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.
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.
- The Antimalarial targets family and the Antimalarial ligands family have been updated, giving a total of 25 P. falciparum (3D7) targets and 65 ligands tagged as antimalarial in the database.
- Continued development of the ligand page to include a table containing Target Candidate Profile (TCP) information.
- Introduced a new TCP tab on the GtoMPdb ligand list page.
- Extended the GtoMPdb search to cover TCP information.
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.
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
- Updated the refined chemical search to used Chemicalize Marvin JS
- Updates to the Guide to Immunopharmacology and Guide to Malaria Pharamcology home pages
- Additional outlinks to Immunopaedia from immuno-relevant ligands