Ligand specificity of odorant receptors

The role of secondary interactions on the preferred conformers of the fenchone-ethanol complex

New atomic-level experimental data on the intermolecular non-covalent interactions between a common odorant and a relevant residue at odorant binding sites are reported. The preferred arrangements and binding interactions of fenchone, a common odorant and ethanol, a mimic of serine's side chain, have been unambiguously identified using a combination of high resolution rotational spectroscopy and computational methods. The observed conformers include homochiral (RR) and heterochiral (RS) conformers, with a slight preference for a heterochiral form, and exhibit primary OH-O hydrogen bonds between fenchone and ethanol. Secondary interactions play a key role in determining the relative configurations of fenchone and ethanol, and in shaping quite a flat potential energy surface, with many conformers close in energy and small barriers for interconversion.

Olfactory Receptors in Non-Chemosensory Organs: The Nervous System in Health and Disease

Olfactory receptors (ORs) and down-stream functional signaling molecules adenylyl cyclase 3 (AC3), olfactory G protein α subunit (Gαolf), OR transporters receptor transporter proteins 1 and 2 (RTP1 and RTP2), receptor expression enhancing protein 1 (REEP1), and UDP-glucuronosyltransferases (UGTs) are expressed in neurons of the human and murine central nervous system (CNS). In vitro studies have shown that these receptors react to external stimuli and therefore are equipped to be functional. However, ORs are not directly related to the detection of odors. Several molecules delivered from the blood, cerebrospinal fluid, neighboring local neurons and glial cells, distant cells through the extracellular space, and the cells’ own self-regulating internal homeostasis can be postulated as possible ligands. Moreover, a single neuron outside the olfactory epithelium expresses more than one receptor, and the mechanism of transcriptional regulation may be different in olfactory epithelia and brain neurons. OR gene expression is altered in several neurodegenerative diseases including Parkinson’s disease (PD), Alzheimer’s disease (AD), progressive supranuclear palsy (PSP) and sporadic Creutzfeldt-Jakob disease (sCJD) subtypes MM1 and VV2 with disease-, region- and subtype-specific patterns. Altered gene expression is also observed in the prefrontal cortex in schizophrenia with a major but not total influence of chlorpromazine treatment. Preliminary parallel observations have also shown the presence of taste receptors (TASRs), mainly of the bitter taste family, in the mammalian brain, whose function is not related to taste. TASRs in brain are also abnormally regulated in neurodegenerative diseases. These seminal observations point to the need for further studies on ORs and TASRs chemoreceptors in the mammalian brain.

Odorant receptors of Drosophila are sensitive to the molecular volume of odorants

Which properties of a molecule define its odor? This is a basic yet unanswered question regarding the olfactory system. The olfactory system of Drosophila has a repertoire of approximately 60 odorant receptors. Molecules bind to odorant receptors with different affinities and activate them with different efficacies, thus providing a combinatorial code that identifies odorants. We hypothesized that the binding affinity of an odorant-receptor pair is affected by their relative sizes. The maximum affinity can be attained when the molecular volume of an odorant matches the volume of the binding pocket. The affinity drops to zero when the sizes are too different, thus obscuring the effects of other molecular properties. We developed a mathematical formulation of this hypothesis and verified it using Drosophila data. We also predicted the volume and structural flexibility of the binding site of each odorant receptor; these features significantly differ between odorant receptors. The differences in the volumes and structural flexibilities of different odorant receptor binding sites may explain the difference in the scents of similar molecules with different sizes.

Aldehyde recognition and discrimination by mammalian odorant receptors via functional group-specific hydration chemistry

The mammalian odorant receptors (ORs) form a chemical-detecting interface between the atmosphere and the nervous system. This large gene family is composed of hundreds of membrane proteins predicted to form as many unique small molecule binding niches within their G-protein coupled receptor (GPCR) framework, but very little is known about the molecular recognition strategies they use to bind and discriminate between small molecule odorants. Using rationally designed synthetic analogs of a typical aliphatic aldehyde, we report evidence that among the ORs showing specificity for the aldehyde functional group, a significant percentage detect the aldehyde through its ability to react with water to form a 1,1-geminal (gem)-diol. Evidence is presented indicating that the rat OR-I7, an often-studied and modeled OR known to require the aldehyde function of octanal for activation, is likely one of the gem-diol activated receptors. A homology model based on an activated GPCR X-ray structure provides a structural hypothesis for activation of OR-I7 by the gem-diol of octanal.

The state of the art of odorant receptor deorphanization: a report from the orphanage

The odorant receptors (ORs) provide our main gateway to sensing the world of volatile chemicals. This involves a complex encoding process in which multiple ORs, each of which detects its own set of odorants, work as an ensemble to produce a distributed activation code that is presumably unique to each odorant. One marked challenge to decoding the olfactory code is OR deorphanization, the identification of a set of activating odorants for a particular receptor. Here, we survey various methods used to try to express defined ORs of interest. We also suggest strategies for selecting odorants for test panels to evaluate the functional expression of an OR. Integrating these tools, while retaining awareness of their idiosyncratic limitations, can provide a multi-tiered approach to OR deorphanization, spanning the initial discovery of a ligand to vetting that ligand in a physiologically relevant setting.

GOMoDo: A GPCRs online modeling and docking webserver

G-protein coupled receptors (GPCRs) are a superfamily of cell signaling membrane proteins that include >750 members in the human genome alone. They are the largest family of drug targets. The vast diversity and relevance of GPCRs contrasts with the paucity of structures available: only 21 unique GPCR structures have been experimentally determined as of the beginning of 2013. User-friendly modeling and small molecule docking tools are thus in great demand. While both GPCR structural predictions and docking servers exist separately, with GOMoDo (GPCR Online Modeling and Docking), we provide a web server to seamlessly model GPCR structures and dock ligands to the models in a single consistent pipeline. GOMoDo can automatically perform template choice, homology modeling and either blind or information-driven docking by combining together proven, state of the art bioinformatic tools. The web server gives the user the possibility of guiding the whole procedure. The GOMoDo server is freely accessible at http://molsim.sci.univr.it/gomodo.

Functional genomics reveals dysregulation of cortical olfactory receptors in Parkinson disease: novel putative chemoreceptors in the human brain

Parkinson disease (PD) is no longer considered a complex motor disorder but rather a systemic disease with variable nonmotor deficits that may include impaired olfaction, depression, mood and sleep disorders, and altered cortical function. Increasing evidence indicates that multiple metabolic defects occur in regions outside the substantia nigra, including the cerebral cortex, even at premotor stages of the disease. We investigated changes in gene expression in the frontal cortex in PD patient brains using a transcriptomics approach. Functional genomics analysis indicated that cortical olfactory receptors (ORs) and taste receptors (TASRs) are altered in PD patients. Olfactory receptors OR2L13, OR1E1, OR2J3, OR52L1, and OR11H1 and taste receptors TAS2R5 and TAS2R50 were downregulated, but TAS2R10 and TAS2R13 were upregulated at premotor and parkinsonian stages in the frontal cortex area 8 in PD patient brains. Furthermore, we present novel evidence that, in addition to the ORs, obligate downstream components of OR function adenylyl cyclase 3 and olfactory G protein (Gαolf), OR transporters, receptor transporter proteins 1 and 2 and receptor expression enhancing protein 1, and OR xenobiotic removing UDP-glucuronosyltransferase 1 family polypeptide A6 are widely expressed in neurons of the cerebral cortex and other regions of the adult human brain. Together, these findings support the concept that ORs and TASRs in the cerebral cortex may have novel physiologic functions that are affected in PD patients.

Modeling of mammalian olfactory receptors and docking of odorants

Olfactory receptors (ORs) belong to the superfamily of G protein-coupled receptors (GPCRs), the second largest class of genes after those related to immunity, and account for about 3 % of mammalian genomes. ORs are present in all multicellular organisms and represent more than half the GPCRs in mammalian species (e.g., the mouse OR repertoire contains >1,000 functional genes). ORs are mainly expressed in the olfactory epithelium where they detect odorant molecules, but they are also expressed in a number of other cells, such as sperm cells, although their functions in these cells remain mostly unknown. It has recently been reported that ORs are present in tumoral tissues where they are expressed at different levels than in healthy tissues. A specific OR is over-expressed in prostate cancer cells, and activation of this OR has been shown to inhibit the proliferation of these cells. Odorant stimulation of some of these receptors results in inhibition of cell proliferation. Even though their biological role has not yet been elucidated, these receptors might constitute new targets for diagnosis and therapeutics. It is important to understand the activation mechanism of these receptors at the molecular level, in particular to be able to predict which ligands are likely to activate a particular receptor ('deorphanization') or to design antagonists for a given receptor. In this review, we describe the in silico methodologies used to model the three-dimensional (3D) structure of ORs (in the more general framework of GPCR modeling) and to dock ligands into these 3D structures.

The mouse eugenol odorant receptor: structural and functional plasticity of a broadly tuned odorant binding pocket

Molecular interactions of odorants with their olfactory receptors (ORs) are of central importance for the ability of the mammalian olfactory system to detect and discriminate a vast variety of odors with a limited set of receptors. How a particular OR binds and distinguishes different odorant molecules remains largely unknown on a structural basis. Here we investigated this question for the mouse eugenol receptor (mOR-EG). By screening a large odorant library, we discovered a wide range of chemical structures activating the receptor in heterologous mammalian cells. Potent agonists comprise (i) benzene, (ii) cyclohexane, or (iii) polycyclic structures substituted with alcohol, aldehyde, keto, ether, or esterified carboxylic groups. To detect those amino acids within the receptor that are in contact with a particular bound odorant molecule, we investigated how distinct mOR-EG point mutants were activated by the different odorant agonists found for the wild-type receptor. We identified 11 amino acids as a part of the receptor's ligand binding pocket. Molecular modeling predicted 10 of these residues in transmembrane helices TM3-TM6 and one in the extracellular loop between TM2 and TM3. These amino acids participate in odorant binding with variable importance depending on the type of odorant, revealing functional "fingerprints" of ligand-receptor interactions.

Insights into the binding of Phenyltiocarbamide (PTC) agonist to its target human TAS2R38 bitter receptor

Humans' bitter taste perception is mediated by the hTAS2R subfamily of the G protein-coupled membrane receptors (GPCRs). Structural information on these receptors is currently limited. Here we identify residues involved in the binding of phenylthiocarbamide (PTC) and in receptor activation in one of the most widely studied hTAS2Rs (hTAS2R38) by means of structural bioinformatics and molecular docking. The predictions are validated by site-directed mutagenesis experiments that involve specific residues located in the putative binding site and trans-membrane (TM) helices 6 and 7 putatively involved in receptor activation. Based on our measurements, we suggest that (i) residue N103 participates actively in PTC binding, in line with previous computational studies. (ii) W99, M100 and S259 contribute to define the size and shape of the binding cavity. (iii) W99 and M100, along with F255 and V296, play a key role for receptor activation, providing insights on bitter taste receptor activation not emerging from the previously reported computational models.

Dissecting the molecular mechanism of drosophila odorant receptors through activity modeling and comparative analysis

To gain insight into the molecular mechanism of odorant receptors (ORs) in Drosophila species, we developed a Quantitative Structure Activity Relationship (QSAR) model that predicts experimentally measured electrophysiological activities between 24 D. melanogaster ORs and 108 odorants. Although the model is limited by the tested odorants,analyzing the model allowed dissection of specific topological and chemical properties necessary for an odorant to elicit excitatory or inhibitory receptor response. Linear odorants with five to eight nonhydrogen atoms at the main chain and hydrogen-bond acceptor and/or hydrogen-bond donor at its ends were found to stimulate strong excitatory response. A comparative sequence analysis of 90 ORs in 15 orthologous groups identified 15 putative specificity-determining residues (SDRs) and 15 globally conserved residues that we postulate as functionally key residues. Mapping to a model of secondary structure resulted in 14 out of 30 key residues locating to the transmembrane (TM) domains. Twelve residues, including six SDRs and six conserved residues, are located at the extracellular halves of the TM domains. Combining the evidence from the QSAR modeling and the comparative sequence analysis, we hypothesize that the Drosophila ORs accept odorants into a binding pocket located on the extracellular halves of its TM domains. The QSAR modeling suggests that the binding pocket is around 15 A in depth and about 6 A in width. Twelve mainly polar or charged key residues, both SDRs and conserved, are located in this pocket and postulated to distinguish docked odorants via primarily geometry fitting and hydrogen-bond interaction.

Mammalian olfactory receptors

Perception of chemical stimuli from the environment is essential to most animals; accordingly, they are equipped with a complex olfactory system capable of receiving a nearly unlimited number of odorous substances and pheromones. This enormous task is accomplished by olfactory sensory neurons (OSNs) arranged in several chemosensory compartments in the nose. The sensitive and selective responsiveness of OSNs to odorous molecules and pheromones is based on distinct receptors in their chemosensory membrane; consequently, olfactory receptors play a key role for a reliable recognition and an accurate processing of chemosensory information. They are therefore considered as key elements for an understanding of the principles and mechanisms underlying the sense of smell. The repertoire of olfactory receptors in mammals encompasses hundreds of different receptor types which are highly diverse and expressed in distinct subcompartments of the nose. Accordingly, they are categorized into several receptor families, including odorant receptors (ORs), vomeronasal receptors (V1Rs and V2Rs), trace amine-associated receptors (TAARs), formyl peptide receptors (FPRs), and the membrane guanylyl cyclase GC-D. This large and complex receptor repertoire is the basis for the enormous chemosensory capacity of the olfactory system.

New vistas in GPCR 3D structure prediction

Human G-protein coupled receptors (hGPCRs) comprise the most prominent family of validated drug targets. More than 50% of approved drugs reveal their therapeutic effects by targeting this family. Accurate models would greatly facilitate the process of drug discovery and development. However, 3-D structure prediction of GPCRs remains a challenge due to limited availability of resolved structure. The X-ray structures have been solved for only four such proteins. The identity between hGPCRs and the potential templates is mostly less than 30%, well below the level at which sequence alignment can be done regularly. In this study, we analyze a large database of human G-protein coupled receptors that are members of family A in order to optimize usage of the available crystal structures for molecular modeling of hGPCRs. On the basis of our findings in this study, we propose to regard specific parts from the trans-membrane domains of the reference receptor helices as appropriate template for constructing models of other GPCRs, while other residues require other techniques for their remodeling and refinement. The proposed hypothesis in the current study has been tested by modeling human beta2-adrenergic receptor based on crystal structures of bovine rhodopsin (1F88) and human A2A adenosine receptor (3EML). The results have shown some improvement in the quality of the predicted models compared to Modeller software.

Molecular tuning of odorant receptors and its implication for odor signal processing

The discovery of the odorant receptor (OR) family by Buck and Axel in 1991 provided a quantum jump in our understanding of olfactory function. However, the study of the responsiveness of ORs to odor ligands was challenging due to the difficulties in deorphanizing the receptors. In this manuscript, we review recent findings of OR responsiveness that have come about through improved OR deorphanization methods, site-directed mutagenesis, structural modeling studies, and studies of OR responses in situ in olfactory sensory neurons. Although there has been a major leap in our understanding of receptor-ligand interactions and how these contribute to the input to the olfactory system, an improvement of our understanding of receptor structure and dynamics and interactions with intracellular and extracellular proteins is necessary.

A new challenge-development of test systems for the infochemical effect

BACKGROUND, AIM, AND SCOPE

Many-if not all-organisms depend on so-called infochemicals, chemical substances in their surroundings which inform the receivers about their biotic and abiotic environment and which allow them to react adequately to these signals. Anthropogenic substances can interfere with this complex chemical communication system. This finding is called infochemical effect. So far, it is not known to what extent anthropogenic discharges act as infochemicals and influence life and reproduction of organisms in the environment because adequate testing methods to identify chemicals which show the infochemical effect and to quantify their effects have not been developed yet. The purpose of this article is to help and find suitable test designs.

MAIN FEATURES

Test systems used in basic research to elucidate the olfactory cascade and the communication of environmental organisms by infochemicals are plentiful. Some of them might be the basis for a quantified ecotoxicological analysis of the infochemical effect. In principle, test systems for the infochemical effect could be developed at each step of the chemosensory signal transduction and processing cascade.

RESULTS

Experimental set-ups were compiled systematically under the aspect whether they might be usable for testing the infochemical effect of single chemicals in standardized quantifying laboratory experiments. For an appropriate ecotoxicological assessment of the infochemical effect, experimental studies of many disciplines, such as molecular biology, neurobiology, physiology, chemical ecology, and population dynamics, should be evaluated in detail before a decision can be made which test system, respectively which test battery, might be suited best. The test systems presented here are based on the knowledge of the genetic sequences for olfactory receptors, binding studies of odorants, signal transmission, and reactions of the receivers on the level of the organisms or the populations. The following basic approaches are conceivable to identify the role of an infochemical: binding studies to the odorant-binding protein or to the odorant receptor binding protein (e.g., by in situ hybridization and immunohistochemical studies), measurement of electrical signals of the receptor cells in the tissue (e.g., electroolfactograms, electroantennograms), registration of phenotypic changes (e.g., observation under the microscope), behavioral tests (e.g., in situ online biomonitoring, use of T-shaped olfactometers, tests of avoidance responses), measurement of population changes (e.g., cell density or turbidity measurements), and multispecies tests with observation of community structure and community function. The main focus of this study is on aquatic organisms.

DISCUSSION

It is evident that the infochemical effect is a very complex sublethal endpoint, and it needs further studies with standardized quantitative methods to elucidate whether and to what extent the ecosystem is affected. The collection of approaches presented here is far from being complete but should serve as a point of depart for further experimental research.

CONCLUSIONS

This article is the first to compare various approaches for testing the infochemical effect. The development of a suitable test system will not be easy as there are a multitude of relevant chemicals, a multitude of relevant receptors, and a multitude of relevant reactions, and it must be expected that the effective concentrations are very low. The chemical communication is of utmost importance for the ecosystem and justifies great endeavors to find solutions to these technical problems.

RECOMMENDATIONS AND PERSPECTIVES

The infochemical effect is a new chapter in ecotoxicology. Will a new endpoint, the so-called infochemical effect, be required in addition to the actual standard test battery of Annex 5 to Commission Directive 92/69/EEC (EC 1992)? Finding the answer to this question is a big challenge that could be met by a comprehensive research project.

Computational molecular biology approaches to ligand-target interactions

Binding of small molecules to their targets triggers complex pathways. Computational approaches are keys for predictions of the molecular events involved in such cascades. Here we review current efforts at characterizing the molecular determinants in the largest membrane-bound receptor family, the G-protein-coupled receptors (GPCRs). We focus on odorant receptors, which constitute more than half GPCRs. The work presented in this review uncovers structural and energetic aspects of components of the cellular cascade. Finally, a computational approach in the context of radioactive boron-based antitumoral therapies is briefly described.

The infochemical effect-a new chapter in ecotoxicology

BACKGROUND, AIM, AND SCOPE

Organisms use chemical cues in their surrounding, so-called infochemicals, as important source of information about their biotic and abiotic environment. The scope of this work is to transfer the knowledge on infochemicals obtained in chemical ecology into ecotoxicology, compare the observations with ecotoxicological standard tests, with other sublethal effects, and deduce consequences for the legal situation of environmental chemicals.

MAIN FEATURES

General principles were elaborated from the compiled information from literature on the structures and roles of natural infochemicals. The experiences gained in chemical ecology and in ecotoxicology led to the discovery of the infochemical effect: Anthropogenic substances can influence the chemical communication of environmental organisms. This finding is supported by a close look at fragrances and other common anthropogenic substances in the environment.

RESULTS

Increasing scientific knowledge shows how complex the chemical communication of environmental organisms is. Infochemicals are released by senders and detected by receivers. The relevant concentrations of infochemicals are very low, usually in the nano- to micromolar range and they do not seem to have common structural features. Knowledge about natural infochemicals is still poor and not consistent. The chemical cues fluctuate specifically in time and space resulting in dynamic response patterns in the ecosystem. Organisms can react to infochemicals in very specific ways by behavioral, morphological, or physiological responses; activities that are relevant for their survival as vital reactions such as flight, food uptake, or mating are affected. Anthropogenic substances at minor concentrations can interfere in the complex chemical communication web of infochemicals, possibly leading to increased vulnerability of populations.

DISCUSSION

The findings show clearly that the actual description of the interplay of organisms in the ecosystem is still very simplified and we are far from understanding the interactions completely. Anthropogenic discharges may play a role on the chemical communication and, hence, on the behavior and interactions of organisms in the ecosystem. The description of the infochemical effect opens a new chapter in ecotoxicology. It is a challenge to develop a suitable test system for the infochemical effect with the knowledge of the multitude of possible reactions and of the high specificity of infochemicals. Problems during the performance and evaluation of standard tests might be related to reactions due to infochemicals in the test systems which have not been considered so far.

CONCLUSIONS

The roles of anthropogenic infochemicals in the environment and the role of natural infochemicals in laboratory tests have been underestimated up to now.

RECOMMENDATIONS AND PERSPECTIVES

The discrepancy between the biological relevance and the lack of data about infochemicals in the environment reveals the necessity of further research. According to the actual findings, infochemicals are so decisive for the interactions in the ecosystem that they should not be neglected in ecotoxicology. The discovery of the infochemical effect is comparable to the detection that environmental substances can act as hormones. Sublethal effects with impacts on the ecosystem, such as the infochemical effect, will receive higher appraisal in the ecotoxicology of the future. It needs to be clarified to which extent anthropogenic discharges disturb the natural chemical communication web. A systematic analysis of this very complex field will be needed to know whether a new ecotoxicological endpoint, the infochemical effect, will have to be taken up in the standard repertoire. The knowledge on infochemicals might require some adjustments of the legal framework on environmental chemicals in future. Looking closer at the infochemical effect will lead to a new understanding of the complexity of environmental communities.

Olfactory coding with all-or-nothing glomeruli

We present a model for olfactory coding based on spatial representation of glomerular responses. In this model distinct odorants activate specific subsets of glomeruli, dependent on the odorant's chemical identity and concentration. The glomerular response specificities are understood statistically, based on experimentally measured distributions of activation thresholds. A simple version of the model, in which glomerular responses are binary (the all-or-nothing model), allows us to account quantitatively for the following results of human/rodent olfactory psychophysics: 1) just noticeable differences in the perceived concentration of a single odor (Weber ratios) are as low as dC/C approximately 0.04; 2) the number of simultaneously perceived odors can be as high as 12; and 3) extensive lesions of the olfactory bulb do not lead to significant changes in detection or discrimination thresholds. We conclude that a combinatorial code based on a binary glomerular response is sufficient to account for several important features of the discrimination capacity of the mammalian olfactory system.