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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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2
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Luo X, Zhang Z, Mu R, Hu G, Liu L, Liu X. Simultaneously Predicting the Pharmacokinetics of CES1-Metabolized Drugs and Their Metabolites Using Physiologically Based Pharmacokinetic Model in Cirrhosis Subjects. Pharmaceutics 2024; 16:234. [PMID: 38399287 PMCID: PMC10893190 DOI: 10.3390/pharmaceutics16020234] [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: 12/13/2023] [Revised: 01/29/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Hepatic carboxylesterase 1 (CES1) metabolizes numerous prodrugs into active ingredients or direct-acting drugs into inactive metabolites. We aimed to develop a semi-physiologically based pharmacokinetic (semi-PBPK) model to simultaneously predict the pharmacokinetics of CES1 substrates and their active metabolites in liver cirrhosis (LC) patients. Six prodrugs (enalapril, benazepril, cilazapril, temocapril, perindopril and oseltamivir) and three direct-acting drugs (flumazenil, pethidine and remimazolam) were selected. Parameters such as organ blood flows, plasma-binding protein concentrations, functional liver volume, hepatic enzymatic activity, glomerular filtration rate (GFR) and gastrointestinal transit rate were integrated into the simulation. The pharmacokinetic profiles of these drugs and their active metabolites were simulated for 1000 virtual individuals. The developed semi-PBPK model, after validation in healthy individuals, was extrapolated to LC patients. Most of the observations fell within the 5th and 95th percentiles of simulations from 1000 virtual patients. The estimated AUC and Cmax were within 0.5-2-fold of the observed values. The sensitivity analysis showed that the decreased plasma exposure of active metabolites due to the decreased CES1 was partly attenuated by the decreased GFR. Conclusion: The developed PBPK model successfully predicted the pharmacokinetics of CES1 substrates and their metabolites in healthy individuals and LC patients, facilitating tailored dosing of CES1 substrates in LC patients.
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Affiliation(s)
| | | | | | | | - Li Liu
- Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing 210009, China; (X.L.); (Z.Z.); (R.M.); (G.H.)
| | - Xiaodong Liu
- Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing 210009, China; (X.L.); (Z.Z.); (R.M.); (G.H.)
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3
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Keefer CE, Chang G, Di L, Woody NA, Tess DA, Osgood SM, Kapinos B, Racich J, Carlo AA, Balesano A, Ferguson N, Orozco C, Zueva L, Luo L. The Comparison of Machine Learning and Mechanistic In Vitro-In Vivo Extrapolation Models for the Prediction of Human Intrinsic Clearance. Mol Pharm 2023; 20:5616-5630. [PMID: 37812508 DOI: 10.1021/acs.molpharmaceut.3c00502] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Accurate prediction of human pharmacokinetics (PK) remains one of the key objectives of drug metabolism and PK (DMPK) scientists in drug discovery projects. This is typically performed by using in vitro-in vivo extrapolation (IVIVE) based on mechanistic PK models. In recent years, machine learning (ML), with its ability to harness patterns from previous outcomes to predict future events, has gained increased popularity in application to absorption, distribution, metabolism, and excretion (ADME) sciences. This study compares the performance of various ML and mechanistic models for the prediction of human IV clearance for a large (645) set of diverse compounds with literature human IV PK data, as well as measured relevant in vitro end points. ML models were built using multiple approaches for the descriptors: (1) calculated physical properties and structural descriptors based on chemical structure alone (classical QSAR/QSPR); (2) in vitro measured inputs only with no structure-based descriptors (ML IVIVE); and (3) in silico ML IVIVE using in silico model predictions for the in vitro inputs. For the mechanistic models, well-stirred and parallel-tube liver models were considered with and without the use of empirical scaling factors and with and without renal clearance. The best ML model for the prediction of in vivo human intrinsic clearance (CLint) was an in vitro ML IVIVE model using only six in vitro inputs with an average absolute fold error (AAFE) of 2.5. The best mechanistic model used the parallel-tube liver model, with empirical scaling factors resulting in an AAFE of 2.8. The corresponding mechanistic model with full in silico inputs achieved an AAFE of 3.3. These relative performances of the models were confirmed with the prediction of 16 Pfizer drug candidates that were not part of the original data set. Results show that ML IVIVE models are comparable to or superior to their best mechanistic counterparts. We also show that ML IVIVE models can be used to derive insights into factors for the improvement of mechanistic PK prediction.
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Affiliation(s)
- Christopher E Keefer
- Translational Modeling and Simulation, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - George Chang
- Translational Modeling and Simulation, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Li Di
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Nathaniel A Woody
- Translational Modeling and Simulation, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - David A Tess
- Translational Modeling and Simulation, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Sarah M Osgood
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Brendon Kapinos
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Jill Racich
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Anthony A Carlo
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Amanda Balesano
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Nicholas Ferguson
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Christine Orozco
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Larisa Zueva
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Lina Luo
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
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4
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Bakrania A, Joshi N, Zhao X, Zheng G, Bhat M. Artificial intelligence in liver cancers: Decoding the impact of machine learning models in clinical diagnosis of primary liver cancers and liver cancer metastases. Pharmacol Res 2023; 189:106706. [PMID: 36813095 DOI: 10.1016/j.phrs.2023.106706] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/17/2023] [Accepted: 02/19/2023] [Indexed: 02/22/2023]
Abstract
Liver cancers are the fourth leading cause of cancer-related mortality worldwide. In the past decade, breakthroughs in the field of artificial intelligence (AI) have inspired development of algorithms in the cancer setting. A growing body of recent studies have evaluated machine learning (ML) and deep learning (DL) algorithms for pre-screening, diagnosis and management of liver cancer patients through diagnostic image analysis, biomarker discovery and predicting personalized clinical outcomes. Despite the promise of these early AI tools, there is a significant need to explain the 'black box' of AI and work towards deployment to enable ultimate clinical translatability. Certain emerging fields such as RNA nanomedicine for targeted liver cancer therapy may also benefit from application of AI, specifically in nano-formulation research and development given that they are still largely reliant on lengthy trial-and-error experiments. In this paper, we put forward the current landscape of AI in liver cancers along with the challenges of AI in liver cancer diagnosis and management. Finally, we have discussed the future perspectives of AI application in liver cancer and how a multidisciplinary approach using AI in nanomedicine could accelerate the transition of personalized liver cancer medicine from bench side to the clinic.
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Affiliation(s)
- Anita Bakrania
- Toronto General Hospital Research Institute, Toronto, ON, Canada; Ajmera Transplant Program, University Health Network, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
| | | | - Xun Zhao
- Toronto General Hospital Research Institute, Toronto, ON, Canada; Ajmera Transplant Program, University Health Network, Toronto, ON, Canada
| | - Gang Zheng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Mamatha Bhat
- Toronto General Hospital Research Institute, Toronto, ON, Canada; Ajmera Transplant Program, University Health Network, Toronto, ON, Canada; Division of Gastroenterology, Department of Medicine, University Health Network and University of Toronto, Toronto, ON, Canada; Department of Medical Sciences, Toronto, ON, Canada.
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5
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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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Ota R, Yamashita F. Application of machine learning techniques to the analysis and prediction of drug pharmacokinetics. J Control Release 2022; 352:961-969. [PMID: 36370876 DOI: 10.1016/j.jconrel.2022.11.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 10/23/2022] [Accepted: 11/07/2022] [Indexed: 11/17/2022]
Abstract
In this review, we describe the current status and challenges in applying machine-learning techniques to the analysis and prediction of pharmacokinetic data. The theory of pharmacokinetics has been developed over decades on the basis of physiology and reaction kinetics. Mathematical models allow the reduction of pharmacokinetic data to parameter values, giving insight and understanding into ADME processes and predicting the outcome of different dosing scenarios. However, much information hidden in the data is lost through conceptual simplification with models. It is difficult to use mechanistic models alone to predict diverse pharmacokinetic time profiles, including inter-drug and inter-individual differences, in a cross-sectional manner. Machine learning is a prediction platform that can handle complex phenomena through data-driven analysis. As a resule, machine learning has been successfully adopted in various fields, including image recognition and language processing, and has been used for over two decades in pharmacokinetic research, primarily in the area of quantitative structure-activity relationships for pharmacokinetic parameters. Machine-learning models are generally known to provide better predictive performance than conventional linear models. Owing to the recent success in deep learning, models with new structures are being consistently proposed. These models include transfer learning and generative adversarial networks, which contribute to the effective use of a limited amount of data by diverting existing similar models or generating pseudo-data. How to make such newly emerging machine learning technologies applicable to meet challenges in the pharmacokinetics/pharmacodynamics field is now the key issue.
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Affiliation(s)
- Ryosaku Ota
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Fumiyoshi Yamashita
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Department of Applied Pharmacy and Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
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Hasanzadeh A, Hamblin MR, Kiani J, Noori H, Hardie JM, Karimi M, Shafiee H. Could artificial intelligence revolutionize the development of nanovectors for gene therapy and mRNA vaccines? NANO TODAY 2022; 47:101665. [PMID: 37034382 PMCID: PMC10081506 DOI: 10.1016/j.nantod.2022.101665] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Gene therapy enables the introduction of nucleic acids like DNA and RNA into host cells, and is expected to revolutionize the treatment of a wide range of diseases. This growth has been further accelerated by the discovery of CRISPR/Cas technology, which allows accurate genomic editing in a broad range of cells and organisms in vitro and in vivo. Despite many advances in gene delivery and the development of various viral and non-viral gene delivery vectors, the lack of highly efficient non-viral systems with low cellular toxicity remains a challenge. The application of cutting-edge technologies such as artificial intelligence (AI) has great potential to find new paradigms to solve this issue. Herein, we review AI and its major subfields including machine learning (ML), neural networks (NNs), expert systems, deep learning (DL), computer vision and robotics. We discuss the potential of AI-based models and algorithms in the design of targeted gene delivery vehicles capable of crossing extracellular and intracellular barriers by viral mimicry strategies. We finally discuss the role of AI in improving the function of CRISPR/Cas systems, developing novel nanobots, and mRNA vaccine carriers.
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Affiliation(s)
- Akbar Hasanzadeh
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
- Radiation Biology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Jafar Kiani
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Noori
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Joseph M. Hardie
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02139 USA
| | - Mahdi Karimi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Research Center for Science and Technology in Medicine, Tehran University of Medical Sciences, Tehran 141556559, Iran
- Applied Biotechnology Research Centre, Tehran Medical Science, Islamic Azad University, Tehran 1584743311, Iran
| | - Hadi Shafiee
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02139 USA
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8
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Ding X, Cui R, Yu J, Liu T, Zhu T, Wang D, Chang J, Fan Z, Liu X, Chen K, Jiang H, Li X, Luo X, Zheng M. Active Learning for Drug Design: A Case Study on the Plasma Exposure of Orally Administered Drugs. J Med Chem 2021; 64:16838-16853. [PMID: 34779199 DOI: 10.1021/acs.jmedchem.1c01683] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The success of artificial intelligence (AI) models has been limited by the requirement of large amounts of high-quality training data, which is just the opposite of the situation in most drug discovery pipelines. Active learning (AL) is a subfield of AI that focuses on algorithms that select the data they need to improve their models. Here, we propose a two-phase AL pipeline and apply it to the prediction of drug oral plasma exposure. In phase I, the AL-based model demonstrated a remarkable capability to sample informative data from a noisy data set, which used only 30% of the training data to yield a prediction capability with an accuracy of 0.856 on an independent test set. In phase II, the AL-based model explored a large diverse chemical space (855K samples) for experimental testing and feedback. Improved accuracy and new highly confident predictions (50K samples) were observed, which suggest that the model's applicability domain has been significantly expanded.
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Affiliation(s)
- Xiaoyu Ding
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Rongrong Cui
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Jie Yu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Tiantian Liu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Tingfei Zhu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Dingyan Wang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Jie Chang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Zisheng Fan
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Xiaomeng Liu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Kaixian Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China.,School of Life Science and Technology, ShanghaiTech University, 393 Huaxiazhong Road, Shanghai 200031, China
| | - Xutong Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xiaomin Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
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Danishuddin, Kumar V, Faheem M, Woo Lee K. A decade of machine learning-based predictive models for human pharmacokinetics: Advances and challenges. Drug Discov Today 2021; 27:529-537. [PMID: 34592448 DOI: 10.1016/j.drudis.2021.09.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/21/2021] [Accepted: 09/22/2021] [Indexed: 11/28/2022]
Abstract
Traditionally, in vitro and in vivo methods are useful for estimating human pharmacokinetics (PK) parameters; however, it is impractical to perform these complex and expensive experiments on a large number of compounds. The integration of publicly available chemical, or medical Big Data and artificial intelligence (AI)-based approaches led to qualitative and quantitative prediction of human PK of a candidate drug. However, predicting drug response with these approaches is challenging, partially because of the adaptation of algorithmic and limitations related to experimental data. In this report, we provide an overview of machine learning (ML)-based quantitative structure-activity relationship (QSAR) models used in the assessment or prediction of PK values as well as databases available for obtaining such data.
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Affiliation(s)
- Danishuddin
- Department of Bio & Medical Big Data (BK4), Division of Life Sciences, Research Institute of Natural Sciences (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Vikas Kumar
- Department of Bio & Medical Big Data (BK4), Division of Life Sciences, Research Institute of Natural Sciences (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Mohammad Faheem
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Keun Woo Lee
- Department of Bio & Medical Big Data (BK4), Division of Life Sciences, Research Institute of Natural Sciences (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea.
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Soltani M, Moradi Kashkooli F, Souri M, Zare Harofte S, Harati T, Khadem A, Haeri Pour M, Raahemifar K. Enhancing Clinical Translation of Cancer Using Nanoinformatics. Cancers (Basel) 2021; 13:2481. [PMID: 34069606 PMCID: PMC8161319 DOI: 10.3390/cancers13102481] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/08/2021] [Accepted: 05/16/2021] [Indexed: 12/14/2022] Open
Abstract
Application of drugs in high doses has been required due to the limitations of no specificity, short circulation half-lives, as well as low bioavailability and solubility. Higher toxicity is the result of high dosage administration of drug molecules that increase the side effects of the drugs. Recently, nanomedicine, that is the utilization of nanotechnology in healthcare with clinical applications, has made many advancements in the areas of cancer diagnosis and therapy. To overcome the challenge of patient-specificity as well as time- and dose-dependency of drug administration, artificial intelligence (AI) can be significantly beneficial for optimization of nanomedicine and combinatorial nanotherapy. AI has become a tool for researchers to manage complicated and big data, ranging from achieving complementary results to routine statistical analyses. AI enhances the prediction precision of treatment impact in cancer patients and specify estimation outcomes. Application of AI in nanotechnology leads to a new field of study, i.e., nanoinformatics. Besides, AI can be coupled with nanorobots, as an emerging technology, to develop targeted drug delivery systems. Furthermore, by the advancements in the nanomedicine field, AI-based combination therapy can facilitate the understanding of diagnosis and therapy of the cancer patients. The main objectives of this review are to discuss the current developments, possibilities, and future visions in naoinformatics, for providing more effective treatment for cancer patients.
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Affiliation(s)
- Madjid Soltani
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran 19967-15433, Iran; (F.M.K.); (M.S.); (S.Z.H.); (T.H.); (A.K.); (M.H.P.)
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- Faculty of Science, School of Optometry and Vision Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
- Advanced Bioengineering Initiative Center, Multidisciplinary International Complex, K. N. Toosi Univesity of Technology, Tehran 14176-14411, Iran
- Centre for Biotechnology and Bioengineering (CBB), University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Farshad Moradi Kashkooli
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran 19967-15433, Iran; (F.M.K.); (M.S.); (S.Z.H.); (T.H.); (A.K.); (M.H.P.)
| | - Mohammad Souri
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran 19967-15433, Iran; (F.M.K.); (M.S.); (S.Z.H.); (T.H.); (A.K.); (M.H.P.)
| | - Samaneh Zare Harofte
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran 19967-15433, Iran; (F.M.K.); (M.S.); (S.Z.H.); (T.H.); (A.K.); (M.H.P.)
| | - Tina Harati
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran 19967-15433, Iran; (F.M.K.); (M.S.); (S.Z.H.); (T.H.); (A.K.); (M.H.P.)
| | - Atefeh Khadem
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran 19967-15433, Iran; (F.M.K.); (M.S.); (S.Z.H.); (T.H.); (A.K.); (M.H.P.)
| | - Mohammad Haeri Pour
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran 19967-15433, Iran; (F.M.K.); (M.S.); (S.Z.H.); (T.H.); (A.K.); (M.H.P.)
| | - Kaamran Raahemifar
- Faculty of Science, School of Optometry and Vision Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
- Data Science and Artificial Intelligence Program, College of Information Sciences and Technology (IST), State College, Penn State University, Pennsylvania, PA 16801, USA
- Department of Chemical Engineering, Faculty of Engineering, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada
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11
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Dawson D, Ingle BL, Phillips KA, Nichols JW, Wambaugh JF, Tornero-Velez R. Designing QSARs for Parameters of High-Throughput Toxicokinetic Models Using Open-Source Descriptors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:6505-6517. [PMID: 33856768 PMCID: PMC8548983 DOI: 10.1021/acs.est.0c06117] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The intrinsic metabolic clearance rate (Clint) and the fraction of the chemical unbound in plasma (fup) serve as important parameters for high-throughput toxicokinetic (TK) models, but experimental data are limited for many chemicals. Open-source quantitative structure-activity relationship (QSAR) models for both parameters were developed to offer reliable in silico predictions for a diverse set of chemicals regulated under the U.S. law, including pharmaceuticals, pesticides, and industrial chemicals. As a case study to demonstrate their utility, model predictions served as inputs to the TK component of a risk-based prioritization approach based on bioactivity/exposure ratios (BERs), in which a BER < 1 indicates that exposures are predicted to exceed a biological activity threshold. When applied to a subset of the Tox21 screening library (6484 chemicals), we found that the proportion of chemicals with BER <1 was similar using either in silico (1133/6484; 17.5%) or in vitro (148/848; 17.5%) parameters. Further, when considering only the chemicals in the Tox21 set with in vitro data, there was a high concordance of chemicals classified with either BER <1 or >1 using either in silico or in vitro parameters (767/848, 90.4%). Thus, the presented QSARs may be suitable for prioritizing the risk posed by many chemicals for which measured in vitro TK data are lacking.
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Affiliation(s)
- Daniel Dawson
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, 109 T.W. Alexander Drive, Research Triangle Park, NC 27709
| | - Brandall L. Ingle
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 109 T.W. Alexander Drive, Research Triangle Park, NC 27709
| | - Katherine A. Phillips
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, 109 T.W. Alexander Drive, Research Triangle Park, NC 27709
| | - John W. Nichols
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, 109 T.W. Alexander Drive, Research Triangle Park, NC 27709
| | - John F. Wambaugh
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, 109 T.W. Alexander Drive, Research Triangle Park, NC 27709
| | - Rogelio Tornero-Velez
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, 109 T.W. Alexander Drive, Research Triangle Park, NC 27709
- Corresponding Author Address correspondence to Rogelio Tornero-Velez at 109 T.W. Alexander Drive, Mail Code E205-01, Research Triangle Park, NC, 27709;
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12
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Predicting blood-to-plasma concentration ratios of drugs from chemical structures and volumes of distribution in humans. Mol Divers 2021; 25:1261-1270. [PMID: 33569705 PMCID: PMC8342319 DOI: 10.1007/s11030-021-10186-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/18/2021] [Indexed: 11/05/2022]
Abstract
Abstract Despite their importance in determining the dosing regimen of drugs in the clinic, only a few studies have investigated methods for predicting blood-to-plasma concentration ratios (Rb). This study established an Rb prediction model incorporating typical human pharmacokinetics (PK) parameters. Experimental Rb values were compiled for 289 compounds, offering reliable predictions by expanding the applicability domain. Notably, it is the largest list of Rb values reported so far. Subsequently, human PK parameters calculated from plasma drug concentrations, including the volume of distribution (Vd), clearance, mean residence time, and plasma protein binding rate, as well as 2702 kinds of molecular descriptors, were used to construct quantitative structure–PK relationship models for Rb. Among the evaluated PK parameters, logVd correlated best with Rb (correlation coefficient of 0.47). Thus, in addition to molecular descriptors selected by XGBoost, logVd was employed to construct the prediction models. Among the analyzed algorithms, artificial neural networks gave the best results. Following optimization using six molecular descriptors and logVd, the model exhibited a correlation coefficient of 0.64 and a root-mean-square error of 0.205, which were superior to those previously reported for other Rb prediction methods. Since Vd values and chemical structures are known for most medications, the Rb prediction model described herein is expected to be valuable in clinical settings. Graphical abstract ![]()
Supplementary informations The online version of this article (10.1007/s11030-021-10186-7) contains supplementary material, which is available to authorized users.
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13
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Weeks J, Li AP, Doshi U, Johanning K, Guiney PD. In vitro evaluation of the metabolic stability of nine fragrance chemicals in trout and human hepatocytes. J Appl Toxicol 2020; 40:1421-1434. [PMID: 32488907 DOI: 10.1002/jat.3995] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 04/01/2020] [Accepted: 04/15/2020] [Indexed: 12/11/2022]
Abstract
In vitro metabolic stability of nine fragrance chemicals: p-tolyl acetate, cashmeran, ethylene brassylate, celestolide, galaxolide, traseolide, ambretone, tonalide and pentadecanolide, was evaluated in trout and human hepatocytes. The compounds were incubated with trout hepatocytes at 12°C and human hepatocytes at 37°C. Quantification of compound disappearance with time was performed using gas chromatography/mass spectrometry. in vivo hepatic intrinsic clearance values were calculated from the in vitro data. Significant metabolism was observed with trout hepatocytes for five of the nine fragrance chemicals, while all nine were metabolized significantly with human hepatocytes. Previously published models were used to examine expected bioaccumulation and persistence in whole organisms. Calculated half-lives due to metabolism of the nine chemicals are significantly shorter for humans than trout: <1 hour and <1 day, respectively. For all chemicals with demonstrated hepatic metabolism, the models indicate a lack of accumulation. For those where metabolism was demonstrated in trout, calculated bioconcentration factors would not be classified as bioaccumulative under prevailing regulatory systems.
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Affiliation(s)
- John Weeks
- S.C. Johnson and Son, Inc., Racine, Wisconsin, US
| | - Albert P Li
- In Vitro ADMET Laboratories LLC, Columbia, Maryland, US
| | - Utkarsh Doshi
- In Vitro ADMET Laboratories LLC, Columbia, Maryland, US.,Altria Client Services LLC, Richmond, Virginia, US
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14
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Hassanzadeh P, Atyabi F, Dinarvand R. The significance of artificial intelligence in drug delivery system design. Adv Drug Deliv Rev 2019; 151-152:169-190. [PMID: 31071378 DOI: 10.1016/j.addr.2019.05.001] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/14/2019] [Accepted: 05/02/2019] [Indexed: 02/07/2023]
Abstract
Over the last decade, increasing interest has been attracted towards the application of artificial intelligence (AI) technology for analyzing and interpreting the biological or genetic information, accelerated drug discovery, and identification of the selective small-molecule modulators or rare molecules and prediction of their behavior. Application of the automated workflows and databases for rapid analysis of the huge amounts of data and artificial neural networks (ANNs) for development of the novel hypotheses and treatment strategies, prediction of disease progression, and evaluation of the pharmacological profiles of drug candidates may significantly improve treatment outcomes. Target fishing (TF) by rapid prediction or identification of the biological targets might be of great help for linking targets to the novel compounds. AI and TF methods in association with human expertise may indeed revolutionize the current theranostic strategies, meanwhile, validation approaches are necessary to overcome the potential challenges and ensure higher accuracy. In this review, the significance of AI and TF in the development of drugs and delivery systems and the potential challenging issues have been highlighted.
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Affiliation(s)
- Parichehr Hassanzadeh
- Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 13169-43551, Iran.
| | - Fatemeh Atyabi
- Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 13169-43551, Iran.
| | - Rassoul Dinarvand
- Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 13169-43551, Iran.
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15
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Wang Y, Liu H, Fan Y, Chen X, Yang Y, Zhu L, Zhao J, Chen Y, Zhang Y. In Silico Prediction of Human Intravenous Pharmacokinetic Parameters with Improved Accuracy. J Chem Inf Model 2019; 59:3968-3980. [DOI: 10.1021/acs.jcim.9b00300] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yuchen Wang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Haichun Liu
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Yuanrong Fan
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Xingye Chen
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Yan Yang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Lu Zhu
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Junnan Zhao
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Yadong Chen
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Yanmin Zhang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
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16
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Baxter LK, Dionisio K, Pradeep P, Rappazzo K, Neas L. Human exposure factors as potential determinants of the heterogeneity in city-specific associations between PM 2.5 and mortality. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2019; 29:557-567. [PMID: 30310133 PMCID: PMC6643264 DOI: 10.1038/s41370-018-0080-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 08/27/2018] [Accepted: 09/17/2018] [Indexed: 06/01/2023]
Abstract
Multi-city population-based epidemiological studies of short-term fine particulate matter (PM2.5) exposures and mortality have observed heterogeneity in risk estimates between cities. Factors affecting exposures, such as pollutant infiltration, which are not captured by central-site monitoring data, can differ between communities potentially explaining some of this heterogeneity. This analysis evaluates exposure factors as potential determinants of the heterogeneity in 312 core-based statistical areas (CBSA)-specific associations between PM2.5 and mortality using inverse variance weighted linear regression. Exposure factor variables were created based on data on housing characteristics, commuting patterns, heating fuel usage, and climatic factors from national surveys. When survey data were not available, air conditioning (AC) prevalence was predicted utilizing machine learning techniques. Across all CBSAs, there was a 0.95% (Interquartile range (IQR) of 2.25) increase in non-accidental mortality per 10 µg/m3 increase in PM2.5 and significant heterogeneity between CBSAs. CBSAs with larger homes, more heating degree days, a higher percentage of home heating with oil had significantly (p < 0.05) higher health effect estimates, while cities with more gas heating had significantly lower health effect estimates. While univariate models did not explain much of heterogeneity in health effect estimates (R2 < 1%), multivariate models began to explain some of the observed heterogeneity (R2 = 13%).
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Affiliation(s)
- Lisa K Baxter
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
| | - Kathie Dionisio
- National Exposure Research Laboratory, Office of Research and Development, Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Prachi Pradeep
- National Center for Computational Toxicology, Office of Research and Development, Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Kristen Rappazzo
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Lucas Neas
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
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17
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Li M, Zhu L, Chen L, Li N, Qi F. Assessment of drug–drug interactions between voriconazole and glucocorticoids. J Chemother 2019; 30:296-303. [PMID: 30843777 DOI: 10.1080/1120009x.2018.1506693] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- MengXue Li
- Pharmaceutical College, Tianjin Medical University, Tianjin, China
| | - LiQin Zhu
- Pharmaceutical College, Tianjin Medical University, Tianjin, China
- Department of Pharmacy, Tianjin First Central Hospital, Tianjin, China
| | - Lu Chen
- Pharmaceutical College, Tianjin Medical University, Tianjin, China
| | - Na Li
- Pharmaceutical College, Tianjin Medical University, Tianjin, China
| | - Fang Qi
- Pharmaceutical College, Tianjin Medical University, Tianjin, China
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18
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Chan TS, Yu H, Moore A, Khetani SR, Tweedie D. Meeting the Challenge of Predicting Hepatic Clearance of Compounds Slowly Metabolized by Cytochrome P450 Using a Novel Hepatocyte Model, HepatoPac. Drug Metab Dispos 2018; 47:58-66. [PMID: 30552098 DOI: 10.1124/dmd.113.053397fullarticlecorrection] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/15/2013] [Indexed: 12/17/2022] Open
Abstract
Generating accurate in vitro intrinsic clearance data is an important aspect of predicting in vivo human clearance. Primary hepatocytes in suspension are routinely used to predict in vivo clearance; however, incubation times have typically been limited to 4-6 hours, which is not long enough to accurately evaluate the metabolic stability of slowly metabolized compounds. HepatoPac is a micropatterened hepatocyte-fibroblast coculture system that can be used for continuous incubations of up to 7 days. This study evaluated the ability of human HepatoPac to predict the in vivo clearance (CL) of 17 commercially available compounds with low to intermediate clearance (<12 ml/min/kg). In vitro half-life for disappearance of each compound was converted to hepatic clearance using the well stirred model, with and without correction for plasma protein binding. Hepatic CL, using three individual donors, was accurately predicted for 11 of 17 compounds (59%; predicted clearance within 2-fold of observed human in vivo clearance values). The accuracy of prediction increased to 82% (14 of 17 compounds) with an acceptance criterion defined as within 3-fold. When considering only low clearance compounds (<5 ml/min per kg), which represented 10 of the 17 compounds, the accuracy of prediction was 70% within 2-fold and 100% within 3-fold. In addition, the turnover of three slowly metabolized compounds (alprazolam, meloxicam, and tolbutamide) in HepatoPac was directly compared with turnover in suspended hepatocytes. The turnover of alprazolam and tolbutamide was approximately 2-fold greater using HepatoPac compared with suspended hepatocytes, which was roughly in line with the extrapolated values (correcting for the longer incubation time and lower cell number with HepatoPac). HepatoPac, but not suspended hepatocytes, demonstrated significant turnover of meloxicam. These results demonstrate the utility of HepatoPac for prediction of in vivo hepatic clearance, particularly with low clearance compounds.
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Affiliation(s)
- Tom S Chan
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Ridgefield, Connecticut (T.S.C., H.Y., D.T.); Hepregen Corporation, Medford, Massachusetts (A.M.); and Mechanical and Biomedical Engineering, Colorado State University, Fort Collins, Colorado (S.R.K.)
| | - Hongbin Yu
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Ridgefield, Connecticut (T.S.C., H.Y., D.T.); Hepregen Corporation, Medford, Massachusetts (A.M.); and Mechanical and Biomedical Engineering, Colorado State University, Fort Collins, Colorado (S.R.K.)
| | - Amanda Moore
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Ridgefield, Connecticut (T.S.C., H.Y., D.T.); Hepregen Corporation, Medford, Massachusetts (A.M.); and Mechanical and Biomedical Engineering, Colorado State University, Fort Collins, Colorado (S.R.K.)
| | - Salman R Khetani
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Ridgefield, Connecticut (T.S.C., H.Y., D.T.); Hepregen Corporation, Medford, Massachusetts (A.M.); and Mechanical and Biomedical Engineering, Colorado State University, Fort Collins, Colorado (S.R.K.)
| | - Donald Tweedie
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Ridgefield, Connecticut (T.S.C., H.Y., D.T.); Hepregen Corporation, Medford, Massachusetts (A.M.); and Mechanical and Biomedical Engineering, Colorado State University, Fort Collins, Colorado (S.R.K.)
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19
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Wood FL, Houston JB, Hallifax D. Clearance Prediction Methodology Needs Fundamental Improvement: Trends Common to Rat and Human Hepatocytes/Microsomes and Implications for Experimental Methodology. Drug Metab Dispos 2017; 45:1178-1188. [DOI: 10.1124/dmd.117.077040] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/06/2017] [Indexed: 01/07/2023] Open
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20
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Madden J, Webb S, Enoch S, Colley H, Murdoch C, Shipley R, Sharma P, Yang C, Cronin M. In silico prediction of skin metabolism and its implication in toxicity assessment. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.comtox.2017.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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21
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Jeong YS, Yim CS, Ryu HM, Noh CK, Song YK, Chung SJ. Estimation of the minimum permeability coefficient in rats for perfusion-limited tissue distribution in whole-body physiologically-based pharmacokinetics. Eur J Pharm Biopharm 2017; 115:1-17. [DOI: 10.1016/j.ejpb.2017.01.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/25/2017] [Accepted: 01/28/2017] [Indexed: 01/12/2023]
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22
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Przybylak K, Madden J, Covey-Crump E, Gibson L, Barber C, Patel M, Cronin M. Characterisation of data resources for in silico modelling: benchmark datasets for ADME properties. Expert Opin Drug Metab Toxicol 2017; 14:169-181. [DOI: 10.1080/17425255.2017.1316449] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- K.R. Przybylak
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool, UK
| | - J.C. Madden
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool, UK
| | | | - L. Gibson
- Lhasa Limited, Granary Wharf House, Leeds, UK
| | - C. Barber
- Lhasa Limited, Granary Wharf House, Leeds, UK
| | - M. Patel
- Lhasa Limited, Granary Wharf House, Leeds, UK
| | - M.T.D. Cronin
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool, UK
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23
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Maass C, Stokes CL, Griffith LG, Cirit M. Multi-functional scaling methodology for translational pharmacokinetic and pharmacodynamic applications using integrated microphysiological systems (MPS). Integr Biol (Camb) 2017; 9:290-302. [PMID: 28267162 PMCID: PMC5729907 DOI: 10.1039/c6ib00243a] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Microphysiological systems (MPS) provide relevant physiological environments in vitro for studies of pharmacokinetics, pharmacodynamics and biological mechanisms for translational research. Designing multi-MPS platforms is essential to study multi-organ systems. Typical design approaches, including direct and allometric scaling, scale each MPS individually and are based on relative sizes not function. This study's aim was to develop a new multi-functional scaling approach for integrated multi-MPS platform design for specific applications. We developed an optimization approach using mechanistic modeling and specification of an objective that considered multiple MPS functions, e.g., drug absorption and metabolism, simultaneously to identify system design parameters. This approach informed the design of two hypothetical multi-MPS platforms consisting of gut and liver (multi-MPS platform I) and gut, liver and kidney (multi-MPS platform II) to recapitulate in vivo drug exposures in vitro. This allows establishment of clinically relevant drug exposure-response relationships, a prerequisite for efficacy and toxicology assessment. Design parameters resulting from multi-functional scaling were compared to designs based on direct and allometric scaling. Human plasma time-concentration profiles of eight drugs were used to inform the designs, and profiles of an additional five drugs were calculated to test the designed platforms on an independent set. Multi-functional scaling yielded exposure times in good agreement with in vivo data, while direct and allometric scaling approaches resulted in short exposure durations. Multi-functional scaling allows appropriate scaling from in vivo to in vitro of multi-MPS platforms, and in the cases studied provides designs that better mimic in vivo exposures than standard MPS scaling methods.
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Affiliation(s)
- Christian Maass
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA.
| | | | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA.
| | - Murat Cirit
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA.
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24
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Pirovano A, Brandmaier S, Huijbregts MAJ, Ragas AMJ, Veltman K, Hendriks AJ. QSARs for estimating intrinsic hepatic clearance of organic chemicals in humans. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2016; 42:190-197. [PMID: 26874337 DOI: 10.1016/j.etap.2016.01.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 01/19/2016] [Accepted: 01/21/2016] [Indexed: 06/05/2023]
Abstract
Quantitative structure-activity relationships (QSARs) were developed to predict the in vitro clearance (CLINT) of xenobiotics metabolised in human hepatocytes (118 compounds) and microsomes (115 compounds). Clearance values were gathered from the scientific literature and multiple linear models were built and validated selecting at most 6 predictors from a pool of over 2000 potential molecular descriptors. For the hepatocytes QSAR, the explained variance (Radj(2)) was 67% and the predictive ability (Rext(2)) was 62%. For the microsomes QSAR, Radj(2) was 50% and Rext(2) 30%. For both liver assays, the most important descriptor relates to electronic properties of the compound. Functional groups of fragments were useful to identify specific compounds that have a deviating reaction rate compared to the others, such as polychlorobiphenyls (PCBs) and organic amides which were poorly metabolised by hepatocytes and microsomes, respectively. For hepatocytes, clearance was predominantly determined by electronic characteristics, while size and shape characteristics were less important and partitioning properties were absent. This may suggest that uptake across the membrane and enzyme binding are not rate-limiting steps. Particularly for hepatocytes the QSAR statistics are encouraging, allowing application of the outcomes in in vitro to in vivo extrapolation.
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Affiliation(s)
- Alessandra Pirovano
- Radboud University Nijmegen, Institute for Wetland and Water Research, Department of Environmental Science, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Stefan Brandmaier
- Helmholtz-Zentrum München - German Research Centre for Environmental Health (GmbH), Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Munich, Germany
| | - Mark A J Huijbregts
- Radboud University Nijmegen, Institute for Wetland and Water Research, Department of Environmental Science, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Ad M J Ragas
- Radboud University Nijmegen, Institute for Wetland and Water Research, Department of Environmental Science, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands; Faculty of Management, Science and Technology, Open University, Heerlen, The Netherlands
| | - Karin Veltman
- University of Michigan, School of Public Health, Department of Environmental Health Sciences, 1415 Washington Heights, Ann Arbor, MI, USA
| | - A Jan Hendriks
- Radboud University Nijmegen, Institute for Wetland and Water Research, Department of Environmental Science, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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25
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Dried blood spot testing: a novel approach for the therapeutic drug monitoring of ziprasidone-treated patients. Bioanalysis 2014; 6:1487-95. [DOI: 10.4155/bio.14.3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: A novel analytical approach, based on dried blood spot (DBS) testing, has been developed, validated and applied for the first time to the analysis of ziprasidone (ZPR) for the therapeutic drug monitoring (TDM) of schizophrenic patients. DBS represent a more feasible but reliable matrix, alternative to blood and plasma. Methods: The assays were carried out using an HPLC method with native fluorescence. Blood drops were applied to DBS cards and dried by microwaves, an internal standard solution was added to the DBS and 5-mm punches were cut out for analysis. ZPR was extracted from DBS with methanol, giving good extraction yields, precision and selectivity results. Results: The method was applied with satisfactory results to DBS samples from psychiatric patients to determine ZPR levels for therapy optimization. Conclusion: This innovative methodology provides reliable and significant TDM information, with important advantages over classical blood sampling in terms of collection, storage and processing.
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26
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Lombardo F, Obach RS, Varma MV, Stringer R, Berellini G. Clearance Mechanism Assignment and Total Clearance Prediction in Human Based upon in Silico Models. J Med Chem 2014; 57:4397-405. [DOI: 10.1021/jm500436v] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Franco Lombardo
- Metabolism
and Pharmacokinetics, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - R. Scott Obach
- Pharmacokinetics,
Dynamics and Metabolism, Pfizer Global Research and Development, Groton, Connecticut 06340, United States
| | - Manthena V. Varma
- Pharmacokinetics,
Dynamics and Metabolism, Pfizer Global Research and Development, Groton, Connecticut 06340, United States
| | - Rowan Stringer
- Metabolism
and Pharmacokinetics, Novartis Institutes for Biomedical Research, Wimblehurst Road Horsham, West Sussex, RH12 5AB, United Kingdom
| | - Giuliano Berellini
- Metabolism
and Pharmacokinetics, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Structure-activity relationship for Fe(III)-salen-like complexes as potent anticancer agents. ScientificWorldJournal 2014; 2014:745649. [PMID: 24955417 PMCID: PMC3997896 DOI: 10.1155/2014/745649] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 02/19/2014] [Indexed: 11/17/2022] Open
Abstract
Quantitative structure activity relationship (QSAR) for the anticancer activity of Fe(III)-salen and salen-like complexes was studied. The methods of density function theory (B3LYP/LANL2DZ) were used to optimize the structures. A pool of descriptors was calculated: 1497 theoretical descriptors and quantum-chemical parameters, shielding NMR, and electronic descriptors. The study of structure and activity relationship was performed with multiple linear regression (MLR) and artificial neural network (ANN). In nonlinear method, the adaptive neuro-fuzzy inference system (ANFIS) was applied in order to choose the most effective descriptors. The ANN-ANFIS model with high statistical significance (R2train = 0.99, RMSE = 0.138, and Q2LOO = 0.82) has better capability to predict the anticancer activity of the new compounds series of this family. Based on this study, anticancer activity of this compound is mainly dependent on the geometrical parameters, position, and the nature of the substituent of salen ligand.
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Sanoh S, Ohta S. Chimeric mice transplanted with human hepatocytes as a model for prediction of human drug metabolism and pharmacokinetics. Biopharm Drug Dispos 2013; 35:71-86. [DOI: 10.1002/bdd.1864] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 09/09/2013] [Accepted: 09/21/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Seigo Sanoh
- Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Shigeru Ohta
- Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
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Chan TS, Yu H, Moore A, Khetani SR, Kehtani SR, Tweedie D. Meeting the challenge of predicting hepatic clearance of compounds slowly metabolized by cytochrome P450 using a novel hepatocyte model, HepatoPac. Drug Metab Dispos 2013; 41:2024-32. [PMID: 23959596 DOI: 10.1124/dmd.113.053397] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Generating accurate in vitro intrinsic clearance data is an important aspect of predicting in vivo human clearance. Primary hepatocytes in suspension are routinely used to predict in vivo clearance; however, incubation times have typically been limited to 4-6 hours, which is not long enough to accurately evaluate the metabolic stability of slowly metabolized compounds. HepatoPac is a micropatterened hepatocyte-fibroblast coculture system that can be used for continuous incubations of up to 7 days. This study evaluated the ability of human HepatoPac to predict the in vivo clearance (CL) of 17 commercially available compounds with low to intermediate clearance (<12 ml/min per kg). In vitro half-life for disappearance of each compound was converted to hepatic clearance using the well stirred model, with and without correction for plasma protein binding. Hepatic CL, using three individual donors, was accurately predicted for 10 of 17 compounds (59%; predicted clearance within 2-fold of observed human in vivo clearance values). The accuracy of prediction increased to 76% (13 of 17 compounds) with an acceptance criterion defined as within 3-fold. When considering only low clearance compounds (<5 ml/min per kg), which represented 10 of the 17 compounds, the accuracy of prediction was 60% within 2-fold and 90% within 3-fold. In addition, the turnover of three slowly metabolized compounds (alprazolam, meloxicam, and tolbutamide) in HepatoPac was directly compared with turnover in suspended hepatocytes. The turnover of alprazolam and tolbutamide was approximately 2-fold greater using HepatoPac compared with suspended hepatocytes, which was roughly in line with the extrapolated values (correcting for the longer incubation time and lower cell number with HepatoPac). HepatoPac, but not suspended hepatocytes, demonstrated significant turnover of meloxicam. These results demonstrate the utility of HepatoPac for prediction of in vivo hepatic clearance, particularly with low clearance compounds.
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Affiliation(s)
- Tom S Chan
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Ridgefield, Connecticut (T.S.C., H.Y., D.T.); Hepregen Corporation, Medford, Massachusetts (A.M.); and Mechanical and Biomedical Engineering, Colorado State University, Fort Collins, Colorado (S.R.K.)
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Poulin P, Haddad S. Hepatocyte Composition-Based Model as a Mechanistic Tool for Predicting the Cell Suspension: Aqueous Phase Partition Coefficient of Drugs in In Vitro Metabolic Studies. J Pharm Sci 2013; 102:2806-18. [DOI: 10.1002/jps.23602] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 04/23/2013] [Accepted: 04/24/2013] [Indexed: 12/21/2022]
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Desbans C, Hilgendorf C, Lutz M, Bachellier P, Zacharias T, Weber JC, Dolgos H, Richert L, Ungell AL. Prediction of fraction metabolized via CYP3A in humans utilizing cryopreserved human hepatocytes from a set of 12 single donors. Xenobiotica 2013; 44:17-27. [DOI: 10.3109/00498254.2013.809617] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Berellini G, Waters NJ, Lombardo F. In silico Prediction of Total Human Plasma Clearance. J Chem Inf Model 2012; 52:2069-78. [DOI: 10.1021/ci300155y] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Giuliano Berellini
- Metabolism and Pharmacokinetics, Novartis Institutes for Biomedical Research, 250 Massachusetts
Avenue, Cambridge Massachusettes 02139, United States
| | - Nigel J. Waters
- Metabolism and Pharmacokinetics, Novartis Institutes for Biomedical Research, 250 Massachusetts
Avenue, Cambridge Massachusettes 02139, United States
| | - Franco Lombardo
- Metabolism and Pharmacokinetics, Novartis Institutes for Biomedical Research, 250 Massachusetts
Avenue, Cambridge Massachusettes 02139, United States
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Paixão P, Gouveia LF, Morais JA. Prediction of the human oral bioavailability by using in vitro and in silico drug related parameters in a physiologically based absorption model. Int J Pharm 2012; 429:84-98. [DOI: 10.1016/j.ijpharm.2012.03.019] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 03/08/2012] [Accepted: 03/09/2012] [Indexed: 12/13/2022]
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Abstract
In silico tools specifically developed for prediction of pharmacokinetic parameters are of particular interest to pharmaceutical industry because of the high potential of discarding inappropriate molecules during an early stage of drug development itself with consequent saving of vital resources and valuable time. The ultimate goal of the in silico models of absorption, distribution, metabolism, and excretion (ADME) properties is the accurate prediction of the in vivo pharmacokinetics of a potential drug molecule in man, whilst it exists only as a virtual structure. Various types of in silico models developed for successful prediction of the ADME parameters like oral absorption, bioavailability, plasma protein binding, tissue distribution, clearance, half-life, etc. have been briefly described in this chapter.
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Affiliation(s)
- A K Madan
- Pt. BD Sharma University of Health Sciences, Rohtak, India.
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35
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Sanoh S, Horiguchi A, Sugihara K, Kotake Y, Tayama Y, Ohshita H, Tateno C, Horie T, Kitamura S, Ohta S. Prediction of In Vivo Hepatic Clearance and Half-Life of Drug Candidates in Human Using Chimeric Mice with Humanized Liver. Drug Metab Dispos 2011; 40:322-8. [DOI: 10.1124/dmd.111.040923] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Sheikh-Bahaei S, Hunt CA. Enabling clearance predictions to emerge from in silico actions of quasi-autonomous hepatocyte components. Drug Metab Dispos 2011; 39:1910-20. [PMID: 21768275 DOI: 10.1124/dmd.111.038703] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We demonstrate the feasibility of using in silico hepatocyte cultures (ISHCs) to provide predictions of the intrinsic clearance (CL) of compounds in hepatocyte cultures. We compare results with predictions obtained using a multiple linear regression method. Our expectation is that the method can be extended to predict in vivo clearance of new compounds in humans. Within ISHCs, mobile "compounds" carry information describing referent compound properties. We used an iterative refinement protocol for ISHC refinement and development of parameterization methods. Quasi-autonomous "hepatocytes" and their components (including "transporters" and "enzymes") use a small, event-specific subset of compound properties to decide how to interact with encountered compounds each simulation cycle. The probability of occurrence for each event is specified by a rule that uses a subset of compound properties known to influence that event in vitro. ISHC experiments mimic in vitro counterparts. In silico clearance is measured the same as in vitro clearance and is used to predict a corresponding CL value. For 39 of 73 compounds having calculated CL S.D.s, 79% of ISHC predictions and 23% of regression predictions were within CL ± 2 S.D. For all 73 compounds, 38% of ISHC predictions and 32% of regression predictions were within a factor of 2 of the referent CL values. ISHC details during simulations stand as a mechanistic hypothesis of how clearance phenomena emerge during in vitro experiments.
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Affiliation(s)
- Shahab Sheikh-Bahaei
- Joint Graduate Group in Bioengineering, University of California, Berkeley, California, USA
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Affiliation(s)
- Melvin J. Yu
- Eisai Incorporated, 4 Corporate Drive, Andover, Massachusetts 01810
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