Current Topics in Medicinal Chemistry

ISSN: 1568-0266

Current Topics in Medicinal Chemistry
Volume 7, Number 1, 2007

Contents

Emerging Therapeutic Opportunities by Targeting Protein–Protein Interactions
Guest Editor: Dr. Rosario González-Muñiz


Editorial Pp. 1-2


PDZ Domain Protein-Protein Interactions: A Case Study with PICK1 Pp. 3-20
Kumlesh K. Dev
[Abstract] [Full text article]


Interfering with Protein-Protein Contact: Molecular Interaction MAPS and Peptide Modulators Pp. 21-32
Erika Nieddu and Stefania Pasa
[Abstract] [Full text article]


Modulation of Protein-Protein Interactions by Stabilizing/Mimicking Protein Secondary Structure Elements Pp. 33-62
M. Jesús Pérez de Vega, Mercedes Martín-Martínez and Rosario González-Muñiz
[Abstract] [Full text article]


Computational Identification of Inhibitors of Protein-Protein Interaction Pp. 63-82
Shijun Zhong, Alba T. Macias and Alexander D. MacKerell Jr.
[Abstract] [Full text article]


Discovery of Inhibitors of Protein-Protein Interactions from Combinatorial Libraries Pp. 83-95
María J. Vicent, Enrique Pérez-Payá and Mar Orzáez
[Abstract] [Full text article]


Pharmacologic Manipulation of Nitric Oxide Signaling: Targeting NOS Dimerization and Protein-Protein Interactions Pp. 97-114
Jeremy S. Paige and Samie R. Jaffrey
[Abstract] [Full text article]


Disrupting β-Amyloid Aggregation for Alzheimer Disease Treatment Pp. 115-126
L.D. Estrada and C. Soto
[Abstract] [Full text article]




Abstracts
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Editorial

During the last years, the explosion in genomics and proteomics has triggered the discovery of new targets for therapeutic intervention based on protein–protein interactions (PPIs). This emanate from the importance of protein associations and networks in a large number of cellular processes, including signal transduction, transcription, cellular trafficking, and mitosis, while the dysregulation of PPIs is in the origin of many pathological states. Protein–protein interconnections are also important inputs on the way to bacterial and viral infections. As a result, the search of modulators either of altered, inappropriate PPIs in human cells or of PPIs crucial to pathogen invasion, survival and replication is an issue of major interest in the field of new medicines. However, protein–protein interactions are clearly more challenging targets than enzymes and receptors that usually bind small molecules: a better understanding of protein complexes and their interconnections, and a deeper knowledge of the structure of protein interfaces and key points of intervention (hot-spots) are still need, and we have to press hard on the development of general strategies to modulate these interactions.

This issue of Current Topics in Medicinal Chemistry, dedicated to “Emerging Therapeutic Opportunities by Targeting Protein-Protein Interactions”, is aimed at describing the state of the art of current research and development in the field.

The first two reviews focus on the complexity of protein–protein networks and the opportunity of interfering within PPIs by means of peptide molecules. Kumlesh K. Dev provides a complete biochemical characterization of the interactions of the PDZ domain of PICK1 with a plethora of proteins, including among others the family of protein kinase receptors, ionotropic and metabotropic glutamate receptors, and different synaptic proteins and transporters. He then makes a brief description of peptides and small molecules able to block PDZ interactions, and highlight their interest as pharmacological tools to study the role of PICK1 in different pathological processes. Erika Nieddu and Stefania Pasa, using c-Myc as a case study, review the way to built and the usefulness of molecular interaction maps (MIMs) for the compilation of available PPI data, the formulation of hypotheses for experimental testing, and the identification of appropriate molecular targets for therapeutic intervention. They selected several examples to illustrate the potential of peptides as starting point to find out PPI inhibitors, and describe a retroinverse peptide analogue, developed as a disruptor of the c-Myc-INI1 interaction, active against proliferation in cancer cell lines.

As in classical medicinal chemistry, the discovery of modulators of protein–protein interactions can follow different approaches according to the degree of knowledge about protein-protein interfaces. The review by Pérez de Vega et al. provides representative examples of rationally designed conformationally restricted peptides and peptidomimetics able to disturb PPIs of therapeutic relevance. The challenge in this case is the identification of essential secondary structural elements (hot-spots) of protein–protein interfaces, followed by the transformation of these protein fragments into mimetics of α–helices, β–sheets, and reverse turns. In the fourth review, Zhong, Macias and MacKerell make convincing arguments in favor of the use of computer-aided drug design and virtual screening for identifying PPI inhibitors. After providing general principles of database screening and a basic protocol for targeting PPIs, they illustrate the usefulness of this alternative rational approach with recent examples from different laboratories. When information about protein complexes is not available, combinatorial chemistry is a valuable tool both for the discovery of PPI modulators and for the identification and subsequent validation of PPIs as potential therapeutic targets. In this context, Vicent et al. highlight the principles of combinatorial approaches and their suitability to target PPIs involved in apoptosis, cell cycle, cell migration, and viral replication, among others.

Paige and Jaffrey provide an extensive examination of the progress in the development of isoform-specific NOS-directed therapeutics, from molecules that target the Arg-binding site to dimerization inhibitors. Moreover, they discuss about emerging approaches directed to stabilize NOS dimmers or to modulate the interaction of NOS isoforms with other proteins, which could be advantageous over dimerization inhibitors to control NO-related diseases.

The contribution by Estrada and Soto begins by providing a clear description of Alzheimer’s disease (AD) and the role of amyloid beta (Aβ) peptide as one of the causative agents of this neurodegenerative process. They then present a critical and thorough examination of the different strategies aimed at correcting the Aβ misfolding and aggregation as therapeutic promising approaches for AD.

The field of PPIs, in its broadest sense, is still in the early stages and will likely receive increased attention in the near future. The advancement in different disciplines, like screening and characterization protocols for the discovery of new PPIs and protein netwoks, assisted by powerful computational tools and by the introduction of protein microarrays, could provide deeper insights into mechanisms of human diseases. Improvements in mass spectrometry, NMR spectroscopy, and nanotechnology could also offer new opportunities for the identification of protein–protein and protein–ligand interactions. The evolution in combinatorial library production, including the exploitation of chemical genetic approaches based on natural products, and the progress on the evaluation processes, specially in silico screening, will undoubtedly facilitate the study of PPI dynamic processes. A big task is in front of the scientific community, and only the combined efforts of specialists in all the above indicated disciplines will help to answer crucial questions that still remain unsolved. We must be open minded and ready to contribute, much work is to be done!


Rosario González-Muñiz
Instituto de Química Médica (CSIC),
Juan de la Cierva, 3,
28006 Madrid,
Spain


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PDZ Domain Protein-Protein Interactions: A Case Study with PICK1
Kumlesh K. Dev

[Full text article]

Using PICK1 as an example this review highlights PDZ domains support a repertoire of protein-protein interactions that regulate the subcellular localisation and function of receptors, ion channels and enzymes. PICK1 is a 416 amino acid protein that contains a PDZ domain, a coiled-coil motif/arfaptin homology domain and an acidic c-terminal. Nearly all proteins thus far reported to interact with PICK1 do so via its single PDZ domain. PICK1 self-associates via its coiled-coil motif and together with its PDZ domain has potential to act as a scaffolding protein. This molecule was first identified as a protein interacting with Cα-kinase (PICK1) and interacts with several members of the glutamate receptor family and receptor tyrosine kinases. The PDZ domain of PICK1 has since been shown to interact with a plethora of proteins including dopamine transporter, prolactin-releasing peptide receptor, ion channels BNaC1/ASIC and many more. The single PDZ domain of PICK1 interacts with a network of proteins that is pivotal in processes such as synaptic plasticity, development and neural guidance as well as many diseased states. The proteins that interact with PICK1 and the functional roles of its PDZ domain are discussed and illustrated are ways to regulate PDZ protein-protein interactions.


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Interfering with Protein-Protein Contact: Molecular Interaction MAPS and Peptide Modulators
Erika Nieddu and Stefania Pasa

[Full text article]

Protein-protein interactions (PPIs) can be useful targets for different pathologies. In fact controlling a function or attempting to repair an anomaly often means interfering with the cross-talk among different proteins.

In order to have a general view of these cross-talks, Molecular Interaction Maps (MIMs) are used, organizing the enormous available information that is added every day and trying to understand the most suitable and accurate targets for any specific cell alteration.

In this paper the c-Myc protein is taken as an example to explain the use of a map. The discovery of a peptidomimetic antagonist of c-Myc, active against proliferation of cancer cell lines, is reported and a possible mechanism of action is explained.

To interfere with a specific protein-protein contact, a good starting point can be to consider a protein entity. Because the interaction between two proteins is normally characterized by a wide zone of contact, relative large inhibitors could be more convenient in the first approaches. Therefore, peptides mimicking the interacting zone can be considered as potential leads in the rational design of effective molecules. Here different examples of peptides as protein-protein interaction inhibitors are reported.


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Modulation of Protein-Protein Interactions by Stabilizing/Mimicking Protein Secondary Structure Elements
M. Jesús Pérez de Vega, Mercedes Martín-Martínez and Rosario González-Muñiz

[Full text article]

In view of the crucial role of protein-protein intercommunication both in biological and pathological processes, the search of modulators of protein-protein interactions (PPIs) is currently a challenging issue. The development of rational strategies to imitate key secondary structure elements of protein interfaces is complementary to other approaches based on the screening of synthetic or virtual libraries. In this sense, the present review provides representative examples of compounds that are able to disturb PPIs of therapeutic relevance, through the stabilization or the imitation of peptide hot-spots detected in contact areas of the interacting proteins. The review is divided into three sections, covering mimetics of the three main secondary structural elements found in proteins, in general, and in protein-protein interfaces, in particular (α–helices, β–sheets, and reverse turns). Once the secondary element has been identified, the first approach typically involves the translation of the primary peptide structure into different cyclic analogues. This is normally followed by gradual decrease of the peptide nature through combination of peptide and non-peptide fragments in the same molecule. The final step usually consists in the development of pertinent organic scaffolds for appending key functional groups in the right spatial disposition, as a means towards totally non-peptide small molecule PPI modulators.


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Computational Identification of Inhibitors of Protein-Protein Interaction
Shijun Zhong, Alba T. Macias and Alexander D. MacKerell Jr.

[Full text article]

The ability to control protein-protein interactions (PPIs) for therapeutic purposes is attractive since many processes in cells involve such interactions. Recent successes in the discovery of small molecules that target protein-protein interactions for drug development have shown that targeting these interactions is indeed feasible. In the present review the use of computer-aided drug design (CADD) via database screening or docking algorithms for identifying inhibitors of protein-protein interactions is introduced. The principles of database screening and a practical protocol for targeting PPIs are described. The recent applications of these approaches to different systems involving protein-protein interactions, including BCL-2, S100B, ERK and p56lck, are presented and provide valuable examples of inhibitor discovery and design.


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Discovery of Inhibitors of Protein-Protein Interactions from Combinatorial Libraries
María J. Vicent, Enrique Pérez-Payá and Mar Orzáez

[Full text article]

Protein-protein interactions play a central role within numerous processes in the cell. The relevance of the processes in which this type of interactions are implicated make them responsible for many pathological situations. In the last decade protein-protein interfaces have shown their potential as new drug targets, and combinatorial chemistry has been defined as a useful tool in this line. This review gives a global vision of the actual situation of combinatorial chemistry, highlighting its applicability to high-throughput drug discovery and giving some crucial examples of its contribution to find modulators of protein-protein interactions.


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Pharmacologic Manipulation of Nitric Oxide Signaling: Targeting NOS Dimerization and Protein-Protein Interactions
Jeremy S. Paige and Samie R. Jaffrey

[Full text article]

Nitric oxide (NO) is an endogenously-produced small molecule that has critical roles in cellular signaling and a variety of physiological processes in many tissues, including the brain, the vasculature, and the immune system. In several medical disorders, NO has been implicated in disease pathology, in most cases due to persistent activation or overproduction of one of three NO synthase (NOS) isoforms. Although NOS inhibitors that are both potent and cell-permeable have been developed, none is currently used in the treatment of any disorder. One reason that NOS inhibitors fail to have therapeutic efficacy may be linked to their very low isoform-selectivity. An additional possibility is that NOS inhibitors, even if they exhibit isoform selectivity, might indiscriminately affect beneficial and pathological NO signaling pathways. In this review, we discuss emerging approaches in the development of isoform-specific NOS-directed therapeutics including dimerization inhibitors, novel L-arginine (L-Arg) binding site inhibitors, and dimer stabilization. Additionally, we suggest novel strategies for the future including targeting subcellular localization of NOS and protein-protein interactions with NOS effectors.


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Disrupting β-Amyloid Aggregation for Alzheimer Disease Treatment
L.D. Estrada and C. Soto

[Full text article]

Alzheimer’s disease is a devastating degenerative disorder for which there is no cure or effective treatment. Although the etiology of Alzheimer’s disease is not fully understood, compelling evidence indicates that deposition of aggregates composed by a misfolded form of the amyloid beta peptide (Aβ) is the central event in the disease pathogenesis. Therefore, an attractive therapeutic strategy is to prevent or reverse Aβ misfolding and aggregation. Diverse strategies have been described to identify inhibitors of this process, including screening of libraries of small molecules chemical compounds, rational design of synthetic peptides, assessment of natural Aβ-binding proteins and stimulation of the immune system by vaccination. In this article we describe these different approaches, their principles and their potential strengths and weaknesses. Overall the available data suggest that the development of drugs to interfere with Aβ misfolding and aggregation is a feasible target that hold great promise for the treatment of Alzheimer’s disease.