GPCR ontology: development and application of a G protein-coupled receptor pharmacology knowledge framework.

MOTIVATION: Novel tools need to be developed to help scientists analyze large amounts of available screening data with the goal to identify entry points for the development of novel chemical probes and drugs. As the largest class of drug targets, G protein-coupled receptors (GPCRs) remain of particular interest and are pursued by numerous academic and industrial research projects. RESULTS: We report the first GPCR ontology to facilitate integration and aggregation of GPCR-targeting drugs and demonstrate its application to classify and analyze a large subset of the PubChem database. The GPCR ontology, based on previously reported BioAssay Ontology, depicts available pharmacological, biochemical and physiological profiles of GPCRs and their ligands. The novelty of the GPCR ontology lies in the use of diverse experimental datasets linked by a model to formally define these concepts. Using a reasoning system, GPCR ontology offers potential for knowledge-based classification of individuals (such as small molecules) as a function of the data. AVAILABILITY: The GPCR ontology is available at http://www.bioassayontology.org/bao_gpcr and the National Center for Biomedical Ontologies Web site.

Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO).

Huge amounts of high-throughput screening (HTS) data for probe and drug development projects are being generated in the pharmaceutical industry and more recently in the public sector. The resulting experimental datasets are increasingly being disseminated via publically accessible repositories. However, existing repositories lack sufficient metadata to describe the experiments and are often difficult to navigate by non-experts. The lack of standardized descriptions and semantics of biological assays and screening results hinder targeted data retrieval, integration, aggregation, and analyses across different HTS datasets, for example to infer mechanisms of action of small molecule perturbagens. To address these limitations, we created the BioAssay Ontology (BAO). BAO has been developed with a focus on data integration and analysis enabling the classification of assays and screening results by concepts that relate to format, assay design, technology, target, and endpoint. Previously, we reported on the higher-level design of BAO and on the semantic querying capabilities offered by the ontology-indexed triple store of HTS data. Here, we report on our detailed design, annotation pipeline, substantially enlarged annotation knowledgebase, and analysis results. We used BAO to annotate assays from the largest public HTS data repository, PubChem, and demonstrate its utility to categorize and analyze diverse HTS results from numerous experiments. BAO is publically available from the NCBO BioPortal at http://bioportal.bioontology.org/ontologies/1533. BAO provides controlled terminology and uniform scope to report probe and drug discovery screening assays and results. BAO leverages description logic to formalize the domain knowledge and facilitate the semantic integration with diverse other resources. As a consequence, BAO offers the potential to infer new knowledge from a corpus of assay results, for example molecular mechanisms of action of perturbagens.

Nutritional state influences Nociceptin/Orphanin FQ peptide receptor expression in the dorsal raphe nucleus.

Agonists of the nociceptin/orphanin FQ (N/OFQ) peptide (NOP) receptor stimulate food intake. Concordantly, neuroanatomical localization of NOP receptor mRNA has revealed it to be highly expressed in brain regions associated with the regulation of energy balance. However, the specific mechanisms and neurochemical pathways through which physiological N/OFQ influences appetite are not well understood. To investigate this, we examined nutritional state-associated changes in NOP receptor mRNA levels throughout the rostrocaudal extent of the rat brain using in situ hybridization histochemistry (ISHH) and quantitative densitometry analysis. We observed a significant downregulation of NOP receptor mRNA in the dorsal raphe nucleus (DRN) of fasted rats compared to free-feeding rats. In contrast, no difference in NOP receptor mRNA expression was observed in the supraoptic, parventricular, ventromedial, arcuate or dorsomedial nuclei of the hypothalamus, the red nucleus, the locus coeruleus or the hypoglossal nucleus in the fasted or fed state. These data suggest that the endogenous N/OFQ system is responsive to changes in energy balance and that NOP receptors specifically within the DRN may be physiologically relevant to N/OFQ's effects on appetite.

Role of central melanocortin pathways in energy homeostasis.

The rise in the global prevalence of human obesity has emphasized the need for a greater understanding of the physiological mechanisms that underlie energy homeostasis. Numerous circulating nutritional cues and central neuromodulatory signals are integrated within the brain to regulate both short- and long-term nutritional state. The central melanocortin system represents a crucial point of convergence for these signals and, thus, has a fundamental role in regulating body weight. The melanocortin ligands, synthesized in discrete neuronal populations within the hypothalamus and brainstem, modulate downstream homeostatic signalling via their action at central melanocortin-3 and -4 receptors. Intimately involved in both ingestive behaviour and energy expenditure, the melanocortin system has garnered much interest as a potential therapeutic target for human obesity.

Nociceptin/orphanin FQ peptide receptor as a therapeutic target for obesity.

Nociceptin/orphanin FQ (N/OFQ) peptide (NOP) receptor is a candidate target for novel therapeutics for a range of conditions, including obesity. This article reviews recent advances in understanding of N/OFQ's involvement in the regulation of food intake and appraises current developments in the rational design of antagonists aimed at the NOP receptor.

Serotonin 5-HT2C receptor agonist promotes hypophagia via downstream activation of melanocortin 4 receptors.

The neurotransmitter serotonin (5-hydroxytryptamine) is a well-established modulator of energy balance. Both pharmacological and genetic evidence implicate the serotonin 2C receptor (5-HT(2C)R) as a critical receptor mediator of serotonin's effects on ingestive behavior. Here we characterized the effect of the novel and selective 5-HT(2C)R agonist BVT.X on energy balance in obese and lean mice and report that BVT.X significantly reduces acute food intake without altering locomotor activity or oxygen consumption. In an effort to elucidate the mechanism of this effect, we examined the chemical phenotype of 5-HT(2C)R-expressing neurons in a critical brain region affecting feeding behavior, the arcuate nucleus of the hypothalamus. We show that 5-HT(2C)Rs are coexpressed with neurons containing proopiomelanocortin, known to potently affect appetite, in the arcuate nucleus of the hypothalamus of the mouse. We then demonstrate that prolonged infusion with BVT.X in obese mice significantly increases Pomc mRNA and reduces body weight, percent body fat, and initial food intake. To evaluate the functional importance of melanocortin circuitry in the effect of BVT.X on ingestive behavior, we assessed mice with disrupted melanocortin pathways. We report that mice lacking the melanocortin 4 receptor are not responsive to BVT.X-induced hypophagia, demonstrating that melanocortins acting on melanocortin 4 receptor are a requisite downstream pathway for 5-HT(2C)R agonists to exert effects on food intake. The data presented here not only indicate that the novel 5-HT(2C)R agonist BVT.X warrants further investigation as a treatment for obesity but also elucidate specific neuronal pathways potently affecting energy balance through which 5-HT(2C)R agonists regulate ingestive behavior.

Homology modeling of opioid receptor-ligand complexes using experimental constraints.

Opioid receptors interact with a variety of ligands, including endogenous peptides, opiates, and thousands of synthetic compounds with different structural scaffolds. In the absence of experimental structures of opioid receptors, theoretical modeling remains an important tool for structure-function analysis. The combination of experimental studies and modeling approaches allows development of realistic models of ligand-receptor complexes helpful for elucidation of the molecular determinants of ligand affinity and selectivity and for understanding mechanisms of functional agonism or antagonism. In this review we provide a brief critical assessment of the status of such theoretical modeling and describe some common problems and their possible solutions. Currently, there are no reliable theoretical methods to generate the models in a completely automatic fashion. Models of higher accuracy can be produced if homology modeling, based on the rhodopsin X-ray template, is supplemented by experimental structural constraints appropriate for the active or inactive receptor conformations, together with receptor-specific and ligand-specific interactions. The experimental constraints can be derived from mutagenesis and cross-linking studies, correlative replacements of ligand and receptor groups, and incorporation of metal binding sites between residues of receptors or receptors and ligands. This review focuses on the analysis of similarity and differences of the refined homology models of mu, delta, and kappa-opioid receptors in active and inactive states, emphasizing the molecular details of interaction of the receptors with some representative peptide and nonpeptide ligands, underlying the multiple modes of binding of small opiates, and the differences in binding modes of agonists and antagonists, and of peptides and alkaloids.