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Wright PSR, Briggs KA, Thomas R, Smith GF, Maglennon G, Mikulskis P, Chapman M, Greene N, Phillips BU, Bender A. Statistical analysis of preclinical inter-species concordance of histopathological findings in the eTOX database. Regul Toxicol Pharmacol 2023; 138:105308. [PMID: 36481279 DOI: 10.1016/j.yrtph.2022.105308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022]
Abstract
Preclinical inter-species concordance can increase the predictivity of observations to the clinic, potentially reducing drug attrition caused by unforeseen adverse events. We quantified inter-species concordance of histopathological findings and target organ toxicities across four preclinical species in the eTOX database using likelihood ratios (LRs). This was done whilst only comparing findings between studies with similar compound exposure (Δ|Cmax| ≤ 1 log-unit), repeat-dosing duration, and animals of the same sex. We discovered 24 previously unreported significant inter-species associations between histopathological findings encoded by the HPATH ontology. More associations with strong positive concordance (33% LR+ > 10) relative to strong negative concordance (12.5% LR- < 0.1) were identified. Of the top 10 most positively concordant associations, 60% were computed between different histopathological findings indicating potential differences in inter-species pathogenesis. We also observed low inter-species target organ toxicity concordance. For example, liver toxicity concordance in short-term studies between female rats and dogs observed an average LR+ of 1.84, and an average LR- of 0.73. This was corroborated by similarly low concordance between rodents and non-rodents for 75 candidate drugs in AstraZeneca. This work provides new statistically significant associations between preclinical species, but finds that concordance is rare, particularly between the absence of findings.
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Affiliation(s)
- Peter S R Wright
- University of Cambridge, Centre for Molecular Science Informatics, Department of Chemistry, Cambridge, United Kingdom.
| | | | | | - Graham F Smith
- AstraZeneca, Data Science and AI, Clinical Pharmacology and Safety Sciences, R&D, Cambridge, United Kingdom
| | - Gareth Maglennon
- AstraZeneca, Oncology Pathology, Clinical Pharmacology and Safety Sciences, R&D, Melbourn, United Kingdom
| | - Paulius Mikulskis
- AstraZeneca, Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, Gothenburg, Sweden
| | - Melissa Chapman
- AstraZeneca, Toxicology, Clinical Pharmacology and Safety Sciences, R&D, Melbourn, United Kingdom
| | - Nigel Greene
- AstraZeneca, Data Science and Artificial Intelligence, Clinical Pharmacology and Safety Sciences, R&D, Boston, MA, USA
| | - Benjamin U Phillips
- AstraZeneca, Data Sciences and Quantitative Biology, Discovery Sciences, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Andreas Bender
- University of Cambridge, Centre for Molecular Science Informatics, Department of Chemistry, Cambridge, United Kingdom.
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2
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Giblin KA, Basili D, Afzal AM, Rosenbrier-Ribeiro L, Greene N, Barrett I, Hughes SJ, Bender A. New Associations between Drug-Induced Adverse Events in Animal Models and Humans Reveal Novel Candidate Safety Targets. Chem Res Toxicol 2020; 34:438-451. [PMID: 33338378 DOI: 10.1021/acs.chemrestox.0c00311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
To improve our ability to extrapolate preclinical toxicity to humans, there is a need to understand and quantify the concordance of adverse events (AEs) between animal models and clinical studies. In the present work, we discovered 3011 statistically significant associations between preclinical and clinical AEs caused by drugs reported in the PharmaPendium database of which 2952 were new associations between toxicities encoded by different Medical Dictionary for Regulatory Activities terms across species. To find plausible and testable candidate off-target drug activities for the derived associations, we investigated the genetic overlap between the genes linked to both a preclinical and a clinical AE and the protein targets found to interact with one or more drugs causing both AEs. We discuss three associations from the analysis in more detail for which novel candidate off-target drug activities could be identified, namely, the association of preclinical mutagenicity readouts with clinical teratospermia and ovarian failure, the association of preclinical reflexes abnormal with clinical poor-quality sleep, and the association of preclinical psychomotor hyperactivity with clinical drug withdrawal syndrome. Our analysis successfully identified a total of 77% of known safety targets currently tested in in vitro screening panels plus an additional 431 genes which were proposed for investigation as future safety targets for different clinical toxicities. This work provides new translational toxicity relationships beyond AE term-matching, the results of which can be used for risk profiling of future new chemical entities for clinical studies and for the development of future in vitro safety panels.
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Affiliation(s)
- Kathryn A Giblin
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.,Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Danilo Basili
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Avid M Afzal
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Lyn Rosenbrier-Ribeiro
- Safety Platforms, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Nigel Greene
- Data Science and Artificial Intelligence, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Ian Barrett
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Samantha J Hughes
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Clark M, Steger-Hartmann T. A big data approach to the concordance of the toxicity of pharmaceuticals in animals and humans. Regul Toxicol Pharmacol 2018; 96:94-105. [PMID: 29730448 DOI: 10.1016/j.yrtph.2018.04.018] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 12/11/2022]
Abstract
Although lack of efficacy is an important cause of late stage attrition in drug development the shortcomings in the translation of toxicities observed during the preclinical development to observations in clinical trials or post-approval is an ongoing topic of research. The concordance between preclinical and clinical safety observations has been analyzed only on relatively small data sets, mostly over short time periods of drug approvals. We therefore explored the feasibility of a big-data analysis on a set of 3,290 approved drugs and formulations for which 1,637,449 adverse events were reported for both humans animal species in regulatory submissions over a period of more than 70 years. The events reported in five species - rat, dog, mouse, rabbit, and cynomolgus monkey - were treated as diagnostic tests for human events and the diagnostic power was computed for each event/species pair using likelihood ratios. The animal-human translation of many key observations is confirmed as being predictive, such as QT prolongation and arrhythmias in dog. Our study confirmed the general predictivity of animal safety observations for humans, but also identified issues of such automated analyses which are on the one hand related to data curation and controlled vocabularies, on the other hand to methodological changes over the course of time.
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Affiliation(s)
- Matthew Clark
- Elsevier R&D Solutions, 1600 JFK Blvd, Philadelphia, PA, 19103, USA.
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Prior H, Baldrick P, de Haan L, Downes N, Jones K, Mortimer-Cassen E, Kimber I. Reviewing the Utility of Two Species in General Toxicology Related to Drug Development. Int J Toxicol 2018. [PMCID: PMC5881785 DOI: 10.1177/1091581818760564] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As part of the safety assessment of new drugs, the use of two species (a rodent and a nonrodent) for regulatory toxicology studies is the typical approach taken for small molecules. For biologics, species selection is dictated by pharmacological relevance, and single species toxicology packages (typically using the nonhuman primate) are common. The UK National Centre for the Replacement, Refinement, and Reduction of Animals in Research and the Association of the British Pharmaceutical Industry are collaborating on a project to review the utility of two species in regulatory toxicology studies, with the aim to explore whether there are wider circumstances when data from a single species could be sufficient to enable safe progression in humans. An international working group consisting of 37 representatives from pharmaceutical and biotechnology companies, contract research organizations, academia, and regulatory bodies is coordinating a large-scale data sharing exercise to examine the potential for changes in current practice to reduce the number of species used for nonclinical safety testing at different stages of development. The challenge will be to determine whether two species toxicology adds significant value or whether in some instances data from a single species are sufficient (across a broader range of molecules than is currently the case) without compromising human safety.
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Affiliation(s)
- Helen Prior
- National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs), London, United Kingdom
| | - Paul Baldrick
- Nonclinical and Biological Discovery Expert Network (NaBDEN), The Association of the British Pharmaceutical Industry (ABPI), London, United Kingdom
| | - Lolke de Haan
- Nonclinical and Biological Discovery Expert Network (NaBDEN), The Association of the British Pharmaceutical Industry (ABPI), London, United Kingdom
| | - Noel Downes
- Nonclinical and Biological Discovery Expert Network (NaBDEN), The Association of the British Pharmaceutical Industry (ABPI), London, United Kingdom
| | - Keith Jones
- Nonclinical and Biological Discovery Expert Network (NaBDEN), The Association of the British Pharmaceutical Industry (ABPI), London, United Kingdom
| | - Elisabeth Mortimer-Cassen
- Nonclinical and Biological Discovery Expert Network (NaBDEN), The Association of the British Pharmaceutical Industry (ABPI), London, United Kingdom
| | - Ian Kimber
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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Sewell F, Edwards J, Prior H, Robinson S. Opportunities to Apply the 3Rs in Safety Assessment Programs. ILAR J 2016; 57:234-245. [PMID: 28053076 PMCID: PMC5886346 DOI: 10.1093/ilar/ilw024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 08/01/2016] [Accepted: 09/01/2016] [Indexed: 12/16/2022] Open
Abstract
Before a potential new medicine can be administered to humans it is essential that its safety is adequately assessed. Safety assessment in animals forms an integral part of this process, from early drug discovery and initial candidate selection to the program of recommended regulatory tests in animals. The 3Rs (replacement, reduction, and refinement of animals in research) are integrated in the current regulatory requirements and expectations and, in the EU, provide a legal and ethical framework for in vivo research to ensure the scientific objectives are met whilst minimizing animal use and maintaining high animal welfare standards. Though the regulations are designed to uncover potential risks, they are intended to be flexible, so that the most appropriate approach can be taken for an individual product. This article outlines current and future opportunities to apply the 3Rs in safety assessment programs for pharmaceuticals, and the potential (scientific, financial, and ethical) benefits to the industry, across the drug discovery and development process. For example, improvements to, or the development of, novel, early screens (e.g., in vitro, in silico, or nonmammalian screens) designed to identify compounds with undesirable characteristics earlier in development have the potential to reduce late-stage attrition by improving the selection of compounds that require regulatory testing in animals. Opportunities also exist within the current regulatory framework to simultaneously reduce and/or refine animal use and improve scientific outcomes through improvements to technical procedures and/or adjustments to study designs. It is important that approaches to safety assessment are continuously reviewed and challenged to ensure they are science-driven and predictive of relevant effects in humans.
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Affiliation(s)
- Fiona Sewell
- Fiona Sewell, PhD, is a Programme Manager in Toxicology and Regulatory Sciences at the UK National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs), London, UK.Joanna Edwards, PhD, is a Programme Manager in Technology Development at the NC3Rs, London, UK.Helen Prior, PhD, is a Programme Manager in Drug Development at the NC3Rs, London, UK.Sally Robinson, PhD, is Head of Laboratory Animal Sciences at AstraZeneca, Alderley Park, UK
| | - Joanna Edwards
- Fiona Sewell, PhD, is a Programme Manager in Toxicology and Regulatory Sciences at the UK National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs), London, UK.Joanna Edwards, PhD, is a Programme Manager in Technology Development at the NC3Rs, London, UK.Helen Prior, PhD, is a Programme Manager in Drug Development at the NC3Rs, London, UK.Sally Robinson, PhD, is Head of Laboratory Animal Sciences at AstraZeneca, Alderley Park, UK
| | - Helen Prior
- Fiona Sewell, PhD, is a Programme Manager in Toxicology and Regulatory Sciences at the UK National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs), London, UK.Joanna Edwards, PhD, is a Programme Manager in Technology Development at the NC3Rs, London, UK.Helen Prior, PhD, is a Programme Manager in Drug Development at the NC3Rs, London, UK.Sally Robinson, PhD, is Head of Laboratory Animal Sciences at AstraZeneca, Alderley Park, UK
| | - Sally Robinson
- Fiona Sewell, PhD, is a Programme Manager in Toxicology and Regulatory Sciences at the UK National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs), London, UK.Joanna Edwards, PhD, is a Programme Manager in Technology Development at the NC3Rs, London, UK.Helen Prior, PhD, is a Programme Manager in Drug Development at the NC3Rs, London, UK.Sally Robinson, PhD, is Head of Laboratory Animal Sciences at AstraZeneca, Alderley Park, UK
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Dambach DM, Misner D, Brock M, Fullerton A, Proctor W, Maher J, Lee D, Ford K, Diaz D. Safety Lead Optimization and Candidate Identification: Integrating New Technologies into Decision-Making. Chem Res Toxicol 2015; 29:452-72. [DOI: 10.1021/acs.chemrestox.5b00396] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Donna M. Dambach
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Dinah Misner
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Mathew Brock
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Aaron Fullerton
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - William Proctor
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Jonathan Maher
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Dong Lee
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Kevin Ford
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Dolores Diaz
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
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The STEP database through the end-users eyes--USABILITY STUDY. Int J Pharm 2015; 492:316-31. [PMID: 26117188 DOI: 10.1016/j.ijpharm.2015.06.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/12/2015] [Accepted: 06/15/2015] [Indexed: 11/22/2022]
Abstract
OBJECTIVES The user-designed database of Safety and Toxicity of Excipients for Paediatrics ("STEP") is created to address the shared need of drug development community to access the relevant information of excipients effortlessly. Usability testing was performed to validate if the database satisfies the need of the end-users. METHOD Evaluation framework was developed to assess the usability. The participants performed scenario based tasks and provided feedback and post-session usability ratings. Failure Mode Effect Analysis (FMEA) was performed to prioritize the problems and improvements to the STEP database design and functionalities. RESULT The study revealed several design vulnerabilities. Tasks such as limiting the results, running complex queries, location of data and registering to access the database were challenging. The three critical attributes identified to have impact on the usability of the STEP database included (1) content and presentation (2) the navigation and search features (3) potential end-users. CONCLUSION Evaluation framework proved to be an effective method for evaluating database effectiveness and user satisfaction. This study provides strong initial support for the usability of the STEP database. Recommendations would be incorporated into the refinement of the database to improve its usability and increase user participation towards the advancement of the database.
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