Using TransR to enhance drug repurposing knowledge graph for COVID-19 and its complications.

Hongxi Zhao, Hongfei Li, Qiaoming Liu, Guanghui Dong, Chang Hou, Yang Li, Yuming Zhao

Journal: Methods (San Diego, Calif.) 2024;221():82-90

PMID: 38104883

Full Text on Elsevier Science View on PubMed

Abstract

MOTIVATION

The COVID-19 pandemic has been spreading globally for four years, yet specific drugs that effectively suppress the virus remain elusive. Furthermore, the emergence of complications associated with COVID-19 presents significant challenges, making the development of therapeutics for COVID-19 and its complications an urgent task. However, traditional drug development processes are time-consuming. Drug repurposing, which involves identifying new therapeutic applications for existing drugs, presents a viable alternative.

RESULT

In this study, we construct a knowledge graph by retrieving information on genes, drugs, and diseases from databases such as DRUGBANK and GNBR. Next, we employ the TransR knowledge representation learning approach to embed entities and relationships into the knowledge graph. Subsequently, we train the knowledge graph using a graph neural network model based on TransR scoring. This trained knowledge graph is then utilized to predict drugs for the treatment of COVID-19 and its complications. Based on experimental results, we have identified 15 drugs out of the top 30 with the highest success rates associated with treating COVID-19 and its complications. Notably, out of these 15 drugs, 10 specifically aimed at treating COVID-19, such as Torcetrapib and Tocopherol, has not been previously identified in the knowledge graph. This finding highlights the potential of our model in aiding healthcare professionals in drug development and research related to this disease.

Address: College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China.; College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China; College of Life Science, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China.; School of Medicine and Health, Harbin Institute of Technology, 150001, Harbin, HeiLongJiang, China; Zhengzhou Research Institute, Harbin Institute of Technology, 450000, Zhengzhou, Henan, China.; College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China. Electronic address: [email protected].; College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China; College of Life Science, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China. Electronic address: [email protected].

DOI: 10.1016/j.ymeth.2023.12.001

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MeSH Terms: Humans, Drug Repositioning, COVID-19, Pandemics, Pattern Recognition, Automated, Drug Development