An Integrative Drug Repurposing Pipeline Using KNIME and Programmatic Data Access: A Case Study on COVID-19 Data

Biomedical information mining is increasingly recognized as a promising technique to accelerate drug discovery and development. Especially, integrative approaches which mine data from several (open) data sources have become more attractive with the increasing possibilities to programmatically access data through Application Programming Interfaces. The use of open data in conjunction with free, platform-independent analytic tools provides the additional advantage
of flexibility, re-usability, and transparency. Here, we present a strategy for performing in silico drug repurposing with the analytics platform KNIME, using data for 38 suggested COVID-19 drug targets as a timely use case. The workflow includes a targeted download of data through web services, data curation (including chemical structure standardization), detection of enriched structural patterns, as well as substructure searches in DrugBank and a recently deposited dataset of antiviral drugs provided by Chemical Abstracts Service. Developed workflows, tutorials with detailed step-by-step instructions, and the information gained by the analysis of COVID-19 data are made freely available to the scientific community. The provided framework can be reused by researchers for other in silico drug repurposing projects, and it should serve as a valuable teaching resource for conveying integrative data mining strategies.