HGNC gene links to GtoPdb

As regular users of GtoPdb will be aware, our target pages include HUGO Gene Nomenclature Committee (HGNC) gene symbols, nomenclature and links to HGNC gene pages (Fig 1).

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Figure 1. GtoPdb gene information including link outs to HGNC pages by clicking on the human gene symbol.

HGNC pages in turn link back to GtoPdb target pages under the “Specialist database” link (Fig 2).

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Figure 2. HGNC gene page showing the link to the IUPHAR/BPS Guide to Pharmacology (GtoPdb) under “Specialist Databases”.

In GtoPdb release 2017.4 there were 2823 HGNC target links. In June 2017 we also added a further 430 HGNC links to GtoPdb peptide ligand pages (Figs 3 and 4). These are either small proteins such as cytokines, or endogenous peptides derived from Swiss-Prot proteins that have an HGNC entry. Implicit in our classification as ligands these will have (in most cases quantitative) reported interactions with cognate receptors.  The peptides will usually correspond to sequences processed from their precursor proteins in HGNC (e.g. the eight angiotensin peptides from Angiotensinogen, AGT).  Note that some of these peptides are cross-linked to other ligand entries which are similar synthetic bioactive sequences that do not exactly match the cleavage cross-references in UniProt.

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Figure 3. GtoPdb peptide ligand page which links to the HGNC gene page by clicking on the gene symbol.

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Figure 4. HGNC gene page for a chemokine ligand showing a link to the GtoPdb ligand page.

For over 50 genes which encode multiple mature peptides, the HGNC page links to the longest peptide sequence included in GtoPdb. This is because HGNC currently only supports one external link per resource, and they are working on providing support for multiple links by the end of this year.

This expansion was driven by importance of these reciprocal links for HGNC users to navigate across to pharmacolgical information. In addtion, going the other way, they enable GtoPdb users to find out more about gene nomenclature and other genetic information via HGNC.

The full list of HGNC in-links to GtoPdb can be downloaded here (as a CSV file as illustrated in Fig 5). Ligand links can be distinguished from target links by the URL.

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Figure 5. Part of the CSV file containing all the HGNC links to GtoPdb showing some of the new ligand links.

 

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Posted in Technical

Hot topic: Activity-based protein profiling reveals off-target proteins of the FAAH inhibitor BIA 10-2474

The historical context for this commentary can be found in this blogpost. This latest report, based on activity-based profiling (ABPP), constitutes the first open biochemical investigation of BIA 10-2474 (1). The ABPP results show it inhibits several lipases that are not targeted by PF04457845, a highly selective and clinically tested FAAH inhibitor. In addition BIA 10-2474 (but not PF04457845) produced substantial alterations in lipid networks in human cortical neurons. The authors are appropriately cautious in not over-extrapolating their findings to causality of pathology recorded in the unfortunate patients (see clinical report in PMID 27806235). However, biochemical and pharmacological questions still remain. One of these is that, given the initial binding interaction is no less than three orders of magnitude lower that PF004457845, it’s not entirely clear why 10-2474 was chosen as the lead. Another question is the basic kinetic parameters for purified enzymes (not just crude cell extracts in vitro) are still not available. This should include at least two methods for confirming irreversibility (e.g. IC50 vs pre-incubation or using a 10-2474 radiolabeled derivative). Word has it that a BIAL paper is in preparation so this aspect might be addressed by new results. Note also there are now two compound suppliers in PubChem offering BIA 10-2474 so more experimental reports could be expected.

The GtoPdb entries below have been updated with key interactions from this paper and will go live at the next release.

BIA 10-2474

PF004457845

FAAH

FAAH2

(1) van Esbroeck ACM et al. (2017). Activity-based protein profiling reveals off-target proteins of the FAAH inhibitor BIA 10-2474. Science, 356(6342): 1084-1087 [PMID:28596366]

Posted in Hot Topics

Hot topic: GPR3 and GPR6, novel molecular targets for cannabidiol

Cannabidiol is a major metabolite from the Cannabis plant, although levels vary dependent on genetic, regional, cultivation and other factors.  It lacks the psychotropic nature of THC, but has been reported to have many biological effects, to the extent that clinical trials for infantile intractable epilepsy are currently ongoing in the US. GPR3 and GPR6 are orphan GPCRs, which have previously been reported to elevate cAMP levels constitutively when expressed in recombinant systems.  Although there was some evidence for activation by sphingosine 1-phosphate, this was not reproduced.  In this report, a number of endogenous and Cannabis-derived metabolites were examined for their effects on β-arrestin2 recruitment in cells expressing either GPR3 or GPR6.  Of these agents, only CBD caused a reduction in β-arrestin2 recruitment in a concentration-dependent manner, with pIC50 values of 5.9 and 6.7 at GPR3 and GPR6, respectively.  The authors suggest that the inverse agonist nature of CBD at these receptors might be of relevance for neurodegenerative disorders, such as Parkinson’s and Alzheimer’s Disease.

Comments by Steve Alexander (@mqzspa)

(1) Laun AS, Song ZH. (2017) GPR3 and GPR6, novel molecular targets for cannabidiol. Biochem Biophys Res Commun. 2017 May 29. pii: S0006-291X(17)31074-4. doi: 10.1016/j.bbrc.2017.05.165. [Epub ahead of print] [PMID:28571738]

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Hot topic: Selectivity determinants of GPCR–G-protein binding

As a detailed comparative sequence/structure/evolution analysis it is relatively unusual (in a good sense) to see such a bioinformatics article in Nature. This tour de force was a collaboration between MRC Laboratory of Molecular Biology, Cambridge UK and the Department of Drug Design and Pharmacology, University of Copenhagen (home of the GPCRdb team). As we know, GPCR signal transduction involves the binding of ligand-activated receptors to their appropriate Gα proteins. In this work selectivity-determining positions for signal transduction (as structural “barcodes”) were inferred by comprehensively comparing the sequence conservation between paralogues and orthologues, incorporating information from recent structures. The residue positions for the interaction interfaces are collated and presented at gpcrdb.org (tab ‘Signal Proteins’) for all human receptors and their 16 Gα proteins. This will be updated (including data from new structures) as a guide to interface determinants of coupling selectivity. Many applications of this resource can be envisaged. These could include: exploring options to target GPCR-G protein interfaces with agents that block coupling between the receptor and G protein intracellularly, protein engineering, structural studies and understanding the consequences of natural variation or rare disease associated mutations occurring in the vicinity of the barcode positions.

Note that all GtoPdb GPCRs have cross-references to GPCRdb (who we collaborate with) so users can navigate structural data (including the barcode positions) via GPCRdb, but also exploit ligand-centric navigation via GtoPdb and links out to genomic variants via the Ensembl links.

[1] Flock et al. (2017). Selectivity determinants of GPCR-G-protein binding. Nature, 545: 317-322. [PMID:28489817].

Comments by by Chris Southan (@cdsouthan)

 

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Hot topics: Crystal structure of full-length glucagon receptor provides insight into relative orientation of extracellular and transmembrane domains in an inactive conformation and importance of dynamic changes in this orientation for activation

It has been quite challenging to gain high resolution structural insights into an intact class B G protein-coupled receptor, despite previous solution of multiple structures for the two dominant domains, the extracellular domain (ECD) and the transmembrane helical bundle domain (TMD) of this family of receptors. Zhang et al. (1) now report a crystal structure of full length glucagon receptor (GCGR) in an inactive conformation stabilized by the non-peptidyl antagonist, NNC0640, and mAb1, bound to the ECD. In this new structure, the ECD is elongated above the TMD, with mAb1 resting on extracellular loop 1 (ECL1), and with the stalk region that links the two dominant receptor domains present in a β-strand conformation lying across the helical bundle between ECL1 and ECL2/ECL3. Of particular interest, hydrogen bonds are formed between the stalk and ECL1 to establish a compact β-sheet. The conformation of the stalk in this structure is different from the α-helical extension of TM1 present in the previous solved structure of the isolated ECD of this receptor (2), with the orientation of the ECD in the new structure quite different from that previously predicted. The authors used data from hydrogen-deuterium exchange, disulfide crosslinking, and molecular dynamics to suggest that the relatively stable β-sheet formed by the stalk and ECL1 plays an important role in controlling accessibility of the orthosteric peptide ligand to its site of docking and in the transition of inactive to active receptor states. A hypothetical model is proposed whereby the C-terminus of glucagon gains access to the peptide-binding groove within the ECD, a step that requires ECD separation from the stalk/ECL1 complex, with this initial ligand-binding event leading to a conformational change in the receptor that is not yet understood, allowing the N-terminus of glucagon to dock within the TMD to activate the receptor. A recent report of the use of cryo-EM to determine the structure of another member of the class B family, the calcitonin receptor, in active conformation in complex with salmon calcitonin and its heterotrimeric G protein (3), also emphasizes the relative mobility of ECD and TMD, and the importance of dynamic changes in orientation of these domains. It will be important to gain more insights into the structure and conformational flexibility of apo-receptors in this family to better understand how the natural peptide ligands gain access to the ECD, and to learn more about other possible sites of contact between ECD and TMD that could contribute to conformational changes in the TMD. These reports emphasize the functional importance and likely variations that will exist in the relative orientations of these key structural domains for this class of GPCRs.

[1] Zhang et al. (2017). Structure of the full-length glucagon class B G-protein-coupled receptor. Nature, doi:10.1038/nature222363. [PMID: 28514451]
[2] Siu et al. (2013). Structure of the human glucagon class B G-protein-coupled receptor. Nature, 488:444-449. [PMID: 23863937]
[3] Liang et al. (2017). Phase-plate cryo-EM structure of a class B GPCR-G-protein complex. Nature,doi: 10.1038/nature22327. [Epub ahead of print] [PMID: 28437792]

Comments by Laurence J. Miller (Mayo Clinic, Scottsdale, AZ, USA)

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Hot topics: Crystal structure of GLP-1 receptor transmembrane domain provides insight into allosteric modulation.

The glucagon-like peptide-1 receptor (GLP-1R) is a major target for treatment of Type 2 diabetes but has been refractory to the development of small molecule compounds as potential therapeutics. Song et al., (1) report the first crystal structures of the GLP-1R transmembrane domain in complex with 2 distinct negative allosteric modulators (NAMs) (PF-06372222 and NNC0640). The work provides insight into inactive state structure for the GLP-1R and key interactions that drive inhibitor potency. Moreover, the work allows modelling of an allosteric agonist (and positive allosteric modulator, PAM), Novo Nordisk compound 2, to reveal a potential mechanism for allosteric receptor activation that is supported by mutagenesis and molecular dynamics simulations. The proposed mechanism would lead to a decreased energy barrier for receptor activation through reorganisation of hydrogen bond networks at the base of the receptor that are important for receptor quiescence, and is consistent with the known pharmacology of the PAM in modulating orthosteric peptide activation of the receptor. This work, combined with novel structures of active class B receptors, opens up new possibilities for design of small molecule compounds to manipulate receptor pharmacology and as potential therapeutic drug leads.

[1] Song et al. (2017) Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators. Nature, doi:10.1038/nature22378. [PMID 28514449]

Comments by Patrick Sexton (Monash Univeristy, Melbourne)

Posted in Hot Topics

Guide to IMMUNOPHARMACOLOGY – beta release v1.0, May 2017

We are pleased to announce the first, public, beta-release of the Guide to IMMUNOPHARMACOLOGY (GtoImmuPdb). The GtoImmuPdb is a Wellcome Trust-funded extension to the existing Guide to PHARMACOLOGY (GtoPdb) and the beta-release (v1.0) marks an important milestone in its production and development. GtoImmuPdb aims to provide improved data exchange between immunology and pharmacology expert communities, so to better support research and development of drugs targeted at modulating immune, inflammatory or infectious components of disease. The underlying GtoPdb schema has been extended to incorporate new immune system specific data types (such as processes, cell types and disease) and the GtoPdb website has been developed to surface this new data and incorporate it into the existing search and browse mechanisms. A new Guide to IMMUNOPHARMACOLOGY portal (Figure 1)(www.guidetoimmunopharmacology.org) has been developed, which serves as a unique immunological access-point to the Guide to PHARMACOLOGY.

portal

The GtoImmuPdb enriches the existing GtoPdb by flagging targets and ligands of immunological relevance and linking these targets to immunological process, cell types and relevant diseases. In terms of processes and cell types, GtoImmuPdb has developed top-level categories (Figure 2), that aim to be meaningful and intuitive to immunologists, against which targets and ligands in the database can be annotated. These categories are underpinned by the use of both the Gene Ontology and the Cell Ontology. Using recognised ontologies provides a controlled vocabulary for higher resolution annotation (Figure 3). It also facilitates interoperability between new data types in GtoImmuPdb and external resources that also use these ontologies.

processs_celltype_browse

process_assoc_bcell

Data linking targets and ligands to disease is also incorporated into GtoImmuPdb, with the curation of disease associations using resources such as OrphaNet, Disease Ontology and OMIM (Figure 4).

ligand_v_disease

As well as the development of the GtoImmuPdb Portal, the web-interface has been further developed with immunological data and users in mind. It has been designed to provide a unique ‘GtoImmuPdb view’ of the data, highlighting content of immunological relevance and prioritising immunological data in search results and display. It includes features that highlight targets, target families and ligands of immunological relevance (Figure 5); toggle buttons to enable the GtoImmuPdb view to be switched on and off (Figure 6); and new pages and sections to display immunological data (Figure 7).

Figure2_Harding

 

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Development of the beta-release is ongoing with regular updates planned over the next few months as the quantity of data captured increases and improvements in the site layout and function are made. One of our priorities over the next 6 months is to undertake rigorous site testing with interested user groups to capture more insight and feedback. We welcome those interested and potential future users to get in touch with us.

This project is supported by a 3-year grant awarded to Professor Jamie Davies at the University of Edinburgh by the Wellcome Trust (WT).

Posted in Guide to Immunopharmacology