bioRxiv - Pharmacology and Toxicology最新文献

{"title":"Enabling Transparent Toxicokinetic Modeling for Public Health Risk Assessment","authors":"Sarah E. Davidson-Fritz, Caroline L. Ring, Celia M. Schacht, Marina V. Evans, Xiaoqing Chang, Miyuki Breen, Gregory S. Honda, Elaina Kenyon, Matthew W. Linakis, Annabel Meade, Robert G. Pearce, Mark A. Sfeir, James P. Sluka, Michael J. Devito, John F. Wambaugh","doi":"10.1101/2024.08.19.608571","DOIUrl":"https://doi.org/10.1101/2024.08.19.608571","url":null,"abstract":"Toxicokinetics describes the absorption, distribution, metabolism, and elimination of chemicals by the body. Predictions from toxicokinetic models provide key information for chemical risk assessment. Traditionally, these predictions extrapolate from experimental animal species data (for example, in rats) to humans. More recently, toxicokinetics has been used for extrapolation from in vitro new approach methods (NAMs) for toxicology to in vivo. Chemical-specific in vivo toxicokinetic data are often unavailable for the thousands of chemicals in commerce. Therefore, large amounts of in vitro data measuring chemical-specific toxicokinetics have been collected. These data enable high-throughput toxicokinetic or HTTK modeling. The httk R package provides a library of chemical-specific data from peer-reviewed HTTK studies. httk further provides a suite of tools for parameterizing and evaluating toxicokinetic models. httk uses the open-source language MCSim to describe models for compartmental and physiologically based toxicokinetics (PBTK), MCSim can convert the model descriptions into a high-speed C code script. New models are integrated into httk using the open-source package development functionality in R, a model documentation file (R script), and the HTTK model description code file (C script). In addition to HTTK models, httk provides a series of functionalities such as unit conversion, model parameterization, Monte Carlo simulations for uncertainty propagation and biological variability, in vivo-derived data for evaluating model predictions, and other model utility functions. Here, we describe in detail how to add new HTTK models to httk and take advantage of the pre-existing data and functionality in the package. As a demonstration, we describe the integration of the gas inhalation PBTK model into httk. Modern modeling approaches, as exemplified by httk, allow for clear communication, reproducibility, and public scrutiny. The intention of httk is to provide a transparent, open-source tool for toxicokinetics, bioinformatics, and public health risk assessment.","PeriodicalId":501518,"journal":{"name":"bioRxiv - Pharmacology and Toxicology","volume":"32 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142184293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of Antiviral Drug Candidates Against Monkeypox DNA Polymerase and Profilin-like Protein A42R Utilizing an In-Silico Approach","authors":"Muhammad Amjid, Muhammad Maroof Khan, Stephen F Pastore, John B Vincent, Tahir Muhammad","doi":"10.1101/2024.08.15.608157","DOIUrl":"https://doi.org/10.1101/2024.08.15.608157","url":null,"abstract":"Monkeypox virus (MPXV) is emerging as a major concern in the field of infectious diseases. Current treatments are limited, highlighting the need for new therapeutic options. The use of computational methods, such as molecular docking and molecular dynamic (MD) simulations, is a valuable approach in identifying potential compounds that can target specific proteins of the virus, like the DNA polymerase and profilin-like protein A42R in this case, with the aim of controlling the disease. Our study focused on screening various libraries of compounds for predicted binding to MPXV DPol and A42R proteins, with the top-performing molecules identified based on their docking scores. Among these, Dorsilurin K and Mangostin in complex with DPol , whereas [2-oxo-2-[3-(3,4,5,6-tetrahydro-2H-azepin-7-ylsulfamoyl)anilino]ethyl] 3,5-dimethylbenzoate and N-[4-[2-[4-(4-methylphenyl)sulfonylpiperazin-1-yl]-2-oxoethoxy]phenyl]furan-2-carboxamide in complex with A42R stand out with notably high docking scores, suggesting they may have a good affinity for binding to the DPol and A42R proteins of MPXV respectively. MD simulations confirmed the stability of these ligand-protein complexes followed by evaluation of the ADMET and oral bioavailability analysis. However, it is important that computational methods can suggest promising candidates, in vitro and eventually in vivo studies are essential to validate these therapeutic candidates. Further studies on these compounds will provide insights into their efficacy, safety, and potential side effects. In conclusion, this study offers promising avenues for developing potential treatments for Monkeypox. If the identified compounds prove effective in further studies, it could be a significant breakthrough in managing this zoonotic disease.","PeriodicalId":501518,"journal":{"name":"bioRxiv - Pharmacology and Toxicology","volume":"66 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142184278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impacts of Disinfection Methods in a Granular Activated Carbon (GAC) Treatment System on Disinfected Drinking Water Toxicity and Antibiotic Resistance Induction Potential","authors":"Yinmei Feng, Stephanie Lau, William Mitch, Caroline Russell, Greg Pope, April Z Gu","doi":"10.1101/2024.08.19.608195","DOIUrl":"https://doi.org/10.1101/2024.08.19.608195","url":null,"abstract":"Granular activated carbon (GAC) treatment followed by chlorination (GAC/Cl2) and chlorination followed by chloramination (Cl2/NH2Cl) are two methods utilized by drinking water treatment facilities to mitigate the formation of disinfection byproducts (DBPs) in treated water. However, the effectiveness of these methods in reducing the overall toxicity of drinking water, driven by DBPs, remains largely unknown. In this study, we evaluate the total toxicity of water samples from a pilot-scale GAC system with post-chlorination (GAC/Cl2), and occasionally pre-chlorination upstream of GAC (Cl2/GAC/Cl2), compared to water treated by chlorination followed by chloramination (Cl2/NH2Cl). The research was conducted at various bromide and iodide levels and across three GAC bed volumes. To assess DNA stress and oxidative stress in water extracts, we employed the yeast toxicogenomic assay and human cell RT-qPCR assay, along with the DBP analysis from in our previous study. Our results indicated that under environmental halogen conditions, GAC/Cl2 typically reduces both genotoxicity and oxidative stress in treated water more effectively than Cl2/NH2Cl and Cl2 treatment. However, Cl2/GAC/Cl2 does not consistently lower toxicity compared to GAC/Cl2. Notably, under high halogen conditions, Cl2/GAC/Cl2 fails to reduce genotoxicity and oxidative stress compared to samples without GAC treatment. Correlation analysis suggested that iodinated DBPs (I-DBPs) and nitrogenous DBPs (N-DBPs) were particularly associated with increased DNA stress and oxidative stress, indicating these classes of DBPs as significant contributors to the observed toxicity. While neither of these two categories of DBPs are regulated by the EPA, it appears that unregulated and unidentified DBPs significantly contribute to the genotoxicity and oxidative stress in drinking water. This research highlights the complex dynamics of water treatment processes and underscores the critical impact of unregulated DBPs on water toxicity.","PeriodicalId":501518,"journal":{"name":"bioRxiv - Pharmacology and Toxicology","volume":"454 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142184277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimising experimental designs for model selection of ion channel drug binding mechanisms","authors":"Frankie Patten-Elliott, Chon Lok R Lei, Simon P Preston, Richard D Wilkinson, Gary R Mirams","doi":"10.1101/2024.08.20.608856","DOIUrl":"https://doi.org/10.1101/2024.08.20.608856","url":null,"abstract":"The rapid delayed rectifier current carried by the human Ether-à-go-go-Related Gene (hERG) channel is susceptible to drug-induced reduction which can lead to an increased risk of cardiac arrhythmia. Establishing the mechanism by which a specific drug compound binds to hERG can help to reduce uncertainty when quantifying pro-arrhythmic risk. In this study, we introduce a methodology for optimising experimental voltage protocols to produce data that enable different proposed models for the drug-binding mechanism to be distinguished. We demonstrate the performance of this methodology via a synthetic data study. If the underlying model of hERG current is known exactly, then the optimised protocols generated show noticeable improvements in our ability to select the true model when compared to a simple protocol used in previous studies. However, if the model is not known exactly, and we assume a discrepancy between the data-generating hERG model and the hERG model used in fitting the models, then the optimised protocols become less effective in determining the 'true' binding dynamics. While the introduced methodology shows promise, we must be careful to ensure that, if applied in a real data study, we have a well-calibrated model of hERG current gating.","PeriodicalId":501518,"journal":{"name":"bioRxiv - Pharmacology and Toxicology","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142184296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ER stress-induced TREM2 downregulation exacerbates platelet activation and myocardial infarction in patients with coronary artery disease","authors":"Xiaowen Wu, Guanxing Pan, Lin Chang, Yulong Zhang, Yangyang Liu, Wei Zhang, Yifan Guo, Ge Zhang, Haoxuan Zhong, Zhiyong Qi, Jianjun Zhang, Ruyi Xue, She Chen, Hu Hu, Jianzeng Dong, Si Zhang, Zhongren Ding","doi":"10.1101/2024.08.20.608887","DOIUrl":"https://doi.org/10.1101/2024.08.20.608887","url":null,"abstract":"Coronary artery disease (CAD) is characterized by the chronic immune-inflammation, excessive endoplasmic reticulum (ER) stress, and platelet hyperactivity; however, whether there is a signaling hub linking these events remains unclear. Here, we identified that triggering receptor expressed on myeloid cells 2 (TREM2), an important pattern recognition receptor of the innate immune system, may serve as one such hub. We found that platelets expressed TREM2 and platelets from CAD patients had decreased TREM2 expression compared to healthy subjects. Decreased TREM2 is associated with platelet hyperactivity in CAD patients. This decrease could be due to excessive ER stress, which downregulated TREM2 through the CHOP-C/EBPα axis. Loss of TREM2 not only enhanced platelet activation in response to ADP, collagen, and collagen-related peptide (CRP), but also amplified the platelet inflammatory response. Loss of TREM2 exacerbated mouse mesenteric arterial thrombosis and aggravated experimental myocardial infarction (MI). Moreover, a TREM2-activating antibody inhibited platelet activation, alleviated arterial thrombosis and pulmonary embolism. In addition, TREM2-activating antibody exhibited cardioprotective roles against experimental MI and reduced the inflammatory burden. Mechanistically, TREM2/DAP12/SHIP1 axis negatively regulated platelet activation through reducing PIP3 levels and inhibiting Akt phosphorylation. We also provided evidence supporting sphingosine-1-phospage (S1P) as a physiological agonist of TREM2. In summary, we find that TREM2 connects chronic immune-inflammation, excessive ER stress, and platelet hyperactivity in CAD patients. Downregulating TREM2 by ER stress exacerbates platelet activation and amplifies inflammation response in patients with CAD. TREM2-activating antibodies may have therapeutic potential for CAD patients.","PeriodicalId":501518,"journal":{"name":"bioRxiv - Pharmacology and Toxicology","volume":"34 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142184279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Title: 4-week GLP immunotoxicity assessment of lactoferrin alpha produced by Komagataella phaffii in Sprague Dawley rats","authors":"Ross Peterson, Robert B Crawford, Lance K Blevins, Norbert E Kaminski, Anthony J Clark, Carrie-Anne Malinczak","doi":"10.1101/2024.08.16.608335","DOIUrl":"https://doi.org/10.1101/2024.08.16.608335","url":null,"abstract":"Oral toxicity and toxicokinetic properties of human lactoferrin (LF) alpha produced in Komagataella Phaffii (effera™) were investigated in adult Sprague-Dawley rats over a 28-day period under good laboratory practice conditions. Main study dosing used groups of 10 rats/sex/dose, and a secondary study evaluating toxicokinetic parameters used 6 rats/sex/dose. The vehicle control group received sodium citrate buffer, test groups received daily doses of 200, 600, and 2000 mg of effera™ per kg body weight, and the comparative control group received 2000 mg bovine LF (bLF)/kg body weight per day. T-cell dependent antibody response against keyhole limpet hemocyanin and immunophenotyping of the spleen were performed as measures of immunotoxicity. Clinical observations, body weight, hematology, coagulation, clinical chemistry, urinalysis, immunotoxicity, gross necropsy, and histopathology were assessed. Toxicokinetic parameters were analyzed as an indication of LF bioavailability, and anti-LF antibody assays were conducted to detect antibodies produced against LF to measure immunogenicity. No treatment related toxicologically significant changes were observed. Based on the absence of toxicologically relevant changes, effera™ is well tolerated in rats at doses up to 2000 mg rhLF/kg/day, an amount ~400 times that of the estimated daily intake at the 90th percentile proposed for human adult use.","PeriodicalId":501518,"journal":{"name":"bioRxiv - Pharmacology and Toxicology","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142223915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The clinical antiprotozoal drug halofuginone promotes weight loss by elevating GDF15 and FGF21","authors":"Suowen Xu, Zhenghong Liu, Tian Tian, Wenqi Zhao, Zhihua Wang, Monan Liu, Mengyun Xu, Fanshun Zhang, Zhidan Zhang, Meijie Chen, Yanjun Yin, Meiming Su, Wenhao Pan, Shiyong Liu, Min-dian Li, Peter Little, Danielle Danielle Kamato, Song-yang Zhang, Dongdong Wang, Stefan Offermanns, John Speakman, Jianping Weng","doi":"10.1101/2024.08.18.608423","DOIUrl":"https://doi.org/10.1101/2024.08.18.608423","url":null,"abstract":"Obesity is a debilitating disease with increasing worldwide prevalence. Despite its high prevalence, specific pharmacologic intervention for obesity is challenging. Here, we report that halofuginone, an FDA-approved anti-scleroderma and anti-protozoal drug, is a promising anti-obesity agent in rodent models. Halofuginone suppressed food intake, increased energy expenditure, and resulted in weight loss in preclinical diet-induced obese mouse models, while also decreasing insulin resistance and hepatic steatosis. By combining genetic and pharmacological tools with transcriptomics, we identified that halofuginone increases FGF21 and GDF15 levels via ATF4. Using knockout mice, we show these hormones are both necessary for its anti-obesity effects. Thus, our study first reports the beneficial metabolic effects of halofuginone and underscores its utility to treat obesity and its associated metabolic complications.","PeriodicalId":501518,"journal":{"name":"bioRxiv - Pharmacology and Toxicology","volume":"56 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142184297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tanshinone IIA potentiates the therapeutic efficacy of glucocorticoid in lipopolysaccharide-treated HEI-OC1 cells through modulation of Foxp3/Nrf2 signaling pathway","authors":"Jie Li, Xiaoyan Zhu, Shiming Ye, Qi Dong, Jie Hou, Jing Liu, Wandong She","doi":"10.1101/2024.08.19.608552","DOIUrl":"https://doi.org/10.1101/2024.08.19.608552","url":null,"abstract":"Glucocorticoids (GC) are commonly used to treat sudden sensorineural hearing loss (SSNHL) , although some patients show resistance to this therapeutic approach. Clinical studies demonstrate the efficacy of tanshinone IIA (TA) in combination with GC for managing various human ailments. However, it remains unclear whether TA can mitigate GC resistance in SSNHL.\u0000Aim of the study: Our aim is to elucidate the role of NRF2-induced transcriptional regulation of HDAC2 in influencing GC resistance and investigate the involvement of TA-related molecular pathways in GC resistance.\u0000Materials and Methods: HEI-OC1 cells are treated with lipopolysaccharide (LPS) to establish an in vitro model for SSNHL. Subsequently, the cells are treated with dexamethasone (DXE) or DXE+TA. RT-qPCR and western blot analyses are employed to measure mRNA and protein levels of Forkhead box P3 (FOXP3), nuclear factor erythroid 2-related factor 2 (NRF2), and histone deacetylase 2 (HDAC2). Cell Counting Kit-8 (CCK-8) and 5-ethynyl-2-deoxyuridine (EdU) assays are conducted to assess cell proliferation. Flow cytometry analysis is performed for apoptosis evaluation. Mechanistic studies involve Chromatin immunoprecipitation (ChIP), luciferase reporter, and DNA pull-down assays.\u0000Results: Treatment with TA+DEX significantly enhances proliferation and suppresses apoptosis in LPS-treated HEI OC1 cells. TA upregulates HDAC2 expression by activating NRF2-mediated transcription of HDAC2, with the NRF2-HDAC2 binding site located at bases 419-429 (ATGACACTCCA) in the promoter sequence of HDAC2. Furthermore, TA upregulates FOXP3 expression to activate NRF2 transcription, with the predicted FOXP3-binding site located at bases 864-870 (GCAAACA) in the promoter sequence of NRF2.\u0000Conclusion: This study's findings suggest that TA enhances the therapeutic effects of GC on proliferation and apoptosis in HEI OC1 cells by up-regulating FOXP3/Nrf2 expression. These results indicate that TA may be promising in ameliorating GC resistance in patients with SSNHL.","PeriodicalId":501518,"journal":{"name":"bioRxiv - Pharmacology and Toxicology","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142184294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Endoplasmic reticulum stress inhibition preserves mitochondrial function and cell survival during early onset of isoniazid-induced oxidative stress","authors":"Truong Thi My Nhung, Nguyen Ky Phat, Trinh Tam Anh, Tran Diem Nghi, Nguyen Quang Thu, Ara Lee, Nguyen Tran Nam Tien, Nguyen Ky Anh, Kimoon Kim, Duc Ninh Nguyen, Dong Hyun Kim, Sang Ki Park, Nguyen Phuoc Long","doi":"10.1101/2024.08.12.607527","DOIUrl":"https://doi.org/10.1101/2024.08.12.607527","url":null,"abstract":"A comprehensive understanding of isoniazid (INH)-mediated hepatotoxic effects is essential for developing strategies to predict and prevent severe liver toxicity in tuberculosis treatment. Our study utilized multi-omics profiling to investigate the toxic effects of INH, revealing significant involvement of endoplasmic reticulum (ER) stress, mitochondrial impairment, redox imbalance, and altered metabolism. Followed-up mechanistic studies revealed that INH triggered the generation of cytosolic reactive oxygen species (ROS) and the activation of the Nrf2 signaling pathway prior to mitochondrial ROS accumulation. Subsequently, INH disrupted mitochondrial function by impairing respiratory complexes I-IV and caused mitochondrial membrane proton leaks without affecting ATP synthase activity, together leading to mitochondrial depolarization and reduced ATP production. These disturbances enhanced mitochondrial fission and mitophagy. While much attention has been given to mitochondrial dysfunction and oxidative stress in INH-induced hepatotoxicity, our findings highlight the potential of inhibiting ER stress during early INH exposure to mitigate cytosolic and mitochondrial oxidative stress. We further revealed the critical role of Nrf2 signaling in protecting liver cells under INH-induced oxidative stress by maintaining redox homeostasis and enabling metabolic reprogramming via regulating the expression of antioxidant genes and cellular lipid abundance. We also identified other antioxidant pathways (e.g., selenocompound metabolism, HIF-1 signaling pathway, and pentose phosphate pathway) as potential alternative mechanisms besides Nrf2 signaling in response to INH-induced oxidative stress. In conclusion, our research emphasizes the importance of ER stress, redox imbalance, metabolic changes, and mitochondrial dysfunction underlying INH-induced hepatotoxicity.","PeriodicalId":501518,"journal":{"name":"bioRxiv - Pharmacology and Toxicology","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142184298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Novel Computational Machine Learning Pipeline to Quantify Similarities in Three-Dimensional Protein Structures","authors":"Shreyas U Hirway, Xiao Xu, Fan Fan","doi":"10.1101/2024.08.14.607969","DOIUrl":"https://doi.org/10.1101/2024.08.14.607969","url":null,"abstract":"Animal models are widely used during drug development. The selection of suitable animal model relies on various factors such as target biology, animal resource availability and legacy species. It is imperative that the selected animal species exhibit the highest resemblance to human, in terms of target biology as well as the similarity in the target protein. The current practice to address cross-species protein similarity relies on pair wise sequence comparison using protein sequences, instead of the biologically relevant 3-dimensional (3D) structure of proteins. We developed a novel quantitative machine learning pipeline using 3D structure-based feature data from the Protein Data Bank, nominal data from UNIPROT and bioactivity data from ChEMBL, all of which were matched for human and animal data. Using the XGBoost regression model, similarity scores between targets were calculated and based on these scores, the best animal species for a target was identified. For real-world application, targets from an alternative source, i.e., AlphaFold, were tested using the model, and the animal species that had the most similar protein to the human counterparts were predicted. These targets were then grouped based on their associated phenotype such that the pipeline could predict an optimal animal species.","PeriodicalId":501518,"journal":{"name":"bioRxiv - Pharmacology and Toxicology","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142184299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}