Allosterism in Drug Discovery: Volume 56 (Drug Discovery Series) - Hardcover

Hardcover

ISBN 10: 1782624597 ISBN 13: 9781782624592

Publisher: Royal Society of Chemistry, 2016

Synopsis

This book, written by the leaders in this young research area, describes the latest developments in allosterism for drug discovery.

About this title

From the Back Cover

Although the concept of allosterism has been known for over half a century, its application in drug discovery has exploded in recent years. The emergence of novel technologies that enable molecular-level ligand-receptor interactions to be studied in unprecedented detail has driven this trend. This book, written by leaders in this research area, describes the latest developments in allosterism for drug discovery.

Bringing together research in a diverse range of scientific disciplines, Allosterism in Drug Discovery is a key reference for academics and industrialists interested in understanding allosteric interactions. The book provides an in-depth review of research using small molecules as chemical probes and drug candidates that interact allosterically with proteins of relevance to life sciences and human disease. Knowledge of these interactions can then be applied in the discovery of the novel therapeutics of the future.

This book will be useful for people working in all disciplines associated with drug discovery in academia or industry, as well as postgraduate students who may be working in the design of allosteric modulators.

From the Inside Flap

Although the concept of allosterism has been known for over half a century, its application in drug discovery has exploded in recent years. The emergence of novel technologies that enable molecular-level ligand-receptor interactions to be studied in unprecedented detail has driven this trend. This book, written by leaders in this research area, describes the latest developments in allosterism for drug discovery.

Bringing together research in a diverse range of scientific disciplines, Allosterism in Drug Discovery is a key reference for academics and industrialists interested in understanding allosteric interactions. The book provides an in-depth review of research using small molecules as chemical probes and drug candidates that interact allosterically with proteins of relevance to life sciences and human disease. Knowledge of these interactions can then be applied in the discovery of the novel therapeutics of the future.

This book will be useful for people working in all disciplines associated with drug discovery in academia or industry, as well as postgraduate students who may be working in the design of allosteric modulators.

Excerpt. © Reprinted by permission. All rights reserved.

Allosterism in Drug Discovery

By Dario Doller

The Royal Society of Chemistry

Copyright © 2017 The Royal Society of Chemistry
All rights reserved.

ISBN: 978-1-78262-459-2

Contents

Chapter 1 Modulation of Biological Targets Using Allosteric Ligands: Food for Thought Dario Doller and Xinyan Huang, 1, 
Chapter 2 Identifying and Quantifying Allosteric Drug Function Terry Kenakin, 24, 
Chapter 3 Targeting Catalytic and Non-Catalytic Functions of Protein Kinases Susanne Müller and Stefan Knapp, 40, 
Chapter 4 Molecular Biology Techniques Applied to GPCR Allosteric and Biased Ligands Mélanie Frauli, Christel Franchet, Ismet Dorange, Arturo Mancini, Billy Breton and Stephan Schann, 65, 
Chapter 5 Examining Allosterism in a Dimeric G-Protein-Coupled Receptor Context Jesús Giraldo, Jordi Ortiz, James Dalton and Bin Zhou, 97, 
Chapter 6 A Unifying Approach to the Duality of "Energetic" Versus "Conformational" Formulations of Allosteric Coupling: Mechanistic Implications for GPCR Allostery H. Ongun Onaran and Tommaso Costa, 131, 
Chapter 7 mGlu2 Receptor Positive Allosteric Modulators A. A. Trabanco, J. M. Cid and G. Tresadern, 156, 
Chapter 8 Muscarinic Receptors Allosteric Modulation Bruce J. Melancon and Corey R. Hopkins, 175, 
Chapter 9 Positive Allosteric Modulators of Opioid Receptors Kristin L. Rockwell and Andrew Alt, 194, 
Chapter 10 mGlu4 PET Ligands as Enablers of Target Biology Understanding Zhaoda Zhang, Pekka Poutiainen and Anna-Liisa Brownell, 220, 
Chapter 11 Allosteric Modulators of Adenosine, P2Y and P2X Receptors Kenneth A. Jacobson and Zhan-Guo Gao, 247, 
Chapter 12 Positive Allosteric Modulators of G-Protein-Coupled Receptors that Act via Covalent Mechanisms of Action Whitney M. Nolte and Philip A. Carpino, 271, 
Chapter 13 Mechanism of Action of a GluN2C- and GluN2D-Selective NMDA Receptor Positive Allosteric Modulator Katie L. Strong, Matthew P. Epplin, Yao Jing, Stephen F. Traynelis and Dennis C. Liotta, 281, 
Chapter 14 Development of AMPA Receptor Modulators as Cognition Enhancers Craig Jamieson and Emma L. Duffy, 310, 
Chapter 15 Allosteric Modulation of Neuronal Nicotinic Acetylcholine Receptors Mark M. Levandoski and Sivaramakrishna Koganti, 334, 
Chapter 16 Allosteric Binding in the Serotonin Transporter – Pharmacology, Structure, Function and Potential Use as a Novel Drug Target Claus J. Loland, Connie Sanchez, Per Plenge, Klaus P. Bøgesø and Benny Bang-Andersen, 360, 
Chapter 17 Allosteric Inhibition of Abl Kinase Anna Lucia Fallacara, Silvia Schenone and Maurizio Botta, 381, 
Chapter 18 Allosteric Modulators of Heat Shock Protein 90 (HSP90) Yen Chin Koay and Shelli McAlpine, 404, 
Subject Index, 427, 

CHAPTER 1

Modulation of Biological Targets Using Allosteric Ligands: Food for Thought

DARIO DOLLER AND XINYAN HUANG

1.1 Drug Discovery in the Early 21st Century

The dawn of the new century found several major pharmaceutical companies facing significant challenges in keeping their pipelines populated with new drugs. For nearly two decades, robust increases in research and development investments had not produced the hoped for number of new medical entities (NMEs) approvals per year. In some therapeutic areas such as diseases of the central nervous system (CNS), and in spite of a growing patient population and major medical needs, only a handful of new drugs were approved during this period, and mostly based on mechanisms already known ("me too" drugs). As a response to this crisis of innovation, and propelled by major discoveries in molecular and cell biology research, in particular in the areas of oncology and immunology, a chemically broad range of new therapeutic modalities emerged, such as antibodies, proteins, nucleic acids, vaccines, cell, or gene therapies. These are generally grouped under the denomination "biologics", to differentiate them from "small molecules". Drugs in the latter group have historically been mostly thought of as acting competitively with endogenous ligands, binding at their target receptors in a model that became known as "lock and key". These two types of drugs differ in terms of a number of attributes, such as molecular weight, preparation, characterization of the active pharmaceutical ingredient (API), physicochemical properties, possible route of administration, pharmacokinetic distribution, metabolism, clearance mechanisms, drug-drug interactions, dosing regimen, safety and toxicology, antigenicity and hypersensitivity, and pharmacology – including side effects. A comparison of these attributes highlights some of the challenges associated with the development of biologics as drugs. (Table 1.1) It also begs the question whether new strategies could be discovered to modulate drug targets with a different type of small molecules. This is, in essence, the promise of what allosteric modulators might do.

1.2 Allostery: A 50-Year Old Concept

Broadly, allostery has been defined as an indirect interaction between topographically distinct binding sites in a protein, mediated by a conformational change. Monod and Jacob used the term for the first time in the printed version of the Proceedings of the 26th Cold Spring Harbor Symposium on Quantitative Biology entitled "Cellular Regulatory Mechanisms" in 1961, in the general discussion written as a conclusion of the conference. The earliest appearance of the term "allostery" in a publication listed in PubMed dates to more than half a century ago. Since then, the concept has evolved and its use expanded notably. Today, allosterism is considered an inherent property of all dynamic proteins and other macromolecules of biological relevance. Examples of important drugs exist that are allosteric modulators of diverse targets such as ion channels, G protein-coupled receptors (GPCRs), and enzymes. Benzodiazepines, one of the earlier drug classes with major impact on society, act as negative (flumazenil, 1) or positive (diazepam, 2; flunitrazepam, 3) allosteric modulators of gamma aminobutyric acid A (GABA) ion channels. The first inhibitors of human immunodeficiency virus reverse transcriptase enzyme (HIVRT) useful in the treatment of AIDS were nucleoside analogs. These compounds act competitively and inhibit the binding of the appropriate deoxynucleotide triphosphate (ATP, TTP, GTP, or CTP) to the reverse transcriptase (RT) enzyme. Nevirapine (4) and efavirenz (5) are non-nucleoside RT inhibitors (NNRTIs). Both nucleoside and non-nucleoside RTIs inhibit the same target, the reverse transcriptase enzyme, an essential viral enzyme which transcribes viral RNA into DNA. Unlike nucleoside RTIs, which bind at the enzyme's active site, NNRTIs bind allosterically at a distinct site away from the active site called the NNRTI pocket. Maraviroc (6) is another antiretroviral drug used in the treatment of HIV infection, which works through a negative allosteric modulation (NAM) mechanism inhibiting the cell-surface chemokine CCR5 receptor. The chemokine receptor CCR5 is a co-receptor for most HIV strains, necessary for the entrance of the virus into the host cell. The drug binds to CCR5 and changes its conformation, thus blocking the HIV protein gp120 from associating with the receptor. HIV is then unable to enter human macrophages and T-cells. Cinacalcet (7), a calcimimetic, is a positive allosteric modulator (PAM) of the calcium-sensing receptor (CaSR), which is activated according to the natural rise and fall of endogenous calcium ion levels. This drug acts by lowering the threshold for activation of feedback on the parathyroid chief cells. Trametinib (8) is a highly selective reversible allosteric inhibitor of mitogen-activated protein kinase (MAPK)-extracellular-signal-regulated kinase enzymes MEK1 and MEK2 activity. Compound 8 is an ATP non-competitive inhibitor that binds MEK at a location adjacent to the ATP binding site. Approved in 2013, it is a first-in-class oral treatment for metastatic melanoma with BRAF V600 mutations (Figure 1.1).

In addition to these marketed drugs, a number of compounds working through allosteric mechanisms are undergoing advanced clinical trials at the time of writing. The serine-threonine kinase AK thyoma oncoprotein homolog (Akt), also known as protein kinase B (PKB), plays a key role in the phosphoinositide 3-kinase-Akt-mammalian target of rapamycin (PI3K-Akt-mTOR) signaling cascade, tightly associated with cell proliferation, survival, migration, angiogenesis and other activities directly linked to tumor genesis and progression. The allosteric Akt inhibitor MK-2206 (9) is currently being evaluated in clinical Phase 1 and 2 studies on breast, colon/rectal and other cancers. The muscarinic Ml receptor positive allosteric modulator (PAM) 1-(4-cyano-4-(pyridine-2-yl)piperidin-1-yl)methyl-4-oxo-4H -quinolizine-3-carboxylic acid (PQCA) (10) has shown in vivo efficacy in a number of preclinical models in both rodents and non-human primates, suggesting this mechanism may have therapeutic potential for the treatment of Alzheimer's disease and cognitive deficits. The metabotropic glutamate receptor 4 (mGluR4) PAM Lu AF21934 (11) has been extensively studied in a number of in vitro and in vivo mechanistic tests. It differentiates from congeners by its remarkable ability to enhance in vitro agonist concentration-response curves for both, the mGluR4 homodimer as well as the mGlu2/4 heterodimer, as opposed to the earlier tool compounds, which are functionally selective for the mGluR4 homodimer (Figure 1.2).

In some cases, strong support was obtained using X-ray crystallography to enable the discovery of allosteric drugs. Phosphodiesterase 4 (PDE4) is an enzyme that hydrolyzes cAMP in cells, and a promising drug target for the treatment of Alzheimer's disease, Huntington's disease, schizophrenia, and depression. Drugs treating these diseases by aiming at central biological targets must cross the blood-brain barrier (BBB) and penetrate into the brain to exert therapeutic benefit, which restricts the available chemical space for potential competitive inhibitors. PDE4 inhibitors exist which are cAMP-competitive marketed drugs, but the lack of subtype selectivity is thought to lead to side effects, including nausea, depression, and weight loss. Studying crystal structures of PDE4 with bound inhibitors exposed the structural basis of this enzyme's regulation and inspired, together with mutagenesis and kinetic studies, the design of subtype-selective negative allosteric modulators of pDE4D with reduced potential to cause the dose-limiting side effects observed with existing active-site-directed PDE4 inhibitors. BPN14770, a first in class PDE4D NAM (structure not disclosed at present time) is being developed with support from the NIH Blueprint Neurotherapeutics Network and is the first compound funded by the program to reach a Phase 1 clinical trial. Likewise, the recent disclosure of crystallographic studies with GPCR ligands confirmed their allosteric nature. Notable examples are the corticotropin-releasing factor-1 (CRF-1) functional inhibitor CP-376395 (12), the mGluR5 NAM mavoglurant (13), the mGluR1 NAM FITM (4-fluoro-N-(4-(6-(isopropylamino)pyrimidin-4yl)thiazol-2-yl)-N -methylbenzamide) (14), and the P2Y receptor non-nucleotide antagonist BPTU (1-(2-(2-(tert-butyl)phenoxy)pyridin-3-yl)-3-(4-(trifluoromethoxy) phenyl)urea) (15). The latter has the peculiarity of being the first structurally characterized selective GPCR ligand located entirely outside of the helical bundle (Figure 1.3).

These last several examples strongly suggest that the use of allosteric ligands has the potential to help solve druggability issues in areas where ligands binding at the orthosteric site present challenges, thus providing a new chemistry modality to deliver therapeutic treatments using small molecules, with which chemists are highly familiar working. Yet, the purposeful targeting of allosteric sites in proteins that are biological targets of drug discovery efforts is a relatively recent undertaking in drug discovery projects.

1.3 Allosteric Drugs: The Right Tool at the Right Time

The pharmaceutical industry has witnessed a major change over the last decade, as it went from working on relatively well-understood biological targets with clinical validation, where efficacy in the patient population was expected, to novel biological targets with unprecedented track records in clinical settings. The reasons for this change are not only scientific, and include social, political, and financial factors, which are beyond the scope of this book. The bottom-line is that today, unmet medical needs and financial incentives dictate the discovery of drugs with enhanced efficacy over existing treatments. A way to achieve this goal is by using novel mechanisms of action. However, the novelty entails a risky task: demonstrating clinical efficacy in a broad patient population, usually requiring phase 3 clinical studies. Late failures are very expensive, and while they might be explicated by our imperfect understanding of disease etiology and flawed replication of human (patho)physiology in the preclinical disease models used, that is no consolation after a billion-dollar drug development exercise yields negative clinical data. The current premise is that translational sciences will, at least in part, mitigate this risk and enhance success rates.

Allosteric drugs were envisioned as having the potential to provide two ways to mitigate the risk of late clinical failure:

1. By providing an alternative molecular mechanism to attack biological targets (clinically validated or not) that require a different, friendlier drug-like chemistry space than originally attempted with orthosteric ligands (e.g., GABA, glutamate or acetylcholine receptors); and

2. Giving novel ways to attack previously intractable targets (e.g., the calcium sensing receptors or sweet taste receptors; voltage gated receptors).

Therefore, it seemed reasonable that some of the same biological targets previously aimed at, and which had been proven recalcitrant to drug discovery efforts using orthosteric ligands, yet not technically invalidated, were given a second life and addressed using allosteric ligands.

1.4 Potential Advantages of Allosteric Modulators Over Orthosteric Ligands ... or are They?

A number of excellent publications have discussed in great detail the potential advantages of using allosteric ligands in drug discovery, including comparisons with their orthosteric counterparts. A review of this literature consistently points to a variety of factors as drivers to encourage the exploration of allosteric ligands as drugs and chemical probes. These include factors such as: being easier to achieve selectivity, lack of intrinsic activity, ability to "dim" endogenous agonist function while preserving spatial and temporal effects, etc. (Figure 1.4). Some of these initial views have evolved as they were challenged by experimental data, suggesting a reconsideration of these idealized properties.

Target selectivity is generally thought to be easier to obtain with allosteric ligands than with orthosteric ligands. This belief would be a consequence of a highly conserved amino acid sequence in the orthosteric binding site. Remote allosteric sites tend to be less well conserved, and sufficiently different that selectivity for allosteric ligands may be expected. For example, when comparing different mGluR subtypes binding the same endogenous agonist (glutamate), the amino acids forming the binding site are indeed highly conserved. Furthermore, these allosteric sites are thought to be an evolutionary artifact and less sensitive to mutations in terms of the receptor functional output, as there would be no endogenous ligands binding at such sites. This would make the design of selective orthosteric ligands somewhat challenging.

However, this thinking may in part be a consequence of how orthosteric analogs were conceived in the past. Historically, these ligands were often designed by constraining the conformation of the endogenous natural ligand and keeping a similar ligand size. Thus, the same amino acids are involved in the binding process of both the endogenous ligand and the putative drug. Indeed, recent work has shown that orthosteric ligand selectivity may be achieved by making analogs with added substituents, so that additional amino acids that may no longer be conserved among receptor subtypes are involved in the binding process. Examples of such selective ligands are LSp4-2022 (16, mGluR4-selective) and LY2812223 (17, mGluR2-selective) (Figure 1.5; glutamate backbone shown in color). Furthermore, evidence suggesting that allosteric sites might play a role in determining receptor function came from the study of the GABA receptor, and the discovery of endogenous ligands binding at the benzodiazepine site, including oleamides, nonpeptidic endozepines and the protein diazepam-binding inhibitor (DBI).

Potent and selective adenosine A1R receptor orthosteric agonists and antagonists have also been discovered and tested in clinical settings for a number of indications. The use of bulky N6-adamantyl substituents on adenosine has led to agonists previously shown to be A1-selective with respect to binding affinity at rat receptors. Recently, the discovery of a series of subtype-selective N6-bicydic and N6 -(2-hydroxy)cyclopentyl derivatives of adenosine as agonists was reported and their A1R/A2R selectivity assessed based on a modified Saccharomyces cerevisiae strains screening platform. In addition, the activity at A1R and A3R of a few select analogs which were active against the A1R in the yeast screen was studied in mammalian CHoki cells; compounds such as 18 and 19 (Figure 1.5) were shown to be highly selective A1R agonists. Preferred compounds based on potency and selectivity contained N6-adamantyl substitution in combination with 5'-N-ethylcarbox-amido or 5'-hydroxymethyl groups.

In some cases, allosteric ligands have provided a path forward to selectively activate CNS receptors when orthosteric ligands failed to do so. One such example is the use of compounds 10, 20 and 21 (Figure 1.6), characterized as having a mixed agonist-positive allosteric modulator profile highly functionally selective for the Ml receptor. Ml agonists such as xanomeline produce beneficial cognitive effects in Alzheimer's disease and schizophrenia patients. Unfortunately, its therapeutic use is limited due to cholinergic side effects (sweating, salivation, gastrointestinal distress). These are suggested to result from nonselective activation of other muscarinic receptor subtypes such as M2 and M3. However, this theory was refuted as the Ml-selective activators 10, 20 and 21 tested in rats, dogs, and cynomologous monkeys still elicited cholinergic side effects such as salivation, diarrhea, and emesis. This suggests that activation of Ml receptors alone is sufficient to produce unwanted cholinergic side effects such as those seen with xanomeline.

(Continues...)

Excerpted from Allosterism in Drug Discovery by Dario Doller. Copyright © 2017 The Royal Society of Chemistry. Excerpted by permission of The Royal Society of Chemistry.
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Edition details

• Publisher: Royal Society of Chemistry
• Publication date: 2016
• Language: English
• ISBN 10: 1782624597
• ISBN 13: 9781782624592
• Binding: Hardcover
• Number of pages: 437
• Editor: Dario Doller