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Molecular BioSystems

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https://www.readbyqxmd.com/read/28098335/not-an-exception-to-the-rule-the-functional-significance-of-intrinsically-disordered-protein-regions-in-enzymes
#1
Shelly DeForte, Vladimir N Uversky
Intrinsically disordered protein regions (IDPRs) are remarkably common and have unique and important biological functions. Enzymes have long been considered an exception to the rule of protein intrinsic disorder due to the structural requirements for catalysis. Although functionally significant IDPRs have been described in several enzymes, there has been no study quantifying the extent of this phenomenon. We have conducted a multilevel computational analysis of missing regions in X-ray crystal structures in the PDB and predicted disorder in 66 representative proteomes...
January 18, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28098303/topologically-inferring-pathway-activity-for-precise-survival-outcome-prediction-breast-cancer-as-a-case
#2
Wei Liu, Wei Wang, Guohua Tian, Wenming Xie, Li Lei, Jiujin Liu, Wanxun Huang, Liyan Xu, Enmin Li
Accurately predicting the survival outcome of patients is of great importance in clinical cancer research. In the past decade, building survival prediction models based on gene expression data has received increasing interest. However, the existing methods are mainly based on individual gene signatures, which are known to have limited prediction accuracy on independent datasets and unclear biological relevance. Here, we propose a novel pathway-based survival prediction method called DRWPSurv in order to accurately predict survival outcome...
January 18, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28098292/an-andrographolide-derivative-agp-26b-exhibiting-anti-angiogenic-activity-in-huvecs-and-zebrafish-via-blocking-the-vegfa-vegfr2-signaling-pathway
#3
Bin Huang, Yuran Peng, Jingjing Li, Shang Li, Yicheng Sun, Decai Wang, Binrui Yang, Judy Yuet-Wa Chan, Huidong Yu, George Pak-Heng Leung, Maggie Pui-Man Hoi, Guo-Chun Zhou, Simon Ming-Yuen Lee
The aim of this study is to investigate the anti-angiogenic properties of andrographolide derivatives AGP-26a (12β-isomer), AGP-26b (12α-isomer) and AGP-26 (4 : 1 mixture of AGP-26a and AGP-26b) in vitro and in vivo. Human umbilical vein endothelial cells (HUVECs) and the Tg(fli-1a:EGFP)y1 zebrafish model were used to identify the anti-angiogenic activities of AGP-26, AGP-26a, and AGP-26b. The results showed that AGP-26b exhibits the strongest inhibitory effect on VEGF-induced proliferation, migration, invasion and formation of capillary-like structures in HUVECs...
January 18, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28092392/the-in-silico-identification-of-human-bile-salt-export-pump-abcb11-inhibitors-associated-with-cholestatic-drug-induced-liver-injury
#4
Lili Xi, Jia Yao, Yuhui Wei, Xin'an Wu, Xiaojun Yao, Huanxiang Liu, Shuyan Li
Drug-induced liver injury (DILI) is one of the major causes of drug attrition and failure. Currently, there is increasing evidence that direct inhibition of the human bile salt export pump (BSEP/ABCB11) by drugs and/or metabolites is one of the most important mechanisms of cholestatic DILI. In the present study, we employ two in silico methods, random forest (RF) and the pharmacophore method, to recognize potential BSEP inhibitors that could cause cholestatic DILI, with the aim of mitigating the risk of cholestatic DILI to some extent...
January 16, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28092388/exploration-and-analysis-of-drug-modes-of-action-through-feature-integration
#5
Mingyuan Xin, Jun Fan, Mingyao Liu, Zhenran Jiang
Identifying drug modes of action (MoA) is of paramount importance for having a good grasp of drug indications in clinical tests. Anticipating MoA can help to discover new uses for approved drugs. Here we first used a drug-set enrichment analysis method to discover significant biological activities in every mode of action category. Then, we proposed a new computational model, a probability ensemble approach based on Bayesian network theory, which integrated chemical, therapeutic, genomic and phenotypic properties of over a thousand of FDA approved drugs to assist with the prediction of MoA...
January 16, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28070584/changes-in-protein-expression-profiles-in-bovine-endometrial-epithelial-cells-exposed-to-e-coli-lps-challenge
#6
Cristian Piras, Yongzhi Guo, Alessio Soggiu, Metasu Chanrot, Viviana Greco, Andrea Urbani, Gilles Charpigny, Luigi Bonizzi, Paola Roncada, Patrice Humblot
E. coli is one of the most frequently involved bacteria in uterine diseases. Lipopolysaccharide (LPS) is a component of the outer membrane of Gram-negative bacteria involved in pathogenic processes leading to post-partum metritis and endometritis in cattle. It also causes inflammation of the endometrium. The increase of cell proliferation by LPS is part of the inflammatory process. The aim of this study was to investigate possible changes in protein expression in relation to the proliferative response of bEECs after challenge with E...
January 10, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28070575/network-pharmacology-based-virtual-screening-of-natural-products-from-clerodendrum-species-for-identification-of-novel-anti-cancer-therapeutics
#7
Barbi Gogoi, Dhrubajyoti Gogoi, Yumnam Silla, Bibhuti Bhushan Kakoti, Brijmohan Singh Bhau
Plant-derived natural products (NPs) play a vital role in the discovery of new drug molecules and these are used for development of novel therapeutic drugs for a specific disease target. Literature review suggests that natural products possess strong inhibitory efficacy against various types of cancer cells. Clerodendrum indicum and Clerodendrum serratum are reported to have anticancer activity; therefore a study was carried out to identify selective anticancer agents from these plants species. In this report, we employed a docking weighted network pharmacological approach to understand the multi-therapeutics potentiality of C...
January 10, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28067383/the-functional-consequences-and-prognostic-value-of-dosage-sensitivity-in-ovarian-cancer
#8
Zichuang Yan, Yongjing Liu, Yunzhen Wei, Ning Zhao, Qiang Zhang, Cheng Wu, Zhiqiang Chang, Yan Xu
Copy number alteration (CNA) represents an important class of genetic variations that may contribute to tumorigenesis, tumor growth and metastatic spread. CNA can directly affect the expression of genes within the CNA regions; however, genes within the CNA regions exhibit heterogeneity in gene dosage sensitivity. In this study, a computational framework was built to identify 1170 dosage-sensitive genes (DSGs) and 1215 dosage-resistant genes (DRGs) that were related to ovarian serous cystadenocarcinoma (OV) through the association between CNA and gene expression...
January 9, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28059425/metabolic-profiling-of-a-myalgic-encephalomyelitis-chronic-fatigue-syndrome-discovery-cohort-reveals-disturbances-in-fatty-acid-and-lipid-metabolism
#9
Arnaud Germain, David Ruppert, Susan M Levine, Maureen R Hanson
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) remains a continuum spectrum disease without biomarkers or simple objective tests, and therefore relies on a diagnosis from a set of symptoms to link the assortment of brain and body disorders to ME/CFS. Although recent studies show various affected pathways, the underlying basis of ME/CFS has yet to be established. In this pilot study, we compare plasma metabolic signatures in a discovery cohort, 17 patients and 15 matched controls, and explore potential metabolic perturbations as the aftermath of the complex interactions between genes, transcripts and proteins...
January 6, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28045162/biochemical-effects-of-venlafaxine-on-astrocytes-as-revealed-by-1-h-nmr-based-metabolic-profiling
#10
Lu Sun, Liang Fang, Bin Lian, Jin-Jun Xia, Chan-Juan Zhou, Ling Wang, Qiang Mao, Xin-Fa Wang, Xue Gong, Zi-Hong Liang, Shun-Jie Bai, Li Liao, Yu Wu, Peng Xie
As a serotonin-norepinephrine reuptake inhibitor [SNRI], venlafaxine is one of the most commonly prescribed clinical antidepressants, with a broad range of antidepressant effects. Accumulating evidence shows that venlafaxine may target astrocytes to exert its antidepressant activity, although the underlying pharmacological mechanisms remained largely unknown. Here, we used a (1)H nuclear magnetic resonance (NMR)-based metabonomics method coupled with multivariate statistical analysis to characterize the metabolic profiling of astrocytes treated with venlafaxine to explore the potential mechanism of its antidepressant effect...
January 3, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28045158/metabolomics-and-proteomics-technologies-to-explore-the-herbal-preparation-affecting-metabolic-disorders-using-high-resolution-mass-spectrometry
#11
Aihua Zhang, Xiaohang Zhou, Hongwei Zhao, Shiyu Zou, Chung Wah Ma, Qi Liu, Hui Sun, Liang Liu, Xijun Wang
An integrative metabolomics and proteomics approach can provide novel insights in the understanding of biological systems. We have integrated proteome and metabolome data sets for a holistic view of the molecular mechanisms in disease. Using quantitative iTRAQ-LC-MS/MS proteomics coupled with UPLC-Q-TOF-HDMS based metabolomics, we determined the protein and metabolite expression changes in the kidney-yang deficiency syndrome (KYDS) rat model and further investigated the intervention effects of the Jinkui Shenqi Pill (JSP)...
January 3, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/27995250/discovery-of-new-dual-binding-tnks-inhibitors-of-wnt-signaling-inhibition-by-pharmacophore-modeling-molecular-docking-and-bioassay
#12
Yinglan Pu, Shuqun Zhang, Zhe Chang, Yunqin Zhang, Dong Wang, Li Zhang, Yan Li, Zhili Zuo
Tankyrases (TNKS), key transmitters in the Wnt signaling pathway which is very conservative in evolution, are vital targets as they are overexpressed widely in many cancers. In this work, 5 inhibitors with novel structures have been discovered and validated using the ligand-based (pharmacophore) virtual screening, docking study, and Luciferase reporter assays for Wnt signaling. Among them, PYL-1, in particular, was the most potent inhibitor with an IC50 value of 9.56 μM against Wnt signaling. The analysis of binding modes was performed to further understand the vital interactions between inhibitors and TNKS 2, and the five hits belong to dual site inhibitors...
December 20, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27975086/ligand-responsive-upregulation-of-3-cite-mediated-translation-in-a-wheat-germ-cell-free-expression-system
#13
Atsushi Ogawa, Yuta Murashige, Junichiro Tabuchi, Taiki Omatsu
We have rationally constructed a novel regulation-type of artificial riboswitch that ligand-dose dependently upregulates translation initiation mediated by a 3' cap-independent translation element (3' CITE) with no major hybridization switches in a plant expression system (wheat germ extract).
December 15, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27966721/integrated-discovery-of-foxo1-dna-stabilizers-from-marine-natural-products-to-restore-chemosensitivity-to-anti-egfr-based-therapy-for-metastatic-lung-cancer
#14
Yingjia Sun, Xinghao Ai, Jingwen Hou, Xiangyun Ye, Ruijun Liu, Shengping Shen, Ziming Li, Shun Lu
The transcription factor forkhead box O1 (FOXO1) negatively regulates activated EGFR signaling by turning on the gene expression of tumor suppressor Kruppel-like factor 6. Here, we propose that the chemosensitivity to anti-EGFR-based lung cancer therapy can be restored by stabilization of the FOXO1-DNA complex architecture using small-molecule marine natural medicines. A synthetic protocol that integrates computational ligand-protein-DNA binding analysis and an experimental fluorescence binding assay was applied against a large library of structurally diverse, drug-like marine natural products to discover novel stabilizers of DNA-bound FOXO1 conformation...
December 14, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27934984/control-of-apoptosis-by-smar1
#15
Md Zubbair Malik, Md Jahoor Alam, Romana Ishrat, Subhash M Agarwal, R K Brojen Singh
The nuclear matrix associated protein SMAR1 is sensitive to p53 and acts as a stress inducer as well as a regulator in the p53 regulatory network. Depending on the amount of stress SMAR1 stimulates, it can drive the p53 dynamics in the system to various dynamical states which correspond to various cellular states. The behavior of p53 in these dynamical states is found to be multifractal, due to the mostly long range correlations and large scale fluctuations imparted by stress. This fractal behavior is exhibited in the topological properties of the networks constructed from these dynamical states, and is a signature of self-organization to optimize information flow in the dynamics...
December 9, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27918060/effect-of-small-molecules-on-cell-reprogramming
#16
REVIEW
M Baranek, A Belter, M Z Naskręt-Barciszewska, M Stobiecki, W T Markiewicz, J Barciszewski
The essential idea of regenerative medicine is to fix or replace tissues or organs with alive and patient-specific implants. Pluripotent stem cells are able to indefinitely self-renew and differentiate into all cell types of the body which makes them a potent substantial player in regenerative medicine. The easily accessible source of induced pluripotent stem cells may allow obtaining and cultivating tissues in vitro. Reprogramming refers to regression of mature cells to its initial pluripotent state. One of the approaches affecting pluripotency is the usage of low molecular mass compounds that can modulate enzymes and receptors leading to the formation of pluripotent stem cells (iPSCs)...
December 5, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27833949/the-emerging-picture-of-cdk9-p-tefb-more-than-20-years-of-advances-since-pitalre
#17
REVIEW
Nikolas Ferreira Dos Santos Paparidis, Maxwell Castro Durvale, Fernanda Canduri
CDK9 is a prominent member of the transcriptional CDKs subfamily, a group of kinases whose function is to control the primary steps of mRNA synthesis and processing by eukaryotic RNA polymerase II. As a cyclin-dependent kinase, CDK9 activation in vivo depends upon its association with T-type cyclins to assemble the positive transcription elongation factor (P-TEFb). Although CDK9/P-TEFb phosphorylates the C-terminal domain of RNAP II in the same positions targeted by CDK7 (TFIIH) and CDK8 (Mediator), the former does not participate in the transcription initiation, but rather plays a unique role by driving the polymerase to productive elongation...
November 11, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27827481/biological-applications-of-xeno-nucleic-acids
#18
REVIEW
Kunihiko Morihiro, Yuuya Kasahara, Satoshi Obika
Xeno nucleic acids (XNAs) are a group of chemically modified nucleic acid analogues that have been applied to various biological technologies such as antisense oligonucleotides, siRNAs and aptamers.
November 9, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27801451/the-discovery-of-new-acetylcholinesterase-inhibitors-derived-from-pharmacophore-modeling-virtual-screening-docking-simulation-and-bioassays
#19
Yunqin Zhang, Shuqun Zhang, Guowei Xu, Hui Yan, Yinglan Pu, Zhili Zuo
Hyperactivity of acetylcholinesterase (AChE) in the brain is the immediate cause of Alzheimer's disease (AD), which is one of the most prevalent fatal diseases afflicting numerous older people. In this research, an in silico study was carried out to find potential AChE inhibitors from a large chemical library. With clustering and lots of comprehensive analysis, some molecules were screened using in vitro bioassays. The IC50 values against AChE ranged from 33.620 to 101.570 μM, while the inhibition ratios at 50 μM ranged from 11...
November 1, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27787525/advances-in-venomics
#20
REVIEW
Vera Oldrati, Miriam Arrell, Aude Violette, Frédéric Perret, Xavier Sprüngli, Jean-Luc Wolfender, Reto Stöcklin
The term "venomics" was coined to describe the global study of venom and venom glands, targeting comprehensive characterization of the whole toxin profile of a venomous animal by means of proteomics, transcriptomics, genomics and bioinformatics studies. This integrative approach is supported by the rapid evolution of protein, RNA and DNA sequencing techniques, as well as databases, knowledge-bases and biocomputing algorithms. The aim of this review is to illustrate advances in the field of venomics during the last decade, addressing each step of the procedure, from sample collection to data treatment...
October 27, 2016: Molecular BioSystems
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