High performance screening, structural and molecular dynamics analysis to identify H1 inhibitors from TCM Database@Taiwan.

Abstract:

:New-type oseltamivir-resistant H1N1 influenza viruses have been a major threat to human health since the 2009 flu pandemic. To resolve the drug resistance issue, we aimed to identify a new type of inhibitors against H1 from traditional Chinese medicine (TCM) by employing the world's largest TCM database () for virtual screening and molecular dynamics (MD). From the virtual screening results, sodium (+)-isolaricireinol-2 alpha-sulfate, sodium 3,4-dihydroxy-5-methoxybenzoic acid methyl ester-4-sulfate, sodium (E)-7-hydroxy-1,7-bis(4-hydroxyphenyl)hept-5-ene-3S-sulfonate, and 3-methoxytyramine-betaxanthin were identified as potential drug-like compounds. MD simulation of the binding poses with the key residues Asp103 and Glu83, as well as other binding site residues, identified higher numbers of hydrogen bonds than N-Acetyl-D-Glucosamine (NAG), the natural ligand of the esterase domain in H1. Ionic bonds, salt bridges, and electrostatic energy also contribute to binding stability. Key binding residues include Lys71, Glu83, Asp103, and Arg238. Structural moieties promoting H-bond or salt bridge formations at these locations greatly contribute to a stable ligand-protein complex. An available sodium atom for ionic interactions with Asp103 can further stabilize the ligands. Based on virtual screening, MD simulation, and interaction energy evaluation, TCM candidates demonstrate good potential as novel H1 inhibitors. In addition, the identified stabilizing features can provide insights for designing highly stable H1 inhibitors.

journal_name

Mol Biosyst

journal_title

Molecular bioSystems

authors

Chang SS,Huang HJ,Chen CY

doi

10.1039/c1mb05320e

subject

Has Abstract

pub_date

2011-12-01 00:00:00

pages

3366-74

issue

12

eissn

1742-206X

issn

1742-2051

journal_volume

7

pub_type

杂志文章
  • Crosstalk between G-protein and Ca2+ pathways switches intracellular cAMP levels.

    abstract::Cyclic adenosine monophosphate and cyclic guanosine monophosphate are universal intracellular messengers whose concentrations are regulated by molecular networks comprised of different isoforms of the synthases adenylate cyclase or guanylate cyclase and the phosphodiesterases which degrade these compounds. In this pap...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/b807993e

    authors: Valeyev NV,Heslop-Harrison P,Postlethwaite I,Gizatullina AN,Kotov NV,Bates DG

    更新日期:2009-01-01 00:00:00

  • A gold nanoparticles based immuno-bioprobe for detection of Vi capsular polysaccharide of Salmonella enterica serovar Typhi.

    abstract::A rapid and sensitive gold-nanobioprobe based immunoassay format has been presented for the detection of capsular Vi polysaccharide of Salmonella enterica serovar Typhi (surface antigen) using anti-Vi antibodies. The Vi antigen was extracted from serovar Typhi cells, under the optimised growth conditions for its over-...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c2mb25048a

    authors: Pandey SK,Suri CR,Chaudhry M,Tiwari RP,Rishi P

    更新日期:2012-07-06 00:00:00

  • Large-scale investigation of oxygen response mutants in Saccharomyces cerevisiae.

    abstract::A genome-wide screen of a yeast non-essential gene-deletion library was used to identify sick phenotypes due to oxygen deprivation. The screen provided a manageable list of 384 potentially novel as well as known oxygen responding (anoxia-survival) genes. The gene-deletion mutants were further assayed for sensitivity t...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c3mb25516f

    authors: Samanfar B,Omidi K,Hooshyar M,Laliberte B,Alamgir M,Seal AJ,Ahmed-Muhsin E,Viteri DF,Said K,Chalabian F,Golshani A,Wainer G,Burnside D,Shostak K,Bugno M,Willmore WG,Smith ML,Golshani A

    更新日期:2013-06-01 00:00:00

  • Combining small molecules for cell reprogramming through an interatomic analysis.

    abstract::The knowledge available about the application and generation of induced pluripotent stem cells (iPSC) has grown since their discovery, and new techniques to enhance the reprogramming process have been described. Among the new approaches to induce iPSC that have gained great attention is the use of small molecules for ...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c3mb70159j

    authors: Feltes BC,Bonatto D

    更新日期:2013-11-01 00:00:00

  • Regulation of stress hormones jasmonates and ethylene by MAPK pathways in plants.

    abstract::Plant stress hormones, such as jasmonates (JAs) and ethylene (ET) are essential in plant defence against stress conditions. JAs are used in cosmetics and food flavouring, and the recently demonstrated anti-cancer activity of JAs highlights their potential in health protection. It reinforces the need for a better under...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/b718578m

    authors: Schweighofer A,Meskiene I

    更新日期:2008-08-01 00:00:00

  • On the basic computational structure of gene regulatory networks.

    abstract::Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and their target genes. The large size of these webs and their entangled nature make it...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/B904960f

    authors: Rodríguez-Caso C,Corominas-Murtra B,Solé RV

    更新日期:2009-12-01 00:00:00

  • BH3 helix-derived biophotonic nanoswitches regulate cytochrome c release in permeabilised cells.

    abstract::Dynamic physical interactions between proteins underpin all key cellular processes and are a highly attractive area for the development of research tools and medicines. Protein-protein interactions frequently involve α-helical structures, but peptides matching the sequences of these structures usually do not fold corr...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c3mb70246d

    authors: Mart RJ,Errington RJ,Watkins CL,Chappell SC,Wiltshire M,Jones AT,Smith PJ,Allemann RK

    更新日期:2013-11-01 00:00:00

  • Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development.

    abstract::Differential gene expression governs the development, function and pathology of multicellular organisms. Transcription regulatory networks study differential gene expression at a systems level by mapping the interactions between regulatory proteins and target genes. While microarray transcription profiles are the most...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/B908108a

    authors: Vermeirssen V,Joshi A,Michoel T,Bonnet E,Casneuf T,Van de Peer Y

    更新日期:2009-12-01 00:00:00

  • Metabolomics study of diabetic retinopathy using gas chromatography-mass spectrometry: a comparison of stages and subtypes diagnosed by Western and Chinese medicine.

    abstract::Diabetic retinopathy (DR) is a serious microvascular syndrome of diabetes, and is one of the most frequent causes of blindness in the world. It has three progressive stages with complex metabolic deregulations in the holistic system of Western medicine. Chinese medicine classifies DR into two different syndrome types;...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c0mb00341g

    authors: Li X,Luo X,Lu X,Duan J,Xu G

    更新日期:2011-07-01 00:00:00

  • Comparative proteome profiling of breast tumor cell lines by gel electrophoresis and mass spectrometry reveals an epithelial mesenchymal transition associated protein signature.

    abstract::The epithelial to mesenchymal transition (EMT) is a cellular program associated with the organ morphogenesis but also with the disease progression. EMT in the cancer field fuels neoplastic progression promoting the resistance to cell death, the resistance to chemotherapy and the acquisition of stem cell properties. Co...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c2mb25401h

    authors: Vergara D,Simeone P,del Boccio P,Toto C,Pieragostino D,Tinelli A,Acierno R,Alberti S,Salzet M,Giannelli G,Sacchetta P,Maffia M

    更新日期:2013-06-01 00:00:00

  • HPLC-MS aided PC12 cell systems: to quantitatively monitor the conversion of nitronyl nitroxide in biological systems with and without NO.

    abstract::Nitronyl nitroxides are capable of preventing cells, tissues, and organs from radical-induced damage through scavenging NO˙, ˙O(2)(-) and ˙OH. In order to explore the conversions of nitronyl nitroxides in biological systems with and without NO˙, HPLC-MS aided PC12 cell systems were developed, and the conversions of 2-...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c1mb05037k

    authors: Wang Y,Jiang X,Liu J,Zhao M,Kang G,Wu J,Peng L,Peng S

    更新日期:2011-05-01 00:00:00

  • Combining radiation, immunotherapy, and antiangiogenesis agents in the management of cancer: the Three Musketeers or just another quixotic combination?

    abstract::With the advent of new cancer therapies in the last few years, the goals of reducing disease burden and improving quality of life are frequently achieved. Yet despite the advances seen with numerous monotherapies, a multimodality approach that targets different aspects of tumor biology may yield the greatest clinical ...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章,评审

    doi:10.1039/b911313b

    authors: Kamrava M,Bernstein MB,Camphausen K,Hodge JW

    更新日期:2009-11-01 00:00:00

  • Chemical biology suggests a role for calcium signaling in mediating sustained JNK activation during apoptosis.

    abstract::Calcium (Ca(2+)) is used as a signaling molecule to regulate many cellular processes. Calcium signaling generally involves transient elevations of the concentration of free Ca(2+) in the cytosol. More pronounced and sustained elevations of intracellular Ca(2+) concentrations are observed during apoptosis (programmed c...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章,评审

    doi:10.1039/b920805d

    authors: Brnjic S,Olofsson MH,Havelka AM,Linder S

    更新日期:2010-05-01 00:00:00

  • TMEM45B promotes proliferation, invasion and migration and inhibits apoptosis in pancreatic cancer cells.

    abstract::In the present study, we focused on the expression and biological functions of TMEM45B in pancreatic cancer tissues and cell lines. Real-time PCR and Western blotting were used to examine the expression levels of TMEM45B in pancreatic cancer tissues and cell lines. The functions of TMEM45B were evaluated using CCK-8, ...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c6mb00203j

    authors: Zhao LC,Shen BY,Deng XX,Chen H,Zhu ZG,Peng CH

    更新日期:2016-05-24 00:00:00

  • Proteomic and ionomic profiling reveals significant alterations of protein expression and calcium homeostasis in cystic fibrosis cells.

    abstract::Cystic fibrosis (CF) is an autosomal recessive disorder associated with mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene and defective chloride transport across the epithelial cell membranes. Abnormal epithelial ion transport is the primary cause of persistent airway infections and chro...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c3mb25594h

    authors: Ciavardelli D,D'Orazio M,Pieroni L,Consalvo A,Rossi C,Sacchetta P,Di Ilio C,Battistoni A,Urbani A

    更新日期:2013-06-01 00:00:00

  • A peptidomimetic siRNA transfection reagent for highly effective gene silencing.

    abstract::RNA interference (RNAi) techniques hold forth great promise for therapeutic silencing of deleterious genes. However, clinical applications of RNAi require the development of safe and efficient methods for intracellular delivery of small interfering RNA (siRNA) oligonucleotides specific to targeted genes. We describe t...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/b603229j

    authors: Utku Y,Dehan E,Ouerfelli O,Piano F,Zuckermann RN,Pagano M,Kirshenbaum K

    更新日期:2006-06-01 00:00:00

  • Modeling the permeability of drug-like molecules through the cell wall of Mycobacterium tuberculosis: an analogue based approach.

    abstract::The emergence of drug resistant strains of Mycobacterium Tuberculosis (Mtb) accentuates the urgent need for the development of novel antitubercular drugs. The major causes of drug resistance are genetic mutations, the influx-efflux transporter system, and the complex cell wall system of Mtb, which can function as perm...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c6mb00457a

    authors: Janardhan S,Ram Vivek M,Narahari Sastry G

    更新日期:2016-10-18 00:00:00

  • Global analysis of the yeast osmotic stress response by quantitative proteomics.

    abstract::Information on extracellular signals and conditions is often transduced by biological systems using cascades of protein phosphorylation that affect the activity of enzymes, the localization of proteins and gene expression. A model to study signal transduction is the response of the yeast Saccharomyces cerevisiae to os...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/b902256b

    authors: Soufi B,Kelstrup CD,Stoehr G,Fröhlich F,Walther TC,Olsen JV

    更新日期:2009-11-01 00:00:00

  • PredcircRNA: computational classification of circular RNA from other long non-coding RNA using hybrid features.

    abstract::Recently circular RNA (circularRNA) has been discovered as an increasingly important type of long non-coding RNA (lncRNA), playing an important role in gene regulation, such as functioning as miRNA sponges. So it is very promising to identify circularRNA transcripts from de novo assembled transcripts obtained by high-...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c5mb00214a

    authors: Pan X,Xiong K

    更新日期:2015-08-01 00:00:00

  • Selective targeting of MAPK family kinases JNK over p38 by rationally designed peptides as potential therapeutics for neurological disorders and epilepsy.

    abstract::Human mitogen-activated protein kinase (MAPK) family members JNK and p38 are two homologous protein-serine/threonine kinases but play distinct roles in the pathological process of neurological disorders. Selective targeting of JNK over p38 has been established as a potential therapeutic approach to epilepsy and other ...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c6mb00297h

    authors: Zhuo ZH,Sun YZ,Jin PN,Li FY,Zhang YL,Wang HL

    更新日期:2016-07-19 00:00:00

  • Phosphorylation of thymidylate synthase affects slow-binding inhibition by 5-fluoro-dUMP and N(4)-hydroxy-dCMP.

    abstract::Endogenous thymidylate synthases, isolated from tissues or cultured cells of the same specific origin, have been reported to show differing slow-binding inhibition patterns. These were reflected by biphasic or linear dependence of the inactivation rate on time and accompanied by differing inhibition parameters. Consid...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c6mb00026f

    authors: Ludwiczak J,Maj P,Wilk P,Frączyk T,Ruman T,Kierdaszuk B,Jarmuła A,Rode W

    更新日期:2016-04-01 00:00:00

  • System properties of ErbB receptor signaling for the understanding of cancer progression.

    abstract::An intracellular signal transduction network constitutes an assembled machinery to control the dynamics of kinase-phosphatase cascade and gene expression. Spatio-temporal analyses of the cellular process can explain the biochemical role of the receptor tyrosine kinases in cancer development from a system point of view...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章,评审

    doi:10.1039/b612800a

    authors: Hatakeyama M

    更新日期:2007-02-01 00:00:00

  • Structural modeling and molecular dynamics studies on the human LMTK3 domain and the mechanism of ATP binding.

    abstract::Estrogen positive breast cancer is a dreadful disease in women worldwide. The human estrogen receptor-α (ERα) pathway plays a critical role in estrogenic signaling and targeting ERα in breast cancer treatment. The key role of Lemur tyrosine kinase-3 (LMTK3) in regulation of ERα has been identified and it is found to b...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c4mb00063c

    authors: Anbarasu K,Jayanthi S

    更新日期:2014-05-01 00:00:00

  • Fluorescent peptide indicator displacement assay for monitoring interactions between RNA and RNA binding proteins.

    abstract::This paper describes a sensitive, non-destructive displacement assay, using a fluorescent peptide indicator, for real-time monitoring of the interactions between RNA and RNA binding proteins (RBPs). The developed fluorescent peptide indicators, each containing a mid-sequence fluorophore unit, allowed sensing of target...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c2mb25470k

    authors: Jeong HS,Choi SM,Kim HW,Park JW,Park HN,Park SM,Jang SK,Rhee YM,Kim BH

    更新日期:2013-05-01 00:00:00

  • Engineering and applications of genetic circuits.

    abstract::In the field of synthetic biology, recent genetic engineering efforts have enabled the construction of novel genetic circuits with diverse functionalities and unique activation mechanisms. Because of these advances, artificial genetic networks are becoming increasingly complex, and are demonstrating more robust behavi...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章,评审

    doi:10.1039/b700547d

    authors: Sayut DJ,Kambam PK,Sun L

    更新日期:2007-12-01 00:00:00

  • Production of long chain alcohols and alkanes upon coexpression of an acyl-ACP reductase and aldehyde-deformylating oxygenase with a bacterial type-I fatty acid synthase in E. coli.

    abstract::Microbial long chain alcohols and alkanes are renewable biofuels that could one day replace petroleum-derived fuels. Here we report a novel pathway for high efficiency production of these products in Escherichia coli strain BL21(DE3). We first identified the acyl-ACP reductase/aldehyde deformylase combinations with th...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c5mb00268k

    authors: Coursolle D,Lian J,Shanklin J,Zhao H

    更新日期:2015-09-01 00:00:00

  • Supervised learning with decision tree-based methods in computational and systems biology.

    abstract::At the intersection between artificial intelligence and statistics, supervised learning allows algorithms to automatically build predictive models from just observations of a system. During the last twenty years, supervised learning has been a tool of choice to analyze the always increasing and complexifying data gene...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章,评审

    doi:10.1039/b907946g

    authors: Geurts P,Irrthum A,Wehenkel L

    更新日期:2009-12-01 00:00:00

  • Glucocorticoid receptors take part in the apoptotic process of human lens epithelial cells, but the glucocorticoid receptor antagonist RU486 does not rescue the cells fully.

    abstract::To identify an agent with specific activity against human lens epithelial cells (HLECs), we confirmed the presence of glucocorticoid receptors (GRs) and GR-α genes and evaluated whether GRs have a relationship with the apoptotic process in cultured HLECs. We also determined whether the inhibitor RU486 could rescue the...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c1mb05045a

    authors: Wang L,Zhao W,Leng F,Ge J,Bu Z,Zhang Y,Liu P

    更新日期:2011-06-01 00:00:00

  • Innate immunomodulation by lipophilic termini of lipopolysaccharide; synthesis of lipid As from Porphyromonas gingivalis and other bacteria and their immunomodulative responses.

    abstract::Synthetic studies of lipid A and LPS partial structures have been performed to investigate the relationship between structures and functions of LPS. Recent studies have suggested several pathological implications of LPS from parasitic bacteria due to its influence on the host immune responses. To address this issue, w...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章

    doi:10.1039/c3mb25477a

    authors: Fujimoto Y,Shimoyama A,Saeki A,Kitayama N,Kasamatsu C,Tsutsui H,Fukase K

    更新日期:2013-05-01 00:00:00

  • High throughput methods of assessing protein stability and aggregation.

    abstract::The significant increase in the demand for purified protein for crystallization and structural studies has made necessary the development of multi-sample methods for identifying solution conditions that affect protein stability and aggregation. Conditions that stabilize proteins can improve protein purification and cr...

    journal_title:Molecular bioSystems

    pub_type: 杂志文章,评审

    doi:10.1039/b814377c

    authors: Senisterra GA,Finerty PJ Jr

    更新日期:2009-03-01 00:00:00