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.

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

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