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Borghese MM, Huang R, MacPherson S, Gaudreau E, Gagné S, Ashley-Martin J, Fisher M, Booij L, Bouchard MF, Arbuckle TE. A descriptive analysis of first trimester urinary concentrations of 14 bisphenol analogues in the MIREC Canadian pregnancy cohort. Int J Hyg Environ Health 2023; 253:114225. [PMID: 37542835 DOI: 10.1016/j.ijheh.2023.114225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/14/2023] [Accepted: 07/22/2023] [Indexed: 08/07/2023]
Abstract
BACKGROUND Concern over the health effects of BPA, particularly for the developing fetus, has led to an increasing use of bisphenol analogues in industrial and consumer products, which may be as hormonally active as BPA. Biomonitoring data for many bisphenol analogues, especially in pregnant populations, are limited. METHODS We measured concentrations of 14 bisphenol analogues in 1st trimester urine samples (n = 1851) from the Maternal-Infant Research on Environmental Chemicals (MIREC) Canadian pregnancy cohort (2008-2011). We examined patterns of exposure according to sociodemographic and sampling characteristics as well as occupation and frequency of consumption of canned fish within the previous 3 months. RESULTS BPA was detected in 89% of participants with a specific gravity standardized geometric mean concentration of 0.990 μg/L. Biphenol 4,4' (BP 4,4'), 4,4'-dihydroxydiphenyl ether (DHDPE), and bisphenol E (BPE) were detected in >97% of participants. Bisphenol F (BPF) and bisphenol S (BPS) were detected in >60% of participants. Specific gravity standardized geometric mean concentrations of these 5 compounds ranged from 0.024 to 0.564 μg/L. Nine bisphenol analogues were detected in <9% of participants. Concentrations of BP 4,4', DHDPE, and BPE were higher in younger women and those with higher pre-pregnancy BMI, lower household income, lower education, and among smokers. We found a similar pattern of differences in BPF for age, education, and smoking status while BPS similarly differed across categories of pre-pregnancy BMI. Participants who were unemployed or working in the service industry had higher molar sum of 7 bisphenol analogues than those working in healthcare, education, or an office setting. Canned fish consumption was not related to bisphenol analogue concentrations. CONCLUSION BP 4,4', DHDPE, BPE, BPF, and BPS were highly detected in 1st trimester urine samples in this large pan-Canadian pregnancy cohort. This suggests widespread exposure to these analogues around 2008-2011 and warrants further investigation into associations with health outcomes.
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Liu F, Patt A, Chen C, Huang R, Xu Y, Mathé EA, Zhu Q. Exploring NCATS In-House Biomedical Data for Evidence-based Drug Repurposing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.21.550045. [PMID: 37546930 PMCID: PMC10401966 DOI: 10.1101/2023.07.21.550045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Drug repurposing is a strategy for identifying new uses of approved or investigational drugs that are outside the scope of the original medical indication. Even though many repurposed drugs have been found serendipitously in the past, the increasing availability of large volumes of biomedical data has enabled more systemic, data-driven approaches for drug candidate identification. At National Center of Advancing Translational Sciences (NCATS), we invent new methods to generate new data and information publicly available to spur innovation and scientific discovery. In this study, we aimed to explore and demonstrate biomedical data generated and collected via two NCATS research programs, the Toxicology in the 21st Century program (Tox21) and the Biomedical Data Translator (Translator) for the application of drug repurposing. These two programs provide complementary types of biomedical data from uncovering underlying biological mechanisms with bioassay screening data from Tox21 for chemical clustering, to enrich clustered chemicals with scientific evidence mined from the Translator towards drug repurposing. 129 chemical clusters have been generated and three of them have been further investigated for drug repurposing candidate identification, which is detailed as case studies.
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Yasgar A, Bougie D, Eastman RT, Huang R, Itkin M, Kouznetsova J, Lynch C, McKnight C, Miller M, Ngan DK, Peryea T, Shah P, Shinn P, Xia M, Xu X, Zakharov AV, Simeonov A. Quantitative Bioactivity Signatures of Dietary Supplements and Natural Products. ACS Pharmacol Transl Sci 2023; 6:683-701. [PMID: 37200814 PMCID: PMC10186358 DOI: 10.1021/acsptsci.2c00194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Indexed: 05/20/2023]
Abstract
Dietary supplements and natural products are often marketed as safe and effective alternatives to conventional drugs, but their safety and efficacy are not well regulated. To address the lack of scientific data in these areas, we assembled a collection of Dietary Supplements and Natural Products (DSNP), as well as Traditional Chinese Medicinal (TCM) plant extracts. These collections were then profiled in a series of in vitro high-throughput screening assays, including a liver cytochrome p450 enzyme panel, CAR/PXR signaling pathways, and P-glycoprotein (P-gp) transporter assay activities. This pipeline facilitated the interrogation of natural product-drug interaction (NaPDI) through prominent metabolizing pathways. In addition, we compared the activity profiles of the DSNP/TCM substances with those of an approved drug collection (the NCATS Pharmaceutical Collection or NPC). Many of the approved drugs have well-annotated mechanisms of action (MOAs), while the MOAs for most of the DSNP and TCM samples remain unknown. Based on the premise that compounds with similar activity profiles tend to share similar targets or MOA, we clustered the library activity profiles to identify overlap with the NPC to predict the MOAs of the DSNP/TCM substances. Our results suggest that many of these substances may have significant bioactivity and potential toxicity, and they provide a starting point for further research on their clinical relevance.
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Patlewicz G, Paul-Friedman K, Houck K, Zhang L, Huang R, Xia M, Brown J, Simmons SO. Evaluating the utility of a high throughput thiol-containing fluorescent probe to screen for reactivity: A case study with the Tox21 library. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 26:10.1016/j.comtox.2023.100271. [PMID: 37388277 PMCID: PMC10304587 DOI: 10.1016/j.comtox.2023.100271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
High-throughput screening (HTS) assays for bioactivity in the Tox21 program aim to evaluate an array of different biological targets and pathways, but a significant barrier to interpretation of these data is the lack of high-throughput screening (HTS) assays intended to identify non-specific reactive chemicals. This is an important aspect for prioritising chemicals to test in specific assays, identifying promiscuous chemicals based on their reactivity, as well as addressing hazards such as skin sensitisation which are not necessarily initiated by a receptor-mediated effect but act through a non-specific mechanism. Herein, a fluorescence-based HTS assay that allows the identification of thiol-reactive compounds was used to screen 7,872 unique chemicals in the Tox21 10K chemical library. Active chemicals were compared with profiling outcomes using structural alerts encoding electrophilic information. Random Forest classification models based on chemical fingerprints were developed to predict assay outcomes and evaluated through 10-fold stratified cross validation (CV). The mean CV Balanced Accuracy of the validation set was 0.648. The model developed shows promise as a tool to screen untested chemicals for their potential electrophilic reactivity based solely on chemical structural features.
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Xu T, Li S, Li AJ, Zhao J, Sakamuru S, Huang W, Xia M, Huang R. Identification of Potent and Selective Acetylcholinesterase/Butyrylcholinesterase Inhibitors by Virtual Screening. J Chem Inf Model 2023; 63:2321-2330. [PMID: 37011147 PMCID: PMC10688023 DOI: 10.1021/acs.jcim.3c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) play important roles in human neurodegenerative disorders such as Alzheimer's disease. In this study, machine learning methods were applied to develop quantitative structure-activity relationship models for the prediction of novel AChE and BChE inhibitors based on data from quantitative high-throughput screening assays. The models were used to virtually screen an in-house collection of ∼360K compounds. The optimal models achieved good performance with area under the receiver operating characteristic curve values ranging from 0.83 ± 0.03 to 0.87 ± 0.01 for the prediction of AChE/BChE inhibition activity and selectivity. Experimental validation showed that the best-performing models increased the assay hit rate by several folds. We identified 88 novel AChE and 126 novel BChE inhibitors, 25% (AChE) and 53% (BChE) of which showed potent inhibitory effects (IC50 < 5 μM). In addition, structure-activity relationship analysis of the BChE inhibitors revealed scaffolds for chemistry design and optimization. In conclusion, machine learning models were shown to efficiently identify potent and selective inhibitors against AChE and BChE and novel structural series for further design and development of potential therapeutics against neurodegenerative disorders.
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Li Z, Liu J, Dong F, Chang N, Huang R, Xia M, Patterson TA, Hong H. Three-Dimensional Structural Insights Have Revealed the Distinct Binding Interactions of Agonists, Partial Agonists, and Antagonists with the µ Opioid Receptor. Int J Mol Sci 2023; 24:ijms24087042. [PMID: 37108204 PMCID: PMC10138646 DOI: 10.3390/ijms24087042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/09/2023] [Accepted: 04/09/2023] [Indexed: 04/29/2023] Open
Abstract
The United States is experiencing the most profound and devastating opioid crisis in history, with the number of deaths involving opioids, including prescription and illegal opioids, continuing to climb over the past two decades. This severe public health issue is difficult to combat as opioids remain a crucial treatment for pain, and at the same time, they are also highly addictive. Opioids act on the opioid receptor, which in turn activates its downstream signaling pathway that eventually leads to an analgesic effect. Among the four types of opioid receptors, the µ subtype is primarily responsible for the analgesic cascade. This review describes available 3D structures of the µ opioid receptor in the protein data bank and provides structural insights for the binding of agonists and antagonists to the receptor. Comparative analysis on the atomic details of the binding site in these structures was conducted and distinct binding interactions for agonists, partial agonists, and antagonists were observed. The findings in this article deepen our understanding of the ligand binding activity and shed some light on the development of novel opioid analgesics which may improve the risk benefit balance of existing opioids.
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Mizrahi I, Shah P, Huang R, Nagamine T, Gozun M, Lee D, Shimabuku L, Khan Z, Lum C, Brodsky M. Echocardiographic Findings in Patients with Methamphetamine Cardiomyopathy. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Romero P, Huang R, Jiménez E, Palma-Hidalgo JM, Ungerfeld EM, Popova M, Morgavi DP, Belanche A, Yáñez-Ruiz DR. Evaluating the effect of phenolic compounds as hydrogen acceptors when ruminal methanogenesis is inhibited in vitro – Part 2. Dairy goats. Animal 2023; 17:100789. [PMID: 37087998 DOI: 10.1016/j.animal.2023.100789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
Most mitigation strategies to reduce enteric methane (CH4) production in the rumen induce an excess of rumen dihydrogen (H2) that is expelled and consequently not redirected to the synthesis of metabolites that can be utilised by the ruminant. We hypothesised that phenolic compounds can be potential H2 acceptors when added to the diet, as they can be degraded to compounds that may be beneficial for the animal, using part of the H2 available when ruminal methanogenesis is inhibited. We performed four in vitro incubation experiments using rumen inoculum from Murciano-Granadina adult goats: Experiment 1 examined the inhibitory potential of Asparagopsis taxiformis (AT) at different concentrations (0, 1, 2, 3, 4 and 5% of the substrate on a DM basis) in 24 h incubations; Experiment 2 investigated the effect of a wide range of phenolic compounds (phenol, catechol, resorcinol, hydroquinone, pyrogallol, phloroglucinol, gallic acid and formic acid) at different doses (0, 2, 4, and 6 mM) on rumen fermentation for 24 h; Experiment 3 evaluated the combined effect of each phenolic compound at 6 mM with AT at 2% DM in sequential batch cultures for 5 days; and Experiment 4 examined the dose-response effect of phloroglucinol at different concentrations (0, 6, 16, 26 and 36 mM) combined with AT in sequential batch cultures for 5 days. Results from Experiment 1 confirmed that AT at 2% DM substantially inhibited CH4 production while significantly increasing H2 accumulation and decreasing the acetate:propionate ratio. Results from Experiment 2 showed that phenolic compounds did not negatively affect rumen fermentation at any dose. In Experiment 3, each phenolic compound at 6 mM combined with AT at 2% DM inhibited CH4 production. Phloroglucinol numerically decreased H2 accumulation and significantly increased total gas production (TGP), volatile fatty acid (VFA) production and the acetate:propionate ratio. In Experiment 4, phloroglucinol at increasing doses supplemented with AT at 2% DM significantly decreased H2 accumulation and the abundances of archaea, protozoa and fungi abundances, and increased TGP, total VFA production and the acetate:propionate ratio in a dose-dependent way. In conclusion, combined treatment with AT and phloroglucinol was successful to mitigate CH4 production while preventing the accumulation of H2, leading to an increase in acetate and total VFA production and therefore an improvement in rumen fermentation in goats.
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Tapan U, Raskina K, Huang R, Schrock A, Sands J, Oxnard G, Tukachinsky H. PPD02.01 Comprehensive Genomic Profiling (CGP) for Diagnostic Clarity in Pulmonary Large-Cell Neuroendocrine Carcinoma (LCNEC). J Thorac Oncol 2023. [DOI: 10.1016/j.jtho.2022.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Huang R, Romero P, Belanche A, Ungerfeld E, Yanez-Ruiz D, Morgavi D, Popova M. Evaluating the effect of phenolic compounds as hydrogen acceptors when ruminal methanogenesis is inhibited in vitro – Part 1. Dairy cows. Animal 2023; 17:100788. [PMID: 37087996 DOI: 10.1016/j.animal.2023.100788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Abstract
Some antimethanogenic feed additives for ruminants promote rumen dihydrogen (H2) accumulation potentially affecting the optimal fermentation of diets. We hypothesised that combining an H2 acceptor with a methanogenesis inhibitor can decrease rumen H2 build-up and improve the production of metabolites that can be useful for the host ruminant. We performed three in vitro incubation experiments using rumen fluid from lactating Holstein cows: Experiment 1 examined the effect of phenolic compounds (phenol, catechol, resorcinol, hydroquinone, pyrogallol, phloroglucinol, and gallic acid) at 0, 2, 4, and 6 mM on ruminal fermentation for 24 h; Experiment 2 examined the combined effect of each phenolic compound from Experiment 1 at 6 mM with two different methanogenesis inhibitors (Asparagopsis taxiformis or 2-bromoethanesulfonate (BES)) for 24 h incubation; Experiment 3 examined the effect of a selected phenolic compound, phloroglucinol, with or without BES over a longer term using sequential incubations for seven days. Results from Experiment 1 showed that phenolic compounds, independently of the dose, did not negatively affect rumen fermentation, whereas results from Experiment 2 showed that phenolic compounds did not decrease H2 accumulation or modify CH4 production when methanogenesis was decreased by up to 75% by inhibitors. In Experiment 3, after three sequential incubations, phloroglucinol combined with BES decreased H2 accumulation by 72% and further inhibited CH4 production, compared to BES alone. Interestingly, supplementation with phloroglucinol (alone or in combination with the CH4 inhibitor) decreased CH4 production by 99% and the abundance of methanogenic archaea, with just a nominal increase in H2 accumulation. Supplementation of phloroglucinol also increased total volatile fatty acid (VFA), acetate, butyrate, and total gas production, and decreased ammonia concentration. This study indicates that some phenolic compounds, particularly phloroglucinol, which are naturally found in plants, could improve VFA production, decrease H2 accumulation and synergistically decrease CH4 production in the presence of antimethanogenic compounds.
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Dranchak PK, Oliphant E, Queme B, Lamy L, Wang Y, Huang R, Xia M, Tao D, Inglese J. In vivo quantitative high-throughput screening for drug discovery and comparative toxicology. Dis Model Mech 2023; 16:dmm049863. [PMID: 36786055 PMCID: PMC10067442 DOI: 10.1242/dmm.049863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 02/01/2023] [Indexed: 02/15/2023] Open
Abstract
Quantitative high-throughput screening (qHTS) pharmacologically evaluates chemical libraries for therapeutic uses, toxicological risk and, increasingly, for academic probe discovery. Phenotypic high-throughput screening assays interrogate molecular pathways, often relying on cell culture systems, historically less focused on multicellular organisms. Caenorhabditis elegans has served as a eukaryotic model organism for human biology by virtue of genetic conservation and experimental tractability. Here, a paradigm enabling C. elegans qHTS using 384-well microtiter plate laser-scanning cytometry is described, in which GFP-expressing organisms revealing phenotype-modifying structure-activity relationships guide subsequent life-stage and proteomic analyses, and Escherichia coli bacterial ghosts, a non-replicating nutrient source, allow compound exposures over two life cycles, mitigating bacterial overgrowth complications. We demonstrate the method with libraries of anti-infective agents, or substances of toxicological concern. Each was tested in seven-point titration to assess the feasibility of nematode-based in vivo qHTS, and examples of follow-up strategies were provided to study organism-based chemotype selectivity and subsequent network perturbations with a physiological impact. We anticipate that this qHTS approach will enable analysis of C. elegans orthologous phenotypes of human pathologies to facilitate drug library profiling for a range of therapeutic indications.
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Huang R, He WJ, Zhang PP, Wang DQ. [Exploring the treatment of sepsis-associated acute lung injury with Liangge Powder via ERK1/2 and PI3K/AKT pathways: based on network pharmacology and whole animal experimentation]. ZHONGHUA LAO DONG WEI SHENG ZHI YE BING ZA ZHI = ZHONGHUA LAODONG WEISHENG ZHIYEBING ZAZHI = CHINESE JOURNAL OF INDUSTRIAL HYGIENE AND OCCUPATIONAL DISEASES 2023; 41:94-103. [PMID: 36882272 DOI: 10.3760/cma.j.cn121094-20220408-00188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Objective: To investigate the therapeutic effect and mechanism of Liangge Powder against sepsis-induced acute lung injury (ALI) . Methods: From April to December 2021, the key components of Liangge Powder and its targets against sepsis-induced ALI were analyzed by network pharmacology, and to enrich for relevant signaling pathways. A total of 90 male Sprague-Dawley rats were randomly assigned to sham-operated group, sepsis-induced ALI model group (model group), Liangge Powder low, medium and high dose group, ten rats in the sham-operated group and 20 rats in each of the remaining four groups. Sepsis-induced ALI model was established by cecal ligation and puncture. Sham-operated group: gavage with 2 ml saline and no surgical treatment. Model group: surgery was performed and 2 ml saline was gavaged. Liangge Powder low, medium and high dose groups: surgery and gavage of Liangge Powder 3.9, 7.8 and 15.6 g/kg, respectively. To measure the wet/dry mass ratio of rats lung tissue and evaluate the permeability of alveolar capillary barrier. Lung tissue were stained with hematoxylin and eosin for histomorphological analysis. The levels of tumor necrosis factor-alpha (TNF-α), interleukin (IL) -6 and IL-1β in bronchoalveolar lavage fluid (BALF) were measured by enzyme-linked immunosorbent assay. The relative protein expression levels of p-phosphatidylinositol 3-kinase (PI3K), p-protein kinase B (AKT), and p-ertracellular regulated protein kinases (ERK) were detected via Western blot analysis. Results: Network pharmacology analysis indicated that 177 active compounds of Liangge Powder were selected. A total of 88 potential targets of Liangge Powder on sepsis-induced ALI were identified. 354 GO terms of Liangge Powder on sepsis-induced ALI and 108 pathways were identified using GO and KEGG analysis. PI3K/AKT signaling pathway was recognized to play an important role for Liangge Powder against sepsis-induced ALI. Compared with the sham-operated group, the lung tissue wet/dry weight ratio of rats in the model group (6.35±0.95) was increased (P<0.001). HE staining showed the destruction of normal structure of lung tissue. The levels of IL-6 [ (392.36±66.83) pg/ml], IL-1β [ (137.11±26.83) pg/ml] and TNF-α [ (238.34±59.36) pg/ml] were increased in the BALF (P<0.001, =0.001, <0.001), and the expression levels of p-PI3K, p-AKT and p-ERK1/2 proteins (1.04±0.15, 0.51±0.04, 2.31±0.41) were increased in lung tissue (P=0.002, 0.003, 0.005). The lung histopathological changes were reduced in each dose group of Liangge Powder compared with the model group. Compared with the model group, the wet/dry weight ratio of lung tissue (4.29±1.26) was reduced in the Liangge Powder medium dose group (P=0.019). TNF-α level [ (147.85±39.05) pg/ml] was reduced (P=0.022), and the relative protein expression levels of p-PI3K (0.37±0.18) and p-ERK1/2 (1.36±0.07) were reduced (P=0.008, 0.017). The wet/dry weight ratio of lung tissue (4.16±0.66) was reduced in the high-dose group (P=0.003). Levels of IL-6, IL-1β and TNF-α[ (187.98±53.28) pg/ml, (92.45±25.39) pg/ml, (129.77±55.94) pg/ml] were reduced (P=0.001, 0.027, 0.018), and relative protein expression levels of p-PI3K, p-AKT and p-ERK1/2 (0.65±0.05, 0.31±0.08, 1.30±0.12) were reduced (P=0.013, 0.018, 0.015) . Conclusion: Liangge Powder has therapeutic effects in rats with sepsis-induced ALI, and the mechanism may be related to the inhibition of ERK1/2 and PI3K/AKT pathway activation in lung tissue.
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Xu T, Kabir M, Sakamuru S, Shah P, Padilha E, Ngan DK, Xia M, Xu X, Simeonov A, Huang R. Predictive Models for Human Cytochrome P450 3A7 Selective Inhibitors and Substrates. J Chem Inf Model 2023; 63:846-855. [PMID: 36719788 PMCID: PMC10664139 DOI: 10.1021/acs.jcim.2c01516] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Inappropriate use of prescription drugs is potentially more harmful in fetuses/neonates than in adults. Cytochrome P450 (CYP) 3A subfamily undergoes developmental changes in expression, such as a transition from CYP3A7 to CYP3A4 shortly after birth, which provides a potential way to distinguish medication effects on fetuses/neonates and adults. The purpose of this study was to build first-in-class predictive models for both inhibitors and substrates of CYP3A7/CYP3A4 using chemical structure analysis. Three metrics were used to evaluate model performance: area under the receiver operating characteristic curve (AUC-ROC), balanced accuracy (BA), and Matthews correlation coefficient (MCC). The performance varied for each CYP3A7/CYP3A4 inhibitor/substrate model depending on the data set type, model type, rebalancing method, and specific feature set. For the active inhibitor/substrate data set, the optimal models achieved AUC-ROC values ranging from 0.77 ± 0.01 to 0.84 ± 0.01. For the selective inhibitor/substrate data set, the optimal models achieved AUC-ROC values ranging from 0.72 ± 0.02 to 0.79 ± 0.04. The predictive power of the optimal models was validated by compounds with known potencies as CYP3A7/CYP3A4 inhibitors or substrates. In addition, we identified structural features significant for CYP3A7/CYP3A4 selective or common inhibitors and substrates. In summary, the top performing models can be further applied as a tool to rapidly evaluate the safety and efficacy of new drugs separately for fetuses/neonates and adults. The significant structural features could guide the design of new therapeutic drugs as well as aid in the optimization of existing medicine for fetuses/neonates.
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Tamalunas A, Wendt A, Springer F, Vigodski V, Huang R, Wang R, Liu Y, Rutz B, Ciotkowska A, Magistro G, Stief C, Hennenberg M. Hexane-extracted saw palmetto (Permixon®) inhibits prostate stromal cell proliferation and growth, and disrupts actin formation. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00102-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Wang R, Huang R, Liu Y, Tamalunas A, Stief C, Hennenberg M. Dihydrotestosterone reduces cholinergic contractions of bladder smooth muscle cells: Novel concepts in the pathogenesis of mixed symptoms in mixed LUTS? Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00732-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Liu Y, Wang R, Huang R, Tamalunas A, Waidelich R, Strittmatter F, Stief C, Hennenberg M. NUAK1 and -2 promote contraction, proliferation and suppression of cell death in human prostate stromal cells: Evidence from isoform-specific silencing. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00096-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Necchi A, Li R, Rose K, Davaro F, Davaro E, Spiess P, Petros G, Bratslavsky G, Jacob J, Pavlick D, Ross J, Huang R, Lin D, Danziger N, Graf R. CDH1-mutated clinically advanced urothelial bladder cancer (UBC): A genomic landscape and real-world clinical outcome study (RWCOS). Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00588-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Tamalunas A, Wendt A, Huang R, Wang R, Liu Y, Rutz B, Ciotkowska A, Magistro G, Stief C, Hennenberg M. Arf1 gef inhibitor golgicide a inhibits adrenergic and non-adrenergic prostate smooth muscle contraction. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00099-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Shi Q, Zhou YJ, Fang JG, Zhong X, Chen LZ, Hou HZ, Ma L, Feng SZ, He JW, Huang R, Wang YF, Yang Y. [Role of preoperative ultrasound-guided inferior parathyroid gland localization and new classification to assist intraoperative search and protection of parathyroid glands]. ZHONGHUA YI XUE ZA ZHI 2022; 102:3842-3848. [PMID: 36540921 DOI: 10.3760/cma.j.cn112137-20220616-01325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Objective: To investigate the role and significance of ultrasound-guided inferior parathyroid gland (IPTG) localization in searching and protecting parathyroid glands before thyroid surgery. Methods: A randomized controlled trial study was conducted. A total of 306 patients (433 cases of lateral parathyroidectomy) who underwent primary thyroidectomy and central lymph node dissection in Beijing Tongren Hosipital from March to October 2021 were enrolled. In order to locate IPTG more quickly and effectively, new IPTG classification and the definition of quadrant position were carried out. The patients were divided into the study group (n=228) and the control group (n=205). The study group underwent ultrasound-guided IPTG examination before operation and measured the distance between the IPTG and the lower pole of the thyroid and the midline of the trachea. During the operation, the IPTG was found and protected depending on the localization. The control group did not use any auxiliary preoperative positioning method. The distribution ratio of IPTG and the coincidence rate between intraoperative validation and ultrasound localization were calculated. Results: There were 306 patients enrolled in the final analysis (95 males and 211 females), with a median age of 41 years old (18-70). Type Ⅱ and Ⅲ IPTG accounted for 77.2% (176/228) of the total cases. The total coincidence rate ranged from 72.8% to 79.4% in different IPTG groups. Type Ⅲ and quadrant 2 IPTG had the highest coincidence rate [92.4% (73/79) and 92.9% (79/85), respectively]. The study group had better in situ retention rate [82.0% (187/228) vs 73.2% (150/205), χ2=4.896, P=0.027] and less implantation rate [8.8% (20/228) vs 16.1% (33/205), χ2=5.393, P=0.020] than those of the control group. The in situ retention rate were better in type Ⅲ IPTG group, compared with those of the control group [94.9% (74/78) vs 77.4% (48/62), χ2=7.898, P=0.005]. There was no permanent hypoparathyroidism in two groups and the temporary hypoparathyroidism rate was 32.0% (24/75) and 34.6% (18/52), respectively (χ2=0.095, P=0.758). Conclusion: Ultrasound-guided IPTG localization examination has important implications for searching and protecting IPTG during operation, which can significantly increase in situ retention rate of IPTG and decrease the implantation rate.
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Ye L, Ngan DK, Xu T, Liu Z, Zhao J, Sakamuru S, Zhang L, Zhao T, Xia M, Simeonov A, Huang R. Prediction of drug-induced liver injury and cardiotoxicity using chemical structure and in vitro assay data. Toxicol Appl Pharmacol 2022; 454:116250. [PMID: 36150479 PMCID: PMC9561045 DOI: 10.1016/j.taap.2022.116250] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/24/2022] [Accepted: 09/14/2022] [Indexed: 11/18/2022]
Abstract
Drug-induced liver injury (DILI) and cardiotoxicity (DICT) are major adverse effects triggered by many clinically important drugs. To provide an alternative to in vivo toxicity testing, the U.S. Tox21 consortium has screened a collection of ∼10K compounds, including drugs in clinical use, against >70 cell-based assays in a quantitative high-throughput screening (qHTS) format. In this study, we compiled reference compound lists for DILI and DICT and compared the potential of Tox21 assay data with chemical structure information in building prediction models for human in vivo hepatotoxicity and cardiotoxicity. Models were built with four different machine learning algorithms (e.g., Random Forest, Naïve Bayes, eXtreme Gradient Boosting, and Support Vector Machine) and model performance was evaluated by calculating the area under the receiver operating characteristic curve (AUC-ROC). Chemical structure-based models showed reasonable predictive power for DILI (best AUC-ROC = 0.75 ± 0.03) and DICT (best AUC-ROC = 0.83 ± 0.03), while Tox21 assay data alone only showed better than random performance. DILI and DICT prediction models built using a combination of assay data and chemical structure information did not have a positive impact on model performance. The suboptimal predictive performance of the assay data is likely due to insufficient coverage of an adequately predictive number of toxicity mechanisms. The Tox21 consortium is currently expanding coverage of biological response space with additional assays that probe toxicologically important targets and under-represented pathways that may improve the prediction of in vivo toxicity such as DILI and DICT.
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Zhu H, Xie D, Yang Y, Wang Y, Huang R, Chen X, Wang B, Peng Y, Wang J, Xiao D, Wu D, Qian C, Deng X. The Immune Response and Intestinal Injury after X-Ray FLASH Irradiation in Murine Breast Cancer Transplanted Models. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bardawil E, Murarka S, Ross W, Huang R, Chohan L, Nijjar J. 8465 Same-Day Discharge (SDD) after Total Laparoscopic Hysterectomy (TLH) in a High-Risk Patient Population. J Minim Invasive Gynecol 2022. [DOI: 10.1016/j.jmig.2022.09.416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Cameo T, Jenkins J, Okuagu C, Huang R, Biest S, Ross W, Bardawil E. Transition to Universal Same Day Discharge (SDD) in Times of Corona Virus Disease-19 (COVID): A Success Story. J Minim Invasive Gynecol 2022. [DOI: 10.1016/j.jmig.2022.09.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Sun FF, Huang R, Meng JL, Yan J, Tang B, Wu GF. [Preliminary clinical effect evaluation of digital head and neck radiotherapy oral positioning stents]. ZHONGHUA KOU QIANG YI XUE ZA ZHI = ZHONGHUA KOUQIANG YIXUE ZAZHI = CHINESE JOURNAL OF STOMATOLOGY 2022; 57:1022-1028. [PMID: 36266075 DOI: 10.3760/cma.j.cn112144-20220701-00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Objective: To develop a designing software of digital oral positioning stent for radiotherapy of head and neck, and to compare its clinical effect with traditional oral positioning stents made by lost wax process. Methods: Thirty patients with nasopharyngeal cancer who received oral examination before radiotherapy in the prosthodontics department from July to December, 2021, were selected and divided into three groups according to the patients' wishes, 10 per group: one group without radiotherapy oral positioning stents, one group with traditional oral positioning stents (traditional stents group), and the third group with digital oral positioning stents (digital stents group). Patients' ages range from 20 years old to 71 years old. There were 15 males and 15 females involved in this study. The manufacturing time and comfort of the two positioning stents were evaluated, and the radiation doses of the radiotherapy target areas and surrounding healthy tissues were statistically analyzed at the end of radiotherapy. Results: The manufacturing time of digital stents group [(209±7) min] was much less than that of traditional stents group [(490±10) min] (t=69.85, P<0.001). The comfort of patients' wearing of digital stents [first wearing: 5 (3, 6) score; at the end of radiotherapy: 4 (3, 5) score] was better than that of traditional ones [first wearing: 7 (3, 7) score; at the end of radiotherapy: 7 (3, 7) score] (U=22.00, P=0.033; U=20.50, P=0.023). There was no significant differences in the target radiation doses among the three groups, and the radiation doses of tongue [traditional stents group: (36.74±5.45) Gy; digital stents group: (35.96±4.98) Gy] and mandible [traditional stents group: (35.46±4.19) Gy; digital stents group: (35.34±3.98) Gy] were significantly lower in the patients wearing oral positioning stents than in the patients without oral positioning stents [tongue: (41.49±4.46) Gy; madible: (39.32±3.52) Gy] (P<0.05). Conclusions: Oral positioning stents for nasopharyngeal carcinoma radiotherapy could greatly reduce the exposure doses of tongue and madible of patients. Digital oral positioning stents designed and manufactured by independently developed software had higher production efficiency than the traditional method, and patients' evaluation of comfort was better.
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Lu X, Luo Z, Huang R, Lo DC, Huang W. High-Throughput Platform for Novel Reaction Discovery. Chemistry 2022; 28:e202201421. [PMID: 35766989 PMCID: PMC11033702 DOI: 10.1002/chem.202201421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Indexed: 11/10/2022]
Abstract
Detecting the formation of new chemical bonds in high-throughput synthesis is limited by the efficiency and scalability of reaction product detection, as conventional methods for isolating product from reaction mixtures are time consuming and labor intensive. Here, we report a miniaturizable purification method that enables the rapid, high-throughput isolation of quaternary ammonium-tagged products from reaction mixtures with excellent purity using inexpensive equipment that easily can be set up in a typical organic chemistry laboratory. This novel purification technique enabled us to establish a high-throughput reaction discovery platform. We validated this platform in a screen of 1536 reactions, and one previously unreported transformation was identified.
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