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Book ; Online ; Thesis: In-silico und In-vitro-Screening von Proteinliganden zur Apoptoseinduktion

Füllbeck, Melanie

2007

Author's details	von Melanie Füllbeck
Language	German
Size	Online-Ressource
Document type	Book ; Online ; Thesis
Thesis / German Habilitation thesis	Humboldt-Univ., Diss--Berlin, 2007
Database	Former special subject collection: coastal and deep sea fishing

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Book ; Online ; Thesis: In-silico und In-vitro-Screening von Proteinliganden zur Apoptoseinduktion

Füllbeck, Melanie [Verfasser]

2007

Author's details	von Melanie Füllbeck
Keywords	Medizin, Gesundheit ; Medicine, Health
Subject code	sg610
Language	German
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article: Natural products: sources and databases.

Füllbeck, Melanie / Michalsky, Elke / Dunkel, Mathias / Preissner, Robert

Natural product reports

2006 Volume 23, Issue 3, Page(s) 347–356

MeSH term(s)	Biological Products/chemistry ; Biological Products/isolation & purification ; Biological Products/pharmacology ; Databases, Factual ; Internet
Chemical Substances	Biological Products
Language	English
Publishing date	2006-06
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2002546-4
ISSN	1460-4752 ; 0265-0568
ISSN (online)	1460-4752
ISSN	0265-0568
DOI	10.1039/b513504b
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Cellular Fingerprints: A Novel Approach Using Large-Scale Cancer Cell Line Data for the Identification of Potential Anticancer Agents

Füllbeck, Melanie / Dunkel, Mathias / Hossbach, Julia / Daniel, Peter T / Preissner, Robert

Chemical biology & drug design. 2009 Nov., v. 74, no. 5

2009

Abstract: The cellular fingerprint, a novel in silico screening approach, was developed to identify new biologically active compounds in combination with structural fingerprints. To this end, high-throughput screening (HTS) data from the National Cancer Institute ... ...

Abstract	The cellular fingerprint, a novel in silico screening approach, was developed to identify new biologically active compounds in combination with structural fingerprints. To this end, high-throughput screening (HTS) data from the National Cancer Institute have been used. To validate this method, we have selected the proapoptotic, natural compound betulinic acid (BA). Because of its antiproliferative effect on a variety of cancer cell lines, the identification of novel BA analogs is of great interest. Novel analogs have been identified and validated in different apoptosis assays. In addition, the novel approach exhibited a strong correlation between structural similarity and biological activity, so that it offers enormous potential for the identification of novel biologically active compounds.
Keywords	neoplasms ; apoptosis
Language	English
Dates of publication	2009-11
Size	p. 439-448.
Publisher	Blackwell Publishing Ltd
Publishing place	Oxford, UK
Document type	Article
ZDB-ID	2216600-2
ISSN	1747-0285 ; 1747-0277
ISSN (online)	1747-0285
ISSN	1747-0277
DOI	10.1111/j.1747-0285.2009.00883.x
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Cellular fingerprints: a novel approach using large-scale cancer cell line data for the identification of potential anticancer agents.

Füllbeck, Melanie / Dunkel, Mathias / Hossbach, Julia / Daniel, Peter T / Preissner, Robert

Chemical biology & drug design

2009 Volume 74, Issue 5, Page(s) 439–448

Abstract	The cellular fingerprint, a novel in silico screening approach, was developed to identify new biologically active compounds in combination with structural fingerprints. To this end, high-throughput screening (HTS) data from the National Cancer Institute have been used. To validate this method, we have selected the proapoptotic, natural compound betulinic acid (BA). Because of its antiproliferative effect on a variety of cancer cell lines, the identification of novel BA analogs is of great interest. Novel analogs have been identified and validated in different apoptosis assays. In addition, the novel approach exhibited a strong correlation between structural similarity and biological activity, so that it offers enormous potential for the identification of novel biologically active compounds.
MeSH term(s)	Animals ; Antineoplastic Agents/pharmacology ; Apoptosis/drug effects ; Combinatorial Chemistry Techniques/methods ; DNA Fragmentation/drug effects ; Drug Design ; Drug Screening Assays, Antitumor/methods ; Flow Cytometry ; Humans ; Inhibitory Concentration 50 ; Jurkat Cells ; Molecular Structure ; Signal Transduction/drug effects ; Triterpenes/chemistry ; Triterpenes/pharmacology
Chemical Substances	Antineoplastic Agents ; Triterpenes ; betulinic acid (4G6A18707N)
Language	English
Publishing date	2009-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2216600-2
ISSN	1747-0285 ; 1747-0277
ISSN (online)	1747-0285
ISSN	1747-0277
DOI	10.1111/j.1747-0285.2009.00883.x
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Computer-assisted identification of small-molecule Bcl-2 modulators.

Füllbeck, Melanie / Gebhardt, Nina / Hossbach, Julia / Daniel, Peter T / Preissner, Robert

Computational biology and chemistry

2009 Volume 33, Issue 6, Page(s) 451–456

Abstract: Apoptosis, the programmed cell death, is a highly regulated process, necessary for normal development and homeostasis of the functions of organisms. The Bcl-2 inhibitors BH3I-1 and BH3I-2 were used as lead compounds to find possible Bcl-2 or Bcl-X(L) ... ...

Abstract	Apoptosis, the programmed cell death, is a highly regulated process, necessary for normal development and homeostasis of the functions of organisms. The Bcl-2 inhibitors BH3I-1 and BH3I-2 were used as lead compounds to find possible Bcl-2 or Bcl-X(L) inhibitors by using computer-assisted screening with our in-house database, containing more than four million commercially available molecules. Identified compounds were further investigated regarding their possible application as a drug.
MeSH term(s)	Apoptosis/drug effects ; Benzamides/chemistry ; Benzamides/pharmacology ; Cell Line ; Computational Biology ; Computer Simulation ; Databases, Factual ; Humans ; Models, Chemical ; Molecular Weight ; Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors ; Thiazoles/chemistry ; Thiazoles/pharmacology
Chemical Substances	3-iodo-5-chloro-N-(2-chloro-5-((4-chlorophenyl)sulphonyl)phenyl)-2-hydroxybenzamide ; 5-(4-bromobenzylidene)-alpha-isopropyl-4-oxo-2-thioxo-3-thazolidineacetic acid ; Benzamides ; Proto-Oncogene Proteins c-bcl-2 ; Thiazoles
Language	English
Publishing date	2009-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1476-928X
ISSN (online)	1476-928X
DOI	10.1016/j.compbiolchem.2009.10.001
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SuperNatural: a searchable database of available natural compounds.

Dunkel, Mathias / Fullbeck, Melanie / Neumann, Stefanie / Preissner, Robert

Nucleic acids research

2005 Volume 34, Issue Database issue, Page(s) D678–83

Abstract: Although tremendous effort has been put into synthetic libraries, most drugs on the market are still natural compounds or derivatives thereof. There are encyclopaedias of natural compounds, but the availability of these compounds is often unclear and ... ...

Abstract	Although tremendous effort has been put into synthetic libraries, most drugs on the market are still natural compounds or derivatives thereof. There are encyclopaedias of natural compounds, but the availability of these compounds is often unclear and catalogues from numerous suppliers have to be checked. To overcome these problems we have compiled a database of approximately 50,000 natural compounds from different suppliers. To enable efficient identification of the desired compounds, we have implemented substructure searches with typical templates. Starting points for in silico screenings are about 2500 well-known and classified natural compounds from a compendium that we have added. Possible medical applications can be ascertained via automatic searches for similar drugs in a free conformational drug database containing WHO indications. Furthermore, we have computed about three million conformers, which are deployed to account for the flexibilities of the compounds when the 3D superposition algorithm that we have developed is used. The SuperNatural Database is publicly available at http://bioinformatics.charite.de/supernatural. Viewing requires the free Chime-plugin from MDL (Chime) or Java2 Runtime Environment (MView), which is also necessary for using Marvin application for chemical drawing.
MeSH term(s)	Anti-Infective Agents/chemistry ; Anti-Infective Agents/therapeutic use ; Clinical Trials as Topic ; Databases, Factual ; Drug Therapy ; Internet ; Pharmaceutical Preparations/chemistry ; User-Computer Interface
Chemical Substances	Anti-Infective Agents ; Pharmaceutical Preparations
Language	English
Publishing date	2005-10-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkj132
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Novel curcumin- and emodin-related compounds identified by in silico 2D/3D conformer screening induce apoptosis in tumor cells.

Füllbeck, Melanie / Huang, Xiaohua / Dumdey, Renate / Frommel, Cornelius / Dubiel, Wolfgang / Preissner, Robert

BMC cancer

2005 Volume 5, Page(s) 97

Abstract: Background: Inhibition of the COP9 signalosome (CSN) associated kinases CK2 and PKD by curcumin causes stabilization of the tumor suppressor p53. It has been shown that curcumin induces tumor cell death and apoptosis. Curcumin and emodin block the CSN- ... ...

Abstract	Background: Inhibition of the COP9 signalosome (CSN) associated kinases CK2 and PKD by curcumin causes stabilization of the tumor suppressor p53. It has been shown that curcumin induces tumor cell death and apoptosis. Curcumin and emodin block the CSN-directed c-Jun signaling pathway, which results in diminished c-Jun steady state levels in HeLa cells. The aim of this work was to search for new CSN kinase inhibitors analogue to curcumin and emodin by means of an in silico screening method. Methods: Here we present a novel method to identify efficient inhibitors of CSN-associated kinases. Using curcumin and emodin as lead structures an in silico screening with our in-house database containing more than 10(6) structures was carried out. Thirty-five compounds were identified and further evaluated by the Lipinski's rule-of-five. Two groups of compounds can be clearly discriminated according to their structures: the curcumin-group and the emodin-group. The compounds were evaluated in in vitro kinase assays and in cell culture experiments. Results: The data revealed 3 compounds of the curcumin-group (e.g. piceatannol) and 4 of the emodin-group (e.g. anthrachinone) as potent inhibitors of CSN-associated kinases. Identified agents increased p53 levels and induced apoptosis in tumor cells as determined by annexin V-FITC binding, DNA fragmentation and caspase activity assays. Conclusion: Our data demonstrate that the new in silico screening method is highly efficient for identifying potential anti-tumor drugs.
MeSH term(s)	Annexin A5/metabolism ; Antineoplastic Agents/pharmacology ; Apoptosis ; COP9 Signalosome Complex ; Caspase 3 ; Caspase 7 ; Caspases/biosynthesis ; Caspases/metabolism ; Cell Line, Tumor ; Cell Survival ; Curcumin/pharmacology ; DNA Fragmentation ; Drug Design ; Drug Screening Assays, Antitumor/methods ; Emodin/pharmacology ; Enzyme Inhibitors/pharmacology ; Gene Expression Regulation, Neoplastic ; HeLa Cells ; Humans ; Models, Chemical ; Models, Statistical ; Multiprotein Complexes/metabolism ; Peptide Hydrolases/metabolism ; Propidium/pharmacology ; Proto-Oncogene Proteins c-jun/metabolism ; Signal Transduction ; Software ; Tetrazolium Salts/pharmacology ; Thiazoles/pharmacology ; Tumor Suppressor Protein p53/metabolism
Chemical Substances	Annexin A5 ; Antineoplastic Agents ; Enzyme Inhibitors ; Multiprotein Complexes ; Proto-Oncogene Proteins c-jun ; Tetrazolium Salts ; Thiazoles ; Tumor Suppressor Protein p53 ; Propidium (36015-30-2) ; Peptide Hydrolases (EC 3.4.-) ; COP9 Signalosome Complex (EC 3.4.19.12) ; CASP3 protein, human (EC 3.4.22.-) ; CASP7 protein, human (EC 3.4.22.-) ; Caspase 3 (EC 3.4.22.-) ; Caspase 7 (EC 3.4.22.-) ; Caspases (EC 3.4.22.-) ; thiazolyl blue (EUY85H477I) ; Curcumin (IT942ZTH98) ; Emodin (KA46RNI6HN)
Language	English
Publishing date	2005-08-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1471-2407
ISSN (online)	1471-2407
DOI	10.1186/1471-2407-5-97
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Design and biological evaluation of photo-switchable inhibitors.

Füllbeck, Melanie / Michalsky, Elke / Jaeger, Ines Stephanie / Henklein, Peter / Kuhn, Hartmut / Rück-Braun, Karola / Preissner, Robert

Genome informatics. International Conference on Genome Informatics

2006 Volume 17, Issue 1, Page(s) 141–151

Abstract: Photo-switchable compounds are becoming increasingly popular for a series of biological applications based on the reversible photo-control of structure and function of biomolecules. Three applications for the usage of BODTCM and hemithioindigo as photo- ... ...

Abstract	Photo-switchable compounds are becoming increasingly popular for a series of biological applications based on the reversible photo-control of structure and function of biomolecules. Three applications for the usage of BODTCM and hemithioindigo as photo-reactive compounds are described here. The structure of the villin headpiece was modified by replacing a part of the backbone with hemithioindigo, aiming at induction of the folding process by irradiation with a defined wavelength. The E-isomer of BODTCM was applied as potential inhibitor of the 12/15-lipoxygenase (12/15-LOX), which is implicated in the pathogenesis of inflammatory diseases. A required death domain for the binding of proapoptotic proteins (e.g. Bak) to the hydrophobic groove of antiapoptotic proteins is the BH3 helix. Inserting hemithioindigo into this short peptide, stabilization towards proteolytic degradation is achieved. Such photo-reactive compounds might be developed as potential drugs for a great variety of diseases.
MeSH term(s)	Azoles/chemical synthesis ; Azoles/pharmacology ; BH3 Interacting Domain Death Agonist Protein/antagonists & inhibitors ; Humans ; Indicators and Reagents/chemical synthesis ; Indicators and Reagents/pharmacology ; Indigo Carmine/analogs & derivatives ; Indigo Carmine/chemistry ; Indigo Carmine/pharmacology ; Jurkat Cells ; Light ; Lipoxygenase Inhibitors/chemical synthesis ; Lipoxygenase Inhibitors/pharmacology ; Microfilament Proteins/chemistry ; Microfilament Proteins/pharmacology ; Organoselenium Compounds/chemical synthesis ; Organoselenium Compounds/pharmacology ; Peptide Fragments/chemistry ; Protein Binding ; Protein Structure, Secondary/drug effects ; Proto-Oncogene Proteins/chemistry ; Substrate Specificity
Chemical Substances	Azoles ; BH3 Interacting Domain Death Agonist Protein ; Bax protein (53-86) ; Indicators and Reagents ; Lipoxygenase Inhibitors ; Microfilament Proteins ; Organoselenium Compounds ; Peptide Fragments ; Proto-Oncogene Proteins ; villin ; ebselen (40X2P7DPGH) ; thioindigo (522-75-8) ; Indigo Carmine (D3741U8K7L)
Language	English
Publishing date	2006
Publishing country	Japan
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	0919-9454
ISSN	0919-9454
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Novel curcumin- and emodin-related compounds identified by in silico 2D/3D conformer screening induce apoptosis in tumor cells

Dubiel Wolfgang / Frommel Cornelius / Dumdey Renate / Huang Xiaohua / Füllbeck Melanie / Preissner Robert

BMC Cancer, Vol 5, Iss 1, p

2005 Volume 97

Abstract: Abstract Background Inhibition of the COP9 signalosome (CSN) associated kinases CK2 and PKD by curcumin causes stabilization of the tumor suppressor p53. It has been shown that curcumin induces tumor cell death and apoptosis. Curcumin and emodin block ... ...

Abstract	Abstract Background Inhibition of the COP9 signalosome (CSN) associated kinases CK2 and PKD by curcumin causes stabilization of the tumor suppressor p53. It has been shown that curcumin induces tumor cell death and apoptosis. Curcumin and emodin block the CSN-directed c-Jun signaling pathway, which results in diminished c-Jun steady state levels in HeLa cells. The aim of this work was to search for new CSN kinase inhibitors analogue to curcumin and emodin by means of an in silico screening method. Methods Here we present a novel method to identify efficient inhibitors of CSN-associated kinases. Using curcumin and emodin as lead structures an in silico screening with our in-house database containing more than 10 6 structures was carried out. Thirty-five compounds were identified and further evaluated by the Lipinski's rule-of-five. Two groups of compounds can be clearly discriminated according to their structures: the curcumin-group and the emodin-group. The compounds were evaluated in in vitro kinase assays and in cell culture experiments. Results The data revealed 3 compounds of the curcumin-group (e.g. piceatannol) and 4 of the emodin-group (e.g. anthrachinone) as potent inhibitors of CSN-associated kinases. Identified agents increased p53 levels and induced apoptosis in tumor cells as determined by annexin V-FITC binding, DNA fragmentation and caspase activity assays. Conclusion Our data demonstrate that the new in silico screening method is highly efficient for identifying potential anti-tumor drugs.
Keywords	Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282 ; Internal medicine ; RC31-1245 ; Medicine ; R ; DOAJ:Oncology ; DOAJ:Medicine (General) ; DOAJ:Health Sciences
Subject code	540 ; 500
Language	English
Publishing date	2005-08-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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