Michael Sabio

X-ray structure breakthroughs in the GPCR transmembrane region.

G-protein-coupled receptor (GPCR) proteins [Lundstrom KH, Chiu ML, editors. G protein-coupled receptors in drug discovery. CRC Press; 2006] are the single largest drug target, representing 25-50% of marketed drugs [Overington JP, Al-Lazikani B, Hopkins AL. How many drug targets are there? Nat Rev Drug Discov 2006;5(12):993-6; Parrill AL. Crystal structures of a second G protein-coupled receptor: triumphs and implications. ChemMedChem 2008;3:1021-3]. While there are six subclasses of GPCR proteins, the hallmark of all GPCR proteins is the transmembrane-spanning region. The general architecture of this transmembrane (TM) region has been known for some time to contain seven alpha-helices. From a drug discovery and design perspective, structural information of the GPCRs has been sought as a tool for structure-based drug design. The advances in the past decade of technologies for structure-based design have proven to be useful in a number of areas. Invoking these approaches for GPCR targets has remained challenging. Until recently, the most closely related structures available for GPCR modeling have been those of bovine rhodopsin. While a representative of class A GPCRs, bovine rhodopsin is not a ligand-activated GPCR and is fairly distant in sequence homology to other class A GPCRs. Thus, there is a variable degree of uncertainty in the use of the rhodopsin X-ray structure as a template for homology modeling of other GPCR targets. Recent publications of X-ray structures of class A GPCRs now offer the opportunity to better understand the molecular mechanism of action at the atomic level, to deploy X-ray structures directly for their use in structure-based design, and to provide more promising templates for many other ligand-mediated GPCRs. We summarize herein some of the recent findings in this area and provide an initial perspective of the emerging opportunities, possible limitations, and remaining questions. Other aspects of the recent X-ray structures are described by Weis and Kobilka [Weis WI, Kobilka BK. Structural insights into G-protein-coupled receptor activation. Curr Opin Struct Biol 2008;18:734-40] and Mustafi and Palczewski [Mustafi D, Palczewski K. Topology of class A G protein-coupled receptors: insights gained from crystal structures of rhodopsins, adrenergic and adenosine receptors. Mol Pharmacol 2009;75:1-12].

Use of the X-ray structure of the β2-adrenergic receptor for drug discovery. Part 2: Identification of active compounds

The recently published X-ray structures of the beta(2)-adrenergic receptor are the first examples of ligand-mediated GPCR crystal structures. We have previously performed computational studies that examine the potential viability of these structures for use in drug design, exploiting known ligand activities. Our previous study and a newly reported beta(2)/Timolol X-ray complex provide validation of the computational approaches. In the present work, we use the X-ray structures to extract, via in silico high-throughput docking, compounds from proprietary and commercial databases and demonstrate the successful identification of active compounds by radioligand binding.

Use of the X-ray structure of the Beta2-adrenergic receptor for drug discovery

The recently reported X-ray structure of the Beta2-adrenergic receptor, the first reported crystal structure of a ligand-mediated GPCR, is used to explore its utility in computer-aided drug design. Validations were conducted with known beta blockers. This was followed by high-throughput docking studies with proprietary and commercial databases to further validate the X-ray structures usefulness as a design tool and to explore the potential for discovery of novel chemical classes acting as Beta2 inhibitors. Our results include the finding of ligands with traditional beta-blocker motifs as well as new motifs, thereby serving to both validate the approach and project its usefulness in the finding and design of novel compounds.

Homology modeling of the serotonin transporter: insights into the primary escitalopram-binding site.

The serotonin transporter (SERT) is one of the neurotransmitter transporters that plays a critical role in the regulation of endogenous amine concentrations and therefore is an important target for therapeutic agents affecting the central nervous system. The recently published, high resolution X‐ray structure of the closely related amino acid transporter, Aquifex aeolicus leucine transporter (LeuT), provides an opportunity to develop a three‐dimensional model of the structure of SERT. We present herein a homology model of SERT using LeuT as the template and containing escitalopram as a bound ligand. Our model explains selectivities known from mutational studies and varying ligand data, which are discussed and illustrated in the paper.

Tricyclic Thiazolopyrazole Derivatives as Metabotropic Glutamate Receptor 4 Positive Allosteric Modulators

There is an increasing amount of evidence to support that activation of the metabotropic glutamate receptor 4 (mGlu4 receptor), either with an orthosteric agonist or a positive allosteric modulator (PAM), provides impactful interventions in diseases such as Parkinsons disease, anxiety, and pain. mGlu4 PAMs may have several advantages over mGlu4 agonists for a number of reasons. As part of our efforts in identifying therapeutics for central nervous system (CNS) diseases such as Parkinsons disease, we have been focusing on metabotropic glutamate receptors. Herein we report our studies with a series of tricyclic thiazolopyrazoles as mGlu4 PAMs.

4-(1-Phenyl-1H-pyrazol-4-yl)quinolines as novel, selective and brain penetrant metabotropic glutamate receptor 4 positive allosteric modulators

4-(1-Phenyl-1H-pyrazol-4-yl)quinoline (1) was identified by screening the Lundbeck compound collection, and characterized as having mGlu4 receptor positive allosteric modulator properties. Compound 1 is selective over other mGlu receptors and a panel of GPCRs, ion channels and enzymes, but has suboptimal lipophilicity and high plasma and brain non-specific binding. In view of the challenges at the hit-to-lead stage previously reported in the development of mGlu4 receptor positive allosteric modulators (PAMs), a thorough structure-mGlu4 PAM activity relationship study was conducted to interrogate the chemical tractability of this chemotype. The central pyrazole ring tolerates the addition of one or two methyl groups. The C-7 position of the quinoline ring provides a site tolerant to hydrophilic substituents, enabling the design of diverse analogs with good in vitro mGlu4 PAM potency and efficacy, as well as improved microsomal turnover in vitro, compared to 1. In spite of the excellent ligand efficiency of 1 (LE=0.43), optimization of in vitro potency for this series reached a plateau around EC(50)=200 nM.

The role of experimental and computational structural approaches in 7TM drug discovery.

Introduction: Starting with the published X-ray structures of ligand-mediated 7TM proteins in 2007, experimental approaches, led by X-ray structure determinations, and computational approaches, led by docking and molecular dynamics, have converged to elaborate our understanding of this field and demonstrate their effectiveness in drug discovery. Areas covered: The authors review the structural information that has emerged for ligand-mediated 7TM proteins, including the class A, B, C, and F receptors, focusing on the 7TM domains for the multi-domain proteins. The authors describe the key regions associated with ligand binding as well as features responsible for function such as activation versus inhibition and biased signaling. Furthermore, the authors summarize the effectiveness of computational studies to help clarify the structure–function information and their use for drug discovery. Expert opinion: There is now a significant amount of structural information covering a range of 7TM protein classes (A, B, C, and F) and activation states. For these and closely related proteins, structure-based drug discovery has proven to be a powerful tool. More structural information is needed with respect to dimerization, 7TM proteins with β-arrestin to help in understanding the control of biased signaling, and full-protein structure determinations for non-class A proteins to help in understanding and controlling their functioning. Finally, the use of the existing structural information to target new sites on these proteins needs further exploration.

Exploration of structure-based drug design opportunities for mGluRs

The metabotropic glutamate receptors (mGluRs) are a subset of the Class C G-Protein Coupled Receptors (GPCRs). Recently, an emerging strategy for drug-discovery efforts targeting mGluRs has been to develop compounds acting at the so-called allosteric site in the 7-transmembrane (7TM) domain, common to all GPCRs, rather than the extracellular (EC) domain containing the orthosteric glutamate-binding site. We examine herein some of the intrinsic relative merits of targeting these two domains. Comparisons are made among amino-acid sequences in the two domains and among X-ray structures and homology models of the EC domain. We show that there is greater sequence diversity in the EC domains than in the transmembrane (TM) domains. Thus, contrary to generally accepted descriptions of there being greater evolutionary pressure to preserve the EC domain, it is the 7TM domain that is more highly conserved. Within the EC domain, the glutamate-binding site of the Venus flytrap region has hitherto received the most attention as a target site. Analysis of examples of the three-dimensional structures of the EC domains at the glutamate-binding site reveals differences as well, thereby supporting the viability of targeting the EC domain, even at the glutamate-binding site, for drug discovery. To exemplify this strategy, we present examples of active compounds identified via high-throughput docking in the EC region.

The computational design of test compounds with potentially specific biological activity: histamine-H2 agonists derived from 5-HT/H2 antagonists.

SummaryThe previously proposed models for the recognition and activation of 5-HT and histamine-H2 receptors, which were employed to explain the antagonist activity of LSD at both of these receptors, as well as the selective antagonism for H2 receptors by SKF-10856 and 9,10-dihydro-LSD, are used herein to design a compound to test the H2-receptor model. The design strategy attempts to construct a compound with potentially selective H2 agonism. The design scheme maintains features which were previously used to explain selective recognition of SKF-10856 and 9,10-dihydro-LSD as well as reintroduces the chemical features proposed to be responsible for H2 activation. The existence of the H2 recognition and activation features in the proposed compound is verified, in a previously proposed model, by computational studies of the molecular electrostatic potentials and shifts in the tautomeric preference.

Theoretical investigations of methanesulphonamide as a hydroxy group equivalent in drugs. Examples from possible β-adrenergic agents and analysis of computational methods

Quantum chemical methods were used to analyse various physical chemical properties and interaction characteristics of methanesulphonamide. Comparison of β-methylsulphonylaminophenethylamine with its hydroxy analogue and certain structural fragments was used to examine the structure–activity relationships of arylhydroxyethylamines. The general role of methanesulphonamide as a hydroxy replacement was examined. In particular, based on the results of the calculations presented here, the differences in proton affinities, proton-donating abilities, or conformational properties do not account for the differences in activities of these compounds. Critical evaluation was made of several quantum chemical methods used in the study of these and other possible drugs, including the semiempirical MNDO and MINDO/3 methods and the ab initio Hartree–Fock method with the STO-3G, 3-21G, and 3-21G(*) basis sets.