1
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Abdelsalam M, Zmyslia M, Schmidtkunz K, Vecchio A, Hilscher S, Ibrahim HS, Schutkowski M, Jung M, Jessen-Trefzer C, Sippl W. Design and synthesis of bioreductive prodrugs of class I histone deacetylase inhibitors and their biological evaluation in virally transfected acute myeloid leukemia cells. Arch Pharm (Weinheim) 2024; 357:e2300536. [PMID: 37932028 DOI: 10.1002/ardp.202300536] [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: 09/25/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023]
Abstract
Although histone deacetylase (HDAC) inhibitors show promise in treating various types of hematologic malignancies, they have some limitations, including poor pharmacokinetics and off-target side effects. Prodrug design has shown promise as an approach to improve pharmacokinetic properties and to improve target tissue specificity. In this work, several bioreductive prodrugs for class I HDACs were designed based on known selective HDAC inhibitors. The zinc-binding group of the HDAC inhibitors was masked with various nitroarylmethyl residues to make them substrates of nitroreductase (NTR). The developed prodrugs showed weak HDAC inhibitory activity compared to their parent inhibitors. The prodrugs were tested against wild-type and NTR-transfected THP1 cells. Cellular assays showed that both 2-nitroimidazole-based prodrugs 5 and 6 were best activated by the NTR and exhibited potent activity against NTR-THP1 cells. Compound 6 showed the highest cellular activity (GI50 = 77 nM) and exhibited moderate selectivity. Moreover, activation of prodrug 6 by NTR was confirmed by liquid chromatography-mass spectrometry analysis, which showed the release of the parent inhibitor after incubation with Escherichia coli NTR. Thus, compound 6 can be considered a novel prodrug selective for class I HDACs, which could be used as a good starting point for increasing selectivity and for further optimization.
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Affiliation(s)
- Mohamed Abdelsalam
- Department of Medicinal Chemistry, Martin-Luther University of Halle-Wittenberg, Halle/Saale, Germany
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Mariia Zmyslia
- Institute of Organic Chemistry, University of Freiburg, Freiburg i. Br., Germany
| | - Karin Schmidtkunz
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg i. Br., Germany
| | - Anita Vecchio
- Department of Medicinal Chemistry, Martin-Luther University of Halle-Wittenberg, Halle/Saale, Germany
| | - Sebastian Hilscher
- Department of Enzymology, Institute of Biochemistry, Martin-Luther-University of Halle-Wittenberg, Halle/Saale, Germany
| | - Hany S Ibrahim
- Department of Medicinal Chemistry, Martin-Luther University of Halle-Wittenberg, Halle/Saale, Germany
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Cairo, Egypt
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry, Martin-Luther-University of Halle-Wittenberg, Halle/Saale, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg i. Br., Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg i. Br., Germany
| | | | - Wolfgang Sippl
- Department of Medicinal Chemistry, Martin-Luther University of Halle-Wittenberg, Halle/Saale, Germany
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2
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Zmyslia M, Fröhlich K, Dao T, Schmidt A, Jessen-Trefzer C. Deep Proteomic Investigation of Metabolic Adaptation in Mycobacteria under Different Growth Conditions. Proteomes 2023; 11:39. [PMID: 38133153 PMCID: PMC10747050 DOI: 10.3390/proteomes11040039] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/22/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
Understanding the complex mechanisms of mycobacterial pathophysiology and adaptive responses presents challenges that can hinder drug development. However, employing physiologically relevant conditions, such as those found in human macrophages or simulating physiological growth conditions, holds promise for more effective drug screening. A valuable tool in this pursuit is proteomics, which allows for a comprehensive analysis of adaptive responses. In our study, we focused on Mycobacterium smegmatis, a model organism closely related to the pathogenic Mycobacterium tuberculosis, to investigate the impact of various carbon sources on mycobacterial growth. To facilitate this research, we developed a cost-effective, straightforward, and high-quality pipeline for proteome analysis and compared six different carbon source conditions. Additionally, we have created an online tool to present and analyze our data, making it easily accessible to the community. This user-friendly platform allows researchers and interested parties to explore and interpret the results effectively. Our findings shed light on mycobacterial adaptive physiology and present potential targets for drug development, contributing to the fight against tuberculosis.
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Affiliation(s)
- Mariia Zmyslia
- Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany; (M.Z.); (T.D.)
| | - Klemens Fröhlich
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland; (K.F.); (A.S.)
| | - Trinh Dao
- Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany; (M.Z.); (T.D.)
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19A, 79104 Freiburg, Germany
- The Center for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland; (K.F.); (A.S.)
| | - Claudia Jessen-Trefzer
- Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany; (M.Z.); (T.D.)
- The Center for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
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3
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Grimmeisen M, Jessen-Trefzer C. Increasing the Selectivity of Light-Active Antimicrobial Agents - Or How To Get a Photosensitizer to the Desired Target. Chembiochem 2023; 24:e202300177. [PMID: 37132365 DOI: 10.1002/cbic.202300177] [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: 03/03/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/04/2023]
Abstract
Photosensitizers combine the inherent reactivity of reactive oxygen species with the sophisticated reaction control of light. Through selective targeting, these light-active molecules have the potential to overcome certain limitations in drug discovery. Ongoing advances in the synthesis and evaluation of photosensitizer conjugates with biomolecules such as antibodies, peptides, or small-molecule drugs are leading to increasingly powerful agents for the eradication of a growing number of microbial species. This review article, therefore, summarizes challenges and opportunities in the development of selective photosensitizers and their conjugates described in recent literature. This provides adequate insight for newcomers and those interested in this field.
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Affiliation(s)
- Michael Grimmeisen
- University of Freiburg, Faculty of Chemistry and Pharmacy, Institute of Organic Chemistry, Albertstraße 21, 79104, Freiburg im Breisgau, Germany
| | - Claudia Jessen-Trefzer
- University of Freiburg, Faculty of Chemistry and Pharmacy, Institute of Organic Chemistry, Albertstraße 21, 79104, Freiburg im Breisgau, Germany
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4
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Ebensperger P, Zmyslia M, Lohner P, Braunreuther J, Deuringer B, Becherer A, Süss R, Fischer A, Jessen-Trefzer C. A Dual‐Metal‐Catalyzed Sequential Cascade Reaction in an Engineered Protein Cage. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202218413] [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: 02/19/2023]
Affiliation(s)
- Paul Ebensperger
- University of Freiburg im Breisgau: Albert-Ludwigs-Universitat Freiburg Institut of Organic Chemistry GERMANY
| | - Mariia Zmyslia
- University of Freiburg im Breisgau: Albert-Ludwigs-Universitat Freiburg Institut of Organic Chemistry GERMANY
| | - Philipp Lohner
- University of Freiburg im Breisgau: Albert-Ludwigs-Universitat Freiburg Institut of Organic Chemistry GERMANY
| | - Judith Braunreuther
- University of Freiburg im Breisgau: Albert-Ludwigs-Universitat Freiburg Institut of Organic Chemistry GERMANY
| | - Benedikt Deuringer
- University of Freiburg im Breisgau: Albert-Ludwigs-Universitat Freiburg Institut of Pharmaceutical Science GERMANY
| | - Anita Becherer
- University of Freiburg im Breisgau: Albert-Ludwigs-Universitat Freiburg Institute of Inorganic and Analytical Chemistry GERMANY
| | - Regine Süss
- University of Freiburg im Breisgau: Albert-Ludwigs-Universitat Freiburg Institut of Pharmaceutical Science GERMANY
| | - Anna Fischer
- University of Freiburg im Breisgau: Albert-Ludwigs-Universitat Freiburg Institute of Inorganic and Analytical Chemistry GERMANY
| | - Claudia Jessen-Trefzer
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg Pharmaceutical Biology and Biotechnology Stefan-Meier-Str. 19 79104 Freiburg GERMANY
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5
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Ebensperger P, Zmyslia M, Lohner P, Braunreuther J, Deuringer B, Becherer A, Süss R, Fischer A, Jessen-Trefzer C. A Dual-Metal-Catalyzed Sequential Cascade Reaction in an Engineered Protein Cage. Angew Chem Int Ed Engl 2023; 62:e202218413. [PMID: 36799770 DOI: 10.1002/anie.202218413] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/18/2023]
Abstract
Herein, we describe the creation of an artificial protein cage housing a dual-metal-tagged guest protein that catalyzes a linear, two-step sequential cascade reaction. The guest protein consists of a fusion protein of HaloTag and monomeric rhizavidin. Inside the protein capsid, we established a ruthenium-catalyzed allylcarbamate deprotection reaction followed by a gold-catalyzed ring-closing hydroamination reaction that led to indoles and phenanthridines with an overall yield of up to 66 % in aqueous solutions. Furthermore, we show that the encapsulation stabilizes the metal catalysts against deactivation by air, proteins and cell lysate.
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Affiliation(s)
- Paul Ebensperger
- Institute of Organic Chemistry, University of Freiburg, Alberstrasse 21, 79104, Freiburg i. Br., Germany
| | - Mariia Zmyslia
- Institute of Organic Chemistry, University of Freiburg, Alberstrasse 21, 79104, Freiburg i. Br., Germany
| | - Philipp Lohner
- Institute of Organic Chemistry, University of Freiburg, Alberstrasse 21, 79104, Freiburg i. Br., Germany
| | - Judith Braunreuther
- Institute of Organic Chemistry, University of Freiburg, Alberstrasse 21, 79104, Freiburg i. Br., Germany
| | - Benedikt Deuringer
- Institute of Pharmaceutical Science, University of Freiburg, Sonnenstrasse 5, 79104, Freiburg i. Br., Germany
| | - Anita Becherer
- Institute of Inorganic and Analytical Chemistry, University of Freiburg, Alberstrasse 21, 79104, Freiburg i. Br., Germany
| | - Regine Süss
- Institute of Pharmaceutical Science, University of Freiburg, Sonnenstrasse 5, 79104, Freiburg i. Br., Germany
| | - Anna Fischer
- Institute of Inorganic and Analytical Chemistry, University of Freiburg, Alberstrasse 21, 79104, Freiburg i. Br., Germany
| | - Claudia Jessen-Trefzer
- Institute of Organic Chemistry, University of Freiburg, Alberstrasse 21, 79104, Freiburg i. Br., Germany
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6
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Hacker SM, Jessen-Trefzer C. Chemical biology in drug discovery. Biol Chem 2022; 403:361-362. [PMID: 35245006 DOI: 10.1515/hsz-2022-0119] [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: 11/15/2022]
Affiliation(s)
- Stephan M Hacker
- Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Claudia Jessen-Trefzer
- Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, D-79104 Freiburg i.Br., Germany
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7
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Ebensperger P, Jessen-Trefzer C. Artificial metalloenzymes in a nutshell: the quartet for efficient catalysis. Biol Chem 2021; 403:403-412. [PMID: 34653321 DOI: 10.1515/hsz-2021-0329] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/05/2021] [Indexed: 12/22/2022]
Abstract
Artificial metalloenzymes combine the inherent reactivity of transition metal catalysis with the sophisticated reaction control of natural enzymes. By providing new opportunities in bioorthogonal chemistry and biocatalysis, artificial metalloenzymes have the potential to overcome certain limitations in both drug discovery and green chemistry or related research fields. Ongoing advances in organometallic catalysis, directed evolution, and bioinformatics are enabling the design of increasingly powerful systems that outperform conventional catalysis in a growing number of cases. Therefore, this review article collects challenges and opportunities in designing artificial metalloenzymes described in recent review articles. This will provide an equitable insight for those new to and interested in the field.
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Affiliation(s)
- Paul Ebensperger
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, D-79104Freiburg i. Br., Germany
| | - Claudia Jessen-Trefzer
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, D-79104Freiburg i. Br., Germany
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8
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Wang X, Bittner T, Milanov M, Kaul L, Mundinger S, Koch HG, Jessen-Trefzer C, Jessen HJ. Pyridinium Modified Anthracenes and Their Endoperoxides Provide a Tunable Scaffold with Activity against Gram-Positive and Gram-Negative Bacteria. ACS Infect Dis 2021; 7:2073-2080. [PMID: 34291902 DOI: 10.1021/acsinfecdis.1c00263] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Due to the emergence of multidrug resistant bacteria, the development of new antibiotics is required. We introduce here asymmetrically modified positively charged bis(methylpyridinium) anthracenes as a novel tunable scaffold, in which the two positive charges can be placed at a defined distance and angle. Our structure-activity relationship reveals that coupling the methylpyridiniums with alkynyl linkers to the central anthracene unit yields antibacterial compounds against a wide range of bacteria, including Escherichia coli, Staphylococcus aureus, and Staphylococcus epidermidis. Also, different mycobacteria, such as Mycobacterium smegmatis and Mycobacterium tuberculosis, are efficiently targeted by these compounds. The antibacterial activity depends on the number of alkynyl linkers and consequently also on the distance of the positive charges in the rigid anthracene scaffold. Additionally, the formation of an anthracene endoperoxide further increases the antibacterial activity, likely due to the release of toxic singlet oxygen that converts the endoperoxide back to the antibacterial anthracene scaffold with half-lives of several hours.
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Affiliation(s)
- Xuan Wang
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Tamara Bittner
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Martin Milanov
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
| | - Laurine Kaul
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology and Biopharmacy, University of Freiburg, 79104 Freiburg, Germany
- Richter Lab, Department of Surgery, Basil Hetzel Institute for Translational Health Research, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5000, Australia
| | - Stephan Mundinger
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZBMZ), Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Claudia Jessen-Trefzer
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Henning J. Jessen
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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9
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Li M, Gašparovič H, Weng X, Chen S, Korduláková J, Jessen-Trefzer C. The Two-Component Locus MSMEG_0244/0246 Together With MSMEG_0243 Affects Biofilm Assembly in M. smegmatis Correlating With Changes in Phosphatidylinositol Mannosides Acylation. Front Microbiol 2020; 11:570606. [PMID: 33013801 PMCID: PMC7516205 DOI: 10.3389/fmicb.2020.570606] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/24/2020] [Indexed: 12/30/2022] Open
Abstract
Ferric and ferrous iron is an essential transition metal for growth of many bacterial species including mycobacteria. The genomic region msmeg_0234 to msmeg_0252 from Mycobacterium smegmatis is putatively involved in iron/heme metabolism. We investigate the genes encoding the presumed two component system MSMEG_0244/MSMEG_0246, the neighboring gene msmeg_0243 and their involvement in this process. We show that purified MSMEG_0243 indeed is a heme binding protein. Deletion of msmeg_0243/msmeg_0244/msmeg_0246 in Mycobacterium smegmatis leads to a defect in biofilm formation and colony growth on solid agar, however, this phenotype is independent of the supplied iron source. Further, analysis of the corresponding mutant and its lipids reveals that changes in morphology and biofilm formation correlate with altered acylation patterns of phosphatidylinositol mannosides (PIMs). We provide the first evidence that msmeg_0244/msmeg_0246 work in concert in cellular lipid homeostasis, especially in the maintenance of PIMs, with the heme-binding protein MSMEG_0243 as potential partner.
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Affiliation(s)
- Miaomaio Li
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Freiburg, Germany
| | - Henrich Gašparovič
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Xing Weng
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Freiburg, Germany
| | - Si Chen
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Freiburg, Germany
| | - Jana Korduláková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Claudia Jessen-Trefzer
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Freiburg, Germany
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10
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Haas TM, Qiu D, Häner M, Angebauer L, Ripp A, Singh J, Koch HG, Jessen-Trefzer C, Jessen HJ. Four Phosphates at One Blow: Access to Pentaphosphorylated Magic Spot Nucleotides and Their Analysis by Capillary Electrophoresis. J Org Chem 2020; 85:14496-14506. [PMID: 32502348 PMCID: PMC7684580 DOI: 10.1021/acs.joc.0c00841] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
complex phosphorylation pattern of natural and modified pentaphosphorylated
magic spot nucleotides is generated in a highly efficient way. A cyclic
pyrophosphoryl phosphoramidite (cPyPA) reagent is used to introduce
four phosphates on nucleosides regioselectively in a one-flask key
transformation. The obtained magic spot nucleotides are used to develop
a capillary electrophoresis UV detection method, enabling nucleotide
assignment in complex bacterial extracts.
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Affiliation(s)
- Thomas M Haas
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Danye Qiu
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Markus Häner
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Larissa Angebauer
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Alexander Ripp
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Jyoti Singh
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Claudia Jessen-Trefzer
- Institute of Pharmaceutical Biology and Biotechnology, University of Freiburg, 79104 Freiburg, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany.,CIBSS, Centre for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
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11
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Unzue A, Jessen-Trefzer C, Spiliotopoulos D, Gaudio E, Tarantelli C, Dong J, Zhao H, Pachmayr J, Zahler S, Bernasconi E, Sartori G, Cascione L, Bertoni F, Śledź P, Caflisch A, Nevado C. Understanding the mechanism of action of pyrrolo[3,2- b]quinoxaline-derivatives as kinase inhibitors. RSC Med Chem 2020; 11:665-675. [PMID: 33479666 PMCID: PMC7557569 DOI: 10.1039/d0md00049c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 02/12/2020] [Accepted: 04/16/2020] [Indexed: 12/02/2022] Open
Abstract
Two novel quinoxaline-based EphA3 tyrosine kinase inhibitors have been designed and characterized in vivo in a relevant lymphoma model, showing high efficacy in the control of tumor size.
The X-ray structure of the catalytic domain of the EphA3 tyrosine kinase in complex with a previously reported type II inhibitor was used to design two novel quinoxaline derivatives, inspired by kinase inhibitors that have reached clinical development. These two new compounds were characterized by an array of cell-based assays and gene expression profiling experiments. A global chemical proteomics approach was used to generate the drug-protein interaction profile, which suggested suitable therapeutic indications. Both inhibitors, studied in the context of angiogenesis and in vivo in a relevant lymphoma model, showed high efficacy in the control of tumor size.
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Affiliation(s)
- Andrea Unzue
- Department of Chemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 , Zürich , Switzerland . ; ; Tel: (+41) 446353945
| | - Claudia Jessen-Trefzer
- Department of Chemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 , Zürich , Switzerland . ; ; Tel: (+41) 446353945
| | - Dimitrios Spiliotopoulos
- Department of Biochemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 , Zürich , Switzerland
| | - Eugenio Gaudio
- Institute of Oncology Research , Faculty of Biomedical Sciences , USI , Bellinzona , Switzerland
| | - Chiara Tarantelli
- Institute of Oncology Research , Faculty of Biomedical Sciences , USI , Bellinzona , Switzerland
| | - Jing Dong
- Department of Biochemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 , Zürich , Switzerland
| | - Hongtao Zhao
- Department of Biochemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 , Zürich , Switzerland
| | - Johanna Pachmayr
- Department of Pharmacy , University of Munich , Butenandstrasse 5-13 , 81377 Munich , Germany
| | - Stefan Zahler
- Department of Pharmacy , University of Munich , Butenandstrasse 5-13 , 81377 Munich , Germany
| | - Elena Bernasconi
- Institute of Oncology Research , Faculty of Biomedical Sciences , USI , Bellinzona , Switzerland
| | - Giulio Sartori
- Institute of Oncology Research , Faculty of Biomedical Sciences , USI , Bellinzona , Switzerland
| | - Luciano Cascione
- Institute of Oncology Research , Faculty of Biomedical Sciences , USI , Bellinzona , Switzerland.,SIB Swiss Institute of Bioinformatics , Lausanne , Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research , Faculty of Biomedical Sciences , USI , Bellinzona , Switzerland.,Oncology Institute of Southern Switzerland (IOSI) , Bellinzona , Switzerland
| | - Paweł Śledź
- Department of Biochemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 , Zürich , Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 , Zürich , Switzerland
| | - Cristina Nevado
- Department of Chemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 , Zürich , Switzerland . ; ; Tel: (+41) 446353945
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12
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Dutta AK, Choudhary E, Wang X, Záhorszka M, Forbak M, Lohner P, Jessen HJ, Agarwal N, Korduláková J, Jessen-Trefzer C. Trehalose Conjugation Enhances Toxicity of Photosensitizers against Mycobacteria. ACS Cent Sci 2019; 5:644-650. [PMID: 31041384 PMCID: PMC6487467 DOI: 10.1021/acscentsci.8b00962] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Indexed: 05/17/2023]
Abstract
Trehalose is a natural glucose-derived disaccharide found in the cell wall of mycobacteria. It enters the mycobacterial cell through a highly specific trehalose transporter system. Subsequently, trehalose is equipped with mycolic acid species and is incorporated into the cell wall as trehalose monomycolate or dimycolate. Here, we investigate the phototoxicity of several photosensitizer trehalose conjugates and take advantage of the promiscuity of the extracellular Ag85 complex, which catalyzes the attachment of mycolic acids to trehalose and its analogues. We find that processing by Ag85 enriches and tethers photosensitizer trehalose conjugates directly into the mycomembrane. Irradiation of the conjugates triggers singlet oxygen formation, killing mycobacterial cells more efficiently, as compared to photosensitizers without trehalose conjugation. The conjugates are potent antimycobacterial agents that are, per se, affected neither by permeability issues nor by detoxification mechanisms via drug efflux. They could serve as interesting scaffolds for photodynamic therapy of mycobacterial infections.
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Affiliation(s)
- Amit K. Dutta
- Institute
of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Eira Choudhary
- NCR-Biotech
Science Cluster, Translational Health Science
and Technology Institute, Gurugram-Faridabad Expressway, third Milestone, Faridabad, 121001 Haryana, India
- Symbiosis
School of Biomedical Sciences, Symbiosis
International University, Lavale, Pune, 412115 Maharashtra, India
| | - Xuan Wang
- Institute
of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Monika Záhorszka
- Department
of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Martin Forbak
- Department
of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Philipp Lohner
- Department
of Pharmaceutical Biology and Biotechnology, Faculty of Chemistry
and Pharmacy, University of Freiburg, Stefan-Meier-Str. 19, 79104 Freiburg, Germany
| | - Henning J. Jessen
- Institute
of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Nisheeth Agarwal
- NCR-Biotech
Science Cluster, Translational Health Science
and Technology Institute, Gurugram-Faridabad Expressway, third Milestone, Faridabad, 121001 Haryana, India
| | - Jana Korduláková
- Department
of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Claudia Jessen-Trefzer
- Department
of Pharmaceutical Biology and Biotechnology, Faculty of Chemistry
and Pharmacy, University of Freiburg, Stefan-Meier-Str. 19, 79104 Freiburg, Germany
- E-mail:
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13
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Li M, Müller C, Fröhlich K, Gorka O, Zhang L, Groß O, Schilling O, Einsle O, Jessen-Trefzer C. Detection and Characterization of a Mycobacterial L-Arabinofuranose ABC Transporter Identified with a Rapid Lipoproteomics Protocol. Cell Chem Biol 2019; 26:852-862.e6. [PMID: 31006617 DOI: 10.1016/j.chembiol.2019.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 09/04/2018] [Revised: 11/23/2018] [Accepted: 03/01/2019] [Indexed: 02/06/2023]
Abstract
Nutrient uptake is essential for survival of organisms, and carbohydrates serve as a crucial carbon and energy source for most microorganisms. Given the importance of mycobacteria as human pathogens a detailed knowledge of carbohydrate uptake transporters is highly desirable, but currently available information is severely limited and mainly based on in silico analyses. Moreover, there is only very little data available on the in vitro characterization of carbohydrate transporters from mycobacterial species. To overcome these significant limitations there is a strong demand for innovative approaches to experimentally match substrates to ATP-binding cassette (ABC) transporters in a straightforward manner. Our study focuses on the model organism Mycobacterium smegmatis and identifies a mycobacterial ABC transport system based on a rapid label-free mass spectrometry lipoproteomics assay with broad applicability. Further validation and X-ray structure analyses reveal a highly selective mycobacterial L-arabinose uptake system.
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Affiliation(s)
- Miaomiao Li
- Department of Pharmaceutical Biology and Biotechnology, Faculty of Chemistry and Pharmacy, University of Freiburg, Stefan-Meier-Straße 19, 79104 Freiburg, Germany
| | - Christoph Müller
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Klemens Fröhlich
- Institute of Surgical Pathology, Faculty of Medicine, University of Freiburg, Breisacher Straße 115A, 79106 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, Albertstraße 19A, 79104 Freiburg, Germany
| | - Oliver Gorka
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Breisacher Straße 66, 79106 Freiburg, Germany
| | - Lin Zhang
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Olaf Groß
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Breisacher Straße 66, 79106 Freiburg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Faculty of Medicine, University of Freiburg, Breisacher Straße 115A, 79106 Freiburg, Germany
| | - Oliver Einsle
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Claudia Jessen-Trefzer
- Department of Pharmaceutical Biology and Biotechnology, Faculty of Chemistry and Pharmacy, University of Freiburg, Stefan-Meier-Straße 19, 79104 Freiburg, Germany.
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14
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Haas TM, Ebensperger P, Eisenbeis VB, Nopper C, Dürr T, Jork N, Steck N, Jessen-Trefzer C, Jessen HJ. Magic spot nucleotides: tunable target-specific chemoenzymatic synthesis. Chem Commun (Camb) 2019; 55:5339-5342. [PMID: 30973558 DOI: 10.1039/c9cc01688k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A tunable chemoenzymatic strategy provides access to the entire class of magic spot nucleotides and modified analogues. The approach combines chemoselective bisphosphorylations using phosphoramidites with regioselective ribonuclease T2 cyclo-phosphate hydrolysis, leading to flexible and simple gram-scale operations.
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Affiliation(s)
- Thomas M Haas
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany. and Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Paul Ebensperger
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany. and Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Verena B Eisenbeis
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany. and Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Christoph Nopper
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany. and Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Tobias Dürr
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany. and Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Jork
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany. and Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Nicole Steck
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany. and Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | | | - Henning J Jessen
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany. and Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
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15
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Zhang S, Zhu J, Zechel DL, Jessen-Trefzer C, Eastman RT, Paululat T, Bechthold A. New WS9326A Derivatives and One New Annimycin Derivative with Antimalarial Activity are Produced by Streptomyces asterosporus DSM 41452 and Its Mutant. Chembiochem 2017; 19:272-279. [PMID: 29148157 DOI: 10.1002/cbic.201700428] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Indexed: 11/10/2022]
Abstract
In this study, we report that Streptomyces asterosporus DSM 41452 is a producer of new molecules related to the nonribosomal cyclodepsipeptide WS9326A and the polyketide annimycin. S. asterosporus DSM 41452 is shown to produce six cyclodepsipeptides and peptides, WS9326A to G. Notably, the compounds WS9326F and WS9326G have not been described before. The genome of S. asterosporus DSM 41452 was sequenced, and a putative WS9326A gene cluster was identified. Gene-deletion experiments confirmed that this cluster was responsible for the biosynthesis of WS9326A to G. Additionally, a gene-deletion experiment demonstrated that sas16 encoding a cytochrome P450 monooxygenase was involved in the synthesis of the novel (E)-2,3-dehydrotyrosine residue found in WS9326A and its derivatives. An insertion mutation within the putative annimycin gene cluster led to the production of a new annimycin derivative, annimycin B, which exhibited modest inhibitory activity against Plasmodium falciparum.
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Affiliation(s)
- Songya Zhang
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strasse 19 VF, 79104, Freiburg im Breisgau, Germany
| | - Jing Zhu
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strasse 19 VF, 79104, Freiburg im Breisgau, Germany
| | - David L Zechel
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, K7L 3N6, Canada
| | - Claudia Jessen-Trefzer
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strasse 19 VF, 79104, Freiburg im Breisgau, Germany
| | - Richard T Eastman
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences/NIH, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Thomas Paululat
- Department of Chemistry and Biology, Universität Siegen, Adolf-Reichwein-Strasse 2, 57068, Siegen, Germany
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strasse 19 VF, 79104, Freiburg im Breisgau, Germany
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16
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Greule A, Marolt M, Deubel D, Peintner I, Zhang S, Jessen-Trefzer C, De Ford C, Burschel S, Li SM, Friedrich T, Merfort I, Lüdeke S, Bisel P, Müller M, Paululat T, Bechthold A. Wide Distribution of Foxicin Biosynthetic Gene Clusters in Streptomyces Strains - An Unusual Secondary Metabolite with Various Properties. Front Microbiol 2017; 8:221. [PMID: 28270798 PMCID: PMC5318452 DOI: 10.3389/fmicb.2017.00221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 11/28/2016] [Accepted: 01/31/2017] [Indexed: 01/13/2023] Open
Abstract
Streptomyces diastatochromogenes Tü6028 is known to produce the polyketide antibiotic polyketomycin. The deletion of the pokOIV oxygenase gene led to a non-polyketomycin-producing mutant. Instead, novel compounds were produced by the mutant, which have not been detected before in the wild type strain. Four different compounds were identified and named foxicins A–D. Foxicin A was isolated and its structure was elucidated as an unusual nitrogen-containing quinone derivative using various spectroscopic methods. Through genome mining, the foxicin biosynthetic gene cluster was identified in the draft genome sequence of S. diastatochromogenes. The cluster spans 57 kb and encodes three PKS type I modules, one NRPS module and 41 additional enzymes. A foxBII gene-inactivated mutant of S. diastatochromogenes Tü6028 ΔpokOIV is unable to produce foxicins. Homologous fox biosynthetic gene clusters were found in more than 20 additional Streptomyces strains, overall in about 2.6% of all sequenced Streptomyces genomes. However, the production of foxicin-like compounds in these strains has never been described indicating that the clusters are expressed at a very low level or are silent under fermentation conditions. Foxicin A acts as a siderophore through interacting with ferric ions. Furthermore, it is a weak inhibitor of the Escherichia coli aerobic respiratory chain and shows moderate antibiotic activity. The wide distribution of the cluster and the various properties of the compound indicate a major role of foxicins in Streptomyces strains.
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Affiliation(s)
- Anja Greule
- Department of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University of Freiburg Freiburg im Breisgau, Germany
| | - Marija Marolt
- Department of Pharmaceutical and Medical Chemistry, Albert-Ludwigs-University of Freiburg Freiburg im Breisgau, Germany
| | - Denise Deubel
- Department of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University of Freiburg Freiburg im Breisgau, Germany
| | - Iris Peintner
- Department of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University of Freiburg Freiburg im Breisgau, Germany
| | - Songya Zhang
- Department of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University of Freiburg Freiburg im Breisgau, Germany
| | - Claudia Jessen-Trefzer
- Department of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University of Freiburg Freiburg im Breisgau, Germany
| | - Christian De Ford
- Department of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University of FreiburgFreiburg im Breisgau, Germany; Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University of FreiburgFreiburg im Breisgau, Germany
| | - Sabrina Burschel
- Institute of Biochemistry, Albert-Ludwigs-University of Freiburg Freiburg im Breisgau, Germany
| | - Shu-Ming Li
- Department of Pharmaceutical Biology, Philipps-University Marburg Marburg, Germany
| | - Thorsten Friedrich
- Institute of Biochemistry, Albert-Ludwigs-University of Freiburg Freiburg im Breisgau, Germany
| | - Irmgard Merfort
- Department of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University of Freiburg Freiburg im Breisgau, Germany
| | - Steffen Lüdeke
- Department of Pharmaceutical and Medical Chemistry, Albert-Ludwigs-University of Freiburg Freiburg im Breisgau, Germany
| | - Philippe Bisel
- Department of Pharmaceutical and Medical Chemistry, Albert-Ludwigs-University of Freiburg Freiburg im Breisgau, Germany
| | - Michael Müller
- Department of Pharmaceutical and Medical Chemistry, Albert-Ludwigs-University of Freiburg Freiburg im Breisgau, Germany
| | - Thomas Paululat
- Department of Chemistry and Biology, University of Siegen Siegen, Germany
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University of Freiburg Freiburg im Breisgau, Germany
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