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Lee KH, Won SJ, Oyinloye P, Shi L. Unlocking the Potential of High-Quality Dopamine Transporter Pharmacological Data: Advancing Robust Machine Learning-Based QSAR Modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583803. [PMID: 38558976 PMCID: PMC10979915 DOI: 10.1101/2024.03.06.583803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The dopamine transporter (DAT) plays a critical role in the central nervous system and has been implicated in numerous psychiatric disorders. The ligand-based approaches are instrumental to decipher the structure-activity relationship (SAR) of DAT ligands, especially the quantitative SAR (QSAR) modeling. By gathering and analyzing data from literature and databases, we systematically assemble a diverse range of ligands binding to DAT, aiming to discern the general features of DAT ligands and uncover the chemical space for potential novel DAT ligand scaffolds. The aggregation of DAT pharmacological activity data, particularly from databases like ChEMBL, provides a foundation for constructing robust QSAR models. The compilation and meticulous filtering of these data, establishing high-quality training datasets with specific divisions of pharmacological assays and data types, along with the application of QSAR modeling, prove to be a promising strategy for navigating the pertinent chemical space. Through a systematic comparison of DAT QSAR models using training datasets from various ChEMBL releases, we underscore the positive impact of enhanced data set quality and increased data set size on the predictive power of DAT QSAR models.
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Affiliation(s)
- Kuo Hao Lee
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Sung Joon Won
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Precious Oyinloye
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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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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Cho K, Hansen PE. Structure Identification of Novel Compounds Using Simple IR,
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C NMR Spectroscopy and Computational Tools. B KOREAN CHEM SOC 2019. [DOI: 10.1002/bkcs.11924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kwang‐Hwi Cho
- School of Systems Biomedical ScienceSoongsil University Seoul 06978 Republic of Korea
| | - Poul Erik Hansen
- Department of Science and EnvironmentRoskilde University Roskilde DK‐4000 Denmark
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Affiliation(s)
- Sona Peter Mbue
- Department of Bioinformatics and Life Science, School of Systems Biomedical Science; Soongsil University; Seoul 156-743 Republic of Korea
| | - Kwang-Hwi Cho
- Department of Bioinformatics and Life Science, School of Systems Biomedical Science; Soongsil University; Seoul 156-743 Republic of Korea
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O'Boyle NM. Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI. J Cheminform 2012; 4:22. [PMID: 22989151 PMCID: PMC3495655 DOI: 10.1186/1758-2946-4-22] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 09/03/2012] [Indexed: 11/10/2022] Open
Abstract
UNLABELLED BACKGROUND There are two line notations of chemical structures that have established themselves in the field: the SMILES string and the InChI string. The InChI aims to provide a unique, or canonical, identifier for chemical structures, while SMILES strings are widely used for storage and interchange of chemical structures, but no standard exists to generate a canonical SMILES string. RESULTS I describe how to use the InChI canonicalisation to derive a canonical SMILES string in a straightforward way, either incorporating the InChI normalisations (Inchified SMILES) or not (Universal SMILES). This is the first description of a method to generate canonical SMILES that takes stereochemistry into account. When tested on the 1.1 m compounds in the ChEMBL database, and a 1 m compound subset of the PubChem Substance database, no canonicalisation failures were found with Inchified SMILES. Using Universal SMILES, 99.79% of the ChEMBL database was canonicalised successfully and 99.77% of the PubChem subset. CONCLUSIONS The InChI canonicalisation algorithm can successfully be used as the basis for a common standard for canonical SMILES. While challenges remain - such as the development of a standard aromatic model for SMILES - the ability to create the same SMILES using different toolkits will mean that for the first time it will be possible to easily compare the chemical models used by different toolkits.
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Affiliation(s)
- Noel M O'Boyle
- Analytical and Biological Chemistry Research Facility, Cavanagh Pharmacy Building, University College Cork, Cork, Co, Cork, Ireland.
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Martin E, Monge A, Duret JA, Gualandi F, Peitsch MC, Pospisil P. Building an R&D chemical registration system. J Cheminform 2012; 4:11. [PMID: 22650418 PMCID: PMC3430593 DOI: 10.1186/1758-2946-4-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 05/11/2012] [Indexed: 11/16/2022] Open
Abstract
Small molecule chemistry is of central importance to a number of R&D companies in diverse areas such as the pharmaceutical, nutraceutical, food flavoring, and cosmeceutical industries. In order to store and manage thousands of chemical compounds in such an environment, we have built a state-of-the-art master chemical database with unique structure identifiers. Here, we present the concept and methodology we used to build the system that we call the Unique Compound Database (UCD). In the UCD, each molecule is registered only once (uniqueness), structures with alternative representations are entered in a uniform way (normalization), and the chemical structure drawings are recognizable to chemists and to a cartridge. In brief, structural molecules are entered as neutral entities which can be associated with a salt. The salts are listed in a dictionary and bound to the molecule with the appropriate stoichiometric coefficient in an entity called “substance”. The substances are associated with batches. Once a molecule is registered, some properties (e.g., ADMET prediction, IUPAC name, chemical properties) are calculated automatically. The UCD has both automated and manual data controls. Moreover, the UCD concept enables the management of user errors in the structure entry by reassigning or archiving the batches. It also allows updating of the records to include newly discovered properties of individual structures. As our research spans a wide variety of scientific fields, the database enables registration of mixtures of compounds, enantiomers, tautomers, and compounds with unknown stereochemistries.
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Affiliation(s)
- Elyette Martin
- Philip Morris International R&D, Philip Morris Products S,A, Neuchâtel, Switzerland.
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