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Lavecchia A. Advancing drug discovery with deep attention neural networks. Drug Discov Today 2024; 29:104067. [PMID: 38925473 DOI: 10.1016/j.drudis.2024.104067] [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: 05/17/2024] [Revised: 06/10/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
In the dynamic field of drug discovery, deep attention neural networks are revolutionizing our approach to complex data. This review explores the attention mechanism and its extended architectures, including graph attention networks (GATs), transformers, bidirectional encoder representations from transformers (BERT), generative pre-trained transformers (GPTs) and bidirectional and auto-regressive transformers (BART). Delving into their core principles and multifaceted applications, we uncover their pivotal roles in catalyzing de novo drug design, predicting intricate molecular properties and deciphering elusive drug-target interactions. Despite challenges, these attention-based architectures hold unparalleled promise to drive transformative breakthroughs and accelerate progress in pharmaceutical research.
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Affiliation(s)
- Antonio Lavecchia
- Drug Discovery Laboratory, Department of Pharmacy, University of Napoli Federico II, I-80131 Naples, Italy.
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Song D, Tang T, Wang R, Liu H, Xie D, Zhao B, Dang Z, Lu G. Enhancing compound confidence in suspect and non-target screening through machine learning-based retention time prediction. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 347:123763. [PMID: 38492749 DOI: 10.1016/j.envpol.2024.123763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/26/2024] [Accepted: 03/09/2024] [Indexed: 03/18/2024]
Abstract
The retention time (RT) of contaminants of emerging concern (CECs) in liquid chromatography-high-resolution mass spectrometry (LC-HRMS) is crucial for database matching in non-targeted screening (NTS) analysis. In this study, we developed a machine learning (ML) model to predict RTs of CECs in NTS analysis. Using 1051 CEC standards, we evaluated Random Forest (RF), XGBoost, Support Vector Regression (SVR), and Artificial Neural Network (ANN) with molecular fingerprints and chemical descriptors to establish an optimal model. The SVR model utilizing chemical descriptors resulted in good predictive capacity with R2ext = 0.850 and r2 = 0.925. The model was further validated through laboratory NTS compound characterization. When applied to examine CEC occurrence in a large wastewater treatment plant, we identified 40 level S1 CECs (confirmed structure by reference standard) and 234 level S2 compounds (probable structure by library spectrum match). The model predicted RTs for level S2 compounds, leading to the classification of 153 level S2 compounds with high confidence (ΔRT <2 min). The model served as a robust filtering mechanism within the analytical framework. This study emphasizes the importance of predicted RTs in NTS analysis and highlights the potential of prediction models. Our research introduces a workflow that enhances NTS analysis by utilizing RT prediction models to determine compound confidence levels.
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Affiliation(s)
- Dehao Song
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Ting Tang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, China.
| | - Rui Wang
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510655, China; Guangxi Key Laboratory of Emerging Contaminants Monitoring, Early Warning and Environmental Health Risk Assessment, Nanning, 530000, China
| | - He Liu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510655, China; Guangxi Key Laboratory of Emerging Contaminants Monitoring, Early Warning and Environmental Health Risk Assessment, Nanning, 530000, China
| | - Danping Xie
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510655, China; Guangxi Key Laboratory of Emerging Contaminants Monitoring, Early Warning and Environmental Health Risk Assessment, Nanning, 530000, China
| | - Bo Zhao
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510655, China; Guangxi Key Laboratory of Emerging Contaminants Monitoring, Early Warning and Environmental Health Risk Assessment, Nanning, 530000, China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, South China University of Technology, Guangzhou, 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, China
| | - Guining Lu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, China
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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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