Protein-Protein Interactions in Drug Discovery E-Book

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

Seitenzahl: 595

Veröffentlichungsjahr: 2013

Beschreibung

Treating protein-protein interactions as a novel and highly promising class of drug targets, this volume introduces the underlying strategies step by step, from the biology of PPIs to biophysical and computational methods for their investigation.
The main part of the book describes examples of protein targets for which small molecule modulators have been developed, covering such diverse fields as cancer, autoimmune disorders and infectious diseases. Tailor-made for the practicing medicinal chemist, this ready reference includes a wide selection of case studies taken straight from the development pipeline of major pharmaceutical companies to illustrate the power and potential of this approach.

From the contents:

* Prediction of intra- and inter-species protein-protein interactions facilitating systems biology studies
* Modulators of protein-protein interactions: The importance of Three-Dimensionality
* Interactive technologies for leveraging the known chemistry of anchor residues
* SH3 Domains as Drug Targets
* P53 MDM2 Antagonists: Towards Non Genotoxic Anticancer Treatments
* Inhibition of LFA-1/ICAM interaction for treatment of autoimmune diseases
* The PIF-binding pocket of AGC kinases
* Peptidic inhibitors of protein-protein interactions for cell adhesion receptors
* The REPLACE Strategy for generating Non-ATP competitive Inhibitors of Cell-Cycle Protein Kinases

and more

Leseprobe

Contents

Cover

Related Titles

Title Page

Copyright

List of Contributors

Preface

A Personal Foreword

Chapter 1: Protein–Protein Interactions: An Overview

1.1 Introduction

1.2 Role of PPIs in Human Physiology

1.3 Regulation of PPIs

1.4 Structural Features of PPI Interfaces

1.5 Identification of PPI Inhibitors

1.6 Conclusions and Outlook

References

Chapter 2: Prediction of Intra- and Interspecies Protein–Protein Interactions Facilitating Systems Biology Studies

2.1 Introduction: Relevance of Interactome Studies to Disease and Drug Discovery

2.2 Our Current Knowledge of Interactomes Identified from Experiments is Incomplete

2.3 Reliability of Interactions Identified Experimentally

2.4 Computational Methods for PPI Prediction

2.5 Sources of Biological Data in Use to Predict PPIs

2.6 Survey of Current Interactomes

References

Chapter 3: Modulators of Protein–Protein Interactions: Importance of Three-Dimensionality

3.1 Introduction

3.2 Study

3.3 Discussion

3.4 Summary

References

Chapter 4: A Leap into the Chemical Space of Protein–Protein Interaction Inhibitors

4.1 Introduction

4.2 Types of Interaction

4.3 Properties of the Interface

4.4 Orthosteric versus Allosteric Modulation

4.5 Leap into the iPPI Chemical Space

4.6 Case Study

4.7 Conclusions

References

Chapter 5: Interactive Technologies for Leveraging the Known Chemistry of Anchor Residues to Disrupt Protein Interactions

5.1 Introduction

5.2 Druggable Sites in PPIs

5.3 Structure-Based Library Design – A Powerful Alternative to High-Throughput Screening

5.4 New MCR Chemistry to Design PPI Antagonists

5.5 Virtual Screening

5.6 New Interactive Modeling Techniques for Medicinal Chemists

5.7 New Ideas: Hit Rate Validation of Anchor-Centered Screening of p53/MDM2/4

5.8 Summary

Acknowledgments

References

Chapter 6: SH3 Domains as Drug Targets

6.1 Introduction

6.2 Structure

6.3 Variability

6.4 SH3 Binding Motifs

6.5 Selectivity

6.6 Drug Target Selection

6.7 Inhibition Strategies: Peptide and Peptoid Inhibitors

6.8 Small-Molecule Inhibitors

6.9 Conclusions

References

Chapter 7: p53/MDM2 Antagonists: Towards Nongenotoxic Anticancer Treatments

7.1 Introduction

7.2 p53/MDM2 PPI is Characterized by Many Cocrystal Structures

7.3 Nutlins: First-In-Class MDM2 Antagonists

7.4 Johnson & Johnson: Benzodiazepines

7.5 Amgen: Chromenotriazolopyrimidines & Piperidones

7.6 University of Michigan: Spirooxindole

7.7 University of Pittsburgh: Ugi based compounds

7.8 University of Newcastle: Some Scaffolds With No Structural Biology Information

7.9 Outlook

Acknowledgments

References

Chapter 8: Inhibition of LFA-1/ICAM Interaction for the Treatment of Autoimmune Diseases

8.1 Introduction

8.2 Integrin Structure and Activation

8.3 Direct Inhibition of the LFA-1/ICAM Interaction

8.4 Allosteric Inhibitors of the LFA-1/ICAM interaction – IDAS Site

8.5 Summary

References

Chapter 9: The PIF Pocket of AGC Kinases: A Target Site for Allosteric Modulators and Protein–Protein Interaction Inhibitors

9.1 Introduction

9.2 Discovery and Physiological Functions of the PIF Pocket

9.3 Properties of the PIF Pocket Relevant to Drug Development

9.4 Small-Molecule PIF Pocket Ligands

9.5 Potential Supportive Effects Enhancing the Cellular Activity of PIF Pocket-Binding Modulators

9.6 Conclusions

References

Chapter 10: Retosiban and Epelsiban: Potent and Selective Orally Available Oxytocin Antagonists

10.1 Introduction

10.2 Aryl-2,5-DKP Template Discovery and Initial Structure–Activity Relationship Studies

10.3 Synthesis of the RRR and RRS 6-Indanyl-3-isobutyl-7-aryl-2,5-DKP Secondary Amides

10.4 Comparison of Crystal Structures of Oxytocin and 2,5-DKPs

10.5 Pharmacokinetics and Property-Based Design

10.6 In Vivo Potency of 2′,4′-Diflurophenyl Dimethylamide 22

10.7 Synthesis of Tertiary Amides

10.8 Summary of Lead Oxytocin Antagonist 2′,4′-Diflurophenyl Dimethylamide 22

10.9 Further Modifications, Five- and Six-Membered Heterocyclic Derivatives

10.10 Five-Membered Heterocyclic Derivatives and Retosiban

10.11 Summary of Lead Oxytocin Antagonist Retosiban 56

10.12 Six-Membered Heterocyclic Derivatives and Epelsiban

10.13 Summary of Lead Oxytocin Antagonist Epelsiban 77

10.14 Comparison of Lead Compounds

10.15 Conclusions

References

Chapter 11: Peptidic Inhibitors of Protein–Protein Interactions for Cell Adhesion Receptors: RGD Peptides and Beyond

11.1 Introduction

11.2 From the Discovery of the RGD Motif in FN to the First Selective Cyclic RGD Peptide

11.3 N-Methylation of c(RGDfV): Cilengitide and Beyond

11.4 isoDGR Sequence as a New Integrin-Binding Motif

11.5 Conclusions

References

Chapter 12: REPLACE Strategy for Generating Non-ATP-Competitive Inhibitors of Cell Cycle Protein Kinases

12.1 Introduction

12.2 Inhibition of CDKs Through the Cyclin Groove

12.3 Inhibitors of PLKs

12.4 Conclusions

References

Index

Related Titles

Methods and Principles in Medicinal Chemistry

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

Editorial Board

H. Buschmann, H. Timmerman, H. van de Waterbeemd, T. Wieland

Previous Volumes of this Series

Kalgutkar, Amit S. / Dalvie, Deepak / Obach, R. Scott / Smith, Dennis A.

Reactive Drug Metabolites

2012

ISBN: 978-3-527-33085-0, Vol. 55

Brown, Nathan (Ed.)

Bioisosteres in Medicinal Chemistry

2012

ISBN: 978-3-527-33015-7, Vol. 54

Gohlke, Holger (Ed.)

Protein-Ligand Interactions

2012

ISBN: 978-3-527-32966-3, Vol. 53

Kappe, C. Oliver / Stadler, Alexander / Dallinger, Doris

Microwaves in Organic and Medicinal Chemistry

Second, Completely Revised and Enlarged Edition

2012

ISBN: 978-3-527-33185-7, Vol. 52

Smith, Dennis A. / Allerton, Charlotte / Kalgutkar, Amit S. / van de Waterbeemd, Han / Walker, Don K.

Pharmacokinetics and Metabolism in Drug Design

Third, Revised and Updated Edition

2012

ISBN: 978-3-527-32954-0, Vol. 51

De Clercq, Erik (Ed.)

Antiviral Drug Strategies

2011

ISBN: 978-3-527-32696-9, Vol. 50

Klebl, Bert / Müller, Gerhard / Hamacher, Michael (Eds.)

Protein Kinases as Drug Targets

2011

ISBN: 978-3-527-31790-5, Vol. 49

Sotriffer, Christoph (Ed.)

Virtual Screening

Principles, Challenges, and Practical Guidelines

2011

ISBN: 978-3-527-32636-5, Vol. 48

Rautio, Jarkko (Ed.)

Prodrugs and Targeted

Delivery Towards Better ADME Properties

2011

ISBN: 978-3-527-32603-7, Vol. 47

Smit, Martine J. / Lira, Sergio A. / Leurs, Rob (Eds.)

Chemokine Receptors as Drug Targets

2011

ISBN: 978-3-527-32118-6, Vol. 46

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List of Contributors

Seshan Ananthasubramanian

University of Pittsburgh

School of Medicine

Department of Biomedical Informatics and Intelligent Systems Program

5607 Baum Blvd, Suite 401

Pittsburgh

PA 15206

USA

Alan D. Borthwick

DrugMolDesign

15 Temple Grove

London NW11 7UA

UK

Carlos J. Camacho

University of Pittsburgh

Department of Computational and Systems Biology

3501 Fifth Avenue

Suite 3064

Biomedical Science Tower 3

Pittsburgh, PA 15260

USA

Alexander S. Dömling

University of Pittsburgh

Department of Pharmacy and Computational and Systems Biology

3501 Fifth Avenue

Suite 3064

Biomedical Science Tower 3

Pittsburgh, PA 15260

USA

and

University of Groningen

Department of Drug Design

A. Deusinglaan 1

9713 AV Groningen

Netherlands

Matthias Engel

University of Saarland

Research Group PhosphoSites

Department of Pharmaceutical and Medicinal Chemistry

Campus C2 2

PO Box 151150

66041 Saarbrücken

Germany

David C. Fry

Roche Research Center

Discovery Technologies

340 Kingsland Street

Nutley, NJ 07110

USA

Madhavi K. Ganapathiraju

University of Pittsburgh

School of Medicine

Department of Biomedical Informatics and Intelligent Systems Program

5607 Baum Blvd, Suite 401

Pittsburgh, PA 15206

USA

Kevin M. Guckian

BiogenIdec Inc.

Medicinal Chemistry

14 Cambridge Center

Cambridge, MA 02142

USA

Andrew D. Hamilton

University of Oxford

Chemistry Research Laboratory

12 Mansfield Road

Oxford OX1 3TA

UK

Tad A. Holak

Max Planck Institute of Biochemistry

NMR Group

Am Klopferspitz 18

82152 Martinsried

Germany

Horst Kessler

Technische Universität München

Institute for Advanced Study and Center of Integrated Protein Science

Department Chemie

Lichtenbergstrasse 4

85747 Garching

Germany

Kareem Khoury

University of Pittsburgh

School of Pharmacy

1104 Salk Hall

3501 Terrace Street

Pittsburgh, PA 15261

USA

Judith Klein-Seetharaman

Institute of Complex Systems

ICS-5: Molecular Biophysics

52425 Jülich

Germany

and

Department of Structural Biology

University of Pittsburgh

School of Medicine Room 2051

Biomedical Science

Tower 3

3501 Fifth Avenue

Pittsburgh, PA 15261

USA

David R. Koes

University of Pittsburgh

Department of Computational and Systems Biology

3501 Fifth Avenue

Suite 3064

Biomedical Science Tower 3

Pittsburgh, PA 15260

USA

C. Labbé

INSERM

U973

35 rue H. Brion

75205 Paris

France

and

Université Paris Diderot

Sorbonne Paris Cité

UMRS 973

MTi

35 rue H. Brion

75205 Paris

France

Guillaume Laconde

INSERM

U973

35 rue H. Brion

75205 Paris

France

and

Université Paris Diderot

Sorbonne Paris Cité

UMRS 973

MTi

35 rue H. Brion

75205 Paris

France

John Liddle

GlaxoSmithKline Research and Development

Department of Medicinal Chemistry

Medicines Research Centre

Gunnels Wood Road

Stevenage SG1 2NY

UK

James Luccarelli

University of Oxford

Chemistry Research Laboratory

12 Mansfield Road

Oxford OX1 3TA

UK

Carlos Mas-Moruno

Technische Universität München

Institute for Advanced Study and Center of Integrated Protein Science

Department Chemie

Lichtenbergstrasse 4

85747 Garching

Germany

Campbell McInnes

University of South Carolina

Pharmaceutical and Biomedical Sciences

South Carolina College of Pharmacy

Coker Life Science Building

715 Sumter Street

Columbia, SC 29208

USA

Christian Ottmann

Max Planck Society

Chemical Genomics Centre

Otto-Hahn-Strasse 15

44227 Dortmund

Germany

Sylvia Schleker

Institute of Complex Systems

ICS-5: Molekulare Biophysik

52425 Jülich

Germany

and

University of Pittsburgh

School of Medicine

Department of Structural Biology

Pittsburgh, PA 15260

USA

Sung-Sau So

Roche Research Center

Discovery Chemistry

340 Kingsland Street

Nutley, NJ 07110

USA

Daniel M. Scott

BiogenIdec Inc.

Medicinal Chemistry

14 Cambridge Center

Cambridge, MA 02142

USA

Olivier Sperandio

INSERM

U973

35 rue H. Brion

75205 Paris

France

and

Université Paris Diderot

Sorbonne Paris Cité

UMRS 973

MTi

35 rue H. Brion

75205 Paris

France

Sam Thompson

University of Oxford

Chemistry Research Laboratory

12 Mansfield Road

Oxford OX1 3TA

UK

Bruno O. Villoutreix

INSERM

U973

35 rue H. Brion

75205 Paris

France

and

Université Paris Diderot

Sorbonne Paris Cité

UMRS 973

MTi

35 rue H. Brion

75205 Paris

France

Preface

In the common definition of the proteome it is considered to be the set of expressed proteins in a given type of cells or an organism at a given time under defined conditions. It is larger than the genome, due to special mechanisms in the biogenesis of proteins, which render them more numerous than the genes at the end. What, however is very special to the proteome is its enriched complexity which arises both from the protein's 3D structure and the functional interaction of the proteins.

Proteins talk to each other. They do it very frequently and in different ways and obviously in large communication networks of sophisticated structure. For yeast, recent research has suggested kind of social life in protein communication:

This distinction suggests a model of organized modularity for the yeast proteome, with modules connected through regulators, mediators or adaptors, the date hubs. Party hubs represent integral elements within distinct modules and, although important for the functions mediated by these modules (and therefore likely to be essential proteins), tend to function at a lower level of the organization of the proteome. We propose that date hubs participate in a wide range of integrated connections required for a global organization of biological modules in the whole proteome network (although some date hubs could simply be ‘shared’ between, and mediate local functions inside, overlapping modules). (...) Finally, it is possible that discriminating between date and party hubs might also help to define new therapeutic drug targets.1

Well, there we are in defining ambitious goals for drug development. Interfering with the party gossip and intruding the clandestine dates of proteins for sake of therapeutic benefits is still the freestyle of drug design. The complexity is huge. Large interfaces that resemble flat landscapes, lacking cosy caves or deep pockets, where small molecules might dock made protein-protein interactions clearly undruggable for a long time. With the advent and success of monoclonal therapeutic antibodies (mAbs) however, this view changed. The benefits of mAbs in the cancer and immune-disease areas showed that interfering with protein-protein interactions (PPIs) is indeed a practicable approach. Unfortunately the proteins parties and dates are taken place inside the cell, with no admittance for mAbs. Hence, the challenge or the ”reaching for high-hanging fruit”2 is to interfere therapeutically by use of small molecules.

In the present volume Alexander Dömling and his co-authors depict a scenario that reveals more than a silver lining on the horizon. There is a variety of new (and old) targets and a plethora of new approaches and insights into molecular mechanisms which raise the hope that in the near future small molecule interference of protein-protein interactions will emerge as a new functional class of therapeutics. Twelve chapters illuminate opportunities, strategies, success stories and pitfalls in the discovery of small molecules targeting protein-protein-interactions.

While this volume grants an encompassing view on the state-of-the-art in the PPI field, it is at the same time structuring the future, since it paves the way for a hopefully greater commitment in drug discovery focusing PPIs.

Not least because of this, the series editors are indebted to the authors and the editor who made this comprehensive issue possible. We are convinced that the book represents an important contribution to the body of knowledge in drug discovery and that it matches the interests of many researches who have adjourned to a promising but rocky field.

In addition, we are very much indebted to Frank Weinreich and Heike Nöthe, both at Wiley-VCH. Their support and ongoing engagement, not only for this book but for the whole series “Methods and Principles in Medicinal Chemistry” adds to the success of this excellent collection of monographs on various topics, all related to drug research.

November 2012

Düsseldorf

Weisenheim am Sand

Zürich

Raimund MannholdHugo KubinyiGerd Folkers

Notes

1. Jing-Dong J. Han, Nicolas Bertin, Tong Hao, Debra S. Goldberg, Gabriel F. Berriz, Lan V. Zhang, Denis Dupuy, Albertha J. M. Walhout∗, Michael E. Cusick, Frederick P. Roth & Marc Vidal. Evidence for dynamically organized modularity in the yeast protein–protein interaction network. Nature, 430, 2004, pp. 88-93

2. James A. Wells and Christopher L. McClendon. Reaching for high-hanging fruit in drug discovery at protein–protein interfaces. Nature 450, 2007, 1001-1009

A Personal Foreword

Therapeutic targeting of protein–protein interactions (PPIs) has been in the past largely the domain of biotech industries. With their exquisite natural selection process, and the resulting high affinity and selectivity towards their targets, monoclonal antibodies (mAbs) and similar biologics have been the only way to target large protein interfaces to effectively compete with the endogenous interaction. Meanwhile, mAbs have overcome their early issues, and the generation of safe, specific, high-affinity, and nonimmunogenic antibodies has become a reality. In fact, a switch of the pharmaceutical industry from focusing traditionally on small molecules towards the biotech drugs has recently been observed based on the therapeutic and business success of the biologics; major takeovers of biotech companies by big pharma excite the industry and shareholders. Severe conditions can meanwhile be treated with mAbs, including some cancers, Crohn's disease, rheumatoid arthritis, transplant rejection, or macular degeneration, just to name a few. However, large biomolecules like mAbs also have intrinsic disadvantages that are hard to overcome, such as lack of oral bioavailability, high cost of goods, and perhaps most importantly mAbs can only target extracellular accessible structures. The majority of PPI drug targets, are, however, localized intracellularly.

The strength of small molecules, in principle, is to overcome exactly the issues of mAbs and similar biologics: they can be made orally bioavailable and decorated with advantageous pharmacokinetics/pharmacodynamics properties, they can be produced orders of magnitude cheaper then biologics, and they can also be designed to penetrate cell membranes to reach intracellular targets. Therefore, small molecules should be ideal to disrupt PPIs. However, PPIs very often consist of large interfaces of greater than 1000 Å2 and do not contain the deep pockets medicinal chemists are used to from other target areas, such as kinases, G-protein-coupled receptors, or proteases. Pocket dimension, form (concave versus convex), and hydrophobicity are, however, key features defining the druggability by small molecules. Analysis of the plethora of available crystal structures of PPIs reveals that only a fraction of PPIs fit the druggability criteria. Nevertheless, while PPIs as a class were considered as undruggable a decade ago, several small molecules advancing into clinical trials recently clearly support the notion that at least a fraction of the PPIs are not only attractive therapeutic targets, but can also be developed to drugs. It can be foreseen that in the future many more small molecules targeting PPIs will emerge for the treatment of unmet medical needs.

This book aims to address an audience including medicinal chemists, organic chemists, and other interested readers. In 12 chapters written by experts in their fields I try to introduce the reader to the problems and opportunities associated with targeting PPIs by small molecules. Introductory overviews pave the way for specific medicinal chemistry showcases on developmental compounds. Additionally, several chapters introduce technologies relevant for PPI drug discovery, including the interactome and computational chemistry.

Ottmann gives an excellent introductory overview on different PPI drug discovery approaches and compound classes, and the structural features of their interacting proteins.

Next, Schleker et al. introduce the reader to different techniques used in systems biology to define the interactome of different species. Scope and limitations of the current experimental and computational identification approaches to obtain interactomes related to human are discussed. Cleary only careful comparison of the large-scale results of orthogonal experimental approaches can lead to meaningful results and a deeper understanding of the interactome's wide regulation of life.

Fry and So stress the importance of three-dimensionality in the modulation of PPIs – a shape feature often under-represented in company screening libraries. From structural analysis based on the Protein Data Bank (PDB) database they deduce simple rules of thumb for when a particular PPI is druggable by small molecules.

Villoutreix et al. introduce the reader to computational chemistry approaches towards PPI drug discovery. Detailed discussions on the relationship and complementarity of the shape of the receptor binding site and the scaffold shape clarify why traditional chemical space is relatively unsuited to find PPI antagonists. The specifics of PPI-targeting compound classes are elaborated in a detailed analysis of many descriptors. Rather novel scaffold and privileged structures are needed to address the PPI interfaces.

Web-based techniques to computationally predict small-molecule PPI inhibitors are introduced by Camacho et al. The AnchorQuery™ approach makes use of the disproportional high importance of anchoring residues in PPIs, and queries the very large chemical space and one-pot accessibility of multicomponent reactions (MCR). Again, the importance of suitably designed libraries for PPIs is stressed.

Luccarelli et al. review the Src homology 3 (SH3) domain as a drug target. SH3 domain proteins comprise a very large class with implications in multiple therapeutic areas. The structural biology is reviewed and, based on the understanding of specific features of the binding pocket, current inhibitor design is discussed.

The PPI of the transcription factor p53 and the oncogene MDM2 is amongst the most intensively studied PPIs with several compounds in late preclinical and early clinical development. Khoury et al. review this area with a focus on small-molecule classes supported by structural biology information, their structure–activity relationships (SARs), and the methods of initial hit finding.

Guckian reviews the area of inhibitors of the lymphocyte function-associated antigen-1/intracellular adhesion molecule (LFA-1/ICAM) interaction for the treatment of autoimmune diseases. LFA-1/ICAM is a case where a recently approved mAb had to be withdrawn from the market due to fatal side-effects. Structural biology as well as different inhibitor classes and their SAR are discussed. Several small molecules are currently being evaluated in clinical trials.

Engel reviews the PIF-binding pocket of the subclass of AGC kinases, which serves as a target site for allosteric modulators and PPI inhibitors. Major advantages of targeting non-ATP sites of kinases would be to obtain more selective compounds and to target kinases previously considered to be nondruggable. The recent discovery of different classes of AGC kinase pocket binders makes this an important area of research.

The discovery and medicinal chemistry evolution of oxytocin receptor antagonists is reviewed by Borthwick and Liddle. Their efforts have led to Retosiban and Epelsiban – two orally bioavailable oxytocin receptor antagonists with superior potency and selectivity for the treatment of preterm birth and related disorders.

Mas-Moruno and Kessler describe peptidic inhibitors targeting cell adhesion receptors (e.g., RGD peptides). Although peptides are not considered as small molecules, much can be learned from the specific modes by which peptides interact with their targets for the development of small-molecule PPI inhibitors.

Last, but not least, McInnes reviews another method to allosterically inhibit the cyclin-dependent kinase (CDK) kinase class by targeting the substrate recognition site. The REPLACE algorithm for the structure-based prediction of PPI binders has been applied to the Polo-box domain of PLK1 (Polo-like kinase 1), resulting in small peptides that are N- and C-capped by organic residues.

The area of small molecules successfully targeting PPIs has recently exploded and therefore only a glimpse of the exciting research in the area can be reflected by the present book. Many interesting works could not be included. To finish, and in the tradition of the Editor's choice, I want to point the reader to several more exciting recent targets.

The small G-protein and oncogene Ras has been recognized for several decades as a major oncology target. A large portion of lung, colon, and pancreas cancer patients bear constitutively active Ras mutations that drive cancer growth. However, until recently no small-molecule drug has been known to directly bind to and effectively modify the downstream pathway. Lately, novel biophysical techniques have shown promise by identifying small molecules inhibiting the Ras effector complex Ras–Sos (Figure 1a) and cocrystal structures solved by two independent groups provide hope that the initial fragment-based hits can be further elaborated towards effective drugs [1,2].

Figure 1 (a) Indole-3-thiocarbonylpiperidine fragment bound to Ras on the Sos interacting interface (PDB ID: 4EPV). (b) Small molecule mimicking the p53 Lys-Me binding to SMYD2 and extending with the dichlorophenyl moiety into a nearby hydrophobic pocket not occupied by the peptide (PDB ID: 3S7B). (c) Small molecule anchoring via the central hydroxyproline ring to the VHL complex and thus inhibiting the contact to HIF-1α (PDB ID: 3ZRC). (d) Cut-away view of the Gewald thiophenodiazepine JQ1 bound into the bromodomain of BRD4 into the Ac-Lys binding site (PDB ID: 3MXF).

Protein lysine methyltransferases are important regulators of epigenetic signaling. The oncogenic protein SMYD2 represses the tumor suppressors p53 and Rb by a PPI. The use of structural biology information cannot be overestimated, and the structure of apo-SMYD2, SMYD2 bound to a methylated p53 peptide, and in complex with a small molecule competitively inhibiting p53 binding was published recently (Figure 1b) [3].

The von Hippel–Lindau (VHL) syndrome is a rare autosomal dominant genetic orphan disease characterized by abnormal angiogenesis in certain parts of the body. The E3 ubiquitin ligase VHL complex primarily targets the hypoxia-inducible factor (HIF)-1α – a transcription factor involved in the regulation of numerous genes (i.e., involved in angiogenesis and cancer). Using in silico methods and structure guided medicinal chemistry the first small molecule ligand for VHL was recently described. The authors used the hydroxyproline motif of HIF-1α as an “anchoring” starting point for their medicinal chemistry efforts (Figure 1c) [4]. Derivatives of the first-generation compounds might evolve into cell-penetrating chemical probes to test the involvement of the VHL complex in disease conditions such as chronic anemia, acute ischemia, and stroke.

Bromodomains are reader elements in the framework of epigenetic control and recognize sequence-specific acetylated lysine side-chains of histones and other proteins. Two small-molecule inhibitors of the LysAc-bromodomain PPI are currently undergoing clinical evaluation for the treatment of artherosclerotic cardiovascular disease, and testis midline and other cancers (Figure 1d) [5,6]. As for many areas in PPIs, the availability of X-ray structures of Apo, Ac-Lys, and ligand-bound protein proved to be invaluable in the early discovery process. A major challenge of the area will be the design of selectivity into the small molecules targeting one of the 61 very similar bromodomains found in the human genome.

I have enjoyed editing this book, and I hope that readers will benefit from the expert reviews on cutting-edge small-molecule PPI research and development.

October 2012

Groningen

Alexander Dömling

References

1. Maurer, T. et al. (2102) Proceedings of the National Academy of Sciences of the United States of America, 109, 5299.

2. Sun, Q. et al. (2102) Angewandte Chemie International Edition, 51, 6140.

3. Ferguson, A.D. et al. (2011) Structure, 19, 1207.

4. Buckley, D.L. et al. (2012) Journal of the American Chemical Society, 134, 4465.

5. Filippakopoulos, P. et al. (2010) Nature, 468, 1067.

6. Nicodeme, E. et al. (2010) Nature, 468, 1119.

1

Protein–Protein Interactions: An Overview

Christian Ottmann

1.1 Introduction

Protein–protein interactions (PPIs) are implicated in almost all biological processes for any given protein engaged in complexes with other proteins for the majority of its lifetime. In this regard, proteins function not merely as single, isolated entities, but display their roles by interacting with other cellular components. The different interaction patterns are at least as important as the intrinsic biochemical activity status (e.g., of a protein kinase) of the protein itself. Therefore, to understand the biological role of a protein it is of the utmost importance to know the underlying PPI network. This holds especially true in the case of diseases where, for example, mutations in oncogene or tumor suppressor proteins are recognized as the cause for malignancies. An impressive recent example for the relevance of the PPI interplay is the finding that active-site inhibitors targeting the oncogenic kinase B-Raf can under certain circumstances activate the underlying signal transduction pathway (mitogen-activated protein kinase (MAPK) pathway) instead of inhibiting it [1–3]. This finding is a strong reminder that nature in the majority of cases ultimately relies on regulating protein function by PPIs. In addition to taking into account this important concept for the drug development process, targeting PPIs significantly enlarges the “druggable genome” that was initially estimated to comprise around 1500 single protein targets [4]. While this number is still several times higher than the 266 human protein targets actually addressed by currently approved drugs [5], there are diseases that lack a good “conventional” target like an enzyme, receptor, or ion channel. By adding the number of PPIs occurring in the human body, the so-called protein–protein “interactome,” this situation will definitely be improved. As the size of the interactome has been estimated to lie between 130 000 [6] and 650 000 [7], successfully addressing PPIs will vastly expand our opportunities for pharmacological intervention.

1.2 Role of PPIs in Human Physiology

Direct physical interactions of proteins are intricately implicated in the majority of processes in living organisms (Figure 1.1). For example, reception and propagation of growth signals can start with the binding of a proteinaceous signaling molecule like the epidermal growth factor (EGF) to its cell surface receptor (EGFR). This binding triggers the intracellular assembly and activation of signaling complexes comprised, for example, of adapter proteins like Grb2 and Sos and small G-proteins like Ras that – again by physically interacting – activate protein kinases like Raf. Activated Raf then stimulates a phosphorylation cascade via the kinases MEK (mitogen-activated protein kinase/extracellular signal-related kinase) and ERK (extracellular signal-related kinase) that ultimately leads to gene activation via transcription factors like Sp1 and Elk [8]. As each of these steps necessitates direct binding of the components of this signal transduction chain, small molecules inhibiting these interactions could disrupt this proproliferative signaling. Furthermore, stabilization of the inhibitory binding of regulatory proteins like the Raf kinase inhibitory protein (RKIP) [9] and 14-3-3 to components of the pathway (e.g., Raf) might also produce a therapeutic benefit.

Figure 1.1 Examples of the role of PPIs in human physiology.

Many cellular functions like motility are related to functional changes in the cytoskeleton. For example, dynamic assembly and disassembly of actin filaments are based on the interaction of actin with itself and with protein partners like ADF/cofilin and profilin [10]. Biological (surface) recognition, like in the immune system, is also mediated by PPIs as in the case of binding of lymphocyte function associated antigen (LFA)-1 presented on the surface of immune cells to intracellular adhesion molecule (ICAM)-1 found on the surface of endothelial cells [11]. This interaction enables immune cells to attach to the walls of blood vessels and to migrate into neighboring tissue to initiate inflammation.

The control of subcellular localization is another important aspect of protein regulation performed by PPIs. For example, the transcription factor NFκB is prevented from nuclear import upon complexation with its negative regulator IκB [12]. The 14-3-3 adapter proteins play a similar role in the case of the FoxO transcription factor family [13]. Also, direct regulation of biochemical activity by PPIs is performed many times by PPIs. The phosphatase calcineurin is activated upon complexation with Ca2+-activated calmodulin and repressed upon binding to cabin (calcineurin binding protein) or calcipressin [14]. Another important process involving PPIs is the functional constitution of transcriptional complexes. While transcription factors of the Tcf (T cell factor) LEF (lymphoid enhancer factor) family can directly bind to DNA, transcription starts only when coactivators like β-catenin additionally interact with Tcf/LEF [15]. Many proteins of disease-causing organisms need host proteins as cofactors for their pathogenic activity. For example, exoenzyme S from Pseudomonas aeruginosa, an opportunistic, pneumonia-causing bacterium, has to interact with host 14-3-3 proteins to be able to transfer an ADP-ribose moiety from NAD+ to small G-proteins like Ras [16], thereby inhibiting its target proteins [17].

1.3 Regulation of PPIs

Given the importance and number of PPIs in the living cell it is no surprise that they have to be tightly orchestrated at any moment in time. The occurrence and perseverance of PPIs is governed by the two principal variables local concentration and intrinsic binding energy of the binary interaction [18]. The first is regulated by transcriptional and translational mechanisms, subcellular (co-)localization, degradation rates, and temporary storage. The second can be influenced by covalent modifications like phosphorylation, and by changes in pH, ionic strength, and temperature (Figure 1.2). Furthermore, additional PPIs can modulate binary interactions. They can be inhibitory when, for example, the interaction interface of one partner is masked by binding to the same interface or by simple sterical obstruction. They can also be stabilized, for example, when the third interacting protein binds simultaneously to both protein partners. Such a “bridging” or “assembly platform” function has been described for the A-kinase anchoring proteins (AKAPs) [19] and the kinase suppressor of Ras (KSR) [20]. It is now clear that the local architecture of such signaling complexes is one of the keys to understand regulation and specificity of signaling events.

Figure 1.2 Factors governing the occurrence and perseverance of PPIs. Important control mechanisms for the oligomerization state of interacting proteins. The association–dissociation equilibrium between monomeric and multimeric states is regulated by the partners' local concentration and their mutual binding affinity. Additional cellular or pharmaceutical factors can compete for one partner or stabilize the dimeric complex. (Adapted from Nooren and Thornton [18].)

1.4 Structural Features of PPI Interfaces

PPIs can be established between identical and nonidentical protomers leading to homo- or heterodimeric complexes, respectively. In the following, a number of examples are discussed in more detail. Small-molecule inhibitors have been identified for these PPIs (Table 1.1), strongly validating the general approach to pharmacologically interfere with the interaction of proteins.

Table 1.1 Small-molecule PPI inhibitors from the pharmaceutical industry.

1.4.1 iNOS Homodimer

An example for a homodimeric protein complex is the inducible nitric oxide synthase (iNOS) that produces the signaling molecule NO from l-arginine [36–38]. To perform its catalytic activity NOS depends on the tightly bound cofactors tetrahydopterin (H4B), flavin adenine dinucleotide (FAD), flavin mononucleotide (FMN), and iron protoporphyrin IX (heme). This enzyme is only active as a homodimer, and the crystal structures of the (dimeric) oxygenase domain [38] explained this fact by showing that the dimerization interface shapes the functional binding sites for the cofactors H4B and heme (Figure 1.3). It also displays a large intersubunit cavity of about 750 Å3 that is separated from the surrounding bulk solvent when a zinc ion is coordinated by two cysteines from protomer A and two cysteines from protomer B. With 69% nonpolar and 31% polar amino acids, the interface of the iNOS dimer shows a distribution that is typical for the majority of known homodimers. The contact surface of roughly 2900 Å2 is rather flat. Nonetheless, mainly due to the special situation characterized by interface-bound cofactors, inhibitors of dimer formation could be identified successfully.

Figure 1.3 Structure of the iNOS homodimer. General topology of the iNOS dimer, and expanded, detailed view of the dimer interface with the cysteine-coordinated zinc ion and the cofactors H4B and heme.

1.4.2 β-Catenin/Tcf4 Complex

The Wnt pathway found to be constitutively activated in many colorectal cancers is dependent on the interaction of β-catenin with transcription factors of the Tcf/LEF family. Normally, the transcriptional coactivator β-catenin can be sequestered in the cytoplasm and the Tcf transcription factor is inhibited by complexation with negative regulators of the Groucho family [39]. Upon Wnt activation, β-catenin is translocated into the nucleus and binds to Tcf to constitute the active transcriptional complex [40]. The crystal structure of the human β-catenin/Tcf4 complex [41,42] revealed the multisite binding nature of the interaction with three regions of Tcf4 to be important for binding to β-catenin (Figure 1.4): (i) an extended N-terminal sequence, (ii) a kinked α-helix, and (iii) a second extended segment followed by the C-terminal α-helix. The binding module of Tcf4 wraps around the 12-membered armadillo-repeat region of β-catenin. Three essential interaction “hotspots” have been identified in the β-catenin/Tcf4 interface; a salt bridge between Tcf4 Asp16 and β-catenin Lys435, a hydrophobic contact of Tcf4 Leu48 to Phe253 and Phe293 of β-catenin, and a second salt bridge between Glu29 of Tcf4 and β-catenin Lys312. Disruption of one (or several) of these contacts by a small-molecule PPI inhibitor may successfully abolish binding of Tcf4 to β-catenin.

Figure 1.4 Complex of Tcf4 (black ribbon) bound to β-catenin (gray ribbon). Three hotspots of the interaction are presented in structural detail with key residues of Tcf4 (black sticks) and β-catenin (light gray sticks) labeled. Polar contacts are shown as black dotted lines.

1.4.3 LEDGF/HIV-IN Complex

For a productive infection HIV depends on the viral integrase (IN) that integrates the genetic material of the virus into the host cell's DNA [43]. The human transcriptional coactivator LEDGF (lens epithelium-derived growth factor) is an essential host protein as cofactor for the function of IN that, among others, locates IN to the nucleus [44]. The interaction is mediated between the catalytic core domain (CCD) of IN and the IN-binding domain (IBD) of LEDGF [45]. The IN CCD/LEDGF IBD complex crystallized as an IN CCD dimer with two LEDGF IBD copies attached at opposing sites (Figure 1.5) [46]. An interhelical loop of IBD binds to a pocket at the IN dimer interface burying approximately 1300 Å2 of protein surface. Binding is driven by the hydrophobic contact of LEDGF residue Ile365 to a pocket concomitantly established by IN residues Leu102, Ala128, Ala129, and Trp132 from one chain of the IN dimer (chain B), and Thr174 and Met178 from the other chain of the dimer (chain A). A second hydrophobic interaction is formed by Phe406 and Val408 of LEDGF that contact Trp31 of chain B of the IN dimer. Furthermore, LEDGF Asp366 makes a bidentate hydrogen bond to the main chain amides of Glu170 and His171 from chain A of IN.

Figure 1.5 Crystal structure of the LEDGF/IN complex. Residues important for the interaction are depicted as black (LEDGF) or light gray (IN) sticks and polar interactions are represented by dotted black lines.

Since mutational studies had shown that Ile365Ala, Asp366Ala, and Phe406Ala substitutions in LEDGF completely abrogate the LEDGF/IN interaction these sites identified in the crystal structure represent promising hotspots for PPI inhibition by small molecules.

1.4.4 HPV E1/E2 Complex

Another PPI that is essential for the pathogenicity of a viral infection is the E1/E2 complex of human papillomavirus (HPV). For successful replication a so-called prereplication complex must be formed that consists in the case of HPV of only two proteins, E1 and E2. E1 is the viral initiator protein that recognizes the viral origin and converts into the functional helicase [47]. For its full function, E1 needs to bind to E2 that helps to target E1 monomers to viral origins and assists in the assembly of the active helicase [48,49]. The overall topology of the HPV E1/E2 complex resembles a “C” with the top and the site formed by the E2 activation domain and the bottom by E1 burying 940 Å2 of surface area per protomer [50]. Several essential contacts especially in the loop region between helices 2 and 3 in E1 have been identified, for example Arg454 that forms a salt bridge with Glu43 of E2. A hydrophobic hotspot is the interaction between Ile461 of E1 and Tyr23 as well as Leu98 of E2 (Figure 1.6).

Figure 1.6 Structure of the HPV E1/E2 complex. Hotspot residues are shown as black (E1) or light gray (E2) sticks and polar contacts are depicted as black dotted lines.

While the interaction surface of the globular E1 is rather flat, the corresponding contact surface of E2 displays some pocket-like features that would allow binding of small molecules. Therefore, it is no surprise that a successfully identified PPI inhibitor of the E1/E2 interaction was found to target E2 rather than E1 [51].

1.4.5 IFN-α/IFNAR Complex

Interferons (IFNs) are important signaling molecules that were discovered in the late 1950s as agents that interfere with the replication of the influenza virus [52], prompting their use as effective antiviral treatments. Due to their recognized role in enhancing immune responses and the modulation of normal and tumor cell survival, IFNs are also used in some cancer and multiple sclerosis therapies [53]. However, in certain pathophysiological conditions such as type I diabetes, IFN signaling can have deleterious effects, leading, for example, to inflammation that results in apoptosis of insulin-producing pancreatic β-cells [54]. Therefore, also the identification of pharmacological agents that attenuate IFN action by inhibiting binding of IFN-α to its receptor (IFNAR) is of therapeutic interest. In this regard, elucidation of the structural basis of IFN-α interactions with IFNAR was considered important. The structure of the IFN-α2/IFNAR2 complex was reported in 2011 (Figure 1.7) [55].

Figure 1.7 Structure of the IFN-α/IFNAR2 complex. Two hotspot regions have been identified in the extensive interface. Residues from IFN-α that contribute to essential contacts are shown as black sticks and those of IFNAR2 are shown as light gray sticks.

Examination of the interaction interface reveals that the single most important amino acid of IFN-α2 for binding to IFNAR2 is Arg33, forming an extensive hydrogen-bond network with the side-chain of Thr44 and the main-chain carbonyl oxygen atoms of Ile45 and Glu50 of the receptor. Mutating Arg33 to alanine reduces the affinity of the interaction by a factor of 4 × 105, literally abrogating the binding of IFN-α2 to IFNAR2 [55]. Another important polar contact is a salt bridge between Arg149 of IFN-α2 and Glu77 of IFNAR2, whose disruption by the mutation Arg149Ala reduces the affinity of the complex by two orders of magnitude. With regard to hydrophobic interaction clusters, two can be found in the IFN-α2/IFNAR2 interface. The first is formed between Leu15 and Met16 of IFN-α2 and Trp100 and Ile103 of IFNAR2. The second involves a hydrophobic patch comprised of Leu26, Phe27, Leu30, and Val142 of IFN-α2 that contacts a corresponding patch in IFNAR2 build from Thr44, Met46, and Leu52. The substitutions of Met148Ala in IFN-α2 or Ile103Ala in IFNAR2 reduces binding 10- to 30-fold.

1.4.6 TNF-α Trimer

A further important protein hormone molecule is the tumor necrosis factor (TNF)-α that is produced predominantly by activated macrophages and lymphocytes, and plays a central role in inflammation processes [56]. TNF-α's name is derived from its activity to induce hemorrhagic necrosis of certain transplantable tumors in mice and its cytotoxicity towards a variety of tumor cells in culture [57,58]. The physiological functions of the molecule are conferred by binding to surface-expressed receptors [59]. Therapeutic antibodies that directly target TNF-α like etanercept (Enbrel™; Amgen Incorporated, Thousand Oaks, CA/Wyeth Pharmaceuticals/Pfizer, Collegeville, PA), infliximab (Remicade™; Centocor, Horsham, PA/Schering-Plough/MSD, Kenilworth, NJ), and adalimumab (Humira™; Abbott Laboratories, Abbott Park, IL) have produced significant advances in the treatment of rheumatoid arthritis and corroborated the feasibility of addressing this signaling protein. Active TNF-α has been shown to be a trimer in solution [60]. The crystal structure of the TNF-α trimer (Figure 1.8) revealed an interface that buries 2200 Å2 of each subunit involving some 40 residues [61]. Eighteen of these are glycine, alanine, valine, leucine, isoleucine, or proline, five are tyrosine or phenylalanine, another eight are uncharged polar, and the remaining nine residues are charged. The latter are responsible for polar intersubunit interactions that are predominant at the top of the dimer where an intrasubunit disulfide bride is also located. Salt bridges can be found between Glu104 of one and Arg103 of the adjacent subunit, and between Lys11 and the terminal carboxylate at Leu157. A hotspot of hydrophobic interactions is formed by a cluster of three tyrosines (Tyr59, Tyr119, and Tyr151). Notably, this is the region that binds a small molecule that has been identified to disrupt the functional TNF-α trimer [23].

Figure 1.8 Structure of the TNF-α trimer. Three areas important for formation of the trimer have been identified, one each at the “front” (top) and the “back” (bottom) of the trimer and one in the center of the molecule.

1.5 Identification of PPI Inhibitors

In the past years numerous PPI interactions have been addressed successfully with small-molecule inhibitors, adding up to several hundred molecules targeting more than 40 protein complexes [62]. In addition to many reports from academic institutions, the pharmaceutical and biotech industry plays an important role (Table 1.1). A wide variety of methodological approaches and techniques have been used for the primary identification of PPI inhibitors. An encoded combinatorial chemistry library was screened in a whole-cell assay for inhibitors of NO production identifying pyrimidinimidazoles that inhibit iNOS activity by disrupting homodimer formation [63]. These molecules were further optimized to yield compound 21b (Table 1.1 and Figure 1.9) that inhibited NO production in A172 cells with IC50s in the subnanomolar range [27]. Small-molecule PPI inhibitors of the β-catenin/Tcf interaction, like ZTM00990 (Figure 1.9), were identified from a library of 7000 purified natural products [64]. The group of Debyser reported the in silico identification of a lead compound disrupting the LEDGF/p75 interaction with HIV IN [65]. To this end, they started their investigations with a 200 000-compound virtual library that was scanned for suitable small molecules. Remarkably, the algorithm employed was so powerful that only 25 compounds had to be tested in a biochemical assay to identify and validate the hit molecule compound 6 (Figure 1.9). A screen for HPV E1/E2 interaction inhibitors with a 140 000-compound library produced one lead structure for further development [30]. A derivative thereof (inhibitor 2, Figure 1.9) was later cocrystalized with E2 revealing the compound bound to the pocket that lies in the contact surface with E1 [51].

Figure 1.9 Small-molecule inhibitors of PPIs.

Recently, Schneider et al. reported the first PPI inhibitor of the IFN-α/IFNAR interaction [66]. Starting from the nuclear magnetic resonance (NMR) structure of unbound IFNAR (Protein Data Bank ID: 1TIF) they identified druggable sites on the protein interaction surface. These were used for the generation of a pharmacophore that was screened against a 556 763-virtual-compound library identifying one lead compound (compound 1, Figure 1.9). To inhibit TNF action, a 285-membered initial library was used as a starting point for a combinatorial fragment assembly strategy that led to the identification of 15 fragments whose possible combinations were subsequently tested. These investigations revealed a molecule (SP307, Figure 1.9) that potently disrupted the TNF-α trimer, thereby abrogating the binding to its receptor [23].

In addition to the examples presented here in more structural detail, there are some “classical” success stories of PPI inhibition with small molecules. Among them, disruption of binding of the ubiquitin ligase MDM2 to the tumor suppressor protein p53 by Nutlin-2 (Figure 1.10) identified by scientists from Roche [22], the benzodiazepinediones (Figure 1.10, TDP665759) from Johnson & Johnson [33], and PB11 from the Dömling group [67] are well-known examples. Furthermore, “SAR (structure–activity relationships) by NMR” was used to identify the precursor fragments of the Bcl-2/Bak inhibitor ABT-737 (Figure 1.10) [21], and “tethering” was employed to identify small molecules that bind to interleukin (IL)-2 and disrupt the interaction with its receptor, IL-2R (SP4206, Figure 1.10) [32]. From a 250 000-compound library, 19 molecules were identified that inhibited the ZipA/FtsZ interaction, such as pyridylpyrimidine 1 (Figure 1.10) [31]. A smaller library was successfully employed in high-throughput screening (HTS) campaigns as in the case of the search for inhibitors of the PICK1 PDZ domain where 44 000 compounds were screened in a fluorescence polarization format, resulting in the identification of FSC231 (Figure 1.10) [68]. In addition, a screen for eIF-4E/eIF-4G interaction inhibitors with only 16 000 compounds yielded successful hits like 4EGI-1 (Figure 1.10) [69]. Recently, a lead structure (pitstop 1, Figure 1.10) was identified by screening 17 000 compounds in an enzyme-linked immunosorbent assay-based assay and were subsequently developed into potent PPI inhibitors of clathrin-mediated endocytosis [70]. This compound binds to the terminal domain of clathrin which disrupts the interaction with clathrin-binding accessory proteins like amphiphysin, AP180, and synaptojanin. The group of Botta reported the identification of a small-molecule inhibitor of the c-Abl/14-3-3 interaction by employing structure-based pharmacophore modeling, virtual screening and molecular docking simulations. They also started with roughly 200 000 compounds, of which finally 14 compounds were tested in cellular and biochemical assays, resulting in the identification of one lead structure (BV02, Figure 1.10) [71]. Furthermore, a low-micromolar-active inhibitor of the HIV Nef–Src homology 3 (SH3) interaction (D1, Figure 1.10) was found by docking a 1990 compound virtual library into a pocket in the Nef–SH3 interface [72].

Figure 1.10 Further inhibitors of PPIs.

1.6 Conclusions and Outlook

The examples of successful inhibition of PPIs illustrate the principal feasibility of this approach in drug development. With an estimated number between 130 000 and 650 000 PPIs in the human body, it is in principle plausible to identify a “druggable” PPI for every disease or (patho)physiological condition. Since nature regulates protein function mainly by interaction with other proteins, the strategy to modulate PPIs with small molecules is an ideal concept to complement more classical approaches of pharmacological intervention. One can, for example, envision that simultaneously targeting a prosurvival pathway with active-site inhibitors and PPI modulators might produce a maximum benefit in cancer therapy. As the examples of the LEDGF/HIV IN, HPV E1/E2, or the ZipA/FtsZ PPI inhibitors show, new active agents against viral or bacterial infections might be also developed based on “hitting” essential (and unique) PPIs in these organisms. Over the last 10 years our knowledge about how to target PPIs with small molecules has dramatically increased, holding great promise for future clinical applications of this kind of compounds.

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