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

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

%d bloggers like this: