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Using chemical and biological data to predict drug toxicity. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:53-64. [PMID: 36639032 DOI: 10.1016/j.slasd.2022.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/19/2022] [Accepted: 12/31/2022] [Indexed: 01/12/2023]
Abstract
Various sources of information can be used to better understand and predict compound activity and safety-related endpoints, including biological data such as gene expression and cell morphology. In this review, we first introduce types of chemical, in vitro and in vivo information that can be used to describe compounds and adverse effects. We then explore how compound descriptors based on chemical structure or biological perturbation response can be used to predict safety-related endpoints, and how especially biological data can help us to better understand adverse effects mechanistically. Overall, the described applications demonstrate how large-scale biological information presents new opportunities to anticipate and understand the biological effects of compounds, and how this can support predictive toxicology and drug discovery projects.
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Arnesdotter E, Rogiers V, Vanhaecke T, Vinken M. An overview of current practices for regulatory risk assessment with lessons learnt from cosmetics in the European Union. Crit Rev Toxicol 2021; 51:395-417. [PMID: 34352182 DOI: 10.1080/10408444.2021.1931027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Risk assessments of various types of chemical compounds are carried out in the European Union (EU) foremost to comply with legislation and to support regulatory decision-making with respect to their safety. Historically, risk assessment has relied heavily on animal experiments. However, the EU is committed to reduce animal experimentation and has implemented several legislative changes, which have triggered a paradigm shift towards human-relevant animal-free testing in the field of toxicology, in particular for risk assessment. For some specific endpoints, such as skin corrosion and irritation, validated alternatives are available whilst for other endpoints, including repeated dose systemic toxicity, the use of animal data is still central to meet the information requirements stipulated in the different legislations. The present review aims to provide an overview of established and more recently introduced methods for hazard assessment and risk characterisation for human health, in particular in the context of the EU Cosmetics Regulation (EC No 1223/2009) as well as the Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) Regulation (EC 1907/2006).
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Affiliation(s)
- Emma Arnesdotter
- Department of Pharmaceutical and Pharmacological Sciences, Research Group of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Vera Rogiers
- Department of Pharmaceutical and Pharmacological Sciences, Research Group of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Tamara Vanhaecke
- Department of Pharmaceutical and Pharmacological Sciences, Research Group of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mathieu Vinken
- Department of Pharmaceutical and Pharmacological Sciences, Research Group of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Brussels, Belgium
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Tcheremenskaia O, Benigni R. Toward regulatory acceptance and improving the prediction confidence of in silico approaches: a case study of genotoxicity. Expert Opin Drug Metab Toxicol 2021; 17:987-1005. [PMID: 34078212 DOI: 10.1080/17425255.2021.1938540] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: Genotoxicity is an imperative component of the human health safety assessment of chemicals. Its secure forecast is of the utmost importance for all health prevention strategies and regulations.Areas covered: We surveyed several types of alternative, animal-free approaches ((quantitative) structure-activity relationship (Q)SAR, read-across, Adverse Outcome Pathway, Integrated Approaches to Testing and Assessment) for genotoxicity prediction within the needs of regulatory frameworks, putting special emphasis on data quality and uncertainties issues.Expert opinion: (Q)SAR models and read-across approaches for in vitro bacterial mutagenicity have sufficient reliability for use in prioritization processes, and as support in regulatory decisions in combination with other types of evidence. (Q)SARs and read-across methodologies for other genotoxicity endpoints need further improvements and should be applied with caution. It appears that there is still large room for improvement of genotoxicity prediction methods. Availability of well-curated high-quality databases, covering a broader chemical space, is one of the most important needs. Integration of in silico predictions with expert knowledge, weight-of-evidence-based assessment, and mechanistic understanding of genotoxicity pathways are other key points to be addressed for the generation of more accurate and trustable results.
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Affiliation(s)
- Olga Tcheremenskaia
- Environmental and Health Department, Istituto Superiore Di Sanità (ISS), Rome, Italy, Rome, Italy
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Aksenova NA, Tcheremenskaia O, Timashev PS, Solovieva AB. Computational prediction of photosensitizers’ toxicity. J PORPHYR PHTHALOCYA 2021. [DOI: 10.1142/s1088424621500334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The percentage of failures in late pharmaceutical development due to toxicity has increased dramatically over the last decade or so, resulting in increased demand for new methods to rapidly and reliably predict the toxicity of compounds. Today, computational toxicology can be used in every phase of drug discovery and development, from profiling large libraries early on, to predicting off-target effects in the mid-discovery phase, and to assess potential mutagenic impurities in development and degradants as part of life-cycle management. In this study, for the first time, in silico approaches were used to analyze the possible dark toxicity of photosensitive systems based on chlorin e6 and assessed possible toxicity of these compositions. By applying quantitative structure-activity relationship models (QSARs) and modeling adverse outcome pathways (AOPs), a potential toxic effect of water-soluble (chlorin e6 and chlorin e6 aminoamid) and hydrophobic (tetraphenylporphyrin) photosensitizers (PS) was predicted. Particularly, PSs’ protein binding ability, reactivity to form peptide adducts, glutathione conjugation, activity in dendritic cells, and gene expression activity in keratinocytes were explored. Using a metabolism simulator, possible PS metabolites were predicted and their potential toxicity was assessed as well. It was shown that all tested porphyrin PS and their predicted metabolites possess low activity in the mentioned processes and therefore are unable to cause significant adverse toxic effects under dark conditions.
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Affiliation(s)
- Nadezhda A. Aksenova
- N.N. Semenov Federal Research Center for Chemical Physics, 4 Kosygin st., Moscow, 119991, Russia
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, 8-2 Trubetskaya st., Moscow, 119991, Russia
| | - Olga Tcheremenskaia
- Environment and Health department, Instituto Superiore di Sanita, 299 Viale Regina Elena, Rome, 00161, Italy
| | - Peter S. Timashev
- N.N. Semenov Federal Research Center for Chemical Physics, 4 Kosygin st., Moscow, 119991, Russia
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, 8-2 Trubetskaya st., Moscow, 119991, Russia
- Chemistry Department, Lomonosov Moscow State University, Leninskiye Gory 13, Moscow 119991, Russia
| | - Anna B. Solovieva
- N.N. Semenov Federal Research Center for Chemical Physics, 4 Kosygin st., Moscow, 119991, Russia
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Jummaat F, Yahya EB, Khalil H.P.S. A, Adnan AS, Alqadhi AM, Abdullah CK, A.K. AS, Olaiya NG, Abdat M. The Role of Biopolymer-Based Materials in Obstetrics and Gynecology Applications: A Review. Polymers (Basel) 2021; 13:633. [PMID: 33672526 PMCID: PMC7923797 DOI: 10.3390/polym13040633] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 12/17/2022] Open
Abstract
Biopolymers have gained tremendous attention in many daily life applications, including medical applications, in the past few years. Obstetrics and gynecology are two fields dealing with sensitive parts of the woman's body and her newborn baby, which are normally associated with many issues such as toxicity, infections, and even gene alterations. Medical professions that use screening, examination, pre, and post-operation materials should benefit from a better understanding of each type of material's characteristics, health, and even environmental effects. The underlying principles of biopolymer-based materials for different obstetric and gynecologic applications may discover various advantages and benefits of using such materials. This review presents the health impact of conventional polymer-based materials on pregnant women's health and highlights the potential use of biopolymers as a safer option. The recent works on utilizing different biopolymer-based materials in obstetric and gynecologic are presented in this review, which includes suture materials in obstetric and gynecologic surgeries, cosmetic and personal care products, vaginal health, and drug delivery; as well as a wound dressing and healing materials. This review highlights the main issues and challenges of biopolymers in obstetric and gynecologic applications.
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Affiliation(s)
- Fauziah Jummaat
- Management & Science University Medical Centre, University Drive, Off Persiaran Olahraga, Section 13, Shah Alam 40100, Malaysia
| | - Esam Bashir Yahya
- School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia; (E.B.Y.); (C.K.A.); (N.G.O.)
| | - Abdul Khalil H.P.S.
- School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia; (E.B.Y.); (C.K.A.); (N.G.O.)
| | - A. S. Adnan
- Management & Science University Medical Centre, University Drive, Off Persiaran Olahraga, Section 13, Shah Alam 40100, Malaysia
| | | | - C. K. Abdullah
- School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia; (E.B.Y.); (C.K.A.); (N.G.O.)
| | - Atty Sofea A.K.
- Hospital Seberang Jaya, Jalan Tun Hussein Onn, Seberang Jaya, Permatang Pauh 13700, Malaysia;
| | - N. G. Olaiya
- School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia; (E.B.Y.); (C.K.A.); (N.G.O.)
| | - Munifah Abdat
- Department of Preventive and Public Health Dentistry, Faculty of Dentistry, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia;
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In Silico Model for Chemical-Induced Chromosomal Damages Elucidates Mode of Action and Irrelevant Positives. Genes (Basel) 2020; 11:genes11101181. [PMID: 33050664 PMCID: PMC7650694 DOI: 10.3390/genes11101181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 11/17/2022] Open
Abstract
In silico tools to predict genotoxicity have become important for high-throughput screening of chemical substances. However, current in silico tools to evaluate chromosomal damage do not discriminate in vitro-specific positives that can be followed by in vivo tests. Herein, we establish an in silico model for chromosomal damages with the following approaches: (1) re-categorizing a previous data set into three groups (positives, negatives, and misleading positives) according to current reports that use weight-of-evidence approaches and expert judgments; (2) utilizing a generalized linear model (Elastic Net) that uses partial structures of chemicals (organic functional groups) as explanatory variables of the statistical model; and (3) interpreting mode of action in terms of chemical structures identified. The accuracy of our model was 85.6%, 80.3%, and 87.9% for positive, negative, and misleading positive predictions, respectively. Selected organic functional groups in the models for positive prediction were reported to induce genotoxicity via various modes of actions (e.g., DNA adduct formation), whereas those for misleading positives were not clearly related to genotoxicity (e.g., low pH, cytotoxicity induction). Therefore, the present model may contribute to high-throughput screening in material design or drug discovery to verify the relevance of estimated positives considering their mechanisms of action.
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Active learning efficiently converges on rational limits of toxicity prediction and identifies patterns for molecule design. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.comtox.2020.100129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Appell M, Tu YS, Compton DL, Evans KO, Wang LC. Quantitative structure-activity relationship study for prediction of antifungal properties of phenolic compounds. Struct Chem 2020. [DOI: 10.1007/s11224-020-01549-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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