The second version of the Probes & Drugs portal this year - 02.2023 - was released with updates of all major data sources (ChEMBL, Guide to Pharmacology, BindingDB, Reactome and others), probe control compound set, highlighted selectivity + selectivity filters and target family distribution visualization.
Apart from the updated ones, we added several new compound sets to the drug sets section. First of all, we added one more drug compound set from ChEMBL (ChEMBL Drugs), where apart from the approved drugs, there are all compounds with assigned non-empty max phase attribute (i.e., compounds that have ever entered the drug discovery/approval pipeline). Upon that, we added two more subsets from the DrugBank and DrugMap databases with only approved drugs. This way, it is fairly easy to compare compounds labelled as approved from different sources. However, it is not a very optimistic comparison, concerning the overall consistency of the data in that area.
From ver. 02.2023, we also added one special probe compound set not containing chemical probes but their control compounds. It is formed simply by all defined control compounds that we have in our database. You can filter these compounds through the compound set filter (Chemical probe controls) or through the probe control tag filter. Currently, it contains 211 standardized compounds.
From the current version, we also decided to highlight targets for which the compounds have the highest selectivity - separately, based on biochemical and cell-based assays. It is represented by the fold change between the first and second most potent target, e.g., if, on the negative logarithmic scale, the first potency value is 7 (100 nM) and the second 5 (10 µM), the fold change is 100x (the compound is 100x more selective on the first target). For more details, you can go to the FAQ section. The new selectivity measure can be also used to filter and order the compounds. For example, here, you can filter all BRD4 ligands with the assigned value from the most selective one.
As the last functional improvement, we added one more visualization among the already existing ones and that is the target family distribution bar chart for currently selected compounds. As a part of the visualization, you can set the potency threshold for a compound-target association for which the target is added to the statistics (e.g., at least 100 nM potency on the target) and also whether you want to add targets with the direct annotation, however, without the exact assigned bioactivity value. Since many of these associations are probably valid and important (mostly primary targets for drugs/chemical probes, or ligands with defined MOA on the target), we let the user decide whether to take them into account or not. Below, you can see the target distribution for our High-quality chemical probes set, currently accounting for 757 compounds.
Between the previous and current versions, we’ve also made a lot of changes in the user interface (front-end generally). We hope that they will contribute to a smoother and uncluttered user experience.
As always, you can download all data used on the portal as a PostgreSQL database dump or the SQLite database in the Download section.
We hope you'll find the new data/features useful and if you have any questions or suggestions or if you stumble upon a bug, don't hesitate to contact us through our contact form.