1
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Herrmann F, Hessmann M, Schaertl S, Berg-Rosseburg K, Brown CJ, Bursow G, Chiki A, Ebneth A, Gehrmann M, Hoeschen N, Hotze M, Jahn S, Johnson PD, Khetarpal V, Kiselyov A, Kottig K, Ladewig S, Lashuel H, Letschert S, Mills MR, Petersen K, Prime ME, Scheich C, Schmiedel G, Wityak J, Liu L, Dominguez C, Muñoz-Sanjuán I, Bard JA. Pharmacological characterization of mutant huntingtin aggregate-directed PET imaging tracer candidates. Sci Rep 2021; 11:17977. [PMID: 34504195 PMCID: PMC8429736 DOI: 10.1038/s41598-021-97334-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/24/2021] [Indexed: 12/14/2022] Open
Abstract
Huntington’s disease (HD) is caused by a CAG trinucleotide repeat expansion in the first exon of the huntingtin (HTT) gene coding for the huntingtin (HTT) protein. The misfolding and consequential aggregation of CAG-expanded mutant HTT (mHTT) underpin HD pathology. Our interest in the life cycle of HTT led us to consider the development of high-affinity small-molecule binders of HTT oligomerized/amyloid-containing species that could serve as either cellular and in vivo imaging tools or potential therapeutic agents. We recently reported the development of PET tracers CHDI-180 and CHDI-626 as suitable for imaging mHTT aggregates, and here we present an in-depth pharmacological investigation of their binding characteristics. We have implemented an array of in vitro and ex vivo radiometric binding assays using recombinant HTT, brain homogenate-derived HTT aggregates, and brain sections from mouse HD models and humans post-mortem to investigate binding affinities and selectivity against other pathological proteins from indications such as Alzheimer’s disease and spinocerebellar ataxia 1. Radioligand binding assays and autoradiography studies using brain homogenates and tissue sections from HD mouse models showed that CHDI-180 and CHDI-626 specifically bind mHTT aggregates that accumulate with age and disease progression. Finally, we characterized CHDI-180 and CHDI-626 regarding their off-target selectivity and binding affinity to beta amyloid plaques in brain sections and homogenates from Alzheimer’s disease patients.
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Affiliation(s)
| | | | | | | | - Christopher J Brown
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, OX14 4RZ, UK
| | | | - Anass Chiki
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | | | | | | | - Madlen Hotze
- Evotec SE, Essener Bogen 7, 22419, Hamburg, Germany
| | | | - Peter D Johnson
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, OX14 4RZ, UK
| | - Vinod Khetarpal
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, CA, 90045, USA
| | - Alex Kiselyov
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, CA, 90045, USA
| | | | | | - Hilal Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | | | - Matthew R Mills
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, OX14 4RZ, UK
| | | | - Michael E Prime
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, OX14 4RZ, UK
| | | | | | - John Wityak
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, CA, 90045, USA
| | - Longbin Liu
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, CA, 90045, USA
| | - Celia Dominguez
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, CA, 90045, USA
| | - Ignacio Muñoz-Sanjuán
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, CA, 90045, USA
| | - Jonathan A Bard
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, CA, 90045, USA.
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2
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Liu L, Johnson PD, Prime ME, Khetarpal V, Lee MR, Brown CJ, Chen X, Clark-Frew D, Coe S, Conlon M, Davis R, Ensor S, Esposito S, Moren AF, Gai X, Green S, Greenaway C, Haber J, Halldin C, Hayes S, Herbst T, Herrmann F, Heßmann M, Hsai MM, Kotey A, Mangette JE, Mills MR, Monteagudo E, Nag S, Nibbio M, Orsatti L, Schaertl S, Scheich C, Sproston J, Stepanov V, Varnäs K, Varrone A, Wityak J, Mrzljak L, Munoz-Sanjuan I, Bard JA, Dominguez C. [ 11C]CHDI-626, a PET Tracer Candidate for Imaging Mutant Huntingtin Aggregates with Reduced Binding to AD Pathological Proteins. J Med Chem 2021; 64:12003-12021. [PMID: 34351166 DOI: 10.1021/acs.jmedchem.1c00667] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The expanded polyglutamine-containing mutant huntingtin (mHTT) protein is implicated in neuronal degeneration of medium spiny neurons in Huntington's disease (HD) for which multiple therapeutic approaches are currently being evaluated to eliminate or reduce mHTT. Development of effective and orthogonal biomarkers will ensure accurate assessment of the safety and efficacy of pharmacologic interventions. We have identified and optimized a class of ligands that bind to oligomerized/aggregated mHTT, which is a hallmark in the HD postmortem brain. These ligands are potentially useful imaging biomarkers for HD therapeutic development in both preclinical and clinical settings. We describe here the optimization of the benzo[4,5]imidazo[1,2-a]pyrimidine series that show selective binding to mHTT aggregates over Aβ- and/or tau-aggregates associated with Alzheimer's disease pathology. Compound [11C]-2 was selected as a clinical candidate based on its high free fraction in the brain, specific binding in the HD mouse model, and rapid brain uptake/washout in nonhuman primate positron emission tomography imaging studies.
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Affiliation(s)
- Longbin Liu
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Peter D Johnson
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Michael E Prime
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Vinod Khetarpal
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Matthew R Lee
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Christopher J Brown
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Xuemei Chen
- Albany Molecular Research, Inc., 1001 Main Street, Buffalo, New York 14203, United States
| | - Daniel Clark-Frew
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Samuel Coe
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Mike Conlon
- Albany Molecular Research, Inc., 1001 Main Street, Buffalo, New York 14203, United States
| | - Randall Davis
- Albany Molecular Research, Inc., 1001 Main Street, Buffalo, New York 14203, United States
| | - Samantha Ensor
- Albany Molecular Research, Inc., 1001 Main Street, Buffalo, New York 14203, United States
| | - Simone Esposito
- IRBM, IRBM Science Park S.p.A., Via Pontina Km 30,600, Pomezia, Rome 00071, Italy
| | - Anton Forsberg Moren
- Department of Clinical Neuroscience, Centre for Psychiatric Research, Karolinska Hospital, Karolinska Institutet, Stockholm S-17176, Sweden
| | - Xinjie Gai
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Samantha Green
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Catherine Greenaway
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - James Haber
- Albany Molecular Research, Inc., 1001 Main Street, Buffalo, New York 14203, United States
| | - Christer Halldin
- Department of Clinical Neuroscience, Centre for Psychiatric Research, Karolinska Hospital, Karolinska Institutet, Stockholm S-17176, Sweden
| | - Sarah Hayes
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Todd Herbst
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Frank Herrmann
- Evotec SE, Manfred Eigen Campus, Essener Bogen 7, Hamburg 22419, Germany
| | - Manuela Heßmann
- Evotec SE, Manfred Eigen Campus, Essener Bogen 7, Hamburg 22419, Germany
| | - Ming Min Hsai
- Albany Molecular Research, Inc., 1001 Main Street, Buffalo, New York 14203, United States
| | - Adrian Kotey
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - John E Mangette
- Albany Molecular Research, Inc., 1001 Main Street, Buffalo, New York 14203, United States
| | - Matthew R Mills
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Edith Monteagudo
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Sangram Nag
- Department of Clinical Neuroscience, Centre for Psychiatric Research, Karolinska Hospital, Karolinska Institutet, Stockholm S-17176, Sweden
| | - Martina Nibbio
- IRBM, IRBM Science Park S.p.A., Via Pontina Km 30,600, Pomezia, Rome 00071, Italy
| | - Laura Orsatti
- IRBM, IRBM Science Park S.p.A., Via Pontina Km 30,600, Pomezia, Rome 00071, Italy
| | - Sabine Schaertl
- Evotec SE, Manfred Eigen Campus, Essener Bogen 7, Hamburg 22419, Germany
| | - Christoph Scheich
- Evotec SE, Manfred Eigen Campus, Essener Bogen 7, Hamburg 22419, Germany
| | - Joanne Sproston
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Vladimir Stepanov
- Department of Clinical Neuroscience, Centre for Psychiatric Research, Karolinska Hospital, Karolinska Institutet, Stockholm S-17176, Sweden
| | - Katarina Varnäs
- Department of Clinical Neuroscience, Centre for Psychiatric Research, Karolinska Hospital, Karolinska Institutet, Stockholm S-17176, Sweden
| | - Andrea Varrone
- Department of Clinical Neuroscience, Centre for Psychiatric Research, Karolinska Hospital, Karolinska Institutet, Stockholm S-17176, Sweden
| | - John Wityak
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Ladislav Mrzljak
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Ignacio Munoz-Sanjuan
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Jonathan A Bard
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Celia Dominguez
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
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3
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Liu L, Prime ME, Lee MR, Khetarpal V, Brown CJ, Johnson PD, Miranda-Azpiazu P, Chen X, Clark-Frew D, Coe S, Davis R, Dickie A, Ebneth A, Esposito S, Gadouleau E, Gai X, Galan S, Green S, Greenaway C, Giles P, Halldin C, Hayes S, Herbst T, Herrmann F, Heßmann M, Jia Z, Kiselyov A, Kotey A, Krulle T, Mangette JE, Marston RW, Menta S, Mills MR, Monteagudo E, Nag S, Nibbio M, Orsatti L, Schaertl S, Scheich C, Sproston J, Stepanov V, Svedberg M, Takano A, Taylor M, Thomas W, Toth M, Vaidya D, Vanräs K, Weddell D, Wigginton I, Wityak J, Mrzljak L, Munoz-Sanjuan I, Bard JA, Dominguez C. Imaging Mutant Huntingtin Aggregates: Development of a Potential PET Ligand. J Med Chem 2020; 63:8608-8633. [PMID: 32662649 DOI: 10.1021/acs.jmedchem.0c00955] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Mutant huntingtin (mHTT) protein carrying the elongated N-terminal polyglutamine (polyQ) tract misfolds and forms protein aggregates characteristic of Huntington's disease (HD) pathology. A high-affinity ligand specific for mHTT aggregates could serve as a positron emission tomography (PET) imaging biomarker for HD therapeutic development and disease progression. To identify such compounds with binding affinity for polyQ aggregates, we embarked on systematic structural activity studies; lead optimization of aggregate-binding affinity, unbound fractions in brain, permeability, and low efflux culminated in the discovery of compound 1, which exhibited target engagement in autoradiography (ARG) studies in brain slices from HD mouse models and postmortem human HD samples. PET imaging studies with 11C-labeled 1 in both HD mice and WT nonhuman primates (NHPs) demonstrated that the right-hand-side labeled ligand [11C]-1R (CHDI-180R) is a suitable PET tracer for imaging of mHTT aggregates. [11C]-1R is now being advanced to human trials as a first-in-class HD PET radiotracer.
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Affiliation(s)
- Longbin Liu
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Michael E Prime
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Matt R Lee
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Vinod Khetarpal
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Christopher J Brown
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Peter D Johnson
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Patricia Miranda-Azpiazu
- Department of Clinical Neuroscience, Centre for Psychiatric Research, Karolinska Hospital, Karolinska Institutet, S-17176 Stockholm, Sweden
| | - Xuemei Chen
- Albany Molecular Research, Inc., 1001 Main St., Buffalo, New York 14203, United States
| | - Daniel Clark-Frew
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Samuel Coe
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Randall Davis
- Albany Molecular Research, Inc., 1001 Main St., Buffalo, New York 14203, United States
| | - Anthony Dickie
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Andreas Ebneth
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Simone Esposito
- IRBM, IRBM Science Park S.p.A., Via Pontina Km 30, 600, 00071 Pomezia (RM), Italy
| | - Elise Gadouleau
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Xinjie Gai
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Sebastien Galan
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Samantha Green
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Catherine Greenaway
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Paul Giles
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Christer Halldin
- Department of Clinical Neuroscience, Centre for Psychiatric Research, Karolinska Hospital, Karolinska Institutet, S-17176 Stockholm, Sweden
| | - Sarah Hayes
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Todd Herbst
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Frank Herrmann
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Manuela Heßmann
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Zhisheng Jia
- Department of Clinical Neuroscience, Centre for Psychiatric Research, Karolinska Hospital, Karolinska Institutet, S-17176 Stockholm, Sweden
| | - Alexander Kiselyov
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Adrian Kotey
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Thomas Krulle
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - John E Mangette
- Albany Molecular Research, Inc., 1001 Main St., Buffalo, New York 14203, United States
| | - Richard W Marston
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Sergio Menta
- IRBM, IRBM Science Park S.p.A., Via Pontina Km 30, 600, 00071 Pomezia (RM), Italy
| | - Matthew R Mills
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Edith Monteagudo
- IRBM, IRBM Science Park S.p.A., Via Pontina Km 30, 600, 00071 Pomezia (RM), Italy
| | - Sangram Nag
- Department of Clinical Neuroscience, Centre for Psychiatric Research, Karolinska Hospital, Karolinska Institutet, S-17176 Stockholm, Sweden
| | - Martina Nibbio
- IRBM, IRBM Science Park S.p.A., Via Pontina Km 30, 600, 00071 Pomezia (RM), Italy
| | - Laura Orsatti
- IRBM, IRBM Science Park S.p.A., Via Pontina Km 30, 600, 00071 Pomezia (RM), Italy
| | - Sabine Schaertl
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Christoph Scheich
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Joanne Sproston
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Vladimir Stepanov
- Department of Clinical Neuroscience, Centre for Psychiatric Research, Karolinska Hospital, Karolinska Institutet, S-17176 Stockholm, Sweden
| | - Marie Svedberg
- Department of Clinical Neuroscience, Centre for Psychiatric Research, Karolinska Hospital, Karolinska Institutet, S-17176 Stockholm, Sweden
| | - Akihiro Takano
- Department of Clinical Neuroscience, Centre for Psychiatric Research, Karolinska Hospital, Karolinska Institutet, S-17176 Stockholm, Sweden
| | - Malcolm Taylor
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Wayne Thomas
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Miklós Toth
- Department of Clinical Neuroscience, Centre for Psychiatric Research, Karolinska Hospital, Karolinska Institutet, S-17176 Stockholm, Sweden
| | - Darshan Vaidya
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Katarina Vanräs
- Department of Clinical Neuroscience, Centre for Psychiatric Research, Karolinska Hospital, Karolinska Institutet, S-17176 Stockholm, Sweden
| | - Derek Weddell
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - Ian Wigginton
- Evotec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, U.K
| | - John Wityak
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Ladislav Mrzljak
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Ignacio Munoz-Sanjuan
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Jonathan A Bard
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
| | - Celia Dominguez
- CHDI Management/CHDI Foundation, 6080 Center Drive, Suite 700, Los Angeles, California 90045, United States
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4
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Mesleh MF, Cross JB, Zhang J, Kahmann J, Andersen OA, Barker J, Cheng RK, Felicetti B, Wood M, Hadfield AT, Scheich C, Moy TI, Yang Q, Shotwell J, Nguyen K, Lippa B, Dolle R, Ryan MD. Fragment-based discovery of DNA gyrase inhibitors targeting the ATPase subunit of GyrB. Bioorg Med Chem Lett 2016; 26:1314-8. [DOI: 10.1016/j.bmcl.2016.01.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/03/2016] [Accepted: 01/05/2016] [Indexed: 11/16/2022]
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5
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Hereng TH, Backe PH, Kahmann J, Scheich C, Bjørås M, Skålhegg BS, Rosendal KR. Structure and function of the human sperm-specific isoform of protein kinase A (PKA) catalytic subunit Cα2. J Struct Biol 2012; 178:300-10. [PMID: 22504716 DOI: 10.1016/j.jsb.2012.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 03/30/2012] [Accepted: 03/31/2012] [Indexed: 10/28/2022]
Abstract
Protein kinase A (PKA) exists as several tissue-specific isoforms that through phosphorylation of serine and threonine residues of substrate proteins act as key regulators of a number of cellular processes. We here demonstrate that the human sperm-specific isoform of PKA named Cα2 is important for sperm motility and thus male fertility. Furthermore, we report on the first three-dimensional crystal structure of human apo Cα2 to 2.1 Å. Apo Cα2 displays an open conformation similar to the well-characterized apo structure of murine Cα1. The asymmetric unit contains two molecules and the core of the small lobe is rotated by almost 13° in the A molecule relative to the B molecule. In addition, a salt bridge between Lys72 and Glu91 was observed for Cα2 in the apo-form, a conformation previously found only in dimeric or ternary complexes of Cα1. Human Cα2 and Cα1 share primary structure with the exception of the amino acids at the N-terminus coded for by an alternative exon 1. The N-terminal glycine of Cα1 is myristoylated and this aliphatic chain anchors the N-terminus to an intramolecular hydrophobic pocket. Cα2 cannot be myristoylated and the crystal structure revealed that the equivalent hydrophobic pocket is unoccupied and exposed. Nuclear magnetic resonance (NMR) spectroscopy further demonstrated that detergents with hydrophobic moieties of different lengths can bind deep into this uncovered pocket. Our findings indicate that Cα2 through the hydrophobic pocket has the ability to bind intracellular targets in the sperm cell, which may modulate protein stability, activity and/or cellular localization.
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6
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Scheich C, Szabadka Z, Vértessy B, Pütter V, Grolmusz V, Schade M. Discovery of novel MDR-Mycobacterium tuberculosis inhibitor by new FRIGATE computational screen. PLoS One 2011; 6:e28428. [PMID: 22164290 PMCID: PMC3229595 DOI: 10.1371/journal.pone.0028428] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 11/08/2011] [Indexed: 11/19/2022] Open
Abstract
With 1.6 million casualties annually and 2 billion people being infected, tuberculosis is still one of the most pressing healthcare challenges. Here we report on the new computational docking algorithm FRIGATE which unites continuous local optimization techniques (conjugate gradient method) with an inherently discrete computational approach in forcefield computation, resulting in equal or better scoring accuracies than several benchmark docking programs. By utilizing FRIGATE for a virtual screen of the ZINC library against the Mycobacterium tuberculosis (Mtb) enzyme antigen 85C, we identified novel small molecule inhibitors of multiple drug-resistant Mtb, which bind in vitro to the catalytic site of antigen 85C.
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Affiliation(s)
| | - Zoltán Szabadka
- Department of Computer Science, Eötvös University, Budapest, Hungary
- Uratim Ltd., Budapest, Hungary
| | - Beáta Vértessy
- Institute of Enzymology, Hungarian Academy of Science, Budapest, Hungary
- Department of Applied Biotechnology, University of Technology and Economics, Budapest, Hungary
| | | | - Vince Grolmusz
- Department of Computer Science, Eötvös University, Budapest, Hungary
- Uratim Ltd., Budapest, Hungary
- * E-mail: (VG); (MS)
| | - Markus Schade
- Combinature Biopharm AG, Berlin, Germany
- * E-mail: (VG); (MS)
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7
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Scheich C, Puetter V, Schade M. Novel Small Molecule Inhibitors of MDR Mycobacterium tuberculosis by NMR Fragment Screening of Antigen 85C. J Med Chem 2010; 53:8362-7. [DOI: 10.1021/jm100993z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [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)
| | | | - Markus Schade
- Combinature Biopharm AG, Robert-Roessle-Strasse 10, 13125 Berlin, Germany
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8
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Cheng R, Felicetti B, Palan S, Toogood-Johnson I, Scheich C, Barker J, Whittaker M, Hesterkamp T. High-resolution crystal structure of human Mapkap kinase 3 in complex with a high affinity ligand. Protein Sci 2010; 19:168-73. [PMID: 19937655 DOI: 10.1002/pro.294] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The Mapkap kinases 2 and 3 (MK2 and MK3) have been implicated in intracellular signaling pathways leading to the production of the pro-inflammatory cytokine tumor necrosis factor alpha. MK2 has been pursued by the biopharmaceutical industry for many years for the development of a small molecule anti-inflammatory treatment and drug-like inhibitors have been described. The development of some of these compounds, however, has been slowed by the absence of a high-resolution crystal structure of MK2. Herein we present a high-resolution (1.9 A) crystal structure of the highly homologous MK3 in complex with a pharmaceutical lead compound. While all of the canonical features of Ser/Thr kinases in general and MK2 in particular are recapitulated in MK3, the detailed analysis of the binding interaction of the drug-like ligand within the adenine binding pocket allows relevant conclusions to be drawn for the further design of potent and selective drug candidates.
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Affiliation(s)
- Robert Cheng
- Evotec (UK) Ltd, 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
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Keminer O, Kraemer J, Kahmann J, Sternberger I, Scheich C, Jungmann J, Schaert S, Winkler D, Ichihara O, Whittaker M, Ullmann D, Hesterkamp T. Novel MK2 inhibitors by fragment screening. Comb Chem High Throughput Screen 2009; 12:697-703. [PMID: 19531016 DOI: 10.2174/138620709788923700] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Accepted: 01/08/2009] [Indexed: 11/22/2022]
Abstract
Inhibitors of MAPKAP kinase 2 (MK2) are expected to attenuate the p38alpha signal transduction pathway in macrophages in a similar way to p38alpha inhibitors and to have a lower propensity for toxic side effects that have slowed the clinical development of the latter. Therefore, novel MK2 inhibitors may find therapeutic application in acute and chronic, TNFalpha-mediated inflammatory conditions like rheumatoid arthritis and others. Herein we have applied fragment screening, using physiologically relevant bioassays and fragment binding mode mapping by protein-observed NMR spectroscopy to the discovery of novel efficient chemical starting points for MK2.
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Schulze JO, Quedenau C, Roske Y, Adam T, Schüler H, Behlke J, Turnbull AP, Sievert V, Scheich C, Mueller U, Heinemann U, Büssow K. Structural and functional characterization of human Iba proteins. FEBS J 2008; 275:4627-40. [DOI: 10.1111/j.1742-4658.2008.06605.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
A vector system is presented that allows generation of E. coli co-expression clones by a standardized, robust cloning procedure. The number of co-expressed proteins is not limited. Five ‘pQLink’ vectors for expression of His-tag and GST-tag fusion proteins as well as untagged proteins and for cloning by restriction enzymes or Gateway cloning were generated. The vectors allow proteins to be expressed individually; to achieve co-expression, two pQLink plasmids are combined by ligation-independent cloning. pQLink co-expression plasmids can accept an unrestricted number of genes. As an example, the co-expression of a heterotetrameric human transport protein particle (TRAPP) complex from a single plasmid, its isolation and analysis of its stoichiometry are shown. pQLink clones can be used directly for pull-down experiments if the proteins are expressed with different tags. We demonstrate pull-down experiments of human valosin-containing protein (VCP) with fragments of the autocrine motility factor receptor (AMFR). The cloning method avoids PCR or gel isolation of restriction fragments, and a single resistance marker and origin of replication are used, allowing over-expression of rare tRNAs from a second plasmid. It is expected that applications are not restricted to bacteria, but could include co-expression in other hosts such as Bacluovirus/insect cells.
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Affiliation(s)
- Christoph Scheich
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestr. 63-73, 14195 Berlin, Germany, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany and Free University of Berlin, Institute of Chemistry and Biochemistry, Takustraße 6, 14195 Berlin, Germany
| | - Daniel Kümmel
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestr. 63-73, 14195 Berlin, Germany, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany and Free University of Berlin, Institute of Chemistry and Biochemistry, Takustraße 6, 14195 Berlin, Germany
| | - Dimitri Soumailakakis
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestr. 63-73, 14195 Berlin, Germany, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany and Free University of Berlin, Institute of Chemistry and Biochemistry, Takustraße 6, 14195 Berlin, Germany
| | - Udo Heinemann
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestr. 63-73, 14195 Berlin, Germany, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany and Free University of Berlin, Institute of Chemistry and Biochemistry, Takustraße 6, 14195 Berlin, Germany
| | - Konrad Büssow
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestr. 63-73, 14195 Berlin, Germany, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany and Free University of Berlin, Institute of Chemistry and Biochemistry, Takustraße 6, 14195 Berlin, Germany
- *To whom correspondence should be addressed. +49 30 9406 2983+49 30 9406 2925
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Berrow NS, Büssow K, Coutard B, Diprose J, Ekberg M, Folkers GE, Levy N, Lieu V, Owens RJ, Peleg Y, Pinaglia C, Quevillon-Cheruel S, Salim L, Scheich C, Vincentelli R, Busso D. Recombinant protein expression and solubility screening in Escherichia coli: a comparative study. Acta Crystallogr D Biol Crystallogr 2006; 62:1218-26. [PMID: 17001098 DOI: 10.1107/s0907444906031337] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Accepted: 08/09/2006] [Indexed: 11/10/2022]
Abstract
Producing soluble proteins in Escherichia coli is still a major bottleneck for structural proteomics. Therefore, screening for soluble expression on a small scale is an attractive way of identifying constructs that are likely to be amenable to structural analysis. A variety of expression-screening methods have been developed within the Structural Proteomics In Europe (SPINE) consortium and to assist the further refinement of such approaches, eight laboratories participating in the network have benchmarked their protocols. For this study, the solubility profiles of a common set of 96 His(6)-tagged proteins were assessed by expression screening in E. coli. The level of soluble expression for each target was scored according to estimated protein yield. By reference to a subset of the proteins, it is demonstrated that the small-scale result can provide a useful indicator of the amount of soluble protein likely to be produced on a large scale (i.e. sufficient for structural studies). In general, there was agreement between the different groups as to which targets were not soluble and which were the most soluble. However, for a large number of the targets there were wide discrepancies in the results reported from the different screening methods, which is correlated with variations in the procedures and the range of parameters explored. Given finite resources, it appears that the question of how to most effectively explore ;expression space' is similar to several other multi-parameter problems faced by crystallographers, such as crystallization.
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Affiliation(s)
- Nick S Berrow
- Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, Oxford, England
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Manjasetty BA, Büssow K, Fieber-Erdmann M, Roske Y, Gobom J, Scheich C, Götz F, Niesen FH, Heinemann U. Crystal structure of Homo sapiens PTD012 reveals a zinc-containing hydrolase fold. Protein Sci 2006; 15:914-20. [PMID: 16522806 PMCID: PMC2242484 DOI: 10.1110/ps.052037006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The human protein PTD012 is the longer product of an alternatively spliced gene and was described to be localized in the nucleus. The X-ray structure analysis at 1.7 A resolution of PTD012 through SAD phasing reveals a monomeric protein and a novel fold. The shorter splice form was also studied and appears to be unfolded and non-functional. The structure of PTD012 displays an alphabetabetaalpha four-layer topology. A metal ion residing between the central beta-sheets is partially coordinated by three histidine residues. X-ray absorption near-edge structure (XANES) analysis identifies the PTD012-bound ion as Zn(2+). Tetrahedral coordination of the ion is completed by the carboxylate oxygen atom of an acetate molecule taken up from the crystallization buffer. The binding of Zn(2+) to PTD012 is reminiscent of zinc-containing enzymes such as carboxypeptidase, carbonic anhydrase, and beta-lactamase. Biochemical assays failed to demonstrate any of these enzyme activities in PTD012. However, PTD012 exhibits ester hydrolase activity on the substrate p-nitrophenyl acetate.
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Manjasetty BA, Niesen FH, Scheich C, Roske Y, Goetz F, Behlke J, Sievert V, Heinemann U, Büssow K. X-ray structure of engineered human Aortic Preferentially Expressed Protein-1 (APEG-1). BMC Struct Biol 2005; 5:21. [PMID: 16354304 PMCID: PMC1352370 DOI: 10.1186/1472-6807-5-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Accepted: 12/14/2005] [Indexed: 11/26/2022]
Abstract
Background Human Aortic Preferentially Expressed Protein-1 (APEG-1) is a novel specific smooth muscle differentiation marker thought to play a role in the growth and differentiation of arterial smooth muscle cells (SMCs). Results Good quality crystals that were suitable for X-ray crystallographic studies were obtained following the truncation of the 14 N-terminal amino acids of APEG-1, a region predicted to be disordered. The truncated protein (termed ΔAPEG-1) consists of a single immunoglobulin (Ig) like domain which includes an Arg-Gly-Asp (RGD) adhesion recognition motif. The RGD motif is crucial for the interaction of extracellular proteins and plays a role in cell adhesion. The X-ray structure of ΔAPEG-1 was determined and was refined to sub-atomic resolution (0.96 Å). This is the best resolution for an immunoglobulin domain structure so far. The structure adopts a Greek-key β-sandwich fold and belongs to the I (intermediate) set of the immunoglobulin superfamily. The residues lying between the β-sheets form a hydrophobic core. The RGD motif folds into a 310 helix that is involved in the formation of a homodimer in the crystal which is mainly stabilized by salt bridges. Analytical ultracentrifugation studies revealed a moderate dissociation constant of 20 μM at physiological ionic strength, suggesting that APEG-1 dimerisation is only transient in the cell. The binding constant is strongly dependent on ionic strength. Conclusion Our data suggests that the RGD motif might play a role not only in the adhesion of extracellular proteins but also in intracellular protein-protein interactions. However, it remains to be established whether the rather weak dimerisation of APEG-1 involving this motif is physiogically relevant.
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Affiliation(s)
- Babu A Manjasetty
- Protein Structure Factory, c/o BESSY GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Case Centre for Proteomics, Case Western Reserve University, Upton, New York 11973, USA
| | - Frank H Niesen
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Charité Universitätsmedizin Berlin, Institut für Medizinische Physik & Biophysik, Ziegelstr. 5-9, 10098 Berlin, Germany
- Structural Genomics Consortium, University of Oxford, Botnar Research Centre, Oxford, OX3 7LD, UK
| | - Christoph Scheich
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Yvette Roske
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
| | - Frank Goetz
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
| | - Joachim Behlke
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Volker Sievert
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Institut für Chemie/Kristallographie, Freie Universität, Takustr. 6, 14195 Berlin, Germany
| | - Konrad Büssow
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
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Büssow K, Scheich C, Sievert V, Harttig U, Schultz J, Simon B, Bork P, Lehrach H, Heinemann U. Structural genomics of human proteins--target selection and generation of a public catalogue of expression clones. Microb Cell Fact 2005; 4:21. [PMID: 15998469 PMCID: PMC1250228 DOI: 10.1186/1475-2859-4-21] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Accepted: 07/05/2005] [Indexed: 11/12/2022] Open
Abstract
Background The availability of suitable recombinant protein is still a major bottleneck in protein structure analysis. The Protein Structure Factory, part of the international structural genomics initiative, targets human proteins for structure determination. It has implemented high throughput procedures for all steps from cloning to structure calculation. This article describes the selection of human target proteins for structure analysis, our high throughput cloning strategy, and the expression of human proteins in Escherichia coli host cells. Results and Conclusion Protein expression and sequence data of 1414 E. coli expression clones representing 537 different proteins are presented. 139 human proteins (18%) could be expressed and purified in soluble form and with the expected size. All E. coli expression clones are publicly available to facilitate further functional characterisation of this set of human proteins.
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Affiliation(s)
- Konrad Büssow
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Christoph Scheich
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Volker Sievert
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Ulrich Harttig
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- RZPD German Resource Center for Genome Research GmbH, Heubnerweg 6, 14059 Berlin, Germany
- DIFE, Arthur-Scheunert-Allee 114–116, 14558 Nuthetal, Germany
| | - Jörg Schultz
- EMBL Heidelberg, Meyerhofstr. 1, 69117 Heidelberg, Germany
- Department of Bioinformatics, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany
| | - Bernd Simon
- EMBL Heidelberg, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Peer Bork
- EMBL Heidelberg, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Hans Lehrach
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Udo Heinemann
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Institut für Chemie/Kristallographie, Freie Universität, Takustr. 6, 14195 Berlin, Germany
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Abstract
The preparation of proteins for structural and functional analysis using the Escherichia coli expression system is often hampered by the formation of insoluble intracellular protein aggregates (inclusion bodies). Transferring those proteins into their native states by in vitro protein folding requires screening for the best buffer conditions and suitable additives. However, it is difficult to assess the success of such a screen if no biological assay is available. We established a fully automated folding screen and a system to detect folded protein that is based on analytical hydrophobic interaction chromatography and tryptophan fluorescence spectroscopy. The system was evaluated with two model enzymes (carbonic anhydrase II and malate dehydrogenase), and was successfully applied to the folding of the p22 subunit of human dynactin, which is expressed in inclusion bodies in E. coli. The described screen allows for high-throughput folding analysis of inclusion body proteins for structural and functional analyses.
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Büssow K, Quedenau C, Sievert V, Tischer J, Scheich C, Seitz H, Hieke B, Niesen FH, Götz F, Harttig U, Lehrach H. A catalog of human cDNA expression clones and its application to structural genomics. Genome Biol 2004; 5:R71. [PMID: 15345055 PMCID: PMC522878 DOI: 10.1186/gb-2004-5-9-r71] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [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: 04/16/2004] [Revised: 07/21/2004] [Accepted: 07/23/2004] [Indexed: 11/10/2022] Open
Abstract
We describe here a systematic approach to the identification of human proteins and protein fragments that can be expressed as soluble proteins in Escherichia coli. A cDNA expression library of 10,825 clones was screened by small-scale expression and purification and 2,746 clones were identified. Sequence and protein-expression data were entered into a public database. A set of 163 clones was selected for structural analysis and 17 proteins were prepared for crystallization, leading to three new structures.
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Affiliation(s)
- Konrad Büssow
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - Claudia Quedenau
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - Volker Sievert
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - Janett Tischer
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - Christoph Scheich
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - Harald Seitz
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - Brigitte Hieke
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - Frank H Niesen
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Institute of Medical Physics and Biophysics, Charité Medical School, Ziegelstraße 5/9, 10117 Berlin, Germany
| | - Frank Götz
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Alpha Bioverfahrenstechnik GmbH, Heinrich-Hertz-Straße 1b, 14532 Kleinmachnow, Germany
| | - Ulrich Harttig
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- RZPD German Resource Center for Genome Research GmbH, Heubnerweg 6, 14059 Berlin, Germany
| | - Hans Lehrach
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
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Manjasetty BA, Delbrück H, Pham DT, Mueller U, Fieber-Erdmann M, Scheich C, Sievert V, Büssow K, Niesen FH, Weihofen W, Loll B, Saenger W, Heinemann U, Neisen FH. Crystal structure of Homo sapiens protein hp14.5. Proteins 2004; 54:797-800. [PMID: 14997576 DOI: 10.1002/prot.10619] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Manjasetty BA, Delbrück H, Pham DT, Mueller U, Fieber-Erdmann M, Scheich C, Sievert V, Büssow K, Niesen FH, Weihofen W, Loll B, Saenger W, Heinemann U. Crystal structure of Homo sapiens protein hp14.5. Proteins 2004. [DOI: 10.1002/prot.20188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Scheich C, Leitner D, Sievert V, Leidert M, Schlegel B, Simon B, Letunic I, Büssow K, Diehl A. Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis. BMC Struct Biol 2004; 4:4. [PMID: 15113422 PMCID: PMC516802 DOI: 10.1186/1472-6807-4-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2004] [Accepted: 03/08/2004] [Indexed: 11/30/2022]
Abstract
Background High-throughput protein structure analysis of individual protein domains requires analysis of large numbers of expression clones to identify suitable constructs for structure determination. For this purpose, methods need to be implemented for fast and reliable screening of the expressed proteins as early as possible in the overall process from cloning to structure determination. Results 88 different E. coli expression constructs for 17 human protein domains were analysed using high-throughput cloning, purification and folding analysis to obtain candidates suitable for structural analysis. After 96 deep-well microplate expression and automated protein purification, protein domains were directly analysed using 1D 1H-NMR spectroscopy. In addition, analytical hydrophobic interaction chromatography (HIC) was used to detect natively folded protein. With these two analytical methods, six constructs (representing two domains) were quickly identified as being well folded and suitable for structural analysis. Conclusion The described approach facilitates high-throughput structural analysis. Clones expressing natively folded proteins suitable for NMR structure determination were quickly identified upon small scale expression screening using 1D 1H-NMR and/or analytical HIC. This procedure is especially effective as a fast and inexpensive screen for the 'low hanging fruits' in structural genomics.
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Affiliation(s)
- Christoph Scheich
- Proteinstrukturfabrik, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, Germany
| | - Dietmar Leitner
- Proteinstrukturfabrik, Heubnerweg 6, 14059 Berlin, Germany
- Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Volker Sievert
- Proteinstrukturfabrik, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, Germany
| | - Martina Leidert
- Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Brigitte Schlegel
- Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Bernd Simon
- Proteinstrukturfabrik, Heubnerweg 6, 14059 Berlin, Germany
- European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Ivica Letunic
- European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Konrad Büssow
- Proteinstrukturfabrik, Heubnerweg 6, 14059 Berlin, Germany
- Max Planck Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, Germany
| | - Anne Diehl
- Proteinstrukturfabrik, Heubnerweg 6, 14059 Berlin, Germany
- Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
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Scheich C, Sievert V, Büssow K. An automated method for high-throughput protein purification applied to a comparison of His-tag and GST-tag affinity chromatography. BMC Biotechnol 2003; 3:12. [PMID: 12885298 PMCID: PMC183854 DOI: 10.1186/1472-6750-3-12] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [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: 03/26/2003] [Accepted: 07/28/2003] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Functional Genomics, the systematic characterisation of the functions of an organism's genes, includes the study of the gene products, the proteins. Such studies require methods to express and purify these proteins in a parallel, time and cost effective manner. RESULTS We developed a method for parallel expression and purification of recombinant proteins with a hexahistidine tag (His-tag) or glutathione S-transferase (GST)-tag from bacterial expression systems. Proteins are expressed in 96-well microplates and are purified by a fully automated procedure on a pipetting robot. Up to 90 microgram purified protein can be obtained from 1 ml microplate cultures. The procedure is readily reproducible and 96 proteins can be purified in approximately three hours. It avoids clearing of crude cellular lysates and the use of magnetic affinity beads and is therefore less expensive than comparable commercial systems. We have used this method to compare purification of a set of human proteins via His-tag or GST-tag. Proteins were expressed as fusions to an N-terminal tandem His- and GST-tag and were purified by metal chelating or glutathione affinity chromatography. The purity of the obtained protein samples was similar, yet His-tag purification resulted in higher yields for some proteins. CONCLUSION A fully automated, robust and cost effective method was developed for the purification of proteins that can be used to quickly characterise expression clones in high throughput and to produce large numbers of proteins for functional studies.His-tag affinity purification was found to be more efficient than purification via GST-tag for some proteins.
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Affiliation(s)
- Christoph Scheich
- Protein Structure Factory, Max Planck Institute of Molecular Genetics, Heubnerweg 6, 14059 Berlin, Germany
| | - Volker Sievert
- Protein Structure Factory, Max Planck Institute of Molecular Genetics, Heubnerweg 6, 14059 Berlin, Germany
| | - Konrad Büssow
- Protein Structure Factory, Max Planck Institute of Molecular Genetics, Heubnerweg 6, 14059 Berlin, Germany
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