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Jin S, Hong Y, Zeng L, Jiang Y, Lin Y, Wei L, Yu Z, Zeng X, Liu X. A general hypergraph learning algorithm for drug multi-task predictions in micro-to-macro biomedical networks. PLoS Comput Biol 2023; 19:e1011597. [PMID: 37956212 PMCID: PMC10681315 DOI: 10.1371/journal.pcbi.1011597] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/27/2023] [Accepted: 10/13/2023] [Indexed: 11/15/2023] Open
Abstract
The powerful combination of large-scale drug-related interaction networks and deep learning provides new opportunities for accelerating the process of drug discovery. However, chemical structures that play an important role in drug properties and high-order relations that involve a greater number of nodes are not tackled in current biomedical networks. In this study, we present a general hypergraph learning framework, which introduces Drug-Substructures relationship into Molecular interaction Networks to construct the micro-to-macro drug centric heterogeneous network (DSMN), and develop a multi-branches HyperGraph learning model, called HGDrug, for Drug multi-task predictions. HGDrug achieves highly accurate and robust predictions on 4 benchmark tasks (drug-drug, drug-target, drug-disease, and drug-side-effect interactions), outperforming 8 state-of-the-art task specific models and 6 general-purpose conventional models. Experiments analysis verifies the effectiveness and rationality of the HGDrug model architecture as well as the multi-branches setup, and demonstrates that HGDrug is able to capture the relations between drugs associated with the same functional groups. In addition, our proposed drug-substructure interaction networks can help improve the performance of existing network models for drug-related prediction tasks.
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Affiliation(s)
- Shuting Jin
- School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, China
- School of Informatics, Xiamen University, Xiamen, China
- Department of AIDD, Shanghai Yuyao Biotechnology Co., Ltd., Shanghai, China
| | - Yue Hong
- School of Informatics, Xiamen University, Xiamen, China
| | - Li Zeng
- Department of AIDD, Shanghai Yuyao Biotechnology Co., Ltd., Shanghai, China
| | - Yinghui Jiang
- School of Informatics, Xiamen University, Xiamen, China
| | - Yuan Lin
- School of Economics, Innovation, and Technology, Kristiania University College, Bergen, Norway
| | - Leyi Wei
- School of Software, Shandong University, Shandong, China
| | - Zhuohang Yu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xiangxiang Zeng
- School of Information Science and Engineering, Hunan University, Hunan, China
| | - Xiangrong Liu
- School of Informatics, Xiamen University, Xiamen, China
- Zhejiang Lab, Hangzhou, China
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Miller SJ, Darji RY, Walaieh S, Lewis JA, Logan R. Senolytic and senomorphic secondary metabolites as therapeutic agents in Drosophila melanogaster models of Parkinson's disease. Front Neurol 2023; 14:1271941. [PMID: 37840914 PMCID: PMC10568035 DOI: 10.3389/fneur.2023.1271941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023] Open
Abstract
Drosophila melanogaster is a valuable model organism for a wide range of biological exploration. The well-known advantages of D. melanogaster include its relatively simple biology, the ease with which it is genetically modified, the relatively low financial and time costs associated with their short gestation and life cycles, and the large number of offspring they produce per generation. D. melanogaster has facilitated the discovery of many significant insights into the pathology of Parkinson's disease (PD) and has served as an excellent preclinical model of PD-related therapeutic discovery. In this review, we provide an overview of the major D. melanogaster models of PD, each of which provide unique insights into PD-relevant pathology and therapeutic targets. These models are discussed in the context of their past, current, and future potential use for studying the utility of secondary metabolites as therapeutic agents in PD. Over the last decade, senolytics have garnered an exponential interest in their ability to mitigate a broad spectrum of diseases, including PD. Therefore, an emphasis is placed on the senolytic and senomorphic properties of secondary metabolites. It is expected that D. melanogaster will continue to be critical in the effort to understand and improve treatment of PD, including their involvement in translational studies focused on secondary metabolites.
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Affiliation(s)
- Sean J. Miller
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, United States
| | - Rayyan Y. Darji
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, United States
| | - Sami Walaieh
- Department of Biology, Eastern Nazarene College, Quincy, MA, United States
| | - Jhemerial A. Lewis
- Department of Biology, Eastern Nazarene College, Quincy, MA, United States
| | - Robert Logan
- Department of Biology, Eastern Nazarene College, Quincy, MA, United States
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