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Chemical Research in Toxicology

American Chemical Society (ACS)

Preprints posted in the last 30 days, ranked by how well they match Chemical Research in Toxicology's content profile, based on 10 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.

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Chemical augmentation of the validated HepaRGTM CYP induction test method Part 2: Additional laboratory study supported by mRNA analysis

Quartermain, E.; Zhang, J.; Marczylo, T.; Gant, T. W.; Jacobs, M. N.

2026-06-20 pharmacology and toxicology 10.64898/2026.06.16.732650 medRxiv
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Cytochrome P450 (CYP)-mediated biotransformation of endogenous and xenobiotic substances can lead to altered exposure, toxicological impact, or adverse drug reactions. CYP induction data are fundamental to regulatory chemical toxicity hazard assessment because they directly affect the in vivo fate of xenobiotics, potentially influencing their safety and efficacy of pharmaceuticals, and impacting the safety assessment of industrial chemicals, and environmental contaminants. Here we report on the third laboratory supplementary validation of an established and previously validated human HepaRGTM in vitro method able to detect CYP1A2, CYP2B6, and CYP3A4 induction, to support the expansion of the chemical applicability domain beyond pharmaceuticals. This study was conducted to support the part 1 study with additional robust data. We established the test method in-house using the 10 previously validated pharmaceutical proficiency chemicals, then tested a further 6 proposed augmentation chemicals, tebuconazole, benfuracarb, chlorpyrifos, N, N-Diethyl-meta-toluamide, fipronil, permethrin, as tested in part 1, and then four additional chemicals: prochloraz, atrazine, pyrimethanil, and chlorpyrifos-methyl. LC-MS/MS was utilised to measure the conversion of a cocktail mixture of prototypical selective CYP probe substrates to their metabolites, in parallel with mRNA measurements. We achieved high concordance with expected classifications for proficiency and additional chemicals. Comparisons with mRNA-based measurements suggested gene expression may serve as a cost-effective pre-screening tool for CYP1A2 and CYP3A4, though with greater uncertainty for CYP2B6. The data support the robustness of the HepaRG method for CYP induction testing and the adoption of the test method in 2026 as an Organisation for Economic Cooperation and Development Test Guideline. Plain language summaryCytochrome P450 (CYP) enzymes metabolize drugs, pesticides, and other chemicals. Chemicals that increase or decrease CYP enzyme activity can change internal exposure levels, potentially leading to unexpected toxicity or impact drug effectiveness. Reliable in vitro methods to assess CYP induction are needed for regulatory chemical safety assessment. This study describes results from a third laboratory applying a previously validated human HepaRG cell-based method to assess induction of CYP1A2, CYP2B6, and CYP3A4. After successful in-house implementation using ten reference pharmaceutical compounds, the method was extended to ten more industrial chemicals. CYP induction was evaluated by measuring enzyme activity and changes in gene expression. The test method showed a high level of agreement with expected induction outcomes. Gene expression data supported enzyme activity results, particularly for CYP1A2 and CYP3A4. These results strengthen confidence in the robustness and wider applicability of the method for Organisation for Economic Cooperation and Development Test Guideline adoption.

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Chemical augmentation of the validated HepaRGTM CYP enzyme induction test method Part 1: The Goliath two laboratory study

Jacobs, M. N.; Kubickova, B.; Person, E.; Kamstra, J. H.; Cabaton, N.; Hoffmann, S.; Jamin, A.; Lacroix, M.; Legler, J.; Munic-Kos, V.; Nijmeijer, S. M.; Sinnige, T. L.; Urien, L.; Zalko, D.

2026-06-20 pharmacology and toxicology 10.64898/2026.06.16.732540 medRxiv
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Cytochrome P450 (CYP) enzymes play a key role in the metabolism of both xenobiotics and endogenous compounds, and the activity of some CYP isoforms are susceptible to induction and/or inhibition by certain chemicals. As CYP induction and inhibition can significantly alter the in vivo fate of xenobiotics i.e., levels of parent chemicals and/or metabolites, and thus toxicity, CYP induction/inhibition data is needed for regulatory chemical toxicity hazard assessment. Utilizing available human in vivo pharmaceutical data, a successful validation was previously conducted on the in vitro HepaRG CYP induction test method for measurement of induction of three key human CYP enzymes CYP1A1/1A2, 2B6 and 3A4. However, further validation data was required to demonstrate applicability of the test method to also accurately detect CYP induction mediated by industrial and pesticidal chemicals. Here we report on the supplementary validation of the HepaRG CYP enzyme induction test method carried out in two laboratories under the auspices of the EU Horizon2020-funded project "GOLIATH", to expand the chemical applicability domain beyond pharmaceutical chemicals. Successful transfer was demonstrated and reproducibility assessed for the original 10 selected proficiency pharmaceuticals, plus three reference inducers together with six additional non-pharmaceutical augmentation chemicals. The method and chemical selection were found to be reliable and relevant for the routine assessment of human CYP induction. For the augmentation chemicals being proposed as additional proficiency chemicals, the test method achieved a reasonable but not optimum reproducibility. Recommendations are proposed to improve the test methods specificity, reflecting the inherent uncertainty around borderline CYP inducing chemicals. Plain language summaryCytochrome P450 (CYP) enzymes help break down drugs and other chemicals in the body. Their activity can be increased (induced) or decreased (inhibited), which can change how toxic a chemical is and when it is excreted. Because of this, CYP data is important for chemical safety assessments. A laboratory-based method using HepaRG cells was previously validated to measure induction of key CYP enzymes (CYP1A1/1A2, CYP2B6 and CYP3A4) using pharmaceutical chemicals. This study aimed to show that it also works well for industrial and pesticidal chemicals. In the EU funded GOLIATH project, two laboratories tested 10 pharmaceutical and 6 non-pharmaceutical chemicals. The method showed good reliability overall and strong reproducibility for pharmaceuticals. For non-pharmaceutical chemicals, results were acceptable but less consistent. The study concludes that the method is useful for routine testing, but improvements are needed to increase accuracy and better handle chemicals that show weak or borderline CYP induction effects.

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Mechanistic characterization of tenuazonic acid-induced cellular stress responses in human esophageal KYSE-510 cells

Grgic, D.; Jobst, M.; Pais, M.; Waesoh, N.; Hager, S.; Del Favero, G.; Marko, D.

2026-07-09 pharmacology and toxicology 10.64898/2026.07.06.736731 medRxiv
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Tenuazonic acid (TeA) is an emerging Alternaria mycotoxin frequently detected in food and feed commodities, raising concerns about its toxicological relevance. Chronic oral exposure to TeA has been reported to induce dysplastic alterations in the esophageal mucosa of mice, while human biomonitoring data indicate an association between TeA exposure and esophageal cancer, although a causal relationship has not yet been established. At a mechanistic level, the effects of TeA in esophageal cells remain poorly characterized. Therefore, this study investigated the impact of TeA on cytotoxicity, oxidative stress, DNA damage, mitochondrial homeostasis, cell-cycle distribution and transcriptomic stress responses in human esophageal KYSE-510 cells. TeA induced a concentration-dependent reduction in metabolic activity and total protein content after 24 h exposure to 0.1-100 M. Significant cytotoxicity was measured starting from 20 M. At sub-cytotoxic concentrations, TeA triggered rapid ROS formation within 5-30 min exposure and induced formamidopyrimidine-DNA glycosylase (FPG) sensitive DNA damage after 1 h exposure (5-7.5 M), indicating oxidative DNA lesions. In addition, TeA altered mitochondrial morphology after 4 h exposure at 7.5 M, manifested by shrinkage of the mitochondrial network area and perinuclear redistribution, while mitochondrial respiration showed only a non-significant tendency towards reduced respiratory capacity. RNA sequencing after 6 h exposure to 10 M TeA revealed oxidative stress-associated transcriptional changes, impaired antioxidant and stress-adaptive responses, and p53-associated stress signaling. Furthermore, TeA induced significant G2/M phase accumulation after 24 h exposure to 1-10 M.

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Ocimum gratissimum essential oil nanoemulsions as a safe topical nanoplatform for antibacterial and wound-healing activities

Fomesseng Negoue, A.; Eya'ane Meva, F.; Fokou, J. B. H.; Voundi Olugu, S. H.; Boudjeka, V.; Ngo Nyobe, J. C.; Belle Ebanda Kedi, P.; Houatchaing Kouemegne, A. M.; Etame Loe, G.

2026-07-07 pharmacology and toxicology 10.64898/2026.07.01.735794 medRxiv
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Background: Natural essential oils exhibit antimicrobial and wound-healing properties, but their therapeutic application is limited by poor water solubility, volatility, and instability. This study developed and characterized a nanoemulsion of Ocimum gratissimum essential oil (OGNe) and evaluated its physicochemical properties, dermal safety, antibacterial activity, and wound-healing potential. Methods: Essential oil was obtained by hydrodistillation and formulated into nanoemulsions by high-speed stirring emulsification. Physicochemical properties, including pH, droplet size, polydispersity index, and storage stability, were determined. Acute dermal toxicity was assessed in Wistar rats following OECD Test Guideline 402. Antibacterial activity was evaluated using broth microdilution, minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and time-kill assays. Wound-healing efficacy was investigated using an excision wound model over 21 days using distilled water and trolamine serving as controls. Results: OGNe exhibited a stable milky appearance, near-neutral pH, and droplet sizes ranging from 26 to 224 nm. No signs of dermal toxicity or behavioral abnormalities were observed after topical administration. The nanoemulsion showed selective antibacterial activity, with the highest susceptibility against Acinetobacter baumannii (MIC = 1.125 L/mL), whereas Escherichia coli remained resistant. Time-kill assays demonstrated concentration-dependent bacteriostatic activity. In vivo, OGNe significantly accelerated wound contraction from day 3 onward (p < 0.0001), achieving healing rates comparable to or exceeding those of trolamine during the inflammatory and proliferative phases. Conclusion: Ocimum gratissimum nanoemulsions represent stable, biocompatible topical formulations that combine selective antibacterial activity with enhanced wound healing, supporting their potential as phytopharmaceutical nanoformulations for the management of acute skin wounds.

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Green-synthesized silver nanoparticles enhance Guibourtia tessmannii antithromboinflammatory therapeutic potential

Eya'ane Meva, F.; Gouli Lougui, L. P.; Nguemfo, E. L.; Fannang, S. v.; Ntoumba, A. A.; Bamal, H.-D.; Beglau, T. H. Y.; Tako Djimefo, A. K.; Mintang Fongang, U. A.; Sone Enone, B.; Tchangou Njiemou, A. F.; Evouna, D. I. M.; Yinyang, J.; Chimi Tchatchouang, G.; Fonye Nyuyfoni, G.; Janiak, C.

2026-07-06 pharmacology and toxicology 10.64898/2026.07.03.736249 medRxiv
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Introduction: Thromboinflammation, which represents the pathological interplay between inflammation and thrombosis, is a leading cause of global mortality. Current therapies are frequently associated with an increased risk of bleeding and do not adequately address the inflammatory component of the disease. The African tree Guibourtia tessmannii represents a promising source of natural anti-inflammatory compounds. This study aimed to synthesize and characterize silver nanoparticles using an aqueous bark extract of G. tessmannii (GT-AgNPs) and to evaluate their anti-inflammatory and anticoagulant properties. Methods: GT-AgNPs were synthesized by reducing silver nitrate with an aqueous extract of G. tessmannii bark. The nanoparticles were comprehensively characterized using UV-Vis spectroscopy, FTIR spectroscopy, powder X-ray diffraction, and scanning electron microscopy. In vitro anti-inflammatory activity was evaluated through inhibition of bovine serum albumin denaturation, whereas in vivo anti-inflammatory activity was assessed using the carrageenan-induced rat paw edema model. Anticoagulant activity was investigated by measuring activated partial thromboplastin time (aPTT) and prothrombin time (PT), corresponding to the intrinsic and extrinsic coagulation pathways, respectively. Results: The synthesis successfully produced GT-AgNPs with an average particle size of approximately 20 nm. Both the aqueous extract and GT-AgNPs exhibited marked anti-inflammatory activity. The nanoparticles achieved 95% inhibition of protein denaturation in vitro and 95% inhibition of carrageenan-induced paw edema in vivo at a dose of 0.4 mg/kg body weight after 5 h. Furthermore, both the extract and GT-AgNPs demonstrated dose-dependent anticoagulant activity. Conclusion: The study demonstrated that GT-AgNPs, synthesized from the bark of G. tessmannii, possess significant anti-inflammatory and anticoagulant properties. These findings highlight the potential of GT-AgNPs as nanotherapeutic candidates for the management of thrombo-inflammatory disorders.

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Suprachoroidal Delivery of Anti-Angiogenic Peptide Microparticles Enables Sustained Activity with Favorable Ocular Safety

Mirando, A. C.; Lima e Silva, R.; Shen, J.; Robinson, T. J.; Green, J. J.; Campochiaro, P. A.; Popel, A. S.; Pandey, N. B.

2026-07-05 pharmacology and toxicology 10.64898/2026.06.30.735614 medRxiv
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Retinal and choroidal vascular diseases are major causes of vision loss that require frequent intravitreal anti-VEGF therapy. Anti-angiogenic peptide AXT107 demonstrated efficacy in preclinical studies and was advanced to the clinical stage. To provide for sustained delivery of the peptide and avoid complications with intravitreal injection, we evaluated suprachoroidal delivery of AXT107 microparticles (MP-AXT107). The original, soluble AXT107 formulation was ineffective at inhibiting laser-induced choroidal neovascularization (CNV) in our rat model and was consequently reformulated as microparticles. MP-AXT107 demonstrated high peptide incorporation efficiency, reproducible morphology, and physical and chemical stability for at least 9 months under refrigerated storage. In the rat CNV model, suprachoroidal MP-AXT107 significantly reduced neovascular area by approximately 60% relative to vehicle controls. Safety and durability were evaluated in a 9-month GLP toxicology study in Gottingen minipigs following a single suprachoroidal injection of vehicle or MP-AXT107 (0.125-1.25 mg/eye). Transient increases in IOP and mild ocular inflammatory findings were observed immediately following administration but resolved rapidly without lasting effects. No treatment-related adverse ocular findings were observed during the remainder of the study, and the highest tested dose (1.25 mg/eye) was established as the no-observed-adverse-effect level. Bioanalysis at study completion demonstrated persistent AXT107 localization primarily within choroid/RPE and scleral tissues, with no signs of systemic exposure. Collectively, these findings demonstrate that suprachoroidal delivery of MP-AXT107 enables sustained anti-angiogenic activity with favorable ocular safety and prolonged tissue retention, supporting further clinical development as a durable therapy for retinal and choroidal vascular diseases.

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Research protocol for a multidimensional environmental and health impact study of petrochemical plant emissions in Calvert city, Kentucky

Huntington-Moskos, L.; Cave, M.; Reynolds, L.; Anderson, L.; Housman, B.; Abolins-Abols, M.; Fratzke, R.; Holm, R.; Smith, T. R.

2026-07-09 occupational and environmental health 10.64898/2026.07.07.26356427 medRxiv
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While exposure to volatile organic compounds such as ethylene dichloride and vinyl chloride monomer is a well-established cause of liver disease, particularly hepatic hemangiosarcoma, characterizing real-world exposure profiles in communities surrounding industrial centers remains challenging. Calvert City, Kentucky (population ~2,500), provides a unique setting characterized by both active industrial emissions and legacy sources of air toxics. To address these complexities, this method paper describes the framework for the Biomonitoring and Environmental Assessment for Community Outreach and Neighborhood Safety (BEACON) study. By utilizing a novel, multi-dimensional exposure assessment strategy, BEACON aims to characterize air toxic exposures and provide actionable data for community health and safety. For the BEACON study, we will leverage Kentucky Department of Air Quality measures of air toxics, analyze urine samples in a small cohort of community volunteers, analyze community urine via wastewater in an adjacent community, geocode citizen odor reporting, assess blood markers in wildlife, survey small and large animal veterinarians in the area for anomalies in morbidity and mortality, and work with the regional health system to enhance vigilance for health issues associated with toxicants present in the area. In addition, blood samples will be collected at three time points and biobanked for future analyses. Efforts will be made to link this study to additional large-scale long-term cohorts where possible. Throughout the project, community engagement will play a critical role by raising awareness, fostering collaboration, and ensuring that the voices of affected residents are heard.

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Pediatric nicotine exposures from devices and liquids: a comparative analysis of U.S. poison center data

Miller, R. S.; Varney, S. M.

2026-07-07 toxicology 10.64898/2026.07.04.26357293 medRxiv
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Introduction: Pediatric nicotine exposures remain an important and preventable public health issue, particularly with the rapid expansion of electronic nicotine delivery systems. This study compared demographic characteristics, exposure circumstances, and clinical outcomes between pediatric cases involving nicotine devices and bottled liquids reported to U.S. poison centers. Method: This retrospective cohort study analyzed National Poison Data System cases from 2011-2022 involving children aged less than 6 years exposed to nicotine devices or bottled liquids. Analyses were limited to cases with definitive medical outcomes. The primary outcome was defined as a moderate or major clinical effect or death. Odds ratios with 95% confidence intervals were calculated, with a secondary analysis restricted to route-concordant exposures. Results: The final cohort included 15,497 cases: 10,168 device exposures and 5,329 liquid exposures. Demographic characteristics were similar between groups. Device exposures more frequently involved inhalation, while ingestion predominated overall. Clinical effects were typically mild and transient, with vomiting and coughing most commonly reported. The primary outcome occurred in 1.9% of device cases and 2.0% of liquid cases (OR = 1.05; 95% CI 0.82-1.34). A secondary analysis restricted to inhalation-only device exposures and ingestion-only liquid exposures similarly found no significant difference in clinically important outcomes (OR = 1.38; 95% CI 0.92-2.12). Two deaths occurred, one in each group. Conclusion: These findings suggest that, despite differences in formulation and route of exposure, nicotine devices and bottled liquids produce broadly similar clinical toxicity profiles in young children. Prevention strategies should address all household nicotine products rather than focusing on specific delivery systems.

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Agnostic material classification using differential de Bruijn graphs of DNA imprints

Cox, R. M.; Ansari, Z. T.; Johnson, C. D.; Marcotte, E. M.; Ellington, A.; Bhadra, S.

2026-06-25 bioinformatics 10.64898/2026.06.23.733838 medRxiv
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The wide variety of physical and chemical properties in materials makes the study of unknown substances challenging. We have previously proposed a theoretical framework for agnostic material characterization based on using nucleic acid imprints of the materials and then analyzing material-specific patterns of derived sequences. Here we demonstrate an experimental and computational pipeline that can agnostically identify and distinguish varied materials based on DNA k-mer imprints and validate the ability of these imprints to distinguish closely related materials. This work lays the foundation for expansion of purely agnostic sensing technologies for the unbiased characterization and categorization of a much wider variety of biotic and abiotic materials.

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Do nanoplastics reshape microglial support of neuronal resilience? A study of microglial bioenergetics and microglia to neuron communication in vitro

Brunialti, E.; Meda, C.; Villa, A.; Parolini, M.; Ciana, P.; Casati, L.

2026-06-25 pharmacology and toxicology 10.64898/2026.06.17.732827 medRxiv
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Nanoplastics (NPs) are emerging environmental contaminants able to cross biological barriers, disrupt cellular and organelle homeostasis, and alter the brain microenvironment. This study investigated whether NPs affect microglia to neuron communication, a key mechanism underlying neuronal resilience, via the nuclear factor erythroid 2 like 2 (NFE2L2) pathway. Using an in vitro model, we evaluated the effects of polystyrene nanoplastics on microglial metabolic fitness and microglia-mediated neuronal stress responses. Increasing NP concentrations induced a dose dependent biphasic effect. Low to intermediate concentrations increased intracellular adenosine triphosphate (ATP) levels in microglia and enhanced microglia-mediated activation of neuronal NFE2L2. In contrast, high NP concentration impaired microglial metabolism, reduced ATP availability, and decreased microglia to neuron communication. These findings indicate that NPs alter microglial energetic status and modulate neuroprotective signalling, potentially contributing to impaired neuron to microglia interactions and increased susceptibility to neurotoxicity.

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Dosimetric Characterization and Workflow Optimization of the FLASH-SARRP for Reliable Preclinical Radiobiological Studies

Knol, M.; Goncalves Jorge, P.; Kunz, L. V.; Korysko, P.; Petit, B.; Durham, A.; Marie-catherine, V.; Tsoutsou, P.; Koutsouvelis, N.; Lascaud, J.

2026-07-07 cancer biology 10.64898/2026.07.06.736680 medRxiv
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Objective: Preclinical small-animal irradiators such as the FLASH-SARRP can support the advancement of photon-FLASH toward the clinic. This study aimed at characterizing the FLASH-SARRP and established a robust quality assurance (QA) workflow to enable accurate and reproducible preclinical experiments. Approach: Custom 3D-printed spacers were designed to ensure reproducible X-ray tube alignment, sample positioning and mounting of the dosimetric tools. Beam characteristics were evaluated using a combined dosimetric approach. High spatially resolved dose distributions were obtained from Gafchromic films, whereas a plastic scintillating fiber was employed to monitor in real-time the temporal pulse structure and synchronization between the two X-ray tubes. Day-to-day variability of the delivery was evaluated over several sessions. Main results: The FLASH-SARRP achieved dose-rates of around 80 Gy/s when both tubes were used simultaneously and provided a homogeneous irradiation field suitable for small-animal studies. A desynchronization between the two tubes was observed with an average delay of 10 ms, resulting in temporal dose-rate heterogeneity. Additionally, a substantial inter-session variability (~11%) was found, whereas the intra-session variability was relatively low (~4%). Inter-session variability was reduced to 5%, approaching the intra-session variability, by adding Gafchromic films/scintillator-based quality assurance (QA) workflow into the irradiation routine. Significance: This work highlights the importance of temporal dosimetry for preclinical FLASH studies. Additionally, a practical QA framework is proposed integrating real-time monitoring with reference dosimetry. The proposed work enables adaptive dose delivery, thereby enhancing the reproducibility of the irradiations, which is crucial for reliable preclinical studies on the FLASH effect.

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Modular in vitro evaluation of Buparlisib-polymeric nanomedicines in 2D and 3D models of glioblastoma

Havelkova, J.; Petrenko, Y.; Stehlikova, A.; Marekova, D.; Peskova, K.; Pechar, M.; Studenovsky, M.; Etrych, T.; Pola, R.; Jendelova, P.

2026-06-23 pharmacology and toxicology 10.64898/2026.06.18.732941 medRxiv
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IntroductionIn this study, we developed a modular in vitro platform that integrates advanced polymer-drug conjugation chemistry with stepwise cytotoxicity screening in both 2D (monolayer) and 3D (spheroids) glioblastoma (GBM) models. Buparlisib was selected as the model therapeutic due to its well-characterised mechanism of action, high blood-brain barrier permeability, and relevance to PI3K-targeted therapy. MethodsTwo mechanistically distinct conjugation strategies were explored using N-(2-hydroxypropyl)methacrylamide-based copolymers. The first strategy was based on a redox-sensitive disulphide linkage designed for intracellular glutathione-triggered release, whereas the second used an azide-bearing derivative compatible with strain-promoted azide-alkyne cycloaddition. Drug release was assessed by high-performance liquid chromatography. Biological activity was systematically evaluated in U87MG, U118MG, and T98G cells under 2D conditions using a resazurin-based metabolic activity assay. Subsequently, the more promising disulphide-based formulations were assessed in 3D spheroids by metabolic activity measurements and live-cell monitoring of spheroid growth dynamics. ResultsFree Buparlisib showed the strongest inhibitory effect, while its modification and polymer conjugation reduced the apparent activity. Nevertheless, the disulphide-based derivative and polymer conjugate retained concentration-dependent activity, whereas the azide-based polymer conjugate showed minimal effects. Moreover, treatment responses differed between cell lines and between 2D and 3D models. DiscussionOverall, linker chemistry, cell-line-specific behaviour, and model dimensionality strongly influenced the biological performance of the polymeric Buparlisib formulations. The redox-sensitive polymer conjugate therefore represents the more promising strategy for further development.

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Computational Design of Two Novel BRAF V600E Inhibitors: Exploiting Sulfoximine Bioisosterism and Chiral Constraints to Evade Paradoxical Activation

Yu, Z. H.; Siegel, J. B.; Morrow, E. R.

2026-06-30 pharmacology and toxicology 10.64898/2026.06.25.734343 medRxiv
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Metastatic melanoma is an aggressive cutaneous malignancy frequently driven by the oncogenic V600E mutation within the BRAF kinase. While first-generation Type IS BRAF inhibitors, such as dabrafenib, are currently prescribed to target this specific molecular vulnerability, paradoxical MAPK pathway activation, and acquired drug resistance necessitate the continuous development of structurally optimized lead molecules. In this study, chemical intuition, bioisosteric replacement, and computational molecular docking were employed to propose two novel BRAFV600E drug candidates. The proposed therapeutics, engineered to incorporate constrained sp3-hybridized aliphatic rings and a sulfoximine bioisostere, demonstrated thermodynamically superior docking scores within the mutant catalytic cleft compared to dabrafenib. Lastly, a homology analysis determined that Mus musculus is a suitable model organism for future preclinical studies and confirmed crucial structural selectivity against microbial off-target kinases.

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Integrating Semantic Retrieval, LLM-based Refinement, and Structured Expert Curation for Scalable AOP Gene Mapping

Schaffert, A.; Fratello, M.; Kangas, K.; Torres Maia, M.; del Giudice, G.; Mobus, L.; Accardi, C.; Al-Abdulraheem, Z.; Campini, L.; Galardo, F.; Federico, A.; Ciancaleoni, G.; Juppi, H.-K.; Paparella, M.; Serra, A.; Greco, D.

2026-06-30 bioinformatics 10.64898/2026.06.25.734475 medRxiv
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Toxicogenomics can support regulatory toxicology, but its use is limited by the difficulty of translating molecular responses into mechanistic, decision-relevant interpretations. Adverse Outcome Pathways (AOPs) provide a framework for this translation, yet omics applications require scalable mapping of Key Events (KEs) to molecular features. Here, we present an AI-assisted, multi-step workflow for KE-to-gene mapping that uses embedding-based semantic retrieval to identify candidate ontology/pathway terms, large language model-assisted refinement to filter these candidates, and double-independent expert group curation with rule-based consolidation to finalize mappings and derive confidence scores. Compared with earlier NLP-based approaches, the workflow improves KE-to-ontology/pathway mapping performance and generates candidate annotations that better align with expert judgment while substantially reducing the need for manual augmentation. Explicit gene and protein mentions in KE titles were additionally grounded to improve specificity, and each curated mapping was assigned curator reason codes to support transparent, traceable, and confidence-aware reuse. Applied across AOP-Wiki, the workflow produced a comprehensive KE-to-gene set resource covering 1,254 KEs across 523 AOPs and linking 15,833 human genes. Utility is demonstrated through CTD-based AOP fingerprinting of curated reference chemical groups, highlighting expanded coverage and confidence-informed interpretation of chemical-associated gene signatures in an AOP context. The workflow and resulting resource provide a practical bridge between toxicogenomics and AOP-based mechanistic interpretation and support routine updating and future extension to additional omics layers within OECD Omics2AOP.

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Development of a Biology-Informed Chemical Mixture Index for Oxidative Stress and Mortality in NHANES 2005-2010: A Survey-Weighted Quantile G-Computation Approach

Rodriguez-Carmona, Y.; Bakulski, K. M.; Walker, E.; Wang, X.; Hao, W.; Mukherjee, B.; Park, S. K.

2026-07-02 occupational and environmental health 10.64898/2026.06.30.26356938 medRxiv
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Background: Current chemical mixture approaches are largely data-driven without considering shared biological mechanisms among mixture components, highlighting the need for biology-informed approaches. Objectives: We constructed an integrated measure of a chemical mixture's oxidative stress potential and assessed its association with mortality in the US population. Methods: The sample comprised 4,574 adults ([&ge;] 20 years) from National Health and Nutrition Examination Survey (NHANES) 2005-2010. To obtain robust estimates, we performed 1,000 repeated random 50:50 splits into training and testing sets. In each training set, we used survey-weighted quantile g-computation to model serum gamma-glutamyl transferase (GGT), an oxidative stress biomarker, as a function of a 30-chemical mixture (blood metals, urinary polycyclic aromatic hydrocarbons (PAHs), pesticides, phenols/parabens, and phthalates), adjusting for sociodemographic, behavioral, and dietary factors. We then applied the fitted model from each training set to the corresponding testing set to derive the environmental risk score for oxidative stress (ERSOS), defined by predicted GGT values. Associations of ERSOS with all-cause, cardiovascular, and cancer mortality over 11 years of follow-up were estimated in the testing sets using survey-weighted Cox proportional hazards models and summarized across the 1,000 repeated splits. Results: Chemicals with the largest positive weights in quantile g-computation included mono-(2-ethyl-5-hydroxyhexyl) phthalate, mono-2-ethyl-5-carboxypentyl phthalate, 2-hydroxyfluorene, methyl paraben, and benzophenone-3; chemicals with the largest negative weights included mono-(2-ethyl-5-oxohexyl) phthalate and PAH metabolites (1-hydroxynaphthalene, 3-hydroxyphenanthrene, and 3-hydroxyfluorene). The median correlation between observed and predicted GGT in the testing sets was 0.43 (2.5th, 97.5th percentiles: 0.40-0.48). A one standard deviation increase in ERSOS was associated with a median hazard ratio of 1.60 (2.5th, 97.5th percentiles: 1.01-2.57) for cardiovascular mortality. No associations were found for all-cause mortality or cancer mortality. Discussion: The proposed survey-weighted quantile g-computation approach may help estimate biology-informed chemical mixture effects in complex survey data, supporting the potential utility for population-generalizable environmental mixture research.

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Environmentally relevant depleted uranium exposure damages mitochondria, decreases cytosolic reductive capacity, and increases global DNA damage accumulation through a ROS-independent mechanism involving slingshot protein phosphatase 1b enrichment.

Kalaniopio, P. H.; Gibbons, L. B.; Allen, R. S.; Matthews, S. M.; Lujan, O. R.; Gaaloul, E.; Wilbanks, J.; Allen, C. M.; Chassman, C. A.; Traustadottir, T.; Propper, C. R.; Salanga, M. C.

2026-07-08 pharmacology and toxicology 10.64898/2026.07.02.736169 medRxiv
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Depleted uranium (DU) is an environmental contaminant with a 30 g/L (ppb; parts per billion) EPA maximum contaminant level (MCL) for drinking water. The mining of uranium and use of DU in modern weapons underly human exposure that disproportionally impacts military and tribal communities in the United States. Uranium's radiotoxic characteristics are understood, but its chemical hazards much less so. In zebrafish (Danio rerio) and human cell cultures we test the hypothesis that exposure to DU negatively impacts cellular function and development through disruption of mitochondrial metabolism. Using a novel shrapnel model with TEM/SEM+EDS, we showed uranium microparticles caused proximity-dependent mitochondrial disruption. In waterborne exposure paradigms, larval movement was reduced and hatching delayed as a result of reduced movement and not enzyme deficiencies in response to 18 ppb DU, below the MCL. Increased DNA damage accumulation was detected in exposed larva and cells. DNA-damage quantitative PCR of DU-exposed larvae showed increased damage in the ahr1 locus (nuclear gene) and decreased mitochondrial DNA (mtDNA) copy number, but mtDNA damage levels varied across experiments. Mitochondrial function was assessed using a resazurin-based assay in the presence and absence of antioxidants and showed diminished cytoplasmic reductive capacity. DU exposure alone did not enrich antioxidant gene expression, contrasting with arsenic exposure, a known ROS-inducer and Nrf2-activator. Sulforaphane (SFN), a potent Nrf2-activator, did not blunt the effects of DU exposure, despite activation of antioxidant response element (ARE) genes (gstp and gss), but did blunt the effects of arsenic exposure. The most enriched transcript in DU-exposed larvae coded for slingshot protein phosphatase (ssh), further exploration revealed ssh1b as the zebrafish-specific ortholog activated in response to DU, and inhibition using an identified SSH1 inhibitor, Sennoside A, partially rescued the metabolic and hatching defects observed. Our data points to a cytotoxic mechanism in which DU disrupts mitochondrial function through ssh1b enrichment that impairs normal mitophagy, leading to decreased cellular reductive potential independent of either ROS production or ARE-activation. Our results suggest that health impacts from DU exposure may be directly linked to impaired mitochondrial functions.

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Soft silicone surface stiffening by oxidation upon deep UV treatment as characterized using nanoindentation

Wilder, A.; Booth, Z.; Obermeyer, C.; Sharmin, S.; Maruthamuthu, V.

2026-06-22 bioengineering 10.64898/2026.06.19.733410 medRxiv
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Silicones are elastomers that have a wide variety of uses, including biomedical applications such as the coating of biomedical devices and as implants. Soft silicones with mechanical properties similar to those of biological tissues have particularly gained use as substrates for cell culture in mechanobiology studies. In this context, it would be desirable to be able to alter their surface mechanical properties with a relatively simple physical treatment. While deep ultraviolet (deep UV) or ultraviolet C (UV-C) treatment has been previously used as a surface treatment method for stiffer silicones formulations, the effect of this treatment on soft silicones relevant for mechanobiology applications is still uncharacterized. We first used nanoindentation to determine the Youngs modulus of two types of soft silicones, Qgel and GEL-8100/Syl (GEL-8100 with Sylgard-184 crosslinker), both with initial moduli in the kilopascal range. We show that nanoindentation in the presence of 1% sodium dodecyl sulfate avoids adhesion between the nanoindentation glass probe and the soft silicones. After deep UV exposure in the presence of air, nanoindentation revealed that the apparent Youngs moduli of the soft silicones Qgel and GEL-8100/Syl increased by 70% and 33%, respectively. The bulk rheology of the soft silicones were not affected, suggesting that this corresponds to a surface stiffening effect with a topical stiffening of at least several hundred kilopascals. Energy-dispersive X-ray spectroscopy results show an increase in the mole fraction of oxygen, consistent with oxidation of the surface. Attenuated Total Reflectance Fourier-Transform Infrared spectra show evidence of Si-OH group formation in GEL-8100/Syl and silicon sub-oxide formation in Qgel. Consistent with this, water contact angle measurements show enhanced hydrophilicity after deep UV treatment. Our results have implications for using soft silicones as substrates in mechanobiology studies and in processes where deep UV light is used in the surface treatment of soft silicones.

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Material-specific quarantine durations for SARS-CoV-2 inactivation on musical instruments and music-related materials

Pastorino, B.; Touret, F.; Creton, M.; Viala, R.; Morand, J. C.; Reyre, F.; Jousserand, M.; Billecard, F.; Charrel, R. N. C.

2026-07-01 microbiology 10.64898/2026.07.01.735763 medRxiv
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The COVID-19 pandemic has imposed a reevaluation of safety protocols across various sectors, including the arts. This study addresses a critical gap in understanding SARS-CoV-2 persistence on materials commonly associated with musical instruments and scores, such as alloys, varnishes, reeds, and paper. While previous research has explored viral survival on various surfaces, limited data exists for materials specific to musical contexts. In this work, we investigate the efficacy of quarantine as a non-destructive method for inactivating SARS-CoV-2 on 16 materials, including brass, silver plating, ABS plastic, ebonite, and various varnishes and paper types. Results revealed significant variability in viral persistence across materials. Non-porous surfaces like metals and ABS plastic cleared infectivity within 3 days, while porous materials such as reeds and music scores required up to 7 days. Gold-plated brass and certain varnishes showed intermediate persistence, with infectivity clearing after 4 days. These findings are in agreement with prior studies indicating that SARS-CoV-2 survival is highly dependent on surface composition, with porous and organic-coated materials retaining viable virus longer due to reduced environmental stress. Our results highlight the feasibility of stratified quarantine protocols based on material type, offering practical guidelines for musicians and institutions and provides critical insights for mitigating SARS-CoV-2 transmission risks in musical settings.

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Targeted Photodegradation of Misfolded Proteins via Self-photosensitizing with Molecularly Produced Light

Wang, H.; Gu, S.; Yu, J.; Yan, J.; Zhang, J.; Jiang, Z.; Yang, J.; Ran, C.

2026-06-22 neuroscience 10.64898/2026.06.16.732486 medRxiv
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Misfolded proteins are tightly associated with various neurodegenerative diseases, and removing these misfolded proteins is one of the actively pursued approaches for seeking therapeutics for these diseases. In this study, we demonstrated that molecularly produced light (molecular light) from ADLumin-5, a self-photosensitizing chemiluminescence compound, could induce photo-oxidation and photodegradation of misfolded proteins, including beta-amyloid, tau, alpha-synucleins, and TDP-43 proteins in vitro. We validated the oxidation and degradation via LC-MS, MADLI-MS, and western blotting. Using beta-amyloid as a showcase, we demonstrated that, upon photo-oxidation and photodegradation, the toxicities of this misfolded protein were significantly reduced. To investigate the therapeutic effects of ADLumin-5 in vivo, we used the 5xFAD mouse model for longitudinal treatment for 4 months. In vivo molecular imaging results indicated that ADLumin-5 could reduce the accumulation of beta-amyloid proteins. Our study presents a novel approach to seek therapeutics for neurodegenerative disease via molecular light-induced degradation of misfolded proteins. In addition, because ADLumin-5 is dual-functional--enabling both photodegradation and in vivo imaging of misfolded protein changes--it can be considered a photo-theranostic agent for neurodegenerative diseases, representing a novel approach to drug discovery for neurodegenerative diseases.

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SonoPatch: Wearable Sonophoresis for On-Demand Physiological Modulation

Shimizu, K.; Whitmore, N. W.; Hossen, A.; Zhang, Y.; Maes, P.

2026-07-07 pharmacology and therapeutics 10.64898/2026.07.03.26357138 medRxiv
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Existing interfaces modulate user experience through visual, auditory, and haptic channels, but direct physiological modulation, which programmatically alters a user's internal state, remains largely underexplored. We present a wearable sonophoresis patch that uses low-frequency acoustic stimulation to deliver psychoactive substances transdermally, and evaluate its potential for programmable physiological modulation in HCI. We tested this in a double-blinded study (N=26) delivering 100 mg caffeine versus sham control, recording physiological signals during rest and a sustained attention task (SART). The planned comparison for heart rate standard deviation during rest was significant (HR-SD p=0.025, d=1.48), with the caffeine group showing suppressed HR~SD consistent with sympathetic activation. Mean heart rate at rest was not significant (p=0.365), but exploratory analyses during the cognitive task revealed significant cardiovascular divergence: heart rate (p=0.003) and heart rate standard deviation (p=0.027) both moved in directions consistent with systemic caffeine delivery, with effects emerging within minutes of device activation and a sustained group effect across all task rounds (p<0.001). These results provide indirect evidence that wearable sonophoresis can deliver substances to modulate user physiology, opening the design space for on-skin chemical interfaces that adapt delivery in real time to change the user's physiological state on demand.