Database release 2018.4

Posted on September 19, 2018 by guidetopharmacology — Leave a comment

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:

SLC6 neurotransmitter transporter family

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still be some time before our PubChem SIDs hit this number since there have been a number of internal deprecations of superseded entries.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