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A systematic analysis of read-across within REACH registration dossiers 对 REACH 注册档案中的交叉阅读进行系统分析
Pub Date : 2024-02-28 DOI: 10.1016/j.comtox.2024.100304
G. Patlewicz , P. Karamertzanis , K. Paul Friedman , M. Sannicola , I. Shah

Read-across is a well-established data-gap filling technique used within analogue or category approaches. Acceptance remains an issue, mainly due to the difficulties of addressing residual uncertainties associated with a read-across prediction and because assessments are expert-driven. Frameworks to develop, assess and document read-across may help reduce variability in read-across results. Data-driven read-across approaches such as Generalised Read-Across (GenRA) include quantification of uncertainties and performance. GenRA also offers opportunities on how New Approach Method (NAM) data can be systematically incorporated to support the read-across hypothesis. Herein, a systematic investigation of differences in expert-driven read-across with data-driven approaches was pursued in terms of building scientific confidence in the use of read-across. A dataset of expert-driven read-across assessments that made use of registration data as disseminated in the public International Uniform Chemical Information Database (IUCLID) (version 6) of Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) Study Results were compiled. A dataset of ∼5000 read-across cases pertaining to repeated dose and developmental toxicity was extracted and mapped to content within EPA’s Distributed Structure Searchable Toxicity database (DSSTox) to retrieve chemical name and structural identification information. Content could be mapped to ∼3600 cases which when filtered for unique cases with curated quantitative structure–activity relationship-ready SMILES resulted in 389 target-source analogue pairs. The similarity between target and the source analogues on the basis of different contexts – from structural similarity using chemical fingerprints to metabolic similarity using predicted metabolic information was evaluated. An attempt was also made to quantify the relative contribution each similarity context played relative to the target-source analogue pairs by deriving a model which predicted known analogue pairs. Finally, point of departure values (PODs) were predicted using the GenRA approach underpinned by data extracted from the EPA’s Toxicity Values Database (ToxValDB). The GenRA predicted PODs were compared with those reported within the REACH dossiers themselves. This study offers generalisable insights on how read-across is already applied for regulatory submissions and expectations on the levels of similarity necessary to make decisions.

横向读数是在模拟或分类方法中使用的一种行之有效的数据缺口填补技术。接受度仍然是一个问题,主要原因是难以解决与读数交叉预测相关的残余不确定性,以及评估是由专家驱动的。开发、评估和记录读数对比的框架可能有助于减少读数对比结果的变异性。数据驱动的读数交叉方法,如广义读数交叉(GenRA),包括对不确定性和性能的量化。GenRA 还提供了如何系统地纳入新方法 (NAM) 数据以支持读数交叉假设的机会。在此,我们对专家驱动的读数交叉与数据驱动的读数交叉之间的差异进行了系统研究,以建立对使用读数交叉的科学信心。我们汇编了一个专家驱动的交叉阅读评估数据集,该数据集使用了公开的国际统一化学品信息数据库(IUCLID)(第 6 版)中发布的化学品注册、评估、许可和限制(REACH)研究结果中的注册数据。提取了 5000 个与重复剂量和发育毒性相关的交叉阅读案例数据集,并将其与美国环保署分布式结构可搜索毒性数据库 (DSSTox) 中的内容进行映射,以检索化学名称和结构识别信息。这些内容可映射到 3600 个案例,在筛选出具有可编辑的定量结构-活性关系 SMILES 的唯一案例后,得出了 389 对目标-来源类似物。根据不同的背景--从使用化学指纹的结构相似性到使用预测代谢信息的代谢相似性--对目标物和源类似物之间的相似性进行了评估。此外,还尝试通过推导预测已知类似物对的模型,量化每种相似性背景对目标-来源类似物对的相对贡献。最后,在从美国环保署毒性值数据库(ToxValDB)中提取的数据的支持下,使用 GenRA 方法对出发点值(POD)进行了预测。GenRA 预测的 POD 值与 REACH 档案中报告的 POD 值进行了比较。这项研究提供了可推广的见解,让我们了解监管呈件是如何应用 "交叉阅读 "的,以及对决策所需的相似性水平的预期。
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引用次数: 0
Computational discovery of potent Escherichia coli DNA gyrase inhibitor: Selective and safer novobiocin analogues 通过计算发现强效大肠杆菌 DNA 回旋酶抑制剂:选择性更强、安全性更高的新生物素类似物
Pub Date : 2024-02-13 DOI: 10.1016/j.comtox.2024.100302
Shweta Singh Chauhan , E. Azra Thaseen , Ramakrishnan Parthasarathi

Bacterial infections caused by resistant strains, especially those conferring multi-drug resistance (MDR), have become a severe health problem worldwide. Novobiocin (NB) is a widely used antibiotic that inhibits the action of DNA gyrase in Escherichia coli (E. coli). The drug's efficiency is hindered by its strong binding with the resistance causing efflux pump AcrAB-TolC on recurrent exposure. Consequently, the discovery of alternate/substitute analogue compounds for the parent drug with higher selectivity could counter drug resistance. In this work, we identified potent analogues of drug NB against the gyrase B enzyme by performing high throughput virtual screening of forty analogues that includes drug-likeness properties, pharmacokinetic parameters analysis, molecular docking, and molecular dynamics (MD) simulations. Our comprehensive pharmacological profiling with intrinsic analysis of selectivity and safety resulted in the identification of four potential compounds, C4 (ZINC218812366), C6 (ZINC221968665), C8 (ZINC49783724) and C10 (ZINC49783727), have better inhibitory and binding capacity against the primary target gyrase B subunit and reduced interaction with the counterpart of resistant target AcrB. These findings provide proof of concept for developing lead compounds targeting gyrase B and help in combatting AcrB-mediated drug resistance.

耐药菌株,尤其是具有多重耐药性(MDR)的耐药菌株引起的细菌感染已成为全球严重的健康问题。新生物素(NB)是一种广泛使用的抗生素,可抑制大肠杆菌(E. coli)中 DNA 回旋酶的作用。该药物在反复接触时会与导致耐药性的外排泵 AcrAB-TolC 发生强结合,从而影响其疗效。因此,发现具有更高选择性的母药替代/替代类似化合物可以对抗耐药性。在这项工作中,我们通过对 40 种类似物进行高通量虚拟筛选,包括药物相似性、药动学参数分析、分子对接和分子动力学(MD)模拟,确定了 NB 药物对回旋酶 B 的强效类似物。我们通过对选择性和安全性的内在分析进行了全面的药理学分析,最终确定了 C4(ZINC218812366)、C6(ZINC221968665)、C8(ZINC49783724)和 C10(ZINC49783727)这四种潜在化合物,它们对主要靶标回旋酶 B 亚基具有更好的抑制和结合能力,并减少了与抗性靶标 AcrB 的相互作用。这些发现为开发靶向回旋酶 B 的先导化合物提供了概念证明,有助于对抗 AcrB 介导的耐药性。
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引用次数: 0
A comparison of machine learning approaches for predicting hepatotoxicity potential using chemical structure and targeted transcriptomic data 比较利用化学结构和靶向转录组数据预测肝毒性潜力的机器学习方法
Pub Date : 2024-02-09 DOI: 10.1016/j.comtox.2024.100301
Tia Tate, Grace Patlewicz, Imran Shah

Animal toxicity testing is time and resource intensive, making it difficult to keep pace with the number of substances requiring assessment. Machine learning (ML) models that use chemical structure information and high-throughput experimental data can be helpful in predicting potential toxicity. However, much of the toxicity data used to train ML models is biased with an unequal balance of positives and negatives primarily since substances selected for in vivo testing are expected to elicit some toxicity effect. To investigate the impact this bias had on predictive performance, various sampling approaches were used to balance in vivo toxicity data as part of a supervised ML workflow to predict hepatotoxicity outcomes from chemical structure and/or targeted transcriptomic data. From the chronic, subchronic, developmental, multigenerational reproductive, and subacute repeat-dose testing toxicity outcomes with a minimum of 50 positive and 50 negative substances, 18 different study-toxicity outcome combinations were evaluated in up to 7 ML models. These included Artificial Neural Networks, Random Forests, Bernouilli Naïve Bayes, Gradient Boosting, and Support Vector classification algorithms which were compared with a local approach, Generalised Read-Across (GenRA), a similarity-weighted k-Nearest Neighbour (k-NN) method. The mean CV F1 performance for unbalanced data across all classifiers and descriptors for chronic liver effects was 0.735 (0.0395 SD). Mean CV F1 performance dropped to 0.639 (0.073 SD) with over-sampling approaches though the poorer performance of KNN approaches in some cases contributed to the observed decrease (mean CV F1 performance excluding KNN was 0.697 (0.072 SD)). With under-sampling approaches, the mean CV F1 was 0.523 (0.083 SD). For developmental liver effects, the mean CV F1 performance was much lower with 0.089 (0.111 SD) for unbalanced approaches and 0.149 (0.084 SD) for under-sampling. Over-sampling approaches led to an increase in mean CV F1 performance (0.234, (0.107 SD)) for developmental liver toxicity. Model performance was found to be dependent on dataset, model type, balancing approach and feature selection. Accordingly tailoring ML workflows for predicting toxicity should consider class imbalance and rely on simple classifiers first.

动物毒性测试需要大量时间和资源,因此很难跟上需要评估的物质数量。使用化学结构信息和高通量实验数据的机器学习(ML)模型有助于预测潜在毒性。然而,用于训练 ML 模型的大部分毒性数据都存在偏差,阳性和阴性数据不平衡,这主要是因为被选中进行体内测试的物质预计会引起一些毒性效应。为了研究这种偏差对预测性能的影响,我们采用了各种取样方法来平衡体内毒性数据,作为监督式 ML 工作流程的一部分,以便从化学结构和/或靶向转录组数据中预测肝毒性结果。从至少 50 种阳性物质和 50 种阴性物质的慢性、亚慢性、发育、多代生殖和亚急性重复剂量测试毒性结果中,在多达 7 个 ML 模型中评估了 18 种不同的研究-毒性结果组合。这些模型包括人工神经网络、随机森林、Bernouilli Naïve Bayes、梯度提升和支持向量分类算法,并与一种本地方法--广义读数交叉(GenRA)--相似性加权 k-近邻(k-NN)方法进行了比较。在所有分类器和描述符的非平衡数据中,慢性肝脏效应的平均 CV F1 性能为 0.735(0.0395 SD)。过度取样方法的平均 CV F1 性能降至 0.639(0.073 标差),尽管在某些情况下 KNN 方法的性能较差也导致了观察到的性能下降(不包括 KNN 的平均 CV F1 性能为 0.697(0.072 标差))。采用取样不足法时,平均 CV F1 为 0.523(0.083 标差)。在发育肝效应方面,不平衡方法的平均 CV F1 性能更低,为 0.089(0.111 标差),而采样不足方法的平均 CV F1 性能为 0.149(0.084 标差)。过度取样方法导致发育期肝脏毒性的平均 CV F1 性能提高(0.234,(0.107 标差))。研究发现,模型性能取决于数据集、模型类型、平衡方法和特征选择。因此,在定制预测毒性的 ML 工作流程时应考虑类的不平衡性,并首先依赖简单的分类器。
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引用次数: 0
Computational discovery of potent Escherichia coli DNA gyrase inhibitor: Selective and safer novobiocin analogues 通过计算发现强效大肠杆菌 DNA 回旋酶抑制剂:选择性更强、安全性更高的新生物素类似物
Pub Date : 2024-02-01 DOI: 10.1016/j.comtox.2024.100302
S. Chauhan, E. A. Thaseen, Ramakrishnan Parthasarathi
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引用次数: 0
Developing and validating read-across workflows that enable decision making for toxicity and potency: Case studies with N-nitrosamines 开发和验证可对毒性和效力做出决策的跨读工作流程:亚硝胺案例研究
Pub Date : 2024-01-29 DOI: 10.1016/j.comtox.2024.100300
Steven Kane, Dan Newman, David J. Ponting, Edward Rosser, Robert Thomas, Jonathan D. Vessey, Samuel J. Webb, William H.J. Wood

To reach conclusions during chemical safety assessments, risk assessors need to ensure sufficient information is present to satisfy the decision criteria. This often requires data to be generated and, in some cases, insufficient knowledge is present, or it is not feasible to generate new data through experiments. Read-across is a powerful technique to fill such data gaps, however the expert-driven process can be time intensive and subjective in nature resulting in variation of approach. To overcome these barriers a prototype software application has been developed by Lhasa Limited to support decision making about the toxicity and potency of chemicals using a read-across approach. The application supports a workflow which allows the user to gather data and knowledge about a chemical of interest and possible read-across candidates. Relevant information is then presented that enables the user to decide if read-across can be performed and, if so, which analogue or category can be considered the most appropriate. Data and knowledge about the toxicity of a compound and potential analogues include assay and metabolism data, toxicophore identification and its local similarity, physico-chemical and pharmacokinetic properties and observed and predicted metabolic profile. The utility of the approach is demonstrated with case studies using N-nitrosamine compounds, where the conclusions from using the workflow supported by the software are concordant with the evidence base. The components of the workflow have been further validated by demonstrating that conclusions are significantly better than would be expect from the distribution of data in test sets. The approach taken demonstrates how software implementing intuitive workflows that guide experts during read-across can support decisions and how validation of the methods can increase confidence in the overall approach.

为了在化学品安全评估过程中得出结论,风险评估人员需要确保有足够的信息来满足决策标准。这通常需要生成数据,而在某些情况下,知识不足或通过实验生成新数据并不可行。读取数据是填补此类数据空白的一项强大技术,但专家驱动的过程可能需要大量时间,而且主观性强,导致方法各异。为了克服这些障碍,拉萨有限公司开发了一个原型软件应用程序,以支持使用 "交叉阅读 "方法对化学品的毒性和效力进行决策。该应用软件支持一个工作流程,允许用户收集有关所关注化学品的数据和知识,以及可能的候选对照品。相关信息随后会显示出来,使用户能够决定是否可以进行交叉分析,如果可以,哪种类似物或类别最合适。有关化合物和潜在类似物毒性的数据和知识包括化验和代谢数据、毒源鉴定及其局部相似性、物理化学和药代动力学特性以及观察到的和预测的代谢概况。利用 N-亚硝胺化合物进行的案例研究证明了该方法的实用性,使用该软件支持的工作流程得出的结论与证据基础一致。工作流程的各个组成部分得到了进一步验证,证明结论明显优于测试集数据分布的预期。所采用的方法表明,实施直观工作流程的软件如何能够指导专家进行交叉阅读,从而为决策提供支持,以及对方法的验证如何能够增强对整体方法的信心。
{"title":"Developing and validating read-across workflows that enable decision making for toxicity and potency: Case studies with N-nitrosamines","authors":"Steven Kane,&nbsp;Dan Newman,&nbsp;David J. Ponting,&nbsp;Edward Rosser,&nbsp;Robert Thomas,&nbsp;Jonathan D. Vessey,&nbsp;Samuel J. Webb,&nbsp;William H.J. Wood","doi":"10.1016/j.comtox.2024.100300","DOIUrl":"https://doi.org/10.1016/j.comtox.2024.100300","url":null,"abstract":"<div><p>To reach conclusions during chemical safety assessments, risk assessors need to ensure sufficient information is present to satisfy the decision criteria. This often requires data to be generated and, in some cases, insufficient knowledge is present, or it is not feasible to generate new data through experiments. Read-across is a powerful technique to fill such data gaps, however the expert-driven process can be time intensive and subjective in nature resulting in variation of approach. To overcome these barriers a prototype software application has been developed by Lhasa Limited to support decision making about the toxicity and potency of chemicals using a read-across approach. The application supports a workflow which allows the user to gather data and knowledge about a chemical of interest and possible read-across candidates. Relevant information is then presented that enables the user to decide if read-across can be performed and, if so, which analogue or category can be considered the most appropriate. Data and knowledge about the toxicity of a compound and potential analogues include assay and metabolism data, toxicophore identification and its local similarity, physico-chemical and pharmacokinetic properties and observed and predicted metabolic profile. The utility of the approach is demonstrated with case studies using <em>N</em>-nitrosamine compounds, where the conclusions from using the workflow supported by the software are concordant with the evidence base. The components of the workflow have been further validated by demonstrating that conclusions are significantly better than would be expect from the distribution of data in test sets. The approach taken demonstrates how software implementing intuitive workflows that guide experts during read-across can support decisions and how validation of the methods can increase confidence in the overall approach.</p></div>","PeriodicalId":37651,"journal":{"name":"Computational Toxicology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139731861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A computational model of endogenous hydrogen peroxide metabolism in hepatocytes, featuring a critical role for GSH 肝细胞内源性过氧化氢代谢的计算模型,GSH 在其中发挥关键作用
Pub Date : 2024-01-23 DOI: 10.1016/j.comtox.2024.100299
L.M. Bilinsky

This paper presents an ordinary differential equation (ODE) model of endogenous H2O2 metabolism in hepatocytes that is unique, at the time of writing, in its ability to accurately compute intracellular H2O2 concentration during incidents of oxidative stress and in its usefulness for constructing PBPK/PD models for ROS-generating xenobiotics. Versions of the model are presented for rat hepatocytes in vitro and mouse liver in vivo. A generic method is given for using the model to create PBPK/PD models which predict intracellular H2O2 concentration and oxidative-stress-induced hepatocyte death; these are identifiable from in vitro data sets reporting cell mortality following xenobiotic exposure at various levels. The procedure is demonstrated for the trivalent arsenical dimethylarsinous acid (DMAIII), which is produced in liver as part of the arsenic elimination pathway. This is the first model of H2O2 metabolism in hepatocytes to feature values for the endogenous rates of H2O2 production by mitochondria and other organelles which are inferred from the physiology literature, and to feature a detailed, realistic treatment of GSH metabolism; the latter is achieved by incorporating a minimal version of Reed and coworkers’ pioneering model of GSH metabolism in liver. Model simulations indicate that critical GSH depletion is the immediate trigger for intracellular H2O2 rising to concentrations associated with apoptosis (>1μM), that this may only occur hours after the xenobiotic concentration peaks (“delay effect”), that when critical GSH depletion does occur, H2O2 concentration rises rapidly in a sequence of two boundary layers, characterized by the kinetics of glutathione peroxidase (first boundary layer) and catalase (second boundary layer), and that intracellular H2O2 concentration >1μM implies critical GSH depletion. There has been speculation that ROS levels in the range associated with apoptosis simply indicate, rather than cause, an apoptotic milieu. Model simulations are consistent with this view. In a result of interest to the wider physiology community, the delay effect is shown to provide a GSH-based mechanism by which cells can distinguish transient elevations in H2O2 concentration, of use in intracellular signaling, from persistent ones indicative of either pathology or the presence of toxins, the second state of affairs eventually triggering apoptosis.

本文介绍了肝细胞内源性 H2O2 代谢的常微分方程 (ODE) 模型,该模型在撰写本文时是独一无二的,因为它能够在氧化应激事件中准确计算细胞内 H2O2 浓度,并可用于构建产生 ROS 的异种生物的 PBPK/PD 模型。本文介绍了该模型在体外大鼠肝细胞和体内小鼠肝脏中的不同版本。给出了使用该模型创建 PBPK/PD 模型的通用方法,该模型可预测细胞内 H2O2 浓度和氧化应激诱导的肝细胞死亡;这些可从体外数据集中识别,这些数据集报告了暴露于不同水平的异种生物后的细胞死亡率。该程序针对三价砷化物二甲基砷酸(DMAIII)进行了演示,该物质在肝脏中产生,是砷消除途径的一部分。这是第一个肝细胞中 H2O2 代谢模型,其特点是线粒体和其他细胞器产生 H2O2 的内源性速率值是根据生理学文献推断出来的,并且对 GSH 代谢进行了详细、现实的处理;后者是通过结合 Reed 和同事的肝脏 GSH 代谢先驱模型的最小版本来实现的。模型模拟表明,临界 GSH 消耗是细胞内 H2O2 上升到与细胞凋亡相关浓度(>;1μM),这可能只发生在异种生物浓度达到峰值数小时之后("延迟效应"),当临界 GSH 耗尽发生时,H2O2 浓度会在两个边界层的序列中迅速上升,这两个边界层的特征是谷胱甘肽过氧化物酶(第一边界层)和过氧化氢酶(第二边界层)的动力学,细胞内 H2O2 浓度为 1μM 意味着临界 GSH 耗尽。有人推测,与细胞凋亡相关范围内的 ROS 水平只是表明而不是导致细胞凋亡的环境。模型模拟与这一观点一致。更广泛的生理学界感兴趣的结果是,延迟效应提供了一种以 GSH 为基础的机制,通过这种机制,细胞可以区分 H2O2 浓度的瞬时升高(用于细胞内信号传导)和持续升高(表明病理或毒素的存在),第二种状态最终会引发细胞凋亡。
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引用次数: 0
Confidence score calculation for the carcinogenic potency categorization approach (CPCA) predictions for N-nitrosamines 亚硝胺类化合物致癌作用力分类法(CPCA)预测的置信度分数计算方法
Pub Date : 2023-12-29 DOI: 10.1016/j.comtox.2023.100298
Suman Chakravarti, Roustem D. Saiakhov, Mounika Girireddy

We present a method for computing confidence in the Carcinogenic Potency Categorization Approach (CPCA) based predictions for N-nitrosamines. Our method relies on capturing local structural variations surrounding the nitrosamine core, which can significantly influence potency and may introduce uncertainty into predictions relying on these features.

We use continuous-valued fingerprints to conduct a specialized neighborhood analysis, grouping nitrosamines with similar local features. Using a reference dataset of 7679 potential Nitrosamine Drug Substance Related Impurities (NDSRIs) with pre-computed CPCA-derived Acceptable Intake (AI) limits, we gauge the prediction confidence for a given query N-nitrosamine by evaluating the distances and CPCA derived potency category distribution among neighboring NDSRIs. Our methodology allows for a nuanced assessment of CPCA's discrete four-level outcomes (i.e. 18/26.5, 100, 400, and 1500 ng AI limits). It enables the differentiation of robust predictions from potentially uncertain ones, for instance, cases where low confidence arises from rare structural features in the query nitrosamine, helpful in regulatory decision-making.

In our analysis of 30 nitrosamines with animal carcinogenicity data, we often observed lower confidence scores when experimental TD50 values significantly disagreed with CPCA-calculated potency. Moreover, lower confidence scores were associated with greater variability in the predicted α-carbon hydroxylation potential of neighboring compounds. In a list of 265 NDSRIs with established regulatory AI limits, approximately 68% received strong confidence scores for accurate CPCA potency class predictions. However, 8% received poor confidence in potency class predictions, as well as lacked sufficient neighbor support due to uncommon structural features.

我们提出了一种方法,用于计算基于致癌性分类方法 (CPCA) 的 N-亚硝胺预测的置信度。我们的方法依赖于捕捉亚硝胺核心周围的局部结构变化,这些变化会显著影响药效,并可能给依赖于这些特征的预测带来不确定性。我们使用连续值指纹进行专门的邻域分析,将具有相似局部特征的亚硝胺分组。我们使用连续值指纹进行专门的邻域分析,对具有相似局部特征的亚硝胺进行分组。我们使用由 7679 个潜在亚硝胺药物物质相关杂质 (NDSRI) 组成的参考数据集(其中包含预先计算的 CPCA 导出的可接受摄入量 (AI) 限值),通过评估邻域 NDSRI 之间的距离和 CPCA 导出的药效类别分布来衡量特定查询 N-亚硝胺的预测可信度。我们的方法允许对 CPCA 的离散四级结果(即 18/26.5、100、400 和 1500 毫微克 AI 限制)进行细致评估。它能够将稳健的预测与潜在的不确定预测区分开来,例如,低置信度是由于查询亚硝胺中罕见的结构特征造成的,这有助于监管决策。在我们对 30 种具有动物致癌性数据的亚硝胺进行的分析中,当实验 TD50 值与 CPCA 计算出的效价明显不一致时,我们经常观察到较低的置信度分数。此外,较低的置信度分数与邻近化合物的预测 α 碳羟化潜力的较大变异性有关。在一份已确定监管 AI 限制的 265 种 NDSRI 清单中,约 68% 的化合物在 CPCA 药效类别准确预测方面获得了较高的置信度分数。但是,有 8% 的化合物在药效类别预测方面的置信度较低,并且由于结构特征不常见而缺乏足够的邻近支持。
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引用次数: 0
Utilizing integrated testing strategy (ITSv1) defined approach and read across to predict skin sensitization of cannabidiol 利用综合测试战略(ITSv1)定义的方法和横向读数预测大麻二酚的皮肤致敏性
Pub Date : 2023-12-23 DOI: 10.1016/j.comtox.2023.100297
Ramez Labib, Ripal Amin, Chris Bartlett, Lisa Hoffman

Cannabidiol (CBD) is increasingly being used as an ingredient in cosmetics, but to date no pre-clinical studies have been published to address the skin sensitization end point. This case study investigated its skin sensitization potential for use in a face cream application at 0.3 % using Next Generation Risk Assessment (NGRA) framework. Based on chemical structure and in-silico prediction using Derek Nexus, CBD was predicted to be weak sensitizer with a resorcinol alert moiety. In vitro testing was conducted confirming it to be sensitizer, but the New Approach Methodologies (NAM) data could not provide sufficient confidence to determine a point of departure (PoD). Integrated testing strategy (ITS)v1 Defined Approach (DA), adopted in OECD Guideline No. 497, was used for skin sensitization potency categorization. However, ITSv1 DA alone is not used for further refinement of the potency prediction based on EC3 (the estimated concentration that produces a stimulation index of 3 in murine local lymph node assay) values. Therefore, the application of read-across using Derek Nexus derived a PoD derived from the LLNA EC3 of 42 %. This led to a favorable NGRA conclusion and to support use of CBD at 0.3 % in face cream application.

大麻二酚(CBD)正越来越多地被用作化妆品成分,但迄今为止,尚未有针对皮肤过敏终点的临床前研究发表。本案例研究采用下一代风险评估(NGRA)框架,研究了在面霜中使用 0.3% 的大麻二酚对皮肤的致敏潜力。根据化学结构和使用 Derek Nexus 进行的室内预测,CBD 被预测为具有间苯二酚警戒分子的弱致敏剂。体外测试证实它是敏化剂,但新方法(NAM)数据无法提供足够的可信度来确定出发点(PoD)。综合测试策略(ITS)v1 定义方法(DA)已在经合组织第 497 号准则中采用,用于皮肤过敏效力分类。不过,仅使用 ITSv1 DA 并不能根据 EC3(在小鼠局部淋巴结试验中产生 3 级刺激指数的估计浓度)值进一步完善药效预测。因此,使用 Derek Nexus 进行交叉分析后,根据 LLNA EC3 得出的 PoD 为 42%。这就得出了有利的 NGRA 结论,并支持在面霜中使用 0.3 % 的 CBD。
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引用次数: 0
Salivary therapeutic monitoring of methadone toxicity in neonates after transplacental transfer from parturient mothers treated with oral methadone guided by PBPK modeling 以 PBPK 模型为指导,对接受口服美沙酮治疗的产妇经胎盘移植后新生儿的美沙酮毒性进行唾液治疗监测
Pub Date : 2023-12-12 DOI: 10.1016/j.comtox.2023.100296
Mo'tasem M. Alsmadi

Opioid use disorders (OUD) during pregnancy are related to neonatal opioid withdrawal syndrome (NOWS). R,S-methadone used to treat OUD and NOWS can penetrate the placenta. High neonatal brain extracellular fluid (bECF) levels of R,S-methadone can induce respiratory depression in newborns. The purpose of this work was to estimate neonatal bECF and saliva levels to establish the neonatal R,S-methadone salivary thresholds for respiratory depression after maternal oral dosing despite the sparse data in pregnancy and newborn populations. An adult physiologically-based pharmacokinetic (PBPK) model for R,S-methadone after intravenous and oral administration was constructed, vetted, and scaled to newborn and pregnancy populations. The pregnancy model predicted the R-methadone and S-methadone doses transplacentally transferred to newborns. Then, the newborn PBPK model was used to estimate newborn exposure after such doses. After maternal oral dosing of R,S-methadone (43.8 mg/day), the neonatal plasma levels were below the respiratory depression threshold. Further, the bECF levels were above the analgesia threshold for more than 96 h. The salivary thresholds for the analgesic effects of R-methadone, S-methadone, and R,S-methadone were estimated herein at 1.7, 43, and 16 ng/mL, respectively. Moreover, the salivary thresholds for the respiratory depression of R-methadone and R,S-methadone were estimated at 58 and 173 ng/mL, respectively. Using neonatal salivary monitoring of methadone can be useful in ensuring newborns' safety during maternal OUD treatment.

怀孕期间阿片类药物使用障碍(OUD)与新生儿阿片类药物戒断综合征(NOWS)有关。用于治疗OUD和NOWS的R、s -美沙酮可以穿透胎盘。高新生儿脑细胞外液(bECF)水平R, s -美沙酮可引起新生儿呼吸抑制。本研究的目的是评估新生儿bECF和唾液水平,以确定母亲口服给药后新生儿R、s -美沙酮唾液阈值对呼吸抑制的影响,尽管在妊娠和新生儿人群中数据较少。建立了R, s -美沙酮静脉和口服给药后的成人生理药代动力学(PBPK)模型,并对其进行了审查,并按比例扩展到新生儿和妊娠人群。妊娠模型预测经胎盘转移给新生儿的r -美沙酮和s -美沙酮剂量。然后,使用新生儿PBPK模型来估计这些剂量后的新生儿暴露。母亲口服R, s -美沙酮(43.8 mg/d)后,新生儿血浆水平低于呼吸抑制阈值。此外,bECF水平高于镇痛阈值的时间超过96小时。本文估计R-美沙酮、s -美沙酮和R, s -美沙酮的镇痛作用的唾液阈值分别为1.7、43和16 ng/mL。此外,R-美沙酮和R, s -美沙酮的呼吸抑制唾液阈值分别为58和173 ng/mL。使用新生儿唾液监测美沙酮可用于确保产妇OUD治疗期间新生儿的安全。
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引用次数: 0
An overview of conceptual-DFT based insights into global chemical reactivity of volatile sulfur compounds (VSCs) 基于概念-DFT 的挥发性硫化合物(VSCs)全球化学反应性洞察概述
Pub Date : 2023-12-12 DOI: 10.1016/j.comtox.2023.100295
Manjeet Bhatia

Volatile sulfur compounds (VSCs) are highly volatile and most frequently associated with oral malodor. The odor quality is associated with the size and shape of the molecule along with stability, hydrogen bonding, extended d-shell electronic behavior, and complicity of d-shell bonding. Chemical reactivity descriptors of VSCs, such as chemical hardness (η), softness (σ), chemical potential (μ), electrophilic index (ω), and electronegativity (χ) are computed at B3LYP/Aug-cc-PVTZ level of theory from the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) in the light of Koopmans’ approximation. Furthermore, the global reactivity parameters are evaluated from the vertical ionization potential (IP) and electron affinity (EA) to support the results of Koopmans’ theorem. These reactivity parameters offer a quantitative measure of the electronic structure and chemical properties of VSCs, offering insights into their stability, reactivity, and interaction with other molecules. A Python-based application is provided for the rapid calculation of these parameters (GitHub: Link).

挥发性硫化合物(VSCs)是高度挥发性的,最常与口腔异味有关。气味质量与分子的大小和形状以及稳定性、氢键、扩展d壳层电子行为和d壳层键的共合性有关。根据Koopmans近似,从最高已占据分子轨道(HOMO)和最低未占据分子轨道(LUMO)出发,在B3LYP/Aug-cc-PVTZ理论水平上计算了VSCs的化学反应性描述符,如化学硬度(η)、柔软度(σ)、化学势(μ)、亲电指数(ω)和电负性(χ)。此外,利用垂直电离势(IP)和电子亲和力(EA)对整体反应性参数进行了评估,以支持Koopmans定理的结果。这些反应性参数提供了VSCs的电子结构和化学性质的定量测量,提供了对其稳定性、反应性和与其他分子相互作用的见解。提供了一个基于python的应用程序来快速计算这些参数(GitHub: Link)。
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引用次数: 0
期刊
Computational Toxicology
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