41 results on '"Ann-Gerd Thorsell"'
Search Results
2. Engineering Af1521 improves ADP-ribose binding and identification of ADP-ribosylated proteins
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Kathrin Nowak, Florian Rosenthal, Tobias Karlberg, Mareike Bütepage, Ann-Gerd Thorsell, Birgit Dreier, Jonas Grossmann, Jens Sobek, Ralph Imhof, Bernhard Lüscher, Herwig Schüler, Andreas Plückthun, Deena M. Leslie Pedrioli, and Michael O. Hottiger more...
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Science - Abstract
ADP-ribose binding macro domains facilitate the enrichment and detection of cellular ADP-ribosylation. Here, the authors generate an engineered macro domain with increased ADP-ribose affinity, improving the identification of ADP-ribosylated proteins by proteomics, western blot and immunofluorescence. more...
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- 2020
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Catalog
3. 14-3-3 proteins activate Pseudomonas exotoxins-S and -T by chaperoning a hydrophobic surface
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Tobias Karlberg, Peter Hornyak, Ana Filipa Pinto, Stefina Milanova, Mahsa Ebrahimi, Mikael Lindberg, Nikolai Püllen, Axel Nordström, Elinor Löverli, Rémi Caraballo, Emily V. Wong, Katja Näreoja, Ann-Gerd Thorsell, Mikael Elofsson, Enrique M. De La Cruz, Camilla Björkegren, and Herwig Schüler more...
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Science - Abstract
The cellular toxicity of Pseudomonas exotoxin-S and -T depends on their activation by 14-3-3 but the underlying molecular mechanism is not fully understood. Here, the authors show that a previously unrecognized 14-3-3:exotoxin binding interface is sufficient for complex formation and toxin activation. more...
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- 2018
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4. Comparative structural analysis of lipid binding START domains.
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Ann-Gerd Thorsell, Wen Hwa Lee, Camilla Persson, Marina I Siponen, Martina Nilsson, Robert D Busam, Tetyana Kotenyova, Herwig Schüler, and Lari Lehtiö
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Medicine ,Science - Abstract
Steroidogenic acute regulatory (StAR) protein related lipid transfer (START) domains are small globular modules that form a cavity where lipids and lipid hormones bind. These domains can transport ligands to facilitate lipid exchange between biological membranes, and they have been postulated to modulate the activity of other domains of the protein in response to ligand binding. More than a dozen human genes encode START domains, and several of them are implicated in a disease.We report crystal structures of the human STARD1, STARD5, STARD13 and STARD14 lipid transfer domains. These represent four of the six functional classes of START domains.Sequence alignments based on these and previously reported crystal structures define the structural determinants of human START domains, both those related to structural framework and those involved in ligand specificity.This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1. more...
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- 2011
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5. Comparative structural analysis of human DEAD-box RNA helicases.
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Patrick Schütz, Tobias Karlberg, Susanne van den Berg, Ruairi Collins, Lari Lehtiö, Martin Högbom, Lovisa Holmberg-Schiavone, Wolfram Tempel, Hee-Won Park, Martin Hammarström, Martin Moche, Ann-Gerd Thorsell, and Herwig Schüler more...
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Medicine ,Science - Abstract
DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members. more...
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- 2010
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6. A Focused DNA-Encoded Chemical Library for the Discovery of Inhibitors of NAD+-Dependent Enzymes
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Raphael M. Franzini, Srikanta Dana, Ann-Gerd Thorsell, Yu Liu, Samuel I. Bloom, Lik Hang Yuen, Anthony J. Donato, Herwig Schüler, Dmitri Kireev, and Dario Neri
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chemistry.chemical_classification ,Synthetic protein ,Extramural ,Drug discovery ,DNA-encoded chemical library ,Nad dependent ,General Chemistry ,Computational biology ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Catalysis ,0104 chemical sciences ,Colloid and Surface Chemistry ,Enzyme ,chemistry ,NAD+ kinase ,Pharmaceutical sciences - Abstract
DNA-encoded chemical libraries are increasingly used in pharmaceutical research because they enable the rapid discovery of synthetic protein ligands. Here we explored whether target-class focused DNA-encoded chemical libraries can be cost-effective tools to achieve robust screening productivity for a series of proteins. The study revealed that a DNA-encoded library designed for NAD+-binding pockets (NADEL) effectively sampled the chemical binder space of enzymes with ADP-ribosyltransferase activity. The extracted information directed the synthesis of inhibitors for several enzymes including PARP15 and SIRT6. The high dissimilarity of NADEL screening fingerprints for different proteins translated into inhibitors that showed selectivity for their target. The discovery of patterns of enriched structures for six out of eight tested proteins is remarkable for a library of 58 302 DNA-tagged structures and illustrates the prospect of focused DNA-encoded libraries as economic alternatives to large library platforms. more...
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- 2019
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7. SIESTA as a universal unbiased proteomics approach for identification and prioritization of enzyme substrates
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Qing Cheng, Tobias Karlberg, Susanna L. Lundström, Sergey Rodin, Herwig Schüler, Alexey Chernobrovkin, Christian M. Beusch, Massimiliano Gaetani, Katja Näreoja, Ákos Végvári, Roman A. Zubarev, Hassan Gharibi, Ann-Gerd Thorsell, Zhaowei Meng, Pierre Sabatier, Elias S.J. Arnér, Amir Ata Saei, and Juan Astorga Wells more...
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Prioritization ,Computer science ,Identification (biology) ,Computational biology ,SIESTA (computer program) ,Proteomics - Abstract
This protocol describes the proteomics technique called System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis or SIESTA 1,2. SIESTA can be used for universal discovery of enzyme substrates that shift in thermal stability or solubility upon post-translational modification (PTM). Experimental design, proteomics sample preparation and data analysis are the key stages of this protocol. Data analysis can be performed using our SIESTA package hosted on GitHub 3. When performed with classical thermal proteome profiling (TPP), the protocol will take 5 days for sample preparation and 14 days of sample analysis by mass spectrometry (the current protocol). If our high-throughput version of TPP called Proteome Integral Solubility Alteration assay (PISA) 4 is used instead, the sample analysis time by mass spectrometry is reduced to 1-2 days for the same number of conditions. more...
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- 2021
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8. System-wide identification and prioritization of enzyme substrates by thermal analysis
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Sergey Rodin, Christian M. Beusch, Katja Näreoja, Herwig Schüler, Pierre Sabatier, Hassan Gharibi, Elias S.J. Arnér, Amir Ata Saei, Alexey Chernobrovkin, Massimiliano Gaetani, Zhaowei Meng, Ann-Gerd Thorsell, Ákos Végvári, Qing Cheng, Susanna L. Lundström, Roman A. Zubarev, Tobias Karlberg, and Juan Astorga Wells more...
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Proteomics ,0301 basic medicine ,Thioredoxin Reductase 1 ,Science ,General Physics and Astronomy ,Computational biology ,Article ,General Biochemistry, Genetics and Molecular Biology ,Substrate Specificity ,03 medical and health sciences ,0302 clinical medicine ,Oxidoreductase ,Proto-Oncogene Proteins ,Drug Discovery ,Humans ,SIESTA (computer program) ,Polymerase ,chemistry.chemical_classification ,Multidisciplinary ,Mass spectrometry ,biology ,Drug discovery ,Carcinoma ,Biochemistry and Molecular Biology ,Proteins ,Substrate (chemistry) ,General Chemistry ,HCT116 Cells ,Enzymes ,030104 developmental biology ,Enzyme ,chemistry ,biology.protein ,Selenoprotein ,Poly(ADP-ribose) Polymerases ,Protein Processing, Post-Translational ,Proto-Oncogene Proteins c-akt ,030217 neurology & neurosurgery ,Biokemi och molekylärbiologi ,Post-translational modifications - Abstract
Despite the immense importance of enzyme–substrate reactions, there is a lack of general and unbiased tools for identifying and prioritizing substrate proteins that are modified by the enzyme on the structural level. Here we describe a high-throughput unbiased proteomics method called System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA). The approach assumes that the enzymatic post-translational modification of substrate proteins is likely to change their thermal stability. In our proof-of-concept studies, SIESTA successfully identifies several known and novel substrate candidates for selenoprotein thioredoxin reductase 1, protein kinase B (AKT1) and poly-(ADP-ribose) polymerase-10 systems. Wider application of SIESTA can enhance our understanding of the role of enzymes in homeostasis and disease, opening opportunities to investigate the effect of post-translational modifications on signal transduction and facilitate drug discovery., The global identification of enzyme substrates is still challenging. Here, the authors develop a method based on proteome-wide thermal shift assays to discover enzyme substrates directly from cell lysates, identifying known and novel oxidoreductase, kinase and poly-(ADP-ribose) polymerase substrates. more...
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- 2021
9. Correction to 'A Focused DNA-Encoded Chemical Library for the Discovery of Inhibitors of NAD+-Dependent Enzymes'
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Ann-Gerd Thorsell, Raphael M. Franzini, Dario Neri, Yu Liu, Herwig Schüler, Srikanta Dana, Dmitri Kireev, Anthony J. Donato, Samuel I. Bloom, and Lik Hang Yuen
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chemistry.chemical_classification ,Colloid and Surface Chemistry ,Enzyme ,chemistry ,Biochemistry ,DNA-encoded chemical library ,Nad dependent ,General Chemistry ,Catalysis - Published
- 2021
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10. Engineering Af1521 improves ADP-ribose binding and identification of ADP-ribosylated proteins
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Jonas Grossmann, Tobias Karlberg, Birgit Dreier, Mareike Bütepage, Deena M. Leslie Pedrioli, Ann-Gerd Thorsell, Bernhard Lüscher, Michael O. Hottiger, Herwig Schüler, Andreas Plückthun, Ralph Imhof, Florian Rosenthal, Jens Sobek, Kathrin Nowak, University of Zurich, and Hottiger, Michael O more...
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Proteomics ,Models, Molecular ,0301 basic medicine ,Protein Conformation ,General Physics and Astronomy ,Protein Engineering ,chemistry.chemical_compound ,Macro domain ,Protein structure ,lcsh:Science ,health care economics and organizations ,Multidisciplinary ,10226 Department of Molecular Mechanisms of Disease ,3100 General Physics and Astronomy ,3. Good health ,Isolation, separation and purification ,PolyADP-ribosylation ,ddc:500 ,Binding domain ,Science ,Protein domain ,Mutagenesis (molecular biology technique) ,610 Medicine & health ,1600 General Chemistry ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,ADP-Ribosylation ,Protein Domains ,1300 General Biochemistry, Genetics and Molecular Biology ,Ribose ,10019 Department of Biochemistry ,Humans ,Binding site ,Adenosine Diphosphate Ribose ,Binding Sites ,030102 biochemistry & molecular biology ,Proteins ,nutritional and metabolic diseases ,social sciences ,General Chemistry ,stomatognathic diseases ,HEK293 Cells ,030104 developmental biology ,chemistry ,Mutagenesis ,Biophysics ,570 Life sciences ,biology ,lcsh:Q ,Salt bridge ,Protein design ,Carrier Proteins ,Protein Processing, Post-Translational ,HeLa Cells - Abstract
Protein ADP-ribosylation is a reversible post-translational modification that regulates important cellular functions. The identification of modified proteins has proven challenging and has mainly been achieved via enrichment methodologies. Random mutagenesis was used here to develop an engineered Af1521 ADP-ribose binding macro domain protein with 1000-fold increased affinity towards ADP-ribose. The crystal structure reveals that two point mutations K35E and Y145R form a salt bridge within the ADP-ribose binding domain. This forces the proximal ribose to rotate within the binding pocket and, as a consequence, improves engineered Af1521 ADPr-binding affinity. Its use in our proteomic ADP-ribosylome workflow increases the ADP-ribosylated protein identification rates and yields greater ADP-ribosylome coverage. Furthermore, generation of an engineered Af1521 Fc fusion protein confirms the improved detection of cellular ADP-ribosylation by immunoblot and immunofluorescence. Thus, this engineered isoform of Af1521 can also serve as a valuable tool for the analysis of cellular ADP-ribosylation under in vivo conditions., ADP-ribose binding macro domains facilitate the enrichment and detection of cellular ADP-ribosylation. Here, the authors generate an engineered macro domain with increased ADP-ribose affinity, improving the identification of ADP-ribosylated proteins by proteomics, western blot and immunofluorescence. more...
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- 2020
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11. 14-3-3 proteins activate Pseudomonas exotoxins-S and -T by chaperoning a hydrophobic surface
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Mahsa Ebrahimi, Enrique M. De La Cruz, Herwig Schüler, A.F. Pinto, Emily V. Wong, Stefina Milanova, Ann-Gerd Thorsell, Elinor Löverli, Peter Hornyak, Camilla Björkegren, Katja Näreoja, Mikael Elofsson, Nikolai Pullen, Mikael J. Lindberg, Rémi Caraballo, Axel Nordström, and Tobias Karlberg more...
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Models, Molecular ,0301 basic medicine ,GTPase-activating protein ,Protein Conformation ,Cell- och molekylärbiologi ,Complex formation ,General Physics and Astronomy ,Crystallography, X-Ray ,medicine.disease_cause ,Protein structure ,Models ,Pseudomonas exotoxin ,lcsh:Science ,ADP Ribose Transferases ,0303 health sciences ,Multidisciplinary ,Crystallography ,biology ,Chemistry ,Phosphopeptide ,Pseudomonas ,GTPase-Activating Proteins ,Biochemistry and Molecular Biology ,3. Good health ,Infectious Diseases ,Pseudomonas aeruginosa ,Host-Pathogen Interactions ,Infection ,Hydrophobic and Hydrophilic Interactions ,Science ,Protein domain ,Bacterial Toxins ,Saccharomyces cerevisiae ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Protein Domains ,medicine ,Escherichia coli ,Binding site ,030304 developmental biology ,Binding Sites ,030102 biochemistry & molecular biology ,030306 microbiology ,Toxin ,Molecular ,General Chemistry ,biology.organism_classification ,Vibrio ,030104 developmental biology ,Emerging Infectious Diseases ,Hydrophobic surfaces ,14-3-3 Proteins ,Biophysics ,X-Ray ,lcsh:Q ,Cell and Molecular Biology ,Biokemi och molekylärbiologi ,Exotoxin ,Molecular Chaperones - Abstract
Pseudomonasare a common cause of hospital acquired infections that may be lethal. ADP-ribosyltransferase activities ofPseudomonasexotoxin-S and -T depend on 14-3-3 proteins inside the host cell. By binding in the 14-3-3 phosphopeptide binding groove, a hydrophobic C-terminal helix of ExoS and ExoT has been thought to be crucial for their activation. However, crystal structures of the 14-3-3β:ExoS and -ExoT complexes presented here reveal an extensive novel binding interface that is sufficient for complex formation and toxin activation. We show that C-terminally truncated ExoS ADP-ribosyltransferase domain lacking the hydrophobic binding motif is active when co-expressed with 14-3-3. Moreover, swapping the hydrophobic C-terminus with a fragment fromVibrioVis toxin creates a 14-3-3 independent toxin that ADP-ribosylates known ExoS targets. Finally, we show that 14-3-3 stabilizes ExoS against thermal aggregation. Together, this indicates that 14-3-3 proteins activate exotoxin ADP-ribosyltransferase domains by chaperoning their hydrophobic surfaces independently of the hydrophobic C-terminal segment.Short summaryCrystal structures of Pseudomonas exotoxins-S and –T identify a novel hydrophobic interface with 14-3-3 proteins, and we show that 14-3-3 activates these toxins independent of their phosphopeptide groove binding C-termini, by preventing their aggregation. more...
- Published
- 2018
12. Design and synthesis of potent inhibitors of the mono(ADP-ribosyl)transferase, PARP14
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Jacob Holechek, Emily Wolf, Robert Lease, Matthew Meyers, Dana Ferraris, Tobias Karlberg, Kristen Upton, Ann-Gerd Thorsell, Herwig Schüler, Adrianna Lucente, and Garrett Schey
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Models, Molecular ,0301 basic medicine ,Dose-Response Relationship, Drug ,Molecular Structure ,Stereochemistry ,Chemistry ,Poly ADP ribose polymerase ,Organic Chemistry ,Clinical Biochemistry ,Pharmaceutical Science ,Poly(ADP-ribose) Polymerase Inhibitors ,Biochemistry ,Structure-Activity Relationship ,03 medical and health sciences ,030104 developmental biology ,Drug Design ,Drug Discovery ,Humans ,Molecular Medicine ,Transferase ,Poly(ADP-ribose) Polymerases ,Selectivity ,Molecular Biology ,IC50 - Abstract
A series of (Z)-4-(3-carbamoylphenylamino)-4-oxobut-2-enyl amides were synthesized and tested for their ability to inhibit the mono-(ADP-ribosyl)transferase, PARP14 (a.k.a. BAL-2; ARTD-8). Two synthetic routes were established for this series and several compounds were identified as sub-micromolar inhibitors of PARP14, the most potent of which was compound 4t, IC50=160nM. Furthermore, profiling other members of this series identified compounds with >20-fold selectivity over PARP5a/TNKS1, and modest selectivity over PARP10, a closely related mono-(ADP-ribosyl)transferase. more...
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- 2017
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13. A Focused DNA-Encoded Chemical Library for the Discovery of Inhibitors of NAD
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Lik Hang, Yuen, Srikanta, Dana, Yu, Liu, Samuel I, Bloom, Ann-Gerd, Thorsell, Dario, Neri, Anthony J, Donato, Dmitri, Kireev, Herwig, Schüler, and Raphael M, Franzini
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ADP Ribose Transferases ,Models, Molecular ,Small Molecule Libraries ,Molecular Structure ,Drug Discovery ,Humans ,Sirtuins ,DNA ,Enzyme Inhibitors - Abstract
DNA-encoded chemical libraries are increasingly used in pharmaceutical research because they enable the rapid discovery of synthetic protein ligands. Here we explored whether target-class focused DNA-encoded chemical libraries can be cost-effective tools to achieve robust screening productivity for a series of proteins. The study revealed that a DNA-encoded library designed for NAD more...
- Published
- 2019
14. System-wide identification and prioritization of enzyme substrates by thermal analysis (SIESTA)
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Katja Näreoja, Sergey Rodin, Pierre Sabatier, Elias S.J. Arnér, Christian M. Beusch, Tobias Karlberg, Alexey Chernobrovkin, Amir Ata Saei, Juan Astorga Wells, Susanna L. Lundström, Ann-Gerd Thorsell, Herwig Schüler, Ákos Végvári, Massimiliano Gaetani, Qing Cheng, and Roman A. Zubarev more...
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chemistry.chemical_classification ,Enzyme ,chemistry ,Drug discovery ,Thioredoxin Reductase 1 ,Substrate (chemistry) ,Identification (biology) ,Computational biology ,Selenoprotein ,Signal transduction ,SIESTA (computer program) - Abstract
Despite the immense importance of enzyme-substrate reactions, there is a lack of generic and unbiased tools for identifying and prioritizing substrate proteins which are modulated in the structural and functional levels through modification. Here we describe a high-throughput unbiased proteomic method called System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA). The approach assumes that enzymatic post-translational modification of substrate proteins might change their thermal stability. SIESTA successfully identifies several known and novel substrate candidates for selenoprotein thioredoxin reductase 1, protein kinase B (AKT1) and poly-(ADP-ribose) polymerase-10 systems in up to a depth of 7179 proteins. Wider application of SIESTA can enhance our understanding of the role of enzymes in homeostasis and disease, open new opportunities in investigating the effect of PTMs on signal transduction, and facilitate drug discovery. more...
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- 2018
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15. Design, synthesis and evaluation of potent and selective inhibitors of mono-(ADP-ribosyl)transferases PARP10 and PARP14
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Robert Lease, Jacob Holechek, Ryan Grant, Tobias Karlberg, Herwig Schüler, Dana Ferraris, Abby Keen, Caitlin McCadden, Ann-Gerd Thorsell, and Evan Callahan
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0301 basic medicine ,Stereochemistry ,Poly ADP ribose polymerase ,Clinical Biochemistry ,Pharmaceutical Science ,Crystal structure ,Poly(ADP-ribose) Polymerase Inhibitors ,01 natural sciences ,Biochemistry ,03 medical and health sciences ,Structure-Activity Relationship ,PARP1 ,Proto-Oncogene Proteins ,Drug Discovery ,Transferase ,Potency ,Humans ,Molecular Biology ,Dose-Response Relationship, Drug ,Molecular Structure ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,Amides ,0104 chemical sciences ,030104 developmental biology ,Design synthesis ,Drug Design ,Molecular Medicine ,Poly(ADP-ribose) Polymerases ,Selectivity ,Ethers - Abstract
A series of diaryl ethers were designed and synthesized to discern the structure activity relationships against the two closely related mono-(ADP-ribosyl)transferases PARP10 and PARP14. Structure activity studies identified 8b as a sub-micromolar inhibitor of PARP10 with ∼15-fold selectivity over PARP14. In addition, 8k and 8m were discovered to have sub-micromolar potency against PARP14 and demonstrated moderate selectivity over PARP10. A crystal structure of the complex of PARP14 and 8b shows binding of the compound in a novel hydrophobic pocket and explains both potency and selectivity over other PARP family members. In addition, 8b, 8k and 8m also demonstrate selectivity over PARP1. Together, this study identified novel, potent and metabolically stable derivatives to use as chemical probes for these biologically interesting therapeutic targets. more...
- Published
- 2018
16. Structural Basis for Lack of ADP-ribosyltransferase Activity in Poly(ADP-ribose) Polymerase-13/Zinc Finger Antiviral Protein
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C. David Andersson, Mirjam Klepsch, Tobias Karlberg, Herwig Schüler, Anna Linusson, and Ann-Gerd Thorsell
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Poly ADP ribose polymerase ,Molecular Sequence Data ,Molecular Dynamics Simulation ,ADP Ribose Transferases ,Crystallography, X-Ray ,Biochemistry ,Stress granule ,Consensus sequence ,Humans ,Amino Acid Sequence ,Molecular Biology ,Peptide sequence ,Polymerase ,Zinc finger ,Sequence Homology, Amino Acid ,biology ,Zinc Fingers ,Cell Biology ,NAD ,ADP-ribosylation ,Protein Structure and Folding ,Mutagenesis, Site-Directed ,biology.protein ,Poly(ADP-ribose) Polymerases - Abstract
The mammalian poly(ADP-ribose) polymerase (PARP) family includes ADP-ribosyltransferases with diphtheria toxin homology (ARTD). Most members have mono-ADP-ribosyltransferase activity. PARP13/ARTD13, also called zinc finger antiviral protein, has roles in viral immunity and microRNA-mediated stress responses. PARP13 features a divergent PARP homology domain missing a PARP consensus sequence motif; the domain has enigmatic functions and apparently lacks catalytic activity. We used x-ray crystallography, molecular dynamics simulations, and biochemical analyses to investigate the structural requirements for ADP-ribosyltransferase activity in human PARP13 and two of its functional partners in stress granules: PARP12/ARTD12, and PARP15/BAL3/ARTD7. The crystal structure of the PARP homology domain of PARP13 shows obstruction of the canonical active site, precluding NAD(+) binding. Molecular dynamics simulations indicate that this closed cleft conformation is maintained in solution. Introducing consensus side chains in PARP13 did not result in 3-aminobenzamide binding, but in further closure of the site. Three-dimensional alignment of the PARP homology domains of PARP13, PARP12, and PARP15 illustrates placement of PARP13 residues that deviate from the PARP family consensus. Introducing either one of two of these side chains into the corresponding positions in PARP15 abolished PARP15 ADP-ribosyltransferase activity. Taken together, our results show that PARP13 lacks the structural requirements for ADP-ribosyltransferase activity. more...
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- 2015
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17. A Potent and Selective PARP11 Inhibitor Suggests Coupling between Cellular Localization and Catalytic Activity
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Ilsa T Kirby, Ana Kojic, Moriah R. Arnold, Herwig Schüler, Tobias Karlberg, Ann Gerd Thorsell, Raashi Sreenivasan, Carsten Schultz, Michael S. Cohen, and Anke Vermehren-Schmaedick
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0301 basic medicine ,MARylation ,Poly ADP ribose polymerase ,Clinical Biochemistry ,Poly(ADP-ribose) Polymerase Inhibitors ,Biochemistry ,03 medical and health sciences ,0302 clinical medicine ,Drug Discovery ,Transferase ,Humans ,Molecular Biology ,Cellular localization ,Polymerase ,Quinazolinones ,Pharmacology ,biology ,Molecular Structure ,Limiting ,Cell biology ,Protein Transport ,030104 developmental biology ,030220 oncology & carcinogenesis ,ADP-ribosylation ,biology.protein ,Biocatalysis ,Molecular Medicine ,Poly(ADP-ribose) Polymerases ,HeLa Cells - Abstract
Summary Poly-ADP-ribose polymerases (PARPs1-16) play pivotal roles in diverse cellular processes. PARPs that catalyze poly-ADP-ribosylation (PARylation) are the best characterized PARP family members because of the availability of potent and selective inhibitors for these PARPs. There has been comparatively little success in developing selective small-molecule inhibitors of PARPs that catalyze mono-ADP-ribosylation (MARylation), limiting our understanding of the cellular role of MARylation. Here we describe the structure-guided design of inhibitors of PARPs that catalyze MARylation. The most selective analog, ITK7, potently inhibits the MARylation activity of PARP11, a nuclear envelope-localized PARP. ITK7 is greater than 200-fold selective over other PARP family members. Using live-cell imaging, we show that ITK7 causes PARP11 to dissociate from the nuclear envelope. These results suggest that the cellular localization of PARP11 is regulated by its catalytic activity. more...
- Published
- 2017
18. Correction to 'Structural Basis for Potency and Promiscuity in Poly(ADP-ribose) Polymerase (PARP) and Tankyrase Inhibitors'
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Tobias Karlberg, A.F. Pinto, T. Ekblad, Lionel Trésaugues, Ann Gerd Thorsell, Michael S. Cohen, Herwig Schüler, Martin Moche, and Mirjam Löw
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Biochemistry ,Chemistry ,Poly ADP ribose polymerase ,Drug Discovery ,Molecular Medicine ,Potency ,Article - Abstract
Selective inhibitors could help unveil the mechanisms by which inhibition of poly(ADP-ribose) polymerases (PARPs) elicits clinical benefits in cancer therapy. We profiled 10 clinical PARP inhibitors and commonly used research tools for their inhibition of multiple PARP enzymes. We also determined crystal structures of these compounds bound to PARP1 or PARP2. Veliparib and niraparib are selective inhibitors of PARP1 and PARP2; olaparib, rucaparib, and talazoparib are more potent inhibitors of PARP1 but are less selective. PJ34 and UPF1069 are broad PARP inhibitors; PJ34 inserts a flexible moiety into hydrophobic subpockets in various ADP-ribosyltransferases. XAV939 is a promiscuous tankyrase inhibitor and a potent inhibitor of PARP1 in vitro and in cells, whereas IWR1 and AZ-6102 are tankyrase selective. Our biochemical and structural analysis of PARP inhibitor potencies establishes a molecular basis for either selectivity or promiscuity and provides a benchmark for experimental design in assessment of PARP inhibitor effects. more...
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- 2019
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19. Structural Basis for Potency and Promiscuity in Poly(ADP-ribose) Polymerase (PARP) and Tankyrase Inhibitors
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A.F. Pinto, Mirjam Löw, Ann Gerd Thorsell, T. Ekblad, Herwig Schüler, Martin Moche, Tobias Karlberg, Michael S. Cohen, and Lionel Trésaugues
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0301 basic medicine ,Models, Molecular ,Indazoles ,Veliparib ,Poly ADP ribose polymerase ,Poly(ADP-ribose) Polymerase Inhibitors ,Piperazines ,Olaparib ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,PARP1 ,Piperidines ,Drug Discovery ,Talazoparib ,Animals ,Humans ,Enzyme Inhibitors ,Rucaparib ,chemistry.chemical_classification ,Tankyrases ,Phenanthrenes ,030104 developmental biology ,Enzyme ,HEK293 Cells ,chemistry ,Biochemistry ,030220 oncology & carcinogenesis ,PARP inhibitor ,Molecular Medicine ,Phthalazines ,Benzimidazoles ,Poly(ADP-ribose) Polymerases - Abstract
Selective inhibitors could help unveil the mechanisms by which inhibition of poly(ADP-ribose) polymerases (PARPs) elicits clinical benefits in cancer therapy. We profiled 10 clinical PARP inhibitors and commonly used research tools for their inhibition of multiple PARP enzymes. We also determined crystal structures of these compounds bound to PARP1 or PARP2. Veliparib and niraparib are selective inhibitors of PARP1 and PARP2; olaparib, rucaparib, and talazoparib are more potent inhibitors of PARP1 but are less selective. PJ34 and UPF1069 are broad PARP inhibitors; PJ34 inserts a flexible moiety into hydrophobic subpockets in various ADP-ribosyltransferases. XAV939 is a promiscuous tankyrase inhibitor and a potent inhibitor of PARP1 in vitro and in cells, whereas IWR1 and AZ-6102 are tankyrase selective. Our biochemical and structural analysis of PARP inhibitor potencies establishes a molecular basis for either selectivity or promiscuity and provides a benchmark for experimental design in assessment of PARP inhibitor effects. more...
- Published
- 2016
20. Small Molecule Microarray Based Discovery of PARP14 Inhibitors
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Bo Peng, Ann Gerd Thorsell, Herwig Schüler, Shao Q. Yao, and Tobias Karlberg
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0301 basic medicine ,Poly ADP ribose polymerase ,High-throughput screening ,Poly(ADP-ribose) Polymerase Inhibitors ,010402 general chemistry ,01 natural sciences ,Catalysis ,Small Molecule Libraries ,03 medical and health sciences ,chemistry.chemical_compound ,Structure-Activity Relationship ,PARP1 ,Drug Discovery ,Transferase ,Humans ,chemistry.chemical_classification ,Nicotinamide ,010405 organic chemistry ,General Medicine ,General Chemistry ,Microarray Analysis ,Combinatorial chemistry ,Small molecule ,0104 chemical sciences ,High-Throughput Screening Assays ,030104 developmental biology ,Enzyme ,chemistry ,Biochemistry ,DNA microarray ,Poly(ADP-ribose) Polymerases - Abstract
Poly(ADP-ribose) polymerases (PARPs) are key enzymes in a variety of cellular processes. Most small-molecule PARP inhibitors developed to date have been against PARP1, and suffer from poor selectivity. PARP14 has recently emerged as a potential therapeutic target, but its inhibitor development has trailed behind. Herein, we describe a small molecule microarray-based strategy for high-throughput synthesis, screening of >1000 potential bidentate inhibitors of PARPs, and the successful discovery of a potent PARP14 inhibitor H10 with >20-fold selectivity over PARP1. Co-crystallization of the PARP14/H10 complex indicated H10 bound to both the nicotinamide and the adenine subsites. Further structure-activity relationship studies identified important binding elements in the adenine subsite. In tumor cells, H10 was able to chemically knockdown endogenous PARP14 activities. more...
- Published
- 2016
21. Discovery of Ligands for ADP-Ribosyltransferases via Docking-Based Virtual Screening
- Author
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Johan Weigelt, Anna Linusson, Tobias Karlberg, Urszula Uciechowska, Herwig Schüler, C. David Andersson, Mikael Elofsson, Anders E. G. Lindgren, T. Ekblad, Ann-Gerd Thorsell, Sara Spjut, Pernilla Wittung-Stafshede, and Moritz S. Niemiec more...
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ADP Ribose Transferases ,Models, Molecular ,Virtual screening ,biology ,Nicotinamide ,DNA repair ,Stereochemistry ,Isothermal titration calorimetry ,Nicotinamide adenine dinucleotide ,Ligands ,Cofactor ,chemistry.chemical_compound ,chemistry ,Biochemistry ,Docking (molecular) ,Drug Discovery ,biology.protein ,Molecular Medicine ,NAD+ kinase - Abstract
The diphtheria toxin-like ADP-ribosyltransferases (ARTDs) are an enzyme family that catalyzes the transfer of ADP-ribose units onto substrate proteins by using nicotinamide adenine dinucleotide (NAD(+)) as a cosubstrate. They have a documented role in chromatin remodelling and DNA repair, and inhibitors of ARTD1 and 2 (PARP1 and 2) are currently in clinical trials for the treatment of cancer. The detailed function of most other ARTDs is still unknown. By using virtual screening, we identified small ligands of ARTD7 (PARP15/BAL3) and ARTD8 (PARP14/BAL2). Thermal-shift assays confirmed that 16 compounds, belonging to eight structural classes, bound to ARTD7/ARTD8. Affinity measurements with isothermal titration calorimetry for two isomers of the most promising hit compound confirmed binding in the low micromolar range to ARTD8. Crystal structures showed anchoring of the hits in the nicotinamide pocket. These results form a starting point in the development of chemical tools for the study of the role and function of ARTD7 and ARTD8. more...
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- 2012
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22. Crystal Structure of Human ADP-ribose Transferase ARTD15/PARP16 Reveals a Novel Putative Regulatory Domain
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Åsa Kallas, Herwig Schüler, Ann-Gerd Thorsell, and Tobias Karlberg
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Sequence Homology, Amino Acid ,biology ,Effector ,Poly ADP ribose polymerase ,Molecular Sequence Data ,Protein domain ,Cell Biology ,Crystallography, X-Ray ,Biochemistry ,Protein Structure, Tertiary ,Protein structure ,ADP-ribosylation ,Protein Structure and Folding ,biology.protein ,Humans ,Transferase ,Amino Acid Sequence ,NAD+ kinase ,Poly(ADP-ribose) Polymerases ,Molecular Biology ,Polymerase - Abstract
ADP-ribosylation is involved in the regulation of DNA repair, transcription, and other processes. The 18 human ADP-ribose transferases with diphtheria toxin homology include ARTD1/PARP1, a cancer drug target. Knowledge of other family members may guide therapeutics development and help evaluate potential drug side effects. Here, we present the crystal structure of human ARTD15/PARP16, a previously uncharacterized enzyme. ARTD15 features an α-helical domain that packs against its transferase domain without making direct contact with the NAD+-binding crevice or the donor loop. Thus, this novel domain does not resemble the regulatory domain of ARTD1. ARTD15 displays auto-mono(ADP-ribosylation) activity and is affected by canonical poly(ADP-ribose) polymerase inhibitors. These results add to a framework that will facilitate research on a medically important family of enzymes. Background: ADP-ribose transferases ARTD1–3/PARP1–3 have an α-helical domain that closes over the NAD+-binding site. Results: Human ARTD15/PARP16 is a mono(ADP-ribose) transferase with a novel α-helical domain that interacts with a catalytic domain loop. Conclusion: The ARTD15 transferase domain is likely regulated by effector binding to the adjacent helical domain. Significance: This provides a basis for understanding the enzymatic mechanism of this previously uncharacterized enzyme. more...
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- 2012
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23. Family-wide chemical profiling and structural analysis of PARP and tankyrase inhibitors
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Herwig Schüler, J. Weigelt, Antonio Macchiarulo, Delal Öncü, Ann-Gerd Thorsell, Roberto Pellicciari, Björn Kull, T. Ekblad, Elisabet Wahlberg, Ewa Pol, Åsa Frostell, Tobias Karlberg, Graeme M. Robertson, N. Markova, and Ekaterina Kouznetsova more...
- Subjects
Biomedical Engineering ,Bioengineering ,Poly(ADP-ribose) Polymerase Inhibitors ,Biology ,Crystallography, X-Ray ,Applied Microbiology and Biotechnology ,Poly (ADP-Ribose) Polymerase Inhibitor ,Olaparib ,Small Molecule Libraries ,chemistry.chemical_compound ,Catalytic Domain ,Tankyrases ,Humans ,Computer Simulation ,Amino Acid Sequence ,Enzyme Inhibitors ,Binding site ,Rucaparib ,Polymerase ,chemistry.chemical_classification ,Binding Sites ,Protein Structure, Tertiary ,Enzyme ,chemistry ,Biochemistry ,Enzyme inhibitor ,biology.protein ,Molecular Medicine ,Poly(ADP-ribose) Polymerases ,Biotechnology - Abstract
Inhibitors of poly-ADP-ribose polymerase (PARP) family proteins are currently in clinical trials as cancer therapeutics, yet the specificity of many of these compounds is unknown. Here we evaluated a series of 185 small-molecule inhibitors, including research reagents and compounds being tested clinically, for the ability to bind to the catalytic domains of 13 of the 17 human PARP family members including the tankyrases, TNKS1 and TNKS2. Many of the best-known inhibitors, including TIQ-A, 6(5H)-phenanthridinone, olaparib, ABT-888 and rucaparib, bound to several PARP family members, suggesting that these molecules lack specificity and have promiscuous inhibitory activity. We also determined X-ray crystal structures for five TNKS2 ligand complexes and four PARP14 ligand complexes. In addition to showing that the majority of PARP inhibitors bind multiple targets, these results provide insight into the design of new inhibitors. more...
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- 2012
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24. Crystal structure of human diphosphoinositol phosphatase 1
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Robert D. Busam, Camilla Persson, B. Martin Hallberg, Martin Hammarström, Ann-Gerd Thorsell, and Susanne Gräslund
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0303 health sciences ,03 medical and health sciences ,Biochemistry ,Structural Biology ,Chemistry ,030302 biochemistry & molecular biology ,Hydrolase ,Phosphatase ,Crystal structure ,Molecular Biology ,030304 developmental biology - Published
- 2009
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25. Sister Chromatid Cohesion Establishment Factor ESCO1 Operates by Substrate-Assisted Catalysis
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Tobias Karlberg, Magdalena Wisniewska, Ann-Gerd Thorsell, Takaharu Kanno, Ekaterina Kouznetsova, Petri Kursula, Camilla Sjögren, and Herwig Schüler
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0301 basic medicine ,Saccharomyces cerevisiae Proteins ,Chromosomal Proteins, Non-Histone ,Protein subunit ,Lysine ,Cell Cycle Proteins ,Saccharomyces cerevisiae ,Crystallography, X-Ray ,Chromosome segregation ,03 medical and health sciences ,Structural Biology ,Acetyl Coenzyme A ,Acetyltransferases ,Catalytic Domain ,Humans ,Molecular Biology ,biology ,Cohesin ,Active site ,Establishment of sister chromatid cohesion ,Molecular Docking Simulation ,030104 developmental biology ,Biochemistry ,Acetylation ,Acetyltransferase ,Mutation ,biology.protein ,Biophysics ,Protein Multimerization ,Protein Binding - Abstract
Sister chromatid cohesion, formed by the cohesin protein complex, is essential for chromosome segregation. In order for cohesion to be established, the cohesin subunit SMC3 needs to be acetylated by a homolog of the ESCO1/Eco1 acetyltransferases, the enzymatic mechanism of which has remained unknown. Here we report the crystal structure of the ESCO1 acetyltransferase domain in complex with acetyl-coenzyme A, and show by SAXS that ESCO1 is a dimer in solution. The structure reveals an active site that lacks a potential catalytic base side chain. However, mutation of glutamate 789, a surface residue that is close to the automodification target lysine 803, strongly reduces autoacetylation of ESCO1. Moreover, budding yeast Smc3 mutated at the conserved residue D114, adjacent to the cohesion-activating acetylation site K112,K113, cannot be acetylated in vivo. This indicates that ESCO1 controls cohesion through substrate-assisted catalysis. Thus, this study discloses a key mechanism for cohesion establishment. more...
- Published
- 2015
26. Structural Basis for Specificity of Common PARP and Tankyrase Inhibitors
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Herwig Schüler, Martin Moche, Mirjam Klepsch, T. Ekblad, A.F. Pinto, Lionel Trésaugues, Tobias Karlberg, and Ann-Gerd Thorsell
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Chemistry ,Poly ADP ribose polymerase ,Genetics ,Cancer research ,Molecular Biology ,Biochemistry ,Biotechnology - Published
- 2015
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27. Triazolo-tetrahydrofluorenones as selective estrogen receptor beta agonists
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Donald M. Sperbeck, Elizabeth T. Birzin, Dann L. Parker, Robert R. Wilkening, Katalin Frisch, Dongfang Meng, Lawrence F. Colwell, Ronald W. Ratcliffe, Stefan Nilsson, Milton L. Hammond, Susan P. Rohrer, Sherrie Lambert, Ann-Gerd Thorsell, and Mark L. Greenlee more...
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Agonist ,medicine.medical_specialty ,medicine.drug_class ,Clinical Biochemistry ,Triazole ,Pharmaceutical Science ,Ligands ,Biochemistry ,Structure-Activity Relationship ,chemistry.chemical_compound ,Internal medicine ,Drug Discovery ,polycyclic compounds ,medicine ,Animals ,Estrogen Receptor beta ,Humans ,Structure–activity relationship ,Selective receptor modulator ,Molecular Biology ,reproductive and urinary physiology ,Estrogen receptor beta ,Fluorenes ,Molecular Structure ,Chemistry ,Organic Chemistry ,Rats ,Bioavailability ,Endocrinology ,Selective estrogen receptor modulator ,Molecular Medicine ,Bioisostere ,Azo Compounds ,hormones, hormone substitutes, and hormone antagonists - Abstract
Several tetrahydrofluorenones with a triazole fused across C7-C8 showed high levels of ERbeta-selectivity and were found to be potent ERbeta-agonists. As a class they demonstrate improved oral bioavailability in the rat over a parent class of 7-hydroxy-tetrahydrofluorenones. The most selective agonist displayed 5.7 nM affinity and 333-fold selectivity for ERbeta. more...
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- 2006
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28. Structure of the ligand-binding domain of oestrogen receptor beta in the presence of a partial agonist and a full antagonist
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Tomas Bonn, Mats Carlquist, Ashley C. W. Pike, Owe Engström, Jan Ljunggren, Ann Gerd Thorsell, Jan-Åke Gustafsson, Andrzej M. Brzozowski, and Roderick E. Hubbard
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Models, Molecular ,Agonist ,medicine.drug_class ,Molecular Sequence Data ,Biology ,Crystallography, X-Ray ,Ligands ,Partial agonist ,General Biochemistry, Genetics and Molecular Biology ,Transactivation ,medicine ,Animals ,Estrogen Receptor beta ,Humans ,Amino Acid Sequence ,Receptor ,Molecular Biology ,Estrogen receptor beta ,Sequence Homology, Amino Acid ,General Immunology and Microbiology ,Ligand ,General Neuroscience ,Genistein ,Rats ,Tamoxifen ,Receptors, Estrogen ,Biochemistry ,Nuclear receptor ,Competitive antagonist ,Raloxifene Hydrochloride ,Biophysics ,hormones, hormone substitutes, and hormone antagonists ,Research Article - Abstract
Oestrogens exert their physiological effects through two receptor subtypes. Here we report the three-dimensional structure of the oestrogen receptor beta isoform (ERbeta) ligand-binding domain (LBD) in the presence of the phyto-oestrogen genistein and the antagonist raloxifene. The overall structure of ERbeta-LBD is very similar to that previously reported for ERalpha. Each ligand interacts with a unique set of residues within the hormone-binding cavity and induces a distinct orientation in the AF-2 helix (H12). The bulky side chain of raloxifene protrudes from the cavity and physically prevents the alignment of H12 over the bound ligand. In contrast, genistein is completely buried within the hydrophobic core of the protein and binds in a manner similar to that observed for ER's endogenous hormone, 17beta-oestradiol. However, in the ERbeta-genistein complex, H12 does not adopt the distinctive 'agonist' position but, instead, lies in a similar orientation to that induced by ER antagonists. Such a sub-optimal alignment of the transactivation helix is consistent with genistein's partial agonist character in ERbeta and demonstrates how ER's transcriptional response to certain bound ligands is attenuated. more...
- Published
- 1999
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29. Chemical probes to study ADP-ribosylation: synthesis and biochemical evaluation of inhibitors of the human ADP-ribosyltransferase ARTD3/PARP3
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Tobias Karlberg, T. Ekblad, Sara Spjut, Mikael Elofsson, Ton Tong Nhan, Ann-Gerd Thorsell, Anders E. G. Lindgren, Herwig Schüler, Victor Hellsten, Johan Weigelt, Anna Linusson, and C. David Andersson
- Subjects
ADP Ribose Transferases ,Models, Molecular ,Stereochemistry ,Stereoisomerism ,GPI-Linked Proteins ,Propanamide ,chemistry.chemical_compound ,Structure-Activity Relationship ,chemistry ,Solubility ,ADP-ribosylation ,Amide ,Drug Discovery ,Molecular Medicine ,Structure–activity relationship ,Humans ,Enzyme Inhibitors ,Selectivity ,Linker ,Quinazolinone ,Quinazolinones - Abstract
The racemic 3-(4-oxo-3,4-dihydroquinazolin-2-yl)-N-[1-(pyridin-2-yl)ethyl]propanamide, 1, has previously been identified as a potent but unselective inhibitor of diphtheria toxin-like ADP-ribosyltransferase 3 (ARTD3). Herein we describe synthesis and evaluation of 55 compounds in this class. It was found that the stereochemistry is of great importance for both selectivity and potency and that substituents on the phenyl ring resulted in poor solubility. Certain variations at the meso position were tolerated and caused a large shift in the binding pose. Changes to the ethylene linker that connects the quinazolinone to the amide were also investigated but proved detrimental to binding. By combination of synthetic organic chemistry and structure-based design, two selective inhibitors of ARTD3 were discovered. more...
- Published
- 2013
30. Recognition of mono-ADP-ribosylated ARTD10 substrates by ARTD8 macrodomains
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Tobias Karlberg, Henning Kleine, Petri Kursula, Annika Gross, Karla L. H. Feijs, Nicolas Herzog, Elisabeth Kremmer, Andreas G. Ladurner, Bernhard Lüscher, Patricia Verheugd, Bianca Nijmeijer, Herwig Schüler, Alexandra H. Forst, and Ann-Gerd Thorsell more...
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Protein domain ,Plasma protein binding ,Molecular Dynamics Simulation ,Biology ,Crystallography, X-Ray ,Protein Structure, Secondary ,Histones ,Mice ,Structure-Activity Relationship ,03 medical and health sciences ,0302 clinical medicine ,Protein structure ,Structural Biology ,Escherichia coli ,Animals ,Humans ,Protein Interaction Domains and Motifs ,Binding site ,Molecular Biology ,030304 developmental biology ,ADP Ribose Transferases ,Adenosine Diphosphate Ribose ,0303 health sciences ,Binding Sites ,HEK 293 cells ,Isothermal titration calorimetry ,Recombinant Proteins ,Isoenzymes ,Molecular Docking Simulation ,Kinetics ,HEK293 Cells ,ran GTP-Binding Protein ,Biochemistry ,030220 oncology & carcinogenesis ,Mutation ,Ran ,Biophysics ,Thermodynamics ,NAD+ kinase ,Protein Binding - Abstract
Summary ADP-ribosyltransferases (ARTs) catalyze the transfer of ADP-ribose from NAD + onto substrates. Some ARTs generate in an iterative process ADP-ribose polymers that serve as adaptors for distinct protein domains. Other ARTs, exemplified by ARTD10, function as mono-ADP-ribosyltransferases, but it has been unclear whether this modification occurs in cells and how it is read. We observed that ARTD10 colocalized with ARTD8 and defined its macrodomains 2 and 3 as readers of mono-ADP-ribosylation both in vitro and in cells. The crystal structures of these two ARTD8 macrodomains and isothermal titration calorimetry confirmed their interaction with ADP-ribose. These macrodomains recognized mono-ADP-ribosylated ARTD10, but not poly-ADP-ribosylated ARTD1. This distinguished them from the macrodomain of macroH2A1.1, which interacted with poly- but not mono-ADP-ribosylated substrates. Moreover, Ran, an ARTD10 substrate, was also read by ARTD8 macrodomains. This identifies readers of mono-ADP-ribosylated proteins, defines their structures, and demonstrates the presence of this modification in cells. more...
- Published
- 2013
31. PARP inhibitor with selectivity toward ADP-ribosyltransferase ARTD3/PARP3
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Sara Spjut, Johan Weigelt, Anna Linusson, Michael O. Hottiger, T. Ekblad, Herwig Schüler, A.F. Pinto, Anders E. G. Lindgren, Mareike Hesse, C.D. Andersson, Tobias Karlberg, Mikael Elofsson, Ann-Gerd Thorsell, University of Zurich, and Elofsson, Mikael more...
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Models, Molecular ,Niacinamide ,1303 Biochemistry ,DNA repair ,Regulator ,Biology ,Poly(ADP-ribose) Polymerase Inhibitors ,Crystallography, X-Ray ,GPI-Linked Proteins ,Biochemistry ,Cell Line ,03 medical and health sciences ,chemistry.chemical_compound ,Inhibitory Concentration 50 ,0302 clinical medicine ,Drug Delivery Systems ,Drug Stability ,Catalytic Domain ,Humans ,Binding site ,Enzyme Inhibitors ,030304 developmental biology ,Quinazolinones ,ADP Ribose Transferases ,0303 health sciences ,Nicotinamide ,Molecular Structure ,General Medicine ,10226 Department of Molecular Mechanisms of Disease ,In vitro ,3. Good health ,Enzyme Activation ,chemistry ,030220 oncology & carcinogenesis ,ADP-ribosyltransferase ,1313 Molecular Medicine ,PARP inhibitor ,Molecular Medicine ,570 Life sciences ,biology ,Poly(ADP-ribose) Polymerases ,Selectivity - Abstract
Inhibiting ADP-ribosyl transferases with PARP-inhibitors is considered a promising strategy for the treatment of many cancers and ischemia, but most of the cellular targets are poorly characterized. Here, we describe an inhibitor of ADP-ribosyltransferase-3/poly(ADP-ribose) polymerase-3 (ARTD3), a regulator of DNA repair and mitotic progression. In vitro profiling against 12 members of the enzyme family suggests selectivity for ARTD3, and crystal structures illustrate the molecular basis for inhibitor selectivity. The compound is active in cells, where it elicits ARTD3-specific effects at submicromolar concentration. Our results show that by targeting the nicotinamide binding site, selective inhibition can be achieved among the closest relatives of the validated clinical target, ADP-ribosyltransferase-1/poly(ADP-ribose) polymerase-1. more...
- Published
- 2013
32. Comparative structural analysis of lipid binding START domains
- Author
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T. Kotenyova, Ann-Gerd Thorsell, Camilla Persson, Herwig Schüler, Marina I. Siponen, Wen Hwa Lee, Robert D. Busam, Lari Lehtiö, and Martina Nilsson
- Subjects
Protein Structure ,Protein domain ,lcsh:Medicine ,Sequence alignment ,Large scale facilities for research with photons neutrons and ions ,Computational biology ,Biology ,Crystallography, X-Ray ,Biochemistry ,Structural genomics ,03 medical and health sciences ,Lipid Mediators ,Protein structure ,Humans ,Biomacromolecule-Ligand Interactions ,lcsh:Science ,Lipid Transport ,030304 developmental biology ,0303 health sciences ,Multidisciplinary ,Tumor Suppressor Proteins ,030302 biochemistry & molecular biology ,Fatty Acids ,GTPase-Activating Proteins ,lcsh:R ,Proteins ,Biological membrane ,Ligand (biochemistry) ,Lipid Metabolism ,Phosphoproteins ,Lipids ,Recombinant Proteins ,Transport protein ,Regulatory Proteins ,Sterols ,Adaptor Proteins, Vesicular Transport ,Palmitoyl-CoA Hydrolase ,lcsh:Q ,Carrier Proteins ,Research Article - Abstract
Background: Steroidogenic acute regulatory (StAR) protein related lipid transfer (START) domains are small globular modules that form a cavity where lipids and lipid hormones bind. These domains can transport ligands to facilitate lipid exchange between biological membranes, and they have been postulated to modulate the activity of other domains of the protein in response to ligand binding. More than a dozen human genes encode START domains, and several of them are implicated in a disease. Principal Findings: We report crystal structures of the human STARD1, STARD5, STARD13 and STARD14 lipid transfer domains. These represent four of the six functional classes of START domains. Significance: Sequence alignments based on these and previously reported crystal structures define the structural determinants of human START domains, both those related to structural framework and those involved in ligand specificity. Enhanced version: This article can also be viewed as an enhanced version (http://plosone.org/enhanced/pone. 0019521/) in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1. more...
- Published
- 2011
33. Structural Basis of Tumor Suppressor in Lung Cancer 1 (TSLC1) Binding to Differentially Expressed in Adenocarcinoma of the Lung (DAL-1/4.1B)*
- Author
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Björn Öbrink, Camilla Persson, Ann-Gerd Thorsell, A. Flores, Robert D. Busam, Martin Hammarström, and B. Martin Hallberg
- Subjects
Immunoglobulins ,Plasma protein binding ,Biology ,Crystallography, X-Ray ,Biochemistry ,Structure-Activity Relationship ,Protein structure ,Adenocarcinoma of the lung ,medicine ,Glycophorin ,Humans ,Cell adhesion ,Protein Structure, Quaternary ,Molecular Biology ,FERM domain ,Cell adhesion molecule ,Tumor Suppressor Proteins ,Microfilament Proteins ,Cell Adhesion Molecule-1 ,Membrane Proteins ,Cell Biology ,Glycophorin C ,Surface Plasmon Resonance ,medicine.disease ,Molecular biology ,Cell biology ,Protein Structure, Tertiary ,Protein Structure and Folding ,biology.protein ,Cell Adhesion Molecules ,Protein Binding - Abstract
Perturbed cell adhesion mechanisms are crucial for tumor invasion and metastasis. A cell adhesion protein, TSLC1 (tumor suppressor in lung cancer 1), is inactivated in a majority of metastatic cancers. DAL-1 (differentially expressed in adenocarcinoma of the lung protein), another tumor suppressor, binds through its FERM domain to the TSLC1 C-terminal, 4.1 glycophorin C-like, cytoplasmic domain. However, the molecular basis for this interaction is unknown. Here, we describe the crystal structure of a complex between the DAL-1 FERM domain and a portion of the TSLC1 cytoplasmic domain. DAL-1 binds to TSLC1 through conserved residues in a well defined hydrophobic pocket in the structural C-lobe of the DAL-1 FERM domain. From the crystal structure, it is apparent that Tyr(406) and Thr(408) in the TSLC1 cytoplasmic domain form the most important interactions with DAL-1, and this was also confirmed by surface plasmon resonance studies. Our results refute earlier exon deletion experiments that indicated that glycophorin C interacts with the α-lobe of 4.1 FERM domains. more...
- Published
- 2010
34. Comparative structural analysis of human DEAD-box RNA helicases
- Author
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Martin Hammarström, P. Schutz, Wolfram Tempel, R. Collins, Hee-Won Park, L. Holmberg-Schiavone, Martin Högbom, Tobias Karlberg, Susanne van den Berg, Herwig Schüler, Martin Moche, Lari Lehtiö, and Ann-Gerd Thorsell more...
- Subjects
Riboswitch ,Models, Molecular ,DEAD box ,Molecular Sequence Data ,Molecular Conformation ,lcsh:Medicine ,Biology ,Crystallography, X-Ray ,DEAD-box RNA Helicases ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Adenosine Triphosphate ,Humans ,Biochemistry/RNA Structure ,Amino Acid Sequence ,lcsh:Science ,Biochemistry/Biomacromolecule-Ligand Interactions ,030304 developmental biology ,Genetics ,0303 health sciences ,Multidisciplinary ,Binding Sites ,DDX5 ,Biochemistry/Structural Genomics ,lcsh:R ,Helicase ,RNA ,RNA Helicase A ,3. Good health ,Protein Structure, Tertiary ,chemistry ,030220 oncology & carcinogenesis ,eIF4A ,Multigene Family ,Molecular Biology/mRNA Transport and Localization ,biology.protein ,lcsh:Q ,Molecular Biology/RNA-Protein Interactions ,Sequence Alignment ,Biochemistry/Transcription and Translation ,DDX47 ,Research Article - Abstract
DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members. more...
- Published
- 2010
35. Crystal structure of human diphosphoinositol phosphatase 1
- Author
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Ann-Gerd, Thorsell, Camilla, Persson, Susanne, Gräslund, Martin, Hammarström, Robert D, Busam, and B Martin, Hallberg
- Subjects
Molecular Sequence Data ,Humans ,Crystallography, X-Ray ,Phosphoric Monoester Hydrolases - Published
- 2009
36. Structural and biophysical characterization of human myo-inositol oxygenase
- Author
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Susanne Gräslund, Astrid Gräslund, Martin Hammarström, Ann-Gerd Thorsell, Robert D. Busam, B. Martin Hallberg, Nina Voevodskaya, and Camilla Persson
- Subjects
Oxygenase ,Stereochemistry ,Biology ,Crystallography, X-Ray ,Biochemistry ,Inositol oxygenase ,Diabetes Complications ,chemistry.chemical_compound ,Oxidoreductase ,Humans ,Inositol ,Amino Acid Sequence ,Binding site ,Molecular Biology ,Peptide sequence ,Sequence Deletion ,chemistry.chemical_classification ,Binding Sites ,Enzyme Catalysis and Regulation ,Inositol Oxygenase ,Active site ,Cell Biology ,Deletion Mutagenesis ,Protein Structure, Tertiary ,chemistry ,Mutagenesis ,biology.protein ,Oxygenases ,lipids (amino acids, peptides, and proteins) - Abstract
Altered inositol metabolism is implicated in a number of diabetic complications. The first committed step in mammalian inositol catabolism is performed by myo-inositol oxygenase (MIOX), which catalyzes a unique four-electron dioxygen-dependent ring cleavage of myo-inositol to D-glucuronate. Here, we present the crystal structure of human MIOX in complex with myo-inosose-1 bound in a terminal mode to the MIOX diiron cluster site. Furthermore, from biochemical and biophysical results from N-terminal deletion mutagenesis we show that the N terminus is important, through coordination of a set of loops covering the active site, in shielding the active site during catalysis. EPR spectroscopy of the unliganded enzyme displays a two-component spectrum that we can relate to an open and a closed active site conformation. Furthermore, based on site-directed mutagenesis in combination with biochemical and biophysical data, we propose a novel role for Lys(127) in governing access to the diiron cluster. more...
- Published
- 2008
37. First structure of a eukaryotic phosphohistidine phosphatase
- Author
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Martin Hammarström, Camilla Persson, Robert D. Busam, B. Martin Hallberg, A. Flores, and Ann-Gerd Thorsell
- Subjects
Models, Molecular ,Binding Sites ,Protein Conformation ,Phosphatase ,Peptide binding ,Cell Biology ,Biology ,Lyase ,Crystallography, X-Ray ,Ligands ,Biochemistry ,Phosphoric Monoester Hydrolases ,Recombinant Proteins ,Serine ,Dephosphorylation ,Protein structure ,Ion binding ,Humans ,Histidine ,Crystallization ,Molecular Biology - Abstract
Phosphatases are a diverse group of enzymes that regulate numerous cellular processes. Much of what is known relates to the tyrosine, threonine, and serine phosphatases, whereas the histidine phosphatases have not been studied as much. The structure of phosphohistidine phosphatase (PHPT1), the first identified eukaryotic-protein histidine phosphatase, has been determined to a resolution of 1.9A using multiple-wavelength anomalous dispersion methods. This enzyme can dephosphorylate a variety of proteins (e.g. ATP-citrate lyase and the beta-subunit of G proteins). A putative active site has been identified by its electrostatic character, ion binding, and conserved protein residues. Histidine 53 is proposed to play a major role in histidine dephosphorylation based on these observations and previous mutational studies. Models of peptide binding are discussed to suggest possible mechanisms for substrate recognition. more...
- Published
- 2006
38. Structure determination of two potential parasitic drug targets of the SAHH family
- Author
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Herwig Shüler, Magdalena Wisniewska, Marina I. Siponen, J. Weigelt, Ann-Gerd Thorsell, and Tobias Karlberg
- Subjects
Drug ,Structural Biology ,Chemistry ,media_common.quotation_subject ,Computational biology ,media_common - Published
- 2009
- Full Text
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39. Erratum to 'Triazolo-tetrahydrofluorenones as selective estrogen receptor beta agonists' [Bioorg. Med. Chem. Lett. 16 (2006) 4652–4656]
- Author
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Mark L. Greenlee, Ronald W. Ratcliffe, Robert R. Wilkening, Elizabeth T. Birzin, Susan P. Rohrer, Ann-Gerd Thorsell, Milton L. Hammond, Sherrie Lambert, Lawrence F. Colwell, Katalin Frisch, Dann L. Parker, Donald M. Sperbeck, Stefan Nilsson, and Dongfang Meng more...
- Subjects
Chemistry ,Organic Chemistry ,Clinical Biochemistry ,Drug Discovery ,Pharmaceutical Science ,Molecular Medicine ,Pharmacology ,Molecular Biology ,Biochemistry ,Estrogen receptor beta - Published
- 2006
- Full Text
- View/download PDF
40. Towards small molecule inhibitors of mono-ADP-ribosyltransferases
- Author
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Anders E. G. Lindgren, Rémi Caraballo, C. David Andersson, Ann-Gerd Thorsell, Herwig Schüler, Anna Linusson, Mikael Elofsson, T. Ekblad, Tobias Karlberg, and Sara Spjut
- Subjects
DNA repair ,Poly ADP ribose polymerase ,Drug Evaluation, Preclinical ,Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) ,Protein degradation ,Small Molecule Libraries ,Inhibitory Concentration 50 ,PARP1 ,Drug Discovery ,Transcriptional regulation ,Humans ,Enzyme Inhibitors ,Medicinsk bioteknologi (med inriktning mot cellbiologi (inklusive stamcellsbiologi), molekylärbiologi, mikrobiologi, biokemi eller biofarmaci) ,Pharmacology ,Diphtheria toxin ,ADP Ribose Transferases ,Poly(ADP-ribose) polymerase ,Chemistry ,ARTD inhibitor ,Organic Chemistry ,Mono-ADP-ribosyltransferase ,General Medicine ,Small molecule ,PARP inhibitor ,Biochemistry ,mART ,Diphtheria toxin-like ADP-ribosyltransferase - Abstract
Protein ADP-ribosylation is a post-translational modification involved in DNA repair, protein degradation, transcription regulation, and epigenetic events. Intracellular ADP-ribosylation is catalyzed predominantly by ADP-ribosyltransferases with diphtheria toxin homology (ARTDs). The most prominent member of the ARTD family, poly(ADP-ribose) polymerase-1 (ARTD1/PARP1) has been a target for cancer drug development for decades. Current PARP inhibitors are generally non-selective, and inhibit the mono-ADP-ribosyltransferases with low potency. Here we describe the synthesis of acylated amino benzamides and screening against the mono-ADP-ribosyltransferases ARTD7/PARP15, ARTD8/PARP14, ARTD10/PARP10, and the poly-ADP-ribosyltransferase ARTD1/PARP1. The most potent compound inhibits ARTD10 with sub-micromolar IC50. more...
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- View/download PDF
41. Structural Insights into the Mode of Action of a Pure Antiestrogen
- Author
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Yi Lin Li, Ashley C. W. Pike, Roderick E. Hubbard, Mats Carlquist, Ann Gerd Thorsell, Julia Walton, A. Marek Brzozowski, and Jan-Åke Gustafsson
- Subjects
Agonist ,Models, Molecular ,medicine.drug_class ,Stereochemistry ,Polyunsaturated Alkamides ,Estrogen receptor ,Biology ,Crystallography, X-Ray ,Ligands ,receptor antagonism ,pure antiestrogen ,Transactivation ,Structural Biology ,transactivation ,Coactivator ,medicine ,Enzyme-linked receptor ,Animals ,Estrogen Receptor beta ,Protein Structure, Quaternary ,Molecular Biology ,Estrogen receptor beta ,Binding Sites ,Estradiol ,Molecular Structure ,Estrogen Antagonists ,Protein Structure, Tertiary ,Rats ,ICI 164,384 ,Nuclear receptor ,Receptors, Estrogen ,Biophysics ,Estrogen-related receptor gamma ,Dimerization ,hormones, hormone substitutes, and hormone antagonists ,estrogen receptor - Abstract
Background: Estrogens exert their effects on target tissues by binding to a nuclear transcription factor termed the estrogen receptor (ER). Previous structural studies have demonstrated that each class of ER ligand (agonist, partial agonist, and SERM antagonist) induces distinctive orientations in the receptor's carboxy-terminal transactivation helix. The conformation of this portion of the receptor determines whether ER can recruit and interact with the components of the transcriptional machinery, thereby facilitating target gene expression. Results: We have determined the structure of rat ERβ ligand binding domain (LBD) in complex with the pure antiestrogen ICI 164,384 at 2.3 A resolution. The binding of this compound to the receptor completely abolishes the association between the transactivation helix (H12) and the rest of the LBD. The structure reveals that the terminal portion of ICI's bulky side chain substituent protrudes from the hormone binding pocket, binds along the coactivator recruitment site, and physically prevents H12 from adopting either its characteristic agonist or AF2 antagonist orientation. Conclusions: The binding mode adopted by the pure antiestrogen is similar to that seen for other ER antagonists. However, the size and resultant positioning of the ligand's side chain substituent produces a receptor conformation that is distinct from that adopted in the presence of other classes of ER ligands. The novel observation that binding of ICI results in the complete destabilization of H12 provides some indications as to a possible mechanism for pure receptor antagonism. more...
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