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At least 19 recordsLinked to original sources

bioRxiv2023

FRESH™ 3D bioprinted cardiac tissue, a bioengineered platform for in-vitro toxicology and pharmacology

There is critical need for a predictive model of human cardiac physiology in the drug development process for assessment of compound toxicology and pharmacology. In vitro two-dimensional monolayer culture of cardiomyocytes provides biochemical and cellular readouts, and in vivo small and large animal models provide information on systemic cardiovascular response. However, there remains a significant gap in these models due to an incomplete recapitulation of adult human cardiovascular physiology, which results in more difficult safety interpretations. Recent efforts in developing in vitro models from engineered heart tissues have demonstrated potential for bridging this gap using human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) in a three-dimensional tissue structure. Here we advance this paradigm by implementing FRESH 3D bioprinting to build human cardiac tissues in a medium throughput, well-plate format with controlled tissue architecture, tailored cellular composition, and native-like physiological function, specifically in its adrenergic agonist drug response. To do this, we combined hiPSC-CMs, endothelial cells and fibroblasts in a cellular bioink and FRESH 3D bioprinted this mixture in the format of a thin tissue strip stabilized on a tissue fixture. Our results confirmed that FRESH 3D bioprinted cardiac tissues could be fabricated directly in a 24-well plate format, were composed of dense and highly aligned hiPSC-CMs at >600 million cells/mL, and within 14 days demonstrated reproducible calcium transients and fast conduction velocity of [~]25 cm/s. Interrogation of these cardiac tissues with the {beta}-adrenergic receptor agonist isoproterenol showed native-like positive chronotropic and inotropic responses, a combination of responses that is not typically observed in 2D monolayer models or standard 3D engineered heart tissue approaches. These results confirm that FRESH 3D bioprinted cardiac tissues represents a novel in vitro platform that enables early in vitro pharmacology and toxicology screening.

bioengineering↗

bioRxiv2025

Pentilludin reduces rat amphetamine and remifentail self-administration with good pharmacologic and toxicologic profiles

Pentilludin is a novel, potent (690 nM) irreversible inhibitor of actions of the receptor type protein tyrosine phosphatase D (PTPRD). Pentilludin displays no in vitro activities in Ames or micronucleus tests, at hERG channels or at targets for currently-licensed drugs. Rats treated with pentilludin doses up to 100 mg/kg/day for two weeks have not been found to display behavioral, hematologic or serum chemistry abnormalities. Treatment with 20 mg/kg sc pentilludin prior to every other M-W-F self-administration session substantially reduces self-administration of amphetamine and more modestly reduces self-administration of remifentanil. Pentilludin provides a novel means for reducing self-administration of psychostimulant and, modestly, opiate drugs in ways that could enhance abstinence in humans.

pharmacology and toxicology↗

bioRxiv2022

Characterization of a strain-specific CD-1 reference genome reveals potential inter- and intra-strain functional variability

BackgroundCD-1 is an outbred mouse stock that is frequently used in toxicology, pharmacology, and fundamental biomedical research. Although inbred strains are typically better suited for such studies due to minimal genetic variability, outbred stocks confer practical advantages over inbred strains, such as improved breeding performance and low cost. Knowledge of the full genetic variability of CD-1 would make it more useful in toxicology, pharmacology, and fundamental biomedical research. ResultsWe performed deep genomic DNA sequencing of CD-1 mice and used the data to identify genome-wide SNPs, indels, and germline transposable elements relative to the mm10 reference genome. We used multiple genome-wide sequencing data types and previously published CD-1 SNPs to validate our called variants. We used the called variants to construct a strain-specific CD-1 reference genome, which we show can improve mappability and reduce experimental biases from genome-wide sequencing data derived from CD-1 mice. Based on previously published ChIP-seq and ATAC-seq data, we find evidence that genetic variation between CD-1 individuals can lead to alterations in transcription factor binding. We also identified a number of variants in the coding region of genes which could have effects on splicing and translation of genes. ConclusionsWe have identified millions of previously unidentified CD-1 variants with the potential to confound studies involving CD-1. We used the identified variants to construct a CD-1-specific reference genome, which can improve accuracy and reduce bias when aligning genomics data derived from CD-1 individuals.

genomics↗

bioRxiv2023

Benchmarking of Small Molecule Feature Representations for hERG, Nav1.5, and Cav1.2 Cardiotoxicity Prediction

In the field of drug discovery, there is a substantial challenge in seeking out chemical structures that possess desirable pharmacological, toxicological, and pharmacokinetic properties. Complications arise when drugs interfere with the functioning of cardiac ion channels, leading to serious cardiovascular consequences. The discontinuation and removal of numerous approved drugs from the market or at late development stages in the pipeline due to such inhibitory effects further highlight the urgency of addressing this issue. Consequently, the early prediction of potential blockers targeting cardiac ion channels during the drug discovery process is of paramount importance. This study introduces a deep learning framework that computationally determines the cardiotoxicity associated with the voltagegated potassium channel (hERG), the voltage-gated calcium channel (Cav1.2), and the voltage-gated sodium channel (Nav1.5) for drug candidates. The predictive capabilities of three feature representations--molecular fingerprints, descriptors, and graph-based numerical representations-- are rigorously benchmarked. Additionally, a novel training and evaluation dataset framework is presented, enabling predictive model training of drug off-target cardiotoxicity using a comprehensive and large curated dataset covering these three cardiac ion channels. To facilitate these predictions, a robust and comprehensive small molecule cardiotoxicity prediction tool named CToxPred has been developed. It is made available as open source under the permissive MIT license at https://github.com/issararab/CToxPred.

pharmacology and toxicology↗

bioRxiv2015

AOP: An R Package For Sufficient Causal Analysis in Pathway-based Screening of Drugs and Chemicals for Adversity

SummaryHow can I quickly find the key events in a pathway that I need to monitor to predict that a/an beneficial/adverse event/outcome will occur? This is a key question when using signaling pathways for drug/chemical screening in pharmacology, toxicology and risk assessment. By identifying these sufficient causal key events, we have fewer events to monitor for a pathway, thereby decreasing assay costs and time, while maximizing the value of the information. I have developed the \"aop\" package which uses back-door analysis of causal networks to identify these minimal sets of key events that are sufficient for making causal predictions.\n\nAvailability and ImplementationThe source for the aop package is available online at Github at https://github.com/DataSciBurgoon/aop and can be installed using the R devtools package. The aop package runs within the R statistical environment. The package has functions that can take pathways (as directed graphs) formatted as a Cytoscape JSON file as input, or pathways can be represented as directed graphs using the R/Bioconductor \"graph\" package. The \"aop\" package has functions that can perform backdoor analysis to identify the minimal set of key events for making causal predictions.\n\nContactlyle.d.burgoon@usace.army.mil

Bioinformatics↗

bioRxiv2020

Ammonia-based enrichment and long-term propagation of zone I hepatocyte-like cells

Zone I and zone III hepatocytes metabolize ammonia through urea cycle and drug by cytochrome P450, respectively. Ammonia has a cytotoxic effect, and can therefore be used as a selection agent for enrichment of hepatocytes. Besides, isolated hepatocytes from livers can be propagated ex vivo under appropriate condition. However, it has not been investigated so far whether ammonia-treated hepatocyte-like cells are able to proliferate in vitro. In this study, we employed the ammonia selection strategy to purify hepatocyte-like cells that were differentiated from human pluripotent stem cells (PSCs) that are embryonic stem cells (ESCs) and induced pluripotent stem cells. Hepatocyte-like cells after exposure to ammonia highly expressed the CPS1 gene that metabolizes ammonia to carbamoyl phosphate. The resistance to cytotoxicity or cell death by ammonia is probably attributed to the metabolic activity of ammonia in the cells. In addition to the ammonia metabolism-related genes, ammonia-selected PSC-derived hepatocytes increased expression of the CYP3A4 gene, one of the cytochrome P450 genes, that is mainly expressed in zone III hepatocytes. Ammonia-selected hepatocyte-like cells derived from both ESCs and iPSCs can be propagated in vitro up to 30 population doublings for more than 190 days without affecting expression of the liver-associated genes, implying that the ammonia-selected cells have immortality or equivalent life span on the appropriate feeder cells like ESCs and iPSCs. The long-term cultivation of ammonia-selected hepatocyte-like cells resulted in the increased expression of hepatocyte-associated genes such as the CPS1 and CYP3A4 genes. The ammonia selection method to enrich a hepatocyte population was also applicable to immortalized cells from the liver. Ammonia treatment in combination with in vitro propagation will be used to obtain large amounts of hepatocytes or hepatocyte-like cells for pharmacology, toxicology and regenerative medicine.

cell biology↗

bioRxiv2021

drda: An R package for dose-response data analysis

Analysis of dose-response data is an important step in many scientific disciplines, including but not limited to pharmacology, toxicology, and epidemiology. The R package drda is designed to facilitate the analysis of dose-response data by implementing efficient and accurate functions with a familiar interface. With drda, it is possible to fit models by the method of least squares, perform goodness of fit tests, and conduct model selection. Compared to other similar packages, drda provides, in general, more accurate estimates in the least-squares sense. This result is achieved by a smart choice of the starting point in the optimization algorithm and by implementing the Newton method with a trust region with analytical gradients and Hessian matrices. In this article, drda is presented through the description of its methodological components and examples of its user-friendly functions. Performance is finally evaluated using a real, large-scale drug sensitivity screening dataset.

bioinformatics↗

bioRxiv2025

High-throughput multi-camera array microscope platform for automated 3D behavioral analysis of freely swimming zebrafish larvae

Understanding the behavioral and morphological dynamics of moving model organisms like the zebrafish larvae requires accurate, high-throughput 3D analysis. However, traditional single-view 2D video tracking fails to capture the full scope of natural 3D movements and postural dynamics. Here, we present a novel high-throughput 24-camera array microscope with a co-designed "mirrored well plate" that allows for snapshot imaging of up to 48 wells over a 118 mm x 82 mm field of view from two orthogonal directions (i.e., a top-view and side-view). Accurate 3D position estimation and tracking is achieved with an efficient machine learning algorithm that scales well to high-throughput measurements. The proposed approach automates parallelized 3D model organism behavioral analysis, providing 3D skeletal tracking, swim bladder morphological dynamics, and kinematics of up to 48 swimming zebrafish larvae at up to several hundred frames per second. The result is an efficient and scalable solution for high-throughput 3D behavioral studies with broad compatibility with standard workflows across laboratories and procedures working with pharmacology, toxicology, and neuroscience.

animal behavior and cognition↗

bioRxiv2026

AOPGraphExplorer 2.0: An Interactive Graph-Based Platform for Multi-Domain Mechanistic Annotation and Exploration of Adverse Outcome Pathways

The Adverse Outcome Pathway (AOP) framework is a cornerstone of modern mechanistic toxicology, providing a structured representation of causal biological events linking molecular initiating events to adverse health outcomes. However, the practical exploration and interpretation of AOPs remain challenging due to the fragmentation of mechanistic knowledge across heterogeneous biological databases and the limited availability of integrated, interactive tools. Here, we present AOPGraphExplorer 2.0, an interactive graph-based platform for the visualization, annotation, and analysis of AOP networks derived from AOP-Wiki. This new version introduces a scalable, modular architecture that integrates multi-domain mechanistic annotations, including biological processes, molecular entities, anatomical context, diseases, and stressors, directly into AOP graphs. AOPGraphExplorer 2.0 enables dynamic filtering of AOP networks based on weight-of-evidence and quantitative understanding scores, supports AOP-, Key Event-, and keyword-centric queries, and generates exportable interactive HTML and machine-readable JSON representations for documentation, sharing, and computational reuse. In addition, the platform provides automated network statistics and annotation coverage summaries, supporting transparent and reproducible analysis. By bridging AOP-Wiki with external biomedical knowledge resources in a unified graph framework, AOPGraphExplorer 2.0 transforms AOP exploration into a multi-domain systems-level analysis workflow. The platform supports hypothesis generation, mechanistic interpretation, and evidence-based decision-making in toxicology, pharmacology, and risk assessment.

systems biology↗

bioRxiv2017

Chronic intermittent nicotine delivery with lung alveolar region-targeted aerosol technology produces circadian blood pharmacokinetics in rats resembling human smokers

IntroductionCigarette smoke is an aerosol containing microparticles that carry nicotine into lung alveolar region where nicotine is rapidly absorbed into circulation. Nicotine exposure in smokers is a chronic intermittent process, with intake during wakefulness and abstinence during sleep resulting in circadian fluctuation of blood nicotine levels. Here we present a smoking-relevant nicotine exposure device and rodent model.\n\nMethodsWe developed a computer controlled integrated platform where freely moving rodents can be exposed to episodic nicotine aerosol on an investigator-designed schedule. Rats were exposed to nicotine aerosol once every half hr in the dark phase of 12/12-hr dark/light cycles for 10 days. Plasma nicotine and its metabolite cotinine levels were determined with a LC-MS/MS method.\n\nResultsWe characterized the aerosol in the breathing zone of the rodent exposure chamber. The droplet size distribution was within the respirable diameter range. The system can generate a wide range of nicotine concentrations in air that meet a variety of experimental needs. We optimized the parameters of aerosol generation and exposure: plasma nicotine and cotinine concentrations reached 30-35 ng/ml and 190-240 ng/ml, respectively. The nicotine levels and circadian patterns resembled the pharmacokinetic pattern of human smokers.\n\nConclusionsWe developed an aerosol system that can produce chronic intermittent nicotine exposure in unanesthetized and unrestrained rodents with route of administration and circadian blood pharmacokinetics resembling human smokers. This methodology is a novel tool for studies of behavior, pharmacology and toxicology of chronic nicotine exposure, nicotine addiction, tobacco-related diseases, teratogenicity, and for discovery of therapeutics.\n\nImplicationsWe developed a method and an alveolar region-targeted aerosol system that provides chronic intermittent nicotine exposure in rodents. The method produces clinically relevant animal models with the route of administration and circadian pharmacokinetics resembling human smokers. This method is a novel tool for understanding the health effects of chronic nicotine exposures such as with tobacco cigarettes, E-cigarettes and other tobacco products, for studies of pharmacology, toxicology, nicotine addiction, tobacco-related diseases, and for discovery of medications.

pharmacology and toxicology↗

bioRxiv2022

Generation of human nociceptor-enriched sensory neurons for the study of pain-related dysfunctions

In vitro models of the peripheral nervous system would benefit from further refinements to better support studies on neuropathies. In particular, the assessment of pain-related signals is still difficult in human cell cultures. Here, we harnessed induced pluripotent stem cells (iPSCs) to generate peripheral sensory neurons enriched in nociceptors. The objective was to generate a culture system with signaling endpoints suitable for pharmacological and toxicological studies. Neurons generated by conventional differentiation protocols expressed moderate levels of P2X3 purinergic receptors and only low levels of TRPV1 capsaicin receptors, when maturation time was kept to the upper practically-useful limit of 6 weeks. As alternative approach, we generated cells with an inducible NGN1 transgene. Ectopic expression of this transcription factor during a defined time window of differentiation resulted in highly-enriched nociceptor cultures, as determined by functional (P2X3 and TRPV1 receptors) and immunocytochemical phenotyping, complemented by extensive transcriptome profiling. Single cell recordings of Ca2+-indicator fluorescence from >9,000 cells were used to establish the "fraction of reactive cells" in a stimulated population as experimental endpoint, that appeared robust, transparent and quantifiable. To provide an example of application to biomedical studies, functional consequences of prolonged exposure to the chemotherapeutic drug oxaliplatin were examined at non-cytotoxic concentrations. We found (i) neuronal (allodynia-like) hypersensitivity to otherwise non-activating mechanical stimulation that could be blocked by modulators of voltage-gated sodium channels; (ii) hyper-responsiveness to TRPV1 receptor stimulation. These findings and several other measured functional alterations indicate that the model is suitable for pharmacological and toxicological studies related to peripheral neuropathies.

pharmacology and toxicology↗

bioRxiv2024

THE PHYTOPHARMACOLOGICAL EVALUATION OF THE METHANOL ROOT EXTRACT OF AZANZA GARCKEANA (MALVACEAE) ON ISOLATED WISTAR RAT UTERINE SMOOTH MUSCLES.

Ethnopharmacological relevancePregnant women in Chongwe, Zambia traditionally use the root of Azanza garckeana (F.Hffm.) Exell & Hillc (Malvalceae) to induce or accelerate labour. A previous study on the plant showed the crude root extracts to possesses uterotonic potential on isolated Wistar rat uterine smooth muscles. The methanol crude root extract was found to be the most potent. AimThe aim of the study was to isolated by bioactivity-guided isolation method the compound with the major uterotonic activity in the root of Azanza garckeana. Materials and methodsThis was a laboratory-based study designed using the uterus isolated from estrogenised adult non-gravid female virgin Wistar rats. The fresh plant materials (leaves and roots) were collected from Chongwe district. The methanol crude extract was obtained by continuous maceration and it was partitioned using hexane, chloroform, ethyl acetate and n-butanol in the increasing order of polarity. The most active fraction was fractionated using column chromatography. One-way ANOVA, Bonferroni post hoc tests were used to analyze data using STATA version 13. Bar charts and dose-response curves were done using Graphpad Prism version 5.00 for Windows (San Diego California USA). ResultsThe final aqueous suspension demonstrated the highest uterotonic potency (EC50 = 2.49 x 10-3mg/ml; 95% CI 1.19 x 10-3 to 5.23 x 10-3 mg/ml, p=0.0001), while sub-fraction pool number 2 (subfractions number 41 to 61) demonstrated the highest uterotonic potency (EC50 at 2.05 x 10-3mg/ml; 95% CI 2.09 x 10-3 to 3.85 x 10-3 mg/ml, p=0.0001). Sub-fraction pool number 2 was suggested to contain the compound with the major uterotonic activity which was suggested to be related to the family of glycosides after High Performance Liquid Chromatography (HPLC) and Fourier Transform Infrared Spectroscopy (FTIR) analysis. ConclusionsThe study suggests the presence of a major uterotonic phytochemical constituent in the methanol root crude extract of Azanza garckeana, which was suggested to be related to the family of glycosides. The study has provided scientific evidence suggesting the root of Azanza garckeana, a plant used traditionally for inducing or accelerating labor possess uterotonic activity. Further pharmacological and toxicological studies need to be undertaken on the plant.

pharmacology and toxicology↗

bioRxiv2025

Planarian behavioral screening is a useful invertebrate model for evaluating seizurogenic chemicals

Detecting adverse health effects of drugs and other chemicals early during chemical/drug development saves significant time and resources. Freshwater planarians are an emerging invertebrate model for rapid, cost-effective neurotoxicity screening. Because planarians exhibit seizure-like behavior when exposed to chemicals that cause seizures in mammals, such as N-methyl-D-aspartate (NMDA) and picrotoxin, they could be a useful first-tier model for seizure screening and thus reduce the need for slow and expensive mammalian tests. However, planarian seizure studies to date have been low-throughput and lacking the necessary standardization and automated analysis to make this model a viable screening solution. Here, we present results from medium-throughput behavioral testing conducted in 48-well plates using two popular models for planarian pharmacological and toxicological studies: Dugesia japonica and Girardia dorotocephala. Planarian behavior was scored using automated image analysis, measuring both translational behavior and body shape changes. We found that known seizurogenic compounds in mammals (NMDA, nicotine, picrotoxin, pilocarpine, and pentylenetetrazole (PTZ)) induced seizure-like behavior in both planarian species within 30 minutes of exposure. We also tested three pesticides (parathion, carbaryl, and permethrin). Parathion and carbaryl, but not permethrin, caused planarian seizure-like activity. While the planarian species responded similarly to most compounds, some compounds showed potency differences of 10-100-fold (pilocarpine and nicotine, respectively). G. dorotocephala planarians were generally more sensitive, but D. japonica planarians displayed more reproducible behaviors. By standardizing both experimental approach and analysis methods and making them available, this work can serve as a framework for future testing of chemicals for seizurogenic potential in planarians.

pharmacology and toxicology↗

bioRxiv2020

One-stop Microfluidic Assembly of Human Brain Organoids to Model Prenatal Cannabis Exposure

Prenatal cannabis exposure (PCE) influences human brain development, but it is challenging to model PCE using animals and current cell culture techniques. Here, we developed a one-stop microfluidic platform to assemble and culture human cerebral organoids from human embryonic stem cells (hESC) to investigate the effect of PCE on early human brain development. By incorporating perfusable culture chambers, air-liquid interface, and one-stop protocol, this microfluidic platform can simplify the fabrication procedure, and produce a large number of organoids (169 organoids per 3.5 cm x 3.5 cm device area) without fusion, as compared with conventional fabrication methods. These one-stop microfluidic assembled cerebral organoids not only recapitulate early human brain structure, biology, and electrophysiology but also have minimal size variation and hypoxia. Under on-chip exposure to the psychoactive cannabinoid, delta-9-tetrahydrocannabinol (THC), cerebral organoids exhibited reduced neuronal maturation, downregulation of cannabinoid receptor type 1 (CB1) receptors, and impaired neurite outgrowth. Moreover, transient on-chip THC treatment also decreased spontaneous firing in microfluidic assembled brain organoids. This one-stop microfluidic technique enables a simple, scalable, and repeatable organoid culture method that can be used not only for human brain organoids, but also for many other human organoids including liver, kidney, retina, and tumor organoids. This technology could be widely used in modeling brain and other organ development, developmental disorders, developmental pharmacology and toxicology, and drug screening.

bioengineering↗

bioRxiv2021

Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose-response study designs.

The application of single-cell RNA sequencing (scRNAseq) for the evaluation of chemicals, drugs, and food contaminants presents the opportunity to consider cellular heterogeneity in pharmacological and toxicological responses. Current differential gene expression analysis (DGEA) methods focus primarily on two group comparisons, not multi-group dose-response study designs used in safety assessments. To benchmark DGEA methods for dose-response scRNAseq experiments, we proposed a multiplicity corrected Bayesian testing approach and compare it against 8 other methods including two frequentist fit-for-purpose tests using simulated and experimental data. Our Bayesian test method outperformed all other tests for a broad range of accuracy metrics including control of false positive error rates. Most notable, the fit-for-purpose and standard multiple group DGEA methods were superior to the two group scRNAseq methods for dose-response study designs. Collectively, our benchmarking of DGEA methods demonstrates the importance in considering study design when determining the most appropriate test methods.

genomics↗

bioRxiv2022

PROTEIN CODING VARIATION IN OUTBRED LABORATORY MOUSE STOCKS PROVIDES A MOLECULAR BASIS FOR DISTINCT RESEARCH APPLICATIONS

Outbred laboratory mice (Mus musculus) are readily available and have high fecundity, making them a popular choice for biomedical research, especially toxicological and pharmacological applications. Direct high throughput genome sequencing (HTS) of these widely used research animals is an important genetic quality control measure that ensures research reproducibility. HTS data have been used to confirm the common origin of outbred stocks and to molecularly define distinct outbred populations. But these data have also revealed unexpected population structure and homozygosity in some populations; genetic features that emerge when outbred stocks are not properly maintained. We used exome sequencing to discover and interrogate protein coding variation in a newly established population of Swiss-derived outbred stock (J:ARC) that is closely related to other, commonly used CD-1 outbred populations. We used these data to describe the genetic architecture of the J:ARC population including heterozygosity, minor allele frequency, LD decay, and we defined the novel, protein-coding sequence variation. These data reveal the expected genetic architecture for a properly maintained outbred stock and provide a basis for on-going genetic quality control. We also compared these data to protein coding variation found in a multiparent outbred stock, the Diversity Outbred (J:DO). We found that the more recently derived, multiparent outbred stock has significantly higher interindividual variability, greater overall genetic variation, higher heterozygosity, and fewer novel variants than the Swiss derived J:ARC stock. However, among the novel variants found in the J:DO stock, significantly more are predicted to be protein-damaging. That individuals from this population can tolerate a higher load of potentially damaging variants highlights the buffering effects of allelic diversity and the differing selective pressures in these stocks. While both outbred stocks offer significant individual heterozygosity, our data provide a molecular basis for their intended applications, where the J:DO are best suited for studies requiring maximum, population-level genetic diversity and power for mapping, while the J:ARC are best suited as a general-purpose outbred stock with robust fecundity, relatively low allelic diversity, and less potential for extreme phenotypic variability.

genetics↗

bioRxiv2023

The impact of molecular variants, crystallization conditions and space group on structure-ligand complexes: A case study on Bacterial Phosphotriesterase Variants and complexes

While attempting to study the 3D structure of proteins with bound ligands, one often encounters considerable difficulties. We illustrate, as an example, the bacterial enzyme phosphotriesterase and specifically examine the effects of multiple factors such as the molecular constructs, ligands used during protein expression and purification, crystallization precipitance, and space group on the visualization of molecular complexes of organophosphate ligands bound to the enzyme. We analyzed twelve crystal structures of the different phosphotriesterase constructs derived by directed evolution in both apo and holo forms (in complex with organophosphate analogs), with resolutions up to 1.38 [A]. Crystals obtained from three different crystallization conditions, crystallized in four space groups, with and without N-terminal tags, were utilized to investigate the impact of these factors on visualizing molecular complexes of ligands bound to the enzyme. The study revealed that residual tags used for protein expression can lodge in the active site and hinder ligand binding. Additionally, the space groups in which the proteins are crystallized can significantly impact the visualization of the organophosphate ligands bound to the phosphotriesterase. The study also reveals that the crystallization precipitants can compete with and even preclude ligand binding, leading to false positives or the incorrect identification of lead drug candidates, which is particularly crucial for ligands with pharmacological and toxicological contexts. Overall, this study provides valuable insights into the challenges and considerations involved in studying the 3D structure of proteins with bound ligands, highlighting the importance of careful experimental design and rigorous data analysis to ensure the accuracy and reliability of the resulting protein-ligand structures.

biochemistry↗

bioRxiv2024

Toxicokinetics for organ-on-chip devices

Organ-on-chip (OOC) devices are an emerging New Approach Method in both pharmacology and toxicology. Such devices use heterotypic combinations of human cells in a micro-fabricated device to mimic in vivo conditions and better predict organ-specific toxicological responses in humans. One drawback of these devices is that they are typically made from polydimethylsiloxane (PDMS), a polymer known to interact with hydrophobic chemicals. Due to this interaction, the actual dose experienced by cells inside OOC devices can differ strongly from the nominal dose. To account for these effects, we have developed a comprehensive toxicokinetic approach to measure and model chemical-PDMS interactions, including partitioning into and diffusion through PDMS. We use these methods to characterize PDMS interactions for ten chemicals, ranging from fluorescent dyes to persistent organic pollutants to organophosphate pesticides. We further show that these methods return physical interaction parameters that can be used to accurately predict time-dependent doses under continuous-flow conditions, as would be present in an OOC device. These results demonstrate the validity of the methods and model across geometries and flow rates.

bioengineering↗