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Kumar V, Singh P, Parate S, Singh R, Ro HS, Song KS, Lee KW, Park YM. Computational insights into allosteric inhibition of focal adhesion kinase: A combined pharmacophore modeling and molecular dynamics approach. J Mol Graph Model 2024; 130:108789. [PMID: 38718434 DOI: 10.1016/j.jmgm.2024.108789] [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: 03/05/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024]
Abstract
Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that modulates integrin and growth factor signaling pathways and is implicated in cancer cell migration, proliferation, and survival. Over the past decade various, FAK kinase, FERM, and FAT domain inhibitors have been reported and a few kinase domain inhibitors are under clinical consideration. However, few of them were identified as multikinase inhibitors. In kinase drug design selectivity is always a point of concern, to improve selectivity allosteric inhibitor development is the best choice. The current research utilized a pharmacophore modeling (PM) approach to identify novel allosteric inhibitors of FAK. The all-available allosteric inhibitor bound 3D structures with PDB ids 4EBV, 4EBW, and 4I4F were utilized for the pharmacophore modeling. The validated PM models were utilized to map a database of 770,550 compounds prepared from ZINC, EXIMED, SPECS, ASINEX, and InterBioScreen, aiming to identify potential allosteric inhibitors. The obtained compounds from screening step were forwarded to molecular docking (MD) for the prediction of binding orientation inside the allosteric site and the results were evaluated with the known FAK allosteric inhibitor (REF). Finally, 14 FAK-inhibitor complexes were selected from the docking study and were studied under molecular dynamics simulations (MDS) for 500 ns. The complexes were ranked according to binding free energy (BFE) and those demonstrated higher affinity for allosteric site of FAK than REF inhibitors were selected. The selected complexes were further analyzed for intermolecular interactions and finally, three potential allosteric inhibitor candidates for the inhibition of FAK protein were identified. We believe that identified scaffolds may help in drug development against FAK as an anticancer agent.
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Affiliation(s)
- Vikas Kumar
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Science, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea; Computational Biophysics Lab, Basque Center for Materials, Applications, and Nanostructures (BCMaterials), Buil. Martina Casiano, Pl. 3 Parque Científico UPV/EHU Barrio Sarriena, Leioa, 48940, Spain.
| | - Pooja Singh
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Shraddha Parate
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden
| | - Rajender Singh
- Division of Crop Improvement and Seed Technology ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Hyeon-Su Ro
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Science, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Kyoung Seob Song
- Department of Medical Science, Kosin University College of Medicine, 194 Wachi-ro, Yeongdo-gu, Busan, 49104, Republic of Korea
| | - Keun Woo Lee
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Science, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea; Angel i-Drug Design (AiDD), 33-3 Jinyangho-ro 44, Jinju, 52650, Republic of Korea.
| | - Yeong-Min Park
- Department of Integrative Biological Sciences and Industry, Sejong University 209, Neugdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea.
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Amorim AM, Piochi LF, Gaspar AT, Preto A, Rosário-Ferreira N, Moreira IS. Advancing Drug Safety in Drug Development: Bridging Computational Predictions for Enhanced Toxicity Prediction. Chem Res Toxicol 2024; 37:827-849. [PMID: 38758610 PMCID: PMC11187637 DOI: 10.1021/acs.chemrestox.3c00352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/19/2024]
Abstract
The attrition rate of drugs in clinical trials is generally quite high, with estimates suggesting that approximately 90% of drugs fail to make it through the process. The identification of unexpected toxicity issues during preclinical stages is a significant factor contributing to this high rate of failure. These issues can have a major impact on the success of a drug and must be carefully considered throughout the development process. These late-stage rejections or withdrawals of drug candidates significantly increase the costs associated with drug development, particularly when toxicity is detected during clinical trials or after market release. Understanding drug-biological target interactions is essential for evaluating compound toxicity and safety, as well as predicting therapeutic effects and potential off-target effects that could lead to toxicity. This will enable scientists to predict and assess the safety profiles of drug candidates more accurately. Evaluation of toxicity and safety is a critical aspect of drug development, and biomolecules, particularly proteins, play vital roles in complex biological networks and often serve as targets for various chemicals. Therefore, a better understanding of these interactions is crucial for the advancement of drug development. The development of computational methods for evaluating protein-ligand interactions and predicting toxicity is emerging as a promising approach that adheres to the 3Rs principles (replace, reduce, and refine) and has garnered significant attention in recent years. In this review, we present a thorough examination of the latest breakthroughs in drug toxicity prediction, highlighting the significance of drug-target binding affinity in anticipating and mitigating possible adverse effects. In doing so, we aim to contribute to the development of more effective and secure drugs.
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Affiliation(s)
- Ana M.
B. Amorim
- Department
of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CNC-UC—Center
for Neuroscience and Cell Biology, University
of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CIBB—Centre
for Innovative Biomedicine and Biotechnology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- PhD
Programme in Biosciences, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- PURR.AI,
Rua Pedro Nunes, IPN Incubadora, Ed C, 3030-199 Coimbra, Portugal
| | - Luiz F. Piochi
- Department
of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CNC-UC—Center
for Neuroscience and Cell Biology, University
of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CIBB—Centre
for Innovative Biomedicine and Biotechnology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Ana T. Gaspar
- Department
of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CNC-UC—Center
for Neuroscience and Cell Biology, University
of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CIBB—Centre
for Innovative Biomedicine and Biotechnology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - António
J. Preto
- CNC-UC—Center
for Neuroscience and Cell Biology, University
of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CIBB—Centre
for Innovative Biomedicine and Biotechnology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- PhD Programme
in Experimental Biology and Biomedicine, Institute for Interdisciplinary
Research (IIIUC), University of Coimbra, Casa Costa Alemão, 3030-789 Coimbra, Portugal
| | - Nícia Rosário-Ferreira
- CNC-UC—Center
for Neuroscience and Cell Biology, University
of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CIBB—Centre
for Innovative Biomedicine and Biotechnology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Irina S. Moreira
- Department
of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CNC-UC—Center
for Neuroscience and Cell Biology, University
of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CIBB—Centre
for Innovative Biomedicine and Biotechnology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
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3
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Kaboudi N, Asl SG, Nourani N, Shayanfar A. Solubilization of drugs using beta-cyclodextrin: Experimental data and modeling. ANNALES PHARMACEUTIQUES FRANÇAISES 2024; 82:663-672. [PMID: 38340807 DOI: 10.1016/j.pharma.2024.02.003] [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: 12/18/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Many drug candidates fail to complete the entire drug development process because of poor physicochemical properties. Solubility is an important physicochemical property which plays a vital role in various stages of drug discovery and development. Several methods have been proposed to enhance the solubility of drugs, and complex formation with cyclodextrins is among them. Beta-cyclodextrin (βCD) is a common excipient for solubilization of drugs. The aim of this study is to develop the mechanistic QSPR models to predict the solubility enhancement of a drug in the presence of βCD. In this study, the solubility enhancement of some drugs in the presence of 10mM βCD at 25°C was experimentally determined or collected from the literature. Two different models to predict the solubilization by βCD were developed by binary logistic regression using structural properties of drugs with more than 80% accuracy. Polar surface area and excess molar refraction are the main parameters for estimating solubilization by βCD. Moreover, other descriptors related to hydrophobicity and the capability of hydrogen bonding formation of molecules could improve the accuracy of the established models.
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Affiliation(s)
- Navid Kaboudi
- Student Research Committee, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saba Ghasemi Asl
- Student Research Committee, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasim Nourani
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Shayanfar
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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Li Y, Liu B, Deng J, Guo Y, Du H. Image-based molecular representation learning for drug development: a survey. Brief Bioinform 2024; 25:bbae294. [PMID: 38920347 PMCID: PMC11200195 DOI: 10.1093/bib/bbae294] [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: 03/12/2024] [Revised: 05/19/2024] [Accepted: 06/08/2024] [Indexed: 06/27/2024] Open
Abstract
Artificial intelligence (AI) powered drug development has received remarkable attention in recent years. It addresses the limitations of traditional experimental methods that are costly and time-consuming. While there have been many surveys attempting to summarize related research, they only focus on general AI or specific aspects such as natural language processing and graph neural network. Considering the rapid advance on computer vision, using the molecular image to enable AI appears to be a more intuitive and effective approach since each chemical substance has a unique visual representation. In this paper, we provide the first survey on image-based molecular representation for drug development. The survey proposes a taxonomy based on the learning paradigms in computer vision and reviews a large number of corresponding papers, highlighting the contributions of molecular visual representation in drug development. Besides, we discuss the applications, limitations and future directions in the field. We hope this survey could offer valuable insight into the use of image-based molecular representation learning in the context of drug development.
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Affiliation(s)
- Yue Li
- Division of Gastroenterology, Dongzhimen Hospital, Beijing University of Chinese Medicine, No. 5 Haiyun Warehouse, 100700, Beijing, China
| | - Bingyan Liu
- School of Computer Science, Beijing University of Posts and Telecommunications, No.10 Xituchen Street, 100876, Beijing, China
| | - Jinyan Deng
- Division of Gastroenterology, Dongzhimen Hospital, Beijing University of Chinese Medicine, No. 5 Haiyun Warehouse, 100700, Beijing, China
| | - Yi Guo
- Division of Gastroenterology, Dongzhimen Hospital, Beijing University of Chinese Medicine, No. 5 Haiyun Warehouse, 100700, Beijing, China
| | - Hongbo Du
- Division of Gastroenterology, Dongzhimen Hospital, Beijing University of Chinese Medicine, No. 5 Haiyun Warehouse, 100700, Beijing, China
- Institute of Liver Disease, Beijing University of Chinese Medicine, No. 5 Haiyun Warehouse, 100700, Beijing, China
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5
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Ahmadi M, Alizadeh B, Ayyoubzadeh SM, Abiyarghamsari M. Predicting Pharmacokinetics of Drugs Using Artificial Intelligence Tools: A Systematic Review. Eur J Drug Metab Pharmacokinet 2024; 49:249-262. [PMID: 38457092 DOI: 10.1007/s13318-024-00883-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND AND OBJECTIVE Pharmacokinetic studies encompass the examination of the absorption, distribution, metabolism, and excretion of bioactive compounds. The pharmacokinetics of drugs exert a substantial influence on their efficacy and safety. Consequently, the investigation of pharmacokinetics holds great importance. However, laboratory-based assessment necessitates the use of numerous animals, various materials, and significant time. To mitigate these challenges, alternative methods such as artificial intelligence have emerged as a promising approach. This systematic review aims to review existing studies, focusing on the application of artificial intelligence tools in predicting the pharmacokinetics of drugs. METHODS A pre-prepared search strategy based on related keywords was used to search different databases (PubMed, Scopus, Web of Science). The process involved combining articles, eliminating duplicates, and screening articles based on their titles, abstracts, and full text. Articles were selected based on inclusion and exclusion criteria. Then, the quality of the included articles was assessed using an appraisal tool. RESULTS Ultimately, 23 relevant articles were included in this study. The clearance parameter received the highest level of investigation, followed by the area under the concentration-time curve (AUC) parameter, in pharmacokinetic studies. Among the various models employed in the articles, Random Forest and eXtreme Gradient Boosting (XGBoost) emerged as the most commonly utilized ones. Generalized Linear Models and Elastic Nets (GLMnet) and Random Forest models showed the most performance in predicting clearance. CONCLUSION Overall, artificial intelligence tools offer a robust, rapid, and precise means of predicting various pharmacokinetic parameters based on a dataset containing information of patients or drugs.
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Affiliation(s)
- Mahnaz Ahmadi
- Student Research Committee, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Medical Nanotechnology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahareh Alizadeh
- Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Mohammad Ayyoubzadeh
- Department of Health Information Management, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
- Health Information Management Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdiye Abiyarghamsari
- Department of Clinical Pharmacy, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, 1991953381, Iran.
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6
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Guo W, Dong Y, Hao GF. Transfer learning empowers accurate pharmacokinetics prediction of small samples. Drug Discov Today 2024; 29:103946. [PMID: 38460571 DOI: 10.1016/j.drudis.2024.103946] [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: 01/08/2024] [Revised: 02/22/2024] [Accepted: 03/05/2024] [Indexed: 03/11/2024]
Abstract
Accurate assessment of pharmacokinetic (PK) properties is crucial for selecting optimal candidates and avoiding downstream failures. Transfer learning is an innovative machine learning approach enabling high-throughput prediction with limited data. Recently, transfer learning methods showed promise in predicting ADME/PK parameters. Given the prolific growth of research on transfer learning for PK prediction, a comprehensive review of its advantages and challenges is imperative. This study explores the fundamentals, classifications, toolkits and applications of various transfer learning techniques for PK prediction, demonstrating their utility through three practical case studies. This work will serve as a reference for drug design researchers.
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Affiliation(s)
- Wenbo Guo
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Yawen Dong
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China.
| | - Ge-Fei Hao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China.
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7
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Yoshikai Y, Mizuno T, Nemoto S, Kusuhara H. Difficulty in chirality recognition for Transformer architectures learning chemical structures from string representations. Nat Commun 2024; 15:1197. [PMID: 38365821 PMCID: PMC10873378 DOI: 10.1038/s41467-024-45102-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 01/11/2024] [Indexed: 02/18/2024] Open
Abstract
Recent years have seen rapid development of descriptor generation based on representation learning of extremely diverse molecules, especially those that apply natural language processing (NLP) models to SMILES, a literal representation of molecular structure. However, little research has been done on how these models understand chemical structure. To address this black box, we investigated the relationship between the learning progress of SMILES and chemical structure using a representative NLP model, the Transformer. We show that while the Transformer learns partial structures of molecules quickly, it requires extended training to understand overall structures. Consistently, the accuracy of molecular property predictions using descriptors generated from models at different learning steps was similar from the beginning to the end of training. Furthermore, we found that the Transformer requires particularly long training to learn chirality and sometimes stagnates with low performance due to misunderstanding of enantiomers. These findings are expected to deepen the understanding of NLP models in chemistry.
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Affiliation(s)
- Yasuhiro Yoshikai
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, Japan
| | - Tadahaya Mizuno
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, Japan.
| | - Shumpei Nemoto
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, Japan
| | - Hiroyuki Kusuhara
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, Japan
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8
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Ciura K. Modeling of small molecule's affinity to phospholipids using IAM-HPLC and QSRR approach enhanced by similarity-based machine algorithms. J Chromatogr A 2024; 1714:464549. [PMID: 38056392 DOI: 10.1016/j.chroma.2023.464549] [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: 10/09/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
Immobilized artificial membrane chromatography (IAM) has been proposed as a more biosimilar alternative to classical lipophilicity measurement. Determination of small molecule's affinity to phospholipids can be supported for predicting their behavior in the human body. Therefore, a better understanding of the molecular interaction mechanism between small xenobiotics and phospholipids can accelerate drug discovery. Here, the quantitative structure-retention relationships (QSRR) approach was integrated with mechanistic descriptors calculated using Chemicalize software to propose an easy-to-interpretation QSRR model. Considering the heterogeneous character of the data set, locally weighted least squares kernel regression belonging to similarity-based machine learning methods have been applied. The results showed that lipophilicity, charge, and maximum projection area determine molecule binding to phospholipids. Full validation of the obtained model based on OECD recommendations has been performed and the applicability domain was defined using the probability-oriented distance-based approach. The high values of predictive squared correlation coefficient (Q2), and small root mean square error of prediction (RMSEP), 0.812 and 6.739, respectively, confirmed that the obtained QSRR model is not well-fitted to the training data but also showed prediction power. Additionally, only 1.5% of molecules from the training set and 2.8% from the validation test are outside the applicability domain, confirming great predictive abilities.
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Affiliation(s)
- Krzesimir Ciura
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, Gdańsk 80-416, Poland; QSAR Lab Ltd., Trzy Lipy 3St., Gdańsk 80-172, Poland.
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9
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Tran TTV, Tayara H, Chong KT. Recent Studies of Artificial Intelligence on In Silico Drug Absorption. J Chem Inf Model 2023; 63:6198-6211. [PMID: 37819031 DOI: 10.1021/acs.jcim.3c00960] [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] [Indexed: 10/13/2023]
Abstract
Absorption is an important area of research in pharmacochemistry and drug development, because the drug has to be absorbed before any drug effects can occur. Furthermore, the ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) profile of drugs can be directly and considerably altered by modulating factors affecting absorption. Many drugs in development fail because of poor absorption. The research and continuous efforts of researchers in recent years have brought many successes and promises in drug absorption property prediction, especially in silico, which helps to reduce the time and cost significantly for screening undesirable drug candidates. In this report, we explicitly provide an overview of recent in silico studies on predicting absorption properties, especially from 2019 to the present, using artificial intelligence. Additionally, we have collected and investigated public databases that support absorption prediction research. On those grounds, we also proposed the challenges and development directions of absorption prediction in the future. We hope this review can provide researchers with valuable guidelines on absorption prediction to facilitate the development of newer approaches in drug discovery.
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Affiliation(s)
- Thi Tuyet Van Tran
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Faculty of Information Technology, An Giang University, Long Xuyen 880000, Vietnam
- Vietnam National University, Ho Chi Minh City, Ho Chi Minh 700000, Vietnam
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Kil To Chong
- Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Republic of Korea
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Habiballah S, Reisfeld B. Adapting physiologically-based pharmacokinetic models for machine learning applications. Sci Rep 2023; 13:14934. [PMID: 37696914 PMCID: PMC10495394 DOI: 10.1038/s41598-023-42165-3] [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: 04/08/2023] [Accepted: 09/06/2023] [Indexed: 09/13/2023] Open
Abstract
Both machine learning and physiologically-based pharmacokinetic models are becoming essential components of the drug development process. Integrating the predictive capabilities of physiologically-based pharmacokinetic (PBPK) models within machine learning (ML) pipelines could offer significant benefits in improving the accuracy and scope of drug screening and evaluation procedures. Here, we describe the development and testing of a self-contained machine learning module capable of faithfully recapitulating summary pharmacokinetic (PK) parameters produced by a full PBPK model, given a set of input drug-specific and regimen-specific information. Because of its widespread use in characterizing the disposition of orally administered drugs, the PBPK model chosen to demonstrate the methodology was an open-source implementation of a state-of-the-art compartmental and transit model called OpenCAT. The model was tested for drug formulations spanning a large range of solubility and absorption characteristics, and was evaluated for concordance against predictions of OpenCAT and relevant experimental data. In general, the values predicted by the ML models were within 20% of those of the PBPK model across the range of drug and formulation properties. However, summary PK parameter predictions from both the ML model and full PBPK model were occasionally poor with respect to those derived from experiments, suggesting deficiencies in the underlying PBPK model.
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Affiliation(s)
- Sohaib Habiballah
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523-1301, USA
| | - Brad Reisfeld
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523-1301, USA.
- School of Public Health, Colorado State University, Fort Collins, CO, 80523-1612, USA.
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11
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Einarson K, Bendtsen KM, Li K, Thomsen M, Kristensen NR, Winther O, Fulle S, Clemmensen L, Refsgaard HH. Molecular Representations in Machine-Learning-Based Prediction of PK Parameters for Insulin Analogs. ACS OMEGA 2023; 8:23566-23578. [PMID: 37426277 PMCID: PMC10324072 DOI: 10.1021/acsomega.3c01218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023]
Abstract
Therapeutic peptides and proteins derived from either endogenous hormones, such as insulin, or de novo design via display technologies occupy a distinct pharmaceutical space in between small molecules and large proteins such as antibodies. Optimizing the pharmacokinetic (PK) profile of drug candidates is of high importance when it comes to prioritizing lead candidates, and machine-learning models can provide a relevant tool to accelerate the drug design process. Predicting PK parameters of proteins remains difficult due to the complex factors that influence PK properties; furthermore, the data sets are small compared to the variety of compounds in the protein space. This study describes a novel combination of molecular descriptors for proteins such as insulin analogs, where many contained chemical modifications, e.g., attached small molecules for protraction of the half-life. The underlying data set consisted of 640 structural diverse insulin analogs, of which around half had attached small molecules. Other analogs were conjugated to peptides, amino acid extensions, or fragment crystallizable regions. The PK parameters clearance (CL), half-life (T1/2), and mean residence time (MRT) could be predicted by using classical machine-learning models such as Random Forest (RF) and Artificial Neural Networks (ANN) with root-mean-square errors of CL of 0.60 and 0.68 (log units) and average fold errors of 2.5 and 2.9 for RF and ANN, respectively. Both random and temporal data splittings were employed to evaluate ideal and prospective model performance with the best models, regardless of data splitting, achieving a minimum of 70% of predictions within a twofold error. The tested molecular representations include (1) global physiochemical descriptors combined with descriptors encoding the amino acid composition of the insulin analogs, (2) physiochemical descriptors of the attached small molecule, (3) protein language model (evolutionary scale modeling) embedding of the amino acid sequence of the molecules, and (4) a natural language processing inspired embedding (mol2vec) of the attached small molecule. Encoding the attached small molecule via (2) or (4) significantly improved the predictions, while the benefit of using the protein language model-based encoding (3) depended on the used machine-learning model. The most important molecular descriptors were identified as descriptors related to the molecular size of both the protein and protraction part using Shapley additive explanations values. Overall, the results show that combining representations of proteins and small molecules was key for PK predictions of insulin analogs.
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Affiliation(s)
- Kasper
A. Einarson
- Danish
Technical University (DTU), Applied Mathematics
and Computer Science, Kongens Lyngby 2800, Denmark
- Novo
Nordisk A/S, Global Drug Discovery, Research
& Early Development (R&ED), Måløv 2760, Denmark
| | | | - Kang Li
- Novo
Nordisk A/S, Digital Science & Innovation, R&ED, Måløv 2760, Denmark
| | - Maria Thomsen
- Novo
Nordisk A/S, Digital Science & Innovation, R&ED, Måløv 2760, Denmark
| | | | - Ole Winther
- Danish
Technical University (DTU), Applied Mathematics
and Computer Science, Kongens Lyngby 2800, Denmark
- Center
for Genomic Medicine, Rigshospitalet (Copenhagen
University Hospital), Copenhagen 2100, Denmark
- Department
of Biology, Bioinformatics Centre, University
of Copenhagen, Copenhagen 2200, Denmark
| | - Simone Fulle
- Novo
Nordisk A/S, Digital Science & Innovation, R&ED, Måløv 2760, Denmark
| | - Line Clemmensen
- Danish
Technical University (DTU), Applied Mathematics
and Computer Science, Kongens Lyngby 2800, Denmark
| | - Hanne H.F. Refsgaard
- Novo
Nordisk A/S, Global Drug Discovery, Research
& Early Development (R&ED), Måløv 2760, Denmark
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12
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Obrezanova O. Artificial intelligence for compound pharmacokinetics prediction. Curr Opin Struct Biol 2023; 79:102546. [PMID: 36804676 DOI: 10.1016/j.sbi.2023.102546] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 02/17/2023]
Abstract
Optimisation of compound pharmacokinetics (PK) is an integral part of drug discovery and development. Animal in vivo PK data as well as human and animal in vitro systems are routinely utilised to evaluate PK in humans. In recent years machine learning and artificial intelligence (AI) emerged as a major tool for modelling of in vivo animal and human PK, enabling prediction from chemical structure early in drug discovery, and therefore offering opportunities to guide the design and prioritisation of molecules based on relevant in vivo properties and, ultimately, predicting human PK at the point of design. This review presents recent advances in machine learning and AI models for in vivo animal and human PK for small-molecule compounds as well as some examples for antibody therapeutics.
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Affiliation(s)
- Olga Obrezanova
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, CB4 0WJ, UK.
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13
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Chou WC, Lin Z. Machine learning and artificial intelligence in physiologically based pharmacokinetic modeling. Toxicol Sci 2023; 191:1-14. [PMID: 36156156 PMCID: PMC9887681 DOI: 10.1093/toxsci/kfac101] [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] [Indexed: 02/03/2023] Open
Abstract
Physiologically based pharmacokinetic (PBPK) models are useful tools in drug development and risk assessment of environmental chemicals. PBPK model development requires the collection of species-specific physiological, and chemical-specific absorption, distribution, metabolism, and excretion (ADME) parameters, which can be a time-consuming and expensive process. This raises a need to create computational models capable of predicting input parameter values for PBPK models, especially for new compounds. In this review, we summarize an emerging paradigm for integrating PBPK modeling with machine learning (ML) or artificial intelligence (AI)-based computational methods. This paradigm includes 3 steps (1) obtain time-concentration PK data and/or ADME parameters from publicly available databases, (2) develop ML/AI-based approaches to predict ADME parameters, and (3) incorporate the ML/AI models into PBPK models to predict PK summary statistics (eg, area under the curve and maximum plasma concentration). We also discuss a neural network architecture "neural ordinary differential equation (Neural-ODE)" that is capable of providing better predictive capabilities than other ML methods when used to directly predict time-series PK profiles. In order to support applications of ML/AI methods for PBPK model development, several challenges should be addressed (1) as more data become available, it is important to expand the training set by including the structural diversity of compounds to improve the prediction accuracy of ML/AI models; (2) due to the black box nature of many ML models, lack of sufficient interpretability is a limitation; (3) Neural-ODE has great potential to be used to generate time-series PK profiles for new compounds with limited ADME information, but its application remains to be explored. Despite existing challenges, ML/AI approaches will continue to facilitate the efficient development of robust PBPK models for a large number of chemicals.
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Affiliation(s)
- Wei-Chun Chou
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, USA
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32608, USA
| | - Zhoumeng Lin
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, USA
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32608, USA
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14
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Stoyanova R, Katzberger PM, Komissarov L, Khadhraoui A, Sach-Peltason L, Groebke Zbinden K, Schindler T, Manevski N. Computational Predictions of Nonclinical Pharmacokinetics at the Drug Design Stage. J Chem Inf Model 2023; 63:442-458. [PMID: 36595708 DOI: 10.1021/acs.jcim.2c01134] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Although computational predictions of pharmacokinetics (PK) are desirable at the drug design stage, existing approaches are often limited by prediction accuracy and human interpretability. Using a discovery data set of mouse and rat PK studies at Roche (9,685 unique compounds), we performed a proof-of-concept study to predict key PK properties from chemical structure alone, including plasma clearance (CLp), volume of distribution at steady-state (Vss), and oral bioavailability (F). Ten machine learning (ML) models were evaluated, including Single-Task, Multitask, and transfer learning approaches (i.e., pretraining with in vitro data). In addition to prediction accuracy, we emphasized human interpretability of outcomes, especially the quantification of uncertainty, applicability domains, and explanations of predictions in terms of molecular features. Results show that intravenous (IV) PK properties (CLp and Vss) can be predicted with good precision (average absolute fold error, AAFE of 1.96-2.84 depending on data split) and low bias (average fold error, AFE of 0.98-1.36), with AutoGluon, Gaussian Process Regressor (GP), and ChemProp displaying the best performance. Driven by higher complexity of oral PK studies, predictions of F were more challenging, with the best AAFE values of 2.35-2.60 and higher overprediction bias (AFE of 1.45-1.62). Multi-Task approaches and pretraining of ChemProp neural networks with in vitro data showed similar precision to Single-Task models but helped reduce the bias and increase correlations between observations and predictions. A combination of GP-computed prediction variance, molecular clustering, and dimensionality-reduction provided valuable quantitative insights into prediction uncertainty and applicability domains. SHAPley Additive exPlanations (SHAPs) highlighted molecular features contributing to prediction outcomes of Vss, providing explanations that could aid drug design. Combined results show that computational predictions of PK are feasible at the drug design stage, with several ML technologies converging to successfully leverage historical PK data sets. Further studies are needed to unlock the full potential of this approach, especially with respect to data set sizes and quality, transfer learning between in vitro and in vivo data sets, model-independent quantification of uncertainty, and explainability of predictions.
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Affiliation(s)
- Raya Stoyanova
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070Basel, Switzerland
| | - Paul Maximilian Katzberger
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070Basel, Switzerland
| | - Leonid Komissarov
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070Basel, Switzerland
| | - Aous Khadhraoui
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070Basel, Switzerland
| | - Lisa Sach-Peltason
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070Basel, Switzerland
| | - Katrin Groebke Zbinden
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070Basel, Switzerland
| | - Torsten Schindler
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070Basel, Switzerland
| | - Nenad Manevski
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070Basel, Switzerland
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15
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Recent Studies of Artificial Intelligence on In Silico Drug Distribution Prediction. Int J Mol Sci 2023; 24:ijms24031815. [PMID: 36768139 PMCID: PMC9915725 DOI: 10.3390/ijms24031815] [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: 12/14/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Drug distribution is an important process in pharmacokinetics because it has the potential to influence both the amount of medicine reaching the active sites and the effectiveness as well as safety of the drug. The main causes of 90% of drug failures in clinical development are lack of efficacy and uncontrolled toxicity. In recent years, several advances and promising developments in drug distribution property prediction have been achieved, especially in silico, which helped to drastically reduce the time and expense of screening undesired drug candidates. In this study, we provide comprehensive knowledge of drug distribution background, influencing factors, and artificial intelligence-based distribution property prediction models from 2019 to the present. Additionally, we gathered and analyzed public databases and datasets commonly utilized by the scientific community for distribution prediction. The distribution property prediction performance of five large ADMET prediction tools is mentioned as a benchmark for future research. On this basis, we also offer future challenges in drug distribution prediction and research directions. We hope that this review will provide researchers with helpful insight into distribution prediction, thus facilitating the development of innovative approaches for drug discovery.
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16
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Kuroda M, Watanabe R, Esaki T, Kawashima H, Ohashi R, Sato T, Honma T, Komura H, Mizuguchi K. Utilizing public and private sector data to build better machine learning models for the prediction of pharmacokinetic parameters. Drug Discov Today 2022; 27:103339. [PMID: 35973660 DOI: 10.1016/j.drudis.2022.103339] [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: 04/23/2022] [Revised: 07/11/2022] [Accepted: 08/11/2022] [Indexed: 11/20/2022]
Abstract
One solution to compensate for the shortage of publicly available data is to collect more quality-controlled data from the private sector through public-private partnerships. However, several issues must be resolved before implementing such a system. Here, we review the technical aspects of public-private partnerships using our initiative in Japan as an example. In particular, we focus on the procedure for collecting data from multiple private sector companies and building prediction models and discuss how merging public and private sector datasets will help to improve the chemical space coverage and prediction performance. Teaser: Japan's first public-private consortium in pharmacokinetics has incorporated data from multiple pharmaceutical companies to create useful predictive models.
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Affiliation(s)
- Masataka Kuroda
- Artificial Intelligence Centre for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8, Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Discovery Technology Laboratories, Mitsubishi Tanabe Pharma Corporation, 1000, Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan.
| | - Reiko Watanabe
- Artificial Intelligence Centre for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8, Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Tsuyoshi Esaki
- Artificial Intelligence Centre for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8, Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; The Centre for Data Science Education and Research, Shiga University, 1-1-1, Banba, Hikone, Shiga 522-8522, Japan
| | - Hitoshi Kawashima
- Artificial Intelligence Centre for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8, Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Rikiya Ohashi
- Artificial Intelligence Centre for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8, Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Discovery Technology Laboratories, Mitsubishi Tanabe Pharma Corporation, 1000, Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Tomohiro Sato
- RIKEN Center for Biosystems Dynamics Research, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Teruki Honma
- RIKEN Center for Biosystems Dynamics Research, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroshi Komura
- Artificial Intelligence Centre for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8, Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; University Research Administration Centre, Osaka Metropolitan University, 1-2-7, Asahi, Abeno-ku, Osaka 545-0051, Japan
| | - Kenji Mizuguchi
- Artificial Intelligence Centre for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8, Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan.
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17
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Li C, Jia WW, Yang JL, Cheng C, Olaleye OE. Multi-compound and drug-combination pharmacokinetic research on Chinese herbal medicines. Acta Pharmacol Sin 2022; 43:3080-3095. [PMID: 36114271 PMCID: PMC9483253 DOI: 10.1038/s41401-022-00983-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/12/2022] [Indexed: 12/02/2022] Open
Abstract
Traditional medicine has provided a basis for health care and disease treatment to Chinese people for millennia, and herbal medicines are regulated as drug products in China. Chinese herbal medicines have two features. They normally possess very complex chemical composition. This makes the identification of the constituents that are together responsible for the therapeutic action of an herbal medicine challenging, because how to select compounds from an herbal medicine for pharmacodynamic study has been a big hurdle in such identification efforts. To this end, a multi-compound pharmacokinetic approach was established to identify potentially important compounds (bioavailable at the action loci with significant exposure levels after dosing an herbal medicine) and to characterize their pharmacokinetics and disposition. Another feature of Chinese herbal medicines is their typical use as or in combination therapies. Coadministration of complex natural products and conventional synthetic drugs is prevalent worldwide, even though it remains very controversial. Natural product–drug interactions have raised wide concerns about reduced drug efficacy or safety. However, growing evidence shows that incorporating Chinese herbal medicines into synthetic drug-based therapies delivers benefits in the treatment of many multifactorial diseases. To address this issue, a drug-combination pharmacokinetic approach was established to assess drug–drug interaction potential of herbal medicines and degree of pharmacokinetic compatibility for multi-herb combination and herbal medicine–synthetic drug combination therapies. In this review we describe the methodology, techniques, requirements, and applications of multi-compound and drug-combination pharmacokinetic research on Chinese herbal medicines and to discuss further development for these two types of pharmacokinetic research.
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18
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Orosz Á, Héberger K, Rácz A. Comparison of Descriptor- and Fingerprint Sets in Machine Learning Models for ADME-Tox Targets. Front Chem 2022; 10:852893. [PMID: 35755260 PMCID: PMC9214226 DOI: 10.3389/fchem.2022.852893] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/14/2022] [Indexed: 01/12/2023] Open
Abstract
The screening of compounds for ADME-Tox targets plays an important role in drug design. QSPR models can increase the speed of these specific tasks, although the performance of the models highly depends on several factors, such as the applied molecular descriptors. In this study, a detailed comparison of the most popular descriptor groups has been carried out for six main ADME-Tox classification targets: Ames mutagenicity, P-glycoprotein inhibition, hERG inhibition, hepatotoxicity, blood–brain-barrier permeability, and cytochrome P450 2C9 inhibition. The literature-based, medium-sized binary classification datasets (all above 1,000 molecules) were used for the model building by two common algorithms, XGBoost and the RPropMLP neural network. Five molecular representation sets were compared along with their joint applications: Morgan, Atompairs, and MACCS fingerprints, and the traditional 1D and 2D molecular descriptors, as well as 3D molecular descriptors, separately. The statistical evaluation of the model performances was based on 18 different performance parameters. Although all the developed models were close to the usual performance of QSPR models for each specific ADME-Tox target, the results clearly showed the superiority of the traditional 1D, 2D, and 3D descriptors in the case of the XGBoost algorithm. It is worth trying the classical tools in single model building because the use of 2D descriptors can produce even better models for almost every dataset than the combination of all the examined descriptor sets.
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Affiliation(s)
- Álmos Orosz
- Plasma Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - Károly Héberger
- Plasma Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - Anita Rácz
- Plasma Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
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