Gisbert Schneider

Hochschule für Technik Zürich, Zürich, Zurich, Switzerland

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Publications (303)1261.02 Total impact

  • Knut Baumann · Gerhard F. Ecker · Jordi Mestres · Gisbert Schneider

    No preview · Article · Jan 2016
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    Erik Gawehn · Jan A. Hiss · Gisbert Schneider
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    ABSTRACT: Artificial neural networks had their first heyday in molecular informatics and drug discovery approximately two decades ago. Currently, we are witnessing renewed interest in adapting advanced neural network architectures for pharmaceutical research by borrowing from the field of “deep learning”. Compared with some of the other life sciences, their application in drug discovery is still limited. Here, we provide an overview of this emerging field of molecular informatics, present the basic concepts of prominent deep learning methods and offer motivation to explore these techniques for their usefulness in computer-assisted drug discovery and design. We specifically emphasize deep neural networks, restricted Boltzmann machine networks and convolutional networks.
    Preview · Article · Dec 2015 · Molecular Informatics
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    ABSTRACT: HtrA proteases and chaperones exhibit important roles in periplasmic protein quality control and stress responses. The genetic inactivation of htrA has been described for many bacterial pathogens. However, in some cases such as the gastric pathogen Helicobacter pylori, HtrA is secreted where it cleaves the tumor-suppressor E-cadherin interfering with gastric disease development, but the generation of htrA mutants is still lacking. Here, we show that the htrA gene locus is highly conserved in worldwide strains. HtrA presence was confirmed in 992 H. pylori isolates in gastric biopsy material from infected patients. Differential RNA-sequencing (dRNA-seq) indicated that htrA is encoded in an operon with two subsequent genes, HP1020 and HP1021. Genetic mutagenesis and complementation studies revealed that HP1020 and HP1021, but not htrA, can be mutated. In addition, we demonstrate that suppression of HtrA proteolytic activity with a newly developed inhibitor is sufficient to effectively kill H. pylori, but not other bacteria. We show that Helicobacter htrA is an essential bifunctional gene with crucial intracellular and extracellular functions. Thus, we describe here the first microbe in which htrA is an indispensable gene, a situation unique in the bacterial kingdom. HtrA can therefore be considered a promising new target for anti-bacterial therapy.
    No preview · Article · Nov 2015 · Molecular Microbiology
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    ABSTRACT: Automated molecular de novo design led to the discovery of an innovative inhibitor of death-associated protein kinase 3 (DAPK3). An unprecedented crystal structure of the inactive DAPK3 homodimer shows the fragment-like hit bound to the ATP pocket. Target prediction software based on machine learning models correctly identified additional macromolecular targets of the computationally designed compound and the structurally related marketed drug azosemide. The study validates computational de novo design as a prime method for generating chemical probes and starting points for drug discovery.
    Full-text · Article · Oct 2015 · Angewandte Chemie International Edition
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    ABSTRACT: High-throughput analysis of cancer cell dissemination and its control by extrinsic and intrinsic cellular factors is hampered by the lack of adequate and efficient analytical tools for quantifying cell motility. Oncology research would greatly benefit from such a methodology that allows to rapidly determine the motile behaviour of cancer cells under different environmental conditions, including inside three-dimensional matrices. We combined automated microscopy imaging of two-and three-dimensional cell cultures with computational image analysis into a single assay platform for studying cell dissemination in high-throughput. We have validated this new approach for medulloblastoma, a metastatic paediatric brain tumour, in combination with the activation of growth factor signalling pathways with established pro-migratory functions. The platform enabled the detection of primary tumour and patient-derived xenograft cell sensitivity to growth factor-dependent motility and dissemination and identified tumour subgroup-specific responses to selected growth factors of excellent diagnostic value.
    Full-text · Article · Oct 2015 · Scientific Reports
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    ABSTRACT: Automatisiertes De-novo-Moleküldesign führte zur Entdeckung eines neuartigen Inhibitors der Death-Associated Proteinkinase 3 (DAPK3). Eine erste Kristallstruktur der inaktiven DAPK3 als Homodimer im Komplex mit dem fragmentartigen Liganden zeigt dessen Bindung in der ATP-Bindetasche. Das verwendete maschinelle Lernverfahren hat neben DAPK3 weitere Targets korrekt vorhergesagt, sowohl für den entworfenen Liganden als auch für den strukturell verwandten und bereits auf dem Markt befindlichen Wirkstoff Azosemid. Die vorliegende Studie bestätigt das Konzept des computergestützten ligandenbasierten De-novo-Moleküldesigns als geeignet für die Erzeugung neuartiger Liganden und potentieller Startpunkte für die Wirkstofffindung.
    Full-text · Article · Oct 2015 · Angewandte Chemie
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    ABSTRACT: 2-Methylerythritol 2,4-cyclodiphosphate synthase (IspF) is an essential enzyme for the biosynthesis of isoprenoid precursors in plants and many human pathogens. The protein is an attractive target for the development of anti-infectives and herbicides. Using a photometric assay, a screen of 40 000 compounds on IspF from Arabidopsis thaliana afforded symmetrical aryl bis-sulfonamides that inhibit IspF from A. thaliana (AtIspF) and Plasmodium falciparum (PfIspF) with IC50 values in the micromolar range. The ortho-bis-sulfonamide structural motif is essential for inhibitory activity. The best derivatives obtained by parallel synthesis showed IC50 values of 1.4 μm against PfIspF and 240 nm against AtIspF. Substantial herbicidal activity was observed at a dose of 2 kg ha(-1) . Molecular modeling studies served as the basis for an in silico search targeted at the discovery of novel, non-symmetrical sulfonamide IspF inhibitors. The designed compounds were found to exhibit inhibitory activities in the double-digit micromolar IC50 range.
    No preview · Article · Oct 2015 · ChemMedChem
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    ABSTRACT: The antimicrobial peptide LL-37 is the sole member of the human cathelicidin family with immune system-modulating properties and roles in autoimmune disease development. Small molecules able to interact with LL-37 and to modulate its functions have not been described yet. Boswellic acids (BAs) are pentacyclic triterpene acids that are bioactive principles of frankincense extracts used as anti-inflammatory remedies. Although various anti-inflammatory modes of action have been proposed for BAs, the pharmacological profile of these compounds is still incompletely understood. Here, we describe the identification of human LL-37 as functional target of BAs. In unbiased target fishing experiments using immobilized BAs as bait and human neutrophils as target source, LL-37 was identified as binding partner assisted by MALDI-TOF mass spectrometry. Thermal stability experiments using circular dichroism spectroscopy confirm direct interaction between BAs and LL-37. Of interest, this binding of BAs resulted in an inhibition of the functionality of LL-37. Thus, the LPS-neutralizing properties of isolated LL-37 were inhibited by 3-O-acetyl-β-BA (Aβ-BA) and 3-O-acetyl-11-keto-β-BA (AKβ-BA) in a cell-free limulus amoebocyte lysate assay with EC50 = 0.2 and 0.8μM, respectively. Also, LL-37 activity was inhibited by these BAs in LL-37-enriched supernatants of stimulated neutrophils or human plasma derived from stimulated human whole blood. Together, we reveal BAs as inhibitors of LL-37, which might be a relevant mechanism underlying the anti-inflammatory properties of BAs and suggests BAs as suitable chemical tools or potential agents for intervention with LL-37 and related disorders.
    No preview · Article · Sep 2015 · Pharmacological Research
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    Full-text · Article · Aug 2015
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    ABSTRACT: A 4.1μs molecular dynamics simulation of the NR4A1 (hNur77) apo-protein has been undertaken and a previously undetected druggable pocket has become apparent that is located remotely from the 'traditional' nuclear receptor ligand-binding site. A NR4A1/bis-indole ligand complex at this novel site has been found to be stable over 1 μs of simulation and to result in an interesting conformational transmission to a remote loop that has the capacity to communicate with a NBRE within a RXR-α/NR4A1 heterodimer. Several features of the simulations undertaken indicate how NR4A1 can be affected by alternate-site modulators.
    Preview · Article · Aug 2015 · PLoS ONE
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    Tiago Rodrigues · Daniel Reker · Jens Kunze · Petra Schneider · Gisbert Schneider
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    ABSTRACT: Fragment-like natural products were identified as ligand-efficient chemical matter for hit-to-lead development and chemical-probe discovery. Relying on a computational method using a topological pharmacophore descriptor and a drug database, several macromolecular targets from distinct protein families were expeditiously retrieved for structurally unrelated chemotypes. The selected fragments feature structural dissimilarity to the reference compounds and suitable target affinity, and they offer opportunities for chemical optimization. Experimental confirmation of hitherto unknown macromolecular targets for the selected molecules corroborate the usefulness of the computational approach and suggests broad applicability to chemical biology and molecular medicine. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    Full-text · Article · Jul 2015 · Angewandte Chemie International Edition in English
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    ABSTRACT: The computer-assisted design and optimization of peptides with selective cancer cell killing activity was achieved through merging the features of anticancer peptides, cell-penetrating peptides, and tumor-homing peptides. Machine-learning classifiers identified candidate peptides that possess the predicted properties. Starting from a template amino acid sequence, peptide cytotoxicity against a range of cancer cell lines was systematically optimized while minimizing the effects on primary human endothelial cells. The computer-generated sequences featured improved cancer-cell penetration, induced cancer-cell apoptosis, and were enabled a decrease in the cytotoxic concentration of co-administered chemotherapeutic agents in vitro. This study demonstrates the potential of multidimensional machine-learning methods for rapidly obtaining peptides with the desired cellular activities. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    No preview · Article · Jun 2015 · Angewandte Chemie International Edition
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    ABSTRACT: Wir stellen hier den rechnergestützten Entwurf und die Optimierung von Peptiden vor, die selektiv Krebszellen zerstören können. Der Designprozess ermöglichte die Verschmelzung von Eigenschaften bekannter Antikrebs-, zellpenetrierender und Tumor-adressierender Peptide. Dabei identifizierten maschinelle Lernverfahren vollautomatisch neue Peptide mit den vorhergesagten Eigenschaften. Ausgehend von einer als Vorlage fungierenden Aminosäuresequenz haben wir systematisch die Toxizität der Peptide gegen eine Reihe von Krebszelllinien optimiert, während gleichzeitig die Aktivität gegen primäre humane Endothelzellen reduziert wurde. Die vom Computer generierten Peptide zeigten verbesserte Krebszellpenetration, lösten Apoptose aus und waren in der Lage, die zytotoxisch wirksame Konzentration von gleichzeitig verabreichten Chemotherapeutika in vitro zu reduzieren. Diese Studie demonstriert das Potenzial mehrdimensionaler maschineller Lernverfahren, innerhalb kurzer Zeit neue Peptide mit den gewünschten Eigenschaften zu erhalten.
    No preview · Article · Jun 2015 · Angewandte Chemie
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    ABSTRACT: Sustained identification of innovative chemical entities is key for the success of chemical biology and drug discovery. We report the fragment-based, computer-assisted de novo design of a small molecule inhibiting Helicobacter pylori HtrA protease. Molecular binding of the designed compound to HtrA was confirmed through biophysical methods, supporting its functional activity in vitro. Hit expansion led to the identification of the currently best-in-class HtrA inhibitor. The results obtained reinforce the validity of ligand-based de novo design and binding-kinetics-guided optimization for the efficient discovery of pioneering lead structures and prototyping drug-like chemical probes with tailored bioactivity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    Full-text · Article · Jun 2015 · Angewandte Chemie International Edition in English
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    ABSTRACT: We present the crystal structures of the SEC14-like domain of supernatant protein factor (SPF) in complex with squalene and 2,3-oxidosqualene. The structures were resolved at 1.75Å (complex with squalene) and 1.6Å resolution (complex with 2,3-oxidosqualene), leading in both cases to clear images of the protein/substrate interactions. Ligand binding is facilitated by removal of the Golgi-dynamics (GOLD) C-terminal domain of SPF, which, as shown in previous structures of the apo-protein, blocked the opening of the binding pocket to the exterior. Both substrates bind into a large hydrophobic cavity, typical of such lipid-transporter family. Our structures report no specific recognition mode for the epoxide group. In fact, for both molecules, ligand affinity is dominated by hydrophobic interactions, and independent investigations by computational models or differential scanning micro-calorimetry reveal similar binding affinities for both ligands. Our findings elucidate the molecular bases of the role of SPF in sterol endo-synthesis, supporting the original hypothesis that SPF is a facilitator of substrate flow within the sterol synthetic pathway. Moreover, our results suggest that the GOLD domain acts as a regulator, as its conformational displacement must occur to favor ligand binding and release during the different synthetic steps. Copyright © 2015 Elsevier Inc. All rights reserved.
    Full-text · Article · May 2015 · Journal of Structural Biology
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    ABSTRACT: Drug metabolism can produce metabolites with physicochemical and pharmacological properties that differ substantially from those of the parent drug, and consequently has important implications for both drug safety and efficacy. To reduce the risk of costly clinical-stage attrition due to the metabolic characteristics of drug candidates, there is a need for efficient and reliable ways to predict drug metabolism in vitro, in silico and in vivo. In this Perspective, we provide an overview of the state of the art of experimental and computational approaches for investigating drug metabolism. We highlight the scope and limitations of these methods, and indicate strategies to harvest the synergies that result from combining measurement and prediction of drug metabolism.
    No preview · Article · Apr 2015 · Nature Reviews Drug Discovery
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    ABSTRACT: The ligand activated transcription factor farnesoid X receptor (FXR) is a crucial regulator of several metabolic and inflammatory pathways and its activation by agonistic ligands seems a valuable therapeutic approach for many disorders. Most known non-steroidal FXR agonists however, have limitations that hinder their clinical development and novel FXR ligands are required. Evaluation of the co-crystal structures of the widely used FXR agonist GW4064 and related compounds in complex with the FXR ligand binding domain indicated that their disubstituted isoxazole moiety is especially relevant for FXR activation. By investigation of GW4064-fragments missing the aromatic tail, we discovered a highly potent and soluble partial FXR agonist (14, ST-1892) as well as a fluorescent FXR ligand (15) as potential pharmacological tool. Copyright © 2015 Elsevier Ltd. All rights reserved.
    Full-text · Article · Apr 2015 · Bioorganic & medicinal chemistry
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    ABSTRACT: We have recently demonstrated that Taspase1-mediated cleavage of the AF4–MLL oncoprotein results in the formation of a stable multiprotein complex which forms the key event for the onset of acute proB leukemia in mice. Therefore, Taspase1 represents a conditional oncoprotein in the context of t(4;11) leukemia. In this report, we used site-directed mutagenesis to unravel the molecular events by which Taspase1 becomes sequentially activated. Monomeric pro-enzymes form dimers which are autocatalytically processed into the enzymatically active form of Taspase1 (αββα). The active enzyme cleaves only very few target proteins, e.g., MLL, MLL4 and TFIIA at their corresponding consensus cleavage sites (CSTasp1) as well as AF4–MLL in the case of leukemogenic translocation. This knowledge was translated into the design of a dominant-negative mutant of Taspase1 (dnTASP1). As expected, simultaneous expression of the leukemogenic AF4–MLL and dnTASP1 causes the disappearance of the leukemogenic oncoprotein, because the uncleaved AF4–MLL protein (328 kDa) is subject to proteasomal degradation, while the cleaved AF4–MLL forms a stable oncogenic multi-protein complex with a very long half-life. Moreover, coexpression of dnTASP1 with a BFP-CSTasp1-GFP FRET biosensor effectively inhibits cleavage. The impact of our findings on future drug development and potential treatment options for t(4;11) leukemia will be discussed.
    Full-text · Article · Apr 2015 · EBioMedicine
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    ABSTRACT: Using computational bioactivity prediction models we identified phosphodiesterase 3B (PDE3B) and cathepsin L as macromolecular targets of de novo designed compounds. By disclosing the most potent cathepsin L activator known to date, small molecule repurposing by target panel prediction represents a feasible route towards innovative leads for chemical biology and molecular medicine.
    Full-text · Article · Apr 2015 · Chemical Communications
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    ABSTRACT: We present the application of the generative topographic map algorithm to visualize the chemical space populated by natural products and synthetic drugs. Generative topographic maps may be used for nonlinear dimensionality reduction and probabilistic modeling. For compound mapping, we represented the molecules by two-dimensional pharmacophore features (chemically advanced template search descriptor). The results obtained suggest a close resemblance of synthetic drugs with natural products in terms of their pharmacophore features, despite pronounced differences in chemical structure. Generative topographic map-based cluster analysis revealed both known and new potential activities of natural products and drug-like compounds. We conclude that the generative topographic map method is suitable for inferring functional similarities between these two classes of compounds and predicting macromolecular targets of natural products. Georg Thieme Verlag KG Stuttgart · New York.
    No preview · Article · Feb 2015 · Planta Medica

Publication Stats

8k Citations
1,261.02 Total Impact Points


  • 2012-2015
    • Hochschule für Technik Zürich
      Zürich, Zurich, Switzerland
  • 2010-2015
    • ETH Zurich
      • • Department of Chemistry and Applied Biosciences
      • • Institute of Pharmaceutical Sciences
      Zürich, Zurich, Switzerland
  • 2014
    • Eawag: Das Wasserforschungs-Institut des ETH-Bereichs
      Duebendorf, Zurich, Switzerland
  • 2011
    • University of Tuebingen
      Tübingen, Baden-Württemberg, Germany
  • 2002-2011
    • Goethe-Universität Frankfurt am Main
      • Institute of Organic Chemistry and Chemical Biology
      Frankfurt, Hesse, Germany
    • Universität Freiburg
      • Institute of Biology I
      Freiburg, Lower Saxony, Germany
  • 2009
    • Technische Universität Braunschweig
      Brunswyck, Lower Saxony, Germany
  • 2005-2009
    • University Hospital Frankfurt
      Frankfurt, Hesse, Germany
  • 2008
    • Columbia University
      New York City, New York, United States
  • 2007
    • Karl-Franzens-Universität Graz
      Gratz, Styria, Austria
  • 1993-2007
    • Freie Universität Berlin
      • • Institute of Biology
      • • Department of Physics
      Berlín, Berlin, Germany
  • 2006
    • Boehringer Ingelheim
      Ingelheim, Rheinland-Pfalz, Germany
  • 2001
    • Stockholm University
      Tukholma, Stockholm, Sweden