1
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Schütz S, Bergsdorf C, Hänni-Holzinger S, Lingel A, Renatus M, Gossert AD, Jahnke W. Intrinsically Disordered Regions in the Transcription Factor MYC:MAX Modulate DNA Binding via Intramolecular Interactions. Biochemistry 2024. [PMID: 38264995 DOI: 10.1021/acs.biochem.3c00608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factor (TF) MYC is in large part an intrinsically disordered oncoprotein. In complex with its obligate heterodimerization partner MAX, MYC preferentially binds E-Box DNA sequences (CANNTG). At promoters containing these sequence motifs, MYC controls fundamental cellular processes such as cell cycle progression, metabolism, and apoptosis. A vast network of proteins in turn regulates MYC function via intermolecular interactions. In this work, we establish another layer of MYC regulation by intramolecular interactions. We used nuclear magnetic resonance (NMR) spectroscopy to identify and map multiple binding sites for the C-terminal MYC:MAX DNA-binding domain (DBD) on the intrinsically disordered regions (IDRs) in the MYC N-terminus. We find that these binding events in trans are driven by electrostatic attraction, that they have distinct affinities, and that they are competitive with DNA binding. Thereby, we observe the strongest effects for the N-terminal MYC box 0 (Mb0), a conserved motif involved in MYC transactivation and target gene induction. We prepared recombinant full-length MYC:MAX complex and demonstrate that the interactions identified in this work are also relevant in cis, i.e., as intramolecular interactions. These findings are supported by surface plasmon resonance (SPR) experiments, which revealed that intramolecular IDR:DBD interactions in MYC decelerate the association of MYC:MAX complexes to DNA. Our work offers new insights into how bHLH-LZ TFs are regulated by intramolecular interactions, which open up new possibilities for drug discovery.
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Affiliation(s)
- Stefan Schütz
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Christian Bergsdorf
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Sandra Hänni-Holzinger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
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2
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Hoegenauer K, An S, Axford J, Benander C, Bergsdorf C, Botsch J, Chau S, Fernández C, Gleim S, Hassiepen U, Hunziker J, Joly E, Keller A, Lopez Romero S, Maher R, Mangold AS, Mickanin C, Mihalic M, Neuner P, Patterson AW, Perruccio F, Roggo S, Scesa J, Schröder M, Shkoza D, Thai B, Vulpetti A, Renatus M, Reece-Hoyes JS. Discovery of Ligands for TRIM58, a Novel Tissue-Selective E3 Ligase. ACS Med Chem Lett 2023; 14:1631-1639. [PMID: 38116426 PMCID: PMC10726445 DOI: 10.1021/acsmedchemlett.3c00259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/06/2023] [Indexed: 12/21/2023] Open
Abstract
Redirecting E3 ligases to neo-substrates, leading to their proteasomal disassembly, known as targeted protein degradation (TPD), has emerged as a promising alternative to traditional, occupancy-driven pharmacology. Although the field has expanded tremendously over the past years, the choice of E3 ligases remains limited, with an almost exclusive focus on CRBN and VHL. Here, we report the discovery of novel ligands to the PRY-SPRY domain of TRIM58, a RING ligase that is specifically expressed in erythroid precursor cells. A DSF screen, followed by validation using additional biophysical methods, led to the identification of TRIM58 ligand TRIM-473. A basic SAR around the chemotype was established by utilizing a competitive binding assay employing a short FP peptide probe derived from an endogenous TRIM58 substrate. The X-ray co-crystal structure of TRIM58 in complex with TRIM-473 gave insights into the binding mode and potential exit vectors for bifunctional degrader design.
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Affiliation(s)
- Klemens Hoegenauer
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Shaojian An
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Jake Axford
- Global Discovery
Chemistry, Novartis Institutes for BioMedical
Research, Cambridge, Massachusetts 02139, United States
| | - Christina Benander
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Christian Bergsdorf
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Josephine Botsch
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Suzanne Chau
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - César Fernández
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Scott Gleim
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Ulrich Hassiepen
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Juerg Hunziker
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Emilie Joly
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Aramis Keller
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Sandra Lopez Romero
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Robert Maher
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Anne-Sophie Mangold
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Craig Mickanin
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Manuel Mihalic
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Philippe Neuner
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Andrew W. Patterson
- Global Discovery
Chemistry, Novartis Institutes for BioMedical
Research, Cambridge, Massachusetts 02139, United States
| | - Francesca Perruccio
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Silvio Roggo
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Julien Scesa
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Martin Schröder
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Dojna Shkoza
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Binh Thai
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Anna Vulpetti
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Martin Renatus
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - John S. Reece-Hoyes
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Cambridge, Massachusetts 02139, United States
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3
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Schütz S, Bergsdorf C, Goretzki B, Lingel A, Renatus M, Gossert AD, Jahnke W. The disordered MAX N-terminus modulates DNA binding of the transcription factor MYC:MAX. J Mol Biol 2022; 434:167833. [PMID: 36174765 DOI: 10.1016/j.jmb.2022.167833] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/05/2022] [Accepted: 09/17/2022] [Indexed: 11/15/2022]
Abstract
The intrinsically disordered protein MYC belongs to the family of basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factors (TFs). In complex with its cognate binding partner MAX, MYC preferentially binds to E-Box promotor sequences where it controls fundamental cellular processes such as cell cycle progression, metabolism, and apoptosis. Intramolecular regulation of MYC:MAX has not yet been investigated in detail. In this work, we use Nuclear Magnetic Resonance (NMR) spectroscopy to identify and map interactions between the disordered MAX N-terminus and the MYC:MAX DNA binding domain (DBD). We find that this binding event is mainly driven by electrostatic interactions and that it is competitive with DNA binding. Using Nuclear Magnetic resonance (NMR) spectroscopy and Surface Plasmon Resonance (SPR), we demonstrate that the MAX N-terminus serves to accelerate DNA binding kinetics of MYC:MAX and MAX:MAX dimers, while it simultaneously provides specificity for E-Box DNA. We also establish that these effects are further enhanced by Casein Kinase 2-mediated phosphorylation of two serine residues in the MAX N-terminus. Our work provides new insights how bHLH-LZ TFs are regulated by intramolecular interactions between disordered regions and the folded DNA binding domain.
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Affiliation(s)
- Stefan Schütz
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Christian Bergsdorf
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Benedikt Goretzki
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Alvar D Gossert
- Department of Biology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland.
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4
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Holdgate GA, Bergsdorf C. Applications of Biophysics in Early Drug Discovery. SLAS Discov 2021; 26:945-946. [PMID: 34415216 DOI: 10.1177/24725552211035123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
| | - Christian Bergsdorf
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
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5
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Di Marco G, Vallese F, Jourde B, Bergsdorf C, Sturlese M, De Mario A, Techer-Etienne V, Haasen D, Oberhauser B, Schleeger S, Minetti G, Moro S, Rizzuto R, De Stefani D, Fornaro M, Mammucari C. A High-Throughput Screening Identifies MICU1 Targeting Compounds. Cell Rep 2021; 30:2321-2331.e6. [PMID: 32075766 PMCID: PMC7034061 DOI: 10.1016/j.celrep.2020.01.081] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/08/2020] [Accepted: 01/22/2020] [Indexed: 01/01/2023] Open
Abstract
Mitochondrial Ca2+ uptake depends on the mitochondrial calcium uniporter (MCU) complex, a highly selective channel of the inner mitochondrial membrane (IMM). Here, we screen a library of 44,000 non-proprietary compounds for their ability to modulate mitochondrial Ca2+ uptake. Two of them, named MCU-i4 and MCU-i11, are confirmed to reliably decrease mitochondrial Ca2+ influx. Docking simulations reveal that these molecules directly bind a specific cleft in MICU1, a key element of the MCU complex that controls channel gating. Accordingly, in MICU1-silenced or deleted cells, the inhibitory effect of the two compounds is lost. Moreover, MCU-i4 and MCU-i11 fail to inhibit mitochondrial Ca2+ uptake in cells expressing a MICU1 mutated in the critical amino acids that forge the predicted binding cleft. Finally, these compounds are tested ex vivo, revealing a primary role for mitochondrial Ca2+ uptake in muscle growth. Overall, MCU-i4 and MCU-i11 represent leading molecules for the development of MICU1-targeting drugs. An HTS identifies MCU-i4 and MCU-i11 as negative modulators of the MCU MCU-i4 and MCU-i11 bind MICU1 MICU1 is required for the activity of MCU-i4 and MCU-i11 MCU-i4 and MCU-i11 impair muscle cell growth
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Affiliation(s)
- Giulia Di Marco
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Francesca Vallese
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Benjamin Jourde
- Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Christian Bergsdorf
- Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Mattia Sturlese
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padua, 35131 Padua, Italy
| | - Agnese De Mario
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | | | - Dorothea Haasen
- Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Berndt Oberhauser
- Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Simone Schleeger
- Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Giulia Minetti
- Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Stefano Moro
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padua, 35131 Padua, Italy
| | - Rosario Rizzuto
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Diego De Stefani
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Mara Fornaro
- Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland.
| | - Cristina Mammucari
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy.
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6
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Markert C, Thoma G, Srinivas H, Bollbuck B, Lüönd RM, Miltz W, Wälchli R, Wolf R, Hinrichs J, Bergsdorf C, Azzaoui K, Penno CA, Klein K, Wack N, Jäger P, Hasler F, Beerli C, Loetscher P, Dawson J, Wieczorek G, Numao S, Littlewood-Evans A, Röhn TA. Discovery of LYS006, a Potent and Highly Selective Inhibitor of Leukotriene A 4 Hydrolase. J Med Chem 2021; 64:1889-1903. [PMID: 33592148 DOI: 10.1021/acs.jmedchem.0c01955] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The cytosolic metalloenzyme leukotriene A4 hydrolase (LTA4H) is the final and rate-limiting enzyme in the biosynthesis of pro-inflammatory leukotriene B4 (LTB4). Preclinical studies have validated this enzyme as an attractive drug target in chronic inflammatory diseases. Despite several attempts, no LTA4H inhibitor has reached the market, yet. Herein, we disclose the discovery and preclinical profile of LYS006, a highly potent and selective LTA4H inhibitor. A focused fragment screen identified hits that could be cocrystallized with LTA4H and inspired a fragment merging. Further optimization led to chiral amino acids and ultimately to LYS006, a picomolar LTA4H inhibitor with exquisite whole blood potency and long-lasting pharmacodynamic effects. Due to its high selectivity and its ability to fully suppress LTB4 generation at low exposures in vivo, LYS006 has the potential for a best-in-class LTA4H inhibitor and is currently investigated in phase II clinical trials in inflammatory acne, hidradenitis suppurativa, ulcerative colitis, and NASH.
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7
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Renner S, Bergsdorf C, Bouhelal R, Koziczak-Holbro M, Amati AM, Techer-Etienne V, Flotte L, Reymann N, Kapur K, Hoersch S, Oakeley EJ, Schuffenhauer A, Gubler H, Lounkine E, Farmer P. Gene-signature-derived IC 50s/EC 50s reflect the potency of causative upstream targets and downstream phenotypes. Sci Rep 2020; 10:9670. [PMID: 32541899 PMCID: PMC7295968 DOI: 10.1038/s41598-020-66533-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/19/2020] [Indexed: 02/02/2023] Open
Abstract
Multiplexed gene-signature-based phenotypic assays are increasingly used for the identification and profiling of small molecule-tool compounds and drugs. Here we introduce a method (provided as R-package) for the quantification of the dose-response potency of a gene-signature as EC50 and IC50 values. Two signaling pathways were used as models to validate our methods: beta-adrenergic agonistic activity on cAMP generation (dedicated dataset generated for this study) and EGFR inhibitory effect on cancer cell viability. In both cases, potencies derived from multi-gene expression data were highly correlated with orthogonal potencies derived from cAMP and cell growth readouts, and superior to potencies derived from single individual genes. Based on our results we propose gene-signature potencies as a novel valid alternative for the quantitative prioritization, optimization and development of novel drugs.
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Affiliation(s)
- Steffen Renner
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Basel, 4056, Switzerland.
| | - Christian Bergsdorf
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Basel, 4056, Switzerland
| | - Rochdi Bouhelal
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Basel, 4056, Switzerland
| | | | - Andrea Marco Amati
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Basel, 4056, Switzerland.,Department of Chemistry & Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Valerie Techer-Etienne
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Basel, 4056, Switzerland
| | | | - Nicole Reymann
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Basel, 4056, Switzerland
| | | | | | | | - Ansgar Schuffenhauer
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Basel, 4056, Switzerland
| | | | - Eugen Lounkine
- Chemical Biology & Therapeutics, NIBR, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA.,Modeling and Informatics, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Pierre Farmer
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Basel, 4056, Switzerland.
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8
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Haffke M, Duckely M, Bergsdorf C, Jaakola VP, Shrestha B. Development of a biochemical and biophysical suite for integral membrane protein targets: A review. Protein Expr Purif 2020; 167:105545. [DOI: 10.1016/j.pep.2019.105545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/18/2019] [Accepted: 11/24/2019] [Indexed: 12/11/2022]
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9
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Abstract
Over the past 30 years, drug discovery has evolved from a pure phenotypic approach to an integrated target-based strategy. The implementation of high-throughput biochemical and cellular assays has enabled the screening of large compound libraries which has become an important and often times the main source of new chemical matter that serve as starting point for medicinal chemistry efforts. In addition, biophysical methods measuring the physical interaction (affinity) between a low molecular weight ligand and a target protein became an integral part of hit validation/optimization to rule out false positives due to assay artifacts. Recent advances in throughput, robustness, and sensitivity of biophysical affinity screening methods have broadened their application in hit identification and validation such that they can now complement classical functional readouts. As a result, new target classes can be accessed that have not been amenable to functional assays. In this chapter, two affinity screening methods, differential scanning fluorimetry and surface plasmon resonance, which are broadly utilized in both academia and pharmaceutical industry are discussed in respect to their use in hit identification and validation. These methods exemplify how assays which differ in complexity, throughput, and information content can support the hit identification/validation process. This chapter focuses on the practical aspects and caveats of these techniques in order to enable the reader to establish their own affinity-based screens in both formats.
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Affiliation(s)
| | - S Kirk Wright
- Novartis Institutes for BioMedical Research, Cambridge, MA, United States
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10
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Kallen J, Bergsdorf C, Arnaud B, Bernhard M, Brichet M, Cobos-Correa A, Elhajouji A, Freuler F, Galimberti I, Guibourdenche C, Haenni S, Holzinger S, Hunziker J, Izaac A, Kaufmann M, Leder L, Martus HJ, von Matt P, Polyakov V, Roethlisberger P, Roma G, Stiefl N, Uteng M, Lerchner A. X-ray Structures and Feasibility Assessment of CLK2 Inhibitors for Phelan-McDermid Syndrome. ChemMedChem 2018; 13:1997-2007. [PMID: 29985556 DOI: 10.1002/cmdc.201800344] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Indexed: 01/15/2023]
Abstract
CLK2 inhibition has been proposed as a potential mechanism to improve autism and neuronal functions in Phelan-McDermid syndrome (PMDS). Herein, the discovery of a very potent indazole CLK inhibitor series and the CLK2 X-ray structure of the most potent analogue are reported. This new indazole series was identified through a biochemical CLK2 Caliper assay screen with 30k compounds selected by an in silico approach. Novel high-resolution X-ray structures of all CLKs, including the first CLK4 X-ray structure, bound to known CLK2 inhibitor tool compounds (e.g., TG003, CX-4945), are also shown and yield insight into inhibitor selectivity in the CLK family. The efficacy of the new CLK2 inhibitors from the indazole series was demonstrated in the mouse brain slice assay, and potential safety concerns were investigated. Genotoxicity findings in the human lymphocyte micronucleus test (MNT) assay are shown by using two structurally different CLK inhibitors to reveal a major concern for pan-CLK inhibition in PMDS.
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Affiliation(s)
- Joerg Kallen
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Christian Bergsdorf
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Bertrand Arnaud
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Mario Bernhard
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Murielle Brichet
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Amanda Cobos-Correa
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Azeddine Elhajouji
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Felix Freuler
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Ivan Galimberti
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Christel Guibourdenche
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Simon Haenni
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Sandra Holzinger
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Juerg Hunziker
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Aude Izaac
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Markus Kaufmann
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Lukas Leder
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Hans-Joerg Martus
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Peter von Matt
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Valery Polyakov
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Patrik Roethlisberger
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Nikolaus Stiefl
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Marianne Uteng
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
| | - Andreas Lerchner
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland
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11
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Numao S, Hasler F, Laguerre C, Srinivas H, Wack N, Jäger P, Schmid A, Osmont A, Röthlisberger P, Houguenade J, Bergsdorf C, Dawson J, Carte N, Hofmann A, Markert C, Hardaker L, Billich A, Wolf RM, Penno CA, Bollbuck B, Miltz W, Röhn TA. Feasibility and physiological relevance of designing highly potent aminopeptidase-sparing leukotriene A4 hydrolase inhibitors. Sci Rep 2017; 7:13591. [PMID: 29051536 PMCID: PMC5648829 DOI: 10.1038/s41598-017-13490-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/25/2017] [Indexed: 01/01/2023] Open
Abstract
Leukotriene A4 Hydrolase (LTA4H) is a bifunctional zinc metalloenzyme that comprises both epoxide hydrolase and aminopeptidase activity, exerted by two overlapping catalytic sites. The epoxide hydrolase function of the enzyme catalyzes the biosynthesis of the pro-inflammatory lipid mediator leukotriene (LT) B4. Recent literature suggests that the aminopeptidase function of LTA4H is responsible for degradation of the tripeptide Pro-Gly-Pro (PGP) for which neutrophil chemotactic activity has been postulated. It has been speculated that the design of epoxide hydrolase selective LTA4H inhibitors that spare the aminopeptidase pocket may therefore lead to more efficacious anti-inflammatory drugs. In this study, we conducted a high throughput screen (HTS) for LTA4H inhibitors and attempted to rationally design compounds that would spare the PGP degrading function. While we were able to identify compounds with preference for the epoxide hydrolase function, absolute selectivity was not achievable for highly potent compounds. In order to assess the relevance of designing such aminopeptidase-sparing LTA4H inhibitors, we studied the role of PGP in inducing inflammation in different settings in wild type and LTA4H deficient (LTA4H KO) animals but could not confirm its chemotactic potential. Attempting to design highly potent epoxide hydrolase selective LTA4H inhibitors, therefore seems to be neither feasible nor relevant.
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Affiliation(s)
- Shin Numao
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Franziska Hasler
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Claire Laguerre
- Analytical Sciences & Imaging, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Honnappa Srinivas
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Nathalie Wack
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Petra Jäger
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Andres Schmid
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Arnaud Osmont
- Analytical Sciences & Imaging, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Patrik Röthlisberger
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Jeremy Houguenade
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Christian Bergsdorf
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Janet Dawson
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Nathalie Carte
- Analytical Sciences & Imaging, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Andreas Hofmann
- Analytical Sciences & Imaging, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Christian Markert
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Liz Hardaker
- Respiratory Research, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Andreas Billich
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Romain M Wolf
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Carlos A Penno
- Analytical Sciences & Imaging, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Birgit Bollbuck
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Wolfgang Miltz
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Till A Röhn
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland.
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12
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Bergsdorf C, Fiez-Vandal C, Sykes DA, Bernet P, Aussenac S, Charlton SJ, Schopfer U, Ottl J, Duckely M. An Alternative Thiol-Reactive Dye to Analyze Ligand Interactions with the Chemokine Receptor CXCR2 Using a New Thermal Shift Assay Format. ACTA ACUST UNITED AC 2015; 21:243-51. [DOI: 10.1177/1087057115619597] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/29/2015] [Indexed: 11/16/2022]
Abstract
Integral membrane proteins (IMPs) play an important role in many cellular events and are involved in numerous pathological processes. Therefore, understanding the structure and function of IMPs is a crucial prerequisite to enable successful targeting of these proteins with low molecular weight (LMW) ligands early on in the discovery process. To optimize IMP purification/crystallization and to identify/characterize LMW ligand-target interactions, robust, reliable, high-throughput, and sensitive biophysical methods are needed. Here, we describe a differential scanning fluorimetry (DSF) screening method using the thiol-reactive BODIPY FL-cystine dye to monitor thermal unfolding of the G-protein-coupled receptor (GPCR), CXCR2. To validate this method, the seven-transmembrane protein CXCR2 was analyzed with a set of well-characterized antagonists. This study showed that the new DSF assay assessed reliably the stability of CXCR2 in a 384-well format. The analysis of 14 ligands with a potency range over 4 log units demonstrated the detection/characterization of LMW ligands binding to the membrane protein target. Furthermore, DSF results cross-validated with the label-free differential static light scattering (DSLS) thermal denaturation method. These results underline the potential of the BODIPY assay format as a general tool to investigate membrane proteins and their interaction partners.
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Affiliation(s)
- Christian Bergsdorf
- Novartis Institutes for BioMedical Research (NIBR), Center for Proteomic Chemistry, Switzerland
| | - Cédric Fiez-Vandal
- Novartis Institutes for BioMedical Research (NIBR), Center for Proteomic Chemistry, Switzerland
- Current affiliation: Heptares Therapeutics Ltd, BioPark, Welwyn Garden City, Hertfordshire, UK
| | - David A. Sykes
- Novartis Institutes for BioMedical Research (NIBR), Respiratory Diseases, Horsham, UK
- Current affiliation: School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, UK
| | - Pascal Bernet
- Novartis Institutes for BioMedical Research (NIBR), Center for Proteomic Chemistry, Switzerland
| | - Sonia Aussenac
- Novartis Institutes for BioMedical Research (NIBR), Center for Proteomic Chemistry, Switzerland
- Current affiliation: Novartis Pharma, Basel, Switzerland
| | - Steven J. Charlton
- Novartis Institutes for BioMedical Research (NIBR), Respiratory Diseases, Horsham, UK
- Current affiliation: School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, UK
| | - Ulrich Schopfer
- Novartis Institutes for BioMedical Research (NIBR), Center for Proteomic Chemistry, Switzerland
| | - Johannes Ottl
- Novartis Institutes for BioMedical Research (NIBR), Center for Proteomic Chemistry, Switzerland
| | - Myriam Duckely
- Novartis Institutes for BioMedical Research (NIBR), Center for Proteomic Chemistry, Switzerland
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13
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Weiler S, Braendlin N, Beerli C, Bergsdorf C, Schubart A, Srinivas H, Oberhauser B, Billich A. Orally active 7-substituted (4-benzylphthalazin-1-yl)-2-methylpiperazin-1-yl]nicotinonitriles as active-site inhibitors of sphingosine 1-phosphate lyase for the treatment of multiple sclerosis. J Med Chem 2014; 57:5074-84. [PMID: 24809814 DOI: 10.1021/jm500338n] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Sphingosine 1-phosphate (S1P) lyase has recently been implicated as a therapeutic target for the treatment of multiple sclerosis (MS), based on studies in a genetic mouse model. Potent active site directed inhibitors of the enzyme are not known so far. Here we describe the discovery of (4-benzylphthalazin-1-yl)-2-methylpiperazin-1-yl]nicotinonitrile 5 in a high-throughput screen using a biochemical assay, and its further optimization. This class of compounds was found to inhibit catalytic activity of S1PL by binding to the active site of the enzyme, as seen in the cocrystal structure of derivative 31 with the homodimeric human S1P lyase. 31 induces profound reduction of peripheral T cell numbers after oral dosage and confers pronounced protection in a rat model of multiple sclerosis. In conclusion, this novel class of direct S1P lyase inhibitors provides excellent tools to further explore the therapeutic potential of T cell-targeted therapies in multiple sclerosis and other autoimmune and inflammatory diseases.
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Affiliation(s)
- Sven Weiler
- Novartis Institutes for BioMedical Research , Basel, CH-4002, Switzerland
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14
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Bergsdorf C, Ottl J. Affinity-based screening techniques: their impact and benefit to increase the number of high quality leads. Expert Opin Drug Discov 2010; 5:1095-107. [DOI: 10.1517/17460441.2010.524641] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christian Bergsdorf
- Novartis Institutes of BioMedical Research, CPC/LFP/LFT, WSJ-88.07.31, CH-4002 Basel, Switzerland ;
| | - Johannes Ottl
- Novartis Institutes of BioMedical Research, CPC/LFP/LFT, WSJ-88.10.03, CH-4002 Basel, Switzerland
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15
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Siehler S, Yamamoto R, Bergsdorf C, Leder L, Reinhardt J, Freuler F, Scheel G. Novel pharmacological insights for adenylyl cyclase 5, a gatekeeper of GPCR signaling. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.lb477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sandra Siehler
- Center for Proteomic ChemistryNovartis Institutes for BioMedical Research (NIBR)BaselSwitzerland
| | - Rina Yamamoto
- Center for Proteomic ChemistryNovartis Institutes for BioMedical Research (NIBR)BaselSwitzerland
| | - Christian Bergsdorf
- Center for Proteomic ChemistryNovartis Institutes for BioMedical Research (NIBR)BaselSwitzerland
| | - Lukas Leder
- Center for Proteomic ChemistryNovartis Institutes for BioMedical Research (NIBR)BaselSwitzerland
| | - Juergen Reinhardt
- Center for Proteomic ChemistryNovartis Institutes for BioMedical Research (NIBR)BaselSwitzerland
| | - Felix Freuler
- Center for Proteomic ChemistryNovartis Institutes for BioMedical Research (NIBR)BaselSwitzerland
| | - Guenther Scheel
- Center for Proteomic ChemistryNovartis Institutes for BioMedical Research (NIBR)BaselSwitzerland
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16
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Bergsdorf C, Kropp-Goerkis C, Kaehler I, Ketscher L, Boemer U, Parczyk K, Bader B. A One-Day, Dispense-Only IP-One HTRF Assay for High-Throughput Screening of Gαq Protein-Coupled Receptors: Towards Cells as Reagents. Assay Drug Dev Technol 2008; 6:39-53. [DOI: 10.1089/adt.2007.108] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Christian Bergsdorf
- Department of Screening, Lead Discovery Berlin, Bayer Schering Pharma AG, Berlin, Germany
| | - Carmen Kropp-Goerkis
- Department of Screening, Lead Discovery Berlin, Bayer Schering Pharma AG, Berlin, Germany
| | - Irene Kaehler
- Department of Protein Supply, Lead Discovery Berlin, Bayer Schering Pharma AG, Berlin, Germany
| | - Lars Ketscher
- Institute of Zoology, Technical University, Dresden, Germany
| | - Ulf Boemer
- Department of Screening, Lead Discovery Berlin, Bayer Schering Pharma AG, Berlin, Germany
| | - Karsten Parczyk
- Department of Screening, Lead Discovery Berlin, Bayer Schering Pharma AG, Berlin, Germany
| | - Benjamin Bader
- Department of Screening, Lead Discovery Berlin, Bayer Schering Pharma AG, Berlin, Germany
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17
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Bergsdorf C, Gewiese N, Stolz A, Mann R, Parczyk K, Bömer U. A Cost-Effective Solution to Reduce Dead Volume of a Standard Dispenser System by a Factor of 5. ACTA ACUST UNITED AC 2006; 11:407-12. [PMID: 16490776 DOI: 10.1177/1087057105285828] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A key trend in high-throughput screening is assay miniaturization to control reagent costs and increase throughput. For this purpose, liquid-handling devices are used that transfer nano-to low-microliter volumes into all currently used microtiter well plates. One drawback of many available dispenser and pipetting systems are high dead volumes. Therefore, the authors were looking for an easy and simple solution to modify their standard liquid-handling device, PerkinElmer’s FlexDrop™ Precision IV, allowing for a dead volume reduction to receive maximum benefit from miniaturized assay formats. Internal reservoirs were developed and constructed by Schering’s Technical Development Laboratory (TDL), which are directly connected to the dispenser banks of FlexDrop™ without tubing. Using these newly built reservoirs, the dead volume was decreased by a factor of 5 in comparison to the manufacturer’s reservoirs without compromising liquid-handling parameters such as accuracy and precision. The modified system displayed a high robustness and reliability under routine high-throughput screening conditions.
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Affiliation(s)
- Christian Bergsdorf
- Department of Assay Development and High-Throughput Screening/Enabling Technologies, Schering AG, Berlin, Germany.
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18
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Rommel O, Dillner J, Fligge C, Bergsdorf C, Wang X, Selinka HC, Sapp M. Heparan sulfate proteoglycans interact exclusively with conformationally intact HPV L1 assemblies: basis for a virus-like particle ELISA. J Med Virol 2005; 75:114-21. [PMID: 15543569 DOI: 10.1002/jmv.20245] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In this article, we demonstrate that interaction of human papillomavirus-like particles (HPV-VLPs) with the putative glucosaminoglycan binding receptor is strictly dependent on conformational integrity. Such conformations are present on VLPs and capsomeres but not on monomers of the major capsid protein, L1, confirming reports that capsomeres can induce virus-neutralizing antibodies. Furthermore, we show the suitability of this specific interaction for development of VLP-based enzyme-linked immunosorbent assays (ELISAs), using heparin for indirect coupling of VLPs to microtiter plates, which may add an intrinsic quality control. This avoids presentation of linear, often highly cross-reactive epitopes of L1. In addition, heparin specifically interacts with a wide variety of HPV types, making it a prime candidate for a universal capture molecule.
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19
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Bergsdorf C, Beyer C, Umansky V, Werr M, Sapp M. Highly efficient transport of carboxyfluorescein diacetate succinimidyl ester into COS7 cells using human papillomavirus-like particles. FEBS Lett 2003; 536:120-4. [PMID: 12586349 DOI: 10.1016/s0014-5793(03)00039-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human papillomavirus virus-like particles (VLPs) have recently been used to deliver genes into mammalian cells in vitro and in vivo. Here, we investigated whether VLPs may serve as an efficient carrier of low molecular weight compounds (e.g. hormones, vitamins, peptides etc.) into cells. COS7 cells were incubated with recombinant HPV-16L1/L2 VLPs labelled with the fluorescence dye carboxyfluorescein diacetate succinimidyl ester. Using flow cytometry, we demonstrate that labelled VLPs can specifically bind to the cell surface followed by their complete internalisation. Our results indicate that VLPs are promising vehicles for highly efficient delivery of low molecular weight compounds into cells.
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Affiliation(s)
- Christian Bergsdorf
- Virofem Diagnostica GmbH, Rheingaustrasse 190-196, P.O. Box 3540, 65174 Wiesbaden, Germany
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20
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Abstract
Biomineralizing organisms use organic molecules to generate species-specific mineral patterns. Here, we describe the chemical structure of long-chain polyamines (up to 20 repeated units), which represent the main organic constituent of diatom biosilica. These substances are the longest polyamine chains found in nature and induce rapid silica precipitation from a silicic acid solution. Each diatom is equipped with a species-specific set of polyamines and silica-precipitating proteins, which are termed silaffins. Different morphologies of precipitating silica can be generated by polyamines of different chain lengths as well as by a synergistic action of long-chain polyamines and silaffins.
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Affiliation(s)
- N Kröger
- Lehrstuhl Biochemie I, Universität Regensburg, 93053 Regensburg, Germany
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21
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Bergsdorf C, Paliga K, Kreger S, Masters CL, Beyreuther K. Identification of cis-elements regulating exon 15 splicing of the amyloid precursor protein pre-mRNA. J Biol Chem 2000; 275:2046-56. [PMID: 10636908 DOI: 10.1074/jbc.275.3.2046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alternative splicing of exon 15 of the amyloid precursor protein (APP) pre-mRNA generates two APP isoform groups APP(ex15) (containing exon 15) and L-APP (without exon 15), which show a cell-specific distribution in non-neuronal cells and neurons of rat. Both APP isoforms differ in regard to functional properties like post-translational modification, APP secretion, and proteolytic production of Abeta peptide from APP molecules. Since Abeta generation is an important factor in the development of Alzheimer's disease, one could anticipate that these major APP isoforms might contribute differentially to the mechanisms underlying neurodegeneration in Alzheimer's disease. In this study, we established an APP minigene system in a murine cell system to identify cis-acting elements controlling exon 15 recognition. A 12. 5-kilobase pair genomic fragment of the murine APP gene contained all cis-regulatory elements to reproduce the splicing pattern of the endogenous APP transcripts. By using this approach, two intronic cis-elements flanking exon 15 were identified that block the inclusion of exon 15 in APP transcripts of non-neuronal cells. Point mutation analysis of these intronic regions indicated that pyrimidine-rich sequences are involved in the splice repressor function. Finally, grafting experiments demonstrated that these regulatory regions cell-specifically enhance the blockage of a chimeric exon in the non-neuronal splicing system.
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Affiliation(s)
- C Bergsdorf
- Center for Molecular Biology Heidelberg (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany.
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22
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Abstract
The outstanding feature of a diatom is the species-specific design and ornamentation of the silica-based cell wall, termed frustulum. A new frustulum is shaped in a specialized organelle (silica deposition vesicle) and secreted. Proteins in the lumen of this organelle may control the biomineralization process and are likely to remain associated with the mature cell wall. Therefore a study of the structures of proteins associated with the diatom cell wall was initiated. The complete primary structures of three cell wall proteins (denoted as frustulins) have been determined. In addition, partial amino acid sequences from two more cell wall components were obtained. From these data, a highly conserved domain has been identified as a common building block of diatom cell wall proteins that is repeated several times per polypeptide chain together with polyproline/hydroxyproline or polyglycine spacers. All frustulins characterized so far, are synthesized as preproteins with a novel type of N-terminal presequence.
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Affiliation(s)
- N Kröger
- Lehrstuhl für Biochemie I, Universität Regensburg, Germany
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23
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Hartmann T, Bergsdorf C, Sandbrink R, Tienari PJ, Multhaup G, Ida N, Bieger S, Dyrks T, Weidemann A, Masters CL, Beyreuther K. Alzheimer's disease betaA4 protein release and amyloid precursor protein sorting are regulated by alternative splicing. J Biol Chem 1996; 271:13208-14. [PMID: 8662794 DOI: 10.1074/jbc.271.22.13208] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We show here that alternative splicing influences the polarized secretion of amyloid precursor protein (APP) as well as the release of its proteolytic 3-4-kDa fragments betaA4 and p3. In Madin-Darby canine kidney II cells stably transfected with various APP isoforms and APP mutants, APPsec was consistently secreted basolaterally. In contrast, Madin-Darby canine kidney II cells transfected with L-APP677, which occurs naturally by alternative splicing of exon 15, secreted this isoform both apically and basolaterally, while maintaining the basolateral sorting of endogenous APPsec. This suggests that the alternative splicing of APP exon 15 modulates the polarized sorting of secretory APP. The same alternative splicing event also decreased the production of betaA4 relative to p3. This is the first example of alternative splicing regulating polarized trafficking of a secretory protein.
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Affiliation(s)
- T Hartmann
- Zentrum für Molekulare Biologie, University of Heidelberg, D-69120 Heidelberg, Federal Republic of Germany
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24
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Zhang D, Sandbrink R, Tienari P, Hartmann T, Bergsdorf C, Paliga K, Förstl H, Masters C, Bevreuther K. 783 Polymorphisms of the Presenilin 2 gene (PS2, STM2 or ES1) in German sporadic Alzheimer's disease patients. Neurobiol Aging 1996. [DOI: 10.1016/s0197-4580(96)80785-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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25
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Abstract
Diatoms possess silica-based cell walls with species-specific structures and ornamentations. Silica deposition in diatoms offers a model to study the processes involved in biomineralization. A new wall is produced in a specialized vesicle (silica deposition vesicle, SDV) and secreted. Thus proteins involved in wall biogenesis may remain associated with the mature cell wall. Here it is demonstrated that EDTA treatment removes most of the proteins present in mature cell walls of the marine diatom Cylindrotheca fusiformis. A main fraction consists of four related glycoproteins with a molecular mass of approximately 75 kDa. These glycoproteins were purified to homogeneity. They consist of repeats of Ca2+ binding domains separated by polypeptide stretches containing hydroxyproline. The proteins in the EDTA extract aggregate and precipitate in the presence of Ca2+. Immunological studies detected related proteins in the cell wall of the freshwater diatom Navicula pelliculosa, indicating that these proteins represent a new family of proteins that are involved in the biogenesis of diatom cell walls.
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Affiliation(s)
- N Kröger
- Lehrstuhl für Biochemie I, Universität Regensburg, Germany
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