Chemical Research in Toxicology最新文献

The mutational outcome of DNA damage as a direct result of constant chemical assault is governed by major factors, including the structure and nature of damage, replication, and repair machinery in vivo. The role of the size of the adduct, adduct-flanking bases, and the type of polymerase involved in the replication pathway is prominently seen through existing in vitro and in vivo studies. In this work, machine learning methods have been developed to predict the critical parameters for the mutational outcome of the adducts when they encounter polymerase in a particular sequence context. We carried out the analysis with three different classification models: Logistic Regression (LR), Decision Tree (DT), and Support Vector Machine (SVM). Using the literature data, mutational results of covalent DNA adducts and abasic sites were used to train the classification models. Following this, we used a generative network method with the available information on the structure of the DNA damage, polymerase, and sequence context to generate synthetic data that accurately mirrors the real data. Further, we employed an Extreme Gradient Boosting Classifier to identify the parameter that most influences the DNA mutational outcome. Metrics such as Accuracy, Sensitivity, Precision, F1 score, and AUC value have been used to evaluate the performance of classifier methods. The proposed Bootstrapped-Variational Autoencoder (BT-VAE) model enhanced the overall prediction accuracy of classifiers by 40%. The SVM model delivered the best performance across all classification metrics in predicting mutational outcomes among the three classification models evaluated. By providing the size of the carcinogen/covalent DNA adduct, polymerase, and flanking base as input, the proposed BT-VAE framework can predict the mutational outcome (match or mismatch for covalent DNA adducts and adenine or nonadenine for abasic site), an additional tool for in vivo and in vitro studies in the field of toxicology.

The Nonclinical Translation Working Group of the IQ Drug-Induced Liver Injury (DILI) Consortium conducted two surveys in 2023 and 2017 to canvas member companies on approaches and experiences in the preceding 5-year periods that inform how DILI risk assessment has evolved in the past decade. Surveys comprised 53 detailed questions to understand the current status, temporal changes, and future direction and to gain insights. Focusing on the 2023 survey for the most contemporary data, responses indicated that DILI still remains a problem during drug development, with 41% of companies in the 2023 survey (50% in 2017) filing at least one clinical expedited safety report in the last 5 years. Most companies have common nonclinical screening approaches, with the majority of companies incorporating target safety assessments, considering physicochemical properties and dose, and using multiple in vitro approaches including cytotoxicity, mitotoxicity, BSEP inhibition, and various reactive metabolite assays, with the utilization of many of these being increased in the 2023 survey compared to the 2017 survey. The impact of in vivo toxicology studies on clinical study design and compound progression is also reviewed in both the 2023 and 2017 surveys. A large majority of companies now report having new modality drugs in their portfolios, including antibody-based and oligonucleotide-based modalities, cell therapies, protein degraders, and peptide-based medicines; yet only 1 or 2 companies report having modality-specific approaches to assess DILI risk despite these modalities having very different mechanisms of causing DILI compared to small molecules. This is a key area for growth in the nonclinical assessment of hepatotoxicity to support these emerging modalities and the tremendous potential that they offer for unmet clinical needs. Collaborative partnerships will be key to driving new capabilities forward in this area, contributing to the development of safer novel therapeutics for patients.

Olaparib, an anticancer drug, has been recently associated with major side effects (hepatotoxicity and hematotoxicity). Human CYP450 3A4/5 metabolizes olaparib and forms dehydrogenated (M11) and hydroxylated (M6, M15) metabolites. The major (dehydrogenated: M11) metabolite is unreactive due to the stability of its amide bonds. Thus, the recently reported toxicities (hepato- and hemato) remain mysterious. Here, we investigate olaparib’s metabolic pathways using Cpd I model systems to gain insights into metabolic preferences, reactive metabolite formation, and associated toxicities. Potential energy surface (PES) analysis using activation (ΔG^‡), reaction (ΔG°) free energies, and molecular docking, dynamics-based accessibility (distance of site of metabolism: SOM from heme-Fe) is utilized to explain metabolic preferences. Quantum chemical calculations showed that the formation of dehydrogenated (M11) and hydroxylated (M6) metabolites is favored relative to aromatic hydroxylated (M15) metabolites (reaction free energies: k_BT = 18.5 kcal/mol as cutoff). The detailed analysis of the metabolic pathway for the major metabolite (M11) formation showed that hydroxylation follows the E1 mechanism, leading to dehydration and the formation of a tetrahydropyrazine derivative. The olaparib piperazine ring C approaches the heme-Fe within activating distance (6 ± 2 Å) in most docked poses and during 200 ns MD simulations. The C10 leading to hydroxylated metabolite (M6) remains at >10 Å, making the reactive M12 formation less likely. Furthermore, the MM-GBSA-based per-residue calculations showed that 13 active-site residues, including Arg105, contribute significantly to the binding energy (avg: −1.24 kcal/mol). DFT-based global and local reactivity (electrophilicity: ω) analysis showed that the 4-acetylphthalazin-1(2H)-one group in the M12 metabolite (formed from M6) is highly electrophilic and might explain the idiosyncratic toxicities. These findings may offer valuable insights into the mechanisms of toxicity and for the design of novel and less toxic olaparib analogs.

Tetrahydrocannabinol (THC), the primary psychoactive compound of cannabis, is the most widely abused substance worldwide, with an annual prevalence of 4.3% of adults and 5.3% of the 15–16 year-old population estimated as of 2022. THC has both acute and chronic effects through the dopaminergic and endocannabinoid systems. This study was conducted to better understand the metabolites and metabolic pathways in biological systems affected by cannabis, which may help find practical diagnostic and treatment approaches for people with cannabis dependence in the future. Metabolomic analysis of urine samples was performed using gas chromatography–mass spectrometry (GC–MS). MetaboAnalyst software was used to determine sample metabolite profiles, which were then subjected to multivariate statistical analysis. From data of over 200 metabolites in each sample of cannabis users, 92 metabolites with a p-value of less than 0.05 were selected for further analyses, of which 38 showed a decrease and 54 showed an increase compared to the nonuser group. Based on 43 metabolites (VIP > 1), subjected to MetaboAnalyst and CPDB, amino acid metabolism (especially arginine, methionine, and cysteine), vitamin metabolism (particularly biotin), and the urea cycle were the primarily affected metabolic pathways. The AUC values of the four metabolites (salsoline, 6-thiourate, procollagen 5-hydroxy-l-lysine, and biotin) with the highest VIP scores were between 0.93 and 0.98, with no significant difference. Metabolites with high VIP scores hold promise as biomarker candidates for identifying cannabis users, and the prominent pathways provide new insights into the understanding of the metabolic effects of cannabis.

Advancement of therapeutic modalities using carbon-based nanomaterials (CBNMs) has mounted in the last few decades. The concept of therapeutic advancement consists of a possible application by understanding the toxicity issues and their fate in the living biological system. Carbon based nanomaterials are recently exploited for their unique properties, and their utilization toward biomedical application such as drug delivery system (DDS), tissue regeneration, nonviral immunotherapy, biosensing, bioimaging, etc. is well reported. Despite such a report, it is very much required to understand their toxicity assessment with fate within the human body. The present review assesses the toxic behavior of various carbonaceous materials and the therapeutic advancement in spite of their toxicity issues. Carbon nanostructures (carbon quantum dot, carbon nanotube, fullerene, graphene, carbon nanohorn, carbon nanodiamond, etc.) impart various cellular toxicities, which are based on their geometric structure as well as chemical composition and physicochemical parameters (size, morphology, surface passivation). Moreover, this review also includes an additional section describing various sources of carbon with their preparation and their properties. Regardless of the toxicity barrier, carbon based materials are still ameliorating the therapeutic advancement with respect to various biomedical applications, which are also highlighted in this review along with their use by suppressing their toxic behavior.

Recent studies have shown that certain peptides and small molecules can induce pseudoanaphylaxis reactions by triggering mast cell degranulation (MCD), resulting in the release of vasoactive and proinflammatory mediators. This mechanism can result in severe adverse drug reactions with potentially life-threatening consequences in humans or loss of tolerability in animal studies, representing a considerable challenge in the development of peptide and small-molecule therapeutics. Therefore, early identification of drug candidates with MCD potential is crucial for an efficient Design–Make–Test–Analyze (DMTA) cycle while promoting the 3Rs principle (replacement, reduction, refinement) in animal research. In the present work, we introduce a proactive risk mitigation strategy aimed at evaluating and minimizing the MCD activity of peptide drug candidates. We developed an ex vivo rat peritoneal mast cell degranulation (rMCD) assay to screen and prioritize candidates that do not exhibit rMCD activity during the lead optimization phase. Importantly, structure–activity relationships (SAR) were established by leveraging rMCD data sets which included ∼3000 diverse peptides across 28 internal programs targeting multiple therapeutic areas. Critical physicochemical properties were identified as predictive calculated parameters for rMCD outcomes. Additionally, we developed a directed message passing neural network (D-MPNN) model that combines structural features with calculated and predicted physicochemical properties, demonstrating strong predictive performance for rMCD outcomes. This model facilitates the early prioritization of peptide drug candidates for rMCD assays during the candidate selection phase and accelerates hit-to-lead and lead optimization by identifying peptides within a series that exhibit minimal rMCD liabilities. Notably, the D-MPNN model outperformed traditional in silico property-based calculators in our prospective validation study. Furthermore, to address species-specific SAR, we also established a human MCD (hMCD) assay, revealing an 80% concordance in MCD outcomes between species. This hMCD assay identifies the MCD liabilities of compounds that differ from those in rats, indicating potential risks in humans. This comprehensive in silico and in vitro approach enables drug discovery teams to advance drug candidates that are free from MCD liability in a resource-efficient manner, thereby increasing the likelihood of success in both nonclinical and clinical studies.

Hydroxyindoles are organic compounds characterized by the presence of a hydroxy group attached to an indole ring (six-membered benzene ring fused to a five-membered pyrrole ring). These compounds are naturally occurring and play a role in the synthesis of various medicinal drugs. One notable example is 4-Hydroxyindole (4-HI), which contains a hydroxy group at the fourth position of the indole ring. In a recent study, we tested various hydroxyindole compounds for their antiferroptotic activity, including 3-hydroxyindole, which demonstrated strong resistance to ferroptosis. Ferroptosis is a regulated form of cell death that occurs due to uncontrolled phospholipid peroxidation and is associated with the development of degenerative conditions, such as neurodegenerative diseases. Here, we tested the hypothesis that 4-HI could protect against ferroptosis, similar to other hydroxyindole compounds. To induce ferroptosis, we utilized established modulators, including erastin, RSL3, and FINO2. We assessed cytotoxicity using the calcein AM assay and measured lipid peroxidation caused by ferroptosis inducers with the C11-BODIPY assay. Our results indicated that 4-HI protects various brain-related cell types, including HT-22, N27, and RBE4 cells, from ferroptosis. We also utilized our newly developed cell-free assay, in which combined iron and arachidonic acid were used to oxidize C11-BODIPY, allowing us to investigate the radical scavenging activity of 4-HI. We discovered that 4-HI exhibits antioxidant effects in cell-free assays, suggesting that its protective action against ferroptosis is likely due to its radical-scavenging capabilities. Interestingly, we found that 4-hydroxyindole-3-carbaldehyde, a structural analog of 4-HI, did not effectively prevent ferroptosis. This suggests that the carbaldehyde group, which is an electron-withdrawing group, may reduce the antiferroptotic activity of 4-HI. In summary, 4-HI appears to be a promising inhibitor of ferroptosis, warranting further research to explore its potential in protecting against neurotoxicity and neurodegeneration associated with this type of cell death.

Skin sensitization is a critical endpoint in human safety risk assessment of chemicals. Risk assessment approaches have evolved, and the field has seen a shift toward adopting new approach methods (NAMs) instead of relying solely on animal or human data. While the direct peptide reactivity assay (DPRA) is considered one of the NAMs of key event (KE) 1 within the OECD guideline 497 in combination with other NAMs for predicting skin sensitization hazard or potency, the assay is limited by the lack of activation features for pre-/pro-haptens. To address this, the peroxidase peptide reactivity assay (PPRA) was developed, utilizing horseradish peroxidase (HRP) and H₂O₂ to facilitate the oxidation and activation of test substances. However, limited information is available on the chemical substrate scope and applicability domain of the PPRA. In this study, we investigated the substrate scope of HRP to gain insights into the mechanism of the PPRA. Based on our analysis, the substrates of HRP include substituted phenols (or aromatic alcohols) and aniline (or aromatic amines) as well as their O- or N-alkyl derivatives. By considering the substrate scope of HRP, depletion patterns and mechanisms in the DPRA/PPRA, and the underlying chemistry of the assays, we categorized chemicals into five distinct chemical groups with unique structural features and depletion patterns in the DPRA/PPRA. This study elucidates the relationship between chemical structures, assay results of the DPRA and PPRA, and their applicability for predicting the skin sensitization potential. These findings contribute to a better understanding of the predictive capabilities of the PPRA and provide valuable insights for incorporating PPRA into next-generation risk assessments (NGRAs).

Electronic nicotine delivery systems (ENDS) are now increasingly used, with commercial electronic cigarettes frequently containing high levels of nicotine and menthol, which is a popular flavoring agent. This has raised multiple concerns about the health risks associated with menthol-flavored ENDS. Although menthol and nicotine are known for their individual effects on respiratory health, their combined impact on pulmonary surfactants remains poorly understood. Therefore, this study aimed at understanding the interactions between the primary components of all ENDS liquids (PG and VG), nicotine and menthol flavoring, and the pulmonary surfactant. This in vitro study used 1,2 dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and a stoichiometric mixture of DPPC/1-palmitoyl-2-Oleoyl-sn-glycero-3-phosphocholine (POPC)/2-Oleoyl-1-palmitoyl-sn-glycero-3- phospho-rac-(1-glycerol) sodium salt (POPG)/cholesterol at 48/32/10/10 to mimic the pulmonary surfactant. These systems were probed using a Langmuir–Blodgett Trough and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. The results indicate a concentration dependence of the impact of different nicotine concentrations combined with menthol on the surfactant mimics. Our findings also reveal the effect of menthol on the surface pressure. The combination of nicotine and menthol appears to alter the conformational state of the surfactant, proximately altering characteristic vibrational groups. Moreover, different behaviors are unveiled between the two model surfactants, particularly attributed to the complexities of the four surfactants mixture. Further research is suggested to address the mechanisms and implications involved with ENDS flavoring and additives on surfactant molecules in biological systems. Establishing well-informed regulations on ENDS consumption and distribution should be developed.

The use of two-dimensional organomodified nanoclays (ONCs) to improve nanocomposite properties continues to grow. Recent evidence suggests that airborne nanoclays in occupational environments pose an inhalation hazard; however, health risks and the underlying mechanisms remain undefined. In vivo studies evaluating pre- and post-incinerated ONC exposures found that cytotoxicity, inflammation, and fibrotic signaling responses are coating- and incineration status-dependent. We hypothesized that physicochemical property differences associated with coating presence/absence and incineration status of nanoclays will elicit changes in key events (KE) in exposed human small airway epithelial (SAECs) and normal lung fibroblast (NHLF) cells that contribute to pulmonary lung fibrosis. Using multiplex high-throughput screening strategies, SAEC and NHLF cells were acutely exposed (0–20 μg/cm²) to pristine nanoclay (CloisNa), an ONC (Clois30B), their incinerated byproducts (I-CloisNa and I-Clois30B), and crystalline silica (CS), to evaluate how ONC characteristics influence several KE in the pulmonary fibrosis adverse outcome pathway. In vitro exposure to pre-incinerated nanoclay induced organic coating-dependent cytotoxicity in SAECs. CloisNa caused disruption of mitochondrial membrane potential, which coincided with loss in viability in both cell types. Clois30B exposure caused dose-dependent SAEC cytotoxicity, micronuclei formation, and mitochondrial hyperpolarization in SAECs and NHLFs. Incinerated nanoclays were noncytotoxic but elicited a SAEC mitochondrial radical and pro-inflammatory response. Direct in vitro exposure to NHLFs exhibited particle-dependent increased live cell count, reactive oxygen species production, and α-smooth muscle actin expression. Nanoclay-exposed NHLFs (0.6 μg/cm²) possessed elevated collagen I levels while the same mass dose in vivo (300 μg/lung) favored elevated fibronectin and collagen III deposition for CloisNa and CS. In conclusion, organic coating presence and incineration status influenced nanoclays’ effects on cellular interaction, membrane integrity, inflammation, fibroblast activation, and collagen accumulation in exposed cell models. Although pre-incinerated nanoclay exposure promoted collagen accumulation in vitro, it was a poor predictor of in vivo model reticular fiber deposition.