Maternal melatonin levels and temporal dietary intake: results from MY-CARE cohort study.

Chrononutrition emerges as a novel approach to promote circadian alignment and metabolic health by means of time-of-the-day dietary intake. However, the relationship between maternal circadian rhythm and temporal dietary intake during pregnancy remains understudied. This study aimed to determine the change in melatonin levels in pregnant women across gestation and its association with temporal energy and macronutrient intake. This was a prospective cohort involving 70 healthy primigravidas. During the second and third trimesters, pregnant women provided salivary samples collected at 9:00, 15:00, 21:00, and 3:00 h over a 24 h day for melatonin assay. Data on chrononutrition characteristics were collected using a 3-day food record. Parameters derived from melatonin measurements including mean, amplitude, maximal level, area under the curve with respect to increase (AUCI), and area under the curve with respect to ground (AUCG) were computed. A rhythmic melatonin secretion over the day that remained stable across trimesters was observed among the pregnant women. There was no significant elevation in salivary melatonin levels as pregnancy advanced. In the second trimester, higher energy intake during 12:00-15:59 h and 19:00-06:59 h predicted a steeper melatonin AUCI (ß=-0.32, p = 0.034) and higher AUCG (ß = 0.26, p = 0.042), respectively. Macronutrient intake within 12:00-15:59 h was negatively associated with mean melatonin (Fat: ß=-0.28, p = 0.041) and AUCG (Carbohydrate: ß=-0.37, p = 0.003; Protein: ß=-0.27, p = 0.036; Fat: ß=-0.32, p = 0.014). As pregnant women progressed from the second to the third trimester, a flatter AUCI was associated with a reduced carbohydrate intake during 12:00-15:59 h (ß=-0.40, p = 0.026). No significant association was detected during the third trimester. Our findings show that higher energy and macronutrient intakes particularly during 12:00-15:59 h and 19:00-06:59 h are associated with the disparities in maternal melatonin levels. Findings suggest the potential of time-based dietary approaches to entrain circadian rhythm in pregnant women.

Mindfulness is Associated with Better Sleep Quality in Young Adults by Reducing Boredom and Bedtime Procrastination.

OBJECTIVE: Bedtime procrastination is a relatively new topic of research and has been found to compromise sleep. Researchers have studied the predictors, but only a few studies have focused on the ways to reduce bedtime procrastination. Mindfulness, a novel variable in this research area, may shed some light on how to decrease bedtime procrastination. This study examined a serial mediation model and hypothesized that the relationship between mindfulness and better sleep quality would be serially mediated by lower levels of boredom and bedtime procrastination. METHODS: This study employed a correlational approach and recruited a sample of 220 participants aged between 17 and 30 (M = 20.34 years, SD = 2.86). In the Qualtrics online survey, participants completed a series of questionnaires measuring mindfulness, boredom, bedtime procrastination, and sleep quality. RESULTS: The analyses provided support for our serial mediation model. Mindfulness predicted a lower level of boredom, which in turn predicted a lower level of bedtime procrastination and subsequently better sleep quality. CONCLUSION: Our findings highlighted the role of mindfulness in curbing bedtime procrastination, setting a foundation for future research on the interventions for sleep issues associated with bedtime procrastination. We discussed the theoretical and practical implications of the findings.

Maternal diet, nutritional status and infant birth weight in Malaysia: a scoping review.

BACKGROUND: Women's diet and nutritional status during pregnancy are important in influencing birth outcomes. We conducted a systematic scoping review of the best available evidence regarding dietary intake of Malaysian pregnant women, and the associations of maternal diet, anthropometry, and nutrition-related co-morbidities with the infant's birth weight (IBW). The study objectives were to examine: (1) the adequacy of micronutrient intake among pregnant women; and (2) the association of maternal factors (anthropometry, diet, plasma glucose and blood pressure) during pregnancy with IBW. METHODS: Eleven search engines such as Proquest, EbscoHost, Scopus, Cochrane Library, Science Direct, Wiley Online Library, PubMed, Google Scholar, MyJournal, BookSC and Inter Library Loan with Medical Library Group were extensively searched to identify the primary articles. Three reviewers independently screened the abstracts and full articles based on the inclusion and exclusion criteria. Extracted data included details about the population characteristics, study methods and key findings related to the review objectives. Seventeen studies published from 1972 to 2021 were included, following the PRISMA-ScR guideline. RESULTS: Studies showed that maternal micronutrient intakes including calcium, iron, vitamin D, folic acid, and niacin fell short of the national recommendations. Increased maternal fruit intake was also associated with increased birth weight. Factors associated with fetal macrosomia included high pre-pregnancy body mass index (BMI), excess gestational weight gain (GWG) and high blood glucose levels. Low pre-pregnancy BMI, inadequate GWG, intake of confectioneries and condiments, and high blood pressure were associated with low birth weight. CONCLUSION: This review identified several factors such as the mother's food habits, comorbidities, BMI and gestational weight gain as the determinants of low birth weight. This implies that emphasis should be given on maternal health and nutrition for the birth outcome.

Prediction of Adverse Drug Reactions by Combining Biomedical Tripartite Network and Graph Representation Model.

As one of the primary contributors to high clinical attrition rates of drugs, toxicity evaluation is of critical significance to new drug discovery. Unsurprisingly, a vast number of computational methods have been developed at various stages of development pipeline to evaluate potential adverse drug reactions (ADRs). Despite previous success of these methods on individual ADR or certain drug family, there are great challenges to toxicity evaluation. In this study, a novel strategy was developed to predict the drug-ADR associations by combining deep learning and the biomedical tripartite network. This heterogeneous network contains biomedical linked data of three entities, for example, drugs, targets, and ADRs. For the first time, GraRep, a deep learning method for distributed representations, is introduced to learn graph representations and identify hidden features from the tripartite network which are further used for ADR prediction. Through this approach, drug-ADR associations could possibly be discovered from a systemic perspective. The accuracy of our method is 0.95 based on internal resource validation and 0.88 based on external resource validation. Moreover, our results show the prediction accuracy using the tripartite network is better than the one with bipartite network, suggesting the model performance can be improved with further enrichment on information. According to the result of 10-fold cross validation, the deep learning model outperforms two traditional methods (topology-based measures and chemical structure-based measures). Additionally, predictive models are also constructed using other deep learning methods, and comparable results are achieved. In summary, the biomedical tripartite network-based deep learning model proposed here proves to offer a promising solution for prediction of ADRs.

Circadian rhythm and its association with birth and infant outcomes: research protocol of a prospective cohort study.

BACKGROUND: Circadian rhythm plays an important role as our internal body's clock that synchronizes behavior and physiology according to the external 24-h light-dark cycle. Past studies have associated disrupted circadian rhythm with higher risk of miscarriages, preterm birth and low birth weights. This paper described the protocol of a prospective cohort study which aims to determine the circadian rhythm in pregnant women, identify its association with maternal factors during pregnancy, gestational weight gain, birth and infant outcomes. METHODS: Ten government maternal and child health clinics in Kuala Lumpur, Malaysia will be randomly selected. Sample size of 438 first-trimester pregnant women will be followed-up until the birth of their infant. Salivary melatonin and cortisol concentration among subsample will be determined using enzyme-linked immunosorbent assay. Data on sleep quality, psychological distress and morningness/eveningness chronotype of pregnant women will be collected using validated questionnaires. Pedometer will be used to measure 5-day physical activity data. Total gestational weight gain will be determined at the end of pregnancy. Utilization of 3-day food record is to capture meal timing and nutrient intake. All measurements will be done in 2nd and 3rd trimester. Birth outcomes will be collected through clinic records and Centers for Disease Control and Prevention (CDC) Neonatal questionnaire. Infants will be followed-up at 6 and 12 months old to obtain anthropometric measurements. DISCUSSION: There is a growing recognition of the role of maternal circadian rhythm, which entrains fetal circadian rhythms that may subsequently have long-term health consequences. The present study will identify the effect of circadian rhythm on pregnancy outcomes and infant growth in the first year of life.

Copy number variation is highly correlated with differential gene expression: a pan-cancer study.

BACKGROUND: Cancer is a heterogeneous disease with many genetic variations. Lines of evidence have shown copy number variations (CNVs) of certain genes are involved in development and progression of many cancers through the alterations of their gene expression levels on individual or several cancer types. However, it is not quite clear whether the correlation will be a general phenomenon across multiple cancer types. METHODS: In this study we applied a bioinformatics approach integrating CNV and differential gene expression mathematically across 1025 cell lines and 9159 patient samples to detect their potential relationship. RESULTS: Our results showed there is a close correlation between CNV and differential gene expression and the copy number displayed a positive linear influence on gene expression for the majority of genes, indicating that genetic variation generated a direct effect on gene transcriptional level. Another independent dataset is utilized to revalidate the relationship between copy number and expression level. Further analysis show genes with general positive linear influence on gene expression are clustered in certain disease-related pathways, which suggests the involvement of CNV in pathophysiology of diseases. CONCLUSIONS: This study shows the close correlation between CNV and differential gene expression revealing the qualitative relationship between genetic variation and its downstream effect, especially for oncogenes and tumor suppressor genes. It is of a critical importance to elucidate the relationship between copy number variation and gene expression for prevention, diagnosis and treatment of cancer.

ß-arrestin2 functions as a key regulator in the sympathetic-triggered immunodepression after stroke.

BACKGROUND: Stroke-induced immunodeficiency syndrome (SIDS) is regarded as a protective mechanism for secondary inflammatory injury as well as a contributor to infection complications. Although stroke-induced hyperactivation of the sympathetic system is proved to facilitate SIDS, the involved endogenous factors and pathways are largely elusive. In this study, we aim to investigate the function of beta-arrestin-2 (ARRB2) in the sympathetic-mediated SIDS. METHODS: Splenic ARRB2 expression and the sympathetic system activity were detected after establishing transient models of middle cerebral artery occlusion (MCAO). In addition, a correlation between ARRB2 expression and the sympathetic system activity was analyzed using a linear correlation analysis. Any SIDS reflected in monocyte dysfunction was investigated by measuring inflammatory cytokine secretion and neurological deficit scores and infarct volume were tested to assess neurological outcome. Further, ARRB2 expression in the monocytes was knocked down in vitro by siRNAs. Following the stimulation of noradrenaline and lipopolysaccharide, cytokine secretion and the nuclear factor-κB (NF-κB) pathway were evaluated to gain insight into the mechanisms related to the contribution of ARRB2 to adrenergic-induced monocyte dysfunction. RESULTS: Splenic ARRB2 expression was significantly increased after stroke and also showed a significant positive correlation with the sympathetic system activity. Stroke-induced monocyte dysfunction resulted in an increase of the interleukin-10 (IL-10) level as well as a decrease of the interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α) and interleukin-1ß (IL-1ß) levels. Also, blockade of adrenergic-activity significantly reversed these cytokine levels, and blockade of adrenergic-activity improved stroke-induced neurological results. However, the improved neurological results had no significant correlation with ARRB2 expression. Furthermore, the in vitro results showed that the deficiency of ARRB2 dramatically repealed adrenergic-induced monocyte dysfunction and the inhibition of NF-κB signaling phosphorylation activity. CONCLUSIONS: ARRB2 is implicated in the sympathetic-triggered SIDS, in particular, monocyte dysfunction after stroke. Accordingly, ARRB2 may be a promising therapeutic target for the immunological management of stroke in a clinic.

Virtual Screening and Experimental Testing of B1 Metallo-ß-lactamase Inhibitors.

The global rise of metallo-ß-lactamases (MBLs) is problematic due to their ability to inactivate most ß-lactam antibiotics. MBL inhibitors that could be coadministered with and restore the efficacy of ß-lactams are highly sought after. In this study, we employ virtual screening of candidate MBL inhibitors without thiols or carboxylates to avoid off-target effects using the Avalanche software package, followed by experimental validation of the selected compounds. As target enzymes, we chose the clinically relevant B1 MBLs NDM-1, IMP-1, and VIM-2. Among 32 compounds selected from an approximately 1.5 million compound library, 6 exhibited IC50 values less than 40 µM against NDM-1 and/or IMP-1. The most potent inhibitors of NDM-1, IMP-1, and VIM-2 had IC50 values of 19 ± 2, 14 ± 1, and 50 ± 20 µM, respectively. While chemically diverse, the most potent inhibitors all contain combinations of hydroxyl, ketone, ester, amide, or sulfonyl groups. Docking studies suggest that these electron-dense moieties are involved in Zn(II) coordination and interaction with protein residues. These novel scaffolds could serve as the basis for further development of MBL inhibitors. A procedure for renaming NDM-1 residues to conform to the class B ß-lactamase (BBL) numbering scheme is also included.

Deciphering chemical interactions between Glycyrrhizae Radix and Coptidis Rhizoma by liquid chromatography with transformed multiple reaction monitoring mass spectrometry.

In this study, we propose an integrated strategy for the efficient identification and quantification of herbal constituents using liquid chromatography with mass spectrometry. First, liquid chromatography with quadrupole time-of-flight mass spectrometry was employed for the chemical profiling of herbs, where a targeted following nontargeted approach was developed to detect trace constituents by using structural correlations and extracted ion chromatograms. Next, ion pairs and parameters of MS2 of quadrupole time-of-flight mass spectrometry were selected to design multiple reaction monitoring transitions for the identified compounds on liquid chromatography with triple quadrupole mass spectrometry. The relative concentration of each constituent was then calculated using a semiquantitative calibration curve. The proposed strategy was applied in a study of chemical interactions between Glycyrrhizae Radix and Coptidis Rhizoma. A total of 140 compounds were identified or tentatively characterized from the herbs, 132 of which were relatively quantified. The visualized quantitative results clearly showed codecoction produced significant constituent concentration variations especially for those with a low polarity. The case study also indicated that the present methodology could provide a reliable, accurate, and labor-saving solution for chemical studies of herbal medicines.

arrayMap 2014: an updated cancer genome resource.

Somatic copy number aberrations (CNA) represent a mutation type encountered in the majority of cancer genomes. Here, we present the 2014 edition of arrayMap (http://www.arraymap.org), a publicly accessible collection of pre-processed oncogenomic array data sets and CNA profiles, representing a vast range of human malignancies. Since the initial release, we have enhanced this resource both in content and especially with regard to data mining support. The 2014 release of arrayMap contains more than 64,000 genomic array data sets, representing about 250 tumor diagnoses. Data sets included in arrayMap have been assembled from public repositories as well as additional resources, and integrated by applying custom processing pipelines. Online tools have been upgraded for a more flexible array data visualization, including options for processing user provided, non-public data sets. Data integration has been improved by mapping to multiple editions of the human reference genome, with the majority of the data now being available for the UCSC hg18 as well as GRCh37 versions. The large amount of tumor CNA data in arrayMap can be freely downloaded by users to promote data mining projects, and to explore special events such as chromothripsis-like genome patterns.

CNARA: reliability assessment for genomic copy number profiles.

BACKGROUND: DNA copy number profiles from microarray and sequencing experiments sometimes contain wave artefacts which may be introduced during sample preparation and cannot be removed completely by existing preprocessing methods. Besides, large derivative log ratio spread (DLRS) of the probes correlating with poor DNA quality is sometimes observed in genome screening experiments and may lead to unreliable copy number profiles. Depending on the extent of these artefacts and the resulting misidentification of copy number alterations/variations (CNA/CNV), it may be desirable to exclude such samples from analyses or to adapt the downstream data analysis strategy accordingly. RESULTS: Here, we propose a method to distinguish reliable genomic copy number profiles from those containing heavy wave artefacts and/or large DLRS. We define four features that adequately summarize the copy number profiles for reliability assessment, and train a classifier on a dataset of 1522 copy number profiles from various microarray platforms. The method can be applied to predict the reliability of copy number profiles irrespective of the underlying microarray platform and may be adapted for those sequencing platforms from which copy number estimates could be computed as a piecewise constant signal. Further details can be found at https://github.com/baudisgroup/CNARA . CONCLUSIONS: We have developed a method for the assessment of genomic copy number profiling data, and suggest to apply the method in addition to and after other state-of-the-art noise correction and quality control procedures. CNARA could be instrumental in improving the assessment of data used for genomic data mining experiments and support the reliable functional attribution of copy number aberrations especially in cancer research.

Niclosamide is a Negative Allosteric Modulator of Group I Metabotropic Glutamate Receptors: Implications for Neuropathic Pain.

PURPOSE: Novel therapeutics are greatly needed that target specific pathological receptors and pathways involved in Neuropathic Pain (NP). Extending our previous work published in this Journal on Group I metabotropic glutamate receptor (mGluR) modulators, we now investigate the therapeutic potential of niclosamide in modulating aberrant glutamate transmission in NP. METHOD: Calcium mobilization assays and cross-receptor selectivity experiments are conducted to characterize the pharmacological activity of niclosamide. A focused series of niclosamide analogues is then prepared to elucidate key structural determinants that emerged from computational molecular modeling analysis on drug-receptor interactions. Finally, niclosamide and a carbamate derivative are studied to assess their efficacy in an NP-evoked mechanical hyperalgesia model in rats. RESULTS: Niclosamide is a low-nanomolar allosteric antagonist of Group I mGluRs with high selectivity for Group I over homologous Group III mGluRs. The phenolic hydroxyl group of niclosamide forms a crucial hydrogen bond with mGluR1/5. Its bioactive coplanar conformation is further stabilized by the nitro substituent on the B ring and an intramolecular bond. Mechanical hyperalgesia in NP rats is reversed by niclosamide through three different dosing routes. CONCLUSION: To our knowledge, this is the first report of the salicylanilide class of compounds as potential treatments for NP.

Progenetix: 12 years of oncogenomic data curation.

DNA copy number aberrations (CNAs) can be found in the majority of cancer genomes and are crucial for understanding the potential mechanisms underlying tumor initiation and progression. Since the first release in 2001, the Progenetix project (http://www.progenetix.org) has provided a reference resource dedicated to provide the most comprehensive collection of genome-wide CNA profiles. Reflecting the application of comparative genomic hybridization techniques to tens of thousands of cancer genomes, over the past 12 years our data curation efforts have resulted in a more than 60-fold increase in the number of cancer samples presented through Progenetix. In addition, new data exploration tools and visualization options have been added. In particular, the gene-specific CNA frequency analysis should facilitate the assignment of cancer genes to related cancer types. In addition, the new user file processing interface allows users to take advantage of the online tools, including various data representation options for proprietary data pre-publication. In this update article, we report recent improvements of the database in terms of content, user interface and online tools.

Qualitative analysis of chemical constituents in traditional Chinese medicine analogous formula cheng-Qi decoctions by liquid chromatography-mass spectrometry.

Cheng-Qi decoctions (CQs), a group of analogous formulas, are well-known traditional Chinese preparations used as purgative remedies to treat 'internal heat'-induced symptoms, which manifest as a bloated and painful abdomen, hard stools, fever and other clinical observations. In this study, HPLC-ESI-MS/MS and UPLC-TOF-MS were employed for separation and structural identification of constituents in CQs. As a result, a total of 90 compounds, including seven anthraquinones, 39 flavones, 21 glycosides, 11 stilbene glycosides, six organic acids, five coumarins and one lignans, were detected and tentatively identified in CQs extracts. The characterization results shed some light on the scientific foundation for clinical application of the CQ analogous formulas. Our results also indicate that the HPLC-MS method is useful for the systemic identification of major constituents in traditional Chinese medicine formulas.

Elucidating the Role of Residue 67 in IMP-Type Metallo-ß-Lactamase Evolution.

Antibiotic resistance in bacteria is ever changing and adapting, as once-novel ß-lactam antibiotics are losing their efficacy, primarily due to the production of ß-lactamases. Metallo-ß-lactamases (MBLs) efficiently inactivate a broad range of ß-lactam antibiotics, including carbapenems, and are often coexpressed with other antibacterial resistance factors. The rapid dissemination of MBLs and lack of novel antibacterials pose an imminent threat to global health. In an effort to better counter these resistance-conferring ß-lactamases, an investigation of their natural evolution and resulting substrate specificity was employed. In this study, we elucidated the effects of different amino acid substitutions at position 67 in IMP-type MBLs on the ability to hydrolyze and confer resistance to a range of ß-lactam antibiotics. Wild-type ß-lactamases IMP-1 and IMP-10 and mutants IMP-1-V67A and IMP-1-V67I were characterized biophysically and biochemically, and MICs for Escherichia coli cells expressing these enzymes were determined. We found that all variants exhibited catalytic efficiencies (kcat/Km) equal to or higher than that of IMP-1 against all tested ß-lactams except penicillins, against which IMP-1 and IMP-1-V67I showed the highest kcat/Km values. The substrate-specific effects of the different amino acid substitutions at position 67 are discussed in light of their side chain structures and possible interactions with the substrates. Docking calculations were employed to investigate interactions between different side chains and an inhibitor used as a ß-lactam surrogate. The differences in binding affinities determined experimentally and computationally seem to be governed by hydrophobic interactions between residue 67 and the inhibitor and, by inference, the ß-lactam substrates.

Identification of Nitazoxanide as a Group I Metabotropic Glutamate Receptor Negative Modulator for the Treatment of Neuropathic Pain: An In Silico Drug Repositioning Study.

PURPOSE: Drug repositioning strategies were employed to explore new therapeutic indications for existing drugs that may exhibit dual negative mGluR1/5 modulating activities as potential treatments for neuropathic pain. METHOD: A customized in silico-in vitro-in vivo drug repositioning scheme was assembled and implemented to search available drug libraries for compounds with dual mGluR1/5 antagonistic activities, that were then evaluated using in vitro functional assays and, for validated hits, in an established animal model for neuropathic pain. RESULTS: Tizoxanide, the primary active metabolite of the FDA approved drug nitazoxanide, fit in silico pharmacophore models constructed for both mGluR1 and mGluR5. Subsequent calcium (Ca++) mobilization functional assays confirmed that tizoxanide exhibited appreciable antagonist activity for both mGluR1 and mGluR5 (IC50 = 1.8 µM and 1.2 µM, respectively). The in vivo efficacy of nitazoxanide administered by intraperitoneal injection was demonstrated in a rat model for neuropathic pain. CONCLUSION: The major aim of the present study was to demonstrate the utility of an in silico-in vitro-in vivo drug repositioning protocol to facilitate the repurposing of approved drugs for new therapeutic indications. As an example, this particular investigation successfully identified nitazoxanide and its metabolite tizoxanide as dual mGluR1/5 negative modulators. A key finding is the vital importance for drug screening libraries to include the structures of drug active metabolites, such as those emanating from prodrugs which are estimated to represent 5-7% of marketed drugs.

Dissecting functional chemome of Xiaoqinglong decoction analogous formulae using network formulaology approach.

Analogous formulae (AF) refer to a set of traditional Chinese medicine (TCM) formulae sharing similar herbs and/or indications. Dissecting functional chemome of analogous formulae could enhance the understanding of the intrinsic nature of TCM. In this study, taking 5 Xiaoqinglong decoction analogous formulae (XQL AF) including Xiaoqinglong decoction, Mahuang Xingren Shigao Gancao decoction, Mahuang Fuzi decoction, Houpu Mahuang decoction and Daqinglong decoction as example, we systematically investigated the relationship between compounds and indications using network formulaology approach. The functional chemome of XQL AF were revealed by network analysis and molecular docking. This successful application in XQL AF suggests network formulaology could be a useful tool for AF-related research and therefore provide a new way to discover the scientific foundation of Zhang Zhongjing's herbal formulae.

[Toxicogenomics and its application in safety evaluation of traditional Chinese medicine].

Toxicogenomics (TGx) refers to a set of technologies that assess genome-wide responses after toxic agent exposure. Altered gene expression patterns that are caused by specific exposures reveal how toxicants may disrupt cellular processes and lead to side effects. Development and application of " omics" technology facilitate the toxicogenomic research which sharing and interpretation of the enormous amount of biological information generated in toxicologic field. In recent years TGx has been widely valued and successfully applied as an effective research tool to evaluate the toxic effects of traditional Chinese medicine (TCM). Here we reviewed current progress in the field of TGx and focused on its application in traditional Chinese medicine safety evaluation, especially in revealing the mechanism, finding potential toxic biomarkers and studying compatibility detoxification of TCM.

LTMap: a web server for assessing the potential liver toxicity by genome-wide transcriptional expression data.

Toxicogenomics (TGx) has played a significant role in mechanistic research related with hepatotoxicity as well as liver toxicity prediction. Currently, several large-scale preclinical TGx data sets were made freely accessible to the public, such as Open TG-GATEs. With the availability of a sufficient amount of microarray data, it is important to integrate this information to provide new insights into the risk assessment of potential drug-induced liver toxicity. Here we developed a web server for evaluating the potential liver toxicity based on genome-wide transcriptomics data, namely LTMap. In LTMap, researchers could compare signatures of query compounds against a pregenerated signature database of 20 123 Affymetrix arrays associated with about 170 compounds retrieved from the largest public toxicogenomics data set Open TG-GATEs. Results from this comparison may lead to the unexpected discovery of similar toxicological responses between chemicals. We validated our computational approach for similarity comparison using three example drugs. Our successful applications of LTMap in these case studies demonstrated its utility in revealing the connection of chemicals according to similar toxicological behaviors. Furthermore, a user-friendly web interface is provided by LTMap to browse and search toxicogenomics data (http://tcm.zju.edu.cn/ltmap).

Pregnane X receptor mediates dyslipidemia induced by the HIV protease inhibitor amprenavir in mice.

Human immunodeficiency virus (HIV) protease inhibitors (PIs) have been used successfully in extending the life span of people infected with HIV. The use of PIs has also been associated with dyslipidemia and an increased risk of cardiovascular disease, but the underlying mechanisms remain elusive. Several PIs have been implicated in activating the nuclear receptor pregnane X receptor (PXR), which acts as a xenobiotic sensor to regulate xenobiotic metabolism in the liver and intestine. Recent studies indicate that PXR may also play an important role in the regulation of lipid homeostasis. In the present study, we identified amprenavir, a widely used HIV PI, as a potent PXR-selective agonist. Computational docking studies combined with site-direct mutagenesis identified several key residues within the ligand-binding pocket of PXR that constitute points of interaction with amprenavir. Amprenavir efficiently activated PXR and induced PXR target gene expression in vitro and in vivo. Short-term exposure to amprenavir significantly increased plasma total cholesterol and atherogenic low-density lipoprotein cholesterol levels in wild-type mice, but not in PXR-deficient mice. Amprenavir-mediated PXR activation stimulated the expression of several key intestinal genes involved in lipid homeostasis. These findings provide critical mechanistic insight for understanding the impact of PIs on cardiovascular disease and demonstrate a potential role of PXR in mediating the adverse effects of HIV PIs in humans.