Graph-DTI: A New Model for Drug-Target Interaction Prediction Based on Heterogenous Network Graph Embedding.

Graph-DTI: A New Model for Drug-Target Interaction Prediction Based on Heterogenous Network Graph Embedding.

Publication date: Jul 13, 2023

In this study, we aimed to develop a new end-to-end learning model called Graph-Drug-Target Interaction (DTI), which integrates various types of information in the heterogeneous network data, and to explore automatic learning of the topology-maintaining representations of drugs and targets, thereby effectively contributing to the prediction of DTI. Precise predictions of DTI can guide drug discovery and development. Most machine learning algorithms integrate multiple data sources and combine them with common embedding methods. However, the relationship between the drugs and target proteins is not well reported. Although some existing studies have used heterogeneous network graphs for DTI prediction, there are many limitations in the neighborhood information between the nodes in the heterogeneous network graphs. We studied the drug-drug interaction (DDI) and DTI from DrugBank Version 3. 0, protein-protein interaction (PPI) from the human protein reference database Release 9, drug structure similarity from Morgan fingerprints of radius 2 and calculated by RDKit, and protein sequence similarity from Smith-Waterman score. Our study consists of three major components. First, various drugs and target proteins were integrated, and a heterogeneous network was established based on a series of data sets. Second, the graph neural networks-inspired graph auto-encoding method was used to extract high-order structural information from the heterogeneous networks, thereby revealing the description of nodes (drugs and proteins) and their topological neighbors. Finally, potential DTI prediction was made, and the obtained samples were sent to the classifier for secondary classification. The performance of Graph-DTI and all baseline methods was evaluated using the sums of the area under the precision-recall curve (AUPR) and the area under the receiver operating characteristic curve (AUC). The results indicated that Graph-DTI outperformed the baseline methods in both performance results. Compared with other baseline DTI prediction methods, the results showed that Graph-DTI had better prediction performance. Additionally, in this study, we effectively classified drugs corresponding to different targets and vice versa. The above findings showed that Graph-DTI provided a powerful tool for drug research, development, and repositioning. Graph-DTI can serve as a drug development and repositioning tool more effectively than previous studies that did not use heterogeneous network graph embedding.

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Concepts Keywords
Drugbank bioinformatics databases
Graphs deep learning
Neighbors drug development
Outperformed feature representation
Waterman topology


Type Source Name
disease MESH drug interaction
drug DRUGBANK Didanosine
drug DRUGBANK Tropicamide
drug DRUGBANK Carboxyamidotriazole
drug DRUGBANK L-Tyrosine
drug DRUGBANK Saquinavir
drug DRUGBANK Aspartame
drug DRUGBANK Temazepam
drug DRUGBANK Vitamin A
drug DRUGBANK Pravastatin
drug DRUGBANK Lovastatin
drug DRUGBANK Cerivastatin
drug DRUGBANK Simvastatin
drug DRUGBANK Atorvastatin
drug DRUGBANK Fluvastatin
drug DRUGBANK Rosuvastatin
drug DRUGBANK Pitavastatin
disease MESH cardiovascular disease
drug DRUGBANK Coenzyme A
drug DRUGBANK Saxagliptin
disease MESH COVID 19
drug DRUGBANK (S)-Des-Me-Ampa
drug DRUGBANK 3 4-Methylenedioxy-N-isopropylamphetamine
drug DRUGBANK Hydralazine
disease MESH hypotension
drug DRUGBANK Hydrogen peroxide
drug DRUGBANK Ezetimibe
disease MESH hypercholesterolemia
drug DRUGBANK Dihydrostreptomycin

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