##plugins.themes.bootstrap3.article.main##

Altankhuyag Avirmed Uranchimeg Erdenedalai Selenge Erdenechimeg Yansen Su Tseren-Onolt Ishdorj

Abstract

Computational drug repurposing methods, particularly biomolecular network-based disease-drug-target interaction models, are essential tools for integrating large-scale heterogenous molecular information and revealing functional mechanisms, as well as for main regulatory modules of interactants which can be useful in developing new drugs. In the present study, a drug-centric network for a parasitic disease (Echinococcosis) and therapeutic drugs have been considered. A complex network with more than 12,000 vertices and more than 33,000 edges representing interactions of 84 echinococcosis-related genes with associated proteins was built and analyzed. The networks of disease similarity and drug similarity were constructed based on the complex network. As a result, three drugs (D08356, D00701, and D00506) associated with three candidate diseases through three pathways and a protein complex have been extracted. This effort tries to predict the anti-echinococcosis effects of the drugs’ combinations with benzimidazole.

Download Statistics

Downloads

Download data is not yet available.

##plugins.themes.bootstrap3.article.details##

Keywords

Biomolecular network, disease, drug combination, network analysis

References
[1] DrugBank | Powering health insights with structured drug data.
[2] KEGG: Kyoto Encyclopedia of Genes and Genomes.
[3] NCBI - National Library of Medicine.
[4] STITCH: chemical association networks.
[5] Eric Alm and Adam P Arkin. Biological networks. Current opinion in structural biology, 13(2):193–202, 2003.
[6] Gary D Bader and Christopher WV Hogue. An automated method for finding molecular complexes in large protein interaction networks. BMC bioinformatics, 4(1):1–27, 2003.
[7] Irene V. Bijnsdorp, Elisa Giovannetti, and Godefridus J. Peters. Analysis of Drug Interactions, pages 421–434. Humana Press, Totowa, NJ, 2011.
[8] Aurora S Blucher, Shannon K McWeeney, Lincoln Stein, and Guanming Wu. Visualization of drug target interactions in the contexts of pathways and networks with reactomefiviz. F1000Research, 8, 2019.
[9] Abdul Talib Bon. Determining the size of centrality in social networks.
[10] Enrico Brunetti, Peter Kern, and Dominique Angèle Vuitton. Expert consensus for the diagnosis and treatment of cystic and alveolar echinococcosis in humans. Acta Tropica, 114(1):1–16, 2010.
[11] Feixiong Cheng, István A Kovács, and Albert-László Barabási. Network-based prediction of drug combinations. Nature communications, 10(1):1–11, 2019.
[12] GeneCards Human Gene Database. GeneCards - Human Genes | Gene Database | Gene Search.
[13] E. Diday and J. C. Simon. Clustering Analysis, pages 47–94. Springer Berlin Heidelberg, Berlin, Heidelberg, 1976.
[14] Joseph El-On. Benzimidazole treatment of cystic echinococcosis. Acta tropica, 85(2):243–252, 2003.
[15] Gihanna Galindez, Julian Matschinske, Tim Daniel Rose, Sepideh Sadegh, Marisol Salgado-Albarrán, Julian Späth, Jan Baumbach, and Josch Konstantin Pauling. Lessons from the covid-19 pandemic for advancing computational drug repurposing strategies. Nature Computational Science, 1(1):33–41, 2021.
[16] Detlef Groth, Stefanie Hartmann, Sebastian Klie, and Joachim Selbig. Principal Components Analysis, pages 527–547. Humana Press, Totowa, NJ, 2013.
[17] Beate Grüner, Petra Kern, Benjamin Mayer, Tilmann Gräter, Andreas Hillenbrand, Thomas EF Barth, Rainer Muche, Doris Henne-Bruns, Wolfgang Kratzer, and Peter Kern. Comprehensive diagnosis and treatment of alveolar echinococcosis: A single-center, long-term observational study of 312 patients in germany. GMS infectious diseases, 5, 2017.
[18] Andrew Hemphill, Britta Stadelmann, Reto Rufener, Markus Spiliotis, Ghalia Boubaker, Joachim Müller, Norbert Müller, Daniela Gorgas, and Bruno Gottstein. Treatment of echinococcosis: albendazole and mebendazole–what else? Parasite, 21, 2014.
[19] Namgil Lee, Hojin Yoo, and Heejung Yang. Cluster analysis of medicinal plants and targets based on multipartite network. Biomolecules, 11(4), 2021.
[20] Elaine L. Leung, Zhi-Wei Cao, Zhi-Hong Jiang, Hua Zhou, and Liang Liu. Network-based drug discovery by integrating systems biology and computational technologies. Briefings in Bioinformatics, 14(4):491–505, 08 2012.
[21] Yongjin Li and Jagdish C Patra. Genome-wide inferring gene–phenotype relationship by walking on the heterogeneous network. Bioinformatics, 26(9):1219–1224, 2010.
[22] Stephani Joy Y Macalino, Vijayakumar Gosu, Sunhye Hong, and Sun Choi. Role of computer-aided drug design in modern drug discovery. Archives of pharmacal research, 38(9):1686–1701, 2015.
[23] Donald P McManus, Wenbao Zhang, Jun Li, and Paul B Bartley. Echinococcosis. The Lancet, 362(9392):1295–1304, 2003.
[24] Pablo Porras Millán. Network analysis of protein interaction data: an introduction. 2017.
[25] Jason Montojo, Khalid Zuberi, Harold Rodriguez, Farzana Kazi, George Wright, Sylva L Donaldson, Quaid Morris, and Gary D Bader. Genemania cytoscape plugin: fast gene function predictions on the desktop. Bioinformatics, 26(22):2927–2928, 2010.
[26] Keiichiro Ono. Cytoscape: An Open Source Platform for Complex Network Analysis and Visualization.
[27] World Health Organization. Echinococcosis. https://www.who.int/en/news-room/fact-sheets/detail/echinococcosis.
[28] Kyungsoo Park. A review of computational drug repurposing. Translational and Clinical Pharmacology, 27(2):59–63, 2019.
[29] Georgios A Pavlopoulos, Maria Secrier, Charalampos N Moschopoulos, Theodoros G Soldatos, Sophia Kossida, Jan Aerts, Reinhard Schneider, and Pantelis G Bagos. Using graph theory to analyze biological networks. BioData mining, 4(1):1–27, 2011.
[30] Victor-Bogdan Popescu, Krishna Kanhaiya, Dumitru Iulian Năstac, Eugen Czeizler, and Ion Petre. Network controllability solutions for computational drug repurposing using genetic algorithms. Scientific reports, 12(1):1–16, 2022.
[31] Victor-Bogdan Popescu, José Ángel Sánchez-Martín, Daniela Schacherer, Sadra Safadoust, Negin Majidi, Andrei Andronescu, Alexandru Nedea, Diana Ion, Eduard Mititelu, Eugen Czeizler, et al. Netcontrol4biomed: a web-based platform for controllability analysis of protein–protein interaction networks. Bioinformatics, 37(21):3976–3978, 2021.
[32] Sudeep Pushpakom, Francesco Iorio, Patrick A Eyers, K Jane Escott, Shirley Hopper, Andrew Wells, Andrew Doig, Tim Guilliams, Joanna Latimer, Christine McNamee, et al. Drug repurposing: progress, challenges and recommendations. Nature reviews Drug discovery, 18(1):41–58, 2019.
[33] Reto Rufener, Luca Dick, Laura D’Ascoli, Dominic Ritler, Amani Hizem, Timothy NC Wells, Andrew Hemphill, and Britta Lundström-Stadelmann. Repurposing of an old drug: in vitro and in vivo efficacies of buparvaquone against echinococcus multilocularis. International Journal for Parasitology: Drugs and Drug Resistance, 8(3):440–450, 2018.
[34] Philippe Sanseau and Jacob Koehler. Editorial: Computational methods for drug repurposing. Briefings in Bioinformatics, 12(4):301–302, 07 2011.
[35] Jack W Scannell, Alex Blanckley, Helen Boldon, and Brian Warrington. Diagnosing the decline in pharmaceutical r&d efficiency. Nature reviews Drug discovery, 11(3):191–200, 2012.
[36] Gisbert Schneider and Uli Fechner. Computer-based de novo design of drug-like molecules. Nature Reviews Drug Discovery, 4(8):649–663, 2005.
[37] Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, and Trey Ideker. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research, 13(11):2498–2504, 2003.
[38] Mar Siles-Lucas, Adriano Casulli, Roberto Cirilli, and David Carmena. Progress in the pharmacological treatment of human cystic and alveolar echinococcosis: compounds and therapeutic targets. PLoS neglected tropical diseases, 12(4):e0006422, 2018.
[39] Nicoleta Siminea, Victor Popescu, Jose Angel Sanchez Martin, Daniela Florea, Georgiana Gavril, Ana-Maria Gheorghe, Corina Iţcuş, Krishna Kanhaiya, Octavian Pacioglu, Laura Ioana Popa, et al. Network analytics for drug repurposing in covid-19. Briefings in bioinformatics, 23(1): bbab490, 2022.
[40] Jianlin Wang, Wenxiu Wang, Chaokun Yan, Junwei Luo, and Ge Zhang. Predicting drug-disease association based on ensemble strategy. Frontiers in Genetics, 12:666575, 2021.
[41] Zikai Wu, Yong Wang, and Luonan Chen. Network-based drug repositioning. Molecular BioSystems, 9(6):1268–1281, 2013.
[42] Wei Zheng, Wei Sun, and Anton Simeonov. Drug repurposing screens and synergistic drug-combinations for infectious diseases. British journal of pharmacology, 175(2):181–191, 2018.
[43] Yadi Zhou, Yuan Hou, Jiayu Shen, Yin Huang, William Martin, and Feixiong Cheng. Network-based drug repurposing for novel coronavirus 2019-ncov/sars-cov-2. Cell discovery, 6(1): 1–18, 2020.
Citation Format
How to Cite
Avirmed, A., Erdenedalai, U., Erdenechimeg, S., Su, Y., & Ishdorj, T.-O. (2022). Biomolecular Network-based Study of a Parasitic Disease and Therapeutic Drugs. ICT Focus, 1(1), 22–34. https://doi.org/10.58873/sict.v1i1.31 (Original work published September 29, 2022)
Section
Articles

Similar Articles

You may also start an advanced similarity search for this article.