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Seal S, Williams DP, Hosseini-Gerami L, Mahale M, Carpenter AE, Spjuth O, Bender A. Improved Detection of Drug-Induced Liver Injury by Integrating Predicted in vivo and in vitro Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575128. [PMID: 38895462 PMCID: PMC11185581 DOI: 10.1101/2024.01.10.575128] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Drug-induced liver injury (DILI) has been significant challenge in drug discovery, often leading to clinical trial failures and necessitating drug withdrawals. The existing suite of in vitro proxy-DILI assays is generally effective at identifying compounds with hepatotoxicity. However, there is considerable interest in enhancing in silico prediction of DILI because it allows for the evaluation of large sets of compounds more quickly and cost-effectively, particularly in the early stages of projects. In this study, we aim to study ML models for DILI prediction that first predicts nine proxy-DILI labels and then uses them as features in addition to chemical structural features to predict DILI. The features include in vitro (e.g., mitochondrial toxicity, bile salt export pump inhibition) data, in vivo (e.g., preclinical rat hepatotoxicity studies) data, pharmacokinetic parameters of maximum concentration, structural fingerprints, and physicochemical parameters. We trained DILI-prediction models on 888 compounds from the DILIst dataset and tested on a held-out external test set of 223 compounds from DILIst dataset. The best model, DILIPredictor, attained an AUC-ROC of 0.79. This model enabled the detection of top 25 toxic compounds compared to models using only structural features (2.68 LR+ score). Using feature interpretation from DILIPredictor, we were able to identify the chemical substructures causing DILI as well as differentiate cases DILI is caused by compounds in animals but not in humans. For example, DILIPredictor correctly recognized 2-butoxyethanol as non-toxic in humans despite its hepatotoxicity in mice models. Overall, the DILIPredictor model improves the detection of compounds causing DILI with an improved differentiation between animal and human sensitivity as well as the potential for mechanism evaluation. DILIPredictor is publicly available at https://broad.io/DILIPredictor for use via web interface and with all code available for download and local implementation via https://pypi.org/project/dilipred/.
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Affiliation(s)
- Srijit Seal
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Rd, CB2 1EW, Cambridge, United Kingdom
- Imaging Platform, Broad Institute of MIT and Harvard, US
| | - Dominic P Williams
- Safety Innovation, Clinical Pharmacology and Safety Sciences, AstraZeneca, Cambridge CB4 0FZ, United Kingdom
- Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0FZ, United Kingdom
| | | | - Manas Mahale
- Bombay College of Pharmacy Kalina Santacruz (E), Mumbai 400 098, India
| | | | - Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-75124, Uppsala, Sweden
| | - Andreas Bender
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Rd, CB2 1EW, Cambridge, United Kingdom
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Fitzpatrick PA, Johansson J, Maglennon G, Wallace I, Hendrickx R, Stamou M, Balogh Sivars K, Busch S, Johansson L, Van Zuydam N, Patten K, Åberg PM, Ollerstam A, Hornberg JJ. A novel in vitro high-content imaging assay for the prediction of drug-induced lung toxicity. Arch Toxicol 2024:10.1007/s00204-024-03800-8. [PMID: 38806719 DOI: 10.1007/s00204-024-03800-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/23/2024] [Indexed: 05/30/2024]
Abstract
The development of inhaled drugs for respiratory diseases is frequently impacted by lung pathology in non-clinical safety studies. To enable design of novel candidate drugs with the right safety profile, predictive in vitro lung toxicity assays are required that can be applied during drug discovery for early hazard identification and mitigation. Here, we describe a novel high-content imaging-based screening assay that allows for quantification of the tight junction protein occludin in A549 cells, as a model for lung epithelial barrier integrity. We assessed a set of compounds with a known lung safety profile, defined by clinical safety or non-clinical in vivo toxicology data, and were able to correctly identify 9 of 10 compounds with a respiratory safety risk and 9 of 9 compounds without a respiratory safety risk (90% sensitivity, 100% specificity). The assay was sensitive at relevant compound concentrations to influence medicinal chemistry optimization programs and, with an accessible cell model in a 96-well plate format, short protocol and application of automated imaging analysis algorithms, this assay can be readily integrated in routine discovery safety screening to identify and mitigate respiratory toxicity early during drug discovery. Interestingly, when we applied physiologically-based pharmacokinetic (PBPK) modelling to predict epithelial lining fluid exposures of the respiratory tract after inhalation, we found a robust correlation between in vitro occludin assay data and lung pathology in vivo, suggesting the assay can inform translational risk assessment for inhaled small molecules.
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Affiliation(s)
- Paul A Fitzpatrick
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R and D, AstraZeneca, Gothenburg, Sweden.
| | - Julia Johansson
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R and D, AstraZeneca, Gothenburg, Sweden
| | - Gareth Maglennon
- AstraZeneca Pathology, Clinical Pharmacology and Safety Sciences, R and D, AstraZeneca, Cambridge, UK
| | - Ian Wallace
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R and D, AstraZeneca, Gothenburg, Sweden
| | - Ramon Hendrickx
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Respiratory and Immunology (R and I), R and D, AstraZeneca, Gothenburg, Sweden
| | - Marianna Stamou
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R and D, AstraZeneca, Gothenburg, Sweden
| | - Kinga Balogh Sivars
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R and D, AstraZeneca, Gothenburg, Sweden
| | - Susann Busch
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R and D, AstraZeneca, Gothenburg, Sweden
| | - Linnea Johansson
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R and D, AstraZeneca, Gothenburg, Sweden
| | - Natalie Van Zuydam
- Data Sciences and Quantitative Biology, Discovery Sciences, R and D, AstraZeneca, Gothenburg, Sweden
| | - Kelley Patten
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R and D, AstraZeneca, Gothenburg, Sweden
| | - Per M Åberg
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R and D, AstraZeneca, Gothenburg, Sweden
| | - Anna Ollerstam
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R and D, AstraZeneca, Gothenburg, Sweden
| | - Jorrit J Hornberg
- Safety Sciences, Clinical Pharmacology and Safety Sciences, R and D, AstraZeneca, Gothenburg, Sweden
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Chemical, Cytotoxic, and Anti-Inflammatory Assessment of Honey Bee Venom from Apis mellifera intermissa. Antibiotics (Basel) 2021; 10:antibiotics10121514. [PMID: 34943726 PMCID: PMC8698958 DOI: 10.3390/antibiotics10121514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/23/2021] [Accepted: 12/08/2021] [Indexed: 12/03/2022] Open
Abstract
The venom from Apis mellifera intermissa, the main honey bee prevailing in Morocco, has been scarcely studied, despite its known potential for pharmacological applications. In the present work, we investigated the composition, the anti-inflammatory activity, and the venom’s cytotoxic properties from fifteen honey bee venom (HBV) samples collected in three regions: northeast, central, and southern Morocco. The chemical assessment of honey bee venom was performed using LC-DAD/ESI/MSn, NIR spectroscopy and AAS spectroscopy. The antiproliferative effect was evaluated using human tumor cell lines, including breast adenocarcinoma, non-small cell lung carcinoma, cervical carcinoma, hepatocellular carcinoma, and malignant melanoma. Likewise, we assessed the anti-inflammatory activity using the murine macrophage cell line. The study provides information on the honey bee venom subspecies’ main components, such as melittin, apamin, and phospholipase A2, with compositional variation depending on the region of collection. Contents of toxic elements such as cadmium, chromium, and plumb were detected at a concentration below 5 ppm, which can be regarded as safe for pharmaceutical use. The data presented contribute to the first study in HBV from Apis mellifera intermissa and highlight the remarkable antiproliferative and anti-inflammatory effects of HBV, suggesting it to be a candidate natural medicine to explore.
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Molecular Human Targets of Bioactive Alkaloid-Type Compounds from Tabernaemontana cymose Jacq. Molecules 2021; 26:molecules26123765. [PMID: 34205626 PMCID: PMC8234993 DOI: 10.3390/molecules26123765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/10/2021] [Accepted: 06/18/2021] [Indexed: 12/29/2022] Open
Abstract
Alkaloids are a group of secondary metabolites that have been widely studied for the discovery of new drugs due to their properties on the central nervous system and their anti-inflammatory, antioxidant and anti-cancer activities. Molecular docking was performed for 10 indole alkaloids identified in the ethanol extract of Tabernaemontana cymosa Jacq. with 951 human targets involved in different diseases. The results were analyzed through the KEGG and STRING databases, finding the most relevant physiological associations for alkaloids. The molecule 5-oxocoronaridine proved to be the most active molecule against human proteins (binding energy affinity average = −9.2 kcal/mol) and the analysis of the interactions between the affected proteins pointed to the PI3K/ Akt/mTOR signaling pathway as the main target. The above indicates that indole alkaloids from T. cymosa constitute a promising source for the search and development of new treatments against different types of cancer.
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Transforming early pharmaceutical assessment of genotoxicity: applying statistical learning to a high throughput, multi end point in vitro micronucleus assay. Sci Rep 2021; 11:2535. [PMID: 33510380 PMCID: PMC7844000 DOI: 10.1038/s41598-021-82115-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/15/2021] [Indexed: 02/06/2023] Open
Abstract
To provide a comprehensive analysis of small molecule genotoxic potential we have developed and validated an automated, high-content, high throughput, image-based in vitro Micronucleus (IVM) assay. This assay simultaneously assesses micronuclei and multiple additional cellular markers associated with genotoxicity. Acoustic dosing (≤ 2 mg) of compound is followed by a 24-h treatment and a 24-h recovery period. Confocal images are captured [Cell Voyager CV7000 (Yokogawa, Japan)] and analysed using Columbus software (PerkinElmer). As standard the assay detects micronuclei (MN), cytotoxicity and cell-cycle profiles from Hoechst phenotypes. Mode of action information is primarily determined by kinetochore labelling in MN (aneugencity) and γH2AX foci analysis (a marker of DNA damage). Applying computational approaches and implementing machine learning models alongside Bayesian classifiers allows the identification of, with 95% accuracy, the aneugenic, clastogenic and negative compounds within the data set (Matthews correlation coefficient: 0.9), reducing analysis time by 80% whilst concurrently minimising human bias. Combining high throughput screening, multiparametric image analysis and machine learning approaches has provided the opportunity to revolutionise early Genetic Toxicology assessment within AstraZeneca. By multiplexing assay endpoints and minimising data generation and analysis time this assay enables complex genotoxicity safety assessments to be made sooner aiding the development of safer drug candidates.
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