45 results on '"Silvio Roggo"'
Search Results
2. Auxin-Inducible Depletion of the Essentialome Suggests Inhibition of TORC1 by Auxins and Inhibition of Vrg4 by SDZ 90-215, a Natural Antifungal Cyclopeptide
- Author
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Nathan A. Snyder, Adam Kim, Louis Kester, Andrew N. Gale, Christian Studer, Dominic Hoepfner, Silvio Roggo, Stephen B. Helliwell, and Kyle W. Cunningham
- Subjects
auxin ,auxin inducible degron ,functional genomics ,glycosylation ,Golgi ,rapamycin ,Genetics ,QH426-470 - Abstract
Gene knockout and knockdown strategies have been immensely successful probes of gene function, but small molecule inhibitors (SMIs) of gene products allow much greater time resolution and are particularly useful when the targets are essential for cell replication or survival. SMIs also serve as lead compounds for drug discovery. However, discovery of selective SMIs is costly and inefficient. The action of SMIs can be modeled simply by tagging gene products with an auxin-inducible degron (AID) that triggers rapid ubiquitylation and proteasomal degradation of the tagged protein upon exposure of live cells to auxin. To determine if this approach is broadly effective, we AID-tagged over 750 essential proteins in Saccharomyces cerevisiae and observed growth inhibition by low concentrations of auxin in over 66% of cases. Polytopic transmembrane proteins in the plasma membrane, Golgi complex, and endoplasmic reticulum were efficiently depleted if the AID-tag was exposed to cytoplasmic OsTIR1 ubiquitin ligase. The auxin analog 1-napthylacetic acid (NAA) was as potent as auxin on AID-tags, but surprisingly NAA was more potent than auxin at inhibiting target of rapamycin complex 1 (TORC1) function. Auxin also synergized with known SMIs when acting on the same essential protein, indicating that AID-tagged strains can be useful for SMI screening. Auxin synergy, resistance mutations, and cellular assays together suggest the essential GMP/GDP-mannose exchanger in the Golgi complex (Vrg4) as the target of a natural cyclic peptide of unknown function (SDZ 90-215). These findings indicate that AID-tagging can efficiently model the action of SMIs before they are discovered and can facilitate SMI discovery.
- Published
- 2019
- Full Text
- View/download PDF
3. Author Correction: Jawsamycin exhibits in vivo antifungal properties by inhibiting Spt14/Gpi3-mediated biosynthesis of glycosylphosphatidylinositol
- Author
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Yue Fu, David Estoppey, Silvio Roggo, Dominik Pistorius, Florian Fuchs, Christian Studer, Ashraf S. Ibrahim, Thomas Aust, Frederic Grandjean, Manuel Mihalic, Klaus Memmert, Vivian Prindle, Etienne Richard, Ralph Riedl, Sven Schuierer, Eric Weber, Jürg Hunziker, Frank Petersen, Jianshi Tao, and Dominic Hoepfner
- Subjects
Science - Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
- Published
- 2020
- Full Text
- View/download PDF
4. Natural Products in Drug Discovery
- Author
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Silvio Roggo
- Subjects
Chemistry ,QD1-999 - Published
- 2007
- Full Text
- View/download PDF
5. Marine Natural Products. Key Advances to the Practical Application of this Resource in Drug Development
- Author
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Mark T. Hamann, Russell Hill, and Silvio Roggo
- Subjects
Alkaloids ,Marine natural products ,Peptides ,Polyketides ,Terpenoids ,Chemistry ,QD1-999 - Abstract
Over a half century has passed since the first discovery of spongothymidine and spongouridine. These sponge-derived natural products initiated a chain of events that has resulted in countless lives saved from viral infections and cancer. In addition these humble marine products inspired the critical evaluation of marine life for the production of novel chemistry and new drug leads. The resulting natural products chemistry from these efforts is unprecedented in regard to structural complexity and biological activity. The drug leads based on marine natural products have however created unique challenges in scaleable production and structural optimization to evaluate toxicity and enhance biological activity. In this report we have focused our discussion on the progress toward the development of general methodologies for the production, optimization and development of rare but promising marine natural product drug leads. Key developments discussed briefly include sourcing, lead optimization, molecular biology and phylogeny, marine microbial culture, and tools for structure assignment.
- Published
- 2007
- Full Text
- View/download PDF
6. Cheminformatic Analysis of Natural Products and their Chemical Space
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Stefan Wetzel, Ansgar Schuffenhauer, Silvio Roggo, Peter Ertl, and Herbert Waldmann
- Subjects
Chemical space ,Chemgps ,Cheminformatics ,Natural products ,Sconp ,Chemistry ,QD1-999 - Abstract
Cheminformatic methods allow the detailed characterization of particular and characteristic properties of natural products (NPs) and comparison with related characteristics of drugs and other compounds. An overview of the most important properties of natural products and analogues and their difference with respect to drugs and synthetic compounds is presented. Moreover, different approaches to charting the chemical space populated by natural products are reviewed and their underlying principles are delineated. Some insights about NP chemical space are described together with possible applications of methods charting chemical space. Strengths and weaknesses of the different approaches will be discussed with respect to possible applications in compound collection design.
- Published
- 2007
- Full Text
- View/download PDF
7. Jawsamycin exhibits in vivo antifungal properties by inhibiting Spt14/Gpi3-mediated biosynthesis of glycosylphosphatidylinositol
- Author
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Eric Weber, Juerg Hunziker, Dominic Hoepfner, Ralph Riedl, Vivian Prindle, Sven Schuierer, Yue Fu, Silvio Roggo, Florian Fuchs, Ashraf S. Ibrahim, Jianshi Tao, Frank Petersen, Manuel Mihalic, David Estoppey, Dominik Pistorius, Christian Studer, Etienne Richard, Klaus Memmert, Thomas Aust, and Frederic Grandjean
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0301 basic medicine ,Male ,Antifungal Agents ,Glycosylphosphatidylinositols ,General Physics and Astronomy ,chemistry.chemical_compound ,Mice ,lcsh:Science ,Lung ,Multidisciplinary ,biology ,Hep G2 Cells ,Hydrogen-Ion Concentration ,Inbred ICR ,Infectious Diseases ,Biochemistry ,Multigene Family ,Mucorales ,lipids (amino acids, peptides, and proteins) ,Infection ,Rhizopus ,Saccharomyces cerevisiae Proteins ,Protein subunit ,Science ,030106 microbiology ,Saccharomyces cerevisiae ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Inhibitory Concentration 50 ,Biosynthesis ,In vivo ,Genetics ,Animals ,Humans ,Reporter ,Cell Proliferation ,Reporter gene ,Cell growth ,Animal ,Glycosyltransferases ,General Chemistry ,biology.organism_classification ,HCT116 Cells ,In vitro ,carbohydrates (lipids) ,030104 developmental biology ,chemistry ,Genes ,Polyketides ,Disease Models ,Fermentation ,lcsh:Q ,K562 Cells - Abstract
Biosynthesis of glycosylphosphatidylinositol (GPI) is required for anchoring proteins to the plasma membrane, and is essential for the integrity of the fungal cell wall. Here, we use a reporter gene-based screen in Saccharomyces cerevisiae for the discovery of antifungal inhibitors of GPI-anchoring of proteins, and identify the oligocyclopropyl-containing natural product jawsamycin (FR-900848) as a potent hit. The compound targets the catalytic subunit Spt14 (also referred to as Gpi3) of the fungal UDP-glycosyltransferase, the first step in GPI biosynthesis, with good selectivity over the human functional homolog PIG-A. Jawsamycin displays antifungal activity in vitro against several pathogenic fungi including Mucorales, and in vivo in a mouse model of invasive pulmonary mucormycosis due to Rhyzopus delemar infection. Our results provide a starting point for the development of Spt14 inhibitors for treatment of invasive fungal infections.
- Published
- 2020
8. Auxin-Inducible Depletion of the Essentialome Suggests Inhibition of TORC1 by Auxins and Inhibition of Vrg4 by SDZ 90-215, a Natural Antifungal Cyclopeptide
- Author
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Silvio Roggo, Louis Kester, Andrew N. Gale, Dominic Hoepfner, Adam Kim, Christian Studer, Kyle W. Cunningham, Stephen B. Helliwell, and Nathan A. Snyder
- Subjects
Genetics, Microbial ,Antifungal Agents ,Saccharomyces cerevisiae Proteins ,glycosylation ,Saccharomyces cerevisiae ,Investigations ,Biology ,QH426-470 ,Peptides, Cyclic ,Naphthaleneacetic Acids ,03 medical and health sciences ,symbols.namesake ,0302 clinical medicine ,Auxin ,Golgi ,Genetics ,Molecular Biology ,Genetics (clinical) ,Gene knockout ,auxin inducible degron ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Gene knockdown ,Indoleacetic Acids ,Drug discovery ,rapamycin ,Endoplasmic reticulum ,fungi ,Membrane Transport Proteins ,food and beverages ,Golgi apparatus ,Cell biology ,Ubiquitin ligase ,chemistry ,biology.protein ,symbols ,Degron ,auxin ,functional genomics ,030217 neurology & neurosurgery ,Transcription Factors - Abstract
Gene knockout and knockdown strategies have been immensely successful probes of gene function, but small molecule inhibitors (SMIs) of gene products allow much greater time resolution and are particularly useful when the targets are essential for cell replication or survival. SMIs also serve as lead compounds for drug discovery. However, discovery of selective SMIs is costly and inefficient. The action of SMIs can be modeled simply by tagging gene products with an auxin-inducible degron (AID) that triggers rapid ubiquitylation and proteasomal degradation of the tagged protein upon exposure of live cells to auxin. To determine if this approach is broadly effective, we AID-tagged over 750 essential proteins in Saccharomyces cerevisiae and observed growth inhibition by low concentrations of auxin in over 66% of cases. Polytopic transmembrane proteins in the plasma membrane, Golgi complex, and endoplasmic reticulum were efficiently depleted if the AID-tag was exposed to cytoplasmic OsTIR1 ubiquitin ligase. The auxin analog 1-napthylacetic acid (NAA) was as potent as auxin on AID-tags, but surprisingly NAA was more potent than auxin at inhibiting target of rapamycin complex 1 (TORC1) function. Auxin also synergized with known SMIs when acting on the same essential protein, indicating that AID-tagged strains can be useful for SMI screening. Auxin synergy, resistance mutations, and cellular assays together suggest the essential GMP/GDP-mannose exchanger in the Golgi complex (Vrg4) as the target of a natural cyclic peptide of unknown function (SDZ 90-215). These findings indicate that AID-tagging can efficiently model the action of SMIs before they are discovered and can facilitate SMI discovery.
- Published
- 2019
9. Phenotypic screen identifies calcineurin-sparing FK506 analogs as BMP potentiators for treatment of acute kidney injury
- Author
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Jinhai Gao, Andreas Harsch, Dong Liu, Deborah Rothman, Stephen M. Canham, Silvio Roggo, Joseph Loureiro, John A. Tallarico, Philipp Krastel, Lloyd B. Klickstein, Gregory A. Michaud, Christy Fryer, Bushell Simon, Savage Nik, Michael Salcius, Kian L. Tan, Joerg Kallen, Feng Cong, Philipp Lustenberger, Manuel Mihalic, Eric T Williams, Aude Izaac, Jian Ding, Patrick J. Devine, Xiaobo Xia, Fred Harbinski, Erhan I. Altinoglu, Shaowen Wang, Rishi K. Jain, Liling Zeng, Xiaolin Gao, and Larraufie Marie-Helene
- Subjects
Male ,Phenotypic screening ,Clinical Biochemistry ,Endogeny ,Biology ,Bone morphogenetic protein ,01 natural sciences ,Biochemistry ,Tacrolimus ,Mice ,Drug Discovery ,medicine ,Animals ,Humans ,Receptor ,Molecular Biology ,Cells, Cultured ,Pharmacology ,Molecular Structure ,010405 organic chemistry ,Acute kidney injury ,Potentiator ,Acute Kidney Injury ,medicine.disease ,0104 chemical sciences ,High-Throughput Screening Assays ,Calcineurin ,Mice, Inbred C57BL ,Disease Models, Animal ,FKBP ,Phenotype ,Bone Morphogenetic Proteins ,Cancer research ,Molecular Medicine - Abstract
Summary Acute kidney injury (AKI) is a life-threatening disease with no known curative or preventive therapies. Data from multiple animal models and human studies have linked dysregulation of bone morphogenetic protein (BMP) signaling to AKI. Small molecules that potentiate endogenous BMP signaling should have a beneficial effect in AKI. We performed a high-throughput phenotypic screen and identified a series of FK506 analogs that act as potent BMP potentiators by sequestering FKBP12 from BMP type I receptors. We further showed that calcineurin inhibition was not required for this activity. We identified a calcineurin-sparing FK506 analog oxtFK through late-stage functionalization and structure-guided design. OxtFK demonstrated an improved safety profile in vivo relative to FK506. OxtFK stimulated BMP signaling in vitro and in vivo and protected the kidneys in an AKI mouse model, making it a promising candidate for future development as a first-in-class therapeutic for diseases with dysregulated BMP signaling.
- Published
- 2020
10. Total synthesis of diaportheone A
- Author
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Silvio Roggo, Mario A. Tan, and Patrik Peter Züger
- Subjects
In situ ,Natural product ,010405 organic chemistry ,Stereochemistry ,Organic Chemistry ,Absolute configuration ,Total synthesis ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Plant use of endophytic fungi in defense ,0104 chemical sciences ,Diaporthe sp ,chemistry.chemical_compound ,chemistry ,Drug Discovery ,Chromone ,Optical rotation - Abstract
Diaportheone A (1), a chromone natural product was previously isolated from the endophytic fungi Diaporthe sp. P 133. Its structure was established by spectroscopic methods, however, its absolute configuration remained undefined. This study dealt on the total synthesis of diaportheone A (1) utilizing the cyclization and in situ thermal syn-elimination of a β-ketosulfoxide. The C-1R absolute configuration of the natural product was established by X-ray crystallography of the synthetic diaportheone A (1) (>99% ee) and comparison with the optical rotation.
- Published
- 2019
11. Author Correction: Jawsamycin exhibits in vivo antifungal properties by inhibiting Spt14/Gpi3-mediated biosynthesis of glycosylphosphatidylinositol
- Author
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Jianshi Tao, Frank Petersen, Eric Weber, David Estoppey, Vivian Prindle, Sven Schuierer, Christian Studer, Dominik Pistorius, Jürg Hunziker, Etienne Richard, Manuel Mihalic, Klaus Memmert, Ralph Riedl, Silvio Roggo, Ashraf S. Ibrahim, Dominic Hoepfner, Yue Fu, Florian Fuchs, Thomas Aust, and Frederic Grandjean
- Subjects
Male ,Antifungal ,Saccharomyces cerevisiae Proteins ,Glycosylphosphatidylinositols ,medicine.drug_class ,Glycosylphosphatidylinositol ,Science ,General Physics and Astronomy ,Saccharomyces cerevisiae ,Article ,General Biochemistry, Genetics and Molecular Biology ,Inhibitory Concentration 50 ,Mice ,chemistry.chemical_compound ,Biosynthesis ,Genes, Reporter ,In vivo ,Target identification ,medicine ,Animals ,Humans ,lcsh:Science ,Author Correction ,Lung ,Antifungal agents ,Cell Proliferation ,Mice, Inbred ICR ,Multidisciplinary ,Chemistry ,Fungi ,Glycosyltransferases ,Hep G2 Cells ,General Chemistry ,Hydrogen-Ion Concentration ,HCT116 Cells ,Disease Models, Animal ,Biochemistry ,Multigene Family ,Polyketides ,Fermentation ,Mucorales ,lcsh:Q ,Pathogens ,K562 Cells ,Rhizopus - Abstract
Biosynthesis of glycosylphosphatidylinositol (GPI) is required for anchoring proteins to the plasma membrane, and is essential for the integrity of the fungal cell wall. Here, we use a reporter gene-based screen in Saccharomyces cerevisiae for the discovery of antifungal inhibitors of GPI-anchoring of proteins, and identify the oligocyclopropyl-containing natural product jawsamycin (FR-900848) as a potent hit. The compound targets the catalytic subunit Spt14 (also referred to as Gpi3) of the fungal UDP-glycosyltransferase, the first step in GPI biosynthesis, with good selectivity over the human functional homolog PIG-A. Jawsamycin displays antifungal activity in vitro against several pathogenic fungi including Mucorales, and in vivo in a mouse model of invasive pulmonary mucormycosis due to Rhyzopus delemar infection. Our results provide a starting point for the development of Spt14 inhibitors for treatment of invasive fungal infections., Biosynthesis of glycosylphosphatidylinositol (GPI) is essential for the integrity of the fungal cell wall. Here, the authors show that the natural product jawsamycin inhibits GPI biosynthesis by targeting a subunit of the fungal UDP-glycosyltransferase, and displays pronounced activity against pathogenic fungi of the order Mucorales.
- Published
- 2020
12. Development of a cyclosporin A derivative with excellent anti-hepatitis C virus potency
- Author
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Feng Sun, David Thomas Parker, Friedrich Schuerch, Silvio Roggo, Xiaolin Li, Zachary Kevin Sweeney, Li Cao, Nicole Meier, Bernard Riss, Christian Guenat, Wei Li, Zhaobo Gao, Jiping Fu, Jibin Zhao, Subramanian Karur, Wang Ruidong, Andrew H. Weiss, Regis Denay, Alexey Rivkin, Su Xu, Harald Schroeder, Michael Paul Capparelli, Simon Ng, Quanbing Wu, Xin Xiong, Weikuan Li, Wosenu Mergo, Christopher Becker, Robert Lowell Simmons, Amy Lu, Gai Yu, Wenjian Xu, Peichao Lu, Nicolas Wenger, Christian Zürcher, Thomas Lochmann, Meiliana Tjandra, Alexandre Luneau, Hongyong Kim, Aregahegn Yifru, Yunshan Peng, Fabrice Gallou, Jianguang Zhou, Roger Aki Fujimoto, and Michael Wang
- Subjects
0301 basic medicine ,Stereochemistry ,Clinical Biochemistry ,Pharmaceutical Science ,Hepacivirus ,Virus Replication ,01 natural sciences ,Biochemistry ,Antiviral Agents ,03 medical and health sciences ,chemistry.chemical_compound ,Cyclosporin a ,Drug Discovery ,Potency ,Chelation ,Molecular Biology ,Cyclophilin ,010405 organic chemistry ,Organic Chemistry ,Chiral ligand ,Transporter ,Stereoisomerism ,Dipeptides ,Quinidine ,0104 chemical sciences ,Claisen rearrangement ,030104 developmental biology ,chemistry ,Cyclization ,Drug Design ,Cyclosporine ,Molecular Medicine ,Derivative (chemistry) - Abstract
Synthetic modification of cyclosporin A at P3-P4 positions led to the discovery of NIM258, a next generation cyclophilin inhibitor with excellent anti-hepatitis C virus potency, with decreased transporter inhibition, and pharmacokinetics suitable for coadministration with other drugs. Herein is disclosed the evolution of the synthetic strategy to from the original medicinal chemistry route, designed for late diversification, to a convergent and robust development synthesis. The chiral centers in the P4 fragment were constructed by an asymmetric chelated Claisen rearrangement in the presence of quinidine as the chiral ligand. Identification of advanced crystalline intermediates enabled practical supply of key intermediates. Finally, macrocyclization was carried out at 10% weight concentration by a general and unconventional "slow release" concept.
- Published
- 2017
13. Evidence for a Functionally Relevant Rocaglamide Binding Site on the eIF4A–RNA Complex
- Author
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Sven Schuierer, Thomas Aust, N. Rao Movva, Bhupinder Bhullar, Britta Knapp, Ralph Riedl, Gabriela Galicia-Vázquez, Silvio Roggo, Stephen B. Helliwell, Jerry Pelletier, Christian Studer, Heather Sadlish, Lena Chang, Dominic Hoepfner, John A. Porco, and C. Gregory Paris
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Genetics ,Binding Sites ,biology ,In silico ,Helicase ,RNA ,Saccharomyces cerevisiae ,General Medicine ,Computational biology ,Models, Biological ,Biochemistry ,Triterpenes ,Article ,chemistry.chemical_compound ,Eukaryotic translation ,Eukaryotic Initiation Factor-4F ,Rocaglamide ,chemistry ,Eukaryotic initiation factor ,eIF4A ,biology.protein ,Molecular Medicine ,Binding site ,Benzofurans - Abstract
Translation initiation is an emerging target in oncology and neurobiology indications. Naturally derived and synthetic rocaglamide scaffolds have been used to interrogate this pathway, however, there is uncertainty regarding their precise mechanism(s) of action. We exploited the genetic tractability of yeast to define the primary effect of both a natural and a synthetic rocaglamide in a cellular context, and characterized the molecular target using biochemical studies and in silico modeling. Chemogenomic profiling and mutagenesis in yeast identified the eIF (eukaryotic Initiation Factor) 4A helicase homologue as the primary molecular target of rocaglamides, and defined a discrete set of residues near the RNA binding motif which confer resistance to both compounds. Three of the eIF4A mutations were characterized regarding their functional consequences on activity and response to rocaglamide inhibition. These data support a model whereby rocaglamides stabilize an eIF4A-RNA interaction to either alter the level and/or impair the activity of the eIF4F complex. Furthermore, in silico modeling supports the annotation of a binding pocket delineated by the RNA substrate and the residues identified from our mutagenesis screen. As expected from the high degree of conservation of the eukaryotic translation pathway, these observations are consistent with previous observations in mammalian model systems. Importantly, we demonstrate that the chemically distinct silvestrol and synthetic rocaglamides share a common mechanism of action, which will be critical for optimization of physiologically stable derivatives. Finally, these data confirm the value of the rocaglamide scaffold for exploring the impact of translational modulation on disease.
- Published
- 2013
14. Oxysterols direct immune cell migration via EBI2
- Author
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Tangsheng Yi, Andreas W. Sailer, Birgit Baumgarten, Miroslava Vanek, Deborah Nguyen, Sébastien Hannedouche, Richard Knochenmuss, Marie-Odile Roy, Inga Preuss, Jason G. Cyster, Charlotte Miault, Yu Chen, João Pereira, Isabelle Christen, Weijun Shen, Silvio Roggo, Peter G. Schultz, Wei Li, Danilo Guerini, Sophie Noël, Lisa M. Kelly, Christian Schmedt, Eric C. Peters, Ratnaningrum Karuna, Thomas Suply, Dong-In Koo, Stephane Laurent, Michel Detheux, Rocco Falchetto, Carsten Spanka, Ben Wen, Andreas Katopodis, François Gessier, Charles Y. Cho, Klaus Seuwen, and Juan Zhang
- Subjects
Multidisciplinary ,Immune system ,Biochemistry ,GPR183 ,Cell migration ,Immune receptor ,Biology ,Receptor ,Acquired immune system ,Hedgehog signaling pathway ,G protein-coupled receptor ,Cell biology - Abstract
The EBI2 receptor (Epstein–Barr virus-induced gene 2, also known as GPR183) was recently shown to be linked to autoimmune disease, and is a critical regulator of the humoral immune response. It is a G-protein-coupled receptor, and its natural ligand has been unknown. Two groups now bring an end to the 'orphan' status of this receptor with identification of specific oxysterols as its natural ligands. The most potent ligand and activator is 7a,25-dihydroxycholesterol, and the EBI2–oxysterol signalling pathway has an important role in the adaptive immune response. Epstein–Barr virus-induced gene 2 (EBI2, also known as GPR183) is a G-protein-coupled receptor that is required for humoral immune responses; polymorphisms in the receptor have been associated with inflammatory autoimmune diseases1,2,3. The natural ligand for EBI2 has been unknown. Here we describe the identification of 7α,25-dihydroxycholesterol (also called 7α,25-OHC or 5-cholesten-3β,7α,25-triol) as a potent and selective agonist of EBI2. Functional activation of human EBI2 by 7α,25-OHC and closely related oxysterols was verified by monitoring second messenger readouts and saturable, high-affinity radioligand binding. Furthermore, we find that 7α,25-OHC and closely related oxysterols act as chemoattractants for immune cells expressing EBI2 by directing cell migration in vitro and in vivo. A critical enzyme required for the generation of 7α,25-OHC is cholesterol 25-hydroxylase (CH25H)4. Similar to EBI2 receptor knockout mice, mice deficient in CH25H fail to position activated B cells within the spleen to the outer follicle and mount a reduced plasma cell response after an immune challenge. This demonstrates that CH25H generates EBI2 biological activity in vivo and indicates that the EBI2–oxysterol signalling pathway has an important role in the adaptive immune response.
- Published
- 2011
15. Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries
- Author
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Ansgar Schuffenhauer, Silvio Roggo, and Peter Ertl
- Subjects
Prioritization ,Biological Products ,Virtual screening ,Natural product ,Combinatorial Chemistry Techniques ,Drug discovery ,Process (engineering) ,Computer science ,General Chemical Engineering ,Reproducibility of Results ,Small Molecule Libraries ,Bayes Theorem ,General Chemistry ,Library and Information Sciences ,computer.software_genre ,Computer Science Applications ,chemistry.chemical_compound ,ROC Curve ,chemistry ,Cheminformatics ,Drug Design ,Data mining ,computer - Abstract
Natural products (NPs) have been optimized in a very long natural selection process for optimal interactions with biological macromolecules. NPs are therefore an excellent source of validated substructures for the design of novel bioactive molecules. Various cheminformatics techniques can provide useful help in analyzing NPs, and the results of such studies may be used with advantage in the drug discovery process. In the present study we describe a method to calculate the natural product-likeness score--a Bayesian measure which allows for the determination of how molecules are similar to the structural space covered by natural products. This score is shown to efficiently separate NPs from synthetic molecules in a cross-validation experiment. Possible applications of the NP-likeness score are discussed and illustrated on several examples including virtual screening, prioritization of compound libraries toward NP-likeness, and design of building blocks for the synthesis of NP-like libraries.
- Published
- 2007
16. FR171456 is a specific inhibitor of mammalian NSDHL and yeast Erg26p
- Author
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Sven Schuierer, Lukas Oberer, Ralph Riedl, Jianshi Tao, Silvio Roggo, John S. Gounarides, Charlotte Miault, Stephen B. Helliwell, Marc Bergdoll, Juan Zhang, Klaus Memmert, Anais Margerit, Dominic Hoepfner, Pierre-Eloi Imbert, Christian N. Parker, Shantanu Karkare, Andreas Hofmann, Stefan Reinker, Hans-Ulrich Naegeli, Mathias Frederiksen, Alban Muller, Hong Yin, Ireos Filipuzzi, Trixie Wagner, Juliet R. Leighton-Davis, Alain Rahier, Philipp Krastel, Vivian Prindle, Celine Fioretto, Richard Knochenmuss, Thomas Aust, N. Rao Movva, Jessica A. Sexton, and Rolf Jeker
- Subjects
3-Hydroxysteroid Dehydrogenases ,Antifungal Agents ,Saccharomyces cerevisiae Proteins ,Saccharomyces cerevisiae ,General Physics and Astronomy ,Saccharomyces ,Article ,General Biochemistry, Genetics and Molecular Biology ,chemistry.chemical_compound ,Drug Resistance, Fungal ,Ergosterol ,Candida albicans ,Replicon ,Binding site ,chemistry.chemical_classification ,Multidisciplinary ,biology ,General Chemistry ,biology.organism_classification ,Yeast ,Cholesterol ,Enzyme ,Biochemistry ,chemistry ,Mutation ,NAD+ kinase - Abstract
FR171456 is a natural product with cholesterol-lowering properties in animal models, but its molecular target is unknown, which hinders further drug development. Here we show that FR171456 specifically targets the sterol-4-alpha-carboxylate-3-dehydrogenase (Saccharomyces cerevisiae—Erg26p, Homo sapiens—NSDHL (NAD(P) dependent steroid dehydrogenase-like)), an essential enzyme in the ergosterol/cholesterol biosynthesis pathway. FR171456 significantly alters the levels of cholesterol pathway intermediates in human and yeast cells. Genome-wide yeast haploinsufficiency profiling experiments highlight the erg26/ERG26 strain, and multiple mutations in ERG26 confer resistance to FR171456 in growth and enzyme assays. Some of these ERG26 mutations likely alter Erg26 binding to FR171456, based on a model of Erg26. Finally, we show that FR171456 inhibits an artificial Hepatitis C viral replicon, and has broad antifungal activity, suggesting potential additional utility as an anti-infective. The discovery of the target and binding site of FR171456 within the target will aid further development of this compound., FR171456 is a bioactive chemical produced by some microorganisms. Here, the authors identify the enzyme NSDHL of the sterol synthesis pathway as the molecular target of FR171456, rendering it the first compound to specifically target this class of enzyme in yeast and mammalian cells.
- Published
- 2015
17. Gift from Nature: Cyclomarin A Kills Mycobacteria and Malaria Parasites by Distinct Modes of Action
- Author
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Silvio Roggo, Cecile Delmas, Nathalie Bürstner, Matthias Rottmann, Jason Murphy, Manuel Mihalic, Jutta Blank, Dominik Pistorius, Nils Ostermann, Dominic Hoepfner, Alexandra Hinniger, Brigitta Liechty, Esther K. Schmitt, Markus Schirle, Jason R. Thomas, Felix Freuler, and Bernd Gerhartz
- Subjects
medicine.medical_treatment ,Plasmodium falciparum ,Plasma protein binding ,Molecular Dynamics Simulation ,Biochemistry ,Microbiology ,Mycobacterium tuberculosis ,chemistry.chemical_compound ,Antimalarials ,Inhibitory Concentration 50 ,Bacterial Proteins ,Hydrolase ,medicine ,Humans ,Binding site ,Molecular Biology ,Biological Products ,Natural product ,Protease ,Binding Sites ,biology ,Organic Chemistry ,Endopeptidase Clp ,biology.organism_classification ,medicine.disease ,Acid Anhydride Hydrolases ,Neoplasm Proteins ,Protein Structure, Tertiary ,chemistry ,Molecular Medicine ,Oligopeptides ,Malaria ,Protein Binding - Abstract
Malaria continues to be one of the most devastating human diseases despite many efforts to limit its spread by prevention of infection or by pharmaceutical treatment of patients. We have conducted a screen for antiplasmodial compounds by using a natural product library. Here we report on cyclomarin A as a potent growth inhibitor of Plasmodium falciparum and the identification of its molecular target, diadenosine triphosphate hydrolase (PfAp3Aase), by chemical proteomics. Using a biochemical assay, we could show that cyclomarin A is a specific inhibitor of the plasmodial enzyme but not of the closest human homologue hFHIT. Co-crystallisation experiments demonstrate a unique binding mode of the inhibitor. One molecule of cyclomarin A binds a dimeric PfAp3Aase and prevents the formation of the enzyme⋅substrate complex. These results validate PfAp3Aase as a new drug target for the treatment of malaria. We have previously elucidated the structurally unrelated regulatory subunit ClpC1 of the ClpP protease as the molecular target of cyclomarin A in Mycobacterium tuberculosis. Thus, cyclomarin A is a rare example of a natural product with two distinct and specific modes of action.
- Published
- 2015
18. Nannocystin A: an Elongation Factor 1 Inhibitor from Myxobacteria with Differential Anti-Cancer Properties
- Author
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Howard R Miller, Eric Weber, Xiaobing Xie, Francesca Perruccio, Felipa A. Mapa, David Estoppey, Markus Schirle, Philipp Krastel, Nathan T. Ross, Ralph Riedl, Kathrin Buntin, Trixie Wagner, Silvio Roggo, Christian Thibaut, Jason R. Thomas, Dominic Hoepfner, Xuewen Pan, Brigitta Liechty, Esther K. Schmitt, Thomas Aust, Klaus Memmert, and Peter Aspesi
- Subjects
Proteomics ,Antifungal Agents ,Macrocyclic Compounds ,Stereochemistry ,Antineoplastic Agents ,Apoptosis ,Catalysis ,Didemnin B ,Structure-Activity Relationship ,Eukaryotic translation ,Peptide Elongation Factor 1 ,Myxobacteria ,Neoplasms ,Candida albicans ,Tumor Cells, Cultured ,Structure–activity relationship ,Humans ,Myxococcales ,Binding site ,Cell Proliferation ,biology ,Molecular Structure ,Chemistry ,General Medicine ,General Chemistry ,Genomics ,biology.organism_classification ,Eukaryotic translation elongation factor 1 alpha 1 ,Elongation factor ,Biochemistry - Abstract
Cultivation of myxobacteria of the Nannocystis genus led to the isolation and structure elucidation of a class of novel cyclic lactone inhibitors of elongation factor 1. Whole genome sequence analysis and annotation enabled identification of the putative biosynthetic cluster and synthesis process. In biological assays the compounds displayed anti-fungal and cytotoxic activity. Combined genetic and proteomic approaches identified the eukaryotic translation elongation factor 1α (EF-1α) as the primary target for this compound class. Nannocystin A (1) displayed differential activity across various cancer cell lines and EEF1A1 expression levels appear to be the main differentiating factor. Biochemical and genetic evidence support an overlapping binding site of 1 with the anti-cancer compound didemnin B on EF-1α. This myxobacterial chemotype thus offers an interesting starting point for further investigations of the potential of therapeutics targeting elongation factor 1.
- Published
- 2015
19. Aspects of Chirality in Natural Products Drug Discovery
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Silvio Roggo, Frank Petersen, Esther K. Schmitt, Ansgar Schuffenhauer, and Philipp Krastel
- Subjects
Chemistry ,Drug discovery ,Stereochemistry ,Chirality (chemistry) - Published
- 2006
20. Structure-Based Design, Synthesis, and Memapsin 2 (BACE) Inhibitory Activity of Carbocyclic and Heterocyclic Peptidomimetics
- Author
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Paolo Paganetti, Gaoqiang Yang, Paul Ramage, Marina Tintelnot-Blomley, Hongying Yun, Jean-Michel Rondeau, Ulf Neumann, Nicolas Moitessier, Stephen Hanessian, Yihua Hou, Malken Bayrakdarian, Christian Ostermeier, Siem Jacob Veenstra, Silvio Roggo, André Strauss, Eric Therrien, and Claudia Betschart
- Subjects
Models, Molecular ,Pyrrolidines ,Molecular model ,Peptidomimetic ,Stereochemistry ,Cyclopentanes ,Crystallography, X-Ray ,Cyclopentanone ,Cathepsin D ,Chemical synthesis ,Pyrrolidine ,Structure-Activity Relationship ,chemistry.chemical_compound ,Endopeptidases ,Drug Discovery ,Aspartic Acid Endopeptidases ,Humans ,Structure–activity relationship ,Furans ,Cyclopentane ,Binding Sites ,Molecular Mimicry ,Pyrrolidinones ,chemistry ,Lactam ,Molecular Medicine ,Amyloid Precursor Protein Secretases ,Peptides - Abstract
Molecular modeling based on the X-ray crystal structure of the Tang-Ghosh heptapeptide inhibitor 1 (OM99-2) of BACE led to the design and synthesis of a series of constrained P(1)' analogues. A cyclopentane ring was incorporated in 1 spanning the P(1)' Ala methyl group and the adjacent methylene carbon atom of the chain. Progressive truncation at the P(2)'-P(4)' sites led to a potent truncated analogue 5 with good selectivity over Cathepsin D. Using the same backbone replacement concept, a series of cyclopentane, cyclopentanone, tetrahydrofuran, pyrrolidine, and pyrrolidinone analogues were synthesized with considerable variation at the P and P' sites. The cyclopentanone and 2-pyrrolidinone analogues 45 and 57 showed low nM BACE inhibition. X-ray cocrystal structures of two analogues 5 and 45 revealed excellent convergence with the original inhibitor 1 structure while providing new insights into other interactions which could be exploited for future modifications.
- Published
- 2005
21. Oxamyl dipeptide caspase inhibitors developed for the treatment of stroke
- Author
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Robert Smidt, Silvio Roggo, Julia Herrmann, Edward D. Robinson, Kathy G. Jahangiri, Teresa Aja, Kip Nalley, Thomas L. Deckwerth, Giorgio Rovelli, Kevin J. Tomaselli, Joe C. Wu, Bastian Hengerer, Steven P. Meduna, André Sauter, Jose-Luis Diaz, Joerg Kallen, Albert Schmitz, Donald S. Karanewsky, Brett R. Ullman, Steven D. Linton, Christoph Wiessner, Robert J. Ternansky, Peter R. Allegrini, and Robert O. Sayers
- Subjects
Peptidomimetic ,Stereochemistry ,Clinical Biochemistry ,Pharmaceutical Science ,Oxamyl ,Apoptosis ,Peptide ,Biochemistry ,Cell Line ,Inhibitory Concentration 50 ,Structure-Activity Relationship ,chemistry.chemical_compound ,Drug Discovery ,Humans ,Structure–activity relationship ,Molecular Biology ,Caspase ,chemistry.chemical_classification ,Dipeptide ,biology ,Organic Chemistry ,Neurodegenerative Diseases ,Dipeptides ,Caspase Inhibitors ,In vitro ,Stroke ,Kinetics ,chemistry ,Enzyme inhibitor ,biology.protein ,Molecular Medicine ,Carbamates - Abstract
Structural modifications were made to a previously described acyl dipeptide caspase inhibitor, leading to the oxamyl dipeptide series. Subsequent SAR studies directed toward the warhead, P2, and P4 regions of this novel peptidomimetic are described herein.
- Published
- 2004
22. Structure–Activity relationships within a series of caspase inhibitors: effect of leaving group modifications
- Author
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Edward D. Robinson, Silvio Roggo, Joe C. Wu, Robert J. Ternansky, Jose-Luis Diaz, Teresa Aja, Kevin J. Tomaselli, Steven P. Meduna, Vincent J. Kalish, Donald S. Karanewsky, Robert O. Sayers, Albert Schmitz, Brett R. Ullman, Julia Herrmann, Kip Nalley, and Thomas L. Deckwerth
- Subjects
chemistry.chemical_classification ,Programmed cell death ,biology ,Chemistry ,Organic Chemistry ,Clinical Biochemistry ,Leaving group ,Pharmaceutical Science ,Inflammation ,Cysteine Proteinase Inhibitors ,Caspase Inhibitors ,Biochemistry ,In vitro ,Structure-Activity Relationship ,Enzyme ,Enzyme inhibitor ,Drug Discovery ,biology.protein ,medicine ,Molecular Medicine ,Structure–activity relationship ,medicine.symptom ,Molecular Biology ,Caspase - Abstract
Various aryloxy methyl ketones of the 1-naphthyloxyacetyl-Val-Asp backbone have been prepared. A systematic study of their structure-activity relationship (SAR) related to caspases 1, 3, 6, and 8 is reported. Highly potent irreversible broad-spectrum caspase inhibitors have been identified. Their efficacy in cellular models of cell death and inflammation are also discussed.
- Published
- 2003
23. The Natural Product Cyclomarin Kills Mycobacterium Tuberculosis by Targeting the ClpC1 Subunit of the Caseinolytic Protease
- Author
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Philipp Krastel, Srinivasa P. S. Rao, Douglas Jeffery, Luis R. Camacho, Christian Zwingelstein, Pornwaratt Niyomrattanakit, Jun Zheng, Kevin Pethe, Christian G. Noble, Vivian Lim, Silvio Roggo, Melvin Au, David Beer, Vasan K. Sambandamurthy, Esther K. Schmitt, Meliana Riwanto, and Charlotte Miault
- Subjects
chemistry.chemical_classification ,Oligopeptide ,Natural product ,Protease ,biology ,Protein subunit ,medicine.medical_treatment ,Antitubercular Agents ,General Chemistry ,Plasma protein binding ,Mycobacterium tuberculosis ,General Medicine ,biology.organism_classification ,Catalysis ,Cyclic peptide ,chemistry.chemical_compound ,Biochemistry ,chemistry ,Bacterial Proteins ,Heat shock protein ,medicine ,Oligopeptides ,Heat-Shock Proteins ,Protein Binding - Published
- 2011
24. Potent nonimmunosuppressive cyclophilin inhibitors with improved pharmaceutical properties and decreased transporter inhibition
- Author
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Brigitte Wiedmann, Michael Wang, Andrew H. Weiss, Silvio Roggo, David Thomas Parker, Robert Elling, Jiping Fu, Zachary Kevin Sweeney, Markus Furegati, Kwan Leung, Robert Lowell Simmons, Aregahegn Yifru, Subramanian Karur, Yunshan Peng, Shengtian Yang, Roger Aki Fujimoto, Lili Xie, Alexey Rivkin, Michael Paul Capparelli, Linda Xiao, Imad Hanna, Charlotte Miault, Simon Ng, Christopher Becker, Wosenu Mergo, Theresa Kasprzyk, Dallas Bednarczyk, Peichao Lu, Mark Knapp, Meiliana Tjandra, Bo Zhou, Xiaolin Li, and Wenjian Xu
- Subjects
Organic Anion Transporters ,Cyclosporins ,Chemistry Techniques, Synthetic ,Hepacivirus ,Pharmacology ,Crystallography, X-Ray ,Virus Replication ,Antiviral Agents ,Cyclophilins ,Structure-Activity Relationship ,Dogs ,Pharmacokinetics ,Cyclosporin a ,Drug Discovery ,polycyclic compounds ,Potency ,Animals ,Humans ,Cyclophilin ,Alisporivir ,Chemistry ,Liver-Specific Organic Anion Transporter 1 ,Multidrug resistance-associated protein 2 ,Transporter ,Hepatitis C ,Multidrug Resistance-Associated Protein 2 ,Rats ,Biochemistry ,Cyclosporine ,Molecular Medicine ,Multidrug Resistance-Associated Proteins ,Hydrophobic and Hydrophilic Interactions ,Cyclophilin D ,Immunosuppressive Agents - Abstract
Nonimmunosuppressive cyclophilin inhibitors have demonstrated efficacy for the treatment of hepatitis C infection (HCV). However, alisporivir, cyclosporin A, and most other cyclosporins are potent inhibitors of OATP1B1, MRP2, MDR1, and other important drug transporters. Reduction of the side chain hydrophobicity of the P4 residue preserves cyclophilin binding and antiviral potency while decreasing transporter inhibition. Representative inhibitor 33 (NIM258) is a less potent transporter inhibitor relative to previously described cyclosporins, retains anti-HCV activity in cell culture, and has an acceptable pharmacokinetic profile in rats and dogs. An X-ray structure of 33 bound to rat cyclophilin D is reported.
- Published
- 2014
25. Long-term protection of brain tissue from cerebral ischemia by peripherally administered peptidomimetic caspase inhibitors
- Author
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Teresa Aja, André Sauter, Donald S. Karanewsky, Markus Rudin, Rachel May, Peter R. Allegrini, Bastian Hengerer, Robert O. Sayers, Christoph Wiessner, Steve Linton, Albert Schmitz, Giorgio Rovelli, Kevin J. Tomaselli, Patricia C. Contreras, Joe C. Wu, Silvio Roggo, Kip Nalley, Lisa M. Adams, and Thomas L. Deckwerth
- Subjects
biology ,business.industry ,Central nervous system ,Ischemia ,Caspase 3 ,Pharmacology ,medicine.disease ,Neuroprotection ,medicine.anatomical_structure ,Apoptosis ,Anesthesia ,medicine.artery ,Drug Discovery ,Middle cerebral artery ,medicine ,biology.protein ,Artery occlusion ,business ,Caspase - Abstract
Apoptotic cell death occurs in the injured and diseased central nervous system. It is mediated by a family of caspases, which are activated by the lethal stimulus and cleave multiple protein substrates that are critical for cell viability. Previous studies demonstrated that caspase-mediated apoptotic cell death contributes to the loss of brain tissue after experimental cerebral ischemia and that peptidic caspase inhibitors can be efficacious in reducing infarct size after icv administration. Here we present the novel small molecule peptidomimetic caspase inhibitor IDN5370/CGP82630, which belongs to the structural class of oxoazepinoindoline caspase inhibitors. It is 10–100-fold more potent than current peptidic inhibitors in inhibiting multiple caspases in vitro and promoting neuronal survival. IDN5370 and a derivative, IDN7866, were tested for their ability to reduce infarct size after permanent and transient cerebral ischemia. When administered icv to rats subjected to permanent middle cerebral artery occlusion (MCAO), IDN5370 significantly reduced cortical infarct as measured by magnetic resonance imaging at 2 days after artery occlusion. Protection of brain tissue persisted for 28 days after artery occlusion. To determine whether compounds of this structural class could reduce infarct size after peripheral administration, IDN7866, which penetrates the blood–brain barrier and inhibits caspase 3 in situ in the hippocampus after kainate-induced seizures, was administered iv in both permanent and transient MCAO models. Infarct size was reduced significantly in both models 24 h after artery occlusion. These results demonstrate that peripherally administered peptidomimetic caspase inhibitors can attenuate brain injury after cerebral ischemia and confer a long-lasting protective effect on the infarcted brain tissue. Drug Dev. Res. 52:579–586, 2001. © 2001 Wiley-Liss, Inc.
- Published
- 2001
26. Glyceraldehyde-3-phosphate Dehydrogenase, the Putative Target of the Antiapoptotic Compounds CGP 3466 and R-(−)-Deprenyl
- Author
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Peter Fürst, Patrick Schindler, Jan van Oostrum, Silvio Roggo, Kaspar Zimmermann, Dieter Müller, Isabelle Lalande, Peter C. Waldmeier, and Eddy A. Kragten
- Subjects
Programmed cell death ,Apoptosis ,Dehydrogenase ,Biosensing Techniques ,Photoaffinity Labels ,Biochemistry ,Neuroprotection ,Cell Line ,Antiparkinson Agents ,Neuroblastoma ,Selegiline ,medicine ,Animals ,Humans ,Molecular Biology ,Glyceraldehyde 3-phosphate dehydrogenase ,Affinity labeling ,Molecular Structure ,Propylamines ,biology ,Muscles ,Brain ,Glyceraldehyde-3-Phosphate Dehydrogenases ,Parkinson Disease ,Cell Biology ,Oligonucleotides, Antisense ,Rats ,Neuroprotective Agents ,Gene Expression Regulation ,Microscopy, Fluorescence ,Mechanism of action ,Cell culture ,Oxepins ,biology.protein ,Rabbits ,medicine.symptom ,Protein Binding - Abstract
R-(-)-Deprenyl (Selegiline) represents one of the drugs currently used for the treatment of Parkinson's disease. This compound was shown to protect neurons or glias from programmed cell death in a variety of models. The mechanism of action of neuroprotection as well as inhibition of apoptosis remains elusive. CGP 3466 is a structurally related analog of R-(-)-deprenyl that exhibits virtually no monoamine oxidase type B inhibiting activity but is neuroprotective in the picomolar concentration range. We showed specific binding of CGP 3466 to glyceraldehyde-3-phosphate dehydrogenase by affinity binding, by affinity labeling, and by means of BIAcore(R) technology. Apoptosis assays based on the human neuroblastoma cell line PAJU established the importance of this interaction for mediating drug-induced inhibition of programmed cell death.
- Published
- 1998
27. ChemInform Abstract: Synthesis of Tools for Target Identification of the Antiapoptotic Compound CGP 3466. Part 1
- Author
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P. Waldmeister, Eddy A. Kragten, P. Fuerst, Kaspar Zimmermann, and Silvio Roggo
- Subjects
Chemistry ,Identification (biology) ,General Medicine ,Computational biology - Published
- 2010
28. ChemInform Abstract: Natural Product-Likeness Score and Its Application for Prioritization of Compound Libraries
- Author
-
Ansgar Schuffenhauer, Peter Ertl, and Silvio Roggo
- Subjects
Prioritization ,Virtual screening ,chemistry.chemical_compound ,Natural product ,chemistry ,Process (engineering) ,Drug discovery ,Cheminformatics ,Bioactive molecules ,General Medicine ,Biochemical engineering - Abstract
Natural products (NPs) have been optimized in a very long natural selection process for optimal interactions with biological macromolecules. NPs are therefore an excellent source of validated substructures for the design of novel bioactive molecules. Various cheminformatics techniques can provide useful help in analyzing NPs, and the results of such studies may be used with advantage in the drug discovery process. In the present study we describe a method to calculate the natural product-likeness scorea Bayesian measure which allows for the determination of how molecules are similar to the structural space covered by natural products. This score is shown to efficiently separate NPs from synthetic molecules in a cross-validation experiment. Possible applications of the NP-likeness score are discussed and illustrated on several examples including virtual screening, prioritization of compound libraries toward NP-likeness, and design of building blocks for the synthesis of NP-like libraries.
- Published
- 2008
29. Natural product-likeness score and its applications in the drug discovery process
- Author
-
Ansgar Schuffenhauer, Silvio Roggo, and Peter Ertl
- Subjects
Prioritization ,Virtual screening ,Natural product ,Chemistry(all) ,Drug discovery ,Bioactive molecules ,General Chemistry ,Data science ,chemistry.chemical_compound ,Chemistry ,chemistry ,Cheminformatics ,Oral Presentation ,Biochemical engineering ,QD1-999 - Abstract
Natural products (NPs) – i.e. secondary metabolites of plants or lower organisms - have been optimized in a very long natural selection process for optimal interactions with biological macromolecules. NPs are therefore an excellent source of validated substructures for the design of novel bioactive molecules. Indeed, many drugs in the current pharmacopeias are NPs, NP derivatives, or are of NP origin. Various cheminformatics techniques can provide useful help in design of new bioactive molecules by taking into account information extracted from structures of NPs. In this presentation we describe a method to calculate natural product-likeness score - a Bayesian measure that characterizes similarity of molecules to the structural space covered by natural products. This score is shown to efficiently separate NPs from synthetic molecules in a cross-validation experiment. Possible applications of the NP-likeness score in drug discovery process are discussed, including virtual screening, prioritization of compound libraries towards NP-likeness and design of building blocks for the synthesis of NP-like combinatorial libraries.
- Published
- 2008
30. The scaffold tree--visualization of the scaffold universe by hierarchical scaffold classification
- Author
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Peter Ertl, Herbert Waldmann, Stefan Wetzel, Silvio Roggo, Marcus A. Koch, and Ansgar Schuffenhauer
- Subjects
Scaffold ,Theoretical computer science ,Databases, Factual ,Computer science ,General Chemical Engineering ,Pyruvate Kinase ,Library and Information Sciences ,Ligands ,Pruning (decision trees) ,Organic Chemicals ,Pesticides ,Hierarchy (mathematics) ,Molecular Structure ,Chemistry ,business.industry ,Pattern recognition ,General Medicine ,General Chemistry ,Classification ,Computer Science Applications ,Tree visualization ,Data set ,Tree (data structure) ,Artificial intelligence ,business ,PubChem ,Universe (mathematics) - Abstract
A hierarchical classification of chemical scaffolds (molecular framework, which is obtained by pruning all terminal side chains) has been introduced. The molecular frameworks form the leaf nodes in the hierarchy trees. By an iterative removal of rings, scaffolds forming the higher levels in the hierarchy tree are obtained. Prioritization rules ensure that less characteristic, peripheral rings are removed first. All scaffolds in the hierarchy tree are well-defined chemical entities making the classification chemically intuitive. The classification is deterministic, data-set-independent, and scales linearly with the number of compounds included in the data set. The application of the classification is demonstrated on two data sets extracted from the PubChem database, namely, pyruvate kinase binders and a collection of pesticides. The examples shown demonstrate that the classification procedure handles robustly synthetic structures and natural products.
- Published
- 2007
31. Inside Cover: Gift from Nature: Cyclomarin A Kills Mycobacteria and Malaria Parasites by Distinct Modes of Action (ChemBioChem 17/2015)
- Author
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Jason R. Thomas, Silvio Roggo, Jutta Blank, Felix Freuler, Manuel Mihalic, Markus Schirle, Cecile Delmas, Nathalie Bürstner, Jason Murphy, Dominic Hoepfner, Dominik Pistorius, Alexandra Hinniger, Brigitta Liechty, Esther K. Schmitt, Bernd Gerhartz, Nils Ostermann, and Matthias Rottmann
- Subjects
Action (philosophy) ,Organic Chemistry ,Diadenosine triphosphate ,medicine ,Molecular Medicine ,Cover (algebra) ,Biology ,medicine.disease ,Molecular Biology ,Biochemistry ,Malaria ,Microbiology - Published
- 2015
32. Small Molecules for Chemogenomicsbased Drug Discovery
- Author
-
Kamal Azzaoui, Ansgar Schuffenhauer, Meir Glick, Sigmar Dressler, Edgar Jacoby, John W. Davies, Jeremy L. Jenkins, Maxim Popov, and Silvio Roggo
- Subjects
Drug discovery ,Chemistry ,Computational biology ,Small molecule - Published
- 2006
33. Structure-activity relationships within a series of caspase inhibitors. Part 2: Heterocyclic warheads
- Author
-
Teresa Aja, Kevin J. Tomaselli, Edward D. Robinson, Joe C. Wu, Steven D. Linton, Xin Gu, Robert O. Sayers, Steven P. Meduna, Kip Nalley, Lalitha Kodandapani, Silvio Roggo, Vincent J. Kalish, Jose-Luis Diaz, Donald S. Karanewsky, Ning Chen, Albert Schmitz, Julia Herrmann, Brett R. Ullman, Joseph J. Krebs, and Robert J. Ternansky
- Subjects
Programmed cell death ,Stereochemistry ,Clinical Biochemistry ,Pharmaceutical Science ,Naphthols ,Cysteine Proteinase Inhibitors ,Biochemistry ,Chemical synthesis ,Models, Biological ,Mice ,Structure-Activity Relationship ,Heterocyclic Compounds ,Drug Discovery ,Animals ,Molecular Biology ,Caspase ,Cells, Cultured ,chemistry.chemical_classification ,Aspartic Acid ,biology ,Bicyclic molecule ,Cell Death ,Organic Chemistry ,Valine ,Ketones ,Caspase Inhibitors ,In vitro ,Enzyme ,chemistry ,Enzyme inhibitor ,biology.protein ,Molecular Medicine ,Cellular model - Abstract
Various heterocyclic hetero-methyl ketones of the 1-naphthyloxyacetyl-Val-Asp backbone have been prepared. A study of their structure-activity relationship (SAR) related to caspase-1, -3, -6, and -8 is reported. Their efficacy in a cellular model of cell death is also discussed. Potent broad-spectrum caspase inhibitors have been identified.
- Published
- 2005
34. Acyl dipeptides as reversible caspase inhibitors. Part 2: further optimization
- Author
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Xian Guo, Robert J. Ternansky, Brett R. Ullman, Lawrence C. Fritz, Robert Smidt, Ning Chen, Albert Schmitz, Lalitha Kodandapani, Donald S. Karanewsky, Jose-Luis Diaz, Steven D. Linton, Vincent J. Kalish, Brian Pham, U. von Krosigk, Kathy G. Jahangiri, Kevin J. Tomaselli, Steven P. Meduna, Joe C. Wu, Silvio Roggo, and Edward D. Robinson
- Subjects
Stereochemistry ,medicine.drug_class ,Acylation ,Clinical Biochemistry ,Pharmaceutical Science ,Carboxamide ,Caspase 8 ,Biochemistry ,Chemical synthesis ,Structure-Activity Relationship ,Drug Discovery ,medicine ,Enzyme Inhibitors ,Molecular Biology ,Caspase ,chemistry.chemical_classification ,biology ,Organic Chemistry ,Dipeptides ,Caspase Inhibitors ,In vitro ,Isoenzymes ,Enzyme ,chemistry ,Enzyme inhibitor ,biology.protein ,Molecular Medicine ,Indicators and Reagents ,Oligopeptides ,Lactone - Abstract
A new structural class of broad spectrum caspase inhibitors was optimized for its activity against caspases 1, 3, 6, 7, and 8. The most potent compound had low nanomolar broad spectrum activity, in particular, single digit nanomolar inhibitory activity against caspase 8.
- Published
- 2002
35. Inhibition of BACE, a promising approach to Alzheimer's disease therapy
- Author
-
Silvio Roggo
- Subjects
Protein Folding ,Isostere ,Protein Conformation ,Cleavage (embryo) ,Structure-Activity Relationship ,Transition state analog ,Alzheimer Disease ,mental disorders ,Drug Discovery ,Endopeptidases ,Amyloid precursor protein ,Peptide bond ,Animals ,Aspartic Acid Endopeptidases ,Humans ,Enzyme Inhibitors ,chemistry.chemical_classification ,Amyloid beta-Peptides ,biology ,Drug discovery ,Active site ,General Medicine ,Enzyme ,chemistry ,Biochemistry ,biology.protein ,Amyloid Precursor Protein Secretases - Abstract
The first proteolytic step in the processing of amyloid precursor protein (APP) to amyloid-beta (Abeta) in the brain is performed by beta-site APP cleaving enzyme (BACE1). This enzyme is a membrane bound aspartic protease with high homology of the catalytic domain to renin and pepsin and of yet unknown physiologic function. It is a primary drug discovery target for Alzheimer s disease therapy. The first potent inhibitors are based on the sequence of APP around the beta-secretase cleavage site EVNL/DAEF, with the scissile Leu-Asp amide bond being replaced by a hydroxyethylene transition state analogue isostere. In addition, lipophilic sidechains have been incorporated and a crystal structure of such an octapeptidic inhibitor bound in the active site is already available. Recent progress in the field of BACE inhibition is reviewed.
- Published
- 2002
36. Synthesis of tools for target identification of the anti-apoptotic compound CGP 3466; Part I
- Author
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Silvio Roggo, Peter Fürst, Peter C. Waldmeier, Kaspar Zimmermann, and Eddy A. Kragten
- Subjects
Tertiary amine ,Stereochemistry ,Clinical Biochemistry ,Pharmaceutical Science ,Apoptosis ,Biochemistry ,Hippocampus ,Chromatography, Affinity ,Structure-Activity Relationship ,Drug Discovery ,Selegiline ,Structure–activity relationship ,Molecule ,Animals ,Molecular Biology ,Fluorescent Dyes ,Neurons ,Molecular Structure ,Chemistry ,Organic Chemistry ,Rats ,Fluorescent labelling ,Neuroprotective Agents ,Oxepins ,Molecular targets ,Molecular Medicine ,Indicators and Reagents - Abstract
Immobilized compounds for BIAcore studies and affinity precipitation as well as a fluorescent-labeled compound were prepared in order to identify the molecular target of the anti-apoptotic, neurorescuing compound CGP 3466 (N-methyl-N-propargyl-10-aminomethyl-dibenzo[b,f]oxepin).
- Published
- 1999
37. Cheminformatic Analysis of Natural Products and their Chemical Space
- Author
-
Silvio Roggo, Ansgar Schuffenhauer, Stefan Wetzel, Peter Ertl, and Herbert Waldmann
- Subjects
Natural products ,Chemistry ,Cheminformatics ,General Medicine ,General Chemistry ,Combinatorial chemistry ,Chemical space ,Natural (archaeology) ,Characterization (materials science) ,Sconp ,Chemgps ,Biochemical engineering ,QD1-999 ,Strengths and weaknesses - Abstract
Cheminformatic methods allow the detailed characterization of particular and characteristic properties of natural products (NPs) and comparison with related characteristics of drugs and other compounds. An overview of the most important properties of natural products and analogues and their difference with respect to drugs and synthetic compounds is presented. Moreover, different approaches to charting the chemical space populated by natural products are reviewed and their underlying principles are delineated. Some insights about NP chemical space are described together with possible applications of methods charting chemical space. Strengths and weaknesses of the different approaches will be discussed with respect to possible applications in compound collection design.
- Published
- 2007
38. Marine Natural Products. Key Advances to the Practical Application of this Resource in Drug Development
- Author
-
Silvio Roggo, Russell T. Hill, and Mark T. Hamann
- Subjects
Natural product ,Resource (biology) ,business.industry ,Terpenoids ,Marine life ,General Medicine ,General Chemistry ,Biology ,Natural (archaeology) ,Biotechnology ,Chemistry ,chemistry.chemical_compound ,Alkaloids ,Lead (geology) ,chemistry ,Drug development ,Marine natural products ,Polyketides ,Key (cryptography) ,Biochemical engineering ,Natural Products Chemistry ,Peptides ,business ,QD1-999 - Abstract
Over a half century has passed since the first discovery of spongothymidine and spongouridine. These sponge-derived natural products initiated a chain of events that has resulted in countless lives saved from viral infections and cancer. In addition these humble marine products inspired the critical evaluation of marine life for the production of novel chemistry and new drug leads. The resulting natural products chemistry from these efforts is unprecedented in regard to structural complexity and biological activity. The drug leads based on marine natural products have however created unique challenges in scaleable production and structural optimization to evaluate toxicity and enhance biological activity. In this report we have focused our discussion on the progress toward the development of general methodologies for the production, optimization and development of rare but promising marine natural product drug leads. Key developments discussed briefly include sourcing, lead optimization, molecular biology and phylogeny, marine microbial culture, and tools for structure assignment.
- Published
- 2007
39. Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries.
- Author
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Peter Ertl, Silvio Roggo, and Ansgar Schuffenhauer
- Published
- 2008
- Full Text
- View/download PDF
40. The Scaffold Tree − Visualization of the Scaffold Universe by Hierarchical Scaffold Classification.
- Author
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Ansgar Schuffenhauer, Peter Ertl, Silvio Roggo, Stefan Wetzel, Marcus A. Koch, and Herbert Waldmann
- Published
- 2007
- Full Text
- View/download PDF
41. Enantioselektive Addition von Arylgruppen an aromatische Aldehyde mit Aryltitan‐Binaphthol‐Derivaten
- Author
-
Albert K. Beck, Dieter Seebach, Silvio Roggo, and Anne Wonnacott
- Subjects
Inorganic Chemistry ,chemistry.chemical_classification ,chemistry.chemical_compound ,chemistry ,Stereochemistry ,Reagent ,Aryl ,Absolute configuration ,Topicity ,Enantioselective synthesis ,Medicinal chemistry ,Aldehyde ,Tetrahydrofuran - Abstract
Die aus chiralem, nicht racemischem Binaphthol, Chlorotriisopropoxytitan und Aryl-magnesiumbromiden in Tetrahydrofuran (THF) in situ erzeugten Organotitanreagentien ubertragen die Arylgruppe mit hoher Enantioselektivitat auf aromatische Aldehyde [Gleichungen (1)–(3)]. So sind praktisch enantiomerenreine Benzhydrole zuganglich (3 – 13, Tab. 1). Die Reaktion verlauft in den Fallen, in welchen die absolute Konfiguration der Benzhydrole bekannt ist, mit relativer Topizitat lk. Enantioselective Addition of Aryl Groups to Aromatic Aldehydes Using Chiral Aryltitanium Binaphthol Derivatives Chiral, non-racemic organotitanium reagents are generated in situ from binaphthol, chlorotriisopropoxytitanium and aryl Grignard reagents in tetrahydrofuran (THF). These reagents transfer aryl groups to aromatic aldehydes with high enantioselectivity [eq. (1)–(3)]. By this method, enantiomerically pure benzhydrols are available (3 – 13, Table 1). In the cases, in which the absolute configuration of the products is known, the reaction occurs with relative topicity lk.
- Published
- 1985
42. Diasterio- und enantioselektive Reduktion von ?-Ketoestern mit Cyclopentanon-, Cyclohexanon-, Piperidon- und Tetralon-Struktur durch nicht fermentierende B�cker-Hefe
- Author
-
Hans Braunschweiger, Silvio Roggo, Jacques Cercus, Dieter Seebach, Thomas Maetzke, and Manfred Krieger
- Subjects
Stereochemistry ,Organic Chemistry ,Enantioselective synthesis ,Substrate (chemistry) ,Cyclohexanone ,Cyclopentanone ,Biochemistry ,Catalysis ,Yeast ,Inorganic Chemistry ,chemistry.chemical_compound ,chemistry ,Drug Discovery ,Tetralone ,Fermentation ,Physical and Theoretical Chemistry ,Selectivity - Abstract
Diastereo- and Enantioselective Reduction of beta;-Keto Esters Derived from Cyclopentanone, Cyclohexanone, Piperidone and Tetralone by ‘Non-fermenting’ Baker's Yeast Under ‘non-fermenting’ conditions, i.e. in tap water, in the absence of nutrients baker's yeast (25–380 g/g of substrate, aerobic) reduces β-keto esters such as those mentioned in the title with better selectivity than under the normally employed ‘fermenting’ conditions (sugar and nutrients, CO2 development). With the β- keto esters containing the tetralone substructure, large amount of yeast are required (250–380 g/g); the substrate disappears in the biomass, and the desired reduction product can be extracted after reaction times of up to a week at 30°. The configuration of most products(16–24) is established. Generally, the (R)-β-keto ester is reduced faster than the (S)-enantiomer (the two esters are in equilibrium under the reactio conditions), and the hydride transfer takes place preferentially from the diastereotopic Re-face. The β-hydroxy esters thus available are useful starting materials for syntheses of enantiomerically pure compounds (EPC).
- Published
- 1987
43. Chirale Alkoxytitan(IV)-Komplexe für enantioselektive nucleophile Additionen an Aldehyde und alsLewis-Säuren inDiels-Alder-Reaktionen
- Author
-
René Imwinkelzied, Anne Wonnacott, Albert K. Beck, Dieter Seebach, and Silvio Roggo
- Subjects
chemistry.chemical_classification ,Nucleophilic addition ,Organic Chemistry ,Acetal ,Enantioselective synthesis ,Biochemistry ,Aldehyde ,Medicinal chemistry ,Catalysis ,Cycloaddition ,Inorganic Chemistry ,chemistry.chemical_compound ,chemistry ,Nucleophile ,Drug Discovery ,Organic chemistry ,Lewis acids and bases ,Physical and Theoretical Chemistry ,Enantiomeric excess - Abstract
Chiral Alkoxytitanium(iv) Complexes for Enantioselective Nucleophilic Additions to Aldehydes and as Lewis Acids in Diels-Alder Reactions A Number of chiral 1,2-1,3 and 1,4-diols were prepared and used as alkoxy ligands on Ti for enantioselective nucleophilic transfer of methyl, butyl, cyclopropyl, allyl, alkinyl, and phenyl groups to aromatic aldehydes, as well as for the enantioselective[4+2]cycloaddition of acrylate to cyclopentadiene. The 1,2-diols were pinane diol 7 and 1,2:5.6-diacetonide-protected mannitol 9 (Scheme 3) and tartrates. The 1,3-diols were obtained from the yeast-reduction products of 2-oxocyclopentane- and 2-oxocyclohexanecarboxylates and excess MeLi, BuLi, or PhLi (or the corresponding Grignard reagents; see4–6.) As 1,4-diols, we used the products 2 and 3 from tartrate acetals and methyl or Pheny1 Grignard reagents, the bis(benzaldehyde) acetal 8 of d-mannitol and o,o'-binaphthol (22). These diols were attached to the Ti-atom by azeotropic removal of i-PrOH from a mixture with [TiCi(i-PrO)3]. Addition of various organometallic reagents R-metal (metal = Li, BR3, MgX, MnC1, CuLiR) was followed by combination with aldehydes at – 75., a warm up period, quenching with aqueous KF solution, and workup (for results see Tables 1–6 and Formulae17–20). The enantiomeric excess of the secondary alcohols obtained varies greatly, certain combinations of chiral ligands, nucleophilic groups, and aldehyde substrates give rise to values as high as 90% ee; see e.g. Table 4. The Ti-complexes of the general formula [Ti(R*O)2Ci2] or [Ti(R*O)2(i-PrO)CI] induced the Diels-Alder addition of methyl acrylate to cyclopentadience to take place at –30.. The best enantioselectivity (50% ee) was observed with the binaphthol derivative (Table 7). The structures of the complexes involved in these reactions are unknown. The substitution on C(2) of the dioxolanes 2 and 3 (derived from tartaric acid) has a pronounced effect on the selectivities of both reactions studied here (Tables 2, 3, and 7). This remote effect (1,6-distance between the stereogenic acetal-C-atom and the Ti-centers) must be caused by conformational changes in the vicinity of the reactive site, i.e. the TiC bond in the nucleophilic addition reactions and the Ti-acrylate-oxygen complexation in the Diels-Alder reaction.
- Published
- 1987
44. ChemInform Abstract: Chiral Alkoxytitanium(IV) Complexes for Enantioselective Nucleophilic Additions to Aldehydes and as Lewis Acids in Diels-Alder Reactions
- Author
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Dieter Seebach, R. Imwinkelried, Silvio Roggo, Albert K. Beck, and A. Wonnacott
- Subjects
Nucleophile ,Chemistry ,Stereochemistry ,Diels alder ,Enantioselective synthesis ,Organic chemistry ,General Medicine ,Lewis acids and bases - Published
- 1987
45. ChemInform Abstract: Diastereo- and Enantioselective Reduction of β-Keto Esters Derived from Cyclopentanone, Cyclohexanone, Piperidone and Tetralone by 'Non-fermenting' Baker′s Yeast
- Author
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Dieter Seebach, Silvio Roggo, Thomas Maetzke, H. Braunschweiger, J. Cercus, and M. Krieger
- Subjects
chemistry.chemical_compound ,Chemistry ,Enantioselective synthesis ,Tetralone ,Cyclohexanone ,Organic chemistry ,Fermentation ,General Medicine ,Cyclopentanone ,Yeast - Published
- 1987
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