Database Release 2020.4

The latest release of the Guide to PHARMACOLOGY database, version 2020.4, has now been made.

Coronavirus

The Guide to Pharmacology coronavirus information page continues to be updated on a regular basis to capture the latest pharmacological strategies under investigation to mitigate against COVID-19.

GtoPdb curates Coronavirus (CoV) proteins under viral protein targets in our hierarchy. This family contains 15 CoV proteins. Updates in this release to the CoV 3C-like (main) protease include outlinks to CHEMBL (CHEMBL3927) and UniProt (P0C6U8); the addition of 4 further 3D structures (3VB3, 2GX4, 6LZE and 6XHL) and and additional 19 curated ligand interactions.

Curation Updates

We’ve added some new targets proteins along with associated pharmacological ligands. These include the following five, that are all oncology targets:

Also added is C-type lectin receptor CLEC4C, an anti-inflammatory target, and N-acetyltransferase 8 like (ANAT), a target for the treatment of Canavan disease which is a rare aspartoacylase deficiency-mediated neurodegenerative condition.

The list of WHO essential medicines has been expanded with the inclusion of many antibiotics and antivirals.

Overall this release sees updates made to targets across 35 targets families. These are listed below with links to family page in the database:

GPCRs
Adenosine receptors
Bradykinin receptors
Calcium-sensing receptor
Complement peptide receptors
Dopamine receptors
Gonadotrophin-releasing hormone receptors
Hydroxycarboxylic acid receptors
Leukotriene receptors
Melanocortin receptors
Melatonin receptors
Motilin receptor
Neuropeptide S receptor
Neurotensin receptors
Prolactin-releasing peptide receptor
QRFP receptor

Ion-Channels
Glycine receptors
P2X receptors
Voltage-gated potassium channels
Voltage-gated proton channel

Catalytic Receptors
Nitric oxide (NO)-sensitive (soluble) guanylyl cyclase
Transmembrane guanylyl cyclases
Tumour necrosis factor (TNF) receptor family

Enzymes
N-Acylethanolamine turnover
2-Acylglycerol ester turnover
Sphingosine 1-phosphate lyase
Sphingosine 1-phosphate phosphatase
Sphingosine 1-phosphate turnover
Sphingosine kinase

Transporters
Neutral amino acid transporter subfamily
SLC14 family of facilitative urea transporters
SLC28 family
SLC29 family
SLC51 family of steroid-derived molecule transporters
SLC8 family of sodium/calcium exchangers

Other Proteins
R7 family of RGS proteins

Website Updates

  • We updated our website tutorial, which now includes details on the advanced search and ligand activity graphs
  • New download files are available from the immunological process and cell type target associations pages
  • A new GPCR targets download files is available on each of the GPCR list page (example here for Class A)
  • Bug fixes for web services
  • Links to AntibioticDB now cover over 230 ligands.

Guide to Malaria Pharmacology (GtoMPdb)

These are the recent advancements made in the GtoMPdb for this database release:

Included in GtoMPdb are 15 of 32 WHO antivirals and with 4 added for this release: atazanavir, abacavir, darunavir and emtricitabine.

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Hot Topics: Soluble ligands as drug targets

Historically, the main classes of drug targets have been receptors, enzymes, ion channels and transporters which are primarily targeted by small molecules. However, advances in molecular biology, genomics, and pharmacology have facilitated the development of different therapeutic modalities which in turn have broadened the types of drug targets. In particular, soluble ligands have growing interest as targets and now constitute 10% of novel targets in clinical trials and are currently the third-largest target class of therapeutic agents targeting human protein products, after enzymes and receptors [1].

A new analysis of ligand-targeting [2], illustrates the different classes of ligand-targeting drugs and targets as well as analysing the success of the different technology platforms. This emerging class of drug targets is very dynamic with 291 agents that target 99 unique ligands reaching clinical development from 1992 to 2020. In the last five years, the number of ligand-targeting agents which are FDA-approved has doubled to 34, while the number of clinically validated ligand targets has doubled to 22. Therapeutic antibodies are the most common class of both approved and investigative ligand-targeting agents, followed by decoy receptors. Several technology platforms are successfully being developed, enhancing the opportunities of drug development using antibody fragments, single-domain antibodies, aptamers, spiegelmers, engineered protein scaffolds, gene therapy, therapeutic vaccines and oligonucleotides. There is an increase in the number of agents that target more than one ligand, as well as the number of unique combinations of ligands. Advances in engineering technology and the ability to effectively and safely target more than one ligand has combined with increased knowledge of disease pathways to effectively utilize bispecific antibodies and decoy receptors, amongst others, to selectively disrupt multiple biological pathways by blocking two (or more) related or unrelated ligands. Cytokines and growth factors are the predominant types of targeted ligands (70%), which is consistent with the three major disease groups being treated by both approved and investigational agents: inflammation and autoimmune diseases, cancer, and ophthalmological diseases.

Several factors contribute to the increasing importance of soluble ligands as drug targets, including the growing understanding of the role of the immune system in many diseases in conjunction with the tractability of cytokines as therapeutic agents, and the relative accessibility of ligands in comparison to their receptors to therapeutic agents. Given the increasing body of evidence that inflammation is involved in many diseases beyond typical inflammation disorders and the position of ligand-targeting drugs at the forefront of anti-inflammatory therapies, there will be continued interest in this class of agents. Furthermore, there is vast territory to explore in the ligand target landscape, as there are almost 600 endogenous human peptides according to IUPHAR/BPS Guide to PHARMACOLOGY (https://www.guidetopharmacology.org) with approximately 150 of these identified as having specifically curated immunopharmacological data associated with them (IUPHAR Guide to IMMUNOPHARMACOLOGY: https://www.guidetoimmunopharmacology.org/immuno/).

In conclusion, ligands as a type of drug target now merit consideration as a distinct and expanding group of targets for a range of therapeutic modalities that can exert their effects through single targets or selected combinations.

Comments by Misty Attwood and Helgi SchiöthUniversity of Uppsala, Uppsala, Sweden. Helgi Schiöth is Chair for NC-IUPHAR Subcommitees for Melanocortin receptors and Prolactin-releasing peptide receptor. Twitter: @FunctPharm

  1. Attwood, M. M., Rask- Andersen, M. & Schiöth, H. B. Orphan drugs and their impact on pharmaceutical development. Trends Pharmacol. Sci. 39, 525–535 (2018). [PMID: 29779531]
  2. Attwood, M.M., Jonsson, J., Rask-Andersen, M & Schiöth, H. B. Soluble ligands as drug targets. Nature Reviews Drug Discovery. Online ahead of print (2020 Sep 2.). [PMID: 32873970]
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GtoPdb pre-release ligands (2020.4)

These are some of the ligands under curation (pre-release) in the Guide to Pharmacology. We expect them to be available on the website at the next database release (2020.4).

Ligand ID: 11132

Name: otilimab

Comment: Otilimab (MOR103, GSK3196165) is a clinical stage fully human IgG1λ antibody that targets the granulocyte-macrophage colony-stimulating factor (GM-CSF; CSF2). It is being investigated as a therapeutic for inflammatory diseases. MOR103 was developed using MorphoSys’ HuCAL® technology, and has been fully out-licensed otilimab to GSK. MOR103 is claimed as MOR-04357 in patent WO2006122797A2 (by BLAST peptide sequence matching).


Ligand ID: 11139

Name: favipiravir

11139

Comment: Favipiravir (T-705) is an orally delivered, guanine (purine) analogue antiviral drug (cf. remdesivir which is administered i.v.). It targets viral RNA-dependent RNA polymerase (RdRP) of RNA viruses and since the catalytic domain of RdRP is well conserved across species, has a broad-spectrum of activity; although Furuta et al. (2002) reported that actvity was weak against non-influenza virus RNA viruses [4]. Favipiravir was originally identified through a chemical library screen against influenza virus RdRP [3]. Chemically, it is a prodrug. In human cells it undergoes phosphoribosylation and phosphorylation to its active form, favipiravir-ribofuranosyl-5′-triphosphate (F-RTP). F-RTP is bound by the RdRP, but it blocks enzyme activity and so terminates chain elongation [5-6].

IUPAC Name: 5-fluoro-2-oxo-1H-pyrazine-3-carboxamide


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Hot Topics: TMEM163 regulates ATP-gated P2X receptor and behaviour

It is now clear that ligand-gated ion channels (LGICs) are not “stand alone” functional units, but form complexes with other components, including scaffolding proteins, regulatory proteins and enzymes. Besides their important physiological roles, these modulating proteins are also potential targets for drug discovery. P2X receptors are LGICs for which ATP is the endogenous agonist. Seven P2X subunits have been identified and they form trimers to produce at least twelve different receptor subtypes. Here, the authors combined a genome-wide open reading frame (ORF) collection with high-throughput functional screening, to search for P2X receptor modulators.

They first created a HEK-293 cell line that stably expressed human P2X2 plus P2X3 receptors, then one-by-one, co-expressed each of 17,284 non-redundant ORFs, which represents 90% of the known human protein-coding genes. They then compared the rise in intracellular [Ca2+] induced by the P2X3 agonist α,β-meATP, using a composite score of four measurements; 1) baseline, 2) peak and 3) steady-state [Ca2+], along with 4) time-course of the decay of the peak. The highest scoring ORFs were then co-expressed with P2X3 receptors in Xenopus laevis oocytes and their effects on ATP-induced ion currents determined. This process led to TMEM163 being identified as a modulator of P2X3 receptors.

TMEM163 comprises 289 amino acids, with a molecular weight of 31 kDa and predicted secondary structure of six transmembrane-spanning domains with intracellular NH2– and COOH-termini. When expressed on its own, TMEM163 had no ATP-dependent activity and when co-expressed, had no effect on the activity of AMPA, kainate, muscarinic or P2X2 receptors, nor on endogenous P2Y receptors in HEK-293 cells. It did, however, potentiate ATP-evoked currents mediated by P2X1 and P2X4 receptors and conversely, inhibited currents carried by P2X7 receptors. Thus TMEM163 appears to selectively modulate P2X receptor activity, but in a subtype-specific manner.

More detailed analysis of its actions showed that TMEM163 potentiated P2X3 receptors by shifting the ATP concentration-response curve (CRC) to the left, with a five-fold decrease in the EC50 and slowing the time-course of current decay. Surprisingly, it also substantially reduced the surface expression of P2X3 receptors. In contrast, the inhibitory effects on P2X7 receptors were associated with a decrease in both the potency of ATP and surface expression of the receptor.

Next, the expression and effects of native TM163 was investigated in mice. In situ hybridisation and an anti-TM163 antibody showed TMEM163 to be present in primary cultures of mouse cerebellar neurones. Infection with a TMEM163 shRNA reduced protein expression by almost half and the peak amplitude of ATP-induced ion currents by a third. The effect on P2X3 receptor protein levels was not reported, however. To study its role in vivo, TMEM163 was knocked-out using CRISPR/Cas9 and pain-associated behaviour induced by ATP injection into the hind-paw studied. There was no difference in paw lifting between wild-type and knock-out mice, but freezing behaviour was reduced by about 50%. Notably, and in contrast to the data obtained using recombinant TMEM163, the total amount of P2X3 protein in dorsal root ganglion was unchanged. The ATP CRC was, however, shifted about five-fold to the right by TMEM163 knock-out, consistent with the leftwards shift seen using the recombinant proteins.

By showing that that TMEM163 selectively modulates P2X receptor activity and in a subtype-specific manner, this study greatly improves our understanding of how native P2X receptors function. As such, TMEM163 is potentially a new target for drug discovery.

Comments by Charles Kennedy, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK. Chair for NC-IUPHAR Subcommitee for P2X receptors.

  1. Salm EJ, Dunn PJ, Shan L, Yamasaki M, Malewicz NM, Miyazaki T, Park J, Sumioka A, Hamer RRL, He WW, Morimoto-Tomita M, LaMotte RH, Tomita S. (2020). TMEM163 regulates ATP-gated P2X receptor and behaviour. Cell Rep, 31: 107704. PMID: 32492420.

 

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Accessing WHO Essential Medicines in GtoPdb

The Guide to Pharmacology (GtoPdb) currently contains data on over 10,000 different ligands which are categorised into an number of different groups or classifications. The ligand list page (https://www.guidetopharmacology.org/GRAC/LigandListForward?type=WHO-essential&database=all) provides a directory of all the ligands described in the database, divided into subsets according to chemical category.

We have recently added a WHO Essential Medicine subset, which contains ligands in GtoPdb that are also in the latest WHO Model List of Essential Medicines (21st list, 2019) (https://www.who.int/medicines/publications/essentialmedicines/en/). This totals 224 ligands in our 2020.3 release.

Selecting the WHO tab from the ligand list page shows this subset (Figure 1). Users can also download this set of ligands (as csv file) by clicking on the link in the top-right.

Accessing WHO tagged GtoPdb compound in PubChem

GtoPdb regularly uploads its set of compounds to PubChem, which provides all GtoPdb ligands with PubChem Substance Identifiers (SIDs), which are in turn mapped (by PubChem) to PubChem Compound Identifiers (CIDs). As part of our PubChem upload process we have developed our curatorial tagging within the depositor comment sections in the substance records (SIDs). This means users are able to make domain-specific queries, to be executed from both the PubChem Substance (SID) and PubChem Compound (CID) interfaces, by using an advanced search of ‘comments’ fields.

We have now added a WHO tag to the comments fields in our PubChem upload (see example for cholorquine, Figure 2). chloroquine2

Figure 2. Depositor comment for Chloroquine (PubChem Substance ID 178102177) showing GtoPdb curatorial tagging to mark substance as included in WHO Essential Medicines List. https://pubchem.ncbi.nlm.nih.gov/substance/178102177#section=Depositor-Comments

Therefore it is now possible, through the query below to easily access the WHO Essential Medicines in GtoPdb through PubChem.

https://www.ncbi.nlm.nih.gov/pcsubstance?term=(%22iuphar%2Fbps%20guide%20to%20pharmacology%22%5BSourceName%5D)%20AND%20%22gtopdb%20who%22%5BComment%5D

pubchem_gtopdb_who


Figure 3. Search result in PubChem for IUPHAR/BPS Guide to PHARMACOLOGY substances that include ‘gtopdb_who’ in the comments. https://www.ncbi.nlm.nih.gov/pcsubstance/?term=(%22iuphar%2Fbps+guide+to+pharmacology%22%5BSourceName%5D)+AND+%22gtopdb+who%22%5BComment%5D

 

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Database Release 2020.3

The latest release of the Guide to PHARMACOLOGY database, version 2020.3, has now been made. A large focus of our curation over the last couple of month since our 2020.2 release We are pleased to have been able to make an expeditious database release (version 2020.2), following on from our last update in March 2020 in order to make public new curation specifically related to SARS-CoV-2.

Coronavirus

The Guide to Pharmacology coronavirus information page continues to be updated on a regular basis to capture the latest pharmacological strategies under investigation to mitigate against COVID-19.

Recently published in BJP is our review that “sets out to identify opportunities for drug discovery in the treatment of COVID‐19 and in so doing, provide a rational roadmap whereby pharmacology and pharmacologists can mitigate against the global pandemic“:

Alexander SPH, Armstrong J, Davenport AP, Davies JA, Faccenda E, Harding SD, Levi-Schaffer F, Maguire JJ, Pawson AJ, Southan C, Spedding MJ. (2020). A rational roadmap for SARS‐CoV‐2/COVID‐19 pharmacotherapeutic research and development. IUPHAR Review 29 Br J Pharmacol. doi: 10.1111/bph.15094. [PMID:32358833]

Content Updates

Main target families with updated in this release:

GPCRs

Ion Channels

NHRs

Enzymes, Catalytic Receptors

New drug target

Acyl-CoA synthetase short chain family member 2 (ACSS2) is an emerging oncology drug target that plays a role in epithelial-mesenchymal transition (EMT) and cancer cell metastasis. Two ACSS2 inhibitor probe compounds have been curated.

AntibioticDB

As part of a collaboration with AntibioticDB (https://www.antibioticdb.com/), we have now begun to identify and tag sets of antibiotic ligands in GtoPdb. Where we have identified mappings between these and compounds in the AntibioticDB repository, we’ve put in place direct links. The newly curated set includes approved and investigational antibiotics and pre-clinical leads, as well as compounds whose development has been discontinued.

teixobactin

Teixobactin ligand summary page (https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=10972). At the bottom, a new specialist database link now existing to the mapped entry in AntibioticDB.

Website Updates

Ligand Summary Pages

The layout of the ligand summary pages has been changed to hopefully provide more of the key information on a ligand at the top of these pages. In the example below we show how this looks for chloroquine.

chloroquine

The main information box now contains:

  • Synonyms
  • Icons to indicate key ligand classifications
  • Drug approval indication
  • GtoPdb curator comments
  • Link to ligand activity graphs

In addition, the 2D ligand structure is display beside this information in a expandable/retractable section where users can also view physico-chemical properties and SMILES/InChI/InChI Keys.

Previously the top part of the ligand summary pages contained too much white space, repetitions of the ligand name and emphasised the ligand ID, physico-chemical properties and to some extent buried comments, SMILES/InChI keys and useful links (such as to the ligand activity graphs).

The reorganisation of the page now emphasises key information. GtoPdb curator comments in particular contain a valuable description of the ligand and provide explanations as to why they have been curated in GtoPdb.

WHO essential medicines

Any ligands included in the World Health Organization (WHO) Model List of Essential Medicines (21st list, 2019) are now tagged in GtoPdb. This means users can easily view these ligands on our ligand list page:

https://www.guidetopharmacology.org/GRAC/LigandListForward?type=WHO-essential&database=all

It is also possible, as it is for all ligand lists, to download this set from this page by clicking the download link in the top-right of the table (see below).

who_list

Other Updates

ChEMBL 27

Both the ligand activity graphs and pharmacology search tools have now been updated to access the latest ChEMBL release (ChEMBL 27).

Links to DrugCentral 2020

We have added links to the DrugCentral 2020 Online Drug Compendium. DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action. It monitors FDA, EMA, and PMDA for new drug approval on regular basis to ensure currency of the resource. Limited information on discontinued and drugs approved outside US is also available however regulatory approval information can’t be verified. The database is developed and maintained by Oleg Ursu and Tudor Oprea and the web application is developed by Jayme Holmes.

We have so far mapped 1433 ligands in GtoPdb to entries in DrugCentral.

 

 

 

 

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Hot Topics: A trio of GPCR peptide publications

This post covers three recent publications with a common theme and whose authors are collaborators with GtoPdb, thus making them as a trio particularly suitable for combined review.  These are; Discovery of Human Signaling Systems: Pairing Peptides to G Protein-Coupled Receptors [1], Novel approaches leading towards peptide GPCR de-orphanisation [2] , and  Advances in therapeutic peptides targeting G protein-coupled receptors [3].  As expected, these are all clearly written, contain  valuable detail  and each includes its own introduction.  Therefore this piece does not need to go over these works per se but simply point out their coverage, domain of application, along with brief explanations of entity linking and/or external look-up options.

For context,  it should be pointed out that historical success in de-orphanising GPCRs (i.e.  reproducibly pairing them with physiologically-relevant endogenous ligands) has been difficult and slow. This remains so,  despite decades of  intense effort from not only all major pharmaceutical companies but also academic groups utilising various flavours of  de-orphanistaion screening approaches and technologies. This was pursued in parallel with cloning (and patenting) the complete repertoire of human GPCRs as they slowly came into view.  Initially done via mining millions of expressed sequence tag (EST) transcripts in the mid 90’s, this later shifted focus to genomic DNA  surfacing between appropriately 1998 and 2000. The modest progress even after the completion of the draft human genome can be discerned from the table below compiled in 2000 [4].

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Progress ~ 2000- 2018 is outlined both in  Concise Guide 2019/20 : G Protein-Coupled Receptors (PMID: 31710717)  [5] and in the Guide to Pharmacology latest parings list .

As the first of this trio of papers, Foster et al.  [1] have significantly advanced the de-orphanisation field in 2019 by integrating computational and experimental approaches for peptide-GPCR pairings.  They began with comparative sequence and structural analyses to gain biological insights into the  human peptide-receptor signalling landscape. They were then able to leverage these features to mine candidate peptide ligands from the entire human genome,  arranged for these to be synthesised and then tested for activity in a broad range of pairing assays that included known ligands as positive controls.  The impressive scope of  results is indicated  in their Fig 7 (below).

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In summary, the 53 peptides with validated receptor-dependent responses first reported in this paper,  has  expanded the known human peptidergic signaling network from 348 to 407 interactions.  It is also important to note that they were unable to reproduce no less than six reported parings in the literature from 2004 to 2016 (i.e. those de-orphanisations could not be verified).

In collaboration with the Copenhagen crew, this paper was curated by the GtoPdb team according to their target mapping stringency and potency thresholds.  Consequently, 11 new peptides have been  annotated with the quantitative ligand binding data reported for the newly de-orphanised receptors.  These are shown below with their PubChem Substance Links  (SIDs) for which GtoPdb (so far) has becomes the only source of these compound structures (CIDs) from over 730 submitters.

CaptureIn PubChem these can be accessed by scrolling down to “Related information”  on the lower right hand facet of PMID: 31675498  and clicking on “PubChem Substance”.  Each entry has a pointer back to GtoPdb from the SID and the nomenclature of  the peptides matches that used in the paper.  However, users wanting to select these entries from within GtoPdb can go to Ligand Search Tools > Search for data by literature reference >   Enter PubMed Id: 31675498 >  Select field to search: PubMed ID.   This brings back 16 entries since it includes the 11 ligands above plus the five receptors for which binding data was curated  (n.b. these instructions apply to the old PubMed interface, so some of this may change for the new interface).  While the version of the article  in Cell journal  itself has no entity outlinks (except for references)  the PubMed Central version has automatically linked the PDB IDs.  All the GPCR protein/gene names should retrieve in GtoPdb or of course GPCRdb

The second article in the trio is a review  by Hauser et al [2].  This  covers some of the same ground as above but includes an assessment of contemporary methodologies of de‐orphanisation.  The informative Figure 1, summarising extensive data mining, is shown below.

Capture

In addition to indicating the ligand status of the GPCRs the circles extend to clinical relevance, disease therapeutic potential,  publication density and tool compounds from ChEMBL.  Note that  while ChEMBL links to compounds with a wide range of potentcies GtoPdb has a more stringent  annotation of smaller number of probe candidates including very recent publications (e.g. these 11 ligands above are not in ChEMBL26).

One of the advantages of publishing in BJP is the provision of author-specified out-links to GtoPdb ligands and targets (see PMID 30087946).  These have been duly added to the  PDF for all GPCRs mentioned in the text as well as any ligands that were already in GtoPdb before this review.  Examples for five links are shown below.

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Clicking on “GPR15” above thus takes us the full annotation for that receptor, including the agonist ligand records shown below.

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Thus GPR15L (71-81)  corresponds to SID 404859015.  The format of Table 1 unfortunately precluded the addition of the live-links for the new ligands.

The last of this trio is an in-depth review by Davenport et. al. [3] that encompasses translation aspects of peptides that modulate GPCRs into clinically effective drugs. This may even eventually extent to analogues of the peptides from the first two papers perhaps even related to new de-orphanisations.  As detailed in this review therapeutic peptides have recently been  undergoing a development technology renaissance via half- life extension, stapling and resistance to proteolysis. These measures  improve pharmacokinetics and oral bioavailability that have hitherto been much less favourable for peptidic structures in comparison to conventional small-molecule drug candidates.  An overview of these peptide approvals and advanced candidates is taken from their Figure 1.

Capture

This comprehensive review goes on to describe in detail 26 synthetic peptides  approved for clinical use  (20 agonists and 6 competitive antagonists) targeting eight class A receptor families.  It also includes a useful  structural perspectives not only on peptide binding sites but also addresses the frequently overlooked aspects associated with unnatural amino acids and chemical modifications.

It seems somewhat anachronistic  that the  Nat Rev Drug Discov  PDFs are entity link-free zones (although this FAIR-gap  has been pointed out to them).  Notwithstanding, the GPCR names should retrieve cleanly from GtoPdb and GPCRdb.  Most of the peptide names in the review should also retrieve their ligand entries from GtoPdb but these will eventually be cross-checked both for the resolution of equivocalities and addition of new development candidates with referenced binding data.

Constituting a well-referenced overview of  the field, these three papers also represent  “good news” for peptides and their analogues.  Notwithstanding,  this slide set outlines some of the challenges for curating peptides and searching them in databases.

**********************************

Comments by Chris Southan, Fellow of the University Edinburgh,  Owner of TW2Informatics ,  Chair of NC-IUPHAR Subcommitees for Proteases and  Drug Targets and Chemistry (DRUTACS),  ORCID 0000-0001-9580-0446.  As declaration of interest (but not conflict!)  Chris was pleased to be a co-supervisor for Alex Hauser’s PhD work on Computational Receptor Biology

[1] Discovery of Human Signaling Systems: Pairing Peptides to G Protein-Coupled Receptors.  Foster SR, Hauser AS, Vedel L, Strachan RT, Huang XP, Gavin AC, Shah SD, Nayak AP, Haugaard-Kedström LM, Penn RB, Roth BL, Bräuner-Osborne H, Gloriam DE. Cell. 2019 Oct 31;179(4):895-908.e21. doi: 10.1016/j.cell.2019.10.010.  PMID: 31675498.

[2]  Novel approaches leading towards peptide GPCR de-orphanisation.  Hauser AS, Gloriam DE, Bräuner-Osborne H, Foster SR. Br J Pharmacol. 2020 Mar;177(5):961-968. doi: 10.1111/bph.14950. Epub 2020 Feb 3. PMID: 31863461.

[3] Advances in therapeutic peptides targeting G protein-coupled receptors.  Anthony P. Davenport AP, Scully CCG , de Graaf C, Brown, AJH,  Maguire JJ.  Nat Rev Drug Discov (2020). https://doi.org/10.1038/s41573-020-0062-z.

[4]  The impact of genomics on drug discovery. Beeley LJ, Duckworth DM, Southan C.  Prog Med Chem. 2000;37:1-43. PMID: 10845246. 

[5]  The Concise Guide to PHARMACOLOGY 2019/20 : G Protein-Coupled Receptors. Alexander SPH, Christopoulos A, Davenport AP, Kelly E, Mathie A, Peters JA, Veale EL, Armstrong JF, Faccenda E, Harding SD, Pawson AJ, Sharman JL, Southan C, Davies JA; CGTP Collaborators. Br J Pharmacol. 2019 Dec;176 Suppl 1:S21-S141. doi: 10.1111/bph.14748.  PMID: 31710717.

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GtoPdb pre-release ligands (2020.3)

These are some of the ligands under curation (pre-release) in the Guide to Pharmacology. We expect them to be available on the website at the next database release (2020.3).

Ligand ID: 10891

Name: aviptadil

10891

Comment: Aviptadil is a vasoactive intestinal peptide analogue, VPAC1 receptor agonist.
The HELM annotation for aviptadil is PEPTIDE1{H.S.D.A.V.F.T.D.N.Y.T.R.L.R.K.Q.M.A.V.K.K.Y.L.N.S.I.L.N}$$$$.


Ligand ID: 10745

Name: MDL-28170

IUPAC: benzyl N-[(2S)-3-methyl-1-oxo-1-[[(2S)-1-oxo-3-phenylpropan-2-yl]amino]butan-2-yl]carbamate

Comment: PRD_002214 is a peptide-like inhibitor of the main protease (MPRO) of SARS-CoV-2. The structure was obtained from the RCSB Protein Data Bank entry 6LU7 which shows the ligand in complex with the protease. The article describing the work has not yet been published (March 12, 2020), but the inhibitor (also referred to as N3) has been deployed in other MPRO crystallisation studies (Yang et al. (2005)).


Ligand ID: 10752

Name: leronlimab

Comment: Leronlimab (PRO140) is a humanized anti-CCR5 (C-C motif chemokine receptor 5) monoclonal antibody [5-6]. It was originally developed by CytoDyn as a novel strategy to manage CCR5-tropic HIV infection.COVID-19: Leronlimab has been administered to a number of patients with severe COVID-19, to determine its potential to reduce cytokine storm caused by this disease.


Ligand ID: 11026

Name: meplazumab

Comment: Meplazumab is a humanized IgG2 monoclonal antibody that targets CD147 (basigin). It is being developed by Jiangsu Pacific Meinuoke Bio Pharmaceutical.

COVID-19
SARS-CoV-2 may utilise CD147 as an additional entry receptor to infect host cells [2]. Meplazumab can block this interaction between CD147 and SARS-CoV-2 spike protein.



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Database Release 2020.2

We are pleased to have been able to make an expeditious database release (version 2020.2), following on from our last update in March 2020 in order to make public new curation specifically related to SARS-CoV-2.

Content Updates

  • GtoPdb now includes a new SARS-Cov-2 protein family which includes 13 members and is included under ‘anti-infective targets’ in our hierarchy
  • The new targets in the SARS-CoV-2 protein family have been mapped to UniProt accessions were possible. Because so little is yet understood about SARS-CoV-2 at the molecular level, much of what is curated for these proteins has been predicted and/or extrapolated from what is known about SARS-CoV and MERS-CoV. We will of course update the pages as and when new data are published.
  • Several new compounds, relevant to SARS-CoV-2 have now been added, including PRD_002214 and compound 13b (virus main protease inhibitors), otamixaban and I-432 (potential TMPRSS2 inhibitors), and β-D-N4-hydroxycytidine (a broad spectrum antiviral compound).

The Guide to Pharmacology coronavirus information page continues to be updated on a regular basis to capture the latest pharmacological strategies under investigation to mitigate against COVID-19.

 

 

Posted in Database updates, Technical

GtoPdb pre-release ligands (2020.2)

These are some of the ligands under curation (pre-release) in the Guide to Pharmacology. We expect them to be available on the website at the next database release (2020.2 – no earlier than April 2020).

  •  Ligand ID: 10716
    • Name: PRD_002214
    • 10716
    • IUPAC: benzyl (2Z,4S)-4-[(2S)-4-methyl-2-[(2S)-3-methyl-2-[(2S)-2-[(5-methyl-1,2-oxazol-3-yl)formamido]propanamido]butanamido]pentanamido]-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate
    • RCSB PDB: PRD_002214
    • Comment: PRD_002214 is a peptide-like inhibitor of the main protease (MPRO) of SARS-CoV-2. The structure was obtained from the RCSB Protein Data Bank entry 6LU7 which shows the ligand in complex with the protease. The article describing the work has not yet been published (March 12, 2020), but the inhibitor (also referred to as N3) has been deployed in other MPRO crystallisation studies (Yang et al. (2005))

  • Ligand ID: 10720
    • Name: compound 13b
    • Click here for structure editor
    • IUPAC: Tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)-butan-2-yl)ami-no)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate
    • Comment: Compound 13b is an inhibitor of SARS-CoV-2 main protease (Mpro) [3]. It is a derivative of the prevoiusly reported α-ketoamide inhibitor compound 11r [PMID: 32045235][1]. Compound 13b has an enhanced plasma half-life compared to 11r, plus it exhibits substantial lung tropism and has shown suitability for inhalation-mediated administration.

  • Ligand ID: 10732
      • Name: otamixaban
      • Click here for structure editor
      • IUPAC: methyl (2R,3R)-2-[(3-carbamimidoylphenyl)methyl]-3-[[4-(1-oxidopyridin-1-ium-4-yl)benzoyl]amino]butanoate
      • Comment: Otamixaban (FXV673) is an anticoagulant that was originally reported by Aventis Pharmaceuticals (Sanofi). It is a potent and selective direct inhibitor of coagulation factor Xa that is delivered intravenously. The INN record stipulates the (2R,3R) configuration. Virtual docking studies suggest that otamixaban may bind to the serine protease TMPRSS2, which is linked to host cell entry by a number of viruses, in particular influenza viruses and respiratory viruses such as SARS-CoV-2. Inhibition of TMPRSS2 is being examined for antiviral activity. The TMPRSS2 inhibitory potential and/or antiviral activity of otamixaban have not yet been determined.

  • Ligand ID: 10733
    • Name: I-432
    • Click here for structure editor
    • IUPAC: 3-[(2R)-3-[4-(2-aminoethyl)piperidin-1-yl]-2-[3-(4,6-dichlorocyclohexa-1,5-dien-1-yl)benzenesulfonamido]-3-oxopropyl]benzene-1-carboximidamide
    • Comment: I-432 is an inhibitor of the serine protease TMPRSS2. TMPRSS2, present in human airway cells, is involved in processes that support infection by a number of viruses, thus inhibitors of this protease are being investigated for anti-viral potential

  • Ligand ID: 10735
    • Name: β-D-N4-hydroxycytidine
    • Click here for structure editor
    • IUPAC: 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-(hydroxyamino)pyrimidin-2-one
    • Comment: Preliminary evidence from a BioRxiv preprint indicate that the ribonucleoside analog β-D-N4-hydroxycytidine (NHC, EIDD-1931) has broad spectrum antiviral activity against SARS-CoV-2, MERS-CoV, SARS-CoV, and related zoonotic group 2b or 2c Bat-CoVs. The potency of NHC/EIDD-2801 against multiple coronaviruses, its therapeutic efficacy, and oral bioavailability in vivo, all highlight its potential utility as an effective antiviral against SARS-CoV-2 and other future zoonotic coronaviruses.

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Database Release 2020.1

We are pleased to announce our first database release of 2020 – version 2020.1.

Coronavirus (Covid-19)

We have added a new coronavirus page to the Guide to Pharmacology which aims to consolidate key pharmacological information and resources related to coronavirus. We have gathered information from various sources, with an aim to cover as many of the pharmacological strategies being considered as we could find. Links are provided to the key ligands and target pages in GtoPdb (where data is available). The page also provides other useful links and resource. We will aim to keep this page updated in this fast changing situation.

Tools

GtoPdb contains a couple of useful tools for searching and visualising pharamcology data – that combine data from ChEMBL with GtoPdb data. In this release we’ve update our site to make accessing the visualisation charts easier

Ligand Activity Charts

This tool provides charts with box plots summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Separate charts are created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

Previously, access to the charts was only found on a ligand’s summary page, under the biological activity tab. We’ve now moved that link so it appears more prominently on these pages.ligSumLink

We have also added a new icon on the ligand list pages which indicated whether there are activity charts available for the ligand. Click the icon takes the users straight to the charts.

iconImage

New ‘bar-chart’ icon added to ligand list to indicate availability of activity charts

Publications

We have published a review of the Guide to Immunopharmacology in Immunology at the start of the year. The review provides a deeper context for how the resource can support research into the development of drugs targeted at modulating immune, inflammatory or infectious components of disease.

Harding, S. D., Faccenda, E., Southan, C., Pawson, A. J., Maffia, P., Alexander, S., Davenport, A. P., Fabbro, D., Levi-Schaffer, F., Spedding, M., & Davies, J. A. (2020). The IUPHAR Guide to Immunopharmacology: connecting immunology and pharmacologyImmunology, 10.1111/imm.13175. Advance online publication. https://doi.org/10.1111/imm.13175

Content Updates

GPCRs:

Ion Channels:

NHRs:

Enzymes and Other Protein Targets:

Guide to Malaria Pharmacology Updates:

  • 3 P. falciparum (3D7) targets have been added to the Antimalarial targets family: PfCLK3, PfPMV and PfNCR1
  • The Antimalarial ligands family now contains a total of 80 ligands tagged as antimalarial in the database

Other Updates

Updated display of ligand clinical trial data

The ligand summary pages have been updated to improve the display of clinical trials information. Key clinical trials involving the ligand are now displayed in a separate table, under the clinical data tab. The table includes link out the clinical trial plus trial title, type, source, curator comments and references.

clinical_trial_snapshot

Approved drug with primary targets download

A new download file of all approved drugs and their primary targets has been added to the download page.

New out-links

  • Marine pharmacology – Marine Pharmacology (Midwestern University): a website aimed at those with an interest in the preclinical and clinical pharmacology of marine compounds and the pharmaceutical potential of the enormous biodiversity of organisms present in the world’s oceans
  • Pharos – Pharos is the user interface to the Knowledge Management Center (KMC) for the Illuminating the Druggable Genome (IDG) program
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Posted in Database updates, Technical

Hot Topics: Virtual screening on the crystal structure of the G protein-coupled melatonin MT1 receptor reveals several new chemical scaffolds with biological activity

Melatonin targets two high-affinity receptors, MT1 and MT2, that belong to the G protein-coupled receptor (GPCR) superfamily (1,2). Drugs acting on melatonin receptors are subscribed for circadian disorders (jet lag, shift work, etc.), insomnia and major depression (3). All marketed drugs are non-selective agonists targeting both receptor types so far. Despite large chemical synthesis campaigns over the last 20 years, the pharmacology of melatonin receptors remains poorly explored with few inverse agonistic and signaling pathway-biased compounds and few  selective compounds, in particular for the MT1 type (2,4). This lack of pharmacological tools goes along with a rather poor diversity in terms of chemical scaffolds currently available (5). Put into this context, a virtual screening looked like a very promising approach to increase the diversity of chemical scaffolds for melatonin receptors, especially now that the crystal structure of the MT1 receptor has been solved (6). The outcome of the virtual screening study performed by Stein et al. (7) met these high expectations. Overall, 15 new chemical scaffolds were identified from the primary docking of over 150 million virtual molecules (7). Some of the primary hits had pEC50 values around 1nM, which is remarkable. In terms of functional properties, primary hits and derivatives showed agonistic and inverse agonistic properties with or without selectivity for MT1 and MT2. Two MT1 selective inverse agonists were further validated in vivo regarding their effects on circadian rhythm parameters in mice under free-running conditions, as well as using an experimental re-entrainment protocol corresponding to an ‘east-bound’ jet lag paradigm.

This study is not only of great value for the melatonin receptor field but will also encourage virtual screening approaches on other GPCRs for which high-resolution structures are available. Compared to other GPCR structures, the MT1 template structure has several limitations as it was in the inactive form despite the presence of the 2‐phenylmelatonin agonist, and it was heavily modified with 9 point mutations and several truncations to facilitate expression and stability (7,8). However, a favorable feature of MT1 for virtual docking might be its ligand binding pocket which is rather small and hydrophobic with only two key residues important for high-affinity binding. This limits the number of poses to be screened by virtual docking. Moreover, although the screening was designed to identify MT1 selective compounds, positive hits included also MT2 selective and non-selective compounds suggesting that virtual screening is currently unable to predict type selective compounds. This might also depend on the quality of the receptor structure and the degree of divergence between receptor types.

In conclusion, this article is a nice example of successful virtual screening on GPCRs, one of the desired benefits of crystal structures, that will accelerate the drug development process towards compounds with improved efficacy and target-selectivity.

This study investigated two MT1-selective inverse agonists, UCSF7447 and UCSF3384, and a selective MT2 agonist, UCSF4226, for their affinities.

Comments by Ralf Jockers, Institut Cochin, CNRS, INSERM, Université de Paris, Paris, France, Chair for NC-IUPHAR Subcommitee for Melatonin receptors.

  1. Dubocovich ML, Delagrange P, Krause DN, Sugden D, Cardinali DP, Olcese J. International Union of Basic and Clinical Pharmacology. LXXV. Nomenclature, classification, and pharmacology of G protein-coupled melatonin receptors. Pharmacol Rev. 2010;62(3):343-380.
  2. Jockers R, Delagrange P, Dubocovich ML, Markus RP, Renault N, Tosini G, Cecon E, Zlotos DP. Update on Melatonin Receptors. IUPHAR Review. Br J Pharmacol. 2016;173(18):2702-2725
  3. Liu J, Clough SJ, Hutchinson AJ, Adamah-Biassi EB, Popovska-Gorevski M, Dubocovich ML. MT1 and MT2 Melatonin Receptors: A Therapeutic Perspective. Annu Rev Pharmacol Toxicol. 2016;56:361-383.
  4. Cecon E, Oishi A, Jockers R. Melatonin receptors: molecular pharmacology and signalling in the context of system bias. Br J Pharmacol. 2017;175:3263–3280.
  5. Zlotos DP, Jockers R, Cecon E, Rivara S, Witt-Enderby PA. MT1 and MT2 Melatonin Receptors: Ligands, Models, Oligomers, and Therapeutic Potential. J Med Chem. 2014;57(8):3161-3185.
  6. Stauch B, Johansson LC, McCorvy JD, Patel N, Han GW, Huang XP, Gati C, Batyuk A, Slocum ST, Ishchenko A, Brehm W, White TA, Michaelian N, Madsen C, Zhu L, Grant TD, Grandner JM, Shiriaeva A, Olsen RHJ, Tribo AR, Yous S, Stevens RC, Weierstall U, Katritch V, Roth BL, Liu W, Cherezov V. Structural basis of ligand recognition at the human MT1 melatonin receptor. Nature. 2019;569(7755):284-288.
  7. Stein RM, Kang HJ, McCorvy JD, Glatfelter GC, Jones AJ, Che T, Slocum S, Huang XP, Savych O, Moroz YS, Stauch B, Johansson LC, Cherezov V, Kenakin T, Irwin JJ, Shoichet BK, Roth BL, Dubocovich ML. Virtual discovery of melatonin receptor ligands to modulate circadian rhythms. Nature. 2020. [PMID: 32040955]
  8. Cecon E, Liu L, Jockers R. Melatonin receptor structures shed new light on melatonin research. J Pineal Res. 2019:e12606.
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Hot Topics: Cardiac Ca2+ Channel Regulation in the Fight-or-Flight Response: the monomeric small G-protein as another piece in the puzzle

Thirty eight years after the discovery that injection of the catalytic subunits of cyclic AMP-dependent protein kinase A (PKA) into isolated pig ventricular cardiac myocytes (1) increases the amplitude of L-type Ca2+ current (today known to be formed by Cav1.2 channels, (2)), we are now getting close to understand the responsible molecular mechanism. Initial research that has focused on direct regulatory mechanisms, such as the activation by the α-subunit of the stimulatory heterotrimeric G-protein Gs (3), and direct phosphorylation of the pore-forming α1- or accessory β2-subunit of the Cav1.2 channel has not provided a conclusive answer. β-adrenergic modulation was not (α1 Ser-1928, (4)) or only partially (α1 Ser-1700/Thr-1704, (5)) prevented in mutant mice lacking predicted phosphorylation sites in α1 or β2 subunits (6). This was further supported by an elegant transgenic approach showing that expression of channel complexes with all PKA consensus sites mutated to alanine in the Cav1.2 α1 and the β2 subunits (7) has no effects on β-adrenergic modulation.

Assuming that other proteins may be involved in this regulatory pathway, Liu et al. (7) used a biotinylation-based proteomic proximity assay to identify proteins in the Cav1.2 neighborhood regulated by isoproterenol treatment in cardiomyocytes. This led to the discovery of the small Ras-like G protein Rad as a potential candidate. It belongs to the family of the Rad, Rem, Rem2 and Gem/Kir (RGK) Ras-like GTP-binding proteins, which were shown earlier to inhibit high-voltage-activated Ca2+ channels by binding to their β-subunits. Indeed, Rad appears to be the long-sought missing piece in the puzzle: in HEK293T Rad-mediated inhibition of cardiac Cav1.2 channels was relieved by PKA phosphorylation. Modulation was prevented either by the simultaneous mutation of the known cardiac PKA phosphorylation sites of Rad to alanine or by inhibiting the interaction of Rad with the β-subunit.

This mechanism may be universal and may also explain the PKA modulation of other types of β-subunit associated high-voltage activated Ca2+ channels in Rad expressing cells. It also provides evidence that the mechanism of PKA modulation of Cav1.2 Ca2+ channels appears to differ in different cell types. Clearly, direct phosphorylation of Ser-1928 of the α1-subunit is not required for β-adrenergic regulation of Cav1.2 in the heart (4,7). However, this residue is required for β-adrenergic stimulation of Ca2+ channels in hippocampal neurons and for hyperglycaemia-induced stimulation of Ca2+ currents in arterial smooth muscle cells (8,9).

Despite compelling evidence for this novel mechanism, several questions remain: First, what is the role of Rad-dependent modulation of the cardiac L-type channel in intact cardiomyocytes, for example in cardiomyocytes expressing Rad with mutated PKA phosphorylation sites. Second, what is the relative importance of Rad versus modulation by direct phosphorylation of Ser-1700 (and Thr-1704), which has also been found to confer some of the PKA activation of L-type current in cardiomyocytes of Ser1700Ala mutant mice (5).

Despite these open questions, we are now getting close to understand the molecular mechanisms underlying the fight-or-flight response.

Comments by Jörg Striessnig, University of Innsbruck, Chair for NC-IUPHAR Subcommitee for Voltage-gated calcium channels, Liaison for NC-IUPHAR subcommittees on Voltage-gated ion channels

  1. Osterrieder W, Brum G, Hescheler J, Trautwein W, Flockerzi V, Hofmann F. (1982) Injection of subunits of cyclic AMP-dependent protein kinase into cardiac myocytes modulates Ca2+ current. Nature 298, 576–8.
  2. Sinnegger-Brauns MJ, Hetzenauer A, Huber IG, Renström E, Wietzorrek G, Berjukov S, et al. (2004) Isoform-specific regulation of mood behavior and pancreatic β cell and cardiovascular function by L-type Ca2+ J Clin Invest. 113: 1430–9.
  3. Yatani A, Codina J, Imoto Y, Reeves JP, Birnbaumer L, Brown AM. (1987) A G protein directly regulates mammalian cardiac calcium channels. Science 238, 1288–92.
  4. Lemke T, Welling A, Christel CJ, Blaich A, Bernhard D, Lenhardt P, et al. (2008) Unchanged beta-adrenergic stimulation of cardiac L-type calcium channels in Cav1.2 phosphorylation site S1928A mutant mice. J Biol Chem. 283, 34738–44.
  5. Fu Y, Westenbroek RE, Scheuer T, Catterall WA. (2014) Basal and beta-adrenergic regulation of the cardiac calcium channel Cav1.2 requires phosphorylation of serine 1700. Proc Natl Acad Sci U S A. 111, 16598–603.
  6. Brandmayr J, Poomvanicha M, Domes K, Ding J, Blaich A, Wegener JW, et al (2012) Deletion of the C-terminal phosphorylation sites in the cardiac beta-subunit does not affect the basic beta-adrenergic response of the heart and the Cav1.2 channel. J Biol Chem. 287, 22584–92.
  7. Liu G, Papa A, Katchman AN, Zakharov SI, Roybal D, Hennessey JA, et al. (2020) Mechanism of adrenergic CaV1.2 stimulation revealed by proximity proteomics. Nature 577, 695–700 [PMID: 31969708].
  8. Qian H, Patriarchi T, Price JL, Matt L, Lee B, Nieves-Cintrón M, et al. (2017) Phosphorylation of Ser1928 mediates the enhanced activity of the L-type Ca2+ channel Cav1.2 by the β2-adrenergic receptor in neurons. Sci Signal. 10 (463), pii: eaaf9659
  9. Nystoriak MA, Nieves-Cintrón M, Patriarchi T, Buonarati OR, Prada MP, Morotti S, et al. (2017) Ser1928 phosphorylation by PKA stimulates the L-type Ca2+ channel Cav1.2 and vasoconstriction during acute hyperglycemia and diabetes. Sci Signal. 10(463), pii: eaaf9647

 

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Hot topics: Cannabinoid receptor stuctures

Two new reports cover further aspects of cannabinoid receptor binding as defined using cryo-EM. These expand on previous reports of the structure of the human CB1 cannabinoid receptor with the antagonists taranabant and  AM6538 bound, and with the agonists MDMB-FUBINACA, AM11542 and AM841 bound. Previously reported also is the structure of the CB2 cannabinoid receptor with the antagonist AM10257 bound.

In the first report (1), a non-selective, high potency agonist WIN55212-2 was bound to a complex of the CB2 cannabinoid receptor with Gi to “complete the set” of agonist- and antagonist-bound versions of CB1 and CB2 receptors. The authors suggest marked similarities in the binding configuration of the agonist WIN55212-2 and the antagonist AM10257. Based on these structures, two novel ligands were generated; one predicted to be an agonist and the other an antagonist. The functional data supported these predictions, although both novel compounds were markedly less potent than their respective positive controls.

In the second report (2), agonist-bound versions of both CB1 and CB2 cannabinoid receptors complexed with Gi were also described to ‘complete and expand the set’. AM12033 is a novel nitrilodimethylheptyl analogue of THC with high affinity at both receptors. Structures using this compound were compared to CB1 receptors bound to the THC-like AM841. The authors suggest similar modes of interaction for agonists at the two receptors, supported by numerous examples of non-selective high potency agonists.

Modelling of the second intracellular loop in both reports suggested a structural basis for the CB2 receptor to couple poorly to Gs. Indeed, a single amino acid variation (L222 in CB1 and P139 in CB2 receptors) was highlighted in both studies and evidenced in the previous literature (https://www.ncbi.nlm.nih.gov/pubmed/23667597).

Comments by Prof. Steve Alexander (@mqzspa), University of Nottingham, UK

(1) Xing C. et al. Cryo-EM Structure of the Human Cannabinoid Receptor CB2-G i Signaling Complex. Cell (2020) doi:10.1016/j.cell.2020.01.007 [PMID:32004460]

(2) Hua T. et al. Activation and Signaling Mechanism Revealed by Cannabinoid Receptor-Gi Complex Structures. Cell  (2020) doi:10.1016/j.cell.2020.01.008 [PMID:32004463]

 

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Hot Topics: A brief update on coronaviruses

The new respiratory coronavirus from Wuhan in China is causing intense research activity in the world. Viruses are evidently associated with respiratory infections ranging in severity from the common cold to pneumonia and death. More than 200 viral types have been associated with the common cold, of which 50% of infections are rhinovirus, but also respiratory syncitial virus, influenza – and coronaviruses, particularly human coronavirus-229E (HCoV-229E), which is ‘relatively benign’. Monocytes are relatively resistant to HcoV-229E infection, but rapidly invades, replicates in, and kills dendritic cells within a few hours of infection (Mesel-Lemoine et al., 2012) [1]. Dendritic cells are the sentinel cells in the respiratory tract, and plasmacytoid dendritic cells are a crucial antiviral defence via interferon production. Thus, these viruses can impair control of viral dissemination and the formation of long-lasting immune memory. The cellular receptor for HcoV-229E is CD-13 (aminopeptidase-N).
The cellular receptors for coronaviruses are critical for cell entry. Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), and HCoV-NL63, bind to angiotensin converting enzyme2, ACE2, on ciliated cells in the respiratory tract, the crystal structure is known (Song et al., 2018) [2]. The SARS-CoV spike (S) glycoprotein (with S1 and S2 sub-units) on the outer envelope binds to ACE2, fusing viral and cellular membranes, triggering conformational transformations. Cleavage of the S1/S2 subunits by proteases is critical. Indeed, Simmons et al (2005) [3] showed that SARS-CoV infection involved receptor binding, conformational changes receptor binding and subsequent cathepsin L (and type II transmembrane serine proteases) proteolysis within endosomes – with inhibitors of cathepsin L preventing viral entry. SARS-CoV may lead to markedly elevated cytokine levels, leading to tissue damage, pneumonitis, and acute respiratory distress syndrome (ARDS). The spike proteins in SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV) are crucial for host specificity and jumping between species, e.g. from bats to humans (Lu et al., 2015) [4], and also the recent cross-over to swine acute diarrhoea syndrome coronavirus (SADS-CoV) to pigs (Zhou et al., 2018) [5]. There is intense interest in the complicated ways whereby coronaviruses engage with their target receptors, are activated and replicate. The rapid evolution of coronaviruses is critical as humans have little or no pre-existing immunity SARS- or MERS-CoV.

ACE2 has been identified as a potential receptor for the novel coronavirus that was identified as the cause of the respiratory disease outbreak in Wuhan in late 2019 (referred to as 2019 – nCoV by the WHO, or Wuhan coronavirus) [6,7 & 9]. 2019-nCoV is a betacoronavirus, and, in common with the SARS-CoV [8], the viral spike protein is postulated to engage ACE2 for viral entry [7]. The data presented by Letko and Munzter [7] is preliminary and has not been peer-reviewed, but a rapid pace of research is needed in the present circumstances. For example, in another recent, preliminary report, ACE2 receptor expression is highly expressed in type II alveolar cells (AT2) with much individual variation and the authors reported that the cells also expressed many genes involved in viral reproduction and transmission [10]. While these findings are preliminary, the rapid publications in bioRxiv and similar archives are crucial in what is now officially a global health emergency. This report is a hot topic in the IUPHAR/BPS Guide to PHARMACOLOGY (https://www.guidetopharmacology.org), and further underlines the importance of immunopharmacology and the IUPHAR Guide to IMMUNOPHARMACOLOGY (https://www.guidetoimmunopharmacology.org/immuno/index.jsp).

Comments by Prof. Michael Spedding, Spedding Reseach Solutions; Prof. Steve Alexander (@mqzspa), University of Nottingham; Dr. Elena Faccenda, University of Edinburgh; and Prof. Francesca Levi-Schaffer, The Hebrew University of Jerusalem.

Note from bioRxiv: bioRxiv is receiving many new papers on coronavirus 2019-nCoV.   A reminder: these are preliminary reports that have not been peer-reviewed. They should not be regarded as conclusive, guide clinical practice/health-related behavior, or be reported in news media as established information.

 

  1. Mesel-Lemoine M, Millet J, Vidalain PO, Law H, Vabret A, Lorin V, Escriou N, Albert ML, Nal B, Tangy F. A human coronavirus responsible for the common cold massively kills dendritic cells but not monocytes. J Virol. 2012 Jul;86(14):7577-87. doi: 10.1128/JVI.00269-12. Epub 2012 May 2. PubMed PMID: 22553325; PubMed Central PMCID: PMC3416289.
  2. Song W, Gui M, Wang X, Xiang Y. Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2. PLoS Pathog. 2018 Aug 13;14(8):e1007236. doi: 10.1371/journal.ppat.1007236. eCollection 2018 Aug. PubMed PMID: 30102747; PubMed Central PMCID: PMC6107290.
  3. Simmons G, Gosalia DN, Rennekamp AJ, Reeves JD, Diamond SL, Bates P. Inhibitors of cathepsin L prevent severe acute respiratory syndrome coronavirus entry. Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11876-81. Epub 2005 Aug 4. PubMed PMID: 16081529; PubMed Central PMCID: PMC1188015.
  4. Lu R, Wang Y, Wang W, Nie K, Zhao Y, Su J, Deng Y, Zhou W, Li Y, Wang H, Wang W, Ke C, Ma X, Wu G, Tan W. Complete Genome Sequence of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) from the First Imported MERS-CoV Case in China. Genome Announc. 2015 Aug 13;3(4). pii: e00818-15. doi: 10.1128/genomeA.00818-15. PubMed PMID: 26272560; PubMed Central PMCID: PMC4536671.
  5. Zhou L, Sun Y, Lan T, Wu R, Chen J, Wu Z, Xie Q, Zhang X, Ma J. Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China. Transbound Emerg Dis. 2019 Mar;66(2):687-695. doi: 10.1111/tbed.13008. Epub 2019 Jan 9. PubMed PMID: 30171801.
  6. Gralinski LE, Menachery VD. Return of the Coronavirus: 2019-nCoV. Viruses. 2020 Jan 24;12(2). pii: E135. doi: 10.3390/v12020135. PubMed PMID: 31991541.
  7. Letko M, Munster V. Functional assessment of cell entry and receptor usage for lineage B β coronaviruses, including 2019-nCoV. bioRxiv 2020.01.22.915660; doi: 10.1101/2020.01.22.915660
  8. Li F, Li W, Farzan M, Harrison SC. Structure of SARS coronavirus spike receptor-binding domain complexed with receptor. Science. 2005 Sep 16;309(5742):1864-8. PubMed PMID: 16166518.
  9. Peng Z, Shi Z-L. (2020) Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin. bioRxiv 2020.01.22.914952; doi: 10.1101/2020.01.22.914952
  10. Yu Zhao, Zixian Zhao, Yujia Wang, Yueqing Zhou, Yu Ma, Wei Zuo.Single-cell RNA expression profiling of ACE2, the putative receptor of Wuhan 2019-nCov bioRxiv 2020.01.26.919985 doi: 10.1101/2020.01.26.919985
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Hot Topics: Cryo-EM structure of a selective T-type calcium channel blocker bound to the Cav3.1 voltage-gated calcium channel

Nieng Yan’s group has now published the cryo-EM structure of the selective T-type Ca2+ channel blocker Z944 bound to the pore-forming α1-subunit of Cav3.1 T-type Ca2+ channels (1). This nicely adds to recent publications reporting of the high-resolution structures of L-type Ca2+ channel blockers (nifedipine, nimodipine, amlodipine, verapamil, diltiazem) bound to the rabbit Cav1.1 skeletal muscle Ca2+ channel (2) and to the model Ca2+ channel CavAb (Ca2+-selectivity engineered into the bacterial homotetrameric Na+-channel NavAb; 3, 4).

Together these three publications provide important insight into how small molecule channel blockers interact with their high affinity binding domains within Ca2+ channels. They also reveal a remarkable similarity between the core structures (i.e. the voltage-sensors and the pore domains) between not only the closely related Cav1.1 and Cav3.1 channels but also their bacterial ancestor CavAb.

Moreover, although some differences exist, the binding poses of L-type Ca2+ channel blockers in the mammalian Cav1.1 and the bacterial CavAb channel are very similar. In both structures verapamil and diltiazem bind within the central cavity, compatible with their pore-blocking properties predicted in functional studies. In contrast, dihydropyridines like nimodipine and nifedipine bind within a fenestration created by adjacent transmembrane S6 helices (IIIS6 and IVS6). These fenestrations penetrate the sides of the central cavities in both voltage gated Na+– and Ca2+ channels and connect them to the surrounding lipid bilayer of the plasma membrane (5). In accordance with functional studies, these dihydropyridines must therefore inhibit L-type channels by allosterically interfering with gating rather than pore block.

These findings raise the important question about how Z944 can selectively inhibit T-type Ca2+ channels. This drug is currently in clinical development for the treatment of epilepsy and neuropathic pain. It appears that Z944 bound to Cav3.1 combines the binding modes of both pore blockers and allosteric blockers. Its phenyl ring projects into the fenestration between repeats II and III (similar to nifedipine binding), whereas the other end of the molecule projects down through the central cavity to the intracellular mouth of the pore. A prominent interaction was found with lysine-1462, a residue unique for T-type channels. Its mutation to L-type residues reduced drug sensitivity in functional studies suggesting that it is one of the determinants for T-type selectivity.

Taken together the accumulating structural insight into drug binding and modulation will greatly facilitate structure-guided drug discovery. This may lead to new oral subtype-selective blockers of voltage-gated Ca2+ channels with therapeutic potential for the treatment of epilepsy (T-type), pain (T-type, N-type), tremor (T-type), primary aldosteronism (Cav1.3 L-type), progression of Parkinsons disease (Cav1.3, R-type) or rare neurodevelopmental disorders (Cav1.3 L-type) (6,7).

Comments by Jörg Striessnig, University of Innsbruck, Chair for NC-IUPHAR Subcommitee for Voltage-gated calcium channels, Liaison for NC-IUPHAR subcommittees on Voltage-gated ion channels

  1. Zhao, Y., Huang, G., Wu, Q., Wu, K., Li, R., Lei, J., Pan, X., and Yan, N. (2019). Cryo-EM structures of apo and antagonist-bound human Cav3.1. Nature. 576, 492–497 [PMID: 31766050].
  2. Zhao, Y., Huang, G., Wu, J., Wu, Q., Gao, S., Yan, Z., Lei, J., and Yan, N. (2019). Molecular Basis for Ligand Modulation of a Mammalian Voltage-Gated Ca2+ Cell 177, 1495-1506 [PMID: 31150622].
  3. Tang, L., El-Din, T.M.G., Swanson, T.M., Pryde, D.C., Scheuer, T., Zheng, N., and Catterall, W.A. (2016). Structural basis for inhibition of a voltage-gated Ca2+ channel by Ca2+ antagonist drugs. Nature 537, 117–121 [PMID: 27556947].
  4. Tang, L., Gamal El-Din, T.M., Lenaeus, M.J., Zheng, N., and Catterall, W.A. (2019). Structural Basis for Diltiazem Block of a Voltage-Gated Ca2+ Mol. Pharmacol. 96, 485–492 [PMID: 31391290].
  5. Payandeh, J., Scheuer, T., Zheng, N., Catterall, W.A., 2011. The crystal structure of a voltage-gated sodium channel. Nature 475, 353–358 [PMID: 21743477].
  6. Pinggera, A., and Striessnig, J. (2016). Cav 1.3 (CACNA1D) L-type Ca2+ channel dysfunction in CNS disorders. J. Physiol. (Lond.) 594, 5839–5849.
  7. Benkert, J., Hess, S., Roy, S., Beccano-Kelly, D., Wiederspohn, N., Duda, J., Simons, C., Patil, K., Gaifullina, A., Mannal, N., et al. (2019). Cav2.3 channels contribute to dopaminergic neuron loss in a model of Parkinson’s disease. Nat. Commun. 10, 5094. doi:10.1038/s41467-019-12834-x
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Hot Topics: Deciphering the crystal structure of the leukotriene receptor CysLT2 opens up for improved therapeutics

Leukotrienes are lipid mediators of inflammation, initially recognized for their role in asthma, but also having potent effects in for example cardiovascular and neurological diseases as well as in cancer. The initial pharmacological classification of leukotriene receptors based on antagonist selectivity in smooth muscle was shown to be valid at the gene and protein levels. Following the recent description of the CysLT1 receptor structure, Gusach et al. now describe the crystal structures of the CysLT2 receptor in complex with dual CysLT1/CysLT2 receptor antagonists (1). This is an important advancement, since it allows to reveal specific characteristics of the two CysLT receptors in terms of ligand recognition and subtype selectivity. In this context, differences in the intracellular helix 8 emerge as particular subtype determinants, which may affect G-protein regulation and β-arrestin binding. The study by Gusach et al. (1) further provides structural insights into the changes in ligand binding and downstream signaling by CysLT2R disease-related single nucleotide polymorphisms (SNP) associated with asthma and cancer. The deciphering of the crystal structures for the CysLT1 and CysLT2 receptors will open up for the design of CysLT receptor antagonists with improved affinity/efficacy or subtype selectivity profiles. The insights into the CysLT receptor genome-structure-function relations may facilitate the prediction of disease associations and potentially further expanding the therapeutic indications of CysLT receptor antagonists.

Comments by Magnus Bäck, MD PhD, (@TransCardio), Karolinska Institutet and University Hospital, Stockholm, Sweden; Chairman NC-IUPHAR subcommittee on Leukotriene Receptors

(1) Gusach, A., Luginina, A., Marin, E. et al. Structural basis of ligand selectivity and disease mutations in cysteinyl leukotriene receptors. Nat Commun 10, 5573 (2019) doi:10.1038/s41467-019-13348-2 [PMID:31811124]

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Hot Topics: New crystal structure of the muscarinic M5 receptor completes the set

Muscarinic receptors consist of 5 G protein-coupled receptors which along with nicotinic ion channels mediate the effects of acetylcholine. Despite years of research on the role of muscarinic receptors in the brain and periphery the Muscarinic M5 receptor has stood out in contrast to M1 -M4 as one which we know little about. The M5 receptor has a unique and unusual distribution in the brain being enriched in mid brain dopamine neurons and in the cerebellum. A lack of selective chemical tools has hampered our ability to study the function of the receptor. Now Vuckovic et al. [1] have solved the X-ray crystal structure of the M5 receptor in complex with the non-selective antagonist tiotropium in the presence of a conformational stabilizing mutation. Since tiotropium was also used to solve the structure of several other muscarinic receptors a direct comparison can be made across the subtypes which will enable the design of selective tool compounds. Significant progress has been made in utilizing crystal structures to design selective orthosteric and allosteric ligands at this family of receptors. This final structure completes the set of muscarinic receptor structures solved and hopefully will pave the way to further understanding of the biology of M5 and its role in disorders such as drug addiction and depression.

Comments by Fiona H. Marshall, Discovery Research UK, MSD (@aston_fm)

(1) Vuckovic Z et al. (2019). Crystal Structure of the M5 Muscarinic Acetylcholine Receptor. Proc Natl Acad Sci USA, DOI: 10.1073/pnas.1914446116. [PMID: 31772027]

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Database Release 2019.5

Our fifth and final database release of 2019 has been made and includes a number of minor content and website updates. Crucially, it comes at a time when we have just published our most recent database update in Nucleic Acids Research:

Armstrong JF, Faccenda E, Harding SD, Pawson AJ, Southan C, Sharman JL, Campo B, Cavanagh DR, Alexander SPH, Davenport AP, Spedding M, Davies JA; NC-IUPHAR. (2019) The IUPHAR/BPS Guide to PHARMACOLOGY in 2020: extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY. Nucl. Acids Res. pii: gkz951. doi: 10.1093/nar/gkz951 [Epub ahead of print]. [Full text]

and we have seen the publication of the 2019/20 Concise Guide to Pharmacology:

Alexander SPH, Kelly E, Mathie A, Peters JA, Veale EL, Faccenda E, Harding SD, Pawson AJ, Sharman JL, Southan C, Buneman OP, Cidlowski JA, Christopoulos A, Davenport AP, Fabbro D, Spedding M, Striessnig J, Davies JA; CGTP Collaborators. (2019) The Concise Guide to PHARMACOLOGY 2019/20 Br J Pharmacol. 176 S1: S1-S493. [Table of Contents]

JWS-SH-BJP-ConciseGuide-01-Pharmacology-1120x600px-BJP

Content Updates

Other Updates

Ligand list download

  • A new download button has been added to the ligand list pages. This enables users to download the specific ligand set they are viewingfor downloading specific sets of ligands (see image below).

Screenshot from 2019-11-15 10-04-37

PlasmoDB links

  • The IUPHAR/MMV Guide to Malaria Pharmacology now includes direct links from targets to PlasmoDB. The detailed target pages now clearly display the PlasmoDB accession for the target. The links are also included in the summary view of the target.

Upcoming presentations at:

We will be presenting on the Guide to Immunopharmacology and the Guide to Malaria Pharmacology at the following meeting over November and December

 

Posted in Database updates, Technical

Hot Topics: 3D structure of the full-length P2X7 receptor provides insight into factors controlling agonist potency and receptor desensitisation

P2X receptors are ligand-gated cation channels for which ATP is the endogenous orthosteric agonist. Seven P2X subunits have been identified and they form trimers to produce at least twelve different receptor subtypes. The tertiary structure of several subtypes have been reported, but they all lack clear information on the conformation of the N- and C-terminal cytoplasmic domains because of the truncated constructs used and the flexibility of these domains. Now, McCarthy et al., (1) report single-particle cryo-EM images of the full-length rat P2X7 receptor in both apo (closed pore) and ATP-bound (open pore) states, which suggest why the affinity of this receptor for ATP is low, indicate how cysteine residues in the C-terminal control desensitisation and reveal a surprising guanine nucleotide binding site in the C-terminal.

The potency of ATP at P2X7 is three orders of magnitude lower than at other P2X subtypes. Whilst these new structures show some differences between the orthosteric ATP binding pocket of P2X7 and P2X3 receptors, these are unlikely to explain the great difference in ATP potency. Notably, however, the entrance to the pocket is much narrower in P2X7 (<11A° orifice) than in P2X3 (17A° orifice) receptors. This and any protein flexibility that opens and closes the entrance would decrease the time ATP spends in the binding pocket, so decreasing its affinity.

A unique feature of P2X7 receptors is an 18-amino acid long cytoplasmic region at the end of TM2 (named the C-cys anchor by the authors) that is cysteine-rich and which links TM2 to the cytoplasmic cap, a structural domain formed by N- and C-terminal residues that determines the rate at which P2X receptors desensitise. The present report shows that the C-cys anchor contains at least four cysteine residues and one serine residue that are palmitoylated and that the aliphatic chains extend into the plasma membrane, anchoring the receptor to the membrane. The authors speculate that this could keep the cytoplasmic cap in place and so limit P2X7 desensitisation. Consistent with this, the receptor, which is normally non-desensitising in the presence of ATP, desensitised rapidly and fully when the C-cys anchor was deleted or the cysteine residues removed by mutation.

A further unique feature of P2X7 receptors compared with other subtypes is the long C-terminal (~200 residues), which the authors term the cytoplasmic ballast. The images show for the first time that each receptor has three globular, wedge-shaped cytoplasmic ballasts, each of which hangs beneath the TM domain of an adjacent subunit. Intriguingly, each cytoplasmic ballast contains a dinuclear zinc ion complex and a high-affinity guanosine nucleotide binding site, the functions of which are unclear.

The P2X7 receptor is of particular therapeutic interest because it is cytotoxic due to its ability to activate the NLRP3 inflammasome and release pro-inflammatory cytokines. This study substantially extends our knowledge and understanding of its pharmacological and biophysical properties and forms the basis of further potential experiments designed to fully characterise how it functions.

Comments by Dr. Charles Kennedy, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde

(1) McCarthy et al. (2019). Full-length P2X7 structures reveal how palmitoylation prevents channel desensitization. Cell. https://doi.org/10.1016/j.cell.2019.09.017. [ScienceDirect: View Article]

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Official Launch of the Guide to MALARIA PHARMACOLOGY

gtommv_bannerWe are delighted to announce the first full public release of the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY (abbreviated to GtoMPdb). This new web resource, designed specifically for malaria pharmacology, has been developed as a joint initiative between the International Union of Basic and Clinical Pharmacology (IUPHAR) and the Medicines for Malaria Venture (MMV). It has been constructed as an extension to the parent Guide to PHARMACOLOGY database (GtoPdb) and incorporates new pharmacological content, including molecular targets in the malaria parasite and interaction data for ligands with antimalarial activity. In addition, a dedicated portal has been developed, in consultation with key opinion leaders in malaria research, to provide quick and focused access to these new data.

Screen Shot 2019-09-26 at 15.32.20The GtoMPdb portal homepage

A more detailed introduction to the project and a chronicle of technical developments can be found in our previous blog posts.

This initiative has enriched the GtoPdb and it is hoped will foster innovation by providing, in a single expert-curated database, results from antimalarial drug discovery programmes and the scientific literature. Following the lastest database release (2019.4), the Antimalarial targets family and the Antimalarial ligands family were updated and now contain a total of 30 P. falciparum (3D7) targets and 72 ligands annotated with antimalarial activity. The GtoMPdb has maintenance funding, ensuring new data curation will continue until June 2020.

We would like to take this opportunity to thank everyone involved in the project and for the helpful feedback we received during beta-testing of the portal. If you have any further feedback or queries about the resource please contact enquiries@guidetopharmacology.org

This project is supported by a grant awarded to Professor Jamie Davies at the University of Edinburgh by Medicines for Malaria Venture (MMV).

 

 

 

 

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Database Release 2019.4

We are very pleased to announce our a new release of the IUPHAR/BPS Guide to Pharmacology. This version (2019.4) is the fourth this year and includes the first full-release of the IUPHAR/MMV Guide to Malaria Pharmacology.

Content Updates

GtoPdb now contains over 9,800 ligands, with around 7,450 having quantitative interaction data to biological targets. 1,442 of the ligands are approved drugs. The database contains over 1,700 human targets with curated interactions, with just over 1,500 of these having quantitative data. Full stats can be found on our About Page.

Here’s a brief summary of some of main curatorial updates:

  • The Lysyl oxidases family has been added to allow the GtoPdb to capture advance in medicinal chemistry and development of lysyl oxidase inhibitors. Lysyl oxidases are extracellular enzymes that are vital for cross-linking fibrillar elastin and collagens and for extracellular matrix stabilisation. LOX and LOXL2 are implicated in fibrosis, tumourigenesis, and metastasis, and are subsequently molecular targets for cancer drug discovery.
  • We have cross-referenced GtoPdb ligands against the World Health Organization (WHO) Model List of Essential Medicines, and now include this subset as a specific ligand category on our ligand list page. This classification is also displayed on ligand summary pages. Currently, 193 ligands in GtoPdb are on the WHO list.

Guide to Malaria Pharmacology (GtoMPdb)

We are delighted to officially launch the first full public release of the IUPHAR/MMV Guide to Malaria Pharmacology. GtoMPdb has been constructed in partnership with the Medicines for Malaria Venture (MMV), an organization dedicated to identifying, developing and delivering new antimalarial therapies that are both effective and affordable. This is in response to the global challenge of over 200 million cases of malaria and 400 000 deaths worldwide, with the majority in the WHO Africa Region.  It provides new pharmacological content, including molecular targets in the malaria parasite and interaction data for ligands with antimalarial activity.  We have pioneered curation of data from assays screening compounds against the whole organism, used routinely in antimalarial drug discovery.

A dedicated portal has been developed to provide quick and focused access to these new data and we have added direct links on the main GtoPbd home page.

home6

GtoPdb home page with new menu bar links to GtoMPdb.

In this database release these are the recent advancements made in the GtoMPdb.

  • The Antimalarial targets family and the Antimalarial ligands family have been updated, giving a total of 30 P. falciparum (3D7) targets and 72 ligands tagged as antimalarial in the database.
  • We have fixed the display of interactions to avoid duplicate rows – now data for a single target, ligand and species will appear together.

You can read more about the launch at this blog post.

Other Updates

Immunopharmacology content statistics

On the immunopharmaoclogy help page we have added a dynamic list of database content stats.

External links in Europe PMC

The GtoPdb has recently been included in the External Links service at Europe PMC (EPMC)  (https://europepmc.org/LabsLink). On EPMC pages, links to target and ligand entries have been added to the papers curated by GtoPdb that include a quantitative description of the ligand-target interaction. It is possible to retrieve all these references at EMPC by running an “Advanced Search” and selecting “IUPHAR/BPS Guide to Pharmacology” from the “External Links” drop-down list (LABS_PUBS:”1969″) as the cross-reference query. This currently gives 1,729 results, which can be further combined as Boolean-type queries against all other types of EPMC indexing including Bibliographic Fields, Filters, Data Links, External Links and Annotations.

empc

External Links for PMC:6452685 – showing links back to GtoPdb targets and ligands.

Bioschemas

We are also working with Bioschemas (http://bioschemas.org/) (35) to add schema.org semantic mark-up to GtoPdb, which will make it simpler for search engines to index the website. Our current focus is on implementing mark-up on all ligand summary pages, including properties from the Bioschemas MolcularEntity profile (https://bioschemas.org/specifications/drafts/MolecularEntity). A first version of the ligand mark-up has been added, but it remains a work in progress as we seek to refine it.

Posted in Database updates, Guide to Immunopharmacology, Guide to Malaria Pharmacology, Technical

Hot Topics: GPR139 as a potential target for increasing opioid safety

The cross-talk between different G protein-coupled receptor signal-transduction pathways is an intriguing concept with important physiological implications [1]. A recent study by Wang et al. [2] has discovered that the actions of opioid drugs on the μ-opioid receptor (MOR) are negatively regulated by an interaction with the undercharacterized GPR139 receptor [3]. These findings implicate GPR139 as a potential target for increasing opioid safety.

The authors first identified opioid modulators using a transgenic C. elegans platform that were engineered to express the human MOR (tgMOR). Using a rapid behavioral readout to screen ∼2,500 mutagenized tgMOR worms, the authors identified ∼900 mutants with abnormal sensitivity to the opioid agonists morphine and fentanyl. In this paradigm, hypersensitive mutants recovered more rapidly from opioid-induced paralysis compared to the tgMOR animals. The authors focused on two mutants, one with homology to the L-type Ca2+ channel that is known to potentiate the nociceptive properties of opioids and the other frpr-13 that shares a phylogeny with the mammalian receptor GPR139. Furthermore, the opioid hypersensitivity in transgenic worms was reversed by the overexpression human GPR139, suggestive of a functional interaction between the receptors.

The authors then performed a variety of supporting in vitro functional assays in HEK293T cells that indicated GPR139 overexpression could attenuate or abolish MOR signaling and cell-surface expression. They also demonstrated that GPR139 and MOR were associating when co-expressed in this model system, although the relevance of this interaction in a native system awaits further investigation. Nevertheless, GPR139 and MOR were co-expressed in mouse neurons in brain regions implicated in opioid reward, analgesia and withdrawal. Moreover, a series of electrophysiological experiments using knockout mice indicated that GPR139 may offset the opioid-mediated inhibitory effects on neuronal firing.

On the basis of these compelling data, the authors then investigated the behavioural correlate of the GPR139 and MOR interaction. Although GPR139 knockout mice were ostensibly healthy, they exhibited consistently increased acute responses to morphine, including in a conditioned place preference paradigm as a measure of opioid reward, as well as in thermal and mechanical pain models. Equally, the GPR139 knockout mice exhibited fewer behavioural signs of withdrawal following the cessation of chronic opioid exposure. In a final set of experiments, the administration of a GPR139 surrogate agonist JNJ-63533054 led to a dose-dependent reduction in morphine analgesia in both pain paradigms in wild-type mice [4]. JNJ-63533054 also markedly suppressed the self-administration of morphine these mice. Strikingly, these effects were absent in the Gpr139−/− mice, strongly implicating GPR139 as a negative regulator of opioid response in vivo.

Taken together, these findings suggest that GPR139 could be pharmacologically targeted in a strategy to increase the safety and efficacy of opioid treatment, which is currently an area of widespread public interest. Intriguingly, this study builds on the previous identification of α-Melanocyte Stimulating Hormone (αMSH) as a potential endogenous ligand for GPR139 [5]. Given that αMSH is derived from the same precursor as another MOR ligand (β-endorphin), these findings may further indicate an important physiological interaction between these receptors. It will be of great interest to dissect the pharmacology of GPR139 activation, particularly in terms of potential therapeutic advantages over the direct inhibition of MOR.

Comments by Simon R. Foster, Postdoctoral Research Fellow at Monash University and David E. Gloriam (@David_Gloriam), Professor at University of Copenhagen and Head of GPCRdb.

(1) Selbie, L. A. & Hill, S. J. G protein-coupled-receptor cross-talk: the fine-tuning of multiple receptor-signalling pathways. Trends in pharmacological sciences 19, 87-93, (1998). [PMID: 9584624]
(2) Wang, D. et al. Genetic behavioral screen identifies an orphan anti-opioid system. Science (New York, N.Y.), eaau2078, (2019). [PMID: 31416932]
(3) Vedel, L., Nohr, A. C., Gloriam, D. E. & Brauner-Osborne, H. Pharmacology and function of the orphan GPR139 G protein-coupled receptor. Basic & clinical pharmacology & toxicology, (2019). [PMID: 31132229]
(4) Liu, C. et al. GPR139, an Orphan Receptor Highly Enriched in the Habenula and Septum, Is Activated by the Essential Amino Acids l-Tryptophan and l-Phenylalanine. Molecular pharmacology 88, 911-925, (2015). [PMID: 26349500]
(5) Nohr, A. C. et al. The orphan G protein-coupled receptor GPR139 is activated by the peptides: Adrenocorticotropic hormone (ACTH), alpha-, and beta-melanocyte stimulating hormone (alpha-MSH, and beta-MSH), and the conserved core motif HFRW. Neurochem Int 102, 105-113, (2017). [PMID: 27916541]

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Hot Topics: Resting-State Structure and Gating Mechanism of a Voltage-Gated Sodium Channel

In this report the Catterall laboratory succeeded in solving the high resolution structure of a voltage-gated Na+-channel (Nav) in its resting state (1). Why is this difficult and why is this important? It is difficult because Navs exist in the resting state only at very negative voltages but not at a zero membrane potential required for structural analysis by X-ray crystallography or cryo-EM. Accordingly, all high resolution structures of Navs, whether pro- or eukaryotic, have so far reported channels with the voltage-sensing domains in the depolarized state, i.e. the positively charges S4 helices of the voltage sensors moved “up” towards the extracellular side. Therefore it is not known how the activation gate of the ion pore (formed by the four S6 helices) is kept closed by the voltage sensor in its resting position, i.e. with the S4-helices “down”. Some predictions about how this might work was inferred from structural work on related voltage-gated ion channels (e.g in a TPC1 channel, 2) or from a study in which a chimeric Nav construct was trapped in a closed (“deactivated”) state by a toxin (3). The elegant work presented here by Wideschaisri and colleagues (1) directly addressed this important question by generating suitable mutants of the bacterial Nav, NavAb (4). One mutant (KAV mutation) was engineered to shift its activation threshold to much higher voltages thus holding the channel in the resting state also at 0 mV for structural studies. Moreover, they introduced disulfide crosslinks locking the voltage-sensor in the desired resting (S4 “down”) or activated (S4 “up”) state. The stabilization of these states in these mutants were verified in functional studies to ensure that the structural data have clear functional correlates. Analysis of the X-ray structures (and cryo-EM structure for the KAV mutant) provided important novel insight into the structural rearrangements associated with the transition from the activated/open to the resting/closed state. This includes changes of the helical structure of S4 associated with its striking inward movement of about 11.5 A compatible with a “sliding helix” model. Rearrangements of the four S4-S5 linkers were found to tighten the “collar” around the S5 and S6 segments thus keeping the pore closed.
All this was possible because they used the bacterial NavAb, for their experiments. This comes with the advantage that this channel exists as a tetramer of identical subunits and therefore the mutations are present in all four voltage-sensors. This also facilitated disulfide cross-linking, because these channels lack endogenous cysteines. The disadvantage of NavAb is that it does not reflect the more complex structure of eukaryotic Nav and voltage-gated Ca2+ channels (Cavs) in which all four voltage-sensing- and pore forming elements are different and are tethered together in a single molecule. Nevertheless, there is no doubt that this “sliding helix” model of electromechanical coupling will also apply to eukarytic Navs and Cavs. Understanding all the conformational rearrangements occurring between resting and activated channel states will provide new opportunities for the discovery of state-dependent and subtype-selective Nav- and Cav- channel blocking drugs.

Comments by Jörg Striessnig, University of Innsbruck

(1) Wisedchaisri, G., Tonggu, L., McCord, E., Gamal El-Din, T.M., Wang, L., Zheng, N., Catterall, W.A., 2019. Resting-State Structure and Gating Mechanism of a Voltage-Gated Sodium Channel. Cell 178, 993-1003. doi: 10.1016/j.cell.2019.06.031. [PMID: 31353218]
(2) Kintzer, A.F., Green, E.M., Dominik, P.K., Bridges, M., Armache, J.-P., Deneka, D., Kim, S.S., Hubbell, W., Kossiakoff, A.A., Cheng, Y., Stroud, R.M., 2018. Structural basis for activation of voltage sensor domains in an ion channel TPC1. Proc. Natl. Acad. Sci. U.S.A. 115, E9095–E9104. doi: 10.1073/pnas.1805651115. [PMID: 30190435]
(3) Xu, H., Li, T., Rohou, A., Arthur, C.P., Tzakoniati, F., Wong, E., Estevez, A., Kugel, C., Franke, Y., Chen, J., Ciferri, C., Hackos, D.H., Koth, C.M., Payandeh, J., 2019. Structural Basis of Nav1.7 Inhibition by a Gating-Modifier Spider Toxin. Cell 176, 702-715.e14. doi: 10.1016/j.cell.2018.12.018. [PMID: 30661758]
(4) Payandeh, J., Scheuer, T., Zheng, N., Catterall, W.A., 2011. The crystal structure of a voltage-gated sodium channel. Nature 475, 353–358. doi: 10.1038/nature10238. [PMID: 21743477]

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Hot Topics: The atlas of aminergic GPCR mutagenesis

G protein-coupled receptors (GPCRs) are an important family of signal-transducing membrane proteins capable of binding various types of ligands from the extracellular space and activating various signalling pathways inside the cell, rendering them one of the largest protein target families in pharmaceutical research [1]. Receptors of the aminergic GPCRs family are particularly rewarding drug targets as they are implicated in various disease areas, and structure-based drug design has enabled the understanding of ligand binding and function, and the development of more than 500 approved drugs targeting these receptors. Advances in structural biology allowed the determination of more than 300 crystal structures of more than 60 GPCR subtypes to date [2], however, these still represent only a small fraction of known receptor-ligand associations [3].

Site-directed mutagenesis (SDM) is a versatile and frequently employed tool in pharmacological investigations used to infer structural features of protein-ligand interactions [4]. Mutation studies complement structural information provided by crystal structures by defining the roles and relative importance of residues involved in binding, functional activity, and selectivity for ligand chemotypes which have not yet been co-crystallized with their receptors. Community-wide GPCR structure modelling challenges have shown that the best models could be constructed by careful incorporation of mutation and SAR data relating to ligand binding [5]. However, an integrated analysis of receptor and ligand structures and SAR, mutation data, and binding mode prediction has been so far lacking.

The study of Vass et al. can be regarded as a meta-analysis of the site-directed mutagenesis literature for aminergic G protein-coupled receptors [6]. Through an exhaustive database and literature search, the researchers from VU University Amsterdam, Polish Academy of Sciences, University of Copenhagen and Sosei Heptares have collected 6692 mutational data points for 34 aminergic GPCR subtypes of 8 species from 302 publications, covering the chemical space of 540 unique ligands from mutagenesis experiments. This large body of mutation data was also annotated with the structure-based GPCR residue numbering enabling a comparison of mutation effects across different GPCR subtypes and sub-families, and mapped onto the residue positions in the available aminergic crystal structures. Mutation effects were binned into four categories: increased effect, no effect, decreased, and abolished effect, and the data is presented in large overview tables for the five aminergic sub-families. For ligands which had not yet been co-crystallized with their respective receptors, the authors provide predicted binding modes using a combined docking and interaction fingerprint approach to rationalize the mutation effects in light of the ligand SAR.

For each receptor sub-family, a discussion of the known structural receptor-ligand interactions, the ligand chemical space, the structural determinants of receptor-ligand interactions from mutation studies in the amine, major, minor pockets, and the extracellular vestibule, and the possibility of mutation effect extrapolation is provided. The authors also discuss mutation effects of the same ligands across different receptors providing insights into the receptor specific determinants of ligand binding. Finally, an overview is provided of some applications, and the possibilities and limitations of using mutation data to guide the design of novel aminergic receptor ligands.

The authors have deposited the data on Zenodo and in the GPCRdb, and a KNIME workflow was also provided using the 3D-e-Chem KNIME nodes to ease further analysis of the data by the readers [7].

Comments by Chris De Graaf (@Chris_de_Graaf), Director Computation Chemistry, Sosei Heptares.

(1) Santos et al. (2017). A comprehensive map of molecular drug targets. Nat Rev Drug Discov. doi: 10.1038/nrd.2016.230. [PMIDs: 27910877]

(2) Munk et al. (2019). An online resource for GPCR structure determination and analysis. Nat Methods. doi: 10.1038/s41592-018-0302-x. [PMIDs: 30664776]

(3) Vass et al. (2018). Chemical Diversity in the G Protein-Coupled Receptor Superfamily. Trends Pharmacol Sci. doi: 10.1016/j.tips.2018.02.004. [PMIDs: 29576399]

(4) a) Munk et al. (2016). Integrating structural and mutagenesis data to elucidate GPCR ligand binding. Curr Opin Pharmacol. doi: 10.1016/j.coph.2016.07.003. [PMIDs: 27475047] b) Arimont et al. (2017) Structural Analysis of Chemokine Receptor–Ligand Interactions. J Med Chem doi: 10.1021/acs.jmedchem.6b0130. [PMIDs: 28165741]. c) Jespers et al. (2018). Structural Mapping of Adenosine Receptor Mutations: Ligand Binding and Signaling Mechanisms. Trends Pharmacol Sci. doi: 10.1016/j.tips.2017.11.001. [PMIDs: 29203139]

(5) a) Kufareva et al. (2011) Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure. doi: 10.1016/j.str.2011.05.012. [PMIDs: 21827947]; b) Kufareva et al. (2014). Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure. doi: 10.1016/j.str.2014.06.012. [PMIDs: 25066135]

(6) Vass et al. (2019). Aminergic GPCR-Ligand Interactions: A Chemical and Structural Map of Receptor Mutation Data. J Med Chem. doi: 10.1021/acs.jmedchem.8b00836. [PMIDs: 30351004]

(7) (a) https://3d-e-chem.github.io/; (b) http://doi.org/10.5281/zenodo.58104

Posted in Hot Topics

Database Release 2019.3

We have now made the third IUPHAR/BPS Guide to Pharmacology database release of 2019 (2019.3). It includes updates focussed on preparation for the next edition of The Concise Guide to PHARMACOLOGY (2019/20), due out later this year.

Content Updates

GtoPdb now contains over 9,600 ligands, with around 7,300 have quantitative interaction data to biological targets. 1,426 of the ligands are approved drugs. The database contains over 1,700 human targets, with just over 1,500 of these having quantitative interaction data. Full stats can be found on our About Page.

Here’s a brief summary of some of main curatorial updates:

  • The cereblon protein has been added as a new target. For simplicity it is included in the Enzymes section of the Guide, as it is an important component of the E3 ubiquitin ligase complex, although it has no intrinsic catalytic activity. Cereblon is included in the Guide as its binding by thalidomide class drugs has been identified as the molecular mechanism that underlies the teratogenicity of this drug class. We have included quantitative data for interactions between cereblon and the three approved thalidomide type drugs (thalidomide, lenalidomide and pomalidomide), as well as an Immunopharmacology comment and information about clinical variants in disease.
  • The neuromedin U receptor family has an updated detailed introduction.
  • Several ‘new to the GtoPdb’ corticotropin releasing factor-1 (CRF-1) receptor antagonists (ligand IDs 10375-10379), their receptor interaction data and histories as clinical candidates have been added, including verucerfont and pexacerfont.
  • Nudix hydrolase 7, an enzyme that is involved in peroxisomal CoA/acyl-CoA homeostasis, and the first reported covalent NUDT7 inhibitor (NUDT7-COV-1) were added.
  • The Guanyly Cyclases were reorganised. A new family, Receptor guanylyl cyclases (RGC) family, was created and the existing RGC family was renamed Transmembrane guanylyl cyclases (and added as a sub-family of the new family). Nitric oxide (NO)-sensitive (soluble) guanylyl cyclase was also moved within this new family. The NPR-C (natriuetic peptide receptor 3) target was moved to the Transmembrane guanylyl cyclases family and the Natriuretic peptide receptor family removed entirely from the Catalytic receptor class.
  • We generated HELM annotation and SMILES for the small cyclic peptide apelin receptor agonist MM07 and these were submitted to PubChem. See reference PMID:25712721

Guide to Malaria Pharmacology (GtoMPdb)

Earlier this year we issue a blog post introducing the Guide to Malaria Pharmacology. This gives a good background to the project and illustrates how we plan to handle curation of this data and how we are developing the new portal that accesses the data.

Thursday 25th of April was World Malaria Day 2019 and to raise awareness we issued a blog post and a news release, in conjunction with Edinburgh Infectious Diseases and the School of Biological Sciences. These highlighted the release of the GtoMPdb and also provided an account of the long association malaria research has had with Edinburgh.

In this database release these are the recent advancements made in the GtoMPdb.

tcp_list

Screenshot showing antimalarial ligands with Target Candidate Profiles (TCPs)

Other Updates

ChEMBL Target Links

Following on from the update to these links in the last release, we’ve finished updating the various place across the GtoPdb site the link out to ChEMBL.

Site search

Our site-wide search now works using ‘*’ as a wildcard indicator at the end of a search string. This helps make our search behaviour more consistent with other web-resources.

Other minor updates

Posted in Database updates, Guide to Malaria Pharmacology, Hot Topics, Technical

Hot Topics: Time to FRET about GPCR activation dynamics?

G protein coupled receptors (GPCRs) are crucial for the transduction of extracellular stimuli to the intracellular space. Upon activation, GPCRs undergo large conformational changes to engage transducers and stimulate intracellular responses. However, the kinetics of agonist induced GPCR conformational changes are relatively understudied. An exception to this is the class A rhodopsin receptor, which has a covalent agonist and fast (< 1ms) activation kinetics. In contrast, other GPCRs are thought to activate across the low to mid millisecond range [1]. For Class C GPCRs, which are distinct from class A receptors in that they contain large extracellular agonist binding domains and exist as obligate dimers, the site of agonist binding is >100Å from where the transducer interacts [2]. Class C GPCR activation involves both dimer rearrangement and activation of the 7-transmembrane (7-TM) domain, which are thought to occur over 20-200ms [3-5]. An outstanding question is whether the activation kinetics of rhodopsin are indeed faster than other GPCRs, or if previous experimental approaches lacked sufficient resolution to reveal fast kinetics in other receptor families.

To this end, Grushevskyi and colleagues have used FRET recordings to detect submillisecond activation dynamics of a prototypical class C GPCR, metabotropic glutamate receptor subtype 1 (mGlu1), demonstrating that mGlu1 undergoes two temporally distinct conformational changes upon activation [6]. Inter-subunit movements were detected by labelling the second intracellular loop of one protomer with CFP and the other with YFP. Intra-subunit changes detected by labelling each protomer with YFP in the second intracellular loop and CFP in the C-terminus. Synchronous activation of receptors was achieved via two complementary methods. UV-induced uncaging of glutamate in intact cells resulted in an increase in inter-subunit FRET and a decrease in intra-subunit FRET, which the authors believe represent movement of protomers towards each other and outward movement of TM6, respectively. Dimer rearrangement occurred with an average time constant of ~2ms, with 7TM conformational changes occurring approximately 10 times slower. Rapid solution exchange in outside-out Xenopus oocyte patches resulted in a similar two-step activation profile. Both methods revealed that initial mGlu1 dimer rearrangement occurs faster than previously reported [4,5], and is only loosely coupled to subsequent 7TM domain conformational changes. Receptor deactivation also occurred in two discrete steps, with inter-subunit rearrangements again preceding intra-subunit conformational changes. Occupancy of both binding sites was required for optimal activation and deactivation kinetics, as inter-subunit rearrangements in both directions were significantly slower in receptor mutants that only bind agonist in one protomer.

This study has revealed the existence of metastable intermediate activation states i.e. states in which the dimer rearrangement or the 7TM conformational changes exist in isolation. How these intermediate states influence mGlu1 signalling is unknown, as the fluorescently labelled mGlu1 dimers are unable to couple to G proteins [3]. Additionally, whether the intra-subunit FRET changes do indeed represent specific TM6 movements is somewhat ambiguous, given that the C-terminus to which CFP is attached is predicted to be highly flexible. However, should this activation mechanism be relevant and applicable across all Class C GPCRs, it may contribute to the complexity of Class C pharmacology. Allosteric agonists of Class C GPCRs bind to sites in the 7TM domain, activating receptors in the absence of orthosteric ligand [2], indicating that the 7TM-active state represents a physiologically relevant signalling conformation. These intermediate receptor activation states may also influence transducer coupling. Different orthosteric/allosteric ligand combinations shifting the balance between the various active states, stabilising unique conformations and engaging distinct downstream signalling pathways could play a part in the biased and probe dependent pharmacology apparent for many Class C GPCR ligands. Exploring multiple GPCRs with different orthosteric and allosteric ligand combinations is a crucial next step in understanding how the kinetics of receptor activation relates to ligand pharmacology. Understanding how drug-like compounds impact receptor activation kinetics and stabilise intermediate receptor states will likely play a large role in rational drug design programs going forward.

Comments by Shane D Hellyer (https://research.monash.edu/en/persons/shane-hellyer) and Karen J Gregory (https://research.monash.edu/en/persons/karen-gregory), Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Australia.

(1) Lohse M.J. et al. (2012). Fluorescence/bioluminescence resonance energy transfer techniques to study G protein-coupled receptor activation and signalling. Pharmacol Rev, 64: 299-336. [PMIDs: 22407612]
(2) Leach K & Gregory K.J. (2017) Molecular insights into allosteric modulation of Class C G protein-coupled receptors. Pharmacol Res, 116: 105-118. [PMIDs: 27965032]
(3) Hlacvackova V et al. (2012) Sequential inter- and intrasubunit rearrangements during activation of dimeric metabotropic glutamate receptor 1. Sci Signal, 5: ra59. [PMIDs: 22894836]
(4) Marcaggi P et al. (2009) Optical measurement of mGluR1 conformational changes reveals fast activation, slow deactivation, and sensitization. PNAS, 106: 11388-11393. [PMIDs: 19549872]
(5) Vafabakhsh R et al. (2015) Conformational dynamics of a class C G-protein-coupled receptor. Nature, 524: 497-501. [PMIDs: 26258295]
(6) Grushevskyi E.O. et al. (2019) Stepwise activation of a class C GPCR begins with millisecond dimer rearrangement. PNAS. pii: 201900261. doi:10.1073/pnas.1900261116. [Epub ahead of print] [PMIDs: 31023886]

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Posted in Hot Topics

World Malaria Day 2019: A New Guide to Malaria Pharmacology

Thursday 25th 2019 is World Malaria Day and we’d like to highlight our new resource, currently under development, called The IUPHAR/MMV Guide to Malaria Pharmacology (GtoMPdb). Based in Edinburgh, this new resource is directed by Professor Jamie Davies and his team and funded by the Medicines for Malaria Venture (MMV).

Malaria and Edinburgh

Malaria and Edinburgh have a long association. This was marked most notably by the announcement by Patrick Manson, at a meeting of the British Medical Association (BMA) in Edinburgh in July 1898, of the discovery by Ronald Ross of the mosquito cycle of the malaria parasite, in a lecture on ‘The mosquito and the malaria parasite’. The first Nobel prize to be awarded to a British subject was awarded in 1902 to Ross for this discovery is now displayed in the Museum of Scotland in Edinburgh. He received the award for showing how the mosquito was the vector for the transmission of malaria. More about Malaria research in Edinburgh.

IUPHAR/MMV Guide to MALARIA PHARMACOLOGY

The IUPHAR/MMV Guide to MALARIA PHARMACOLOGY (GtoMPdb) database portal is a new extension to the existing Guide to PHARMACOLOGY database (GtoPdb). GtoMPdb is being developed as a joint initiative between Medicines for Malaria Venture (MMV) and the International Union of Basic and Clinical Pharmacology (IUPHAR), with the aim of adding curated antimalarial data to GtoPdb and providing a purpose-built portal that is optimized for the malaria research community.

The parent Guide to PHARMACOLOGY database (GtoPdb) has been extended to incorporate the additional information required to describe the activity and target interactions of antimalarial compounds. It provides a searchable database with quantitative information on Plasmodium molecular targets and the prescription medicines and experimental drugs that act on them. The development of this resource is important because until now there has been no single purpose-built portal into open access, expert curated information on Plasmodium molecular targets and the antimalarial compounds that act on them, including approved drugs, clinical candidates and research leads. This initiative will facilitate access by the malaria research community to lead, target and efficacy data integrated from disparate global R&D efforts.

More information about IUPHAR and MMV, and the project can be found here: https://www.guidetomalariapharmacology.org/malaria/gtmpAbout.jsp.

This blog post gives more detailed information about the development of GtoMPdb.

See also the Edinburgh Infectious Disease news page.

Expert Advisory Committee for the IUPHAR/MMV Guide to Malaria Pharmacology project

David R. Cavanagh, UK (https://www.ed.ac.uk/profile/dr-david-cavanagh)
Mark J. Coster, Australia
Michael P. Pollastri, USA
Laurent Rénia, Singapore
J. Alexandra Rowe, UK (http://alexrowe.bio.ed.ac.uk/)
Chris Swain, UK
Matthew H. Todd, UK
Elizabeth A. Winzeler, USA

Scientific Advisors for IUPHAR/MMV Guide to Malaria Pharmacology project

Jeremy N. Burrows, Switzerland
Brice Campo, Switzerland
Stephen P.H. Alexander, UK
Anthony P. Davenport, UK
Jamie A. Davies, UK
F. Javier Gamo, Spain
Michael Spedding, France
Stephen A. Ward, UK

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Posted in Guide to Malaria Pharmacology

Hot Topics: Rise up against statistical significance, probably.

A recent commentary in Nature has the provocative title “Retire Statistical Significance” (1, with a list of more than 800 signatories) and has been widely interpreted as a call for the entire concept of statistical significance to be abandoned. Closer reading of the commentary suggests that the main message of the paper is a call to stop the use of P values or confidence intervals in a categorical or binary sense in order to be absolute as to whether a result supports or refutes a scientific hypothesis. This remains a radical proposal but perhaps does not signal the end for statistical tests in biomedical research just yet.

For pharmacologists, particularly those who wish to publish in the British Journal of Pharmacology (BJP), the proposals in Amrhein et al. (1) are a problem. They appear to directly contradict advice given in the guidelines for publication in the BJP, introduced by Curtis et al. (2), namely: “when comparing groups, a level of probability (P) deemed to constitute the threshold for statistical significance should be defined in Methods, and not varied later in Results (by presentation of multiple levels of significance).” In other words, statistical tests must produce a categorical outcome based on a P value of a defined threshold (normally as P = 0.05, or a 95% confidence interval) for all data sets in the paper.

So, which is correct? How should potential future authors in BJP and elsewhere approach this? In the spirit of the Amrhein et al. (1) article, I do not propose to make a binary choice here. After all, in the wider sense, both approaches seek to address the same issues of reliability and reproducibility in scientific research; issues which are particularly problematic in the area of biomedical science and thus pharmacology. The BJP approach is based around objectivity and removal of bias (whether unconscious or not). Here, decisions are largely taken away from the experimenter with a predefined statistical threshold coupled to a number of guidance statements around experimental design. There is much merit in this approach, and the journal does encourage authors to make appropriate caveats (3) but, inevitably, when such absolute, categorical decisions are made, P = 0.04 will take science in a different direction to P = 0.06. As Colquhoun (4) and others have shown, much too often this will be the wrong direction.

For this reason, I prefer the Amrhein et al. (1) proposals, but, to my mind, they come with at least two requirements. One of these requirements is data transparency and availability. If authors do not provide a statement about statistical significance, it is incumbent on them to make their data freely available so others, particularly those researchers working closely in the field, can study the data in detail in order to support or refute the messages of the paper, ideally, perhaps, in the form of post-publication peer review. A second requirement is trust. In the absence of a statistical significance rule book or convention (however flawed), authors must provide a subjective narrative around the results and readers must expect that they can trust this narrative to be both informed and unbiased. However transparent and available the underlying data, most readers will rely on the authors to guide their understanding and interpretation of the research. In an environment where “researchers’ careers depend more on publishing results with ‘impact’ than on publishing results that are correct” (5), this is surely the big challenge.

Comments by Alistair Mathie (@AlistairMathie), The Medway School of Pharmacy

(1) Amrhein V, Greenland S & McShane B. (2019). Scientists rise up against statistical significance. Nature, 567(7748):305-307. doi: 10.1038/d41586-019-00857-9. [PMID:30894741]

(2) Curtis MJ et al. (2019). Experimental design and analysis and their reporting: new guidance for publication in BJP. Br J Pharmacol, 172(14):3461-71. doi: 10.1111/bph.12856. [PMID:26114403]

(3) Curtis MJ et al. (2019). Experimental design and analysis and their reporting II: updated and simplified guidance for authors and peer reviewers. Br J Pharmacol, 175(7):987-993. doi: 10.1111/bph.14153. [PMID:29520785]

(4) Colquhoun D. (2019). An investigation of the false discovery rate and the misinterpretation of p-values. R Soc Open Sci, 1(3):140216. doi: 10.1098/rsos.140216. eCollection 2014 Nov. [PMID:26064558]

(5) Casadevall A. (2019). Duke University’s huge misconduct fine is a reminder to reward rigour. Nature, 568(7). [World View: Article]

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Posted in Hot Topics, Uncategorized

Database Release 2019.2

We are pleased to announce a new IUPHAR/BPS Guide to Pharmacology database release! This release, 2019.2, is the second of the year and includes updates focussed on preparation for the next edition of The Concise Guide to PHARMACOLOGY (2019/20), due out later this year.

Content Updates

GtoPdb now contains over 9,600 ligands, with around 7,300 have quantitative interaction data to biological targets. 1,416 of the ligands are approved drugs. The database contains over 1,700 human targets, with just over 1,500 of these having quantitative interaction data. Full stats can be found on our About Page.

Over 200 new ligands have been added in this release, with more than 50% of these having quantitative interaction data.

In preparation for the next Concise Guide to PHARMACOLOGY our expert subcommittees have been providing update across all target classes.

Guide to Malaria Pharmacology (GtoMPdb)

Earlier this month we issue a blog post introducing the Guide to Malaria Pharmacology. This gave a very good background to the project and illustrated how we plan to handle curation of this data and how we are developing the new portal that accesses the data.

In this database release these are the recent advancements made in the GtoMPdb.

  • The Antimalarial targets family and the Antimalarial ligands family have been updated, giving a total of 25 P. falciparum (3D7) targets and 57 ligands tagged as antimalarial in the database.
  • New species P. yoelii
  • Extended GtoMPdb search to cover parasite lifecycle stages and malaria species

Other Updates

ChEMBL Target Links

Our target out-links to ChEMBL have been updated, many thanks to Anna Gaulton for her support in this. Not only have we update our exisitng links, but we have added around ~800 new outlinks.

Contributor Lists

As part of the preparation for the next Concise Guide to PHARMACOLOGY we have update a substantial portion of our contributor records.

Endogenous/natural ligands

Work has been undertaken to review the curation of endogenous/natural ligand lists with an attempt to correlate this with ligands marked as endogenous in the interaction data. We hope to soon provide a downloadable list of all natural/endogenous ligands for targets.

Bug Fixes

  • Google Analytics tracker fixed for GtoMPdb
  • Family overviews have internal links corrected for ligands
  • Out links to HGNC
  • Interaction table style modified improve style and better handle wrapped text

 

Posted in Database updates

Guide to MALARIA PHARMACOLOGY: introducing a new resource

gtommv_bannerWe are pleased to make public the first beta-release (v1.0) of the Guide to MALARIA PHARMACOLOGY (GtoMPdb), a new extension to the existing Guide to PHARMACOLOGY (GtoPdb). The GtoMPdb is being developed as a joint initiative between Medicines for Malaria Venture (MMV) and the International Union of Basic and Clinical Pharmacology (IUPHAR), with the aim of adding curated antimalarial data to GtoPdb and providing a purpose-built portal that is optimized for the malaria research community.

We have implemented a number of changes to the existing database structure and web interface that were necessary for the capture and presentation of antimalarial data. Many antimalarial compounds have a poorly understood mechanism of action and an unknown molecular target and we have extended the interactions table and updated the web interface to accommodate this. A new “whole organism” assay type has been introduced to capture data from the whole cell assays used routinely in antimalarial drug discovery. Both changes are illustrated below.

Figure 1: The interactions table on an antimalarial ligand summary page

Screen Shot 2019-02-25 at 15.02.56.png

In addition, we have put in place the ability to tag both targets and ligands of relevance to malaria and provide curatorial comments. These comments surface on the website (see Figure 2 below) and are incorporated into the site search.

Figure 2: Malaria comments tab on an antimalarial ligand summary page

Screen Shot 2019-02-25 at 11.42.59.png

A new GtoMPdb portal (www.guidetomalariapharmacology.org) is being developed to provide tailored routes into browsing the antimalarial data in addition to the existing ligand and target browse/search functionality available on the parent GtoPdb site. For beta-release v1.0 we have implemented customised views of the data that include parasite lifecycle and target species activity, with access from either the menu-bar or panels on the homepage (see figure 3 below).

Figure 3: The GtoMPdb portal homepage

Screen Shot 2019-02-25 at 11.11.59.png

The GtoMPdb uses a set of top-level Plasmodium lifecycle stages (collective categories for one or more developmental forms of the parasite) against which interactions in the database can be annotated and which form the basis of organising, navigating and searching for parasitic lifecycle activity. We have developed a new Parasite Lifecycle homepage that provides a short introduction and links to additional pages for each of the top-level lifecycle stages. These in turn contain a more detailed description and a table of interactions for that lifecycle stage (illustrated in Figure 4).

Figure 4: Plasmodium liver stage page, an example of the new Parasite Lifecycle Stage pages

Screen Shot 2019-02-25 at 11.17.10.png

The Target Species homepage provides a short description for Plasmodium species that are of clinical or research importance. It also includes a resource section and links to individual pages for species that have annotated interactions in the database. The figure below illustrates an example of an individual species page. The interactions table displays affinity data for the species but also provides additional details, when available, for the strain used.

Figure 5: Plasmodium falciparum page, an example of the new Target Species pages

Screen Shot 2019-02-25 at 11.27.29.png

Development of the beta-release will continue 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.

If you have any feedback or queries about the resource please contact enquiries@guidetopharmacology.org

This project is supported by a grant awarded to Professor Jamie Davies at the University of Edinburgh by Medicines for Malaria Venture (MMV).

Posted in Guide to Malaria Pharmacology, Technical

Hot Topics: Exciting Times for Ion Channel Pharmacology

Whilst life is always exciting as an ion channel pharmacologist, the last few months have been particularly so, with a large number of publications showing structures of ion channels with regulatory molecules bound to them. In just the last month, the journal, Science, has published several such papers. Three of these concern voltage-gated sodium channels (NaV1.2, NaV1.7) and the binding of potent and selective toxins from animals [1-3]. Another reveals the structure of the primary human cooling and menthol sensor channel TRPM8 bound to synthetic cooling and menthol-like compounds [4].

In the most recent paper [5], Schewe and colleagues extend their outstanding work on selectivity-filter gating of K2P potassium (K) channels (Schewe et al. (2016). Cell. PMID: 26919430), to identify a binding site for negatively charged activators of these channels (styled the “NCA binding site”). Activators which bind to this site open a number of different K2P channels (e.g. K2P2.1 (TREK-1) and K2P10.1 (TREK-2)) and several other potassium channels such as hERG channels (KV11.1) and BKCa channels (KCa1.1), all of which are gated at their selectivity filter. This is exciting, because it is notoriously difficult to design, or even identify, activator compounds for ion channels. This work together with the identification of a separate “cryptic binding site” for K2P channel activators (PMID: 28693035) opens possibilities for rationale design of activator compounds targeting these binding sites, which would provide potential novel therapeutic approaches for the treatment of several conditions including chronic pain, arrhythmias, epilepsy and migraine (PMID: 30573346).

One potential problem, identified by Schewe et al, is the promiscuity of the NCA binding site across several K channel families. However, there are enough structural differences in the region around the NCA-binding site between the channel types to overcome this. Provocatively, Schewe et al even suggest that the simultaneous activation of several different K channel types at once may even be advantageous in certain acute conditions such as ischemic stroke and status epilepticus.

Comments by Alistair Mathie (@AlistairMathie) and Emma L. Veale (@Ve11Emma), The Medway School of Pharmacy

(1) Clairfeuille T et al. (2019). Structural basis of α-scorpion toxin action on Nav channels. Science, pii: eaav8573. doi: 10.1126/science.aav8573. [PMIDs:30733386].

(2) Shen H et al. (2019). Structures of human Nav1.7 channel in complex with auxiliary subunits and animal toxins. Science, pii: eaaw2493. doi: 10.1126/science.aaw2493. [Epub ahead of print]. [PMIDs:30765606].

(3) Pan X et al. (2019). Molecular basis for pore blockade of human NaNa+ channel Nav1.2 by the μ-conotoxin KIIIA. Science, pii: eaaw2999. doi: 10.1126/science.aaw2999. [Epub ahead of print]. [PMIDs:30765605].

(4) Yin Y et al. (2019). Structural basis of cooling agent and lipid sensing by the cold-activated TRPM8 channel. Science, pii: eaav9334. doi: 10.1126/science.aav9334. [Epub ahead of print]. [PMIDs:30733385].

(5) Schewe M et al. (2019). A pharmacological master key mechanism that unlocks the selectivity filter gate in K+ channels. Science, 363(6429):875-880. doi: 10.1126/science.aav0569.. [PMIDs:30792303].

 

Posted in Hot Topics

Hot Topics: Ligand biological activity predicted by cleaning positive and negative chemical correlations

New machine learning algorithm for drug discovery that is twice as efficient as the industry standard and identified potential ligands for the M1 receptor, a potential target for the treatment of Alzheimer’s disease.

A paper from Lee et al. [1] (University of Cambridge) in collaboration with Pfizer, describes the development of an algorithm to use machine learning to separate pharmacologically relevant chemical patterns from irrelevant ones. The algorithm compared active versus inactive molecules at the muscarinic acetylcholine receptor, M1 and uses machine learning to identify components of the compounds are important for binding and which arose by chance. Lee et al. built a model using historic data using ~5,000 compounds that were screened for agonist activity, of which 222 were active. Six million molecules from the e−Molecules database were computationally screened. From these ~100 molecules were purchased and screened in CHO cells expressing the M1 receptor with four compounds identified as agonists (EC50 range 80-300nM).

Comments by Anthony Davenport, IUPHAR/BPS Guide to PHARMACOLOGY, University of Cambridge

(1) Lee AA et al. (2019). Ligand biological activity predicted by cleaning positive and negative chemical correlations. PNAS, https://doi.org/10.1073/pnas.1810847116. [Epub ahead of print]. [PNAS: Article]

Posted in Hot Topics

Hot Topics: An online resource for GPCR structure determination and analysis

G protein-coupled receptors (GPCRs) transduce physiological and sensory stimuli into appropriate cellular responses and mediate the actions of one-third of drugs. Structures of GPCRs are therefore extremely valuable for understanding basic receptor function and rational drug design. Today, 310 structures of 59 distinct receptors (https://gpcrdb.org/structure/statistics) have revealed the general bases of receptor activation, signalling, drug action and allosteric modulation. However, there are still no structures for the vast majority – 85% – of the 398 non-olfactory GPCRs and for 52% structure models can only be based on low-homology templates.

To accelerate the determination of GPCR structures and to help assess the quality of the available templates based on the modifications and methods, a recent article in Nature Methods presents “An Online Resource for GPCR Structure Determination and Analysis” [1]. This surveyes the construct engineering and experimental methods and reagens used to produce all available GPCR crystal and cryo-EM structures. Furthermore, it describes and interactive resource integrated in GPCRdb (www.gpcrdb.org) to assist users in designing new constructs and browsing appropriate experimental conditions for structure studies.

Comments by David E. Gloriam, University of Copenhagen (@David_Gloriam)

(1) Munk C et al. (2019). An online resource for GPCR structure determination and analysis. J Med Chem, doi:10.1038/s41592-018-0302-x. [PMID:30664776]

 

Posted in Hot Topics

Database Release 2019.1

Our first database release of 2019 (2019.1) is now available. This update contains the following new features and content changes:

Content Updates

GtoPdb contains over 9,400 ligands, with around 7,200 have quantitative interaction data to biological targets. Just over 1,400 of the ligands are approved drugs. The database contains over 1,700 human targets, with near 1,500 of these having quantitative interaction data. Full stats can be found on the About Page.

Targets curated in this release:

GPCRs:

Ion-Channels:

Guide to IMMUNOPHARMACOLOGY

Official Launch, October 2018

At the beginning of October 2018 we held a meeting in Edinburgh focussed on the launch of the IUPHAR Guide to IMMUNOPHARMACOLOGY. Invited speakers contributed to productive discussions on the varying challenges and opportunities in immunopharmacology research. The meeting page has links to the slidesets from the meeting (where permission was granted) and to the meeting report which summarises the presentations, discussions and outcomes.

Immunopaedia

We have begun to incorporate direct links from our ligand pages to the Immunopaedia resource. Immunopaedia promotes education, knowledge and research in immunology globally; it is an immediate source of immunology information for healthcare professionals, students and researchers. Their clinical case studies utilise doctors’ real-world experiences to demonstrate diagnostic methods and treatments as well as explain immunological pathways of diseases. In close collaboration with colleagues at Immunopaedia we have put in place links to relevant case studies from our ligand summary pages (e.g. rituximab).

Guide to Malaria PHARAMCOLOGY

The first public beta-release (v1.0) of the IUPHAR/MMV Guide to Malaria PHARMACOLOGY (www.guidetomalariapharmacology.org) is available in this release! The new portal has been designed to provide tailored routes into browsing the antimalarial data.

At this stage, the data curated in GtoMPdb and viewed on the Antimalarial targets family and the Antimalarial ligands family. In total the are 15 P. falciparum (3D7) targets and 50 ligands tagged as antimalarial in the database. A detailed blog-post on the release will be posted soon.

As well as being able to browse via target or ligand, users can also navigate data via parasite lifecycle stage and via target species. Search tools extended to cover GtoMPdb data, up weighting results relevant to malaria pharmacology.

Other Updates

Drug Approvals

There has been a substantially increased our coverage of European Medicines Agency (EMA) drug approval data in 2019.1. There are 414 approved drugs with EMA marked as a source, up from 274 in 2018.1.   In addition, at about this time of  year  considerable interest is generated from reviews of the previous year’s FDA Drug Approvals (see https://cdsouthan.blogspot.com/2019/01/2018-approved-drugs-in-pubchem.html)

Reaching 59, 2018 was welcomed as a particularly prolific year.  However, for our own capture, we have various exclusion criteria such as antiinfectives (with some exceptions including the antimalarials mentioned above), already-approved mixture components, topicals, non-antibody biologicals, undefined extracts (e.g. fish oil) and inorganics. Thus our scorecard stands at 26 chemical entities that form PubChem Compound Identifiers. We also have database records and PubChem Substance submissions for 11 of the 12 newly-approved antibodies (excepting the anti-HIV one).  Note the exact PubChem CID and SID counts will be linked here in a week or so and reviewed in forthcoming a blog post.

New Target: Vanin 1

Novel targets, as defined by first documentation of disease-targeted chemical modulators  (or new probes to explore roles of under-studied proteins) are relatively infrequent.  However, this release sees the first entry of Vanin 1 where inhibition is being explored as a novel mechanism for the treatment of inflammatory diseases.  This Boehringer filing WO2018228934 on Vanin inhibition with SAR for 44 compounds was found via filtered browsing of recent WO patents in SureChEMBL looking for new immunopharmacology indications in particular.

Update to CDK library to v2.2

We have updated the Chemical Development Kit (CDK) library to version 2.2. This is used by the Guide to Pharmacology to calculate molecular properties of ligands curated in the database. As part of this update, we performed a re-calculation of all molecular properties in the database. As a consequence, you may notice some difference between the properties in 2018.4 and 2019.1.

Chemicalize Pro API (Marvin JS update)

A key feature of the IUPHAR Guide to Pharmacology website is the ability to perform searches by chemical structure (http://www.guidetopharmacology.org/GRAC/chemSearch.jsp). The chemical structure search tool utilises Marvin JS by ChemAxon. In the 2019.1 release we have updated the API control to use Chemicalize Pro (https://pro.chemicalize.com/). This update simplifies the integration of Marvin JS into our website.

Page navigation

We have updated our webpages to feature a drop-down navigation bar, which is revealed when users scroll-down on longer pages. Many pages on GtoPdb are quite long, particularly detailed targets pages (e.g. CB1 receptor) – the new drop-down menu keeps key menu items, and most importantly the site search, in focus at all time.

Detailed target pages

Minor adjustments to the top-section of these pages to layout GtoImmuPdb and GtoMPdb icons and toggle button.

Posted in Database updates, Guide to Immunopharmacology, Guide to Malaria Pharmacology

Hot Topics: New Cannabinoid Receptors Structures

Cannabinoid receptors respond to multiple endogenous fatty acid derivatives and are often divided into neuronal-associated CB1 receptors and immune cell-associated CB2 receptors. Both receptors are GPCR, coupled predominantly to Gi, and have cytoprotective properties. The predominant psychotropic agent in Cannabis, THC, acts as a partial agonist at both receptors. CB1 patho/physiological responses are often characterised as analgesic, rewarding, orexigenic, hypothermic and amnestic, while CB2 receptors are mostly associated with anti-inflammatory effects.

In many countries, synthetic cannabinoids have become a social issue, with a prevalence of use amongst the homeless and incarcerated, with even a number of deaths attributed to these agents. Although all the molecular mechanisms of action of these synthetic cannabinoids are yet to be defined, one feature they have in common is a high potency and high efficacy profile at CB1 receptors. Kumar and colleagues [1] report a CB1 receptor:Gi complex, where the receptor is bound to a synthetic cannabinoid, MDMB-FUBINACA. The authors report an agonist binding-evoked conformational switch involving residues in TM3 and TM6, which they suggest underlies the high affinity of this synthetic cannabinoid. Furthermore, they conduct in silico simulations to suggest a lateral path of entry for the synthetic cannabinoid between TM1 and TM7 rather than the ‘traditional’ extracellular point of ingress. This lateral diffusion model has been suggested for a number of lipid-binding GPCR.

There is a second cannabinoid receptor crystal structure in the same journal, which focusses on the CB2 receptor [2]. Based on the primary sequences of the two human receptors, there is limited structural identity between CB1 and CB2 (~40 %), although the overlap is much higher in the transmembrane domains, as might be expected, given they bind a number of structurally-diverse ligands with little discrimination (e.g. CP55940, WIN55212-2 and HU210). Li et al report the first crystal structure of the CB2 receptor. In this version, a novel high affinity antagonist/inverse agonist AM10257 was bound to the receptor for crystallisation. The resultant structure shows a number of similarities with the antagonist-bound structure of the CB1 receptor, although notably the extracellular portions of the two receptors diverged markedly. Slightly surprisingly, a close resemblance to the agonist-bound CB1 receptor was identified, which lead them to investigate CB1 receptor function of the novel CB2 antagonist, which turned out to be a low efficacy CB1 receptor agonist.

Comments by Steve Alexander (@mqzspa)

[1] Kumar KK et al. (2018). Structure of a Signaling Cannabinoid Receptor 1-G Protein Complex. Cell, pii: S0092-8674(18)31565-4. doi: 10.1016/j.cell.2018.11.040. [Epub ahead of print]. [PMID:30639101].

[2] Li X et al. (2018). Crystal Structure of the Human Cannabinoid Receptor CB2. Cell, pii: S0092-8674(18)31625-8. doi: 10.1016/j.cell.2018.12.011. [Epub ahead of print]. [PMID:30639103].

Posted in Hot Topics

GtoPdb at BPS Pharmacology 2018

The IUPHAR/BPS Guide to Pharmacology was represented at the recent BPS Pharmacology 2018 meeting (London, UK, 18-20 Dec 2018).

Tuesday 18th Dec

On Tuesday we had two significant presentations. Firstly, a late-breaking poster on the IUPHAR/MMV Guide to Malaria Pharmacology. This is an under-development extension to the database to curate in anti-malarial ligands and Plasmodium targets for approved drugs.

Poster: Introducing a new resource: the capture of drugs, leads and targets in the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY (Presented by Dr. Chris Southan & Dr. Simon D. Harding)

Secondly, Dr. Southan presented on the challenges and tribulations of curating peptides in the Guide to Pharmacology. His slides are available below.

Oral Presentation: Tribulations of curating published key bioactive peptides for the Guide to PHARMACOLOGY

Thursday 20th Dec

On the Thursday by three more presentations. Firstly, Dr. Harding presented a flash presentation and poster on new features and updates to the Guide to Pharmacology in 2018, which was awarded the daily flash poster prize.

Poster: The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: new features and updates

Also during the poster session Dr. Southan presented his second poster looking at how we can identify the most pharmacologically significant proteins.

Poster: Will the real pharmacologically significant proteins please stand up?

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Posted in Events, Guide to Immunopharmacology, Guide to Malaria Pharmacology

Hot Topics: GPR37/GPR37L1 and the putative pairing with prosaptide/PSAP

Comments by Dr. Nicola J. Smith, National Heart Foundation Future Leader Fellow & Group Leader, Molecular Pharmacology Laboratory, Victor Chang Cardiac Research Institute, Australia

As is often the case with orphan GPCRs, assigning the endogenous ligand has been controversial for the closely related peptide family orphans, GPR37 and GPR37L1. In 2013, Randy Hall and his team (PubMed: 23690594) first reported an association between both centrally-expressed orphan GPCRs and prosaposin (PSAP) and prosaptide (TX14A), the synthetic active epitope of PSAP. Since that time there has been much debate in the field about whether this pairing is correct, with some authors corroborating the findings (PubMed: 24371137; 30010619, 28795439) and others not (PubMed: 23396314; 27072655; 28688853). Note that Head Activator, found in Hydra, was earlier reported as a ligand (PubMed: 16443751) but was quickly discredited (PubMed:28688853; 23686350).

A recent paper by Sergey Kasparov’s laboratory in Bristol has added further fuel to the fire. In a series of well controlled experiments, Liu et al. (PubMed: 30260505) provided convincing evidence that prosaptide is cyto- and neuro-protective and promotes chemotaxis. They are also the first group to demonstrate an effect of prosaptide at a more physiologically plausible potency. At the same time, Bang et al. (PubMed: 30010619) published a ground-breaking paper linking GPR37 expression to macrophage function. Moreover, they proposed a second, more potent ligand for GPR37 (GPR37L1 was not studied): the pro-resolving mediator neuroprotectin D1 (NPD1). Using HEK293 cells expressing GPR37, NPD1 was a potent stimulator of Gαi/o-dependent calcium flux; findings that were corroborated in macrophages isolated from wild type, but not GPR37 knock-out, mice (PubMed: 30010619). Thus, it may be that the endogenous ligand for GPR37 (and perhaps GPR37L1?) is not a peptide after all, but a lipid.

These two studies, while exciting, do little to help us resolve the conundrum that is PSAP/prosaptide and GPR37/GPR37L1. At the very least, it seems likely that prosaptide, if not the highest affinity endogenous ligand at GPR37, is certainly capable of signalling through GPR37 to stimulate Gαi/o signal transduction (whether it is the most potent endogenous agonist will be shown in time as independent groups seek to validate the actions of NPD1).

But what of GPR37L1? This is harder to answer as a number of studies linking GPR37L1 to PSAP/prosaptide have been performed in double GPR37/GPR37L1 knock-out backgrounds or inappropriate tissue models. For example, in the original paper connecting prosaptide to the receptors, the authors claimed prosaptide acted through both GPR37 and GPR37L1 in primary astrocytes, despite the fact that their Western blots demonstrated marked GPR37 expression in comparison to GPR37L1 in the cells (PubMed: 23690594). More recently, they failed to recapitulate this initial pairing in a HEK293 model (PubMed: 28688853). The absence of GPR37L1 in primary astrocytes is consistent with the animal knock-out work of Marazziti et al. (PubMed: 24062445), who showed that GPR37L1 protein was barely detectable before post-natal day 15, which is after the window for isolating primary astrocyte cultures (confirmed by PubMed: 28795439). Coleman et al. (PubMed: 27072655) overcame this expression issue, with difficulty, by using cerebellar slice cultures in vitro to examine Gαs, but not prosaptide, signalling in wild type and knock-out tissue.

In the neuroprotection paper by Liu et al. (PubMed: 30260505) it is clear that prosaptide or PSAP are exhibiting an effect on the cells. By depleting astrocytes of PSAP and then reintroducing prosaptide exogenously, there is an obvious effect on cell migration, cytotoxicity and neuroprotection – phenotypes that are all lost when shRNA knocking down expression of both GPR37 and GPR37L1 are used. Frustratingly, though, the use of a double knock-down approach makes it impossible to ascribe a specific effect to GPR37L1. While GPR37 and GPR37L1 are very closely related by phylogeny and have highly similsar binding sites (PubMed: 27992882), this does not mean that prosaptide is a ligand at both receptors, nor that both receptors signal via the same G proteins (another area of controversy for GPR37L1, where contradictory studies including two by the same team show either Gαi/o or Gαs signaling: PubMed: 23690594, 30260505 vs 27072655, 28688853). Thus, the failure to use single receptor knock-out/knock-downs, or isolate cells with endogenous expression of GPR37L1, represent major limitations in these studies.

Other than the confounding effects of both GPR37 and GPR37L1 deletion in tested cells, what are other reasons that could explain the inconsistencies between studies? Kasparov and colleagues (PubMed: 30260505) attribute this to cellular background, stating that previous studies that failed to confirm prosaptide/GPR37L1 coupling (PubMed: 27072655, 28688853) used HEK293 cells that must be lacking in the necessary endogenous machinery for signal transduction (PubMed: 30260505). To support this claim, they turned to the PRESTO-Tango assay in HEK293 cells to demonstrate prosaptide stimulation could not lead to GPR37L1-dependent recruitment of beta-arrestin. The assay choice is surprising because previous beta-arrestin-based screens at GPR37L1 have failed to show that the receptor can indeed recruit arrestins (PubMed: 23396314, 25895059), and Liu et al. (PubMed: 30260505) did not provide evidence that recruitment was intact in a more physiologically relevant cellular background. Most puzzling though is that the original paper that identified prosaptide and PSAP as GPR37/37L1 ligands used HEK293 cells to make the original pairing (PubMed: 23690594). They also refute the physiological relevance of high constitutive Gαs signalling reported by Coleman et al., even though Coleman et al. demonstrated higher cAMP accumulation in cerebellar brain slices from wild type mice when compared to GPR37L1-/- (PubMed: 27072655).

Further muddying the waters, the physiological role of GPR37L1 itself remains enigmatic. For example, Min et al. (PubMed: 20100464) initially reported GPR37L1 null mice to have a staggering 62 mmHg increase in systolic blood pressure when compared to a cardiac-specific overexpressing model, with the presence of concomitant left ventricular hypertrophy. However, Coleman et al. (PubMed: 29625592) found a far more marginal cardiovascular phenotype, with a small increase in blood pressure evident in female mice only. Notably, male GPR37L1 knock-out mice appeared to be more susceptible to cardiovascular stressors, while females were cardioprotected (PubMed: 29625592). In terms of a developmental phenotype, Marazziti et al. (PubMed: 24062445) found that GPR37L1 null mice displayed precocious cerebellar development with enhanced performance in a rotarod test up to 1 year of age. More recently, though, Jolly et al. (PubMed: 28795439) failed to confirm a behavioural difference in their own GPR37L1 knock out mice. The links between GPR37L1 and neurological defects are also confounded by the fact that GPR37 also needs to be deleted in mice for a clear phenotype to be evident. For example, while a single point mutation in GPR37L1 (K349N) in a highly consanguineous family appeared to be causative of fatal progressive myoclonus epilepsy, the mouse phenotype was most pronounced in double GPR37/GPR37L1 knock-out animals (PubMed: 28688853). In vitro studies of the GPR37L1 K349N mutant found no difference between it and the wild type receptor in terms of receptor expression, processing, signalling or ubiquitination (PubMed: 28688853). In the absence of a transgenic K349N mutant mouse, or any confirmed synthetic agonists or antagonists, the authors then assessed seizure susceptibility in knock-out mice of either GPR37L1, GPR37 or both receptors. Interestingly, using the 6Hz-induced seizure model, the GPR37-/- mice appeared to have a more pronounced phenotype than the GPR37L1-/- mice, while double KO mice were extremely susceptible to seizures at all frequencies tested. GPR37 and double KO mice both displayed more spontaneous seizures, although curiously in the flurothyl-induced seizure model only GPR37L1-/- differed from wild type. Thus, conclusive links between GPR37L1 and a specific physiological or pathophysiological state remain to be provided and it seems in general that we are far from understanding the true biology and pharmacology of the receptor.

 

Posted in Hot Topics

Hot Topics: Somatic APP gene recombination in normal and Alzheimer’s disease neurons

A new facet of the human brain has been reported [1] involving a first example of somatic gene recombination in neurons, representing a normal neural mechanism whose disruption could underlie the most common (sporadic) forms of Alzheimer’s disease. Mosaic and somatic recombination of Amyloid Precursor Protein (APP) was identified in this well-known Alzheimer’s disease gene, where increased copies and mutations in rare families or Down syndrome are considered causal. Recombination generates thousands of previously unknown gene variants characterized as “genomic complementary DNAs” or “gencDNAs” that could show identical sequences to cDNAs copied from brain-specific spliced RNAs, as well as myriad truncated forms characterized by exonic deletions and “intraexonic junctions” to produce novel sequences that become “retro-inserted” into the genome of single neurons, with neurons showing from 0 to 13 copies. Recombination appeared to require gene transcription, reverse transcriptase activity and DNA strand breaks. Both forms and numbers of APP gencDNAs were altered and increased in sporadic Alzheimer’s disease. Recombination might normally provide a way to alter post-mitotic neuronal genomes to “record” preferred gene variants for later “playback” without a need for gene splicing, towards optimizing or fine-tuning gene expression, representing a form of memory. The involvement of reverse transcriptase activities implicate potential Alzheimer’s disease therapeutics using reverse transcriptase inhibitors, a possibility supported epidemiologically by relatively rare cases of Alzheimer’s disease in aged HIV patients. Recombination could generate new therapeutic targets. Other recombined genes and affected diseases are possible.

Comments by Jerold Chun, Sanford Burnham Prebys Medical Discovery Institute

(1) Lee MH et al. (2018). Somatic APP gene recombination in Alzheimer’s disease and normal neurons. Nature, doi: 10.1038/s41586-018-0718-6. [Epub ahead of print]. [PMID:30464338].

Posted in Hot Topics

Hot Topics: Cellular thermal shift assays to measure ligand-to-target engagement

The cellular thermal shift assay (CETSA) was introduced in July of 2013 as a means to investigate drug target engagement inside live cells and tissues (1). The underlying principle of CETSA is simple – it relies on the thermostability of each investigated protein and how this is altered by ligand binding. Experimentally these changes are assessed by applying a transient heat-pulse to the samples. This results in rapid rearrangements of established equilibria such that proteins denature and aggregate unless stabilised by ligand (1,2). The simplicity of CETSA has allowed prompt adoption in the literature but the importance of rapid changes in ligand binding is still not well recognised.

To explore these considerations we systematically varied both the heat-pulse temperature and duration in CETSA using p38a as our model system (3). Studies spanning seven different heating times and over a 13°C temperature interval show apparent potency changes over four orders of magnitude. These studies demonstrate how quantitative comparisons with functional cellular data require an understanding of the temperature dependence of the interactions under study. Our publications also discuss critical technology developments that allow shorter heating times.  These can now be down in the 10s of seconds range to minimize ligand rearrangements and heat-induced changes to cell permeability.

Comments by Dr. Thomas Lundbäck,  Associate Director, Mechanistic Biology & Profiling, Discovery Sciences, AstraZeneca R&D, Gothenburg,  Sweden,  thomas.lundback@astrazeneca.com

  1. Martinez Molina, D.; Jafari, R.; Ignatushchenko, M.; Seki, T.; Larsson, E. A.; Dan, C.; Sreekumar, L.; Cao, Y.; Nordlund, P., Monitoring drug target engagement in cells and tissues using the cellular thermal shift assay. Science 2013, 341 (6141), 84-7 (PMID 23828940).
  2.  Jafari, R.; Almqvist, H.; Axelsson, H.; Ignatushchenko, M.; Lundbäck, T.; Nordlund, P.; Martinez Molina, D., The cellular thermal shift assay for evaluating drug-target interactions in cells. Nat Protoc 2014, 9 (9), 2100-22 (PMID 25101824).
  3.  Seashore-Ludlow, B.; Axelsson, H.; Almqvist, H.; Dahlgren, B.; Jonsson, M.; Lundbäck, T., Quantitative Interpretation of Intracellular Drug Binding and Kinetics Using the Cellular Thermal Shift Assay. Biochemistry Nov 2018 (PMID 30418016).
Posted in Hot Topics

Immunopharmacology: challenges, opportunities and research tools. Edinburgh 1st-2nd October 2018.

At the beginning of October 2018 we held a meeting in Edinburgh focussed on the launch of the IUPHAR Guide to IMMUNOPHARMACOLOGY. Invited speakers contributed to productive discussions on the varying challenges and opportunities in immunopharmacology research.

Immunopharmacology: The New Frontier

There has been immense progress in immunopharmacology, but there are insufficient links between the immunological and pharmacological sciences. Thus, we have set up several initiatives.

  • IUPHAR set up an immunopharmacology section (Immuphar) chaired by Francesca Levi-Schaffer.

  • IUPHAR has signed an agreement with International Union of Immunological Sciences (IUIS, President Alberto Mantovani, who has also made major contributions to the field of check-point inhibitors) to ensure collaboration and cooperation.

  • IUPHAR, NC-IUPHAR (chair Steve Alexander), the University of Edinburgh (PI, Pr Jamie Davies) and the Edinburgh database group (IUPHAR/BPS Guide to Pharmacology; www.guidetopharmacology.org) have been able to set up a new database on the drug targets in immunopharmacology, financed by a major grant from the Wellcome Trust. This is www.guidetoimmunopharmacology.org, which has been recently launched and is freely available to all. The BPS finance two staff in the Edinburgh group for which IUPHAR is immensely grateful.

  • To celebrate this launch, a focussed immunopharmacology meeting was organised, which included the Anthony Harmar memorial lecture. This report provides a a summary of the meeting presentations, discussions and outcomes.

The launch of GtoImmuPdb has also been reported in a Nature Review Immunology Web Watch article: Harding SD et al. (2018). A new guide to immunopharmacology. Nat Rev Immunol, 18(12):729. [PMID:30327546]

Please read our detail meeting report which summarises the presentations, discussions and outcomes. Download the Meeting Report (PDF)

Access slidesets from the presentations below (or on our website):

Meeting Presentations

Anthony Harmer Memorial Lecture: Decision-making in lung immunity Prof. Tracy Hussell Download slides: pptx | pdf
The Guide to IMMUNOPHARMACOLOGY Dr. Elena Faccenda, Dr. Chris Southan and Dr. Simon Harding Download slides: pptx | pdf
Macrophage plasticity in immunopathology and cancer: from bench to bedside Prof. Alberto Mantovani Download slides: pptx | pdf
Targeting Pattern Recognition Receptor signalling for therapeutic approaches Prof. Clare Bryant slides not available
Discovering the right target in inflammatory disease Prof. Iain McInnes slides not available
Is Atherosclerosis a Systemic or a Vascular Immune Disease? Prof. Pasquale Maffia slides not available
Inhibit Activation or Activate Inhibition of Mast Cells and Eosinophils: Which Weapon is Better to Fight Allergic Diseases? Prof. Francesca Levi-Schaffer Download slides: pptx | pdf
IUPHAR: natural products and immunology Prof. Michael Spedding Download slides: pptx | pdf
Human type I interferon up regulation – worth targeting? Prof. Yanick Crow Download slides: pptx | pdf
A review on kinase targets in immunological indications Dr. Dorian Fabbro Download slides: pdf
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Posted in Events, Guide to Immunopharmacology

The Anthony Harmar Memorial Lecture 2018: Prof. Tracy Hussell

Prof. Tracy Hussell

Lung Disease: think about disease in a different way

Hussell Tracey (Altered)Tracy Hussell is Director, Manchester Collaborative Centre for Inflammation Research (MCCIR) and Professor of Inflammatory Disease, University of Manchester, Oxford Road, Manchester, M13 9PT.

To be healthy is an active process so health must be continually maintained. Is disease a process that can’t sense it is healthy again? We all have different set points. Sterile inflammation can be created by a single missing factor. Generally, while the lung epithelium is intact, then the tissue is non-activated. Epithelial damage is a critical driver, which may permanently change macrophages and the basal state in the lung. Airways macrophages are critical – when washed out, tissues change very quickly.

CD200R transmits negative signal to macrophages and ligand is on epithelium cells. Then antigen relieves signal. Axl continually recognises gas 6 on apoptosis so don’t activate with apoptosis.

Resolution of inflammation gives a different macrophage population – twice as many as before inflammation, which may survey the environment, resolving from a severe inflammatory event, to a new state. There are therapeutic ways of going back, but chronic obstructive pulmonary disease (COPD) and asthma have a permanently active state. MiRNAs are changed in resolved inflammation, therefore let-7b is increased, modifying Toll response changes. Patient becomes less responsive to bacteria – patients are retuned to not die when challenged, but have also lost miRNAs. The basement membrane is normally very thin but becomes permanently changed (Burgstaller et al., 2017, Eur Respir J. 2017 doi: 10.1183/13993003. PMID: 28679607). The tissue is changed, so not just immune effects.

Hyaluranon is a major constituent of the inflamed lung. Is the lung inflamed or is it just because there are a lot of retained immune cells? The latter. Why does matrix persist? Hyaluronic acid synthase is increased (clearance unchanged, hyaluronase unchanged). Matrix turnover means that there are more activated immune cells. The impact of viral infections on lung matrix affects its mechanical stability and structural support. The composition of matrix also indirectly controls inflammation by influencing cell adhesion, migration, survival, proliferation and differentiation. Hyaluronan is a significant component of the lung extracellular matrix and production and degradation must be carefully balanced. Tracy discovered an imbalance in hyaluronan production following resolution of a severe lung influenza virus infection, driven by hyaluronan synthase 2 from epithelial cells, endothelial cells and fibroblasts. Furthermore hyaluronan, due to elevated TNF, sequesters CD44-expressing macrophages. Intranasal hyaluronidase reduces lung hyaluronan restoring function. Hyaluronidase is already used clinically. Digestion of HA restores lung function. Hyaluronidase (available for clinical trials) appears an interesting option. (Hussell T et al., Eur Respir Rev., 2018, doi: 10.1183/16000617.0032-2018. PMID: 29950305).

In cancer the matrix is abnormal, and the immune system is paralysed. In many instances the matrix is stiff. It may be possible to think differently about reactivating the immune system here.

In severe cell death, macrophages clear apoptotic cells, TAMs recognise external phosphatidyl serine. Reverse signalling to STAT1 turning off inflammation, so while apoptosis is going on the tissue is vulnerable to bacterial attack. Axl receptor only in lung so this represents a unique opportunity for targeted therapy. Changed matrix, lost apoptosis, but poorly cleared even if immunity suppressed.

Eight days after influenza, basal cells proliferate requiring Axl receptor to show that damage has happened. Basal cell show hyperplasia if apoptosis continues – most lung disease has this as a hallmark. Axl antagonists allows faster repair. Type 1 interferons (IFNs): Neuropeptide receptors alter away homeostasis Gfra2 part of GDNF family massively increased on lung TAMs. Needs to co-stimulate with ret which is induced by type 1 IFNs. The virus may act via TLR7/8, in epithelium. MMP2 is specifically increased to degrade collagen type IV to degrade basement membrane. Two chemokines bind CXCR2. CCL18 macrophages that drive resolution, no homologue in rodents.

Is COPD then associated with inflamed tissues or trapped inflammatory cells? Possibly like tumours. Will check-point inhibitors also release antigen presenting cells? New therapeutic options await validation.

Slide Downloads: PPTX | PDF


tonyharmar

Anthony Harmar, Professor of Pharmacology in Edinburgh.

In addition to being a brilliant pharmacologist, Tony set up the IUPHAR Edinburgh database group which initiated IUPHAR-DB, which expanded into the IUPHAR/BPS Guide to Pharmacology database (www.guidetopharmacology.org).

 

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Posted in Events

Hot Topics: Piezo channels and mechano-transduction in sensory neurons

Piezo channels (Piezo1 and Piezo2) are excitatory ion channels which respond directly to a variety of forms of mechanical stimuli. Two recent papers describe some of the critical roles of Piezo channels in sensory neuron transduction (1, 2). In the first, Murthy et al. (1) demonstrate that Piezo2 mediates both inflammatory and nerve-injury sensitized mechanical pain in mice. In the second, Zeng et al. (2), show that both Piezo1 and Piezo2 are responsible for the baro-receptor reflex that regulates blood pressure and cardiac function.

For researchers interested in studying the roles of Piezo channels in mechano-transduction, useful pharmacological tools, at least for Piezo1, in the form of allosteric activators (3) and an inhibitor (4), have already emerged. Named Yoda1, Jedi1, Jedi2 and Dooku1, they are. May the force………

Comments by Alistair Mathie (@AlistairMathie) and Emma L. Veale (@Ve11Emma), The Medway School of Pharmacy

(1) Murthy SE et al. (2018). The mechanosensitive ion channel Piezo2 mediates sensitivity to mechanical pain in mice. Sci Transl Med. doi: 10.1126/scitranslmed.aat9897. [PMID: 30305457].
(2) Zeng WZ et al. (2018). PIEZOs mediate neuronal sensing of blood pressure and the baroreceptor reflex. Science doi: 10.1126/science.aau6324. [PMID: 30361375].
(3) Wang Y et al. (2018). A lever-like transduction pathway for long-distance chemical- and mechano-gating of the mechanosensitive Piezo1 channel. Nat Commun. 9(1):1300. doi: 10.1038/s41467-018-03570-9. [PMID: 29610524].
(4) Evans EL et al. (2018). Yoda1 analogue (Dooku1) which antagonizes Yoda1-evoked activation of Piezo1 and aortic relaxation. Br J Pharmacol. 175(10):1744-1759. doi: 10.1111/bph.14188. [PMID: 29498036].

Posted in Hot Topics

Hot Topics: Role of RTP type D on reward association with cocaine administration

The receptor tyrosine phosphatase (RTP) family is a relatively small group of cell-surface proteins with a simple intracellular enzymatic function in the dephosphorylation of phosphotyrosine proteins. There is less known about the endogenous extracellular ligands which regulate RTP activities in physiological conditions, although some RTPs are activated by cell-surface proteins thought to be expressed on neighbouring cells.

This report [1] from the National Institute on Drug Abuse in the USA focusses on the role of RTP type D on reward associated with cocaine administration. They identify that RTP type D heterozygous knockout mice exhibit lower reward responses to cocaine, and that a novel small molecule that appears to target the enzymatic function of RTP type D is able to reduce cocaine-induced place preference and self-administration in wild type, but not heterozygous knockout mice.

Comments by Steve Alexander (@mqzspa)

(1) Uhl GR et al. (2018). β-Subunit of the voltage-gated Ca2+ channel Cav1.2 drives signaling to the nucleus via H-Ras. Proc Natl Acad Sci USA, pii: 201720446. doi: 10.1073/pnas.1720446115. [Epub ahead of print] [PMID: 30348770]

Posted in Hot Topics

Hot topic: (but in this case, stale beer) the long overdue primary pharmacological characterisation of BIA 10-2747

The unfortunate French clinical trial disaster in which the FAAH inhibitor BIA 10-2747 (ligand ID 9001)  left one participant dead and several others with serious neurological adverse events, occurred back in January 2016.  However, the primary publication that describes the properties of this lead compound from its Portuguese originators BIAL has only now appeared in September of 2018 (1).  It is more typical for pharmaceutical medicinal chemistry teams to report their initial in vitro optimisation of a clinical candidate well in advance of Phase 1 (i.e. we might have expected to see this paper circa 2017).  While much has been written about 10-2747 in the last two years, very little peer-reviewed data has appeared (see this slide set and blog post).  In this context, the only BIAL journal paper so far on this compound is a disappointment.  The SAR of the series is only reported as % inhibition determinations rather than the more standardised and usefully comparative IC50s (this means we would actually not curate interaction data from such a paper but we have added the reference to the ligand entry). In addition, they do not address experimentally the irreversibility topic over which there has been some confusion. We would also quibble with the use of  “potent” in the title since an independent report of the initial IC50 binding  (i.e. without pre-incubation for inactivation) was only 7.5 uM (2).

Comments by Chris Southan (@cdsouthan)

  1. Kiss et al  (2018). Discovery of a Potent, Long-Acting, and CNS-Active Inhibitor (BIA 10-2474) of Fatty Acid Amide Hydrolase.  ChemMedChem, [Epub ahead of print]. [PMID:30113139].
  2. van Esbroeck 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 Topics: Cryo-EM structure of the active, Gs-protein complexed, human CGRP receptor

In this multi-author, multi-centre publication [1] lead by Denise Wootten and Patrick Sexton from the Monash Institute of Pharmacological Sciences, there is reported a 3.3 Angstrom structure of one of the more unusual G protein-coupled receptors. The CGRP receptor is a target for the recently FDA-approved monoclonal antibody erenumab targetting migraine. The receptor is unusual because of its modulation by a trio of accessory proteins exemplified here by RAMP1, which influence both the pharmacological and signalling profiles of the GPCR. Recent structural approaches to studies of GPCR have moved into investigations where a G protein is included. The Liang paper has a Gs heterotrimer attached, and, in addition, has the natural ligand, CGRP bound to the receptor. The report on this six molecule complex thus allows a major advance into the interaction between a GPCR, its endogenous agonist, the requisite G protein AND a modulatory protein.

Comments by Steve Alexander (@mqzspa)

(1) Liang YL et al. (2018). Cryo-EM structure of the active, Gs-protein complexed, human CGRP receptor. Nature, doi: 10.1038/s41586-018-0535-y. [Epub ahead of print]. [PMID: 30175587]

Posted in Hot Topics

Hot Topics: β-Subunit of the voltage-gated Ca2+ channel Cav1.2 drives signaling to the nucleus via H-Ras

This paper [1] extends previous studies demonstrating a key role of voltage-gated L-type Ca2+ channels in the modulation of activity-dependent gene transcription. Earlier work in cultured neurons had already shown that L-type channel activity is required to activate gene expression through different signaling pathways, including the Ras/MAPK pathway [2-4]. This is confirmed in the present study (primarily in experiments with HEK-293 cells) but there are important differences in the way nuclear signaling gets activated. In contrast to previous models [2], it is shown that the Ras/MAPK pathway is turned on by a direct physical interaction of the L-type channel (only Cav1.2 was studied) with Ras through the channel’s beta-subunit. Moreover, this interaction requires binding of extracellular Ca2+ to the pore-forming alpha1-subunit but no Ca2+ influx through the channel. Also no binding of calmodulin to the channel is required. This strongly suggests a direct conformational coupling of Cav1.2 to Ras activation and adds to other evidence of conformational coupling of L-type Ca2+ channels [5-6]. However, further experiments are required to demonstrate that this mechanism also exists in neurons.

Comments by Jörg Striessnig, University of Innsbruck

(1) Servili E et al. (2018). β-Subunit of the voltage-gated Ca2+ channel Cav1.2 drives signaling to the nucleus via H-Ras. Proc Natl Acad Sci USA, 115(37):E8624-E8633. doi: 10.1073/pnas.1805380115. [PMID: 30150369]

(2) Dolmetsch RE et al. (2001). Signaling to the nucleus by an L-type calcium channel-calmodulin complex through the MAP kinase pathway. Science, 294(5541):333-9. [PMID: 11598293]

(3) Wu GY et al. (2018). Activity-dependent CREB phosphorylation: convergence of a fast, sensitive calmodulin kinase pathway and a slow, less sensitive mitogen-activated protein kinase pathway. Cold Spring Harbor Perspect Biol, 98(5):2808-13. [PMID: 11226322]

(4) Hagenston AM & Bading H (2018). Calcium signaling in synapse-to-nucleus communication. Mol Pharmacol, 3(11):a004564. doi: 10.1101/cshperspect.a004564. [Epub ahead of print]. [PMID: 30021858]

(5) Krey JF et al. (2013). Timothy syndrome is associated with activity-dependent dendritic retraction in rodent and human neurons. Nat Neurosci 16:201-9. [PMID: 23313911]

(6) Li B et al. (2016). Sequential ionic and conformational signaling by calcium channels drives neuronal gene expression. Science 351:863-7. [PMID: 26912895]

Posted in Hot Topics

Database release 2018.4

Our fourth database release of the year, 2018.4, is now available (n.b. the PubChem update statistics and link sets will be posted in a couple of weeks).   This update contains the following new features and content changes:

Content Updates

GPCRs:

NHRs:

Ion Channels:

Enzymes:

Catalytic Receptors:

Transporters:

Other Proteins:

Guide to IMMUNOPHARMACOLOGY

Recently added immunology/inflammation targets with novel pharmacological modulators include:

  • Fc fragment of IgG receptor IIIa (FCGR3A)
  • RAS guanyl releasing protein 1 (RASGRP1)
  • transglutaminase 2 (TGM2)
  • sialic acid binding Ig like lectin 8 (SIGLEC8)
  • CD37
  • signal transducer and activator of transcription 3 (STAT3)
  • signal transducer and activator of transcription 6 (STAT6)

In response to publication of ‘Ion channelopathies of the immune system’ (Vaeth and Feske, 2018; PMID:29635109), we have updated the immune cell type and GtoImmuPdb curation for the ion channels and transporters that the article and the ‘Guide’ have in common.

Guide to Malaria PHARAMCOLOGY

The Antimalarial targets family and the Antimalarial ligands family have been updated, giving a total of 9 P. falciparum (3D7) targets and 41 ligands tagged as antimalarial in the database.

Peptide Curation

Over the summer a MSc student, Lin Yakai, worked on a project to investigate GtoPdb peptide ligand structures and develop ways of converting these into standardised specifications (SMILES, InChi, HELM etc.). Using SugarNSplice software (SnS) we have been able to convert some peptides to SMILES format and submit these to PubChem – creating new CIDs from our SID structures. At this stage, we have converted ~400 peptides and on this release have curated the SMILES of around 40 peptides back into GtoPdb.  One of these includes the venerable “Entothelin-1” (Ligand ID 989)  that now specifies not only peptide sequence but also points to the CID.  There is a preliminary slide set on this topic but we will publish a detailed blog post in due course.

Other Announcements

  • We have now broken the 10,000 barrier for ligand IDs on the development server. However, it will still be some time before our PubChem SIDs hit this number since there have been a number of internal deprecations of superseded entries.
  • Ligand 10083 represents a new precedent in being curated from ChemRxiv,  The Preprint Server for Chemistry https://chemrxiv.org/ (where we have two papers that were subsequently published by ACS Omega). This gives us the advantage of being able to pick up key bioactive chemistry from open manuscripts many months before the papers are accepted and indexed in PubMed (using a DOI to enter the reference in our system).  This case was a cell-penetrant KDM5B covalent inhibitor with therapeutic relevance to immunopharmacology and cancer. The authors are from the Structural Genomics Consortium (SGC)
  • Nearly three years after the clinical trial fatality in January 2016  the primary pharmacological characterization paper for BIA-10-2747 has finally appeared (see Hot Topic report)

New website features

Extension to web-services

With the continuing development of the GtoImmuPdb we are pleased to announce that target and ligands of immunological relevance, as well as the new immunopharmacology data types can now be retrieved via our web services.

For example, targets tagged in the database as relevant to immunopharmacology can be retrieved form the following URL:

http://www.guidetopharmacology.org/services/targets?immuno=true

The API has also been extended to return immuno processes and cell types for specific targets. Here is an example retrieving cell types associated with CD86 (target ID 2735):

http://www.guidetopharmacology.org/services/targets/2745/immunoCelltypes

We have also introduced disease data to the web services, so summarised data for any disease in GtoPdb can be retrieved, here using Psoriasis (disease ID 801) as an example:

http://www.guidetopharmacology.org/services/diseases/801

Downloads

We have extended the file formats to include both csv and tsv formats on our downloads page.

Stats

We have extended our about page to include a few extra statistics on ligand counts with clinical use summaries and interactions.

Posted in Database updates, Guide to Immunopharmacology, Guide to Malaria Pharmacology

July 2018 News, Updates and Hot Topics

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July 2018

News, Updates and Hot Topics


Database release 2018.3:

Our third database release of the year, 2018.3, is now available. This update contains the following new features and content changes:

  • Updates across several target classes.
  • The existing Antimalarial targets family has been updated with 5 new P. falciparum (3D7) targets:
    • PfATP4 (Plasmodium falciparum ATPase4)
    • PfDHFR-TS (Plasmodium falciparum bifunctional dihydrofolate reductase-thymidylate synthase)
    • PfDXR (Plasmodium falciparum 1-deoxy-D-xylulose 5-phosphate reductoisomerase)
    • PfeEF2 (Plasmodium falciparum elongation factor 2)
    • PfPI4K (Plasmodium falciparum phosphatidylinositol 4-kinase)
  • A new Antimalarial ligands family has been created and contains 30 ligands all tagged as an antimalarial in the database. Of these 30, 20 are new ligands curated for this release.
  • GtoImmuPdb now public

The IUPHAR Guide to IMMUNOPHARMACOLOGY is now at its first public release and is no longer considered a beta version. We will continue to develop the portal and specific immuno interfaces as well as continuing curation towards its official launch in October 2018 (see blog post here


Recent Papers from the Team

We are pleased to point to three.  Two were close in succession, both initially as pre-prints in ChemRxiv and later accepted in ACS Omega.  Both are Open Acess and will be full-text indexed in  PubMed Central and European PubMed Central in due course.

“SynPharm: A Guide to PHARMACOLOGY Database Tool for Designing Drug Control into Engineered Proteins” Ireland et.al.DOI/10.1021/acsomega.8b00659

“Challenges of Connecting Chemistry to Pharmacology: Perspectives from Curating the IUPHAR/BPS Guide to PHARMACOLOGY”  Southan et. al. DOI/10.1021/acsomega.8b00884.

The third has been on the Current Protocols in Bioinformatics website for some months but was only just recently indexed in PubMed as “Accessing Expert-Curated Pharmacological Data in the IUPHAR/BPS Guide to PHARMACOLOGY”  Sharman et. al. PMID 30040201.


Hot Topics

The Guide to PHARMACOLOGY hot topics are new and significant pharmacology, drug discovery and key human genomics papers. These are often communicated to us through our expert subcommittee members. All hot topic papers are listed on the hot topics page on the website (http://www.guidetopharmacology.org/hotTopics.jsp). For a selection, we commission concise commentaries from our expert contacts and these are posted onto our blog (https://blog.guidetopharmacology.org/category/hot-topics/).

Here we summarise the latest hot topic commentaries:

New pharmacological tools reiterate lack of direct connection between Angiotensin 1–7 and the MAS1 GPCR

Comments by Sadashiva S. Karnik (karnicks@ccf.org.uk) and Kalyan Tirupula

A new type of deorphanization conundrum confronted in pairing the GPCR, MAS1 with the hormonal peptide angiotensin 1–7 (Ang1-7) was emphasised in recent IUPHAR reviews… Read more.

Structural details for coupling of the agonist-occupied µ opioid receptor (amongst others) to the Gi protein

Comments by Eamonn Kelly (E.Kelly@bristol.ac.uk) and Katy Sutcliffe

Every few years in the field of receptor pharmacology, a technological advance occurs that drives the field forward in terms of insight and understanding. Over the past couple of years, the cryo-EM technique (the development of which won the 2017 Nobel Prize in Chemistry for Dubochet, Frank, and Henderson) for resolving protein structures… Read more.

Systems Medicine, Disease Maps and the future of Systems Biology

Comments by Steven Watterson (@systemsbiology), University of Ulster

What will Systems Biology look like in the future? Up to now, it has focussed on the development of standards, software tools and databases that enabled us to study the dynamics of physiological function mechanistically. Read more.

Structure of the adenosine-bound human adenosine A1 receptor–Gi complex

Comments by Steve Alexander (@mqzspa)

The A1 adenosine receptor is, for most people, a molecular target they can become conscious of when they block it, which happens frequently. Rapid consumption of higher doses of caffeine, in products like Italian espresso or Turkish coffee, provokes a … Read more.

Commentary on the distinction between Cannabis and cannabinoids

Commentary by Steve Alexander (@mqzspa) & Anthony Davenport

The Cannabis plant is a natural product from which more than 100 apparently unique metabolites (cannabinoids) have been identified. Many of these have been found in human plasma following consumption of Cannabis preparations. Read more.

(Update): From double to triple whammy for BACE1 inhibitors

Comments by Chris Southan (@cdsouthan)

19 June 2018 update. Announced only about a week after the events described below,  yet a third clinical candidate, lanabecestat  (AZD-3293, LY3314814) has also bitten the dust (4).  The two PhIII trials were stopped because they were deemed unlikely to meet their primary endpoints. Read more.

Cryo-EM structure of the adenosine A2A receptor coupled to an engineered heterotrimeric G protein

Comments by Steve Alexander (@mqzspa)

The A2A adenosine receptor is densely expressed in dopamine-rich areas of the brain and in the vasculature. It is the target of an adjunct medication for Parkinson’s Disease, istradefylline in Japan, an A2A receptor antagonist. Read more.

Conformational plasticity in the selectivity filter of the TRPV2 ion channel

Comments by Steve Alexander (@mqzspa)

The TRPV2 ion channel is the less well-characterised relative of the TRPV1 or vanilloid receptor that is activated by capsaicin. TRPV2 channels have many similarities to the TRPV1 channels, in that they are homotetrameric and respond to some of the same ligands (natural products such as cannabinoids) as well as being triggered at elevated temperatures. Read more.

3D structure of the P2X3 receptor bound to a negative allosteric modifier, identifies a binding site that is a target for development of novel therapeutic agents

Comments by Dr. Charles Kennedy, University of Strathclyde

Negative allosteric modulators (NAMs) are of great interest in drug development because they offer improved scope for the production of receptor antagonists with enhanced subtype-selectivity. Indeed, many NAMs are already on the market or undergoing clinical trials. NAMs act byRead more.

3D structures of the closed acid-sensing ion channel (ASIC) shed light on the activation mechanism of these neuronal ion channels

Comments by Stephen Kellenberger, Université de Lausanne, Switzerland

ASICs are potential drug targets of interest. Their activation mechanism has however remained elusive. ASICs are neuronal, proton-gated, sodium-permeable channels that are expressed in the central and peripheral nervous system of vertebrates. Read more.

Engineered mini G proteins provide a useful tool for studying the activation of GPCRs in living cells

Comments by Shane C. Wright and Gunnar Schulte, Karolinska Institute

In order to stabilize the GPCR-G protein complex, an agonist must be bound to the receptor and the alpha subunit of the heterotrimer must be in a nucleotide-free state. Read more.

Unexplored therapeutic opportunities in the human genome

Comments by Chris Southan, IUPHAR/BPS Guide to PHARMACOLOGY, @cdsouthan

Contemporary drug discovery is dominated by two related  themes. The first of these is target validation upon which the sustainability of pharmaceutical R&D (in both the commercial and academic sectors) crucially depends. Read more.


Publications

Ireland SM, Southan C, Dominguez-Monedero, Harding SD, Sharman JL, Davies JD. (2018). SynPharm: A Guide to PHARMACOLOGY Database Tool for Designing Drug Control into Engineered Proteins. ACS Omega, 3 (7), pp 7993–8002, doi: 10.1021/acsomega.8b00659.

Southan C, Sharman JL, Faccenda E, Pawson AJ, Harding SD, Davies JA. (2018). Challenges of Connecting Chemistry to Pharmacology: Perspectives from Curating the IUPHAR/BPS Guide to PHARMACOLOGY. ACS Omega, 3 (7), pp 8408–8420, doi: 10.1021/acsomega.8b00884.

Davenport AP, Kuc RE, Southan C, Maguire JJ. (2018). New drugs and emerging therapeutic targets in the endothelin signaling pathway and prospects for personalized precision medicine. Physiol. Res., (Suppl. 1): S37-S54, doi: 10.1021/acsomega.8b00659. [PMID:29947527]

 

Reviews

Caraci F, Calabrese F, Molteni R, Bartova L, Dold M, Leggio GM, Fabbri C, Mendlewicz J, Racagni G, Kasper S, Riva MA, Drago F. (2018) International Union of Basic and Clinical Pharmacology CIV: The Neurobiology of Treatment-resistant Depression: From Antidepressant Classifications to Novel Pharmacological Targets. Pharmacol Rev. 70: 475-504. [PMID:29884653]


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Posted in Hot Topics

Hot Topics: Direct activation of neuronal KV7 channels by GABA and gabapentin – a novel mechanism for reducing neuronal excitability

The potassium channels KV7.2-KV7.5 (KCNQ2-5; GtoPdb target IDs 561-564) regulate neuronal excitability in the mammalian nervous system. The best characterised neuronal KV7 channels give rise to the M current (1) and are mediated predominantly by hetero-tetramers of KV7.2 and KV7.3 subunits (2). Established anticonvulsant agents such as retigabine are known to dampen neuronal excitability by activating neuronal KV7 channels. A tryptophan in the S5 transmembrane region of neuronal KV7 channels is essential for retigabine sensitivity with KV7.3 channels particularly sensitive. Importantly, this residue is not present in the cardiac KV7.1 (KCNQ1) channel, reducing the potential for cardiac side effects.

Now, a pair of studies (3, 4) has shown that this same region of the channel also contributes to a high affinity binding site for GABA and related metabolites (3). GABA activates channels comprised of KV7.3 and KV7.5, including heteromeric KV7.2/7.3 channels, with high potency but low efficacy. GABA does not, however, activate KV7.2 or KV7.4 homomeric channels or cardiac KV7.1 channels. The synthetic anticonvulsant and antinociceptive agent gabapentin activates the same KV7 subunits, although pregabalin does not, despite the overlapping therapeutic efficacy of these two compounds (4).

These results are of considerable pharmacological interest. They suggest a novel mechanism for GABA in regulating neuronal excitability through activation of KV7 channels. They indicate that both GABA and gabapentin will interfere with the action of therapeutically useful activators of KV7 channels such as retigabine. However, perhaps of most value given the relative difficulty in identifying potassium channel openers compared to blockers (5), this work identifies a new chemical class of potential therapeutic activators of neuronal KV7 channels that target an identified region of these channels.

Comments by Emma L. Veale (@Ve11Emma) and Alistair Mathie (@AlistairMathie)

(1) Brown, D.A. & Adams P.R. (1980). Muscarinic suppression of a novel voltage-sensitive K+ current in a vertebrate neurone. Nature, 283. 673-676. [PMID: 6965523].

(2) Wang H.S. et al. (1998). KCNQ2 and KCNQ3 potassium channel subunits: molecular correlates of the M-channel. Science, 282. 1890-1893. [PMID: 9836639].

(3) Manville R.W. et al. (2018). Direct neurotransmitter activation of voltage-gated potassium channels. Nature Commun., 9(1). 1847. [PMID: 29748663].

(4) Manville R.W. & Abbott G. (2018). Gabapentin is a potent activator of KCNQ3 and KCNQ5 potassium channels. Mol. Pharmacol., doi: 10.1124/mol.118.112953. [PMID: 30021858].

(5) Liin, S.I. et al. (2018). Biaryl sulfonamide motifs up- or down-regulate ion channel activity by activating voltage sensors. J. Gen. Physiol., doi: 10.1085/jgp.201711942. [PMID: 30002162].

Posted in Hot Topics