TY - JOUR

T1 - Exploration of databases and methods supporting drug repurposing

T2 - A comprehensive survey

AU - Tanoli, Ziaurrehman

AU - Seemab, Umair

AU - Scherer, Andreas

AU - Wennerberg, Krister

AU - Tang, Jing

AU - Vähä-Koskela, Markus

N1 - Funding Information: The work was financially supported by European Research Council (ERC) starting grant agreement DrugComb (No. 716063), Academy of Finland grant (No. 317680), European Commission H2020 EOSC-life (No. 824087) and Medicinska Underst?dsf?reningen Liv och H?lsa. Publisher Copyright: © 2020 The Author(s) 2020. Published by Oxford University Press. All rights reserved.

PY - 2021

Y1 - 2021

N2 - Drug development involves a deep understanding of the mechanisms of action and possible side effects of each drug, and sometimes results in the identification of new and unexpected uses for drugs, termed as drug repurposing. Both in case of serendipitous observations and systematic mechanistic explorations, confirmation of new indications for a drug requires hypothesis building around relevant drug-related data, such as molecular targets involved, and patient and cellular responses. These datasets are available in public repositories, but apart from sifting through the sheer amount of data imposing computational bottleneck, a major challenge is the difficulty in selecting which databases to use from an increasingly large number of available databases. The database selection is made harder by the lack of an overview of the types of data offered in each database. In order to alleviate these problems and to guide the end user through the drug repurposing efforts, we provide here a survey of 102 of the most promising and drug-relevant databases reported to date. We summarize the target coverage and types of data available in each database and provide several examples of how multi-database exploration can facilitate drug repurposing.

AB - Drug development involves a deep understanding of the mechanisms of action and possible side effects of each drug, and sometimes results in the identification of new and unexpected uses for drugs, termed as drug repurposing. Both in case of serendipitous observations and systematic mechanistic explorations, confirmation of new indications for a drug requires hypothesis building around relevant drug-related data, such as molecular targets involved, and patient and cellular responses. These datasets are available in public repositories, but apart from sifting through the sheer amount of data imposing computational bottleneck, a major challenge is the difficulty in selecting which databases to use from an increasingly large number of available databases. The database selection is made harder by the lack of an overview of the types of data offered in each database. In order to alleviate these problems and to guide the end user through the drug repurposing efforts, we provide here a survey of 102 of the most promising and drug-relevant databases reported to date. We summarize the target coverage and types of data available in each database and provide several examples of how multi-database exploration can facilitate drug repurposing.

KW - Biomolecular databases

KW - Disease databases

KW - Drug databases

KW - Drug repositioning

KW - Drug-target interaction databases

UR - http://www.scopus.com/inward/record.url?scp=85103474432&partnerID=8YFLogxK

U2 - 10.1093/bib/bbaa003

DO - 10.1093/bib/bbaa003

M3 - Review

C2 - 32055842

AN - SCOPUS:85103474432

VL - 22

SP - 1656

EP - 1678

JO - Briefings in Bioinformatics

JF - Briefings in Bioinformatics

SN - 1467-5463

IS - 2

ER -