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Review

Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning

1
Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden
2
Department of Animal Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
3
National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
4
Department of Medical Biology, Faculty of Medicine, Atatürk University, 25240 Erzurum, Turkey
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Department of Molecular and Clinical Medicine, University of Gothenburg, The Wallenberg Laboratory, Sahlgrenska University Hospital, SE-41345 Gothenburg, Sweden
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Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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BioInnovation Institute, DK-2200 Copenhagen N, Denmark
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Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, UK
*
Author to whom correspondence should be addressed.
Cancers 2020, 12(9), 2694; https://doi.org/10.3390/cancers12092694
Received: 30 July 2020 / Revised: 14 September 2020 / Accepted: 16 September 2020 / Published: 21 September 2020
(This article belongs to the Collection Application of Bioinformatics in Cancers)
Drug repurposing is an accelerated route for drug development and a promising approach for finding medications for orphan and common diseases. Here, we compiled databases that comprise both computationally- or experimentally-derived data, and categorized them based on quiddity and origin of data, further focusing on those that present high throughput omic data or drug screens. These databases were then contextualized with genome-wide screening methods such as CRISPR/Cas9 and RNA interference, as well as state of art systems biology approaches that enable systematic characterizations of multi-omic data to find new indications for approved drugs or those that reached the latest phases of clinical trials.
Modern drug discovery through de novo drug discovery entails high financial costs, low success rates, and lengthy trial periods. Drug repositioning presents a suitable approach for overcoming these issues by re-evaluating biological targets and modes of action of approved drugs. Coupling high-throughput technologies with genome-wide essentiality screens, network analysis, genome-scale metabolic modeling, and machine learning techniques enables the proposal of new drug–target signatures and uncovers unanticipated modes of action for available drugs. Here, we discuss the current issues associated with drug repositioning in light of curated high-throughput multi-omic databases, genome-wide screening technologies, and their application in systems biology/medicine approaches. View Full-Text
Keywords: drug repositioning; genomic screens; machine learning; systems pharmacology; systems medicine drug repositioning; genomic screens; machine learning; systems pharmacology; systems medicine
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MDPI and ACS Style

Mohammadi, E.; Benfeitas, R.; Turkez, H.; Boren, J.; Nielsen, J.; Uhlen, M.; Mardinoglu, A. Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning. Cancers 2020, 12, 2694. https://doi.org/10.3390/cancers12092694

AMA Style

Mohammadi E, Benfeitas R, Turkez H, Boren J, Nielsen J, Uhlen M, Mardinoglu A. Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning. Cancers. 2020; 12(9):2694. https://doi.org/10.3390/cancers12092694

Chicago/Turabian Style

Mohammadi, Elyas, Rui Benfeitas, Hasan Turkez, Jan Boren, Jens Nielsen, Mathias Uhlen, and Adil Mardinoglu. 2020. "Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning" Cancers 12, no. 9: 2694. https://doi.org/10.3390/cancers12092694

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