Structure of class C GPCR metabotropic glutamate receptor 5 transmembrane domain

Generic GPCR residue numbers - aligning topology maps while minding the gaps

Generic residue numbers facilitate comparisons of, for example, mutational effects, ligand interactions, and structural motifs. The numbering scheme by Ballesteros and Weinstein for residues within the class A GPCRs (G protein-coupled receptors) has more than 1100 citations, and the recent crystal structures for classes B, C, and F now call for a community consensus in residue numbering within and across these classes. Furthermore, the structural era has uncovered helix bulges and constrictions that offset the generic residue numbers. The use of generic residue numbers depends on convenient access by pharmacologists, chemists, and structural biologists. We review the generic residue numbering schemes for each GPCR class, as well as a complementary structure-based scheme, and provide illustrative examples and GPCR database (GPCRDB) web tools to number any receptor sequence or structure.

Mammalian olfactory receptors: molecular mechanisms of odorant detection, 3D-modeling, and structure-activity relationships

This chapter describes the main characteristics of olfactory receptor (OR) genes of vertebrates, including generation of this large multigenic family and pseudogenization. OR genes are compared in relation to evolution and among species. OR gene structure and selection of a given gene for expression in an olfactory sensory neuron (OSN) are tackled. The specificities of OR proteins, their expression, and their function are presented. The expression of OR proteins in locations other than the nasal cavity is regulated by different mechanisms, and ORs display various additional functions. A conventional olfactory signal transduction cascade is observed in OSNs, but individual ORs can also mediate different signaling pathways, through the involvement of other molecular partners and depending on the odorant ligand encountered. ORs are engaged in constitutive dimers. Ligand binding induces conformational changes in the ORs that regulate their level of activity depending on odorant dose. When present, odorant binding proteins induce an allosteric modulation of OR activity. Since no 3D structure of an OR has been yet resolved, modeling has to be performed using the closest G-protein-coupled receptor 3D structures available, to facilitate virtual ligand screening using the models. The study of odorant binding modes and affinities may infer best-bet OR ligands, to be subsequently checked experimentally. The relationship between spatial and steric features of odorants and their activity in terms of perceived odor quality are also fields of research that development of computing tools may enhance.

Metabotropic glutamate receptors as drug targets: what's new?

The question in the title: 'what's new?' has two facets. First, are 'clinical' expectations met with success? Second, is the number of CNS disorders targeted by mGlu drugs still increasing? The answer to the first question is 'no', because development program with promising drugs in the treatment of schizophrenia, Parkinson's disease, and Fragile X syndrome have been discontinued. Nonetheless, we continue to be optimistic because there is still the concrete hope that some of these drugs are beneficial in targeted subpopulations of patients. The answer to the second question is 'yes', because mGlu ligands are promising targets for 'new' disorders such as type-1 spinocerebellar ataxia and absence epilepsy. In addition, the increasing availability of pharmacological tools may push mGlu7 and mGlu8 receptors into the clinical scenario. After almost 30 years from their discovery, mGlu receptors are still alive.

Structural biology: 'seeing' crystals the XFEL way

X-ray free-electron lasers (XFELs) offer opportunities beyond classic X-ray crystallography, particularly for proteins that are difficult to crystallize.

Large scale expression and purification of the rat 5-HT2c receptor

5-HT2c G-protein coupled receptors located in the central nervous system bind the endogenous neurotransmitters serotonin and couple to G protein to mediate excitatory neurotransmission, which inhibits dopamine and norepinephrine release in the brain. Thus, 5-HT2c receptors play important roles in cognitive function and are potent drug targets. Structural information is needed to elucidate the molecular mechanism of ligand-binding and receptor-activation of the 5-HT2c receptor. Lacking of an efficient expression system that produces sufficient amounts of active and homogenous receptors hinders progress in the functional and structural characterization of the 5-HT2c receptor. We present here a protocol which can be used easily to obtain milligram amount of purified rat 5-HT2c receptors. We established this protocol by protein engineering and optimization of expression and purification based on radioligand-binding assay. The purified and well-characterized rat 5-HT2c receptors are active, stable, homogenous, and ready for 2-dimensional and 3-dimensional crystallization experiments.

Discovery of GPCR ligands for probing signal transduction pathways

G protein-coupled receptors (GPCRs) are seven integral transmembrane proteins that are the primary targets of almost 30% of approved drugs and continue to represent a major focus of pharmaceutical research. All of GPCR targeted medicines were discovered by classical medicinal chemistry approaches. After the first GPCR crystal structures were determined, the docking screens using these structures lead to discovery of more novel and potent ligands. There are over 360 pharmaceutically relevant GPCRs in the human genome and to date about only 30 of structures have been determined. For these reasons, computational techniques such as homology modeling and molecular dynamics simulations have proven their usefulness to explore the structure and function of GPCRs. Furthermore, structure-based drug design and in silico screening (High Throughput Docking) are still the most common computational procedures in GPCRs drug discovery. Moreover, ligand-based methods such as three-dimensional quantitative structure–selectivity relationships, are the ideal molecular modeling approaches to rationalize the activity of tested GPCR ligands and identify novel GPCR ligands. In this review, we discuss the most recent advances for the computational approaches to effectively guide selectivity and affinity of ligands. We also describe novel approaches in medicinal chemistry, such as the development of biased agonists, allosteric modulators, and bivalent ligands for class A GPCRs. Furthermore, we highlight some knockout mice models in discovering biased signaling selectivity.

Computational studies to predict or explain G protein coupled receptor polypharmacology

Since G protein-coupled receptors (GPCRs) belong to a very large superfamily of evolutionarily related receptors (>800 members in humans), and due to the rapid progress on their structural biology, they are ideal candidates for polypharmacology studies. Broad screening and bioinformatics/chemoinformatics have been applied to understanding off-target effects of GPCR ligands. It is now feasible to approach the question of GPCR polypharmacology using molecular modeling and the available X-ray GPCR structures. As an example, large and sterically constrained adenosine derivatives (potent adenosine receptor ligands with low conformational freedom and multiple extended substituents) were screened for binding at diverse receptors. Unanticipated off-target interactions, including at biogenic amine receptors, were then modeled using a structure-based approach to provide a consistent understanding of recognition. A conserved Asp in TM3 changed its role from counterion for biogenic amines to characteristic H-bonding to adenosine. The same systematic approach could potentially be applied to many GPCRs or other receptors using other sets of congeneric ligands.

G-protein-coupled receptor type A heteromers as an emerging therapeutic target

INTRODUCTION

The discovery of receptor-receptor interactions (RRIs) in the early 1980s provided evidence that G-protein-coupled receptors (GPCRs) operate not only as monomers but also as heteromers, in which integration of the incoming signals takes place already at the plasma membrane level through allosteric RRIs. These integrative mechanisms give sophisticated dynamics to the structure and function of these receptor assemblies in terms of modulation of recognition, G-protein signaling and selectivity and switching to β-arrestin signaling.

AREAS COVERED

The present review briefly describes the concept of direct RRI and the available data on the mechanisms of oligomer formation. Further, pharmacological data concerning the best characterized heteromers involving type A GPCRs will be analyzed to evaluate their profile as possible targets for the treatment of various diseases, in particular of impacting diseases of the CNS.

EXPERT OPINION

GPCR heteromers have the potential to open a completely new field for pharmacology with likely a major impact in molecular medicine. Novel pharmacological strategies for the treatment of several pathologies have already been proposed. However, several challenges still exist to accurately characterize the role of the identified heteroreceptor complexes in pathology and to develop heteromer-specific ligands capable of efficiently exploiting their pharmacological features.

The influence of alignment-free sequence representations on the semi-supervised classification of class C G protein-coupled receptors: semi-supervised classification of class C GPCRs

G protein-coupled receptors (GPCRs) are integral cell membrane proteins of relevance for pharmacology. The tertiary structure of the transmembrane domain, a gate to the study of protein functionality, is unknown for almost all members of class C GPCRs, which are the target of the current study. As a result, their investigation must often rely on alignments of their amino acid sequences. Sequence alignment entails the risk of missing relevant information. Various approaches have attempted to circumvent this risk through alignment-free transformations of the sequences on the basis of different amino acid physicochemical properties. In this paper, we use several of these alignment-free methods, as well as a basic amino acid composition representation, to transform the available sequences. Novel semi-supervised statistical machine learning methods are then used to discriminate the different class C GPCRs types from the transformed data. This approach is relevant due to the existence of orphan proteins to which type labels should be assigned in a process of deorphanization or reverse pharmacology. The reported experiments show that the proposed techniques provide accurate classification even in settings of extreme class-label scarcity and that fair accuracy can be achieved even with very simple transformation strategies that ignore the sequence ordering.

Overlapping binding sites drive allosteric agonism and positive cooperativity in type 4 metabotropic glutamate receptors

Type 4 metabotropic glutamate (mGlu4) receptors are emerging targets for the treatment of various disorders. Accordingly, numerous mGlu4-positive allosteric modulators (PAMs) have been identified, some of which also display agonist activity. To identify the structural bases for their allosteric action, we explored the relationship between the binding pockets of mGlu4 PAMs with different chemical scaffolds and their functional properties. By use of innovative mGlu4 biosensors and second-messenger assays, we show that all PAMs enhance agonist action on the receptor through different degrees of allosteric agonism and positive cooperativity. For example, whereas VU0155041 and VU0415374 display equivalent efficacies [log(τ(B)) = 1.15 ± 0.38 and 1.25 ± 0.44, respectively], they increase the ability of L-AP4 to stabilize the active conformation of the receptor by 4 and 39 times, respectively. Modeling and docking studies identify 2 overlapping binding pockets as follows: a first site homologous to the pocket of natural agonists of class A GPCRs linked to allosteric agonism and a second one pointing toward a site topographically homologous to the Na(+) binding pocket of class A GPCRs, occupied by PAMs exhibiting the strongest cooperativity. These results reveal that intrinsic efficacy and cooperativity of mGlu4 PAMs are correlated with their binding mode, and vice versa, integrating structural and functional knowledge from different GPCR classes.

Location-dependent signaling of the group 1 metabotropic glutamate receptor mGlu5

Although G protein-coupled receptors are primarily known for converting extracellular signals into intracellular responses, some receptors, such as the group 1 metabotropic glutamate receptor, mGlu5, are also localized on intracellular membranes where they can mediate both overlapping and unique signaling effects. Thus, besides "ligand bias," whereby a receptor's signaling modality can shift from G protein dependence to independence, canonical mGlu5 receptor signaling can also be influenced by "location bias" (i.e., the particular membrane and/or cell type from which it signals). Because mGlu5 receptors play important roles in both normal development and in disorders such as Fragile X syndrome, autism, epilepsy, addiction, anxiety, schizophrenia, pain, dyskinesias, and melanoma, a large number of drugs are being developed to allosterically target this receptor. Therefore, it is critical to understand how such drugs might be affecting mGlu5 receptor function on different membranes and in different brain regions. Further elucidation of the site(s) of action of these drugs may determine which signal pathways mediate therapeutic efficacy.

Rapid Computational Prediction of Thermostabilizing Mutations for G Protein-Coupled Receptors

G protein-coupled receptors (GPCRs) are highly dynamic and often denature when extracted in detergents. Deriving thermostable mutants has been a successful strategy to stabilize GPCRs in detergents, but this process is experimentally tedious. We have developed a computational method to predict the position of the thermostabilizing mutations for a given GPCR sequence. We have validated the method against experimentally measured thermostability data for single mutants of the β₁-adrenergic receptor (β₁AR), adenosine A_2A receptor (A_2AR) and neurotensin receptor 1 (NTSR1). To make these predictions we started from homology models of these receptors of varying accuracies and generated an ensemble of conformations by sampling the rigid body degrees of freedom of transmembrane helices. Then, an all-atom force field function was used to calculate the enthalpy gain, known as the “stability score” upon mutation of every residue, in these receptor structures, to alanine. For all three receptors, β₁AR, A_2AR, and NTSR1, we observed that mutations of hydrophobic residues in the transmembrane domain to alanine that have high stability scores correlate with high experimental thermostability. The prediction using the stability score improves when using an ensemble of receptor conformations compared to a single structure, showing that receptor flexibility is important. We also find that our previously developed LITiCon method for generating conformation ensembles is similar in performance to predictions using ensembles obtained from microseconds of molecular dynamics simulations (which is computationally hundred times slower than LITiCon). We improved the thermostability prediction by including other properties such as residue-based stress and the extent of allosteric communication by each residue in the stability score. Our method is the first step toward a computational method for rapid prediction of thermostable mutants of GPCRs.

2013 Philip S. Portoghese Medicinal Chemistry Lectureship: drug discovery targeting allosteric sites

The identification of sites on receptors topographically distinct from the orthosteric sites, so-called allosteric sites, has heralded novel approaches and modes of pharmacology for target modulation. Over the past 20 years, our understanding of allosteric modulation has grown significantly, and numerous advantages, as well as caveats (e.g., flat structure-activity relationships, species differences, "molecular switches"), have been identified. For multiple receptors and proteins, numerous examples have been described where unprecedented levels of selectivity are achieved along with improved physiochemical properties. While not a panacea, these novel approaches represent exciting opportunities for tool compound development to probe the pharmacology and therapeutic potential of discrete molecular targets, as well as new medicines. In this Perspective, in commemoration of the 2013 Philip S. Portoghese Medicinal Chemistry Lectureship ( Lindsley , C. W. Adventures in allosteric drug discovery . Presented at the 246th National Meeting of the American Chemical Society, Indianapolis, IN, September 10, 2013 ; The 2013 Portoghese Lectureship ), several vignettes of drug discovery campaigns targeting novel allosteric mechanisms will be recounted, along with lessons learned and guidelines that have emerged for successful lead optimization.

Structured and disordered facets of the GPCR fold

The seven-transmembrane (7TM) helix fold of G-protein coupled receptors (GPCRs) has been adapted for a wide variety of physiologically important signaling functions. Here, we discuss the diversity in the structured and disordered regions of GPCRs based on the recently published crystal structures and sequence analysis of all human GPCRs. A comparison of the structures of rhodopsin-like receptors (class A), secretin-like receptors (class B), metabotropic receptors (class C) and frizzled receptors (class F) shows that the relative arrangement of the transmembrane helices is conserved across all four GPCR classes although individual receptors can be activated by ligand binding at varying positions within and around the transmembrane helical bundle. A systematic analysis of GPCR sequences reveals the presence of disordered segments in the cytoplasmic side, abundant post-translational modification sites, evidence for alternative splicing and several putative linear peptide motifs that have the potential to mediate interactions with cytosolic proteins. While the structured regions permit the receptor to bind diverse ligands, the disordered regions appear to have an underappreciated role in modulating downstream signaling in response to the cellular state. An integrated paradigm combining the knowledge of structured and disordered regions is imperative for gaining a holistic understanding of the GPCR (un)structure-function relationship.

Opportunities and challenges in the discovery of allosteric modulators of GPCRs for treating CNS disorders

Novel allosteric modulators of G protein-coupled receptors (GPCRs) are providing fundamental advances in the development of GPCR ligands with high subtype selectivity and novel modes of efficacy that have not been possible with traditional approaches. As new allosteric modulators are advancing as drug candidates, we are developing an increased understanding of the major advantages and broad range of activities that can be achieved with these agents through selective modulation of specific signalling pathways, differential effects on GPCR homodimers versus heterodimers, and other properties. This understanding creates exciting opportunities, as well as unique challenges, in the optimization of novel therapeutic agents for disorders of the central nervous system.

The receptor concept in 3D: from hypothesis and metaphor to GPCR-ligand structures

The first mentioning of the word "receptor" for the structure with which a bioactive compound should react for obtaining its specific influence on a physiological system goes back to the years around 1900. The receptor concept was adapted from the lock and key theory for the enzyme substrate and blockers interactions. Through the years the concept, in the beginning rather being a metaphor, not a model, was refined and became reality in recent years. Not only the structures of receptors were elucidated, also the receptor machineries were unraveled. Following a brief historical review we will describe how the recent breakthroughs in the experimental determination of G protein-coupled receptor (GPCR) crystal structures can be complemented by computational modeling, medicinal chemistry, biochemical, and molecular pharmacological studies to obtain new insights into the molecular determinants of GPCR-ligand binding and activation. We will furthermore discuss how this information can be used for structure-based discovery of novel GPCR ligands that bind specific (allosteric) binding sites with desired effects on GPCR functional activity.