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Li Y, Liu X, Li L, Zhang T, Gao Y, Zeng K, Wang Q. Characterization of the metabolism of eupalinolide A and B by carboxylesterase and cytochrome P450 in human liver microsomes. Front Pharmacol 2023; 14:1093696. [PMID: 36762117 PMCID: PMC9905117 DOI: 10.3389/fphar.2023.1093696] [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: 11/09/2022] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
Eupalinolide A (EA; Z-configuration) and eupalinolide B (EB; E-configuration) are bioactive cis-trans isomers isolated from Eupatorii Lindleyani Herba that exert anti-inflammatory and antitumor effects. Although one pharmacokinetic study found that the metabolic parameters of the isomers were different in rats, metabolic processes relevant to EA and EB remain largely unknown. Our preliminary findings revealed that EA and EB are rapidly hydrolyzed by carboxylesterase. Here, we investigated the metabolic stability and enzyme kinetics of carboxylesterase-mediated hydrolysis and cytochrome P450 (CYP)-mediated oxidation of EA and EB in human liver microsomes (HLMs). We also explored differences in the hydrolytic stability of EA and EB in human liver microsomes and rat liver microsomes (RLMs). Moreover, cytochrome P450 reaction phenotyping of the isomers was performed via in silico methods (i.e., using a quantitative structure-activity relationship model and molecular docking) and confirmed using human recombinant enzymes. The total normalized rate approach was considered to assess the relative contributions of five major cytochrome P450s to EA and EB metabolism. We found that EA and EB were eliminated rapidly, mainly by carboxylesterase-mediated hydrolysis, as compared with cytochrome P450-mediated oxidation. An inter-species difference was observed as well, with faster rates of EA and EB hydrolysis in rat liver microsomes. Furthermore, our findings confirmed EA and EB were metabolized by multiple cytochrome P450s, among which CYP3A4 played a particularly important role.
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Affiliation(s)
- Yingzi Li
- Department of Toxicology, School of Public Health, Peking University, Beijing, China
| | - Xiaoyan Liu
- Department of Toxicology, School of Public Health, Peking University, Beijing, China
| | - Ludi Li
- Department of Toxicology, School of Public Health, Peking University, Beijing, China
| | - Tao Zhang
- Department of Toxicology, School of Public Health, Peking University, Beijing, China
| | - Yadong Gao
- Department of Toxicology, School of Public Health, Peking University, Beijing, China
| | - Kewu Zeng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China,*Correspondence: Kewu Zeng, ; Qi Wang,
| | - Qi Wang
- Department of Toxicology, School of Public Health, Peking University, Beijing, China,Key Laboratory of State Administration of Traditional Chinese Medicine for Compatibility Toxicology, Beijing, China,Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing, China,*Correspondence: Kewu Zeng, ; Qi Wang,
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Jawarkar R, Bakal RL, Zaki ME, Al-Hussain S, Ghosh A, Gandhi A, Mukerjee N, Samad A, Masand VH, Lewaa I. QSAR based virtual screening derived identification of a novel hit as a SARS CoV-229E 3CL pro Inhibitor: GA-MLR QSAR modeling supported by molecular Docking, molecular dynamics simulation and MMGBSA calculation approaches. ARAB J CHEM 2022; 15:103499. [PMID: 34909066 PMCID: PMC8524701 DOI: 10.1016/j.arabjc.2021.103499] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/10/2021] [Indexed: 12/26/2022] Open
Abstract
Congruous coronavirus drug targets and analogous lead molecules must be identified as quickly as possible to produce antiviral therapeutics against human coronavirus (HCoV SARS 3CLpro) infections. In the present communication, we bear recognized a HIT candidate for HCoV SARS 3CLpro inhibition. Four Parametric GA-MLR primarily based QSAR model (R2:0.84, R2adj:0.82, Q2loo: 0.78) was once promoted using a dataset over 37 structurally diverse molecules along QSAR based virtual screening (QSAR-VS), molecular docking (MD) then molecular dynamic simulation (MDS) analysis and MMGBSA calculations. The QSAR-based virtual screening was utilized to find novel lead molecules from an in-house database of 100 molecules. The QSAR-vS successfully offered a hit molecule with an improved PEC50 value from 5.88 to 6.08. The benzene ring, phenyl ring, amide oxygen and nitrogen, and other important pharmacophoric sites are revealed via MD and MDS studies. Ile164, Pro188, Leu190, Thr25, His41, Asn46, Thr47, Ser49, Asn189, Gln191, Thr47, and Asn141 are among the key amino acid residues in the S1 and S2 pocket. A stable complex of a lead molecule with the HCoV SARS 3CLpro was discovered using MDS. MM-GBSA calculations resulted from MD simulation results well supported with the binding energies calculated from the docking results. The results of this study can be exploited to develop a novel antiviral target, such as an HCoV SARS 3CLpro Inhibitor.
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Key Words
- 3CLpro, 3C like Protease
- FDA, Food and Drug Administration
- GA-MLR
- GA-MLR, Genetic Algorithm Multilinear Regression
- HCoV SARS 3CLpro
- HCoV-HKU1, Human coronavirus HKU1
- HCoV-NL63, Human coronavirus NL63
- HCoVs, human coronaviruses
- Lead
- MD, Molecular Docking
- MDS, molecular dynamic simulation
- MERS, Middle East Respiratory Syndrome
- MMGBSA calculations
- MMGBSA, Molecular Mechanics Generalized Born and Surface Area
- Molecular docking and MD simulation
- OECD, Organization for Economic Corporation and Development
- QSAR based virtual screening
- QSAR, Quantitative Structure Activity Relationship
- RNA, Ribo-nucleic acid
- SARS, severe acute respiratory sign
- VS, Virtual Screening
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Affiliation(s)
- R.D. Jawarkar
- Department of Medicinal Chemistry, Dr. Rajendra Gode Institute of Pharmacy, University-Mardi Road, Amravati, Maharashtra, 444603, India,Corresponding authors at: Department of Medicinal Chemistry, Dr. Rajendra Gode College of Pharmacy, Mardi Road, Amravati, Maharashtra, India and (Rahul D. Jawarkar). Department of Chemistry, Faculty of Science, Al-Imam Mohammad Ibn Saud Islamic university, Riyadh 13318, Saudi Arabia (Magdi E.A. Zaki)
| | - Ravindrakumar L. Bakal
- Department of Medicinal Chemistry, Dr. Rajendra Gode Institute of Pharmacy, University-Mardi Road, Amravati, Maharashtra, 444603, India
| | - Magdi E.A. Zaki
- Department of Chemistry, Faculty of Science, Al-Imam Mohammad Ibn Saud Islamic university, Riyadh 13318, Saudi Arabia
| | - Sami Al-Hussain
- Department of Chemistry, Faculty of Science, Al-Imam Mohammad Ibn Saud Islamic university, Riyadh 13318, Saudi Arabia,Corresponding authors at: Department of Medicinal Chemistry, Dr. Rajendra Gode College of Pharmacy, Mardi Road, Amravati, Maharashtra, India and (Rahul D. Jawarkar). Department of Chemistry, Faculty of Science, Al-Imam Mohammad Ibn Saud Islamic university, Riyadh 13318, Saudi Arabia (Magdi E.A. Zaki)
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, Assam 781014, India
| | - Ajaykumar Gandhi
- Department of Chemistry, Government College of Arts and Science, Aurangabad, Maharashtra 431 004, India
| | - Nobendu Mukerjee
- Department of Microbiology; Ramakrishna Mission Vivekananda Centenary College, Akhil Mukherjee Rd, Chowdhary Para, Rahara, Khardaha, Kolkata, West Bengal 700118, India
| | - Abdul Samad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Vijay H. Masand
- Department of Chemistry, Vidyabharti Mahavidyalaya, Camp Road, Amravati Maharashtra, India
| | - Israa Lewaa
- Department of Business Administration, Faculty of Business Administration, Economics & Political Science, The British University in Egypt (BUE), Cairo, Egypt
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3
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Liu J, Guo W, Sakkiah S, Ji Z, Yavas G, Zou W, Chen M, Tong W, Patterson TA, Hong H. Machine Learning Models for Predicting Liver Toxicity. Methods Mol Biol 2022; 2425:393-415. [PMID: 35188640 DOI: 10.1007/978-1-0716-1960-5_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Liver toxicity is a major adverse drug reaction that accounts for drug failure in clinical trials and withdrawal from the market. Therefore, predicting potential liver toxicity at an early stage in drug discovery is crucial to reduce costs and the potential for drug failure. However, current in vivo animal toxicity testing is very expensive and time consuming. As an alternative approach, various machine learning models have been developed to predict potential liver toxicity in humans. This chapter reviews current advances in the development and application of machine learning models for prediction of potential liver toxicity in humans and discusses possible improvements to liver toxicity prediction.
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Affiliation(s)
- Jie Liu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Wenjing Guo
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Sugunadevi Sakkiah
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Zuowei Ji
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Gokhan Yavas
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Wen Zou
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Minjun Chen
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Weida Tong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Tucker A Patterson
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Huixiao Hong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA.
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Kohlbacher SM, Langer T, Seidel T. QPHAR: quantitative pharmacophore activity relationship: method and validation. J Cheminform 2021; 13:57. [PMID: 34372940 PMCID: PMC8351372 DOI: 10.1186/s13321-021-00537-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/21/2021] [Indexed: 11/10/2022] Open
Abstract
QSAR methods are widely applied in the drug discovery process, both in the hit‐to‐lead and lead optimization phase, as well as in the drug-approval process. Most QSAR algorithms are limited to using molecules as input and disregard pharmacophores or pharmacophoric features entirely. However, due to the high level of abstraction, pharmacophore representations provide some advantageous properties for building quantitative SAR models. The abstract depiction of molecular interactions avoids a bias towards overrepresented functional groups in small datasets. Furthermore, a well‐crafted quantitative pharmacophore model can generalise to underrepresented or even missing molecular features in the training set by using pharmacophoric interaction patterns only. This paper presents a novel method to construct quantitative pharmacophore models and demonstrates its applicability and robustness on more than 250 diverse datasets. fivefold cross-validation on these datasets with default settings yielded an average RMSE of 0.62, with an average standard deviation of 0.18. Additional cross-validation studies on datasets with 15–20 training samples showed that robust quantitative pharmacophore models could be obtained. These low requirements for dataset sizes render quantitative pharmacophores a viable go-tomethod for medicinal chemists, especially in the lead-optimisation stage of drug discovery projects.![]()
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Affiliation(s)
- Stefan M Kohlbacher
- Division of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| | - Thierry Langer
- Division of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| | - Thomas Seidel
- Division of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, University of Vienna, Althanstraße 14, 1090, Vienna, Austria.
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5
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Wang Y, Yang X, Zhang S, Guo TL, Zhao B, Du Q, Chen J. Polarizability and aromaticity index govern AhR-mediated potencies of PAHs: A QSAR with consideration of freely dissolved concentrations. CHEMOSPHERE 2021; 268:129343. [PMID: 33359989 DOI: 10.1016/j.chemosphere.2020.129343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/12/2020] [Accepted: 12/13/2020] [Indexed: 06/12/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants associated with adverse human effects including cancer, and the aryl hydrocarbon receptor (AhR) is a key ligand-activated transcription factor mediating their toxicity. However, there is presently a lack of data on AhR potencies of PAHs. Simple, transparent, interpretable and predictive quantitative structure-activity relationship (QSAR) models are helpful, especially with the consideration of freely dissolved concentrations linked to bioavailability. Here, QSAR models on AhR-mediated luciferase activity of PAHs were developed with nominal median effect concentrations (EC50, nom) and freely dissolved concentration (EC50, free) as endpoints, and quantum chemical and Dragon descriptors as predictor variables. Results indicated that only the EC50, free model met the acceptable criteria of QSAR model (determination coefficient (R2) > 0.600, leave-one-out cross validation (QLOO2) > 0.500, and external validation coefficient (QEXT2) > 0.500), implying that it has good goodness-of-fit, robustness and external predictive power. Molecular polarizability and aromaticity index reflecting the partition behavior and intermolecular interactions can effectively predict AhR-mediated potencies of PAHs. The results highlight the necessity of adoption of the freely dissolved concentration in the QSAR modeling and more in silico models need to be further developed for different animal models (in vivo or in vitro).
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Affiliation(s)
- Ying Wang
- Key Laboratory for Ecological Environment in Coastal Areas, Ministry of Ecology and Environment, National Marine Environmental Monitoring Center, 42 Linghe Street, Dalian, 116023, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
| | - Xianhai Yang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing, 210094, China
| | - Songyan Zhang
- Engineering Laboratory of Shenzhen Natural Small Molecule Innovative Drugs, Health Science Center, Shenzhen University, 3688 Nanhai Avenue, Shenzhen, 518060, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
| | - Tai L Guo
- Department of Veterinary Biosciences and Diagnostic Imaging, College of Veterinary Medicine, University of Georgia, 501 D.W. Brooks Drive, Athens, GA, 30602, USA
| | - Bin Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China.
| | - Qiong Du
- Appraisal Center for Environment and Engineering, Ministry of Ecology and Environment, 8 Dayangfang, Anwai Beiyuan, Chaoyang District, Beijing, 100012, China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (China Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian, 116024, China.
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Drug properties and host factors contribute to biochemical presentation of drug-induced liver injury: a prediction model from a machine learning approach. Arch Toxicol 2021; 95:1793-1803. [PMID: 33666709 DOI: 10.1007/s00204-021-03013-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/25/2021] [Indexed: 12/19/2022]
Abstract
Drug-induced liver injury (DILI) presentation varies biochemically and histologically. Certain drugs present quite consistent injury patterns, i.e., DILI signatures. In contrast, others are manifested as broader types of liver injury. The variety of DILI presentations by a single drug suggests that both drugs and host factors may contribute to the phenotype. However, factors determining the DILI types have not been yet elucidated. Identifying such factors may help to accurately predict the injury types based on drugs and host information and assist the clinical diagnosis of DILI. Using prospective DILI registry datasets, we sought to explore and validate the associations of biochemical injury types at the time of DILI recognition with comprehensive information on drug properties and host factors. Random forest models identified a set of drug properties and host factors that differentiate hepatocellular from cholestatic damage with reasonable accuracy (69-84%). A simplified logistic regression model developed for practical use, consisting of patient's age, drug's lipoaffinity, and hybridization ratio, achieved a fair prediction (68-74%), but suggested potential clinical usability, computing the likelihood of liver injury type based on two properties of drugs taken by a patient and patient's age. In summary, considering both drug and host factors in evaluating DILI risk and phenotypes open an avenue for future DILI research and aid in the refinement of causality assessment.
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Hunter FM, Bento AP, Bosc N, Gaulton A, Hersey A, Leach AR. Drug Safety Data Curation and Modeling in ChEMBL: Boxed Warnings and Withdrawn Drugs. Chem Res Toxicol 2021; 34:385-395. [PMID: 33507738 PMCID: PMC7888266 DOI: 10.1021/acs.chemrestox.0c00296] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Indexed: 12/15/2022]
Abstract
The safety of marketed drugs is an ongoing concern, with some of the more frequently prescribed medicines resulting in serious or life-threatening adverse effects in some patients. Safety-related information for approved drugs has been curated to include the assignment of toxicity class(es) based on their withdrawn status and/or black box warning information described on medicinal product labels. The ChEMBL resource contains a wide range of bioactivity data types, from early "Discovery" stage preclinical data for individual compounds through to postclinical data on marketed drugs; the inclusion of the curated drug safety data set within this framework can support a wide range of safety-related drug discovery questions. The curated drug safety data set will be made freely available through ChEMBL and updated in future database releases.
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Affiliation(s)
- Fiona M.I. Hunter
- European Bioinformatics Institute, European
Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge
CB10 1SD, United Kingdom
| | - A. Patrícia Bento
- European Bioinformatics Institute, European
Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge
CB10 1SD, United Kingdom
| | - Nicolas Bosc
- European Bioinformatics Institute, European
Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge
CB10 1SD, United Kingdom
| | - Anna Gaulton
- European Bioinformatics Institute, European
Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge
CB10 1SD, United Kingdom
| | - Anne Hersey
- European Bioinformatics Institute, European
Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge
CB10 1SD, United Kingdom
| | - Andrew R. Leach
- European Bioinformatics Institute, European
Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge
CB10 1SD, United Kingdom
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Mechanism-based integrated assay systems for the prediction of drug-induced liver injury. Toxicol Appl Pharmacol 2020; 394:114958. [PMID: 32198022 DOI: 10.1016/j.taap.2020.114958] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/29/2020] [Accepted: 03/13/2020] [Indexed: 12/18/2022]
Abstract
Drug-induced liver injury (DILI) can cause hepatic failure and result in drug withdrawal from the market. It has host-related and compound-dependent mechanisms. Preclinical prediction of DILI risk is very challenging and safety assessments based on animals inadequately forecast human DILI risk. In contrast, human-derived in vitro cell culture-based models could improve DILI risk prediction accuracy. Here, we developed and validated an innovative method to assess DILI risk associated with various compounds. Fifty-four marketed and withdrawn drugs classified as DILI risks of "most concern", "less concern", and "no concern" were tested using a combination of four assays addressing mitochondrial injury, intrahepatic lipid accumulation, inhibition of bile canalicular network formation, and bile acid accumulation. Using the inhibitory potencies of the drugs evaluated in these in vitro tests, an algorithm with the highest available DILI risk prediction power was built by artificial neural network (ANN) analysis. It had an overall forecasting accuracy of 73%. We excluded the intrahepatic lipid accumulation assay to avoid overfitting. The accuracy of the algorithm in terms of predicting DILI risks was 62% when it was constructed by ANN but only 49% when it was built by the point-added scoring method. The final algorithm based on three assays made no DILI risk prediction errors such as "most concern " instead of "no concern" and vice-versa. Our mechanistic approach may accurately predict DILI risks associated with numerous candidate drugs.
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10
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Gonzalez-Jimenez A, McEuen K, Chen M, Suzuki A, Robles-Diaz M, Medina-Caliz I, Bessone F, Hernandez N, Arrese M, Parana R, Lucena MI, Stephens C, Andrade RJ. The influence of drug properties and host factors on delayed onset of symptoms in drug-induced liver injury. Liver Int 2019; 39:401-410. [PMID: 30195258 DOI: 10.1111/liv.13952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/22/2018] [Accepted: 08/27/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS Most patients with drug-induced liver injury (DILI) manifest clinical symptoms while on therapy, while some patients manifest days or weeks after drug cessation (delayed onset). This challenges DILI causality assessment and diagnosis. Factors contributing to the delayed onset phenotype are currently unknown. We explored factors contributing to delayed onset of DILI by analysing culprit drug properties, host factors and their interactions in a large patient population from the Spanish DILI Registry. METHODS Clinical information from 388 patients (69 presented delayed onset) and drug properties of 43 causative drugs (45 active ingredients) were analysed. A two-tier regression-based model was used to assess host/drug interactions affecting the probability of delayed onset. RESULTS Antibacterial and anti-inflammatory drugs accounted for the delayed onset cases. Drug property of <50% hepatic metabolism (odds ratio [OR] 11.06, 95% confidence interval [95% CI]: 4.4-32.2, P = 0.0003), daily dose ≥1000 mg (OR: 2.77, 95% CI: 1.3-6.1, P = 0.0063) and the absence of pre-existing conditions in a patient (OR: 2.55, 95% CI: 1.3-4.9, P = 0.0043) were independently associated with delayed onset. The findings were consistent when externally validated using Latin American DILI Network cases (N = 131). Likewise, drug properties of mitochondrial liability and Pauling electronegativity were associated with delayed onset, but dependent on specific host factors such as age, sex and pre-existing cardiac diseases. CONCLUSIONS This study demonstrated that delayed onset, a specific DILI phenotype, is explained by complex interactions among drug properties and host factors and provided mechanistic hypotheses for future studies. These findings can help improve the diagnostic capability and causality assessment.
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Affiliation(s)
- Andres Gonzalez-Jimenez
- Unidad de Gestión Clínica del Aparato Digestivo, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd, Málaga, Spain
| | - Kristin McEuen
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
| | - Minjun Chen
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
| | - Ayako Suzuki
- Gastroenterology, Duke University, Durham, North Carolina, USA.,Gastroenterology, Durham VA Medical Center, Durham, North Carolina, USA
| | - Mercedes Robles-Diaz
- Unidad de Gestión Clínica del Aparato Digestivo, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd, Málaga, Spain
| | - Inmaculada Medina-Caliz
- Unidad de Gestión Clínica del Aparato Digestivo, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd, Málaga, Spain
| | - Fernando Bessone
- Facultad de Medicina, Hospital Provincial del Centenario, Universidad de Rosario, Rosario, Argentina
| | - Nelia Hernandez
- Facultad de Medicina, Hospital de Clínicas, UDELAR, Montevideo, Uruguay
| | - Marco Arrese
- Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile y Centro de Envejecimiento y Regeneración (CARE), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Raymundo Parana
- Hospital Universitario Prof. Edgard Santos, Universidad Federal da Bahía, Salvador de Bahía, Brazil
| | - M Isabel Lucena
- Unidad de Gestión Clínica del Aparato Digestivo, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd, Málaga, Spain.,UICEC IBIMA, Plataforma SCReN (Spanish Clinical Research Network), Servicio de Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Málaga, Spain
| | - Camilla Stephens
- Unidad de Gestión Clínica del Aparato Digestivo, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd, Málaga, Spain
| | - Raúl J Andrade
- Unidad de Gestión Clínica del Aparato Digestivo, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd, Málaga, Spain
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Mode-of-Action-Guided, Molecular Modeling-Based Toxicity Prediction: A Novel Approach for In Silico Predictive Toxicology. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2019. [DOI: 10.1007/978-3-030-16443-0_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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12
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Li Y, Idakwo G, Thangapandian S, Chen M, Hong H, Zhang C, Gong P. Target-specific toxicity knowledgebase (TsTKb): a novel toolkit for in silico predictive toxicology. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2018; 36:219-236. [PMID: 30426823 DOI: 10.1080/10590501.2018.1537148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
As the number of man-made chemicals increases at an unprecedented pace, efforts of quickly screening and accurately evaluating their potential adverse biological effects have been hampered by prohibitively high costs of in vivo/vitro toxicity testing. While it is unrealistic and unnecessary to test every uncharacterized chemical, it remains a major challenge to develop alternative in silico tools with high reliability and precision in toxicity prediction. To address this urgent need, we have developed a novel mode-of-action-guided, molecular modeling-based, and machine learning-enabled modeling approach for in silico chemical toxicity prediction. Here we introduce the core element of this approach, Target-specific Toxicity Knowledgebase (TsTKb), which consists of two main components: Chemical Mode of Action (ChemMoA) database and a suite of prediction model libraries.
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Affiliation(s)
- Yan Li
- a Bennett Aerospace Inc. , Cary , NC , USA
| | - Gabriel Idakwo
- b School of Computing Science and Computer Engineering , University of Southern Mississippi , Hattiesburg , MS , USA
| | - Sundar Thangapandian
- c Environmental Laboratory , US Army Engineer Research and Development Center , Vicksburg , MS , USA
| | - Minjun Chen
- d Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, US Food and Drug Administration , Jefferson , AR , USA
| | - Huixiao Hong
- d Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, US Food and Drug Administration , Jefferson , AR , USA
| | - Chaoyang Zhang
- b School of Computing Science and Computer Engineering , University of Southern Mississippi , Hattiesburg , MS , USA
| | - Ping Gong
- c Environmental Laboratory , US Army Engineer Research and Development Center , Vicksburg , MS , USA
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Selvaraj C, Sakkiah S, Tong W, Hong H. Molecular dynamics simulations and applications in computational toxicology and nanotoxicology. Food Chem Toxicol 2017; 112:495-506. [PMID: 28843597 DOI: 10.1016/j.fct.2017.08.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 08/08/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022]
Abstract
Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations.
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Affiliation(s)
- Chandrabose Selvaraj
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Sugunadevi Sakkiah
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
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