Update on Guide to Pharmacology during the ELIXIR UK All Hands Meeting in Dundee in Dec 2019

1. IUPHAR/BPS Guide to PHARMACOLOGY
Simon Harding & Chris Southan
University of Edinburgh, UK
www.guidetopharmacology.org
10 DECEMBER
ELIXIR-UK ALL-HANDS, DUNDEE, 2019
1WWW.GUIDETOPHARMACOLOGY.ORG

2. www.guidetoimmunopharmacology.org
A knowledge-base that connects immunology with pharmacology
Targets and ligands linked to immunological processes, cell type and disease
IUPHAR/BPS Guide to Pharmacology
www.guidetopharmacology.org
Open, expert-driven database of pharmacological targets and the substances that act on them: ~1,700 human drug
targets, ~9,700 ligands, including ~1,300 approved drugs
Updated quarterly, accessible via website, download and web service API
Includes Bioschemas mark-up for ligands (Molecular Entities)
IUPHAR/MMV Guide to Malaria Pharmacology
Curation of antimalarial compounds and Plasmodium molecular
targets for approved drugs: www.guidetomalariapharmacology.org

3. WWW.GUIDETOPHARMACOLOGY.ORG 3
Database report
https://www.guidetopharmacology.org/pdfs/GtoPdb_Database_Report_April_2019.pdf

4. Guide to MALARIA PHARMACOLOGY
4
Aim to curate antimalarial compounds and
Plasmodium molecular targets for approved
drugs
Developed with funding and scientific
support from the Medicines for Malaria
Venture (MMV)
www.guidetomalariapharmacology.org
WWW.GUIDETOPHARMACOLOGY.ORG

5. Guide to MALARIA PHARMACOLOGY
• Our last database release (2019.4)
contains:
• 72 ligands tagged as in GtoMPdb
• 30 targets tagged as in GtoMPdb
• Curated ligands include
• antimalarial leads
• drugs in preclinical and clinical
development
• approved medicines
ble 4. GtoMPdb data counts for targets, ligands and interactions (database release 2019.4).
Guide to Malaria Pharmacology Content Breakdown
Targets 30
Ligands 72
Ligands (Approved drugs) 19
Ligands (WHO essential lists) 17
Targets with quantitative ligand interactions 20
Targets with approved drug interactions 4
Ligands with interactions 67
Ligands with interaction to known targets 38
Ligands with interaction to unknown targets 34
Ligands with quantitative interactions (approved drugs) 65 (18)
Ligands with clinical use summaries (approved drugs) 39 (19)

6. WWW.GUIDETOPHARMACOLOGY.ORG 6
BioSchemas
<!-- BioSchemas Mark-Up For Ligands -->
<script type="application/ld+json">
{
"@context": "http://schema.org",
"@id": "https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=5535",
"@type": "MolecularEntity",
"@type": "DataRecord",
"dct:conformsTo": "https://bioschemas.org/types/MolecularEntity/",
"includedInDataset" : {
"@type": "Dataset",
"@id": "https://www.guidetopharmacology.org/index.jsp#dataset"
},
"mainEntity": {
"@id": "https://identifiers.org/iuphar.ligand:5535",
"name": "chloroquine",
"alternateName": [
"Aralen&reg;","chloraquine","Malaquin&reg;"
],
"description": "Chloroquine is a 4-aminoquinoline and used primarily as an antimalarial drug. <br>The approved drug is a racemic mixture and we show the chemical structure without stereochemistry
to represent the mixture. The non-isomeric structure is also represented in the PubChem, ChEMBL and ChEBI entries listed in the links table below, while the two enantiomers forming the racemate are
represented by <a href="https://pubchem.ncbi.nlm.nih.gov/compound/444810">PubChem CID 444810</a> and <a href="https://pubchem.ncbi.nlm.nih.gov/compound/639540">PubChem CID
639540</a>.<br>Marketed formulations may contain chloroquine phosphate (<a href="https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=64927&loc=ec_rcs" target="_blank">PubChem CID
64927</a>).<br><br>The <b>Malaria</b> tab on this ligand page provides additional curator comments of relevance to the Guide to MALARIA PHARMACOLOGY.",
"identifier": "5535",
"inChI": "InChI=1S/C18H26ClN3/c1-4-22(5-2)12-6-7-14(3)21-17-10-11-20-18-13-15(19)8-9-16(17)18/h8-11,13-14H,4-7,12H2,1-3H3,(H,20,21)",
"inChIKey": "WHTVZRBIWZFKQO-UHFFFAOYSA-N",
"iupacName": "N'-(7-chloroquinolin-4-yl)-N,N-diethylpentane-1,4-diamine",
"molecularWeight": 319.18,
"smiles": "CCN(CCCC(Nc1ccnc2c1ccc(c2)Cl)C)CC",
"url": https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=5535
}
}
</script>
Addingschema.org semantic mark-up to GtoPdb
Our current focus is on implementing mark-up on all
ligand summary pages but also beginning to engage
on including mark-up for proteins.
Thanks to Alasdair Gray!
(https://bioschemas.org/specifications/drafts/Molec
ularEntity).

7. 7
Publications
WWW.GUIDETOPHARMACOLOGY.ORG

8. 8
Publications
WWW.GUIDETOPHARMACOLOGY.ORG
Immunology paper submitted!
Connecting pharmacology and
immunology
Update on GtoPdb published in NAR
last month and…

9. Interoperable entities between ELIXIR resources
9WWW.GUIDETOPHARMACOLOGY.ORG
Document > assay > result > compound > protein target
We can compare D-A-R-C-P between GtoPdb and ChEMBL

10. Document X-refs in UniProt
10WWW.GUIDETOPHARMACOLOGY.ORG

11. UniProt x-ref protein counts
11WWW.GUIDETOPHARMACOLOGY.ORG
17695389
ChEMBL 7158 GtoPdb 2013
244

12. PubChem
Compound
(CIDs)
12WWW.GUIDETOPHARMACOLOGY.ORG

13. Substance (SID) tagging in PubChem
13WWW.GUIDETOPHARMACOLOGY.ORG

14. PubChem CID counts
14WWW.GUIDETOPHARMACOLOGY.ORG
53721866798
ChEMBL 1872170 GtoPdb 7662
2290

15. Further info
15WWW.GUIDETOPHARMACOLOGY.ORG
https://cdsouthan.blogspot.com/2018/08/an-initial-look-at-elixir-chemistry.html
https://europepmc.org/article/PPR/PPR102764