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Mao J, Akhtar J, Zhang X, Sun L, Guan S, Li X, Chen G, Liu J, Jeon HN, Kim MS, No KT, Wang G. Comprehensive strategies of machine-learning-based quantitative structure-activity relationship models. iScience 2021; 24:103052. [PMID: 34553136 PMCID: PMC8441174 DOI: 10.1016/j.isci.2021.103052] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Early quantitative structure-activity relationship (QSAR) technologies have unsatisfactory versatility and accuracy in fields such as drug discovery because they are based on traditional machine learning and interpretive expert features. The development of Big Data and deep learning technologies significantly improve the processing of unstructured data and unleash the great potential of QSAR. Here we discuss the integration of wet experiments (which provide experimental data and reliable verification), molecular dynamics simulation (which provides mechanistic interpretation at the atomic/molecular levels), and machine learning (including deep learning) techniques to improve QSAR models. We first review the history of traditional QSAR and point out its problems. We then propose a better QSAR model characterized by a new iterative framework to integrate machine learning with disparate data input. Finally, we discuss the application of QSAR and machine learning to many practical research fields, including drug development and clinical trials.
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Affiliation(s)
- Jiashun Mao
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Computational Science and Material Design, Shenzhen, Guangdong 518055 China
| | - Javed Akhtar
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen, Guangdong 518055, China
| | - Xiao Zhang
- Shanghai Rural Commercial Bank Co., Ltd, Shanghai 200002, China
| | - Liang Sun
- Department of Physics, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Shenghui Guan
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Computational Science and Material Design, Shenzhen, Guangdong 518055 China
| | - Xinyu Li
- School of Life and Health Sciences and Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Guangming Chen
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen, Guangdong 518055, China
| | - Jiaxin Liu
- Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyeon-Nae Jeon
- Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Min Sung Kim
- Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Kyoung Tai No
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea
| | - Guanyu Wang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Computational Science and Material Design, Shenzhen, Guangdong 518055 China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen, Guangdong 518055, China
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Hall A, Chanteux H, Ménochet K, Ledecq M, Schulze MSED. Designing Out PXR Activity on Drug Discovery Projects: A Review of Structure-Based Methods, Empirical and Computational Approaches. J Med Chem 2021; 64:6413-6522. [PMID: 34003642 DOI: 10.1021/acs.jmedchem.0c02245] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This perspective discusses the role of pregnane xenobiotic receptor (PXR) in drug discovery and the impact of its activation on CYP3A4 induction. The use of structural biology to reduce PXR activity on drug discovery projects has become more common in recent years. Analysis of this work highlights several important molecular interactions, and the resultant structural modifications to reduce PXR activity are summarized. The computational approaches undertaken to support the design of new drugs devoid of PXR activation potential are also discussed. Finally, the SAR of empirical design strategies to reduce PXR activity is reviewed, and the key SAR transformations are discussed and summarized. In conclusion, this perspective demonstrates that PXR activity can be greatly diminished or negated on active drug discovery projects with the knowledge now available. This perspective should be useful to anyone who seeks to reduce PXR activity on a drug discovery project.
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Affiliation(s)
- Adrian Hall
- UCB, Avenue de l'Industrie, Braine-L'Alleud 1420, Belgium
| | | | | | - Marie Ledecq
- UCB, Avenue de l'Industrie, Braine-L'Alleud 1420, Belgium
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Ma S, Hwang S, Lee S, Acree WE, No KT. Incorporation of Hydrogen Bond Angle Dependency into the Generalized Solvation Free Energy Density Model. J Chem Inf Model 2018; 58:761-772. [PMID: 29561152 DOI: 10.1021/acs.jcim.7b00410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To describe the physically realistic solvation free energy surface of a molecule in a solvent, a generalized version of the solvation free energy density (G-SFED) calculation method has been developed. In the G-SFED model, the contribution from the hydrogen bond (HB) between a solute and a solvent to the solvation free energy was calculated as the product of the acidity of the donor and the basicity of the acceptor of an HB pair. The acidity and basicity parameters of a solute were derived using the summation of acidities and basicities of the respective acidic and basic functional groups of the solute, and that of the solvent was experimentally determined. Although the contribution of HBs to the solvation free energy could be evenly distributed to grid points on the surface of a molecule, the G-SFED model was still inadequate to describe the angle dependency of the HB of a solute with a polarizable continuum solvent. To overcome this shortcoming of the G-SFED model, the contribution of HBs was formulated using the geometric parameters of the grid points described in the HB coordinate system of the solute. We propose an HB angle dependency incorporated into the G-SFED model, i.e., the G-SFED-HB model, where the angular-dependent acidity and basicity densities are defined and parametrized with experimental data. The G-SFED-HB model was then applied to calculate the solvation free energies of organic molecules in water, various alcohols and ethers, and the log P values of diverse organic molecules, including peptides and a protein. Both the G-SFED model and the G-SFED-HB model reproduced the experimental solvation free energies with similar accuracy, whereas the distributions of the SFED on the molecular surface calculated by the G-SFED and G-SFED-HB models were quite different, especially for molecules having HB donors or acceptors. Since the angle dependency of HBs was included in the G-SFED-HB model, the SFED distribution of the G-SFED-HB model is well described as compared to that of the G-SFED model.
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Affiliation(s)
- Songling Ma
- Department of Biotechnology , Yonsei University , Seoul 120-749 , Korea.,Bioinformatics and Molecular Design Research Center , Seoul 120-749 , Korea
| | - Sungbo Hwang
- Department of Biotechnology , Yonsei University , Seoul 120-749 , Korea
| | - Sehan Lee
- Department of Biotechnology , Yonsei University , Seoul 120-749 , Korea.,Gulf Ecology Division , U.S. Environmental Protection Agency , Gulf Breeze , Florida 32561 , United States
| | - William E Acree
- Department of Chemistry , University of North Texas , 1155 Union Circle Drive #305070 , Denton , Texas 76230-5017 , United States
| | - Kyoung Tai No
- Department of Biotechnology , Yonsei University , Seoul 120-749 , Korea.,Bioinformatics and Molecular Design Research Center , Seoul 120-749 , Korea
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Lee K, You H, Choi J, No KT. Development of pharmacophore-based classification model for activators of constitutive androstane receptor. Drug Metab Pharmacokinet 2016; 32:172-178. [PMID: 28366619 DOI: 10.1016/j.dmpk.2016.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/21/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
Abstract
Constitutive androstane receptor (CAR) is predominantly expressed in the liver and is important for regulating drug metabolism and transport. Despite its biological importance, there have been few attempts to develop in silico models to predict the activity of CAR modulated by chemical compounds. The number of in silico studies of CAR may be limited because of CAR's constitutive activity under normal conditions, which makes it difficult to elucidate the key structural features of the interaction between CAR and its ligands. In this study, to address these limitations, we introduced 3D pharmacophore-based descriptors with an integrated ligand and structure-based pharmacophore features, which represent the receptor-ligand interaction. Machine learning methods (support vector machine and artificial neural network) were applied to develop an in silico model with the descriptors containing significant information regarding the ligand binding positions. The best classification model built with a solvent accessibility volume-based filter and the support vector machine showed good predictabilities of 87%, and 85.4% for the training set and validation set, respectively. This demonstrates that our model can be used to accurately predict CAR activators and offers structural information regarding ligand/protein interactions.
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Affiliation(s)
- Kyungro Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Hwan You
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Jiwon Choi
- Bioinformatics & Molecular Design Research Center, Yonsei University, Seoul 03722, South Korea
| | - Kyoung Tai No
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea; Bioinformatics & Molecular Design Research Center, Yonsei University, Seoul 03722, South Korea.
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