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[Preprint]. 2023 Jul 4:arXiv:2305.15453v2.

Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing

Andreas Maier¹, Michael Hartung¹, Mark Abovsky^{2

3}, Klaudia Adamowicz¹, Gary D Bader^{4

5

6

7

8}, Sylvie Baier⁹, David B Blumenthal¹⁰, Jing Chen¹¹, Maria L Elkjaer^{12

13

14}, Carlos Garcia-Hernandez¹⁵, Mohamed Helmy^{4

5

6}, Markus Hoffmann^{9

16

17}, Igor Jurisica^{2

3

18

19}, Max Kotlyar^{2

3}, Olga Lazareva^{20

21

22}, Hagai Levi²³, Markus List⁹, Sebastian Lobentanzer²⁴, Joseph Loscalzo²⁵, Noel Malod-Dognin¹⁵, Quirin Manz⁹, Julian Matschinske^{1

9}, Miles Mee^{4

5

6}, Mhaned Oubounyt¹, Alexander R Pico²⁶, Rudolf T Pillich¹¹, Julian M Poschenrieder^{1

9}, Dexter Pratt¹¹, Nataša Pržulj^{15

27

28}, Sepideh Sadegh^{1

9

29}, Julio Saez-Rodriguez²⁴, Suryadipto Sarkar¹⁰, Gideon Shaked²³, Ron Shamir²³, Nico Trummer⁹, Ugur Turhan¹, Ruisheng Wang²⁵, Olga Zolotareva^{1

9}, Jan Baumbach^{1

30}

Affiliations

¹ Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.
² Division of Orthopaedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre, Osteoarthritis Research Program, Krembil Research Institute, UHN, Toronto, Canada.
³ Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, 60 Leonard Avenue, 5KD-407, Toronto, ON, M5T 0S8, Canada.
⁴ Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
⁵ The Donnelly Centre, University of Toronto, Toronto, ON, Canada.
⁶ Department of Computer Science, University of Toronto, Toronto, ON, Canada.
⁷ Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
⁸ The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
⁹ Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany.
¹⁰ Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany.
¹¹ Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
¹² Department of Neurology, Odense University Hospital, Odense, Denmark.
¹³ Institute of Clinical Research, University of Southern Denmark, Odense, Denmark.
¹⁴ Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.
¹⁵ Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain.
¹⁶ Institute for Advanced Study (Lichtenbergstrasse 2a, D-85748 Garching, Germany), Technical University of Munich, Germany.
¹⁷ National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America.
¹⁸ Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada.
¹⁹ Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.
²⁰ Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
²¹ Junior Clinical Cooperation Unit Multiparametric methods for early detection of prostate cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
²² European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany.
²³ Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel.
²⁴ Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany.
²⁵ Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
²⁶ Institute of Data Science and Biotechnology, Gladstone Institutes, 1650 Owens Street, San Francisco, 94158, California, USA.
²⁷ Department of Computer Science, University College London, London WC1E 6BT, UK.
²⁸ ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
²⁹ Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.
³⁰ Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.

PMID: 37332567
PMCID: PMC10274948

Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing

Andreas Maier et al. ArXiv. 2023.

[Preprint]. 2023 Jul 4:arXiv:2305.15453v2.

Authors

Affiliations

¹ Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.
² Division of Orthopaedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre, Osteoarthritis Research Program, Krembil Research Institute, UHN, Toronto, Canada.
³ Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, 60 Leonard Avenue, 5KD-407, Toronto, ON, M5T 0S8, Canada.
⁴ Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
⁵ The Donnelly Centre, University of Toronto, Toronto, ON, Canada.
⁶ Department of Computer Science, University of Toronto, Toronto, ON, Canada.
⁷ Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
⁸ The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
⁹ Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany.
¹⁰ Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany.
¹¹ Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
¹² Department of Neurology, Odense University Hospital, Odense, Denmark.
¹³ Institute of Clinical Research, University of Southern Denmark, Odense, Denmark.
¹⁴ Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.
¹⁵ Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain.
¹⁶ Institute for Advanced Study (Lichtenbergstrasse 2a, D-85748 Garching, Germany), Technical University of Munich, Germany.
¹⁷ National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America.
¹⁸ Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada.
¹⁹ Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.
²⁰ Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
²¹ Junior Clinical Cooperation Unit Multiparametric methods for early detection of prostate cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
²² European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany.
²³ Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel.
²⁴ Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany.
²⁵ Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
²⁶ Institute of Data Science and Biotechnology, Gladstone Institutes, 1650 Owens Street, San Francisco, 94158, California, USA.
²⁷ Department of Computer Science, University College London, London WC1E 6BT, UK.
²⁸ ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
²⁹ Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.
³⁰ Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.

PMID: 37332567
PMCID: PMC10274948

Update in

Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing.
Maier A, Hartung M, Abovsky M, Adamowicz K, Bader GD, Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Helmy M, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, List M, Lobentanzer S, Loscalzo J, Malod-Dognin N, Manz Q, Matschinske J, Mee M, Oubounyt M, Pastrello C, Pico AR, Pillich RT, Poschenrieder JM, Pratt D, Pržulj N, Sadegh S, Saez-Rodriguez J, Sarkar S, Shaked G, Shamir R, Trummer N, Turhan U, Wang RS, Zolotareva O, Baumbach J. Maier A, et al. Nucleic Acids Res. 2024 Jul 5;52(W1):W481-W488. doi: 10.1093/nar/gkae388. Nucleic Acids Res. 2024. PMID: 38783119 Free PMC article.

Abstract

In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network medicine tools have emerged to identify potential drug repurposing candidates. However, these tools often require complex installation and lack intuitive visual network mining capabilities. To tackle these challenges, we introduce Drugst.One, a platform that assists specialized computational medicine tools in becoming user-friendly, web-based utilities for drug repurposing. With just three lines of code, Drugst.One turns any systems biology software into an interactive web tool for modeling and analyzing complex protein-drug-disease networks. Demonstrating its broad adaptability, Drugst.One has been successfully integrated with 21 computational systems medicine tools. Available at https://drugst.one, Drugst.One has significant potential for streamlining the drug discovery process, allowing researchers to focus on essential aspects of pharmaceutical treatment research.

Keywords: Biomedical data analysis; Biomedical network exploration; Data visualization; Drug repurposing; Interactive network enrichment; Network integration; Systems medicine.

PubMed Disclaimer

Conflict of interest statement

JSR reports funding from GSK, Pfizer and Sanofi and fees from Travere Therapeutics and Astex Pharmaceuticals.

Figures

**Figure 1:**
Drugst.One enables web developers to add a fully functional network explorer to any website with minimal coding effort (biomedical web tool before (A) and after (B) Drugst.One integration). (C): A network can be explored manually or by using network medicine algorithms to identify disease mechanisms and drug repurposing candidates. Associated diseases and tissue-specific expression are additional information layers to gain insight into the network context.

**Figure 2:**
The Drugst.One ecosystem: The Drugst.One server (A) updates weekly from online databases (B), executes computationally demanding tasks, and provides data to the Drugst.One plugin (**D i** and **D ii**). The frontend is loaded from the content delivery system (CDS), (C), receives the network data from the developer integrating Drugst.One (E), and presents it to the user. Drugst.One can also be accessed programmatically through a Python package (F).

**Figure 3:**
Participants of WikiPathway WP1991 displayed in Drugst.One. Adjacent diseases and drugs are enabled, as well as diseases linked to drugs targeting this smooth muscle cell proliferation and differentiation pathway. Normalized median expression values for ‘Artery - Aorta’ are overlaid as pie charts, where 360° represent the maximum observed transcripts per million (TPM) in the selected tissue and all other TPMs are exponentially scaled.

See this image and copyright information in PMC

References

1. Hufsky F, Lamkiewicz K, Almeida A, Aouacheria A, Arighi C, Bateman A, et al. Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Brief Bioinform. 2021;22: 642–663. - PMC - PubMed
1. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O’Meara MJ, et al. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv. 2020. doi:10.1101/2020.03.22.002386 - DOI
1. Zolotareva O, Kleine M. A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. J Integr Bioinform. 2019;16. doi:10.1515/jib-2018-0069 - DOI - PMC - PubMed
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This is a preprint.

Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing

Affiliations

Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing

Authors

Affiliations

Update in

Abstract

Conflict of interest statement

Figures

References

Publication types

LinkOut - more resources

Full Text Sources