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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Hommel U, Hurth K, Rondeau JM, Vulpetti A, Ostermeier D, Boettcher A, Brady JP, Hediger M, Lehmann S, Koch E, Blechschmidt A, Yamamoto R, Tundo Dottorello V, Haenni-Holzinger S, Kaiser C, Lehr P, Lingel A, Mureddu L, Schleberger C, Blank J, Ramage P, Freuler F, Eder J, Bornancin F. Discovery of a selective and biologically active low-molecular weight antagonist of human interleukin-1β. Nat Commun 2023; 14:5497. [PMID: 37679328 PMCID: PMC10484922 DOI: 10.1038/s41467-023-41190-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Human interleukin-1β (hIL-1β) is a pro-inflammatory cytokine involved in many diseases. While hIL-1β directed antibodies have shown clinical benefit, an orally available low-molecular weight antagonist is still elusive, limiting the applications of hIL-1β-directed therapies. Here we describe the discovery of a low-molecular weight hIL-1β antagonist that blocks the interaction with the IL-1R1 receptor. Starting from a low affinity fragment-based screening hit 1, structure-based optimization resulted in a compound (S)-2 that binds and antagonizes hIL-1β with single-digit micromolar activity in biophysical, biochemical, and cellular assays. X-ray analysis reveals an allosteric mode of action that involves a hitherto unknown binding site in hIL-1β encompassing two loops involved in hIL-1R1/hIL-1β interactions. We show that residues of this binding site are part of a conformationally excited state of the mature cytokine. The compound antagonizes hIL-1β function in cells, including primary human fibroblasts, demonstrating the relevance of this discovery for future development of hIL-1β directed therapeutics.
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Affiliation(s)
- Ulrich Hommel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland.
| | - Konstanze Hurth
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland.
| | - Jean-Michel Rondeau
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Anna Vulpetti
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Daniela Ostermeier
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Andreas Boettcher
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Jacob Peter Brady
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Michael Hediger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Sylvie Lehmann
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Elke Koch
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Anke Blechschmidt
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Rina Yamamoto
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | | | | | - Christian Kaiser
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Philipp Lehr
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Luca Mureddu
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Christian Schleberger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Jutta Blank
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Paul Ramage
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Felix Freuler
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Joerg Eder
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Frédéric Bornancin
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland.
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3
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Tréton G, Sayer C, Schürz M, Jaritsch M, Müller A, Matea CT, Stanojlovic V, Melo-Benirschke H, Be C, Krembel C, Rodde S, Haffke M, Hintermann S, Marzinzik A, Ripoche S, Blöchl C, Hollerweger J, Auer D, Cabrele C, Huber CG, Hintersteiner M, Wagner T, Lingel A, Meisner-Kober N. Quantitative and functional characterisation of extracellular vesicles after passive loading with hydrophobic or cholesterol-tagged small molecules. J Control Release 2023; 361:694-716. [PMID: 37567507 DOI: 10.1016/j.jconrel.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 03/27/2023] [Revised: 07/03/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
Extracellular vesicles (EVs) are nanosized intercellular messengers that bear enormous application potential as biological drug delivery vehicles. Much progress has been made for loading or decorating EVs with proteins, peptides or RNAs using genetically engineered donor cells, but post-isolation loading with synthetic drugs and using EVs from natural sources remains challenging. In particular, quantitative and unambiguous data assessing whether and how small molecules associate with EVs versus other components in the samples are still lacking. Here we describe the systematic and quantitative characterisation of passive EV loading with small molecules based on hydrophobic interactions - either through direct adsorption of hydrophobic compounds, or by membrane anchoring of hydrophilic ligands via cholesterol tags. As revealed by single vesicle imaging, both ligand types bind to CD63 positive EVs (exosomes), however also non-specifically to other vesicles, particles, and serum proteins. The hydrophobic compounds Curcumin and Terbinafine aggregate on EVs with no apparent saturation up to 106-107 molecules per vesicle as quantified by liquid chromatography - high resolution mass spectrometry (LC-HRMS). For both compounds, high density EV loading resulted in the formation of a population of large, electron-dense vesicles as detected by quantitative cryo-transmission electron microscopy (TEM), a reduced EV cell uptake and a toxic gain of function for Curcumin-EVs. In contrast, cholesterol tagging of a hydrophilic mdm2-targeted cyclic peptide saturated at densities of ca 104-105 molecules per vesicle, with lipidomics showing addition to, rather than replacement of endogenous cholesterol. Cholesterol anchored ligands did not change the EVs' size or morphology, and such EVs retained their cell uptake activity without inducing cell toxicity. However, the cholesterol-anchored ligands were rapidly shed from the vesicles in presence of serum. Based on these data, we conclude that (1) both methods allow loading of EVs with small molecules but are prone to unspecific compound binding or redistribution to other components if present in the sample, (2) cholesterol anchoring needs substantial optimization of formulation stability for in vivo applications, whereas (3) careful titration of loading densities is warranted when relying on hydrophobic interactions of EVs with hydrophobic compounds to mitigate changes in physicochemical properties, loss of EV function and potential cell toxicity.
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Affiliation(s)
- Gwenola Tréton
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Claudia Sayer
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Melanie Schürz
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Maria Jaritsch
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Anna Müller
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Cristian-Tudor Matea
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Vesna Stanojlovic
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Heloisa Melo-Benirschke
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Celine Be
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Caroline Krembel
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Stephane Rodde
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Matthias Haffke
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Samuel Hintermann
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas Marzinzik
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Sébastien Ripoche
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Constantin Blöchl
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Julia Hollerweger
- GMP Unit, Spinal Cord Injury & Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
| | - Daniela Auer
- GMP Unit, Spinal Cord Injury & Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
| | - Chiara Cabrele
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Christian G Huber
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | | | - Trixie Wagner
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland.
| | - Nicole Meisner-Kober
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria.
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4
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Lorthiois E, Gerspacher M, Beyer KS, Vaupel A, Leblanc C, Stringer R, Weiss A, Wilcken R, Guthy DA, Lingel A, Bomio-Confaglia C, Machauer R, Rigollier P, Ottl J, Arz D, Bernet P, Desjonqueres G, Dussauge S, Kazic-Legueux M, Lozac'h MA, Mura C, Sorge M, Todorov M, Warin N, Zink F, Voshol H, Zecri FJ, Sedrani RC, Ostermann N, Brachmann SM, Cotesta S. JDQ443, a Structurally Novel, Pyrazole-Based, Covalent Inhibitor of KRAS G12C for the Treatment of Solid Tumors. J Med Chem 2022; 65:16173-16203. [PMID: 36399068 DOI: 10.1021/acs.jmedchem.2c01438] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [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: 11/19/2022]
Abstract
Rapid emergence of tumor resistance via RAS pathway reactivation has been reported from clinical studies of covalent KRASG12C inhibitors. Thus, inhibitors with broad potential for combination treatment and distinct binding modes to overcome resistance mutations may prove beneficial. JDQ443 is an investigational covalent KRASG12C inhibitor derived from structure-based drug design followed by extensive optimization of two dissimilar prototypes. JDQ443 is a stable atropisomer containing a unique 5-methylpyrazole core and a spiro-azetidine linker designed to position the electrophilic acrylamide for optimal engagement with KRASG12C C12. A substituted indazole at pyrazole position 3 results in novel interactions with the binding pocket that do not involve residue H95. JDQ443 showed PK/PD activity in vivo and dose-dependent antitumor activity in mouse xenograft models. JDQ443 is now in clinical development, with encouraging early phase data reported from an ongoing Phase Ib/II clinical trial (NCT04699188).
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Affiliation(s)
- Edwige Lorthiois
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Marc Gerspacher
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Kim S Beyer
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Andrea Vaupel
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Catherine Leblanc
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Rowan Stringer
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Andreas Weiss
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Rainer Wilcken
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Daniel A Guthy
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | | | - Rainer Machauer
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Pascal Rigollier
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Johannes Ottl
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Dorothee Arz
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | | | | | - Solene Dussauge
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | | | | | - Christophe Mura
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Mickaël Sorge
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Milen Todorov
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Nicolas Warin
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Florence Zink
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Hans Voshol
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Frederic J Zecri
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts02139, United States
| | - Richard C Sedrani
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | - Nils Ostermann
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
| | | | - Simona Cotesta
- Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland
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5
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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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6
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Vulpetti A, Lingel A, Dalvit C, Schiering N, Oberer L, Henry C, Lu Y. Efficient Screening of Target-Specific Selected Compounds in Mixtures by 19F NMR Binding Assay with Predicted 19F NMR Chemical Shifts. ChemMedChem 2022; 17:e202200163. [PMID: 35475323 DOI: 10.1002/cmdc.202200163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 03/28/2022] [Revised: 04/26/2022] [Indexed: 11/06/2022]
Abstract
Ligand-based 19 F NMR screening is a highly effective and well-established hit-finding approach. The high sensitivity to protein binding makes it particularly suitable for fragment screening. Different criteria can be considered for generating fluorinated fragment libraries. One common strategy is to assemble a large, diverse, well-designed and characterized fragment library which is screened in mixtures, generated based on experimental 19 F NMR chemical shifts. Here, we introduce a complementary knowledge-based 19 F NMR screening approach, named 19 Focused screening, enabling the efficient screening of putative active molecules selected by computational hit finding methodologies, in mixtures assembled and on-the-fly deconvoluted based on predicted 19 F NMR chemical shifts. In this study, we developed a novel approach, named LEFshift , for 19 F NMR chemical shift prediction using rooted topological fluorine torsion fingerprints in combination with a random forest machine learning method. A demonstration of this approach to a real test case is reported.
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Affiliation(s)
- Anna Vulpetti
- Novartis Pharma AG, Global Discovery Chemistry, Novartis Campus, 4002, Basel, SWITZERLAND
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Claudio Dalvit
- Novartis Institutes for BioMedical Research Basel, Protease Platform, SWITZERLAND
| | - Nikolaus Schiering
- Novartis Institutes for BioMedical Research Basel, Protease Platform, SWITZERLAND
| | - Lukas Oberer
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
| | - Chrystelle Henry
- Novartis Institutes for BioMedical Research Basel, Protein Science, SWITZERLAND
| | - Yipin Lu
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, SWITZERLAND
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7
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Huang Y, Sendzik M, Zhang J, Gao Z, Sun Y, Wang L, Gu J, Zhao K, Yu Z, Zhang L, Zhang Q, Blanz J, Chen Z, Dubost V, Fang D, Feng L, Fu X, Kiffe M, Li L, Luo F, Luo X, Mi Y, Mistry P, Pearson D, Piaia A, Scheufler C, Terranova R, Weiss A, Zeng J, Zhang H, Zhang J, Zhao M, Dillon MP, Jeay S, Qi W, Moggs J, Pissot-Soldermann C, Li E, Atadja P, Lingel A, Oyang C. Discovery of the Clinical Candidate MAK683: An EED-Directed, Allosteric, and Selective PRC2 Inhibitor for the Treatment of Advanced Malignancies. J Med Chem 2022; 65:5317-5333. [PMID: 35352560 DOI: 10.1021/acs.jmedchem.1c02148] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polycomb Repressive Complex 2 (PRC2) plays an important role in transcriptional regulation during animal development and in cell differentiation, and alteration of PRC2 activity has been associated with cancer. On a molecular level, PRC2 catalyzes methylation of histone H3 lysine 27 (H3K27), resulting in mono-, di-, or trimethylated forms of H3K27, of which the trimethylated form H3K27me3 leads to transcriptional repression of polycomb target genes. Previously, we have shown that binding of the low-molecular-weight compound EED226 to the H3K27me3 binding pocket of the regulatory subunit EED can effectively inhibit PRC2 activity in cells and reduce tumor growth in mouse xenograft models. Here, we report the stepwise optimization of the tool compound EED226 toward the potent and selective EED inhibitor MAK683 (compound 22) and its subsequent preclinical characterization. Based on a balanced PK/PD profile, efficacy, and mitigated risk of forming reactive metabolites, MAK683 has been selected for clinical development.
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Affiliation(s)
- Ying Huang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Martin Sendzik
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States.,Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeff Zhang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Zhenting Gao
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Yongfeng Sun
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Long Wang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Justin Gu
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Kehao Zhao
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Zhengtian Yu
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Lijun Zhang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Qiong Zhang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Joachim Blanz
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Zijun Chen
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Valérie Dubost
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Douglas Fang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Lijian Feng
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Xingnian Fu
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Michael Kiffe
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Ling Li
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Fangjun Luo
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Xiao Luo
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Yuan Mi
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Prakash Mistry
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - David Pearson
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Alessandro Piaia
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Clemens Scheufler
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Remi Terranova
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Andreas Weiss
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Jue Zeng
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Hailong Zhang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Jiangwei Zhang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Mengxi Zhao
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Michael P Dillon
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Sebastien Jeay
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Wei Qi
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Jonathan Moggs
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | | | - En Li
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Peter Atadja
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States.,Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Counde Oyang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
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8
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Lingel A, Vulpetti A, Reinsperger T, Proudfoot A, Denay R, Frommlet A, Henry C, Hommel U, Gossert AD, Luy B, Frank AO. Innentitelbild: Comprehensive and High‐Throughput Exploration of Chemical Space Using Broadband
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F NMR‐Based Screening (Angew. Chem. 35/2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009848] [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: 11/09/2022]
Affiliation(s)
- Andreas Lingel
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Anna Vulpetti
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Tony Reinsperger
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance Karlsruhe Institute of Technology (KIT) 76131 Karlsruhe Germany
| | - Andrew Proudfoot
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
| | - Regis Denay
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Alexandra Frommlet
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
| | - Christelle Henry
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Ulrich Hommel
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Alvar D. Gossert
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance Karlsruhe Institute of Technology (KIT) 76131 Karlsruhe Germany
| | - Andreas O. Frank
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
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9
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Lingel A, Vulpetti A, Reinsperger T, Proudfoot A, Denay R, Frommlet A, Henry C, Hommel U, Gossert AD, Luy B, Frank AO. Inside Cover: Comprehensive and High‐Throughput Exploration of Chemical Space Using Broadband
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F NMR‐Based Screening (Angew. Chem. Int. Ed. 35/2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/anie.202009848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Andreas Lingel
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Anna Vulpetti
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Tony Reinsperger
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance Karlsruhe Institute of Technology (KIT) 76131 Karlsruhe Germany
| | - Andrew Proudfoot
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
| | - Regis Denay
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Alexandra Frommlet
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
| | - Christelle Henry
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Ulrich Hommel
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Alvar D. Gossert
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance Karlsruhe Institute of Technology (KIT) 76131 Karlsruhe Germany
| | - Andreas O. Frank
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
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10
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Lingel A, Vulpetti A, Reinsperger T, Proudfoot A, Denay R, Frommlet A, Henry C, Hommel U, Gossert AD, Luy B, Frank AO. Comprehensive and High-Throughput Exploration of Chemical Space Using Broadband 19 F NMR-Based Screening. Angew Chem Int Ed Engl 2020; 59:14809-14817. [PMID: 32363632 DOI: 10.1002/anie.202002463] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 02/17/2020] [Revised: 04/27/2020] [Indexed: 12/20/2022]
Abstract
Fragment-based lead discovery has become a fundamental approach to identify ligands that efficiently interact with disease-relevant targets. Among the numerous screening techniques, fluorine-detected NMR has gained popularity owing to its high sensitivity, robustness, and ease of use. To effectively explore chemical space, a universal NMR experiment, a rationally designed fragment library, and a sample composition optimized for a maximal number of compounds and minimal measurement time are required. Here, we introduce a comprehensive method that enabled the efficient assembly of a high-quality and diverse library containing nearly 4000 fragments and screening for target-specific binders within days. At the core of the approach is a novel broadband relaxation-edited NMR experiment that covers the entire chemical shift range of drug-like 19 F motifs in a single measurement. Our approach facilitates the identification of diverse binders and the fast ligandability assessment of new targets.
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Affiliation(s)
- Andreas Lingel
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA.,Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Anna Vulpetti
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Tony Reinsperger
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Andrew Proudfoot
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Regis Denay
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Alexandra Frommlet
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Christelle Henry
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Ulrich Hommel
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Alvar D Gossert
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Andreas O Frank
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
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11
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Lingel A, Vulpetti A, Reinsperger T, Proudfoot A, Denay R, Frommlet A, Henry C, Hommel U, Gossert AD, Luy B, Frank AO. Comprehensive and High‐Throughput Exploration of Chemical Space Using Broadband
19
F NMR‐Based Screening. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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]
Affiliation(s)
- Andreas Lingel
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Anna Vulpetti
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Tony Reinsperger
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance Karlsruhe Institute of Technology (KIT) 76131 Karlsruhe Germany
| | - Andrew Proudfoot
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
| | - Regis Denay
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Alexandra Frommlet
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
| | - Christelle Henry
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Ulrich Hommel
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Alvar D. Gossert
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance Karlsruhe Institute of Technology (KIT) 76131 Karlsruhe Germany
| | - Andreas O. Frank
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
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12
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Han W, Ma X, Balibar CJ, Baxter Rath CM, Benton B, Bermingham A, Casey F, Chie-Leon B, Cho MK, Frank AO, Frommlet A, Ho CM, Lee PS, Li M, Lingel A, Ma S, Merritt H, Ornelas E, De Pascale G, Prathapam R, Prosen KR, Rasper D, Ruzin A, Sawyer WS, Shaul J, Shen X, Shia S, Steffek M, Subramanian S, Vo J, Wang F, Wartchow C, Uehara T. Two Distinct Mechanisms of Inhibition of LpxA Acyltransferase Essential for Lipopolysaccharide Biosynthesis. J Am Chem Soc 2020; 142:4445-4455. [DOI: 10.1021/jacs.9b13530] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wooseok Han
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Xiaolei Ma
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Carl J. Balibar
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | | | - Bret Benton
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Alun Bermingham
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Fergal Casey
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Barbara Chie-Leon
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Min-Kyu Cho
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Andreas O. Frank
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Alexandra Frommlet
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Chi-Min Ho
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Patrick S. Lee
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Min Li
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Sylvia Ma
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Hanne Merritt
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Elizabeth Ornelas
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Gianfranco De Pascale
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Ramadevi Prathapam
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Katherine R. Prosen
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Dita Rasper
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Alexey Ruzin
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - William S. Sawyer
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jacob Shaul
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Xiaoyu Shen
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Steven Shia
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Micah Steffek
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Sharadha Subramanian
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jason Vo
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Feng Wang
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Charles Wartchow
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Tsuyoshi Uehara
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
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13
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Proudfoot A, Frank AO, Frommlet A, Lingel A. Selective Methyl Labeling of Proteins: Enabling Structural and Mechanistic Studies As Well As Drug Discovery Applications by Solution-State NMR. Methods Enzymol 2018; 614:1-36. [PMID: 30611421 DOI: 10.1016/bs.mie.2018.08.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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] [Indexed: 01/08/2023]
Abstract
Escherichia coli expression protocols for selective labeling of methyl groups in proteins have been essential in expanding the size range of targets that can be studied by biomolecular NMR. Based on the initial work achieving selective labeling of isoleucine, leucine, and valine residues, additional methods were developed over the past years which enabled the individual and/or simultaneous combinatorial labeling of all methyl containing amino acids. Together with the introduction of new methyl-optimized NMR experiments, this now allows the detailed characterization of protein-ligand interactions as well as mechanistic and dynamic processes of protein-protein complexes up to 1MDa in size. In this chapter, we provide a general introduction to selective labeling of proteins using E. coli-based expression systems, describe the considerations taken into account prior to the selective labeling of a protein, and include the protocols used to produce such proteins. An overview of applications using selectively labeled proteins with an emphasis on examples relevant to the drug discovery process is then presented.
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Affiliation(s)
- Andrew Proudfoot
- Structural and Biophysical Chemistry, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, United States
| | - Andreas O Frank
- Structural and Biophysical Chemistry, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, United States
| | - Alexandra Frommlet
- Structural and Biophysical Chemistry, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, United States
| | - Andreas Lingel
- Structural and Biophysical Chemistry, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, United States; Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland.
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14
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Skepper CK, Moreau RJ, Appleton BA, Benton BM, Drumm JE, Feng BY, Geng M, Hu C, Li C, Lingel A, Lu Y, Mamo M, Mergo W, Mostafavi M, Rath CM, Steffek M, Takeoka KT, Uehara K, Wang L, Wei JR, Xie L, Xu W, Zhang Q, de Vicente J. Discovery and Optimization of Phosphopantetheine Adenylyltransferase Inhibitors with Gram-Negative Antibacterial Activity. J Med Chem 2018; 61:3325-3349. [DOI: 10.1021/acs.jmedchem.7b01861] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Colin K. Skepper
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Robert J. Moreau
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brent A. Appleton
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Bret M. Benton
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Joseph E. Drumm
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brian Y. Feng
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mei Geng
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Cheng Hu
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Cindy Li
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Andreas Lingel
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Yipin Lu
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mulugeta Mamo
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Wosenu Mergo
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mina Mostafavi
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Christopher M. Rath
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Micah Steffek
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kenneth T. Takeoka
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kyoko Uehara
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Lisha Wang
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Jun-Rong Wei
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Lili Xie
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Wenjian Xu
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Qiong Zhang
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Javier de Vicente
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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15
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Moreau RJ, Skepper CK, Appleton BA, Blechschmidt A, Balibar CJ, Benton BM, Drumm JE, Feng BY, Geng M, Li C, Lindvall MK, Lingel A, Lu Y, Mamo M, Mergo W, Polyakov V, Smith TM, Takeoka K, Uehara K, Wang L, Wei JR, Weiss AH, Xie L, Xu W, Zhang Q, de Vicente J. Fragment-Based Drug Discovery of Inhibitors of Phosphopantetheine Adenylyltransferase from Gram-Negative Bacteria. J Med Chem 2018; 61:3309-3324. [DOI: 10.1021/acs.jmedchem.7b01691] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Robert J. Moreau
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Colin K. Skepper
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brent A. Appleton
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Anke Blechschmidt
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Carl J. Balibar
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Bret M. Benton
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Joseph E. Drumm
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brian Y. Feng
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mei Geng
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Cindy Li
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mika K. Lindvall
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Yipin Lu
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mulugeta Mamo
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Wosenu Mergo
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Valery Polyakov
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Thomas M. Smith
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kenneth Takeoka
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kyoko Uehara
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Lisha Wang
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Jun-Rong Wei
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Andrew H. Weiss
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Lili Xie
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Wenjian Xu
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Qiong Zhang
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Javier de Vicente
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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16
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Proudfoot A, Bussiere DE, Lingel A. High-Confidence Protein–Ligand Complex Modeling by NMR-Guided Docking Enables Early Hit Optimization. J Am Chem Soc 2017; 139:17824-17833. [DOI: 10.1021/jacs.7b07171] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Andrew Proudfoot
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Dirksen E. Bussiere
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Andreas Lingel
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
- Global
Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
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17
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Qi W, Zhao K, Gu J, Huang Y, Wang Y, Zhang H, Zhang M, Zhang J, Yu Z, Li L, Teng L, Chuai S, Zhang C, Zhao M, Chan H, Chen Z, Fang D, Qi F, Feng L, Feng L, Gao Y, Ge H, Ge X, Lingel A, Li G, Lin Y, Liu Y, Luo F, Shi M, Wang L, Wang Z, Yu Y, Zeng J, Zeng C, Zhang L, Zhang Q, Zhou S, Oyang C, Atadja P, Li E. Abstract LB-288: An allosteric PRC2 inhibitor targeting the H3K27me3 binding pocket of EED. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-lb-288] [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: 11/16/2022]
Abstract
Abstract
Polycomb repressive complex 2 (PRC2) consists of three core subunits, EZH2, EED and SUZ12 and plays pivotal roles in transcriptional regulation through its histone H3K27 methyltransferase activity. Dysregulation of PRC2 is observed in multiple human cancers, for example, the catalytic subunit EZH2 is overexpressed in a wide range of human cancers and gain-of-function mutations of EZH2 within its catalytic site have been reported in human B-cell lymphoma, parathyroid carcinoma and melanoma. Small molecule inhibitors that compete with the cofactor S-adenosylmethionine (SAM) have been reported and showed anti-lymphoma efficacy in pre-clinical studies. EED within the PRC2 complex allosterically activate the enzymatic activity by binding to tri-methylated H3K27 (H3K27me3). Here we report the discovery of EED226, a potent and selective PRC2 inhibitor directly binding to the H3K27me3 binding pocket of EED. EED226 induces conformational change upon binding EED leading to loss of PRC2 activity. EED226 shows similar activity as SAM-competitive inhibitors in blocking H3K27 methylation of PRC2 target genes and inducing regression of human lymphoma xenograft tumors. Interestingly, EED226 also effectively inhibits PRC2 containing mutant EZH2 protein resistant to SAM-competitive inhibitors. Together, we show EED226 inhibits PRC2 activity via an allosteric mechanism and offers opportunity for treatment of PRC2-dependent cancers.
Citation Format: Wei Qi, Kehao Zhao, Justin Gu, Ying Huang, Youzhen Wang, Hailong Zhang, Man Zhang, Jeff Zhang, Zhengtian Yu, Ling Li, Lin Teng, Shannon Chuai, Chao Zhang, Mengxi Zhao, HoMan Chan, Zijun Chen, Douglas Fang, Fei Qi, Leying Feng, Lijian Feng, Yuan Gao, Hui Ge, Xinjian Ge, Andreas Lingel, Guobin Li, Ying Lin, Yueqin Liu, Fangjun Luo, Minlong Shi, Long Wang, Zhaofu Wang, Yanyan Yu, Jue Zeng, Chenhui Zeng, Lijun Zhang, Qiong Zhang, Shaolian Zhou, Counde Oyang, Peter Atadja, En Li. An allosteric PRC2 inhibitor targeting the H3K27me3 binding pocket of EED [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-288. doi:10.1158/1538-7445.AM2017-LB-288
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Affiliation(s)
- Wei Qi
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Kehao Zhao
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Justin Gu
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Ying Huang
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Youzhen Wang
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Hailong Zhang
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Man Zhang
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Jeff Zhang
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Zhengtian Yu
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Ling Li
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Lin Teng
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Shannon Chuai
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Chao Zhang
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Mengxi Zhao
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - HoMan Chan
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Zijun Chen
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Douglas Fang
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Fei Qi
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Leying Feng
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Lijian Feng
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Yuan Gao
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Hui Ge
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Xinjian Ge
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Andreas Lingel
- 2Novartis Institutes of BioMedical Research, Emeryville, CA
| | - Guobin Li
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Ying Lin
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Yueqin Liu
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Fangjun Luo
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Minlong Shi
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Long Wang
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Zhaofu Wang
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Yanyan Yu
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Jue Zeng
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Chenhui Zeng
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Lijun Zhang
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Qiong Zhang
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Shaolian Zhou
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Counde Oyang
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - Peter Atadja
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
| | - En Li
- 1Novartis Institutes of BioMedical Research (China), Shanghai, China
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18
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Jansen JM, Wartchow C, Jahnke W, Fong S, Tsang T, Pfister K, Zavorotinskaya T, Bussiere D, Cheng JM, Crawford K, Dai Y, Dove J, Fang E, Feng Y, Florent JM, Fuller J, Gossert AD, Hekmat-Nejad M, Henry C, Klopp J, Lenahan WP, Lingel A, Ma S, Meyer A, Mishina Y, Narberes J, Pardee G, Ramurthy S, Rieffel S, Stuart D, Subramanian S, Tandeske L, Widger S, Widmer A, Winterhalter A, Zaror I, Hardy S. Inhibition of prenylated KRAS in a lipid environment. PLoS One 2017; 12:e0174706. [PMID: 28384226 PMCID: PMC5383040 DOI: 10.1371/journal.pone.0174706] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/14/2017] [Indexed: 12/30/2022] Open
Abstract
RAS mutations lead to a constitutively active oncogenic protein that signals through multiple effector pathways. In this chemical biology study, we describe a novel coupled biochemical assay that measures activation of the effector BRAF by prenylated KRASG12V in a lipid-dependent manner. Using this assay, we discovered compounds that block biochemical and cellular functions of KRASG12V with low single-digit micromolar potency. We characterized the structural basis for inhibition using NMR methods and showed that the compounds stabilized the inactive conformation of KRASG12V. Determination of the biophysical affinity of binding using biolayer interferometry demonstrated that the potency of inhibition matches the affinity of binding only when KRAS is in its native state, namely post-translationally modified and in a lipid environment. The assays we describe here provide a first-time alignment across biochemical, biophysical, and cellular KRAS assays through incorporation of key physiological factors regulating RAS biology, namely a negatively charged lipid environment and prenylation, into the in vitro assays. These assays and the ligands we discovered are valuable tools for further study of KRAS inhibition and drug discovery.
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Affiliation(s)
- Johanna M. Jansen
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
- * E-mail:
| | - Charles Wartchow
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Wolfgang Jahnke
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Susan Fong
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Tiffany Tsang
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Keith Pfister
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Tatiana Zavorotinskaya
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Dirksen Bussiere
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Jan Marie Cheng
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Kenneth Crawford
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Yumin Dai
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Jeffrey Dove
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Eric Fang
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Yun Feng
- Department of Oncology, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Jean-Michel Florent
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - John Fuller
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Alvar D. Gossert
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Mohammad Hekmat-Nejad
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Chrystèle Henry
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Julia Klopp
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - William P. Lenahan
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Andreas Lingel
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Sylvia Ma
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Arndt Meyer
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Yuji Mishina
- Department of Oncology, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Jamie Narberes
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Gwynn Pardee
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Savithri Ramurthy
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Sebastien Rieffel
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Darrin Stuart
- Department of Oncology, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Sharadha Subramanian
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Laura Tandeske
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Stephania Widger
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Armin Widmer
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Aurelie Winterhalter
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Isabel Zaror
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Stephen Hardy
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
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19
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Huang Y, Zhang J, Yu Z, Zhang H, Wang Y, Lingel A, Qi W, Gu J, Zhao K, Shultz MD, Wang L, Fu X, Sun Y, Zhang Q, Jiang X, Zhang J, Zhang C, Li L, Zeng J, Feng L, Zhang C, Liu Y, Zhang M, Zhang L, Zhao M, Gao Z, Liu X, Fang D, Guo H, Mi Y, Gabriel T, Dillon MP, Atadja P, Oyang C. Discovery of First-in-Class, Potent, and Orally Bioavailable Embryonic Ectoderm Development (EED) Inhibitor with Robust Anticancer Efficacy. J Med Chem 2017; 60:2215-2226. [DOI: 10.1021/acs.jmedchem.6b01576] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ying Huang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Jeff Zhang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Zhengtian Yu
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Hailong Zhang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Youzhen Wang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Wei Qi
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Justin Gu
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Kehao Zhao
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Michael D. Shultz
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Long Wang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Xingnian Fu
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Yongfeng Sun
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Qiong Zhang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Xiangqing Jiang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Jiangwei Zhang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Chunye Zhang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Ling Li
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Jue Zeng
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Lijian Feng
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Chao Zhang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Yueqin Liu
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Man Zhang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Lijun Zhang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Mengxi Zhao
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Zhenting Gao
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Xianghui Liu
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Douglas Fang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Haibing Guo
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Yuan Mi
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Tobias Gabriel
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Michael P. Dillon
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Peter Atadja
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
| | - Counde Oyang
- Novartis Institutes for BioMedical Research, 4218 Jinke Road, Shanghai 201203, China
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20
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Li L, Zhang H, Zhang M, Zhao M, Feng L, Luo X, Gao Z, Huang Y, Ardayfio O, Zhang JH, Lin Y, Fan H, Mi Y, Li G, Liu L, Feng L, Luo F, Teng L, Qi W, Ottl J, Lingel A, Bussiere DE, Yu Z, Atadja P, Lu C, Li E, Gu J, Zhao K. Discovery and Molecular Basis of a Diverse Set of Polycomb Repressive Complex 2 Inhibitors Recognition by EED. PLoS One 2017; 12:e0169855. [PMID: 28072869 PMCID: PMC5224880 DOI: 10.1371/journal.pone.0169855] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/24/2016] [Indexed: 01/23/2023] Open
Abstract
Polycomb repressive complex 2 (PRC2), a histone H3 lysine 27 methyltransferase, plays a key role in gene regulation and is a known epigenetics drug target for cancer therapy. The WD40 domain-containing protein EED is the regulatory subunit of PRC2. It binds to the tri-methylated lysine 27 of the histone H3 (H3K27me3), and through which stimulates the activity of PRC2 allosterically. Recently, we disclosed a novel PRC2 inhibitor EED226 which binds to the K27me3-pocket on EED and showed strong antitumor activity in xenograft mice model. Here, we further report the identification and validation of four other EED binders along with EED162, the parental compound of EED226. The crystal structures for all these five compounds in complex with EED revealed a common deep pocket induced by the binding of this diverse set of compounds. This pocket was created after significant conformational rearrangement of the aromatic cage residues (Y365, Y148 and F97) in the H3K27me3 binding pocket of EED, the width of which was delineated by the side chains of these rearranged residues. In addition, all five compounds interact with the Arg367 at the bottom of the pocket. Each compound also displays unique features in its interaction with EED, suggesting the dynamics of the H3K27me3 pocket in accommodating the binding of different compounds. Our results provide structural insights for rational design of novel EED binder for the inhibition of PRC2 complex activity.
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Affiliation(s)
- Ling Li
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Hailong Zhang
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Man Zhang
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Mengxi Zhao
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Lijian Feng
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Xiao Luo
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Zhenting Gao
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Ying Huang
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Ophelia Ardayfio
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Ji-Hu Zhang
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Ying Lin
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Hong Fan
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Yuan Mi
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Guobin Li
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Lei Liu
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Leying Feng
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Fangjun Luo
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Lin Teng
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Wei Qi
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Johannes Ottl
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Dirksen E. Bussiere
- Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Zhengtian Yu
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Peter Atadja
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Chris Lu
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - En Li
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Justin Gu
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Kehao Zhao
- China Novartis Institutes for BioMedical Research, Shanghai, China
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21
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Lingel A, Sendzik M, Huang Y, Shultz MD, Cantwell J, Dillon MP, Fu X, Fuller J, Gabriel T, Gu J, Jiang X, Li L, Liang F, McKenna M, Qi W, Rao W, Sheng X, Shu W, Sutton J, Taft B, Wang L, Zeng J, Zhang H, Zhang M, Zhao K, Lindvall M, Bussiere DE. Structure-Guided Design of EED Binders Allosterically Inhibiting the Epigenetic Polycomb Repressive Complex 2 (PRC2) Methyltransferase. J Med Chem 2017; 60:415-427. [DOI: 10.1021/acs.jmedchem.6b01473] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Andreas Lingel
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Martin Sendzik
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Ying Huang
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Michael D. Shultz
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - John Cantwell
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Michael P. Dillon
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Xingnian Fu
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - John Fuller
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Tobias Gabriel
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Justin Gu
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Xiangqing Jiang
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Ling Li
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Fang Liang
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Maureen McKenna
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Wei Qi
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Weijun Rao
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Xijun Sheng
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Wei Shu
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - James Sutton
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Benjamin Taft
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Long Wang
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Jue Zeng
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Hailong Zhang
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Maya Zhang
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Kehao Zhao
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Mika Lindvall
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Dirksen E. Bussiere
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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22
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Proudfoot A, Frank AO, Ruggiu F, Mamo M, Lingel A. Facilitating unambiguous NMR assignments and enabling higher probe density through selective labeling of all methyl containing amino acids. J Biomol NMR 2016; 65:15-27. [PMID: 27130242 DOI: 10.1007/s10858-016-0032-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/19/2016] [Indexed: 05/05/2023]
Abstract
The deuteration of proteins and selective labeling of side chain methyl groups has greatly enhanced the molecular weight range of proteins and protein complexes which can be studied using solution NMR spectroscopy. Protocols for the selective labeling of all six methyl group containing amino acids individually are available, however to date, only a maximum of five amino acids have been labeled simultaneously. Here, we describe a new methodology for the simultaneous, selective labeling of all six methyl containing amino acids using the 115 kDa homohexameric enzyme CoaD from E. coli as a model system. The utility of the labeling protocol is demonstrated by efficiently and unambiguously assigning all methyl groups in the enzymatic active site using a single 4D (13)C-resolved HMQC-NOESY-HMQC experiment, in conjunction with a crystal structure. Furthermore, the six fold labeled protein was employed to characterize the interaction between the substrate analogue (R)-pantetheine and CoaD by chemical shift perturbations, demonstrating the benefit of the increased probe density.
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Affiliation(s)
- Andrew Proudfoot
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Andreas O Frank
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Fiorella Ruggiu
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Mulugeta Mamo
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA.
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Peng C, Frommlet A, Perez M, Cobas C, Blechschmidt A, Dominguez S, Lingel A. Fast and Efficient Fragment-Based Lead Generation by Fully Automated Processing and Analysis of Ligand-Observed NMR Binding Data. J Med Chem 2016; 59:3303-10. [DOI: 10.1021/acs.jmedchem.6b00019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chen Peng
- Mestrelab Research S.L., Feliciano
Barrera 9B − Baixo, 15706 Santiago de Compostela, Spain
| | - Alexandra Frommlet
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Manuel Perez
- Mestrelab Research S.L., Feliciano
Barrera 9B − Baixo, 15706 Santiago de Compostela, Spain
| | - Carlos Cobas
- Mestrelab Research S.L., Feliciano
Barrera 9B − Baixo, 15706 Santiago de Compostela, Spain
| | - Anke Blechschmidt
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Santiago Dominguez
- Mestrelab Research S.L., Feliciano
Barrera 9B − Baixo, 15706 Santiago de Compostela, Spain
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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Jansen J, Jahnke W, Fong S, Tandeske L, Wartchow C, Pfister K, Zavorotinskaya T, Blechschmidt A, Bussiere D, Dai Y, Dove J, Fang E, Farley D, Florent JM, Fuller J, Gokhin S, Gossert A, Hekmat-Nejad M, Henry C, Klopp J, Lenahan B, Lingel A, Meyer A, Narberes J, Pardee G, Paris CG, Ramurthy S, Renhowe P, Rieffel S, Shoemaker K, Subramanian S, Tsang T, Widger S, Widmer A, Zaror I, Hardy S. Abstract B38: Inhibiting mutated KRAS, a broken switch of effector pathways. Mol Cancer Res 2015. [DOI: 10.1158/1557-3125.rasonc14-b38] [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: 11/16/2022]
Abstract
Abstract
Mutated forms of KRAS are no longer able to switch effectors between “on” and “off” states. It is known that the function of KRAS is controlled by key parts in the C-terminus, including six consecutive lysines, a terminal prenyl moiety and a terminal carboxymethyl functional group. We set out to discover compounds which would inhibit the function of mutated KRAS as an activator for effectors. This campaign yielded several compounds that blocked biochemical and cellular functions of KRAS with low micromolar activity while not affecting markers outside of KRAS pathways in cells. In order to understand the mode of binding of these compounds to KRAS, we generated different forms of the protein, including unprenylated truncated and fully processed full-length protein. NMR studies with truncated protein (amino acids 1-169) identified a site at which compound binding stabilized the inactive conformation of KRAS. This site is located adjacent to switch-II and is similar to sites described by others. The Kd determined for this binding event is almost 3 orders of magnitude higher than the IC50 and EC50 values measured in biochemical and cellular assays. In order to understand this difference, we developed a biophysical assay using the Fortebio system which enabled binding studies in a system with full-length prenylated protein in the presence of lipids, to match the context of the biochemical and cellular assays. Micromolar binding to the full-length prenylated KRAS protein was observed in the Fortebio assay and binding was not observed in the absence of prenylation, consistent with the near millimolar Kd observed by NMR for truncated KRAS. Curiously, similar micromolar binding was seen to a peptide derived from the C-terminus of KRAS (amino acids 168-185) with and without prenyl modification while related compounds that do not bind to the full-length prenylated KRAS also do not bind to these peptides. It is still unclear whether binding to the terminal peptide in lipid context is related to the binding site adjacent to switch-II. From a drug discovery perspective, it remains to be confirmed whether current inhibitors can be optimized.
Citation Format: Johanna Jansen, Wolfgang Jahnke, Susan Fong, Laura Tandeske, Charles Wartchow, Keith Pfister, Tatiana Zavorotinskaya, Anke Blechschmidt, Dirksen Bussiere, Yumin Dai, Jeff Dove, Eric Fang, David Farley, Jean-Michel Florent, John Fuller, Simona Gokhin, Alvar Gossert, Mohammad Hekmat-Nejad, Chrystèle Henry, Julia Klopp, Bill Lenahan, Andreas Lingel, Arndt Meyer, Jamie Narberes, Gwynn Pardee, C Gregory Paris, Savithri Ramurthy, Paul Renhowe, Sebastien Rieffel, Kevin Shoemaker, Sharadha Subramanian, Tiffany Tsang, Stephania Widger, Armin Widmer, Isabel Zaror, Stephen Hardy. Inhibiting mutated KRAS, a broken switch of effector pathways. [abstract]. In: Proceedings of the AACR Special Conference on RAS Oncogenes: From Biology to Therapy; Feb 24-27, 2014; Lake Buena Vista, FL. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(12 Suppl):Abstract nr B38. doi: 10.1158/1557-3125.RASONC14-B38
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Affiliation(s)
- Johanna Jansen
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Wolfgang Jahnke
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland,
| | - Susan Fong
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Laura Tandeske
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | | | - Keith Pfister
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | | | | | | | - Yumin Dai
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Jeff Dove
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Eric Fang
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - David Farley
- 3Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | - John Fuller
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Simona Gokhin
- 3Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Alvar Gossert
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland,
| | | | - Chrystèle Henry
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland,
| | - Julia Klopp
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland,
| | - Bill Lenahan
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Andreas Lingel
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Arndt Meyer
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland,
| | - Jamie Narberes
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Gwynn Pardee
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | | | | | - Paul Renhowe
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | | | - Kevin Shoemaker
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | | | - Tiffany Tsang
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | | | - Armin Widmer
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland,
| | - Isabel Zaror
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Stephen Hardy
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
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Kryshtafovych A, Moult J, Bartual SG, Bazan JF, Berman H, Casteel DE, Christodoulou E, Everett JK, Hausmann J, Heidebrecht T, Hills T, Hui R, Hunt JF, Seetharaman J, Joachimiak A, Kennedy MA, Kim C, Lingel A, Michalska K, Montelione GT, Otero JM, Perrakis A, Pizarro JC, van Raaij MJ, Ramelot TA, Rousseau F, Tong L, Wernimont AK, Young J, Schwede T. Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Proteins 2011; 79 Suppl 10:6-20. [PMID: 22020785 PMCID: PMC3692002 DOI: 10.1002/prot.23196] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
One goal of the CASP community wide experiment on the critical assessment of techniques for protein structure prediction is to identify the current state of the art in protein structure prediction and modeling. A fundamental principle of CASP is blind prediction on a set of relevant protein targets, that is, the participating computational methods are tested on a common set of experimental target proteins, for which the experimental structures are not known at the time of modeling. Therefore, the CASP experiment would not have been possible without broad support of the experimental protein structural biology community. In this article, several experimental groups discuss the structures of the proteins which they provided as prediction targets for CASP9, highlighting structural and functional peculiarities of these structures: the long tail fiber protein gp37 from bacteriophage T4, the cyclic GMP-dependent protein kinase Iβ dimerization/docking domain, the ectodomain of the JTB (jumping translocation breakpoint) transmembrane receptor, Autotaxin in complex with an inhibitor, the DNA-binding J-binding protein 1 domain essential for biosynthesis and maintenance of DNA base-J (β-D-glucosyl-hydroxymethyluracil) in Trypanosoma and Leishmania, an so far uncharacterized 73 residue domain from Ruminococcus gnavus with a fold typical for PDZ-like domains, a domain from the phycobilisome core-membrane linker phycobiliprotein ApcE from Synechocystis, the heat shock protein 90 activators PFC0360w and PFC0270w from Plasmodium falciparum, and 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae.
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Affiliation(s)
- Andriy Kryshtafovych
- Genome Center, University of California-Davis, 451 Health Sciences Drive, Davis, CA 95616, USA
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26
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Dueber EC, Schoeffler AJ, Lingel A, Elliott JM, Fedorova AV, Giannetti AM, Zobel K, Maurer B, Varfolomeev E, Wu P, Wallweber HJA, Hymowitz SG, Deshayes K, Vucic D, Fairbrother WJ. Antagonists Induce a Conformational Change in cIAP1 That Promotes Autoubiquitination. Science 2011; 334:376-80. [DOI: 10.1126/science.1207862] [Citation(s) in RCA: 177] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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27
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Maun HR, Wen X, Lingel A, de Sauvage FJ, Lazarus RA, Scales SJ, Hymowitz SG. Hedgehog pathway antagonist 5E1 binds hedgehog at the pseudo-active site. J Biol Chem 2010; 285:26570-80. [PMID: 20504762 DOI: 10.1074/jbc.m110.112284] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Proper hedgehog (Hh) signaling is crucial for embryogenesis and tissue regeneration. Dysregulation of this pathway is associated with several types of cancer. The monoclonal antibody 5E1 is a Hh pathway inhibitor that has been extensively used to elucidate vertebrate Hh biology due to its ability to block binding of the three mammalian Hh homologs to the receptor, Patched1 (Ptc1). Here, we engineered a murine:human chimeric 5E1 (ch5E1) with similar Hh-binding properties to the original murine antibody. Using biochemical, biophysical, and x-ray crystallographic studies, we show that, like the regulatory receptors Cdon and Hedgehog-interacting protein (Hhip), ch5E1 binding to Sonic hedgehog (Shh) is enhanced by calcium ions. In the presence of calcium and zinc ions, the ch5E1 binding affinity increases 10-20-fold to tighter than 1 nm primarily because of a decrease in the dissociation rate. The co-crystal structure of Shh bound to the Fab fragment of ch5E1 reveals that 5E1 binds at the pseudo-active site groove of Shh with an epitope that largely overlaps with the binding site of its natural receptor antagonist Hhip. Unlike Hhip, the side chains of 5E1 do not directly coordinate the Zn(2+) cation in the pseudo-active site, despite the modest zinc-dependent increase in 5E1 affinity for Shh. Furthermore, to our knowledge, the ch5E1 Fab-Shh complex represents the first structure of an inhibitor antibody bound to a metalloprotease fold.
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Affiliation(s)
- Henry R Maun
- Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080, USA
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Abstract
We report near complete NMR backbone and side chain assignments of the human cytokine interleukin-33 (IL-33) in solution. IL-33 is the latest addition to the family of interleukin-1 homologous cytokines and was shown to be involved in inflammation and autoimmune diseases.
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Affiliation(s)
- Andreas Lingel
- Department of Protein Engineering, Genentech, South San Francisco, CA 94080, USA
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29
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Lingel A, Weiss TM, Niebuhr M, Pan B, Appleton BA, Wiesmann C, Bazan JF, Fairbrother WJ. Structure of IL-33 and its interaction with the ST2 and IL-1RAcP receptors--insight into heterotrimeric IL-1 signaling complexes. Structure 2009; 17:1398-410. [PMID: 19836339 PMCID: PMC2766095 DOI: 10.1016/j.str.2009.08.009] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 07/20/2009] [Accepted: 08/04/2009] [Indexed: 10/20/2022]
Abstract
Members of the interleukin-1 (IL-1) family of cytokines play major roles in host defense and immune system regulation in infectious and inflammatory diseases. IL-1 cytokines trigger a biological response in effector cells by assembling a heterotrimeric signaling complex with two IL-1 receptor chains, a high-affinity primary receptor and a low-affinity coreceptor. To gain insights into the signaling mechanism of the novel IL-1-like cytokine IL-33, we first solved its solution structure and then performed a detailed biochemical and structural characterization of the interaction between IL-33, its primary receptor ST2, and the coreceptor IL-1RAcP. Using nuclear magnetic resonance data, we obtained a model of the IL-33/ST2 complex in solution that is validated by small-angle X-ray scattering (SAXS) data and is similar to the IL-1beta/IL-1R1 complex. We extended our SAXS analysis to the IL-33/ST2/IL-1RAcP and IL-1beta/IL-1R1/IL-1RAcP complexes and propose a general model of the molecular architecture of IL-1 ternary signaling complexes.
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Affiliation(s)
- Andreas Lingel
- Department of Protein Engineering, Genentech, South San Francisco, CA 94080, USA
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30
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Bourhis E, Lingel A, Phung Q, Fairbrother WJ, Cochran AG. Phosphorylation of a Borealin Dimerization Domain Is Required for Proper Chromosome Segregation. Biochemistry 2009; 48:6783-93. [DOI: 10.1021/bi900530v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Bosanac I, Maun HR, Scales SJ, Wen X, Lingel A, Bazan JF, de Sauvage FJ, Hymowitz SG, Lazarus RA. The structure of SHH in complex with HHIP reveals a recognition role for the Shh pseudo active site in signaling. Nat Struct Mol Biol 2009; 16:691-7. [PMID: 19561609 DOI: 10.1038/nsmb.1632] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 06/04/2009] [Indexed: 12/26/2022]
Abstract
Hedgehog (Hh) signaling is crucial for many aspects of embryonic development, whereas dysregulation of this pathway is associated with several types of cancer. Hedgehog-interacting protein (Hhip) is a surface receptor antagonist that is equipotent against all three mammalian Hh homologs. The crystal structures of human HHIP alone and bound to Sonic hedgehog (SHH) now reveal that HHIP is comprised of two EGF domains and a six-bladed beta-propeller domain. In the complex structure, a critical loop from HHIP binds the pseudo active site groove of SHH and directly coordinates its Zn2+ cation. Notably, sequence comparisons of this SHH binding loop with the Hh receptor Patched (Ptc1) ectodomains and HHIP- and PTC1-peptide binding studies suggest a 'patch for Patched' at the Shh pseudo active site; thus, we propose a role for Hhip as a structural decoy receptor for vertebrate Hh.
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Affiliation(s)
- Ivan Bosanac
- Department of Structural Biology, Genentech, Inc., South San Francisco, California, USA
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32
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Jinek M, Eulalio A, Lingel A, Helms S, Conti E, Izaurralde E. The C-terminal region of Ge-1 presents conserved structural features required for P-body localization. RNA 2008; 14:1991-1998. [PMID: 18755833 PMCID: PMC2553738 DOI: 10.1261/rna.1222908] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Accepted: 07/07/2008] [Indexed: 05/26/2023]
Abstract
The removal of the 5' cap structure by the DCP1-DCP2 decapping complex irreversibly commits eukaryotic mRNAs to degradation. In human cells, the interaction between DCP1 and DCP2 is bridged by the Ge-1 protein. Ge-1 contains an N-terminal WD40-repeat domain connected by a low-complexity region to a conserved C-terminal domain. It was reported that the C-terminal domain interacts with DCP2 and mediates Ge-1 oligomerization and P-body localization. To understand the molecular basis for these functions, we determined the three-dimensional crystal structure of the most conserved region of the Drosophila melanogaster Ge-1 C-terminal domain. The region adopts an all alpha-helical fold related to ARM- and HEAT-repeat proteins. Using structure-based mutants we identified an invariant surface residue affecting P-body localization. The conservation of critical surface and structural residues suggests that the C-terminal region adopts a similar fold with conserved functions in all members of the Ge-1 protein family.
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Affiliation(s)
- Martin Jinek
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
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Lingel A, Simon B, Izaurralde E, Sattler M. The structure of the flock house virus B2 protein, a viral suppressor of RNA interference, shows a novel mode of double-stranded RNA recognition. EMBO Rep 2006; 6:1149-55. [PMID: 16270100 PMCID: PMC1369214 DOI: 10.1038/sj.embor.7400583] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2005] [Revised: 10/18/2005] [Accepted: 10/19/2005] [Indexed: 11/08/2022] Open
Abstract
We report the structure of the flock house virus B2 protein, a potent suppressor of RNA interference (RNAi) in animals and plants. The B2 protein is a homodimer in solution and contains three alpha-helices per monomer. Chemical shift perturbation shows that an antiparallel arrangement of helices (alpha2/alpha2') forms an elongated binding interface with double-stranded RNA (dsRNA). This implies a novel mode of dsRNA recognition and provides insights into the mechanism of RNAi suppression by B2.
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MESH Headings
- Amino Acid Sequence
- Amino Acids/chemistry
- Amino Acids, Aromatic/chemistry
- Dimerization
- Hydrophobic and Hydrophilic Interactions
- Models, Molecular
- Nuclear Magnetic Resonance, Biomolecular
- Protein Binding
- Protein Conformation
- Protein Folding
- Protein Structure, Secondary
- Protein Subunits/chemistry
- RNA Interference
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Solutions
- Spectrum Analysis, Raman
- Static Electricity
- Viral Proteins/chemistry
- Viral Proteins/isolation & purification
- Viral Proteins/metabolism
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Affiliation(s)
- Andreas Lingel
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Bernd Simon
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Elisa Izaurralde
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Tel: +49 6221 388 103; Fax: +49 6221 387 306; E-mail:
| | - Michael Sattler
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Tel: +49 6221 387 552; Fax: +49 6221 387 306; E-mail:
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Abstract
Gene silencing mediated by RNA interference (RNAi) depends on short interfering RNAs (siRNAs) and micro RNAs (miRNAs). These RNAs have unique features, namely a defined size of 19-21 base pairs, and characteristic two-nucleotide single-stranded 3' overhangs and 5' monophosphate groups. These molecular features of siRNAs and miRNAs are produced by RNase III enzymes, which are a hallmark of gene silencing induced by double-stranded RNA. Recent structural studies of components of the RNAi pathway, including PAZ, Piwi and RNase III domains, as well as full-length Argonaute and viral p19 proteins, have revealed distinct and novel modes of sequence-independent recognition of the characteristic features of siRNAs and miRNAs in the RNAi pathway.
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Affiliation(s)
- Andreas Lingel
- EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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35
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Abstract
RNA interference involves endonucleolytic cleavage of mRNAs at a site determined by complementary siRNAs. Initial cleavage leads to rapid degradation of the message, resulting in a corresponding reduction in the level of the encoded protein. Despite intensive study, the identity of the endonucleolytic activity (designated slicer) has remained obscure. Now, a combination of structural and biochemical analyses provide compelling evidence that human Argonaute2 (Ago2), a protein already known to be a key player in the RNAi pathway, is in fact the missing endonuclease.
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36
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37
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Lingel A, Simon B, Izaurralde E, Sattler M. Nucleic acid 3'-end recognition by the Argonaute2 PAZ domain. Nat Struct Mol Biol 2004; 11:576-7. [PMID: 15156196 DOI: 10.1038/nsmb777] [Citation(s) in RCA: 247] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2004] [Accepted: 04/29/2004] [Indexed: 11/09/2022]
Abstract
We describe the solution structures of the Argonaute2 PAZ domain bound to RNA and DNA oligonucleotides. The structures reveal a unique mode of single-stranded nucleic acid binding in which the two 3'-terminal nucleotides are buried in a hydrophobic cleft. We propose that the PAZ domain contributes to the specific recognition of siRNAs by providing a binding pocket for their characteristic two-nucleotide 3' overhangs.
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Affiliation(s)
- Andreas Lingel
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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38
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Lingel A, Simon B, Izaurralde E, Sattler M. Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature 2003; 426:465-9. [PMID: 14615801 DOI: 10.1038/nature02123] [Citation(s) in RCA: 294] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2003] [Accepted: 10/15/2003] [Indexed: 11/08/2022]
Abstract
RNA interference is a conserved mechanism that regulates gene expression in response to the presence of double-stranded (ds)RNAs. The RNase III-like enzyme Dicer first cleaves dsRNA into 21-23-nucleotide small interfering RNAs (siRNAs). In the effector step, the multimeric RNA-induced silencing complex (RISC) identifies messenger RNAs homologous to the siRNAs and promotes their degradation. The Argonaute 2 protein (Ago2) is a critical component of RISC. Both Argonaute and Dicer family proteins contain a common PAZ domain whose function is unknown. Here we present the three-dimensional nuclear magnetic resonance structure of the Drosophila melanogaster Ago2 PAZ domain. This domain adopts a nucleic-acid-binding fold that is stabilized by conserved hydrophobic residues. The nucleic-acid-binding patch is located in a cleft between the surface of a central beta-barrel and a conserved module comprising strands beta3, beta4 and helix alpha3. Because critical structural residues and the binding surface are conserved, we suggest that PAZ domains in all members of the Argonaute and Dicer families adopt a similar fold with nucleic-acid binding function, and that this plays an important part in gene silencing.
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Affiliation(s)
- Andreas Lingel
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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Iwai H, Lingel A, Pluckthun A. Cyclic green fluorescent protein produced in vivo using an artificially split PI-PfuI intein from Pyrococcus furiosus. J Biol Chem 2001; 276:16548-54. [PMID: 11278952 DOI: 10.1074/jbc.m011639200] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.0] [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: 11/06/2022] Open
Abstract
A cyclic protein was produced in vivo using the intein from Pyrococcus furiosus PI-PfuI in a novel approach to create a circular permutation of the precursor protein by introducing new termini in the intein domain. Green fluorescent protein (GFP) was cyclized with this method in vivo on milligram scales. There was no by-product of linear or polymerized species isolated, unlike with other in vitro or in vivo cyclization methods utilizing inteins. Cyclized GFP unfolded at half the rate of the linear form upon chemical denaturation and required >2 days in 7 m guanidine hydrochloride until a residual fast folding phase (consistent with a persistent cis-proline) had disappeared. Cyclic GFP might become a novel tool for studying the role of termini and backbone topology in various biological processes such as protein degradation and translocation in vivo as well as in vitro.
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Affiliation(s)
- H Iwai
- Biochemisches Institut der Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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