Discovery of azaleatin as a potential allosteric inhibitor for dengue NS2B-NS3 protease using and studies.

The rise in dengue cases in tropical and sub-tropical areas has become a significant health concern. At present, there is no definitive cure for dengue fever, which underscores the importance of identifying potent inhibitors. Dengue NS2B-NS3 protease is the prime drug target due to its vital function for replication.

Differential Correlations Informed Metabolite Set Enrichment Analysis to Decipher Metabolic Heterogeneity of Disease.

Metabolic pathways are regarded as functional and basic components of the biological system. In metabolomics, metabolite set enrichment analysis (MSEA) is often used to identify the altered metabolic pathways (metabolite sets) associated with phenotypes of interest (POI), e.g.

Concordance-Based Batch Effect Correction for Large-Scale Metabolomics.

For a large-scale metabolomics study, sample collection, preparation, and analysis may last several days, months, or even (intermittently) over years. This may lead to apparent batch effects in the acquired metabolomics data due to variability in instrument status, environmental conditions, or experimental operators. Batch effects may confound the true biological relationships among metabolites and thus obscure real metabolic changes.

iMSEA: A Novel Metabolite Set Enrichment Analysis Strategy to Decipher Drug Interactions.

Drug combinations are commonly used to treat various diseases to achieve synergistic therapeutic effects or to alleviate drug resistance. Nevertheless, some drug combinations might lead to adverse effects, and thus, it is crucial to explore the mechanisms of drug interactions before clinical treatment. Generally, drug interactions have been studied using nonclinical pharmacokinetics, toxicology, and pharmacology.

Immune Checkpoint Molecules and Glucose Metabolism in HIV-Induced T Cell Exhaustion.

The progressive decline of CD8 cytotoxic T cells in human immunodeficiency virus (HIV)-infected patients due to infection-triggered cell exhaustion and cell death is significantly correlated with disease severity and progression into the life-threatening acquired immunodeficiency syndrome (AIDS) stage. T cell exhaustion is a condition of cell dysfunction despite antigen engagement, characterized by augmented surface expression of immune checkpoint molecules such as programmed cell death protein 1 (PD-1), which suppress T cell receptor (TCR) signaling and negatively impact the proliferative and effector activities of T cells. T cell function is tightly modulated by cellular glucose metabolism, which produces adequate energy to support a robust reaction when battling pathogen infection.

iSegMSI: An Interactive Strategy to Improve Spatial Segmentation of Mass Spectrometry Imaging Data.

Spatial segmentation is a critical procedure in mass spectrometry imaging (MSI)-based biochemical analysis. However, the commonly used unsupervised MSI segmentation methods may lead to inappropriate segmentation results as the MSI data is characterized by high dimensionality and low signal-to-noise ratio. This process can be improved by the incorporation of precise prior knowledge, which is hard to obtain in most cases.

Phytochemistry, Bioactivities and Traditional Uses of .

() is a flowering tree best known for its essential oil, which has long been used as a fragrance ingredient for perfume and cosmetics. In addition, the plant has been used in traditional medicine in Asia and dates back hundreds of years. To date, there is a limited number of publications on the bioactivities of , which focused on its tyrosinase inhibition, antimicrobial, antidiabetic, anti-inflammatory, and antioxidant activities.

NMF-Based Approach for Missing Values Imputation of Mass Spectrometry Metabolomics Data.

In mass spectrometry (MS)-based metabolomics, missing values (NAs) may be due to different causes, including sample heterogeneity, ion suppression, spectral overlap, inappropriate data processing, and instrumental errors. Although a number of methodologies have been applied to handle NAs, NA imputation remains a challenging problem. Here, we propose a non-negative matrix factorization (NMF)-based method for NA imputation in MS-based metabolomics data, which makes use of both global and local information of the data.

Sparse PLS-Based Method for Overlapping Metabolite Set Enrichment Analysis.

Metabolite set enrichment analysis (MSEA) has gained increasing research interest for identification of perturbed metabolic pathways in metabolomics. The method incorporates predefined metabolic pathways information in the analysis where metabolite sets are typically assumed to be mutually exclusive to each other. However, metabolic pathways are known to contain common metabolites and intermediates.

Edible Bird's Nest: The Functional Values of the Prized Animal-Based Bioproduct From Southeast Asia-A Review.

Edible Bird's Nest (EBN) is the most prized health delicacy among the Chinese population in the world. Although some scientific characterization and its bioactivities have been studied and researched, no lights have been shed on its actual composition or mechanism. The aim of this review paper is to address the advances of EBN as a therapeutic animal bioproduct, challenges and future perspectives of research involving EBN.

DeepPSP: A Global-Local Information-Based Deep Neural Network for the Prediction of Protein Phosphorylation Sites.

Identification of phosphorylation sites is an important step in the function study and drug design of proteins. In recent years, there have been increasing applications of the computational method in the identification of phosphorylation sites because of its low cost and high speed. Most of the currently available methods focus on using local information around potential phosphorylation sites for prediction and do not take the global information of the protein sequence into consideration.

Suppresses Inflammation and Glycolysis in Lipopolysaccharide-Activated RAW264.7 Macrophages.

Macrophage activation is a key event that triggers inflammatory response. The activation is accompanied by metabolic shift such as upregulated glucose metabolism. There are accumulating evidences showing the anti-inflammatory activity of .

Identifying Significant Metabolic Pathways Using Multi-Block Partial Least-Squares Analysis.

In metabolomics, identification of metabolic pathways altered by disease, genetics, or environmental perturbations is crucial to uncover the underlying biological mechanisms. A number of pathway analysis methods are currently available, which are generally based on equal-probability, topological-centrality, or model-separability methods. In brief, prior identification of significant metabolites is needed for the first two types of methods, while each pathway is modeled separately in the model-separability-based methods.

H NMR-Based Metabolic Profiles Delineate the Anticancer Effect of Vitamin C and Oxaliplatin on Hepatocellular Carcinoma Cells.

Hepatocellular carcinoma (HCC) is a leading cause of cancer death worldwide. Because of its high recurrence rate and heterogeneity, effective treatment for advanced stage of HCC is currently lacking. There are accumulating evidences showing the therapeutic potential of pharmacologic vitamin C (VC) on HCC.

Deciphering the metabolic perturbation in hepatic alveolar echinococcosis: a H NMR-based metabolomics study.

Background: Hepatic alveolar echinococcosis (HAE) is caused by the growth of Echinococcus multilocularis larvae in the liver. It is a chronic and potentially lethal parasitic disease. Early stage diagnosis for this disease is currently not available due to its long asymptomatic incubation period.

Metabolic Response in Rats following Electroacupuncture or Moxibustion Stimulation.

Electroacupuncture and moxibustion are traditional Chinese medicine practices that exert therapeutic effects through stimulation of specific meridian acupoints. However, the biological basis of the therapies has been difficult to establish; thus the current practices still rely on ancient TCM references. Here, we used a rat model to study perturbations in cortex, liver, and stomach metabolome and plasma hormones following electroacupuncture or moxibustion treatment on either stomach meridian or gallbladder meridian acupoints.

Metabolomics analysis of herb-partitioned moxibustion treatment on rats with diarrhea-predominant irritable bowel syndrome.

Background: Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder, which is commonly treated with antidiarrhoeal, antispasmodics, serotonergic agents or laxative agents. These treatments provide relief for IBS symptoms but may also lead to undesired side effects. Previously, herb-partitioned moxibustion (HPM) treatment has been demonstrated to be effective in ameliorating symptoms of IBS.

Metabolic Effect of Dietary Taurine Supplementation on Nile Tilapia (Oreochromis nilotictus) Evaluated by NMR-Based Metabolomics.

Taurine is indispensable in aquatic diets that are based solely on plant protein, and it promotes growth of many fish species. However, the physiological and metabolome effects of taurine on fish have not been well described. In this study, H NMR-based metabolomics approaches were applied to investigate the metabolite variations in Nile tilapia (Oreochromis nilotictus) muscle in order to visualize the metabolic trajectory and reveal the possible mechanisms of metabolic effects of dietary taurine supplementation on tilapia growth.

H NMR-based Investigation of Metabolic Response to Electro-Acupuncture Stimulation.

Acupuncture is a traditional Chinese medicine therapy that has been found useful for treating various diseases. The treatments involve the insertion of fine needles at acupoints along specific meridians (meridian specificity). This study aims to investigate the metabolic basis of meridian specificity using proton nuclear magnetic resonance (H NMR)-based metabolomics.

NMR-based metabolomics Reveals Alterations of Electro-acupuncture Stimulations on Chronic Atrophic Gastritis Rats.

Chronic atrophic gastritis (CAG) is a common gastrointestinal disease which has been considered as precancerous lesions of gastric carcinoma. Previously, electro-acupuncture stimulation has been shown to be effective in ameliorating symptoms of CAG. However the underlying mechanism of this beneficial treatment is yet to be established.

Metabolomics, Lipidomics and Pharmacometabolomics of Human Hypertension.

Hypertension is a common but complex human disease, which can lead to a heart attack, stroke, kidney disease or other complications. Since the pathogenesis of hypertension is heterogeneous and multifactorial, it is crucial to establish a comprehensive metabolomic approach to elucidate the molecular mechanism of hypertension. Although there have been limited metabolomic, lipidomic and pharmacometabolomic studies investigating this disease to date, metabolomic studies on hypertension have provided greater insights into the identification of disease-specific biomarkers, predicting treatment outcome and monitor drug safety and efficacy.

The Influence of OLR1 and PCSK9 Gene Polymorphisms on Ischemic Stroke: Evidence from a Meta-Analysis.

Both OLR1 and PCSK9 genes are associated with atherosclerosis, cardiovascular disease and ischemic stroke. The overall prevalence of PCSK9 rs505151 and OLR1 rs11053646 variants in ischemic stroke were 0.005 and 0.

(1) H NMR Metabolic Profiling of Biofluids from Rats with Gastric Mucosal Lesion and Electroacupuncture Treatment.

Gastric mucosal lesion (GML) is a common gastrointestinal disorder with multiple pathogenic mechanisms in clinical practice. In traditional Chinese medicine (TCM), electroacupuncture (EA) treatment has been proven as an effective therapy for GML, although the underlying healing mechanism is not yet clear. Here, we used proton nuclear magnetic resonance- ((1)H NMR-) based metabolomic method to investigate the metabolic perturbation induced by GML and the therapeutic effect of EA treatment on stomach meridian (SM) acupoints.

Celastrol Protects against Antimycin A-Induced Insulin Resistance in Human Skeletal Muscle Cells.

Mitochondrial dysfunction and inflammation are widely accepted as key hallmarks of obesity-induced skeletal muscle insulin resistance. The aim of the present study was to evaluate the functional roles of an anti-inflammatory compound, celastrol, in mitochondrial dysfunction and insulin resistance induced by antimycin A (AMA) in human skeletal muscle cells. We found that celastrol treatment improved insulin-stimulated glucose uptake activity of AMA-treated cells, apparently via PI3K/Akt pathways, with significant enhancement of mitochondrial activities.