Illuminating the druggable genome through patent bioactivity data

The patent literature is a potentially valuable source of bioactivity data. In this article we describe a process to prioritise 3.7 million life science relevant patents obtained from the SureChEMBL database (https://www.surechembl.org/), according to how likely they were to contain bioactivity data for potent small molecules on less-studied targets, based on the classification developed by the Illuminating the Druggable Genome (IDG) project. The overall goal was to select a smaller number of patents that could be manually curated and incorporated into the ChEMBL database. Using relatively simple annotation and filtering pipelines, we have been able to identify a substantial number of patents containing quantitative bioactivity data for understudied targets that had not previously been reported in the peer-reviewed medicinal chemistry literature. We quantify the added value of such methods in terms of the numbers of targets that are so identified, and provide some specific illustrative examples. Our work underlines the potential value in searching the patent corpus in addition to the more traditional peer-reviewed literature. The small molecules found in these patents, together with their measured activity against the targets, are now accessible via the ChEMBL database.

An open source chemical structure curation pipeline using RDKit

BACKGROUND

The ChEMBL database is one of a number of public databases that contain bioactivity data on small molecule compounds curated from diverse sources. Incoming compounds are typically not standardised according to consistent rules. In order to maintain the quality of the final database and to easily compare and integrate data on the same compound from different sources it is necessary for the chemical structures in the database to be appropriately standardised.

RESULTS

A chemical curation pipeline has been developed using the open source toolkit RDKit. It comprises three components: a Checker to test the validity of chemical structures and flag any serious errors; a Standardizer which formats compounds according to defined rules and conventions and a GetParent component that removes any salts and solvents from the compound to create its parent. This pipeline has been applied to the latest version of the ChEMBL database as well as uncurated datasets from other sources to test the robustness of the process and to identify common issues in database molecular structures.

CONCLUSION

All the components of the structure pipeline have been made freely available for other researchers to use and adapt for their own use. The code is available in a GitHub repository and it can also be accessed via the ChEMBL Beaker webservices. It has been used successfully to standardise the nearly 2 million compounds in the ChEMBL database and the compound validity checker has been used to identify compounds with the most serious issues so that they can be prioritised for manual curation.

The Global Phosphorylation Landscape of SARS-CoV-2 Infection

The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected millions and killed hundreds of thousands of people worldwide, highlighting an urgent need to develop antiviral therapies. Here we present a quantitative mass spectrometry-based phosphoproteomics survey of SARS-CoV-2 infection in Vero E6 cells, revealing dramatic rewiring of phosphorylation on host and viral proteins. SARS-CoV-2 infection promoted casein kinase II (CK2) and p38 MAPK activation, production of diverse cytokines, and shutdown of mitotic kinases, resulting in cell cycle arrest. Infection also stimulated a marked induction of CK2-containing filopodial protrusions possessing budding viral particles. Eighty-seven drugs and compounds were identified by mapping global phosphorylation profiles to dysregulated kinases and pathways. We found pharmacologic inhibition of the p38, CK2, CDK, AXL, and PIKFYVE kinases to possess antiviral efficacy, representing potential COVID-19 therapies.

ChEMBL: towards direct deposition of bioassay data

ChEMBL is a large, open-access bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012, 2014 and 2017 Nucleic Acids Research Database Issues. In the last two years, several important improvements have been made to the database and are described here. These include more robust capture and representation of assay details; a new data deposition system, allowing updating of data sets and deposition of supplementary data; and a completely redesigned web interface, with enhanced search and filtering capabilities.

Reply to "Missed opportunities in large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery"

In response to Krstajic's letter to the editor concerning our published paper, we here take the opportunity to reply, to re-iterate that no errors in our work were identified, to provide further details, and to re-emphasise the outputs of our study. Moreover, we highlight that all of the data are freely available for the wider scientific community (including the aforementioned correspondent) to undertake follow-on studies and comparisons.

[Effect of the prolonged use of intrauterine devices and oral contraceptive on iron nutrition]

The aim of this work was to study the effect of prolonged use of intrauterine devices (IUD) and oral contraceptives (OCO) normally prescribed at outpatient clinics of the Health Service on iron nutrition. Two hundred twenty three healthy women, aged 20 to 39 years were studied. Of these, 100 were using IUD and 97 OCO for three to five years and 26 were not using any pharmacological or mechanical contraceptive method (control group). Serum ferritin was significantly higher in the OCO group compared to IUD and control groups (58.9 +/- 2.2; 26.2 +/- 2.1 and 21.1 +/- 2.4 ng/ml respectively). There was a positive correlation between serum ferritin and hemoglobin in IUD and control groups and between ferritin and transferrin saturation in the OCO and control groups. The frequency of storage iron depletion (defined as a serum ferritin < 12 ng/ml) was 6.3, 0 and 25% in the IUD, OCO and control groups respectively. The numbers for iron-deficient erythropoiesis (defined as a transferrin saturation < 15%) were 7, 3 and 4% and for iron deficiency anemia, 6.5, 0 and 8%. It is concluded that the chronic use of IUDs leads to iron depletion and that measures to improve iron nutrition among women using them should be adopted.