure 4.8

Figure 4.9

Figure 4.10

Figure 4.11

Figure 4.12

Figure 5.1

Figure 5.2

Figure 5.3

Figure 5.4

Figure 5.5

Figure 5.6

Figure 5.7

Figure 5.8

Figure 5.9

Scheme 5.1

Figure 5.10

Figure 5.11

Figure 5.12

Figure 5.13

Figure 5.14

Figure 5.15

Figure 5.16

Figure 6.1

Figure 6.2

Figure 6.3

Figure 6.4

Figure 6.5

Figure 6.6

Figure 6.7

Figure 6.8

Figure 6.9

Figure 6.10

Figure 6.11

Figure 6.12

Figure 6.13

Figure 6.14

Figure 6.15

Figure 6.16

Figure 6.17

Figure 6.18

Figure 6.19

Figure 7.1

Figure 7.2

Figure 7.3

Figure 7.4

Figure 7.5

Figure 7.6

Figure 8.1

Figure 8.2

Figure 8.3

Figure 8.4

Figure 8.5

Figure 8.6

Figure 8.7

Figure 8.8

Figure 8.9

Figure 8.10

Figure 8.11

Figure 8.12

Figure 8.13

Figure 8.14

Figure 8.15

Figure 8.16

Figure 8.17

Figure 8.18

Figure 8.19

Figure 10.1

Figure 10.2

Figure 10.3

Figure 10.4

Figure 10.5

Figure 10.6

Figure 10.7

Figure 11.1

Figure 11.2

Figure 11.3

Figure 11.4

Figure 11.5

Figure 11.6

Figure 11.7

Figure 11.8

Figure 11.9

Figure 11.10

Figure 11.11

Figure 11.12

Figure 11.13

Figure 11.14

Figure 11.15

Figure 11.16

Figure 11.17

Figure 11.18

Figure 11.19

Figure 11.20

Figure 12.1

Figure 12.2

Figure 12.3

Figure 12.4

Figure 12.5

Figure 12.6

Figure 12.7

Guide

Cover

Table of Contents

Preface

Chapter 1

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Methods and Principles in Medicinal Chemistry

Edited by R. Mannhold, H. Kubinyi, G. Folkers

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Vol. 51

Phosphodiesterases and Their Inhibitors

Edited by

Spiros Liras

Andrew S. Bell

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List of Contributors

Christopher W. am Ende

Pfizer Worldwide Research and Development

Eastern Point Road

Neuroscience Medicinal Chemistry

Groton, CT 06340

USA

Andrew S. Bell

Imperial College London

Department of Chemistry

Exhibition Road

London SW7 2AZ

UK

Thomas A. Chappie

Pfizer Worldwide Research and Development

Worldwide Medicinal Chemistry

620 Memorial Drive

Cambridge, MA 02139

USA

Michelle M. Claffey

Pfizer Worldwide Research and Development

Neuroscience Medicinal Chemistry

Eastern Point Road

Groton, CT 06340

USA

Etzer Darout

Pfizer Worldwide Research and Development

Worldwide Medicinal Chemistry

620 Memorial Drive

Cambridge, MA 02139

USA

Rainer Gewald

BioCrea GmbH

Meissner Strasse 191

01445 Radebau

Germany

Christopher J. Helal

Pfizer Worldwide Research and Development

Neuroscience Medicinal Chemistry

Eastern Point Road

Groton, CT 06340

USA

Xinjun Hou

Pfizer Worldwide Research and Development

Neuroscience Medicinal Chemistry

700 Main Street

Cambridge, MA 02139

USA

John M. Humphrey

Pfizer Worldwide Research and Development

Neuroscience Medicinal Chemistry

Eastern Point Road

Groton, CT 06340

USA

Hengming Ke

The University of North Carolina

Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center

120 Mason Farm Rd

Chapel Hill, NC 27599-7260

USA

Bethany L. Kormos

Pfizer Worldwide Research and Development

Eastern Point Road

Neuroscience Medicinal Chemistry

Groton, CT 06340

USA

Spiros Liras

Pfizer Worldwide Research and Development

Worldwide Medicinal Chemistry

620 Memorial Drive

Cambridge, MA 02139

USA

Hai-Bin Luo

Sun Yat-Sen University

School of Pharmaceutical Sciences

Xingang Xi Road

Guangzhou, 510006

P. R. China

Elnaz Menhaji-Klotz

Pfizer Worldwide Research and Development

Worldwide Medicinal Chemistry

620 Memorial Drive

Cambridge, MA 02139

USA

Dafydd R. Owen

Pfizer Worldwide Research and Development

Worldwide Medicinal Chemistry

620 Memorial Drive

Cambridge, MA 02139

USA

Jayvardhan Pandit

Pfizer Pharmatherapeutics Research

Centre for Chemical Innovation and Excellence

Structural Biology and Biophysics Group

Eastern Point Road

Groton, CT 06340

USA

Michael P. Pollastri

Northeastern University

Department of Chemistry & Chemical Biology

102 Hurtig, 360 Huntington Avenue

Boston, MA 02115

USA

Nigel A. Swain

Worldwide Medicinal Chemistry

Pfizer Neusentis

The Portway Building

Granta Park

Cambridge CB21 6GSUK

Patrick Verhoest

Pfizer Worldwide Research and Development

Groton Laboratories

Eastern Point Road

Groton, CT 06340

USA

Yiqian Wan

Sun Yat-Sen University

School of Chemistry and Chemical Engineering

Xingang Xi Road

Guangzhou 510275

P. R. China

Yousheng Wang

Beijing Technology and Business University

School of Chemical and Environmental Engineering

Bioengineering Department

Fucheng Road, Beijing 100048

P. R. China

Jennifer L. Woodring

Northeastern University

Department of Chemistry & Chemical Biology

102 Hurtig, 360 Huntington Avenue

Boston, MA 02115

USA

Stephen W. Wright

Pfizer Global Research and Development

Worldwide Medicinal Chemistry

Eastern Point Road

Groton, CT 06340

USA

Preface

Cyclic nucleotide phosphodiesterases (PDEs) cleave the phosphodiester bond in the second messenger molecules cAMP and cGMP. They regulate localization, duration, and amplitude of cyclic nucleotide signaling within subcellular domains. Thus, PDEs are important regulators of signal transduction mediated by these second messenger molecules and thereby potential drug targets of prime interest.

PDEs presently comprise 11 subfamilies and at least 21 isoforms with numerous splice variants; they differ in structure, substrate specificity, inhibitor selectivity, tissue and cell distribution, regulation by kinases, protein–protein interaction, and subcellular distribution. Phosphodiesterases are classified by the cyclic nucleotide substrate that they hydrolyze. PDEs 1, 2, 3, 10, and 11 are dual substrate enzymes. PDEs 4, 7, and 8 hydrolyze only cAMP, whereas PDEs 5, 6, and 9 hydrolyze only cGMP.

Initial pharmacological studies on PDE inhibitors concerned ingredients from coffee, cacao, and tea, later on identified as xanthines that act by inhibiting PDEs. The diuretic, inotropic, and bronchodilator properties of theophylline anticipated the clinical goals, later on approached with weakly selective PDE inhibitors in the 1980s, such as the PDE3 inhibitors amrinone and milrinone for cardiovascular indications and the PDE4 inhibitor roflumilast for severe COPD. Both PDE3 and PDE4 inhibition resulted in nausea and severe side effects such as sudden cardiac arrest. Thus, PDE inhibitor research declined in the late 1980s.

In the mid-1990s, the quantum leap in PDE and PDE inhibitor research was the finding that sildenafil – a PDE5 inhibitor – efficiently treats male erectile dysfunction. The discovery of its clinical utility reanimated PDE research, leading to the identification of the PDE sub families 6–11. Except PDE6, the other more recently discovered PDEs represent potential targets for various clinical indications.

The therapeutic potential of PDEs has been explored in many disease areas, including psychiatry, neurology, inflammation, vascular disease, and respiratory diseases.

For instance, PDE4 inhibitors are evaluated for inflammatory disorders, for the treatment of cognitive disorders, depression, and anxiety, and also for the treatment of atopic dermatitis, and PDE10 inhibitors for the treatment of schizophrenia and Huntington's disease. PDE5 inhibitors are active for several indications, including renal disease. Mixed PDE 3/5 inhibitors are evaluated for the treatment of asthma, atherosclerosis, and intermittent claudication. Recently, PDE9, PDE2, and PDE1 inhibitors entered clinical trials for the treatment of cognitive disorders.

This volume provides the reader with a comprehensive up-to-date overview of medicinal chemistry aspects in the development of selective inhibitors for all therapeutically relevant PDE subfamilies. PDEs are very attractive targets, particularly as they are inhibited by a wide range of different, drug-like chemotypes. Beginning with an overview of the gene family, this book focuses on new and emerging PDE targets and their inhibitors. Drug development options for all major human PDE families are discussed and cover a plethora of diverse therapeutic fields. Separate chapters describe the impact of structural biology on the development of selective inhibitors. Finally, emerging chemotherapeutic applications of PDE inhibitors against malaria and other tropical diseases are discussed.

The series editors are grateful to Spiros Liras and Andy Bell for organizing this volume and to work with such excellent authors. We also thank Frank Weinreich and Heike Nöthe from Wiley-VCH for their valuable contributions to this book and to the entire book series.

Düsseldorf

Raimund Mannhold

Weisenheim am Sand

Hugo Kubinyi

Zürich January 2014

Gerd Folkers

A Personal Foreword

The phosphodiesterase family has attracted the attention of medicinal chemists for over 40 years. Inevitably, this period has seen a number of high and low points. After early setbacks, when multiple inhibitors of PDE3 were found to increase mortality in patients with congestive heart failure, the field exploded following the observation that a selective PDE5 inhibitor, sildenafil (Viagra), could be useful as a treatment for male erectile dysfunction and for pulmonary hypertension. The timing of this discovery in the mid-1990s could not have been more propitious for PDE research, since advances in molecular biology enabled the identification and isolation of six further members of the PDE family, as well multiple sub types and splice variants. Several members of the family were also found to be amenable to structural biology, allowing the design of selective inhibitors against many of the PDE orthologs. From a medicinal chemistry point of view, PDEs are highly attractive at targets, particularly as they are inhibited by a wide range of different, drug-like chemotypes. Despite the continued level of interest in PDE inhibitors in the past decade, there has been no holistic and broad review of the subject, focusing specifically on the medicinal chemistry.

In this volume, we have brought together contributions from the pharmaceutical industry and academia, across multiple therapeutic areas and disciplines, to capture the current level of interest across the whole PDE gene family. Beginning with an overview of the gene family, this book focuses on new and emerging PDE targets and their inhibitors. Drug development options for all major human PDE families are discussed and cover diverse therapeutic fields, such as neurological/psychiatric, cardiovascular/metabolic, pain, and allergy/respiratory diseases. Separate chapters describe the impact of structural biology on the development of selective inhibitors. Finally, emerging chemotherapeutic applications of PDE inhibitors against malaria and other tropical diseases are discussed. We hope that this book will further stimulate interest in the field and lead to a new generation of medicines based on novel indications for additional members of the PDE gene family.

Finally, we would like to thank all the authors and contributors to this volume as well as the support and encouragement of Dr. Heike Nöthe and Dr. Frank Weinreich of Wiley-VCH and Dr. Tony Wood at Pfizer. We are also greatly indebted to Ms. Michele Occhipinti for the finalization and assemblage of the manuscripts for submission to the publisher.

Cambridge, MA

Spiros Liras

London, England January 2014

Andrew S. Bell

1Introduction

Andrew S. Bell and Spiros Liras

The cyclic nucleotide phosphodiesterases (PDEs) are a group of regulatory enzymes that affect intracellular signaling by inactivating the second messengers cyclic guanosine monophosphate (cGMP) and cyclic adenosine monophosphate (cAMP) to the corresponding nucleotides (Figure 1.1). The PDEs are critical in maintaining levels of these cyclic nucleotides within the narrow tolerances required for normal cell operation.

Figure 1.1 Hydrolysis of cyclic nucleotides by PDEs.

The superfamily of PDEs is encoded by 21 different genes that are grouped into 11 subfamilies according to primary sequence homology, composition of the N-terminal regulatory domain, and inhibitor sensitivity. The family has also been split into three sets based on their substrate preferences (Table 1.1). In addition, more than 60 splice variants have been reported.

Table 1.1 Substrate preferences of each class of PDE

cAMP-specific

cGMP-specific

Mixed

PDE4

PDE5

PDE1

PDE7

PDE6

PDE2

PDE8

PDE9

PDE3

PDE10

PDE11

Signal transduction cascades regulated by the PDEs are diverse and include a multitude of central and peripheral processes, such as cell proliferation and cell death, neuroplasticity, gene activation, insulin reaction, locomotion, neurotransmission, metabolism, vascular smooth muscle contraction and growth, and olfactory, taste, and visual responses. Pharmacological intervention of these signaling cascades through selective PDE inhibition is of great therapeutic interest for both central and peripheral targets.

The biological importance and druggability of these enzymes have led to market success with inhibitors for three of the PDE family members across multiple diseases (Table 1.2). The earliest examples include the PDE3 inhibitors amrinone and milrinone for cardiovascular indications, followed by PDE4 inhibitor roflumilast for severe chronic obstructive pulmonary disease. Unfortunately, both PDE3 and PDE4 inhibition result in highly undesirable side effects: sudden cardiac arrest and severe nausea, respectively. As a result, research into novel PDE inhibitors diminished in the late 1980s.

Table 1.2 Peak sales of PDE inhibitors, post-1997

USAN

Structure

Launch date

Target

Indication

Peak sales ($, million)

Amrinone

1983

PDE3

Cardiotonic

20

Milrinone

1989

PDE3

Cardiotonic

228

Roflumilast

2010

PDE4

COPD

104

Sildenafil

1998

PDE5

MED/PH

3119

Vardenafil

2003

PDE5

MED

517

Tadalafil

2003

PDE5

MED/PH/BPH

2222

Udenafil

2009

PDE5

MED

24

Mirodenafil

2009?

PDE5

MED

7.5

Avanafil

2012

PDE5

MED

2.4

Abbreviations

: COPD: chronic obstructive pulmonary disease; MED: male erectile dysfunction; PH: pulmonary hypertension; BPH: benign prostatic hypertrophy.

The commercial breakthrough for PDE inhibitors came from the discovery that the PDE5 inhibitor sildenafil was efficacious in the treatment of male erectile dysfunction. The approval of sildenafil under the brand name Viagra® was followed by the commercialization of closely related analogs, vardenafil (Levitra®/Staxyn®/Vivanza®) and tadalafil (Cialis®/Adcirca®). Two other sildenafil analogs (udenafil (Zydena®) and mirodenafil (Mvix®)) have been launched in some countries. A second generation of PDE5 inhibitors is still in development, with the most advanced example, avanafil (Stendra™), launched first in 2012. Sildenafil was also the first PDE5 inhibitor to be approved for the treatment of pulmonary hypertension (Revatio®), an indication closer to its original target, angina. Tadalafil is also approved for the treatment of pulmonary hypertension; in addition, it has been approved for benign prostatic hypertrophy.

The discovery of clinical utility for PDE5 inhibitors triggered a renaissance in PDE research, leading to the identification of the last six subfamilies of PDEs. These included additional cGMP-hydrolyzing enzymes PDEs 6, 9, 10, and 11, which emerged as potential selectivity targets for the PDE5 inhibitors under development. PDE6 is located predominantly in the eye and remains undesirable off-target pharmacology, but the remainder are potential targets for alternative clinical indications. Pharmaceutical research in pursuit of selective PDE inhibitors for various conditions exploded in the 1990s and the field remains highly active today. In all, more than 1000 original patents for various PDEs have appeared in the literature since 1994. Patent activity peaked in 2004–2005 following the characterization and preclinical validation of targets including PDE10 (Chapter 4) and PDE9 (Chapter 7) and breakthroughs in structural biology and molecular modeling that enabled the generation of hypotheses that led to the discovery of selective PDE4 subtype inhibitors (Chapter 3). Since 2004 there has been a steady flow of more than 70 patents a year from major pharmaceutical companies, biotechnology firms, and academia (Figure 1.2). PDE4 and its subtypes, PDE10 and PDE5 (Chapter 2), have dominated patent activity for a broad spectrum of potential therapeutic indications, including schizophrenia, cognitive decline, vascular disease, and stroke, among others.

Figure 1.2 PDE inhibitor patent landscape 1994–2013 (Data source: Thomson_Reuters Integrity).

Although not yet resulting in clinical candidates that have advanced to proof-of-concept studies, several other PDEs have been explored by medicinal chemists in various companies. Recent advances in the field are summarized in separate chapters on PDE1 (Chapter 9), PDE2 (Chapter 5), PDE7 (Chapter 10), and PDE8 (Chapter 8). The only unexploited mammalian PDEs are PDE6 (due to known undesirable visual effects) and PDE11.

Although all of the approved agents target mammalian PDEs, there is evidence for the existence of PDE orthologs across the whole spectrum of eukaryotes including fungi and parasites. The PDEs from Trypanosoma cruzi and Plasmodium falciparum, the causative agents of Chagas disease and malaria, respectively, have received the most interest (Chapter 11).

All of the PDE inhibitors characterized to date have been shown to interact with the catalytic domain of their respective PDE. Despite there being only two substrates, PDEs appear to be capable of tolerating a wide range of chemotypes as inhibitors, which in turn favors the identification of selective inhibitors, often through structure-aided drug design (Chapters 2 and 6). The first crystal structure reported of any PDE domain was that of the catalytic domain of PDE4B in 2000; this was the starting point for a host of structural studies in this important gene family. Crystal structures have been reported of the catalytic domains of PDE1, 2, 3, 4, 5, 7, 8, 9, and 10, by themselves or in complex with inhibitors, substrates, or products. Unfortunately, structural information on PDE regulatory domains is still lacking, and so far only PDE2 has a crystal structure with all its regulatory domains identified.

As a result of the large investment in the biology of PDEs, which occurred after the discovery and commercialization of sildenafil, today the clinical pipeline across the industry remains highly active. Currently, the clinical exploration of the therapeutic potential of numerous PDEs spans many disease areas, including psychiatry, neurology, inflammation, vascular disease, and respiratory diseases, among others. Some of the compounds that highlight the diversity of the current clinical pipeline include PDE4 inhibitors for inflammatory disorders (OCID-2987, Phase 2; GRC-4039, Phase 2). PDE4 inhibitors are also being evaluated for the treatment of cognitive disorders (HT-0712, Phase 2), as topical agents for atopic dermatitis (HT-0712, HT-0712, and AN-2898, all in Phase 2), and for the treatment of depression and anxiety (GSK-356278, Phase 1). The clinical pipeline is also populated with PDE10 inhibitors in various phases of clinical development for the treatment of schizophrenia and Huntington's disease (PF-2545920, Phase 2 for schizophrenia, Phase 1 for Huntington's disease; OMS-182410 and EVP-6308, both in Phase 1 for schizophrenia). PDE5 inhibitors are active in the clinical pipeline for many indications; worth highlighting is Pfizer's PF-00489791, currently in Phase 2 for renal disease. INDI-702 is a PDE3/5 inhibitor in Phase 3 clinical trials for the treatment of asthma, atherosclerosis, and intermittent claudication. Recently, PDE9, PDE2, and PDE1 inhibitors entered clinical trials for the treatment of cognitive disorders. Overall the diversity of this pipeline offers the promise of new drugs from this gene family.

The growth in PDE research had a profound impact on medicinal chemistry strategies and design principles, which the reader will appreciate in the subsequent chapters. Excellent application of structure-based drug design has been reported in the context of discovering the new generation of PDE inhibitors. Design principles for the use of conserved water have been developed; structural hypotheses for generating exquisitely selective agents have been explored and validated. Design principles that challenged legacy knowledge in terms of central nervous system penetration were developed, and new knowledge emerged that allowed medicinal chemists to expand design space for penetration and other tissue targeting.

2Toward a New Generation of PDE5 Inhibitors through Advances in Medicinal Chemistry

Dafydd R. Owen

2.1 Introduction

Fifteen years after approval, the prototypical phosphodiesterase 5 (PDE5) inhibitor sildenafil (1, Figure 2.1) still represents a landmark in drug discovery. A first-in-class medicine for what was at the time a poorly served indication, PDE5 inhibitors were a breakthrough therapy in sexual health and have rightly garnered much attention in the clinic and through a predictable public intrigue. The erectile dysfunction market is now well served with oral therapies and many years of patient experience and understanding on the efficacy and safety of PDE5 inhibitors. Since the initial approval of sildenafil for male erectile dysfunction (MED) in 1998, competitors were launched in 2003 (vardenafil (2) and tadalafil (3), Figure 2.1), which have themselves now had more than a decade on the market. The in vitro and in vivo pharmacological profiles of these agents have been previously reviewed, and much of the focus for their differentiation was based on pharmacokinetic (PK) parameters that governed speed of onset and duration of action in MED [1–4]. Pharmacological selectivity differences over other PDEs, particularly subtypes 6 and 11, also significantly differentiate these drugs. The efficacy and safety of these medications, combined with an ongoing interest in mechanisms governed by cyclic guanosine monophosphate (cGMP)-regulated processes, have seen a number of attempts to understand the potential utility of PDE5 inhibitors for indications beyond MED. Sildenafil and tadalafil have earned approval for the treatment of pulmonary arterial hypertension (PAH), and sildenafil sees annual sales of $500 million for this indication alone, with double-digit sales growth reported in 2011 and 2012. Efforts to expand the number of indications of these approved agents continue. The impact and profile of these drugs has inspired reviews of the field on several occasions. Two excellent discussions of PDE5 chemotypes up to 2010 are available [5], and other reviews on PDE5 and its potential therapeutic utility have appeared in recent years [6–13].

Figure 2.1 Sildenafil (1), vardenafil (2), and tadalafil (3).

This chapter reviews the medicinal chemistry behind the discovery of novel chemotypes that have appeared since the sildenafil, vardenafil, and tadalafil were approved as the first wave of PDE5 inhibitors. Particular attention is paid to the discovery of two clinical candidates from Pfizer. The Pfizer PDE5 program moved away from its sildenafil template franchise to deliver structurally orthogonal, highly selective PDE5 inhibitors with once-daily dosing pharmacokinetic profiles. In the past decade, PDE5 researchers have continued to design and synthesize compounds with new PDE selectivity and pharmacokinetic profiles suitable for chronic dosing conditions. A number of templates have been discovered in this time for what appears to be a safe and well-tolerated PDE5 mechanism with many potential uses to researchers, and hopefully patients, beyond MED.

2.2 The First-Generation Agents

The profiles of the first-generation agents are briefly summarized here. Sildenafil entered the market as a first-in-class agent for MED and has since been approved for PAH [14]. It has a relatively short half-life, which is suitable for its use in sexual health. It has a low to moderate volume of distribution and moderate to high clearance. It is sometimes associated with visual disturbances due to off-target activity against PDE6, which is found in the retina. Sildenafil is highly selective over other PDE family members. Vardenafil is a very close, almost regioisomeric, analog of sildenafil and is more potent as a PDE5 inhibitor [15]. With a lower dose but a similar pharmacokinetics and associated pro re nata (p.r.n.) dosing regimen as sildenafil, vardenafil has found relatively little clinical differentiation as an agent second to market. As the third agent of the first wave, tadalafil represents a truly orthogonal chemotype and has a half-life of approximately 17 h in humans [16]. Unlike vardenafil, it is a significant structural departure from sildenafil, and this comes with not only the differentiated PK profile but also an alternate PDE family selectivity.

Tadalafil is far less active against PDE6 (780-fold selective over PDE5), and consequently virtually no vision side effects associated with PDE6 inhibition are reported. Tadalafil has low PDE11 selectivity. It has a slower onset of action but a longer duration of action than sildenafil and vardenafil. Its fused tetracyclic structure offers very few rotatable bonds for metabolism, and this drives very low clearance. Its structural rigidity is also likely to minimize off-target pharmacology. Any potential for solubility-based problems from the neutral template and rigid molecular conformation is mitigated by some three-dimensionality to the structure and its low clinical dose [17]. All three agents have parameters that could be addressed in a new generation of PDE5 research for other indications, whether it is enhanced selectivity, duration of action, onset of action, or increased central nervous system (CNS) penetration. As treatments for MED and PAH, there is little doubt that these PDE5 inhibitors have been transformative medicines of great benefit to patients [18].

2.3 PDE5 as a Mechanism and Alternative Indications Beyond MED

For PDE5, a number of these potential further indications were described in a 2010 review [5], and perhaps the best way to summarize these opportunities is simply to list them. The following indications have had the use of PDE5 investigated according to ClinicalTrials.gov: heart failure, erectile dysfunction, Duchenne muscular dystrophy, type 2 diabetes, diabetic nephropathy, chronic kidney disease, Raynaud's syndrome, cardiac allograft vasculopathy, Becker muscular dystrophy, hypertension, schizophrenia, multiple myeloma, aortic stenosis, COPD, head and neck squamous cell carcinoma, sickle cell disease, depression, prostatic hyperplasia, active digital ulcers, ischemic stroke, cerebral vasospasm, chronic fatigue syndrome, meconium aspiration syndrome, Waldenström's macroglobulinemia, traumatic brain injury, angina pectoris, dysmenorrhea, female sexual arousal disorder, lymphangioma, Ménière's disease, pre-eclampsia, and prostatitis. Selected preclinical examples of interest mentioned in the literature over the past 3 years are for PDE5 in Alzheimer's disease, benign prostatic hyperplasia, skin wrinkles, metabolic syndrome, dementia, peripheral nerve regeneration, breast tumors, multiple sclerosis, human African trypanosomiasis, hearing loss, circadian rhythm disorders, premature ejaculation, and memory loss.

2.4 A Summary of PDE5 Chemotypes Reported Post-2010

Although the first wave of agents has already been defined as sildenafil, vardenafil, and tadalafil, two other sildenafil-related structures have also been launched. Udenafil (4, Figure 2.2) and mirodenafil (5) are both approved for MED in South Korea [19,20]. The 2012 approval of the structurally novel avanafil (6) saw the addition of a third chemotype to the field of PDE5 inhibitors [21].

Figure 2.2 Udenafil (4), mirodenafil (5), and avanafil (6).

Many of the structures published and patented after 2010 remain related to sildenafil and tadalafil chemotypes. Since the informative chemotype [22] and patent [23] reviews of recent years, relatively few novel chemical series have been disclosed. The structures in Figure 2.3, taken from 2010 to the present, show some novelty with respect to previously reviewed and disclosed structures [23–27]. The peak of PDE5 patenting was in 2005 with 29 patents. There were 10 patent filings in 2010 and just 3 in 2011.

Figure 2.3 PDE5 chemotypes disclosed since 2010.

2.5 Second-Generation PDE5 Inhibitors from Pfizer: Pyrazolopyrimidines

The chronic dosing requirements for PDE5 inhibitors for the wide range of potential additional indications beyond MED highlighted the need and opportunity for a new generation of research at Pfizer. As useful as the short half-life and associated p.r.n. dosing regimen for sildenafil was (in the context of MED), Pfizer set itself the goal of identifying a new class of PDE5 inhibitors featuring pharmacokinetics suitable for once-daily dosing, with an improved selectivity profile for use in potential chronic dose indications. Should such a molecule be identified, this would constitute an attractive, differentiated profile from the three marketed inhibitors known at the time. Since the discovery of sildenafil, further PDE family members had been characterized (PDE7–11). Along with the challenges associated with modulating half-life, little was known about how to improve PDE6 selectivity, let alone the potential for staying clear of PDE7–11 activity. Pfizer has published on three chemical templates addressed in their post-sildenafil research efforts in seeking novel PDE5 inhibitors [28–30]. The initial, conservative, second-generation agents focused on staying close to sildenafil's pyrazolopyrimidinone template. Despite the apparent success of clinical candidate nominations, the conversion of the sildenafil template into a highly potent and selective template came at the price of optimal human pharmacokinetics. Pyrazolopyrimidinones UK-343664 (12, Figure 2.4) and its improved counterpart, UK-371800 (13, Figure 2.4), both displayed nonlinear oral pharmacokinetics to some degree across the dosing ranges investigated. Ultimately neither compound was deemed sufficiently optimized for progression beyond Phase 2 trials as a chronically administered PDE5 inhibitor. With a decade's worth of medicinal chemistry hindsight, the human P-glycoprotein and cytochrome P450 3A4 (CYP3A4) activity, which came about through the nomination of these relatively large molecules (with molecular weight (MWt) > 520), are believed to be responsible for the non-dose-proportional areas under the curve (AUCs) seen in the clinic with these compounds [31]. A further iteration of clinical candidate nomination took place where the molecular parameters responsible for the pharmacokinetic shortcomings of UK-343664 and UK-371800 were solved. A smaller, less lipophilic candidate (14, Figure 2.4) was identified from the same pyrazolopyrimidinone template where elimination of the metabolic soft spots responsible for the short half-life of sildenafil was matched with the required PDE potency and selectivity expected of a next-generation candidate.

Figure 2.4 Pfizer's sildenafil template follow-up clinical candidates.

The deliberate attempt to introduce new, less vigorous routes of metabolism through the incorporation of a ketone (ketoreductase proved to be a useful non-P450 metabolic pathway for the template) successfully eliminated the primary reasons for nonlinear pharmacokinetics found in the previous candidates. The most notable observation from the disclosure was not related to pharmacokinetics – an observed “flip” in the binding mode for the template. The loyally conserved pyrazolopyrimidinone core was able to orient itself in a completely reversed interaction, while still accommodating the PDE5 pharmacophore of the binding site. This binding mode was also adopted by both UK-343664 (12) and UK-371800 (13) as well, although at the time of their design, this knowledge was not available. Dramatic improvements in PDE6 selectivity based on small changes in inhibitor structure suggested that something significant had occurred in the binding mode. No further information has been reported on the ketone compound 14; however, the observation that pyrazolopyrimidinone could be so versatile in its binding mode directed researchers away from its conservative, sildenafil core modification strategy in the next generation of PDE5 templates (Figure 2.5).

Figure 2.5 Despite considerable 2D similarity between 14 (a) and sildenafil (1, (b)), 14 adopts a “flipped” binding mode when comparing the pyrazolopyrimidinone cores.

Novel chemical series for PDE5 were sought through a full file high-throughput screening (HTS) campaign and specific criteria were set for potential lead matter to offer the best chance of securing a clinical candidate with the desired potency, selectivity, and PK profile. Initial interest would be shown in hits displaying potency and selectivity of PDE5 IC50 < 50 nM and >10-fold selectivity over PDE family members. Leads were subjected to a strict physicochemical property analysis, with MWt < 400, cLogP < 4, and LogD 1–2 deemed attractive. Chemical tractability in terms of design and synthesis space were also assessed as criteria. In reality, the clinical candidates that were secured from this campaign (in two orthogonal chemotypes, as it turned out) did not meet this harsh and inflexible characterization of lead-like attractiveness for their HTS hits. Both candidate successes were optimizations of what were, on first inspection, “significantly flawed” hits against the criteria set out above. Importantly, these hits were not blindly discarded by strict enforcement of perceived rules or the use of prejudicial medicinal chemistry instincts. The chemistry strategies that were used delivered attractive-looking clinical candidates with the desired profile – highly potent and selective PDE5 inhibitors with once-daily dosing pharmacokinetics.

An important legacy of the sildenafil template work and its associated candidates was the delivery of a more robust protein crystallography platform for the catalytic domain of PDE5. The high-throughput soaking method for X-ray crystallography that resulted from having a chimeric PDE5 protein (a function of conserving the PDE5 binding site yet creating an artificial stabilizing region in the protein produced for crystallography) supported a rational, structure-based design program that helped place value on chemical series at the HTS triage stage. Compounds could go from chemical resynthesis to a solved cocrystal structure within a week. Chemical tractability of series in terms of access to monomer-rich, template-enabled parallel synthesis space was highly valued. Pfizer's file enrichment activities of preceding years had been designed to yield HTS enabled for parallel synthesis – as they had been synthesized by these methods in the first place. A series of PDE5-active 6-nitro-2,4-diaminoquinazolines identified from HTS met the criteria for parallel synthesis potential, but failed most other measures of chemotype attractiveness laid out at the start of the program (compound 15, Figure 2.6). Physicochemical properties were well off track (cLogP 5.4, MWt 545), and a nitro group was not an acceptable functional group for long-term incorporation in the chemotype (despite the role it played in binding, as seen in the crystal structure). Although one round of design did keep the nitro group in place, it was eventually removed to look at a simple 2,4-substituted quinazoline template in two dimensions of regioisomeric amine monomer usage. This used the dichloroquinazoline as core in a two-step parallel synthesis protocol (compound 16, Figure 2.6).

Figure 2.6 Pyrimidine-based templates amenable to parallel chemistry.

This was followed up with 2,4-diamino substitutions on closely related pyrimidine-based cores. Unlike the lead matter triaged from the HTS, compounds designed and synthesized in a prospective manner during this library work were subjected to constraints on their physicochemistry and attractiveness. Features likely to secure a desirable PK profile were also incorporated by design through selective monomer usage and computational library design software [32]. One of the core variants identified had echoes of the pyrazolopyrimidinone found in sildenafil. Pyrazolopyrimidine 17 (Figure 2.6) met potency, selectivity, and physicochemical requirements for a promising lead. The moderated basic center, identified by using piperazine as a monomer, secured a very promising human half-life prediction of over 12 h based on a rat PK study. The X-ray structure revealed an obvious strategy to improve potency (Figure 2.7). The so-called PDE5 alkoxy pocket could be easily accessed through extension of the N-1 methyl group in 17 off the pyrazole within the bicyclic core. This maneuver would also tackle PDE10 selectivity because this PDE isoform did not possess a pocket of similar depth in the same region of the protein. This left fellow cGMP PDEs 6 and 11 as the most likely selectivity challenges throughout the forthcoming lead optimization phase for the series.

Figure 2.7 Pyrazolopyrimidine lead 17 bound in PDE5. The N-1 methyl points toward the empty alkoxy pocket.

The synthetically enabled nature of the pyrazolopyrimidine template saw N-1 alkylation improve PDE5 potency as predicted, when substituents greater than the original methyl were used in the alkoxy pocket. The selection of ethoxyethyl became the optimized compromise between potent, overlipophilic options (such as benzyl) and a group of sufficient size to realize the predicted PDE10 selectivity. This aliphatic ether did little to alter the PDE6 and PDE11 selectivities of the lead, but PDE10 activity was eliminated. Unlike the piperazine found in sildenafil, which was shown to be directed toward solvent by an X-ray cocrystal structure (Figure 2.5), the basic center attached to pyrazolopyrimidine template occupied an area buried into the protein (Figure 2.7). The substituent was involved in both hydrophobic interactions from the piperazine carbon atoms and an associated network of water and metal ions solvating the amino NH functionality. Despite the theoretical design space offered by this prototype, with an apparently unoptimized amine-linked substituent, no compelling alternative to piperazine was identified (as judged by a ligand efficiency analysis of subsequent analogs [33]). No selectivity advantages were realized against PDE6 and PDE11 through these changes either. The synthetically most challenging position to modify in the template proved to be the most rewarding as incorporation of a C-3 methyl amide brought about PDE6 and PDE11 selectivities of >100-fold and PDE5 activity of under 1 nM (18, Figure 2.8). Given its polar nature, the C-3 amide also improved molecular physicochemistry even further, with the optimized compound 18 having a cLogP of 2.5 and a MWt of 467. However, the numerous advantages conferred by the amide incorporation compromised the permeability of this C-3 variant. The high proportion of template heteroatoms in general, combined with the presence of three H-bond donors, exposed flaws for the compound in Caco-2 assays of membrane permeability. Ultimately basic amides failed to overcome permeability issues.

Figure 2.8 Basic, neutral, and acidic templates tested in pyrazolopyrimidines.

Sacrificing some of the exceptional potency of the piperazine amides led to a foray into neutral chemotypes by looking at N-ethylamine as a C-5 substituent (19, Figure 2.8) and replacing the basic piperazine found in 18. Unlike the basic series, three H-bond donors were tolerated in the Caco-2 assay for the neutral chemotype 19