1
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Pesch V, Flores-Fernandez JM, Reithofer S, Ma L, Özdüzenciler P, Busch Y, Sriraman A, Wang Y, Amidian S, Kroepel CVM, Müller L, Lien Y, Rudtke O, Frieg B, Schröder GF, Wille H, Tamgüney G. Vaccination with structurally adapted fungal protein fibrils induces immunity to Parkinson's disease. Brain 2024; 147:1644-1652. [PMID: 38428032 PMCID: PMC11068327 DOI: 10.1093/brain/awae061] [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: 08/14/2023] [Revised: 01/05/2024] [Accepted: 02/10/2024] [Indexed: 03/03/2024] Open
Abstract
The pathological misfolding and aggregation of soluble α-synuclein into toxic oligomers and insoluble amyloid fibrils causes Parkinson's disease, a progressive age-related neurodegenerative disease for which there is no cure. HET-s is a soluble fungal protein that can form assembled amyloid fibrils in its prion state. We engineered HET-s(218-298) to form four different fibrillar vaccine candidates, each displaying a specific conformational epitope present on the surface of α-synuclein fibrils. Vaccination with these four vaccine candidates prolonged the survival of immunized TgM83+/- mice challenged with α-synuclein fibrils by 8% when injected into the brain to model brain-first Parkinson's disease or by 21% and 22% when injected into the peritoneum or gut wall, respectively, to model body-first Parkinson's disease. Antibodies from fully immunized mice recognized α-synuclein fibrils and brain homogenates from patients with Parkinson's disease, dementia with Lewy bodies and multiple system atrophy. Conformation-specific vaccines that mimic epitopes present only on the surface of pathological fibrils but not on soluble monomers, hold great promise for protection against Parkinson's disease, related synucleinopathies and other amyloidogenic protein misfolding disorders.
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Affiliation(s)
- Verena Pesch
- Institut für Biologische Informationsprozesse, Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - José Miguel Flores-Fernandez
- Department of Biochemistry and Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB T6G 2M8, Canada
| | - Sara Reithofer
- Institut für Biologische Informationsprozesse, Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Liang Ma
- Institut für Biologische Informationsprozesse, Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Pelin Özdüzenciler
- Institut für Biologische Informationsprozesse, Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Yannick Busch
- Institut für Biologische Informationsprozesse, Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Aishwarya Sriraman
- Department of Biochemistry and Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB T6G 2M8, Canada
| | - YongLiang Wang
- Department of Biochemistry and Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB T6G 2M8, Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Sara Amidian
- Department of Biochemistry and Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB T6G 2M8, Canada
| | - Chiara V M Kroepel
- Institut für Biologische Informationsprozesse, Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Laura Müller
- Institut für Biologische Informationsprozesse, Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Yi Lien
- Institut für Biologische Informationsprozesse, Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Olivia Rudtke
- Institut für Biologische Informationsprozesse, Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Benedikt Frieg
- Institut für Biologische Informationsprozesse, Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Gunnar F Schröder
- Institut für Biologische Informationsprozesse, Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
- Physics Department, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Wille
- Department of Biochemistry and Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB T6G 2M8, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB T6G 2M8, Canada
| | - Gültekin Tamgüney
- Institut für Biologische Informationsprozesse, Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
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2
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Schmitz B, Frieg B, Homeyer N, Jessen G, Gohlke H. Extracting binding energies and binding modes from biomolecular simulations of fragment binding to endothiapepsin. Arch Pharm (Weinheim) 2024; 357:e2300612. [PMID: 38319801 DOI: 10.1002/ardp.202300612] [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: 10/20/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024]
Abstract
Fragment-based drug discovery (FBDD) aims to discover a set of small binding fragments that may be subsequently linked together. Therefore, in-depth knowledge of the individual fragments' structural and energetic binding properties is essential. In addition to experimental techniques, the direct simulation of fragment binding by molecular dynamics (MD) simulations became popular to characterize fragment binding. However, former studies showed that long simulation times and high computational demands per fragment are needed, which limits applicability in FBDD. Here, we performed short, unbiased MD simulations of direct fragment binding to endothiapepsin, a well-characterized model system of pepsin-like aspartic proteases. To evaluate the strengths and limitations of short MD simulations for the structural and energetic characterization of fragment binding, we predicted the fragments' absolute free energies and binding poses based on the direct simulations of fragment binding and compared the predictions to experimental data. The predicted absolute free energies are in fair agreement with the experiment. Combining the MD data with binding mode predictions from molecular docking approaches helped to correctly identify the most promising fragments for further chemical optimization. Importantly, all computations and predictions were done within 5 days, suggesting that MD simulations may become a viable tool in FBDD projects.
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Affiliation(s)
- Birte Schmitz
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Benedikt Frieg
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Nadine Homeyer
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gisela Jessen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich, Germany
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3
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Frieg B, Han M, Giller K, Dienemann C, Riedel D, Becker S, Andreas LB, Griesinger C, Schröder GF. Cryo-EM structures of lipidic fibrils of amyloid-β (1-40). Nat Commun 2024; 15:1297. [PMID: 38351005 PMCID: PMC10864299 DOI: 10.1038/s41467-023-43822-x] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/21/2023] [Indexed: 02/16/2024] Open
Abstract
Alzheimer's disease (AD) is a progressive and incurable neurodegenerative disease characterized by the extracellular deposition of amyloid plaques. Investigation into the composition of these plaques revealed a high amount of amyloid-β (Aβ) fibrils and a high concentration of lipids, suggesting that fibril-lipid interactions may also be relevant for the pathogenesis of AD. Therefore, we grew Aβ40 fibrils in the presence of lipid vesicles and determined their structure by cryo-electron microscopy (cryo-EM) to high resolution. The fold of the major polymorph is similar to the structure of brain-seeded fibrils reported previously. The majority of the lipids are bound to the fibrils, as we show by cryo-EM and NMR spectroscopy. This apparent lipid extraction from vesicles observed here in vitro provides structural insights into potentially disease-relevant fibril-lipid interactions.
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Affiliation(s)
- Benedikt Frieg
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Mookyoung Han
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Karin Giller
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Dietmar Riedel
- Laboratory of Electron Microscopy, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Loren B Andreas
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
| | - Gunnar F Schröder
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany.
- Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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4
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Zielinski M, Peralta Reyes FS, Gremer L, Schemmert S, Frieg B, Schäfer LU, Willuweit A, Donner L, Elvers M, Nilsson LNG, Syvänen S, Sehlin D, Ingelsson M, Willbold D, Schröder GF. Cryo-EM of Aβ fibrils from mouse models find tg-APP ArcSwe fibrils resemble those found in patients with sporadic Alzheimer's disease. Nat Neurosci 2023; 26:2073-2080. [PMID: 37973869 PMCID: PMC10689242 DOI: 10.1038/s41593-023-01484-4] [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: 06/18/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023]
Abstract
The use of transgenic mice displaying amyloid-β (Aβ) brain pathology has been essential for the preclinical assessment of new treatment strategies for Alzheimer's disease. However, the properties of Aβ in such mice have not been systematically compared to Aβ in the brains of patients with Alzheimer's disease. Here, we determined the structures of nine ex vivo Aβ fibrils from six different mouse models by cryogenic-electron microscopy. We found novel Aβ fibril structures in the APP/PS1, ARTE10 and tg-SwDI models, whereas the human type II filament fold was found in the ARTE10, tg-APPSwe and APP23 models. The tg-APPArcSwe mice showed an Aβ fibril whose structure resembles the human type I filament found in patients with sporadic Alzheimer's disease. A detailed assessment of the Aβ fibril structure is key to the selection of adequate mouse models for the preclinical development of novel plaque-targeting therapeutics and positron emission tomography imaging tracers in Alzheimer's disease.
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Affiliation(s)
- Mara Zielinski
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich, Germany
- JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | | | - Lothar Gremer
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich, Germany.
- JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Sarah Schemmert
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich, Germany
| | - Benedikt Frieg
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich, Germany
- JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Luisa U Schäfer
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich, Germany
- JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Antje Willuweit
- Institute of Neuroscience and Medicine, Medical Imaging Physics (INM-4), Forschungszentrum Jülich, Jülich, Germany
| | - Lili Donner
- Department of Vascular and Endovascular Surgery, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Margitta Elvers
- Department of Vascular and Endovascular Surgery, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Lars N G Nilsson
- Department of Pharmacology, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Stina Syvänen
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Dag Sehlin
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Martin Ingelsson
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
- Krembil Brain Institute, University Health Network, Toronto, Ontario, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, Departments of Medicine and Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Dieter Willbold
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich, Germany.
- JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Gunnar F Schröder
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich, Germany.
- JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany.
- Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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5
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Becker N, Frieg B, Gremer L, Kupreichyk T, Gardon L, Freiburg P, Neudecker P, Willbold D, Gohlke H, Heise H. Atomic Resolution Insights into pH Shift Induced Deprotonation Events in LS-Shaped Aβ(1-42) Amyloid Fibrils. J Am Chem Soc 2023; 145:2161-2169. [PMID: 36653015 PMCID: PMC9896559 DOI: 10.1021/jacs.2c09231] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Alzheimer's disease is a neurodegenerative disorder associated with the deposition of misfolded aggregates of the amyloid-β protein (Aβ). Aβ(1-42) is one of the most aggregation-prone components in senile plaques of AD patients. We demonstrated that relatively homogeneous Aβ(1-42) fibrils with one predominant fold visible in solid-state NMR spectra can be obtained at acidic pH. The structure of these fibrils differs remarkably from some other polymorphs obtained at neutral pH. In particular, the entire N-terminal region is part of the rigid fibril core. Here, we investigate the effects of a pH shift on the stability and the fold of these fibrils at higher pH values. Fibril bundling at neutral pH values renders cryo-EM studies impractical, but solid-state NMR spectroscopy, molecular dynamics simulations, and biophysical methods provide residue-specific structural information under these conditions. The LS-fold of the Aβ(1-42) fibrils does not change over the complete pH range from pH 2 to pH 7; in particular, the N-terminus remains part of the fibril core. We observe changes in the protonation state of charged residues starting from pH 5 on a residue-specific level. The deprotonation of the C-terminal carboxyl group of A42 in the intermolecular salt bridge with D1 and K28 is slow on the NMR time scale, with a local pKa of 5.4, and local conformations of the involved residues are affected by deprotonation of A42. Thus, we demonstrate that this fibril form is stable at physiological pH values.
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Affiliation(s)
- Nina Becker
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Benedikt Frieg
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,John
von Neumann Institute for Computing (NIC), Jülich Supercomputing
Centre (JSC), Forschungszentrum Jülich
GmbH, 52425 Jülich, Germany
| | - Lothar Gremer
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Tatsiana Kupreichyk
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Luis Gardon
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Patrick Freiburg
- Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Philipp Neudecker
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Dieter Willbold
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,John
von Neumann Institute for Computing (NIC), Jülich Supercomputing
Centre (JSC), Forschungszentrum Jülich
GmbH, 52425 Jülich, Germany,Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany,
| | - Henrike Heise
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany,
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6
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Ibáñez de Opakua A, Geraets JA, Frieg B, Dienemann C, Savastano A, Rankovic M, Cima-Omori MS, Schröder GF, Zweckstetter M. Molecular interactions of FG nucleoporin repeats at high resolution. Nat Chem 2022; 14:1278-1285. [PMID: 36138110 PMCID: PMC9630130 DOI: 10.1038/s41557-022-01035-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/02/2022] [Indexed: 12/01/2022]
Abstract
Proteins that contain repeat phenylalanine-glycine (FG) residues phase separate into oncogenic transcription factor condensates in malignant leukaemias, form the permeability barrier of the nuclear pore complex and mislocalize in neurodegenerative diseases. Insights into the molecular interactions of FG-repeat nucleoporins have, however, remained largely elusive. Using a combination of NMR spectroscopy and cryoelectron microscopy, we have identified uniformly spaced segments of transient β-structure and a stable preformed α-helix recognized by messenger RNA export factors in the FG-repeat domain of human nucleoporin 98 (Nup98). In addition, we have determined at high resolution the molecular organization of reversible FG–FG interactions in amyloid fibrils formed by a highly aggregation-prone segment in Nup98. We have further demonstrated that amyloid-like aggregates of the FG-repeat domain of Nup98 have low stability and are reversible. Our results provide critical insights into the molecular interactions underlying the self-association and phase separation of FG-repeat nucleoporins in physiological and pathological cell activities. ![]()
Proteins rich in phenylalanine-glycine (FG) repeats can phase separate through FG–FG interactions. The molecular interactions of an important FG-repeat protein, nucleoporin 98, have now been studied in liquid-like transient and amyloid-like cohesive states. These interactions underlie the behaviour of FG-repeat proteins and their function in physiological and pathological cell activities.
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Affiliation(s)
| | - James A Geraets
- Institute of Biological Information Processing (Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Benedikt Frieg
- Institute of Biological Information Processing (Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Christian Dienemann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | | | - Marija Rankovic
- Max Planck Institute for Multidisciplinary Sciences, Department of NMR-based Structural Biology, Göttingen, Germany
| | | | - Gunnar F Schröder
- Institute of Biological Information Processing (Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany. .,Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases, Göttingen, Germany. .,Max Planck Institute for Multidisciplinary Sciences, Department of NMR-based Structural Biology, Göttingen, Germany.
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7
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Bhatia S, Spanier L, Bickel D, Dienstbier N, Woloschin V, Vogt M, Pols H, Lungerich B, Reiners J, Aghaallaei N, Diedrich D, Frieg B, Schliehe-Diecks J, Bopp B, Lang F, Gopalswamy M, Loschwitz J, Bajohgli B, Skokowa J, Borkhardt A, Hauer J, Hansen FK, Smits SHJ, Jose J, Gohlke H, Kurz T. Development of a First-in-Class Small-Molecule Inhibitor of the C-Terminal Hsp90 Dimerization. ACS Cent Sci 2022; 8:636-655. [PMID: 35647282 PMCID: PMC9136973 DOI: 10.1021/acscentsci.2c00013] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Indexed: 05/04/2023]
Abstract
Heat shock proteins 90 (Hsp90) are promising therapeutic targets due to their involvement in stabilizing several aberrantly expressed oncoproteins. In cancerous cells, Hsp90 expression is elevated, thereby exerting antiapoptotic effects, which is essential for the malignant transformation and tumor progression. Most of the Hsp90 inhibitors (Hsp90i) under investigation target the ATP binding site in the N-terminal domain of Hsp90. However, adverse effects, including induction of the prosurvival resistance mechanism (heat shock response or HSR) and associated dose-limiting toxicity, have so far precluded their clinical approval. In contrast, modulators that interfere with the C-terminal domain (CTD) of Hsp90 do not inflict HSR. Since the CTD dimerization of Hsp90 is essential for its chaperone activity, interfering with the dimerization process by small-molecule protein-protein interaction inhibitors is a promising strategy for anticancer drug research. We have developed a first-in-class small-molecule inhibitor (5b) targeting the Hsp90 CTD dimerization interface, based on a tripyrimidonamide scaffold through structure-based molecular design, chemical synthesis, binding mode model prediction, assessment of the biochemical affinity, and efficacy against therapy-resistant leukemia cells. 5b reduces xenotransplantation of leukemia cells in zebrafish models and induces apoptosis in BCR-ABL1+ (T315I) tyrosine kinase inhibitor-resistant leukemia cells, without inducing HSR.
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Affiliation(s)
- Sanil Bhatia
- Department
of Pediatric Oncology, Hematology and Clinical Immunology, Medical
Faculty, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- Phone: (+49) 211 81 04896.
| | - Lukas Spanier
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - David Bickel
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Niklas Dienstbier
- Department
of Pediatric Oncology, Hematology and Clinical Immunology, Medical
Faculty, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Vitalij Woloschin
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Melina Vogt
- Department
of Pediatric Oncology, Hematology and Clinical Immunology, Medical
Faculty, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Henrik Pols
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Beate Lungerich
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Jens Reiners
- Center
for Structural Studies, Heinrich Heine University
Düsseldorf, Düsseldorf 40225, Germany
| | - Narges Aghaallaei
- Department
of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen 72076, Germany
| | - Daniela Diedrich
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Benedikt Frieg
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- John
von Neumann Institute for Computing (NIC), Jülich Supercomputing
Centre (JSC), Institute of Biological Information Processing (IBI-7:
Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4:
Bioinformatics), Forschungszentrum Jülich
GmbH, Jülich 52425, Germany
| | - Julian Schliehe-Diecks
- Department
of Pediatric Oncology, Hematology and Clinical Immunology, Medical
Faculty, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Bertan Bopp
- Institute
for Pharmaceutical and Medicinal Chemistry, PharmaCampus, Westphalian Wilhelms University, Münster 48149, Germany
| | - Franziska Lang
- Department
of Pediatric Oncology, Hematology and Clinical Immunology, Medical
Faculty, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Mohanraj Gopalswamy
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Jennifer Loschwitz
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Baubak Bajohgli
- Department
of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen 72076, Germany
| | - Julia Skokowa
- Department
of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen 72076, Germany
| | - Arndt Borkhardt
- Department
of Pediatric Oncology, Hematology and Clinical Immunology, Medical
Faculty, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Julia Hauer
- Department
of Pediatrics, Pediatric Hematology and Oncology, University Hospital Carl Gustav Carus, Dresden 01307, Germany
- Partner
Site Dresden, National Center for Tumor
Diseases (NCT), Dresden 01307, Germany
| | - Finn K. Hansen
- Pharmaceutical
and Cell Biological Chemistry, Pharmaceutical
Institute University of Bonn, Bonn 53121, Germany
| | - Sander H. J. Smits
- Center
for Structural Studies, Heinrich Heine University
Düsseldorf, Düsseldorf 40225, Germany
- Institute
of Biochemistry, Heinrich Heine University
Düsseldorf, Düsseldorf 40225, Germany
| | - Joachim Jose
- Institute
for Pharmaceutical and Medicinal Chemistry, PharmaCampus, Westphalian Wilhelms University, Münster 48149, Germany
| | - Holger Gohlke
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- John
von Neumann Institute for Computing (NIC), Jülich Supercomputing
Centre (JSC), Institute of Biological Information Processing (IBI-7:
Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4:
Bioinformatics), Forschungszentrum Jülich
GmbH, Jülich 52425, Germany
- Phone: (+49)
211 81 13662.
| | - Thomas Kurz
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- Phone: (+49)
211 81 14984.
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8
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Kondapuram M, Frieg B, Yüksel S, Schwabe T, Sattler C, Lelle M, Schweinitz A, Schmauder R, Benndorf K, Gohlke H, Kusch J. Functional and structural characterization of interactions between opposite subunits in HCN pacemaker channels. Commun Biol 2022; 5:430. [PMID: 35534535 PMCID: PMC9085832 DOI: 10.1038/s42003-022-03360-6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
Hyperpolarization-activated and cyclic nucleotide (HCN) modulated channels are tetrameric cation channels. In each of the four subunits, the intracellular cyclic nucleotide-binding domain (CNBD) is coupled to the transmembrane domain via a helical structure, the C-linker. High-resolution channel structures suggest that the C-linker enables functionally relevant interactions with the opposite subunit, which might be critical for coupling the conformational changes in the CNBD to the channel pore. We combined mutagenesis, patch-clamp technique, confocal patch-clamp fluorometry, and molecular dynamics (MD) simulations to show that residue K464 of the C-linker is relevant for stabilizing the closed state of the mHCN2 channel by forming interactions with the opposite subunit. MD simulations revealed that in the K464E channel, a rotation of the intracellular domain relative to the channel pore is induced, which is similar to the cAMP-induced rotation, weakening the autoinhibitory effect of the unoccupied CL-CNBD region. We suggest that this CL-CNBD rotation is considerably involved in activation-induced affinity increase but only indirectly involved in gate modulation. The adopted poses shown herein are in excellent agreement with previous structural results. Interactions between opposite subunits of HCN channels are relevant for stabilizing the auto-inhibited state of the channel. Like cAMP-binding, K464E-mutation breaks these interactions to favor a channel’s pre-activated state.
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Affiliation(s)
- Mahesh Kondapuram
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Benedikt Frieg
- John von Neumann-Institut für Computing (NIC), Jülich Supercomputing Centre (JSC), and Institut für Biologische Informationsprozesse (IBI-7: Strukturbiochemie), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Sezin Yüksel
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Tina Schwabe
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Christian Sattler
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Marco Lelle
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Andrea Schweinitz
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Ralf Schmauder
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Klaus Benndorf
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Holger Gohlke
- John von Neumann-Institut für Computing (NIC), Jülich Supercomputing Centre (JSC), and Institut für Biologische Informationsprozesse (IBI-7: Strukturbiochemie), Forschungszentrum Jülich GmbH, Jülich, Germany. .,Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany. .,Institut für Bio- und Geowissenschaften (IBG-4: Bioinformatik), Forschungszentrum Jülich GmbH, Jülich, Germany.
| | - Jana Kusch
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany.
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9
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Cukkemane A, Becker N, Zielinski M, Frieg B, Lakomek NA, Heise H, Schröder GF, Willbold D, Weiergräber OH. Conformational heterogeneity coupled with β-fibril formation of a scaffold protein involved in chronic mental illnesses. Transl Psychiatry 2021; 11:639. [PMID: 34921141 PMCID: PMC8683410 DOI: 10.1038/s41398-021-01765-1] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/23/2021] [Accepted: 12/07/2021] [Indexed: 12/17/2022] Open
Abstract
Chronic mental illnesses (CMIs) pose a significant challenge to global health due to their complex and poorly understood etiologies and hence, absence of causal therapies. Research of the past two decades has revealed dysfunction of the disrupted in schizophrenia 1 (DISC1) protein as a predisposing factor involved in several psychiatric disorders. DISC1 is a multifaceted protein that serves myriads of functions in mammalian cells, for instance, influencing neuronal development and synapse maintenance. It serves as a scaffold hub forming complexes with a variety (~300) of partners that constitute its interactome. Herein, using combinations of structural and biophysical tools, we demonstrate that the C-region of the DISC1 protein is highly polymorphic, with important consequences for its physiological role. Results from solid-state NMR spectroscopy and electron microscopy indicate that the protein not only forms symmetric oligomers but also gives rise to fibrils closely resembling those found in certain established amyloid proteinopathies. Furthermore, its aggregation as studied by isothermal titration calorimetry (ITC) is an exergonic process, involving a negative enthalpy change that drives the formation of oligomeric (presumably tetrameric) species as well as β-fibrils. We have been able to narrow down the β-core region participating in fibrillization to residues 716-761 of full-length human DISC1. This region is absent in the DISC1Δ22aa splice variant, resulting in reduced association with proteins from the dynein motor complex, viz., NDE-like 1 (NDEL1) and lissencephaly 1 (LIS1), which are crucial during mitosis. By employing surface plasmon resonance, we show that the oligomeric DISC1 C-region has an increased affinity and shows cooperativity in binding to LIS1 and NDEL1, in contrast to the noncooperative binding mode exhibited by the monomeric version. Based on the derived structural models, we propose that the association between the binding partners involves two neighboring subunits of DISC1 C-region oligomers. Altogether, our findings highlight the significance of the DISC1 C-region as a crucial factor governing the balance between its physiological role as a multifunctional scaffold protein and aggregation-related aberrations with potential significance for disease.
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Affiliation(s)
- Abhishek Cukkemane
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany. .,Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Nina Becker
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XJülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Mara Zielinski
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Benedikt Frieg
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Nils-Alexander Lakomek
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XJülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Henrike Heise
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XJülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Gunnar F. Schröder
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.8385.60000 0001 2297 375XJülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany ,grid.411327.20000 0001 2176 9917Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany. .,Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany. .,Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany.
| | - Oliver H. Weiergräber
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.8385.60000 0001 2297 375XJülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
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10
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El Harrar T, Frieg B, Davari MD, Jaeger KE, Schwaneberg U, Gohlke H. Aqueous ionic liquids redistribute local enzyme stability via long-range perturbation pathways. Comput Struct Biotechnol J 2021; 19:4248-4264. [PMID: 34429845 PMCID: PMC8355836 DOI: 10.1016/j.csbj.2021.07.001] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 01/25/2023] Open
Abstract
Ionic liquids (IL) and aqueous ionic liquids (aIL) are attractive (co-)solvents for biocatalysis due to their unique properties. On the other hand, the incubation of enzymes in IL or aIL often reduces enzyme activity. Recent studies proposed various aIL-induced effects to explain the reduction, classified as direct effects, e.g., local dehydration or competitive inhibition, and indirect effects, e.g., structural perturbations or disturbed catalytic site integrity. However, the molecular origin of indirect effects has largely remained elusive. Here we show by multi-μs long molecular dynamics simulations, free energy computations, and rigidity analyses that aIL favorably interact with specific residues of Bacillus subtilis Lipase A (BsLipA) and modify the local structural stability of this model enzyme by inducing long-range perturbations of noncovalent interactions. The perturbations percolate over neighboring residues and eventually affect the catalytic site and the buried protein core. Validation against a complete experimental site saturation mutagenesis library of BsLipA (3620 variants) reveals that the residues of the perturbation pathways are distinguished sequence positions where substitutions highly likely yield significantly improved residual activity. Our results demonstrate that identifying these perturbation pathways and specific IL ion-residue interactions there effectively predicts focused variant libraries with improved aIL tolerance.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Benedikt Frieg
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52428 Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- DWI – Leibniz Institute for Interactive Materials e.V., 52074 Aachen, Germany
| | - Holger Gohlke
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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11
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Frieg B, Görg B, Gohlke H, Häussinger D. Glutamine synthetase as a central element in hepatic glutamine and ammonia metabolism: novel aspects. Biol Chem 2021; 402:1063-1072. [PMID: 33962502 DOI: 10.1515/hsz-2021-0166] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/22/2021] [Indexed: 12/27/2022]
Abstract
Glutamine synthetase (GS) in the liver is expressed in a small perivenous, highly specialized hepatocyte population and is essential for the maintenance of low, non-toxic ammonia levels in the organism. However, GS activity can be impaired by tyrosine nitration of the enzyme in response to oxidative/nitrosative stress in a pH-sensitive way. The underlying molecular mechanism as investigated by combined molecular simulations and in vitro experiments indicates that tyrosine nitration can lead to a fully reversible and pH-sensitive regulation of protein function. This approach was also used to understand the functional consequences of several recently described point mutations of human GS with clinical relevance and to suggest an approach to restore impaired GS activity.
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Affiliation(s)
- Benedikt Frieg
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Boris Görg
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
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12
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Frieg B, Görg B, Qvartskhava N, Jeitner T, Homeyer N, Häussinger D, Gohlke H. Mechanism of Fully Reversible, pH-Sensitive Inhibition of Human Glutamine Synthetase by Tyrosine Nitration. J Chem Theory Comput 2020; 16:4694-4705. [PMID: 32551588 DOI: 10.1021/acs.jctc.0c00249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Glutamine synthetase (GS) catalyzes an ATP-dependent condensation of glutamate and ammonia to form glutamine. This reaction-and therefore GS-are indispensable for the hepatic nitrogen metabolism. Nitration of tyrosine 336 (Y336) inhibits human GS activity. GS nitration and the consequent loss of GS function are associated with a broad range of neurological diseases. The mechanism by which Y336 nitration inhibits GS, however, is not understood. Here, we show by means of unbiased MD simulations, binding, and configurational free energy computations that Y336 nitration hampers ATP binding but only in the deprotonated and negatively charged state of residue 336. By contrast, for the protonated and neutral state, our computations indicate an increased binding affinity for ATP. pKa computations of nitrated Y336 within GS predict a pKa of ∼5.3. Thus, at physiological pH, nitrated Y336 exists almost exclusively in the deprotonated and negatively charged state. In vitro experiments confirm these predictions, in that, the catalytic activity of nitrated GS is decreased at pH 7 and 6 but not at pH 4. These results indicate a novel, fully reversible, pH-sensitive mechanism for the regulation of GS activity by tyrosine nitration.
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Affiliation(s)
- Benedikt Frieg
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Boris Görg
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Natalia Qvartskhava
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Thomas Jeitner
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, United States
| | - Nadine Homeyer
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
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13
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Frieg B, Gremer L, Heise H, Willbold D, Gohlke H. Binding modes of thioflavin T and Congo red to the fibril structure of amyloid-β(1-42). Chem Commun (Camb) 2020; 56:7589-7592. [PMID: 32510059 DOI: 10.1039/d0cc01161d] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Binding modes for the amyloid-β(1-42) fibril fluorescent dyes thioflavin T and Congo red were predicted by molecular dynamics simulations and binding free energy calculations. Both probes bind on the fibril surface to primarily hydrophobic grooves, with their long axis oriented almost parallel to the fibril axis. The computed binding affinities are in agreement with experimental values. The binding modes also explain observables from previous structural studies and, thus, provide a starting point for the systematic search and design of novel molecules, which may improve in vitro diagnostics for Alzheimer's disease.
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Affiliation(s)
- Benedikt Frieg
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, Jülich, Germany
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14
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Kater L, Frieg B, Berninghausen O, Gohlke H, Beckmann R, Kedrov A. Partially inserted nascent chain unzips the lateral gate of the Sec translocon. EMBO Rep 2019; 20:e48191. [PMID: 31379073 PMCID: PMC6776908 DOI: 10.15252/embr.201948191] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/10/2019] [Accepted: 07/16/2019] [Indexed: 12/25/2022] Open
Abstract
The Sec translocon provides the lipid bilayer entry for ribosome-bound nascent chains and thus facilitates membrane protein biogenesis. Despite the appreciated role of the native environment in the translocon:ribosome assembly, structural information on the complex in the lipid membrane is scarce. Here, we present a cryo-electron microscopy-based structure of bacterial translocon SecYEG in lipid nanodiscs and elucidate an early intermediate state upon insertion of the FtsQ anchor domain. Insertion of the short nascent chain causes initial displacements within the lateral gate of the translocon, where α-helices 2b, 7, and 8 tilt within the membrane core to "unzip" the gate at the cytoplasmic side. Molecular dynamics simulations demonstrate that the conformational change is reversed in the absence of the ribosome, and suggest that the accessory α-helices of SecE subunit modulate the lateral gate conformation. Site-specific cross-linking validates that the FtsQ nascent chain passes the lateral gate upon insertion. The structure and the biochemical data suggest that the partially inserted nascent chain remains highly flexible until it acquires the transmembrane topology.
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Affiliation(s)
- Lukas Kater
- Gene Center Munich, Ludwig-Maximilian-University, Munich, Germany
| | - Benedikt Frieg
- John von Neumann Institute for Computing, Jülich Supercomputing Centre, Institute for Complex Systems - Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Jülich, Germany
| | | | - Holger Gohlke
- John von Neumann Institute for Computing, Jülich Supercomputing Centre, Institute for Complex Systems - Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Roland Beckmann
- Gene Center Munich, Ludwig-Maximilian-University, Munich, Germany
| | - Alexej Kedrov
- Gene Center Munich, Ludwig-Maximilian-University, Munich, Germany.,Synthetic Membrane Systems, Institute for Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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15
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Kondapuram M, Yüksel S, Schwabe T, Frieg B, Gohlke H, Schmauder R, Benndorf K, Kusch J. Opposing Subunits Interact to Stabilize the Closed State in HCN2 Channels. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.617] [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: 11/29/2022] Open
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16
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Bhatia S, Diedrich D, Frieg B, Ahlert H, Stein S, Bopp B, Lang F, Zang T, Kröger T, Ernst T, Kögler G, Krieg A, Lüdeke S, Kunkel H, Rodrigues Moita AJ, Kassack MU, Marquardt V, Opitz FV, Oldenburg M, Remke M, Babor F, Grez M, Hochhaus A, Borkhardt A, Groth G, Nagel-Steger L, Jose J, Kurz T, Gohlke H, Hansen FK, Hauer J. Targeting HSP90 dimerization via the C terminus is effective in imatinib-resistant CML and lacks the heat shock response. Blood 2018; 132:307-320. [PMID: 29724897 PMCID: PMC6225350 DOI: 10.1182/blood-2017-10-810986] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [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: 10/12/2017] [Accepted: 04/19/2018] [Indexed: 12/12/2022] Open
Abstract
Heat shock protein 90 (HSP90) stabilizes many client proteins, including the BCR-ABL1 oncoprotein. BCR-ABL1 is the hallmark of chronic myeloid leukemia (CML) in which treatment-free remission (TFR) is limited, with clinical and economic consequences. Thus, there is an urgent need for novel therapeutics that synergize with current treatment approaches. Several inhibitors targeting the N-terminal domain of HSP90 are under investigation, but side effects such as induction of the heat shock response (HSR) and toxicity have so far precluded their US Food and Drug Administration approval. We have developed a novel inhibitor (aminoxyrone [AX]) of HSP90 function by targeting HSP90 dimerization via the C-terminal domain. This was achieved by structure-based molecular design, chemical synthesis, and functional preclinical in vitro and in vivo validation using CML cell lines and patient-derived CML cells. AX is a promising potential candidate that induces apoptosis in the leukemic stem cell fraction (CD34+CD38-) as well as the leukemic bulk (CD34+CD38+) of primary CML and in tyrosine kinase inhibitor (TKI)-resistant cells. Furthermore, BCR-ABL1 oncoprotein and related pro-oncogenic cellular responses are downregulated, and targeting the HSP90 C terminus by AX does not induce the HSR in vitro and in vivo. We also probed the potential of AX in other therapy-refractory leukemias. Therefore, AX is the first peptidomimetic C-terminal HSP90 inhibitor with the potential to increase TFR in TKI-sensitive and refractory CML patients and also offers a novel therapeutic option for patients with other types of therapy-refractory leukemia because of its low toxicity profile and lack of HSR.
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MESH Headings
- Animals
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Binding Sites
- Biomarkers, Tumor
- Cell Cycle/drug effects
- Cell Line, Tumor
- Cell Survival/drug effects
- Disease Models, Animal
- Drug Resistance, Neoplasm/drug effects
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/chemistry
- HSP90 Heat-Shock Proteins/antagonists & inhibitors
- HSP90 Heat-Shock Proteins/chemistry
- HSP90 Heat-Shock Proteins/metabolism
- Heat-Shock Response/drug effects
- Humans
- Imatinib Mesylate/chemistry
- Imatinib Mesylate/pharmacology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Mice
- Models, Molecular
- Molecular Conformation
- Molecular Structure
- Protein Binding
- Protein Interaction Domains and Motifs
- Protein Kinase Inhibitors/chemistry
- Protein Kinase Inhibitors/pharmacology
- Protein Multimerization/drug effects
- Spectrum Analysis
- Structure-Activity Relationship
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
| | - Daniela Diedrich
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Benedikt Frieg
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing, Jülich Supercomputing Centre, Institute for Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Heinz Ahlert
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
| | - Stefan Stein
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Germany
| | - Bertan Bopp
- Institute for Pharmaceutical and Medicinal Chemistry, PharmaCampus, Westphalian Wilhelms University, Münster, Germany
| | - Franziska Lang
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
| | - Tao Zang
- Institute for Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Tobias Kröger
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Thomas Ernst
- Hematology/Oncology, Internal Medicine II, Jena University Hospital, Jena, Germany
| | - Gesine Kögler
- Institute for Transplantation Diagnostics and Cell Therapeutics and
| | - Andreas Krieg
- Department of Surgery (A), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Steffen Lüdeke
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany
| | - Hana Kunkel
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Germany
| | - Ana J Rodrigues Moita
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Matthias U Kassack
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Viktoria Marquardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Division of Pediatric Neuro-Oncogenomics, German Cancer Consortium, partner site University Hospital Düsseldorf, Düsseldorf, Germany
| | - Friederike V Opitz
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
| | - Marina Oldenburg
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
| | - Marc Remke
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Division of Pediatric Neuro-Oncogenomics, German Cancer Consortium, partner site University Hospital Düsseldorf, Düsseldorf, Germany
| | - Florian Babor
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
| | - Manuel Grez
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Germany
| | - Andreas Hochhaus
- Hematology/Oncology, Internal Medicine II, Jena University Hospital, Jena, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
| | - Georg Groth
- Institute for Biochemical Plant Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; and
| | - Luitgard Nagel-Steger
- Institute for Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Joachim Jose
- Institute for Pharmaceutical and Medicinal Chemistry, PharmaCampus, Westphalian Wilhelms University, Münster, Germany
| | - Thomas Kurz
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing, Jülich Supercomputing Centre, Institute for Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Finn K Hansen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Leipzig University, Leipzig, Germany
| | - Julia Hauer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
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17
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Kroeger T, Frieg B, Zhang T, Hansen FK, Marmann A, Proksch P, Nagel-Steger L, Groth G, Smits SHJ, Gohlke H. EDTA aggregates induce SYPRO orange-based fluorescence in thermal shift assay. PLoS One 2017; 12:e0177024. [PMID: 28472107 PMCID: PMC5417642 DOI: 10.1371/journal.pone.0177024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 01/19/2017] [Accepted: 03/29/2017] [Indexed: 12/16/2022] Open
Abstract
Ethylenediaminetetraacetic acid (EDTA) is widely used in the life sciences as chelating ligand of metal ions. However, formation of supramolecular EDTA aggregates at pH > 8 has been reported, which may lead to artifactual assay results. When applied as a buffer component at pH ≈ 10 in differential scanning fluorimetry (TSA) using SYPRO Orange as fluorescent dye, we observed a sharp change in fluorescence intensity about 20°C lower than expected for the investigated protein. We hypothesized that this change results from SYPRO Orange/EDTA interactions. TSA experiments in the presence of SYPRO Orange using solutions that contain EDTA-Na+ but no protein were performed. The TSA experiments provide evidence that suggests that at pH > 9, EDTA4- interacts with SYPRO Orange in a temperature-dependent manner, leading to a fluorescence signal yielding a "denaturation temperature" of ~68°C. Titrating Ca2+ to SYPRO Orange and EDTA solutions quenched fluorescence. Ethylene glycol tetraacetic acid (EGTA) behaved similarly to EDTA. Analytical ultracentrifugation corroborated the formation of EDTA aggregates. Molecular dynamics simulations of free diffusion of EDTA-Na+ and SYPRO Orange of in total 27 μs suggested the first structural model of EDTA aggregates in which U-shaped EDTA4- arrange in an inverse bilayer-like manner, exposing ethylene moieties to the solvent, with which SYPRO Orange interacts. We conclude that EDTA aggregates induce a SYPRO Orange-based fluorescence in TSA. These results make it relevant to ascertain that future TSA results are not influenced by interference between EDTA, or EDTA-related molecules, and the fluorescent dye.
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Affiliation(s)
- Tobias Kroeger
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Benedikt Frieg
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tao Zhang
- Institute for Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, Jülich, Germany
| | - Finn K. Hansen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andreas Marmann
- Institute for Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Peter Proksch
- Institute for Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Luitgard Nagel-Steger
- Institute for Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, Jülich, Germany
| | - Georg Groth
- Institute for Biochemical Plant Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sander H. J. Smits
- Institute for Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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18
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Krieger V, Ciglia E, Thoma R, Vasylyeva V, Frieg B, de Sousa Amadeu N, Kurz T, Janiak C, Gohlke H, Hansen FK. α-Aminoxy Peptoids: A Unique Peptoid Backbone with a Preference for cis-Amide Bonds. Chemistry 2017; 23:3699-3707. [PMID: 28090689 DOI: 10.1002/chem.201605100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Indexed: 12/13/2022]
Abstract
α-Peptoids, or N-substituted glycine oligomers, are an important class of peptidomimetic foldamers with proteolytic stability. Nevertheless, the presence of cis/trans-amide bond conformers, which contribute to the high flexibility of α-peptoids, is considered as a major drawback. A modified peptoid backbone with an improved control of the amide bond geometry could therefore help to overcome this limitation. Herein, we have performed the first thorough analysis of the folding propensities of α-aminoxy peptoids (or N-substituted 2-aminoxyacetic acid oligomers). To this end, the amide bond geometry and the conformational properties of a series of model α-aminoxy peptoids were investigated by using 1D and 2D NMR experiments, X-ray crystallography, natural bond orbital (NBO) analysis, circular dichroism (CD) spectroscopy, and molecular dynamics (MD) simulations revealing a unique preference for cis-amide bonds even in the absence of cis-directing side chains. The conformational analysis based on the MD simulations revealed that α-aminoxy peptoids can adopt helical conformations that can mimic the spatial arrangement of peptide side chains in a canonical α-helix. Given their ease of synthesis and conformational properties, α-aminoxy peptoids represent a new member of the peptoid family capable of controlling the amide isomerism while maintaining the potential for side-chain diversity.
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Affiliation(s)
- Viktoria Krieger
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Emanuele Ciglia
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Roland Thoma
- Institute of Inorganic and Structural Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Vera Vasylyeva
- Institute of Inorganic and Structural Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Benedikt Frieg
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Nader de Sousa Amadeu
- Institute of Inorganic and Structural Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Thomas Kurz
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Christoph Janiak
- Institute of Inorganic and Structural Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Finn K Hansen
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany.,Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Leipzig University, Brüderstrasse 34, 04103, Leipzig, Germany
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19
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Diedrich D, Moita AJR, Rüther A, Frieg B, Reiss GJ, Hoeppner A, Kurz T, Gohlke H, Lüdeke S, Kassack MU, Hansen FK. Frontispiece: α-Aminoxy Oligopeptides: Synthesis, Secondary Structure, and Cytotoxicity of a New Class of Anticancer Foldamers. Chemistry 2016. [DOI: 10.1002/chem.201684962] [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: 11/10/2022]
Affiliation(s)
- Daniela Diedrich
- Institut für Pharmazeutische und Medizinische Chemie; Heinrich-Heine-Universität Düsseldorf; 40225 Düsseldorf Germany
| | - Ana J. Rodrigues Moita
- Institut für Pharmazeutische und Medizinische Chemie; Heinrich-Heine-Universität Düsseldorf; 40225 Düsseldorf Germany
| | - Anja Rüther
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; 79104 Freiburg Germany
| | - Benedikt Frieg
- Institut für Pharmazeutische und Medizinische Chemie; Heinrich-Heine-Universität Düsseldorf; 40225 Düsseldorf Germany
| | - Guido J. Reiss
- Institut für Anorganische Chemie und Strukturchemie; Heinrich-Heine-Universität Düsseldorf; 40225 Düsseldorf Germany
| | - Astrid Hoeppner
- X-Ray Facility and Crystal Farm; Heinrich-Heine-Universität Düsseldorf; 40225 Düsseldorf Germany
| | - Thomas Kurz
- Institut für Pharmazeutische und Medizinische Chemie; Heinrich-Heine-Universität Düsseldorf; 40225 Düsseldorf Germany
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie; Heinrich-Heine-Universität Düsseldorf; 40225 Düsseldorf Germany
| | - Steffen Lüdeke
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; 79104 Freiburg Germany
| | - Matthias U. Kassack
- Institut für Pharmazeutische und Medizinische Chemie; Heinrich-Heine-Universität Düsseldorf; 40225 Düsseldorf Germany
| | - Finn K. Hansen
- Institut für Pharmazeutische und Medizinische Chemie; Heinrich-Heine-Universität Düsseldorf; 40225 Düsseldorf Germany
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20
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Diedrich D, Moita AJR, Rüther A, Frieg B, Reiss GJ, Hoeppner A, Kurz T, Gohlke H, Lüdeke S, Kassack MU, Hansen FK. α-Aminoxy Oligopeptides: Synthesis, Secondary Structure, and Cytotoxicity of a New Class of Anticancer Foldamers. Chemistry 2016; 22:17600-17611. [PMID: 27573537 DOI: 10.1002/chem.201602521] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Indexed: 11/11/2022]
Abstract
α-Aminoxy peptides are peptidomimetic foldamers with high proteolytic and conformational stability. To gain an improved synthetic access to α-aminoxy oligopeptides we used a straightforward combination of solution- and solid-phase-supported methods and obtained oligomers that showed a remarkable anticancer activity against a panel of cancer cell lines. We solved the first X-ray crystal structure of an α-aminoxy peptide with multiple turns around the helical axis. The crystal structure revealed a right-handed 28 -helical conformation with precisely two residues per turn and a helical pitch of 5.8 Å. By 2D ROESY experiments, molecular dynamics simulations, and CD spectroscopy we were able to identify the 28 -helix as the predominant conformation in organic solvents. In aqueous solution, the α-aminoxy peptides exist in the 28 -helical conformation at acidic pH, but exhibit remarkable changes in the secondary structure with increasing pH. The most cytotoxic α-aminoxy peptides have an increased propensity to take up a 28 -helical conformation in the presence of a model membrane. This indicates a correlation between the 28 -helical conformation and the membranolytic activity observed in mode of action studies, thereby providing novel insights in the folding properties and the biological activity of α-aminoxy peptides.
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Affiliation(s)
- Daniela Diedrich
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Ana J Rodrigues Moita
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Anja Rüther
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Benedikt Frieg
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Guido J Reiss
- Institut für Anorganische Chemie und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Astrid Hoeppner
- X-Ray Facility and Crystal Farm, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Thomas Kurz
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Steffen Lüdeke
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Matthias U Kassack
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Finn K Hansen
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
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21
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Frieg B, Görg B, Homeyer N, Keitel V, Häussinger D, Gohlke H. Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies. PLoS Comput Biol 2016; 12:e1004693. [PMID: 26836257 PMCID: PMC4737493 DOI: 10.1371/journal.pcbi.1004693] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 12/03/2015] [Indexed: 12/15/2022] Open
Abstract
Glutamine synthetase (GS) catalyzes ATP-dependent ligation of ammonia and glutamate to glutamine. Two mutations of human GS (R324C and R341C) were connected to congenital glutamine deficiency with severe brain malformations resulting in neonatal death. Another GS mutation (R324S) was identified in a neurologically compromised patient. However, the molecular mechanisms underlying the impairment of GS activity by these mutations have remained elusive. Molecular dynamics simulations, free energy calculations, and rigidity analyses suggest that all three mutations influence the first step of GS catalytic cycle. The R324S and R324C mutations deteriorate GS catalytic activity due to loss of direct interactions with ATP. As to R324S, indirect, water-mediated interactions reduce this effect, which may explain the suggested higher GS residual activity. The R341C mutation weakens ATP binding by destabilizing the interacting residue R340 in the apo state of GS. Additionally, the mutation is predicted to result in a significant destabilization of helix H8, which should negatively affect glutamate binding. This prediction was tested in HEK293 cells overexpressing GS by dot-blot analysis: Structural stability of H8 was impaired through mutation of amino acids interacting with R341, as indicated by a loss of masking of an epitope in the glutamate binding pocket for a monoclonal anti-GS antibody by L-methionine-S-sulfoximine; in contrast, cells transfected with wild type GS showed the masking. Our analyses reveal complex molecular effects underlying impaired GS catalytic activity in three clinically relevant mutants. Our findings could stimulate the development of ATP binding-enhancing molecules by which the R324S mutant can be repaired extrinsically. Glutamine synthetase (GS) catalyzes the ATP-dependent ligation of ammonia and glutamate to glutamine, which makes the enzyme essential for human nitrogen metabolism. Three mutations in human GS, R324C, R324S, and R341C, had been identified previously that lead to a glutamine deficiency, resulting in neonatal death in the case of R324C and R341C. However, the molecular mechanisms underlying this impairment of GS activity have remained elusive. Our results from computational biophysics approaches suggest that all three mutants influence the first step of GS’ catalytic cycle, namely ATP or glutamate binding. The analyses reveal a complex set of effects including the loss of direct interactions to substrates, the involvement of water-mediated interactions that alleviate part of the mutation effect, and long-range effects between the catalytic site and structural parts distant from it. As to the latter, experimental validation is in line with our prediction of a significant destabilization of helix H8 in the R341C mutant, which should negatively affect glutamate binding. Finally, our findings could stimulate the development of ATP-binding enhancing molecules for the R324S mutant, which has been suggested to have residual activity, that way extrinsically “repairing” the mutant.
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Affiliation(s)
- Benedikt Frieg
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Düsseldorf, Germany
| | - Boris Görg
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich-Heine-University, Düsseldorf, Germany
| | - Nadine Homeyer
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Düsseldorf, Germany
| | - Verena Keitel
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich-Heine-University, Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology, and Infectious Diseases, Heinrich-Heine-University, Düsseldorf, Germany
- * E-mail: (DH); (HG)
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University, Düsseldorf, Germany
- * E-mail: (DH); (HG)
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22
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Khosa S, Frieg B, Mulnaes D, Kleinschrodt D, Hoeppner A, Gohlke H, Smits SHJ. Structural basis of lantibiotic recognition by the nisin resistance protein from Streptococcus agalactiae. Sci Rep 2016; 6:18679. [PMID: 26727488 PMCID: PMC4698656 DOI: 10.1038/srep18679] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 08/18/2015] [Accepted: 11/23/2015] [Indexed: 11/09/2022] Open
Abstract
Lantibiotics are potent antimicrobial peptides. Nisin is the most prominent member and contains five crucial lanthionine rings. Some clinically relevant bacteria express membrane-associated resistance proteins that proteolytically inactivate nisin. However, substrate recognition and specificity of these proteins is unknown. Here, we report the first three-dimensional structure of a nisin resistance protein from Streptococcus agalactiae (SaNSR) at 2.2 Å resolution. It contains an N-terminal helical bundle, and protease cap and core domains. The latter harbors the highly conserved TASSAEM region, which lies in a hydrophobic tunnel formed by all domains. By integrative modeling, mutagenesis studies, and genetic engineering of nisin variants, a model of the SaNSR/nisin complex is generated, revealing that SaNSR recognizes the last C-terminally located lanthionine ring of nisin. This determines the substrate specificity of SaNSR and ensures the exact coordination of the nisin cleavage site at the TASSAEM region.
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Affiliation(s)
- Sakshi Khosa
- Institute of Biochemistry, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Benedikt Frieg
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Daniel Mulnaes
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Diana Kleinschrodt
- Protein Production Facility, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Astrid Hoeppner
- Crystal and X-ray Facility, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
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23
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Frieg B, Homeyer N, Häussinger D, Gohlke H. Glutamine synthetase mutations that cause glutamine deficiency: mechanistic insights from molecular dynamics simulations. Eur J Med Res 2014. [PMCID: PMC4118431 DOI: 10.1186/2047-783x-19-s1-s15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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24
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Ota K, Möri A, Alexander WR, Frieg B, Schild M. Influence of the mode of matrix porosity determination on matrix diffusion calculations. J Contam Hydrol 2003; 61:131-145. [PMID: 12598100 DOI: 10.1016/s0169-7722(02)00139-0] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The theoretical basis for matrix diffusion in fractured rocks and the methodology for the determination of diffusion coefficients in the laboratory are well established. One significant problem, however, remains in that it is difficult to quantify the degree of sample disturbance affecting the geometrical, geophysical and hydraulic properties of the rock matrix. A new technique, with in situ rock impregnation with resin, for examining the diffusion-accessible rock matrix has been developed and successfully adopted to the rock matrix behind a water-conducting fracture in host crystalline rocks at Nagra's Grimsel Test Site in Switzerland and JNC's Kamaishi In Situ Test Site in Japan. In line with the results of a large number of natural analogue and laboratory studies, the existence of an in situ interconnected pore network was substantiated. Matrix porosities determined on the laboratory samples from both the sites are 1.5-3 times higher than in situ values, irrespective of the technique applied. On the Grimsel granodiorite matrix, matrix porosity existing in situ and artefacts of stress release and physical disturbance, induced by sampling and sample preparation, were clearly distinguished, allowing in situ porosity to be quantified. Laboratory work with conventional techniques tends to overestimate the porosity of the rock matrix, hence leading to an overestimation of in situ matrix diffusion. The implications of these differences to a repository performance assessment are assessed with a couple of examples from existing assessments, and recommendations for future approaches to the examination of in situ matrix porosity are made.
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Affiliation(s)
- K Ota
- JNC (Japan Nuclear Cycle Development Institute), Tono Geoscience Centre, 959-31 Jorinji, Toki, Gifu 509-5102, Japan.
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25
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Smith PA, Alexander WR, Kickmaier W, Ota K, Frieg B, McKinley IG. Development and testing of radionuclide transport models for fractured rock: examples from the Nagra/JNC Radionuclide Migration Programme in the Grimsel Test Site, Switzerland. J Contam Hydrol 2001; 47:335-348. [PMID: 11288587 DOI: 10.1016/s0169-7722(00)00161-3] [Citation(s) in RCA: 9] [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] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The joint Swiss National Co-operative for the Disposal of Radioactive Waste (Nagra)/Japan Nuclear Cycle Development Institute (JNC) Radionuclide Migration Programme has now been on-going for over a decade in Nagra's Grimsel Test Site (GTS). The main aim of the programme has been the direct testing of radionuclide transport models in as realistic manner as possible. Although it will never be possible to fully test these models due to the large time and distance scales involved, tests of the model assumptions in scaled down but otherwise realistic conditions will contribute to developing confidence in the predictive power of the models. In this paper, the Nagra/JNC approach is highlighted with examples from a large programme of field, laboratory and natural analogue studies based around the GTS. The successes and failures are discussed as in the general approach to the thorough testing of predictive transport codes which will be used in repository performance assessment (PA). Some of the work is still on-going and this represents the first presentation of a unique set of results and conclusions.
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Affiliation(s)
- P A Smith
- Safety Assessment Management Ltd., UK.
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