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Zhang B, Niu D, Zhang L, Zhang Q, Li Z. MSH-DTI: multi-graph convolution with self-supervised embedding and heterogeneous aggregation for drug-target interaction prediction. BMC Bioinformatics 2024; 25:275. [PMID: 39179993 PMCID: PMC11342675 DOI: 10.1186/s12859-024-05904-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 08/16/2024] [Indexed: 08/26/2024] Open
Abstract
BACKGROUND The rise of network pharmacology has led to the widespread use of network-based computational methods in predicting drug target interaction (DTI). However, existing DTI prediction models typically rely on a limited amount of data to extract drug and target features, potentially affecting the comprehensiveness and robustness of features. In addition, although multiple networks are used for DTI prediction, the integration of heterogeneous information often involves simplistic aggregation and attention mechanisms, which may impose certain limitations. RESULTS MSH-DTI, a deep learning model for predicting drug-target interactions, is proposed in this paper. The model uses self-supervised learning methods to obtain drug and target structure features. A Heterogeneous Interaction-enhanced Feature Fusion Module is designed for multi-graph construction, and the graph convolutional networks are used to extract node features. With the help of an attention mechanism, the model focuses on the important parts of different features for prediction. Experimental results show that the AUROC and AUPR of MSH-DTI are 0.9620 and 0.9605 respectively, outperforming other models on the DTINet dataset. CONCLUSION The proposed MSH-DTI is a helpful tool to discover drug-target interactions, which is also validated through case studies in predicting new DTIs.
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Affiliation(s)
- Beiyi Zhang
- College of Computer Science and Technology, Qingdao University, Ningxia Road, Qingdao, 266071, Shandong, China
| | - Dongjiang Niu
- College of Computer Science and Technology, Qingdao University, Ningxia Road, Qingdao, 266071, Shandong, China
| | - Lianwei Zhang
- College of Computer Science and Technology, Qingdao University, Ningxia Road, Qingdao, 266071, Shandong, China
| | - Qiang Zhang
- College of Computer Science and Technology, Qingdao University, Ningxia Road, Qingdao, 266071, Shandong, China
| | - Zhen Li
- College of Computer Science and Technology, Qingdao University, Ningxia Road, Qingdao, 266071, Shandong, China.
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2
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Jin Q, Zhang X, Huo D, Xie H, Zhang D, Liu L, Zhao Y, Chen X. Predicting drug synergy using a network propagation inspired machine learning framework. Brief Funct Genomics 2024; 23:429-440. [PMID: 38183214 DOI: 10.1093/bfgp/elad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/14/2023] [Accepted: 12/04/2023] [Indexed: 01/07/2024] Open
Abstract
Combination therapy is a promising strategy for cancers, increasing therapeutic options and reducing drug resistance. Yet, systematic identification of efficacious drug combinations is limited by the combinatorial explosion caused by a large number of possible drug pairs and diseases. At present, machine learning techniques have been widely applied to predict drug combinations, but most studies rely on the response of drug combinations to specific cell lines and are not entirely satisfactory in terms of mechanism interpretability and model scalability. Here, we proposed a novel network propagation-based machine learning framework to predict synergistic drug combinations. Based on the topological information of a comprehensive drug-drug association network, we innovatively introduced an affinity score between drug pairs as one of the features to train machine learning models. We applied network-based strategy to evaluate their therapeutic potential to different cancer types. Finally, we identified 17 specific-, 21 general- and 40 broad-spectrum antitumor drug combinations, in which 69% drug combinations were validated by vitro cellular experiments, 83% drug combinations were validated by literature reports and 100% drug combinations were validated by biological function analyses. By quantifying the network relationships between drug targets and cancer-related driver genes in the human protein-protein interactome, we show the existence of four distinct patterns of drug-drug-disease relationships. We also revealed that 32 biological pathways were correlated with the synergistic mechanism of broad-spectrum antitumor drug combinations. Overall, our model offers a powerful scalable screening framework for cancer treatments.
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Affiliation(s)
- Qing Jin
- Department of Pharmacogenomics, College of Bioinformatics and Science Technology, Harbin Medical University, Harbin, China
| | - Xianze Zhang
- Department of Pharmacogenomics, College of Bioinformatics and Science Technology, Harbin Medical University, Harbin, China
| | - Diwei Huo
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hongbo Xie
- Department of Pharmacogenomics, College of Bioinformatics and Science Technology, Harbin Medical University, Harbin, China
| | - Denan Zhang
- Department of Pharmacogenomics, College of Bioinformatics and Science Technology, Harbin Medical University, Harbin, China
| | - Lei Liu
- Department of Pharmacogenomics, College of Bioinformatics and Science Technology, Harbin Medical University, Harbin, China
| | - Yashuang Zhao
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Xiujie Chen
- Department of Pharmacogenomics, College of Bioinformatics and Science Technology, Harbin Medical University, Harbin, China
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Yao R, Shen Z, Xu X, Ling G, Xiang R, Song T, Zhai F, Zhai Y. Knowledge mapping of graph neural networks for drug discovery: a bibliometric and visualized analysis. Front Pharmacol 2024; 15:1393415. [PMID: 38799167 PMCID: PMC11116974 DOI: 10.3389/fphar.2024.1393415] [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: 02/29/2024] [Accepted: 04/12/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction In recent years, graph neural network has been extensively applied to drug discovery research. Although researchers have made significant progress in this field, there is less research on bibliometrics. The purpose of this study is to conduct a comprehensive bibliometric analysis of graph neural network applications in drug discovery in order to identify current research hotspots and trends, as well as serve as a reference for future research. Methods Publications from 2017 to 2023 about the application of graph neural network in drug discovery were collected from the Web of Science Core Collection. Bibliometrix, VOSviewer, and Citespace were mainly used for bibliometric studies. Results and Discussion In this paper, a total of 652 papers from 48 countries/regions were included. Research interest in this field is continuously increasing. China and the United States have a significant advantage in terms of funding, the number of publications, and collaborations with other institutions and countries. Although some cooperation networks have been formed in this field, extensive worldwide cooperation still needs to be strengthened. The results of the keyword analysis clarified that graph neural network has primarily been applied to drug-target interaction, drug repurposing, and drug-drug interaction, while graph convolutional neural network and its related optimization methods are currently the core algorithms in this field. Data availability and ethical supervision, balancing computing resources, and developing novel graph neural network models with better interpretability are the key technical issues currently faced. This paper analyzes the current state, hot spots, and trends of graph neural network applications in drug discovery through bibliometric approaches, as well as the current issues and challenges in this field. These findings provide researchers with valuable insights on the current status and future directions of this field.
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Affiliation(s)
| | | | | | | | | | | | - Fei Zhai
- Faculty of Medical Device, Shenyang Pharmaceutical University, Shenyang, China
| | - Yuxuan Zhai
- Faculty of Medical Device, Shenyang Pharmaceutical University, Shenyang, China
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An H, Liu X, Cai W, Shao X. Explainable Graph Neural Networks with Data Augmentation for Predicting p Ka of C-H Acids. J Chem Inf Model 2024; 64:2383-2392. [PMID: 37706462 DOI: 10.1021/acs.jcim.3c00958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
The pKa of C-H acids is an important parameter in the fields of organic synthesis, drug discovery, and materials science. However, the prediction of pKa is still a great challenge due to the limit of experimental data and the lack of chemical insight. Here, a new model for predicting the pKa values of C-H acids is proposed on the basis of graph neural networks (GNNs) and data augmentation. A message passing unit (MPU) was used to extract the topological and target-related information from the molecular graph data, and a readout layer was utilized to retrieve the information on the ionization site C atom. The retrieved information then was adopted to predict pKa by a fully connected network. Furthermore, to increase the diversity of the training data, a knowledge-infused data augmentation technique was established by replacing the H atoms in a molecule with substituents exhibiting different electronic effects. The MPU was pretrained with the augmented data. The efficacy of data augmentation was confirmed by visualizing the distribution of compounds with different substituents and by classifying compounds. The explainability of the model was studied by examining the change of pKa values when a specific atom was masked. This explainability was used to identify the key substituents for pKa. The model was evaluated on two data sets from the iBonD database. Dataset1 includes the experimental pKa values of C-H acids measured in DMSO, while dataset2 comprises the pKa values measured in water. The results show that the knowledge-infused data augmentation technique greatly improves the predictive accuracy of the model, especially when the number of samples is small.
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Affiliation(s)
- Hongle An
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Xuyang Liu
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Wensheng Cai
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Xueguang Shao
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
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5
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Chen S, Li M, Semenov I. MFA-DTI: Drug-target interaction prediction based on multi-feature fusion adopted framework. Methods 2024; 224:79-92. [PMID: 38430967 DOI: 10.1016/j.ymeth.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/16/2024] [Accepted: 02/23/2024] [Indexed: 03/05/2024] Open
Abstract
The identification of drug-target interactions (DTI) is a valuable step in the drug discovery and repositioning process. However, traditional laboratory experiments are time-consuming and expensive. Computational methods have streamlined research to determine DTIs. The application of deep learning methods has significantly improved the prediction performance for DTIs. Modern deep learning methods can leverage multiple sources of information, including sequence data that contains biological structural information, and interaction data. While useful, these methods cannot be effectively applied to each type of information individually (e.g., chemical structure and interaction network) and do not take into account the specificity of DTI data such as low- or zero-interaction biological entities. To overcome these limitations, we propose a method called MFA-DTI (Multi-feature Fusion Adopted framework for DTI). MFA-DTI consists of three modules: an interaction graph learning module that processes the interaction network to generate interaction vectors, a chemical structure learning module that extracts features from the chemical structure, and a fusion module that combines these features for the final prediction. To validate the performance of MFA-DTI, we conducted experiments on six public datasets under different settings. The results indicate that the proposed method is highly effective in various settings and outperforms state-of-the-art methods.
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Affiliation(s)
- Siqi Chen
- School of Information Science and Engineering, Chongqing Jiaotong University, Chongqing, 400074, China.
| | - Minghui Li
- Beidahuang Industry Group General Hospital, Harbin, 150006, China
| | - Ivan Semenov
- College of Intelligence and Computing, Tianjin University, Tianjin, 300072, China
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Cao J, Chen Q, Qiu J, Wang Y, Lan W, Du X, Tan K. NGCN: Drug-target interaction prediction by integrating information and feature learning from heterogeneous network. J Cell Mol Med 2024; 28:e18224. [PMID: 38509739 PMCID: PMC10955156 DOI: 10.1111/jcmm.18224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/14/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
Drug-target interaction (DTI) prediction is essential for new drug design and development. Constructing heterogeneous network based on diverse information about drugs, proteins and diseases provides new opportunities for DTI prediction. However, the inherent complexity, high dimensionality and noise of such a network prevent us from taking full advantage of these network characteristics. This article proposes a novel method, NGCN, to predict drug-target interactions from an integrated heterogeneous network, from which to extract relevant biological properties and association information while maintaining the topology information. It focuses on learning the topology representation of drugs and targets to improve the performance of DTI prediction. Unlike traditional methods, it focuses on learning the low-dimensional topology representation of drugs and targets via graph-based convolutional neural network. NGCN achieves substantial performance improvements over other state-of-the-art methods, such as a nearly 1.0% increase in AUPR value. Moreover, we verify the robustness of NGCN through benchmark tests, and the experimental results demonstrate it is an extensible framework capable of combining heterogeneous information for DTI prediction.
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Affiliation(s)
- Junyue Cao
- College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Qingfeng Chen
- School of Computer, Electronics and InformationGuangxi UniversityNanningChina
| | - Junlai Qiu
- School of Computer, Electronics and InformationGuangxi UniversityNanningChina
| | - Yiming Wang
- School of Computer, Electronics and InformationGuangxi UniversityNanningChina
| | - Wei Lan
- School of Computer, Electronics and InformationGuangxi UniversityNanningChina
| | - Xiaojing Du
- School of Computer, Electronics and InformationGuangxi UniversityNanningChina
| | - Kai Tan
- School of Computer, Electronics and InformationGuangxi UniversityNanningChina
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7
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Zhang C, Zang T, Zhao T. KGE-UNIT: toward the unification of molecular interactions prediction based on knowledge graph and multi-task learning on drug discovery. Brief Bioinform 2024; 25:bbae043. [PMID: 38348746 PMCID: PMC10939374 DOI: 10.1093/bib/bbae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 12/29/2023] [Accepted: 01/23/2024] [Indexed: 02/15/2024] Open
Abstract
The prediction of molecular interactions is vital for drug discovery. Existing methods often focus on individual prediction tasks and overlook the relationships between them. Additionally, certain tasks encounter limitations due to insufficient data availability, resulting in limited performance. To overcome these limitations, we propose KGE-UNIT, a unified framework that combines knowledge graph embedding (KGE) and multi-task learning, for simultaneous prediction of drug-target interactions (DTIs) and drug-drug interactions (DDIs) and enhancing the performance of each task, even when data availability is limited. Via KGE, we extract heterogeneous features from the drug knowledge graph to enhance the structural features of drug and protein nodes, thereby improving the quality of features. Additionally, employing multi-task learning, we introduce an innovative predictor that comprises the task-aware Convolutional Neural Network-based (CNN-based) encoder and the task-aware attention decoder which can fuse better multimodal features, capture the contextual interactions of molecular tasks and enhance task awareness, leading to improved performance. Experiments on two imbalanced datasets for DTIs and DDIs demonstrate the superiority of KGE-UNIT, achieving high area under the receiver operating characteristics curves (AUROCs) (0.942, 0.987) and area under the precision-recall curve ( AUPRs) (0.930, 0.980) for DTIs and high AUROCs (0.975, 0.989) and AUPRs (0.966, 0.988) for DDIs. Notably, on the LUO dataset where the data were more limited, KGE-UNIT exhibited a more pronounced improvement, with increases of 4.32$\%$ in AUROC and 3.56$\%$ in AUPR for DTIs and 6.56$\%$ in AUROC and 8.17$\%$ in AUPR for DDIs. The scalability of KGE-UNIT is demonstrated through its extension to protein-protein interactions prediction, ablation studies and case studies further validate its effectiveness.
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Affiliation(s)
- Chengcheng Zhang
- Department of Computer Science, Harbin Institute of Technology, Harbin, 150001, China
| | - Tianyi Zang
- Department of Computer Science, Harbin Institute of Technology, Harbin, 150001, China
| | - Tianyi Zhao
- School of Medicine and Health, Harbin Institute of Technology, Harbin, 150001, China
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Son J, Kim D. Applying network link prediction in drug discovery: an overview of the literature. Expert Opin Drug Discov 2024; 19:43-56. [PMID: 37794688 DOI: 10.1080/17460441.2023.2267020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/02/2023] [Indexed: 10/06/2023]
Abstract
INTRODUCTION Network representation can give a holistic view of relationships for biomedical entities through network topology. Link prediction estimates the probability of link formation between the pair of unconnected nodes. In the drug discovery process, the link prediction method not only enables the detection of connectivity patterns but also predicts the effects of one biomedical entity to multiple entities simultaneously and vice versa, which is useful for many applications. AREAS COVERED The authors provide a comprehensive overview of network link prediction in drug discovery. Link prediction methodologies such as similarity-based approaches, embedding-based approaches, probabilistic model-based approaches, and preprocessing methods are summarized with examples. In addition to describing their properties and limitations, the authors discuss the applications of link prediction in drug discovery based on the relationship between biomedical concepts. EXPERT OPINION Link prediction is a powerful method to infer the existence of novel relationships in drug discovery. However, link prediction has been hampered by the sparsity of data and the lack of negative links in biomedical networks. With preprocessing to balance positive and negative samples and the collection of more data, the authors believe it is possible to develop more reliable link prediction methods that can become invaluable tools for successful drug discovery.
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Affiliation(s)
- Jeongtae Son
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Dongsup Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
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Zhang Y, Liu C, Liu M, Liu T, Lin H, Huang CB, Ning L. Attention is all you need: utilizing attention in AI-enabled drug discovery. Brief Bioinform 2023; 25:bbad467. [PMID: 38189543 PMCID: PMC10772984 DOI: 10.1093/bib/bbad467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/03/2023] [Accepted: 11/25/2023] [Indexed: 01/09/2024] Open
Abstract
Recently, attention mechanism and derived models have gained significant traction in drug development due to their outstanding performance and interpretability in handling complex data structures. This review offers an in-depth exploration of the principles underlying attention-based models and their advantages in drug discovery. We further elaborate on their applications in various aspects of drug development, from molecular screening and target binding to property prediction and molecule generation. Finally, we discuss the current challenges faced in the application of attention mechanisms and Artificial Intelligence technologies, including data quality, model interpretability and computational resource constraints, along with future directions for research. Given the accelerating pace of technological advancement, we believe that attention-based models will have an increasingly prominent role in future drug discovery. We anticipate that these models will usher in revolutionary breakthroughs in the pharmaceutical domain, significantly accelerating the pace of drug development.
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Affiliation(s)
- Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Caiqi Liu
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, No.150 Haping Road, Nangang District, Harbin, Heilongjiang 150081, China
- Key Laboratory of Molecular Oncology of Heilongjiang Province, No.150 Haping Road, Nangang District, Harbin, Heilongjiang 150081, China
| | - Mujiexin Liu
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tianyuan Liu
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Japan
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Cheng-Bing Huang
- School of Computer Science and Technology, Aba Teachers University, Aba, China
| | - Lin Ning
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang, China
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China
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10
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Mo X, Tang R, Liu H. A relation-aware heterogeneous graph convolutional network for relationship prediction. Inf Sci (N Y) 2023. [DOI: 10.1016/j.ins.2022.12.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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11
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Wang L, Song Y, Wang H, Zhang X, Wang M, He J, Li S, Zhang L, Li K, Cao L. Advances of Artificial Intelligence in Anti-Cancer Drug Design: A Review of the Past Decade. Pharmaceuticals (Basel) 2023; 16:253. [PMID: 37259400 PMCID: PMC9963982 DOI: 10.3390/ph16020253] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/25/2023] [Accepted: 02/06/2023] [Indexed: 10/13/2023] Open
Abstract
Anti-cancer drug design has been acknowledged as a complicated, expensive, time-consuming, and challenging task. How to reduce the research costs and speed up the development process of anti-cancer drug designs has become a challenging and urgent question for the pharmaceutical industry. Computer-aided drug design methods have played a major role in the development of cancer treatments for over three decades. Recently, artificial intelligence has emerged as a powerful and promising technology for faster, cheaper, and more effective anti-cancer drug designs. This study is a narrative review that reviews a wide range of applications of artificial intelligence-based methods in anti-cancer drug design. We further clarify the fundamental principles of these methods, along with their advantages and disadvantages. Furthermore, we collate a large number of databases, including the omics database, the epigenomics database, the chemical compound database, and drug databases. Other researchers can consider them and adapt them to their own requirements.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kang Li
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin 150081, China
| | - Lei Cao
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin 150081, China
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12
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Ren ZH, You ZH, Zou Q, Yu CQ, Ma YF, Guan YJ, You HR, Wang XF, Pan J. DeepMPF: deep learning framework for predicting drug-target interactions based on multi-modal representation with meta-path semantic analysis. J Transl Med 2023; 21:48. [PMID: 36698208 PMCID: PMC9876420 DOI: 10.1186/s12967-023-03876-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/05/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Drug-target interaction (DTI) prediction has become a crucial prerequisite in drug design and drug discovery. However, the traditional biological experiment is time-consuming and expensive, as there are abundant complex interactions present in the large size of genomic and chemical spaces. For alleviating this phenomenon, plenty of computational methods are conducted to effectively complement biological experiments and narrow the search spaces into a preferred candidate domain. Whereas, most of the previous approaches cannot fully consider association behavior semantic information based on several schemas to represent complex the structure of heterogeneous biological networks. Additionally, the prediction of DTI based on single modalities cannot satisfy the demand for prediction accuracy. METHODS We propose a multi-modal representation framework of 'DeepMPF' based on meta-path semantic analysis, which effectively utilizes heterogeneous information to predict DTI. Specifically, we first construct protein-drug-disease heterogeneous networks composed of three entities. Then the feature information is obtained under three views, containing sequence modality, heterogeneous structure modality and similarity modality. We proposed six representative schemas of meta-path to preserve the high-order nonlinear structure and catch hidden structural information of the heterogeneous network. Finally, DeepMPF generates highly representative comprehensive feature descriptors and calculates the probability of interaction through joint learning. RESULTS To evaluate the predictive performance of DeepMPF, comparison experiments are conducted on four gold datasets. Our method can obtain competitive performance in all datasets. We also explore the influence of the different feature embedding dimensions, learning strategies and classification methods. Meaningfully, the drug repositioning experiments on COVID-19 and HIV demonstrate DeepMPF can be applied to solve problems in reality and help drug discovery. The further analysis of molecular docking experiments enhances the credibility of the drug candidates predicted by DeepMPF. CONCLUSIONS All the results demonstrate the effectively predictive capability of DeepMPF for drug-target interactions. It can be utilized as a useful tool to prescreen the most potential drug candidates for the protein. The web server of the DeepMPF predictor is freely available at http://120.77.11.78/DeepMPF/ , which can help relevant researchers to further study.
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Affiliation(s)
- Zhong-Hao Ren
- grid.460132.20000 0004 1758 0275School of Information Engineering, Xijing University, Xi’an, 710100 China
| | - Zhu-Hong You
- grid.440588.50000 0001 0307 1240School of Computer Science, Northwestern Polytechnical University, Xi’an, 710129 China
| | - Quan Zou
- grid.54549.390000 0004 0369 4060Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054 China
| | - Chang-Qing Yu
- grid.460132.20000 0004 1758 0275School of Information Engineering, Xijing University, Xi’an, 710100 China
| | - Yan-Fang Ma
- grid.417234.70000 0004 1808 3203Department of Galactophore, The Third People’s Hospital of Gansu Province, Lanzhou, 730020 China
| | - Yong-Jian Guan
- grid.460132.20000 0004 1758 0275School of Information Engineering, Xijing University, Xi’an, 710100 China
| | - Hai-Ru You
- grid.440588.50000 0001 0307 1240School of Computer Science, Northwestern Polytechnical University, Xi’an, 710129 China
| | - Xin-Fei Wang
- grid.460132.20000 0004 1758 0275School of Information Engineering, Xijing University, Xi’an, 710100 China
| | - Jie Pan
- grid.460132.20000 0004 1758 0275School of Information Engineering, Xijing University, Xi’an, 710100 China
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Fu Y, Yang R, Zhang L. Association prediction of CircRNAs and diseases using multi-homogeneous graphs and variational graph auto-encoder. Comput Biol Med 2022; 151:106289. [PMID: 36401973 DOI: 10.1016/j.compbiomed.2022.106289] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/19/2022] [Accepted: 11/06/2022] [Indexed: 11/12/2022]
Abstract
As a non-coding RNA molecule with closed-loop structure, circular RNA (circRNA) is tissue-specific and cell-specific in expression pattern. It regulates disease development by modulating the expression of disease-related genes. Therefore, exploring the circRNA-disease relationship can reveal the molecular mechanism of disease pathogenesis. Biological experiments for detecting circRNA-disease associations are time-consuming and laborious. Constrained by the sparsity of known circRNA-disease associations, existing algorithms cannot obtain relatively complete structural information to represent features accurately. To this end, this paper proposes a new predictor, VGAERF, combining Variational Graph Auto-Encoder (VGAE) and Random Forest (RF). Firstly, circRNA homogeneous graph structure and disease homogeneous graph structure are constructed by Gaussian interaction profile (GIP) kernel similarity, semantic similarity, and known circRNA-disease associations. VGAEs with the same structure are employed to extract the higher-order features by the encoding and decoding of input graph structures. To further increase the completeness of the network structure information, the deep features acquired from the two VGAEs are summed, and then train the RF with sparse data processing capability to perform the prediction task. On the independent test set, the Area Under ROC Curve (AUC), accuracy, and Area Under PR Curve (AUPR) of the proposed method reach up to 0.9803, 0.9345, and 0.9894, respectively. On the same dataset, the AUC, accuracy, and AUPR of VGAERF are 2.09%, 5.93%, and 1.86% higher than the best-performing method (AEDNN). It is anticipated that VGAERF will provide significant information to decipher the molecular mechanisms of circRNA-disease associations, and promote the diagnosis of circRNA-related diseases.
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Affiliation(s)
- Yao Fu
- The School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai, 264209, China.
| | - Runtao Yang
- The School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai, 264209, China.
| | - Lina Zhang
- The School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai, 264209, China.
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14
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Tangmanussukum P, Kawichai T, Suratanee A, Plaimas K. Heterogeneous network propagation with forward similarity integration to enhance drug-target association prediction. PeerJ Comput Sci 2022; 8:e1124. [PMID: 36262151 PMCID: PMC9575853 DOI: 10.7717/peerj-cs.1124] [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: 06/17/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Identification of drug-target interaction (DTI) is a crucial step to reduce time and cost in the drug discovery and development process. Since various biological data are publicly available, DTIs have been identified computationally. To predict DTIs, most existing methods focus on a single similarity measure of drugs and target proteins, whereas some recent methods integrate a particular set of drug and target similarity measures by a single integration function. Therefore, many DTIs are still missing. In this study, we propose heterogeneous network propagation with the forward similarity integration (FSI) algorithm, which systematically selects the optimal integration of multiple similarity measures of drugs and target proteins. Seven drug-drug and nine target-target similarity measures are applied with four distinct integration methods to finally create an optimal heterogeneous network model. Consequently, the optimal model uses the target similarity based on protein sequences and the fused drug similarity, which combines the similarity measures based on chemical structures, the Jaccard scores of drug-disease associations, and the cosine scores of drug-drug interactions. With an accuracy of 99.8%, this model significantly outperforms others that utilize different similarity measures of drugs and target proteins. In addition, the validation of the DTI predictions of this model demonstrates the ability of our method to discover missing potential DTIs.
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Affiliation(s)
- Piyanut Tangmanussukum
- Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Thitipong Kawichai
- Department of Mathematics and Computer Science, Academic Division, Chulachomklao Royal Military Academy, Nakhon Nayok, Thailand
| | - Apichat Suratanee
- Department of Mathematics, Faculty of Applied Science, King Mongkut’s University of Technology North Bangkok, Bangkok, Thailand
- Intelligent and Nonlinear Dynamics Innovations Research Center, Science and Technology Research Institute, King Mongkut’s University of Technology North Bangkok, Bangkok, Thailand
| | - Kitiporn Plaimas
- Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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15
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Lu D, Pan R, Wu W, Zhang Y, Li S, Xu H, Huang J, Xia J, Wang Q, Luan X, Lv C, Zhang W, Meng G. FL-DTD: an integrated pipeline to predict the drug interacting targets by feedback loop-based network analysis. Brief Bioinform 2022; 23:6632928. [PMID: 35794722 DOI: 10.1093/bib/bbac263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 11/12/2022] Open
Abstract
Drug target discovery is an essential step to reveal the mechanism of action (MoA) underlying drug therapeutic effects and/or side effects. Most of the approaches are usually labor-intensive while unable to identify the tissue-specific interacting targets, especially the targets with weaker drug binding affinity. In this work, we proposed an integrated pipeline, FL-DTD, to predict the drug interacting targets of novel compounds in a tissue-specific manner. This method was built based on a hypothesis that cells under a status of homeostasis would take responses to drug perturbation by activating feedback loops. Therefore, the drug interacting targets can be predicted by analyzing the network responses after drug perturbation. We evaluated this method using the expression data of estrogen stimulation, gene manipulation and drug perturbation and validated its good performance to identify the annotated drug targets. Using STAT3 as a target protein, we applied this method to drug perturbation data of 500 natural compounds and predicted five compounds with STAT3 interacting activities. Experimental assay validated the STAT3-interacting activities of four compounds. Overall, our evaluation suggests that FL-DTD predicts the drug interacting targets with good accuracy and can be used for drug target discovery.
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Affiliation(s)
- Dong Lu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Rongrong Pan
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Wenxuan Wu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Yanyan Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Shensuo Li
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Hong Xu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Jialan Huang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Jianhua Xia
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Qun Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Xin Luan
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Chao Lv
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Weidong Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
| | - Guofeng Meng
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Cailun 1200, 201203, Shanghai, China
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