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Chen F, Elgaher WAM, Winterhoff M, Büssow K, Waqas FH, Graner E, Pires-Afonso Y, Casares Perez L, de la Vega L, Sahini N, Czichon L, Zobl W, Zillinger T, Shehata M, Pleschka S, Bähre H, Falk C, Michelucci A, Schuchardt S, Blankenfeldt W, Hirsch AKH, Pessler F. Citraconate inhibits ACOD1 (IRG1) catalysis, reduces interferon responses and oxidative stress, and modulates inflammation and cell metabolism. Nat Metab 2022; 4:534-546. [PMID: 35655026 PMCID: PMC9170585 DOI: 10.1038/s42255-022-00577-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 04/20/2022] [Indexed: 01/08/2023]
Abstract
Although the immunomodulatory and cytoprotective properties of itaconate have been studied extensively, it is not known whether its naturally occurring isomers mesaconate and citraconate have similar properties. Here, we show that itaconate is partially converted to mesaconate intracellularly and that mesaconate accumulation in macrophage activation depends on prior itaconate synthesis. When added to human cells in supraphysiological concentrations, all three isomers reduce lactate levels, whereas itaconate is the strongest succinate dehydrogenase (SDH) inhibitor. In cells infected with influenza A virus (IAV), all three isomers profoundly alter amino acid metabolism, modulate cytokine/chemokine release and reduce interferon signalling, oxidative stress and the release of viral particles. Of the three isomers, citraconate is the strongest electrophile and nuclear factor-erythroid 2-related factor 2 (NRF2) agonist. Only citraconate inhibits catalysis of itaconate by cis-aconitate decarboxylase (ACOD1), probably by competitive binding to the substrate-binding site. These results reveal mesaconate and citraconate as immunomodulatory, anti-oxidative and antiviral compounds, and citraconate as the first naturally occurring ACOD1 inhibitor.
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Affiliation(s)
- F Chen
- Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Research Group Biomarkers for Infectious Diseases, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - W A M Elgaher
- Helmholtz Institute for Pharmaceutical Research Saarland - Helmholtz Centre for Infection Research, Saarbrücken, Germany
| | - M Winterhoff
- Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Research Group Biomarkers for Infectious Diseases, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - K Büssow
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - F H Waqas
- Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Research Group Biomarkers for Infectious Diseases, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - E Graner
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Y Pires-Afonso
- Neuro-Immunology Group, Department of Cancer Research, LIH Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - L Casares Perez
- Division of Molecular Medicine, University of Dundee, Dundee, UK
| | - L de la Vega
- Division of Molecular Medicine, University of Dundee, Dundee, UK
| | - N Sahini
- Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Research Group Biomarkers for Infectious Diseases, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - L Czichon
- Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Research Group Biomarkers for Infectious Diseases, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - W Zobl
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Hannover, Germany
| | - T Zillinger
- Institute of Clinical Chemistry and Clinical Pharmacology, University Medical Centre Bonn, Bonn, Germany
- Institute of Immunology, Philipps-University Marburg, Marburg, Germany
| | - M Shehata
- Institute of Medical Virology, Justus-Liebig-University Giessen, Giessen, Germany
- National Research Centre, Giza, Egypt
| | - S Pleschka
- Institute of Medical Virology, Justus-Liebig-University Giessen, Giessen, Germany
- German Center for Infection Research partner site Giessen, Giessen, Germany
| | - H Bähre
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - C Falk
- Department of Transplantation Immunology, Hannover Medical School, Hannover, Germany
| | - A Michelucci
- Neuro-Immunology Group, Department of Cancer Research, LIH Luxembourg Institute of Health, Luxembourg, Luxembourg
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - S Schuchardt
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Hannover, Germany
| | - W Blankenfeldt
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - A K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland - Helmholtz Centre for Infection Research, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - F Pessler
- Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, Braunschweig, Germany.
- Research Group Biomarkers for Infectious Diseases, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany.
- Centre for Individualised Infection Medicine, Hannover, Germany.
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Della Volpe S, Linciano P, Listro R, Tumminelli E, Amadio M, Bonomo I, Elgaher WAM, Adam S, Hirsch AKH, Boeckler FM, Vasile F, Rossi D, Collina S. Identification of N,N-arylalkyl-picolinamide derivatives targeting the RNA-binding protein HuR, by combining biophysical fragment-screening and molecular hybridization. Bioorg Chem 2021; 116:105305. [PMID: 34482166 DOI: 10.1016/j.bioorg.2021.105305] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 04/29/2021] [Revised: 07/26/2021] [Accepted: 08/23/2021] [Indexed: 12/31/2022]
Abstract
Hu proteins are members of the RNA-binding protein (RBP) family and play a pivotal role in the regulation of post-transcriptional processes. Through interaction with selected mRNAs, RBPs regulate their function and stability; as a consequence, RBP dysregulation can cause abnormal translation of key proteins involved in several pathologies. In the past few years, this observation has sparked interest to develop new treatments against these pathologies by using small molecules able to modulate RBP activity. Among the four Hu proteins, we have directed our efforts towards the isoform HuR, which is mainly involved in cancer, inflammation and retinopathy. Aimed at developing compounds able to modulate the stability of HuR-mRNA complexes, in the present work, we applied a biophysical fragment screening by assessing a library of halogen-enriched heterocyclic fragments (HEFLibs) via Surface Plasmon Resonance (SPR) and Saturation Transfer Difference (STD) NMR to select promising fragments able to interact with HuR. One selected fragment and a few commercially available congeners were exploited to design and synthesize focused analogues of compound N-(3-chlorobenzyl)-N-(3,5-dihydroxyphenethyl)-4-hydroxybenzamide (1), our previously reported hit. STDNMR spectroscopy, molecular modeling, and SPR offered further insight into the HuR-small molecule interaction and showed that fragment-based approaches represent a promising and yet underexplored strategy to tackle such unusual targets. Lastly, fluorescence polarization (FP) studies revealed the capability of the new compounds to interfere with the formation of the HuR-mRNA complex. This is, to our knowledge, the first fragment-based campaign performed on the Hu protein class, and one of the few examples in the larger RBP field and constitutes an important step in the quest for the rational modulation of RBPs and related RNA functions by small molecules.
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Affiliation(s)
- S Della Volpe
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus building E8.1, 66123 Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany.
| | - P Linciano
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy.
| | - R Listro
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy.
| | - E Tumminelli
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus building E8.1, 66123 Saarbrücken, Germany.
| | - M Amadio
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy.
| | - I Bonomo
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
| | - W A M Elgaher
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus building E8.1, 66123 Saarbrücken, Germany.
| | - S Adam
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus building E8.1, 66123 Saarbrücken, Germany.
| | - A K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus building E8.1, 66123 Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany.
| | - F M Boeckler
- Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany; Center for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - F Vasile
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy.
| | - D Rossi
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy.
| | - S Collina
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy.
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Swier LJYM, Monjas L, Reeßing F, Oudshoorn RC, Aisyah, Primke T, Bakker MM, van Olst E, Ritschel T, Faustino I, Marrink SJ, Hirsch AKH, Slotboom DJ. Insight into the complete substrate-binding pocket of ThiT by chemical and genetic mutations. Medchemcomm 2017; 8:1121-1130. [PMID: 30108823 DOI: 10.1039/c7md00079k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/24/2017] [Indexed: 01/12/2023]
Abstract
Energy-coupling factor (ECF) transporters are involved in the uptake of micronutrients in bacteria. The transporters capture the substrate by high-affinity binding proteins, the so-called S-components. Here, we present the analysis of two regions of the substrate-binding pocket of the thiamine-specific S-component in Lactococcus lactis, ThiT. First, interaction of the thiazolium ring of thiamine with residues Trp34, His125 and Glu84 by π-π-stacking and cation-π is studied, and second, the part of the binding pocket that extends from the hydroxyl group. We mutated either the transported ligand (chemically) or the protein (genetically). Surprisingly, modifications in the thiazolium ring by introducing substituents with opposite electronic effects had similar effects on the binding affinity. We hypothesize that the electronic effects are superseeded by steric effects of the added substituents, which renders the study of isolated interactions difficult. Amino acid substitutions in ThiT indicate that the electrostatic interaction facilitated by residue Glu84 of ThiT and thiamine is necessary for picomolar affinity. Deazathiamine derivatives that explore the subpocket of the binding site extending from the hydroxyl group of thiamine bind with high affinity to ThiT and may be developed into selective inhibitors of thiamine transport by ECF transporters. Molecular-dynamics simulations suggest that two of these derivatives may not only bind to ThiT, but could also be transported.
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Affiliation(s)
- L J Y M Swier
- Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands . ; Tel: +31 50 363 4187
| | - L Monjas
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands . ; Tel: +31 50 363 4275
| | - F Reeßing
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands . ; Tel: +31 50 363 4275
| | - R C Oudshoorn
- Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands . ; Tel: +31 50 363 4187
| | - Aisyah
- Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands . ; Tel: +31 50 363 4187
| | - T Primke
- Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands . ; Tel: +31 50 363 4187
| | - M M Bakker
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands . ; Tel: +31 50 363 4275
| | - E van Olst
- Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands . ; Tel: +31 50 363 4187
| | - T Ritschel
- Centre for Molecular and Biomolecular Informatics (CMBI) , Radboudumc , 6525 GA Nijmegen , The Netherlands
| | - I Faustino
- Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands . ; Tel: +31 50 363 4187
| | - S J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands . ; Tel: +31 50 363 4187
| | - A K H Hirsch
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands . ; Tel: +31 50 363 4275
| | - D J Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands . ; Tel: +31 50 363 4187
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Monjas L, Swier LJYM, de Voogd AR, Oudshoorn RC, Hirsch AKH, Slotboom DJ. Design and synthesis of thiamine analogues to study their binding to the ECF transporter for thiamine in bacteria. Med Chem Commun 2016. [DOI: 10.1039/c6md00022c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work presents new small molecules that bind to the protein ThiT, which confers substrate specificity to the Energy-Coupling Factor (ECF) transporter for thiamine. Further development of the molecules may lead to compounds with antimicrobial activity.
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Affiliation(s)
- L. Monjas
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - L. J. Y. M. Swier
- Groningen Biomolecular Sciences and Biotechnology Institute
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - A. R. de Voogd
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - R. C. Oudshoorn
- Groningen Biomolecular Sciences and Biotechnology Institute
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - A. K. H. Hirsch
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - D. J. Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute
- University of Groningen
- 9747 AG Groningen
- The Netherlands
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Masini T, Lacy B, Monjas L, Hawksley D, de Voogd AR, Illarionov B, Iqbal A, Leeper FJ, Fischer M, Kontoyianni M, Hirsch AKH. Validation of a homology model of Mycobacterium tuberculosis DXS: rationalization of observed activities of thiamine derivatives as potent inhibitors of two orthologues of DXS. Org Biomol Chem 2015; 13:11263-77. [DOI: 10.1039/c5ob01666e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We present the a homology model ofM. tuberculosisDXS that we validated by identifying thiamine and thiamine diphosphate analogues as potent inhibitors of DXS.
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Masini T, Pilger J, Kroezen BS, Illarionov B, Lottmann P, Fischer M, Griesinger C, Hirsch AKH. De novo fragment-based design of inhibitors of DXS guided by spin-diffusion-based NMR spectroscopy. Chem Sci 2014. [DOI: 10.1039/c4sc00588k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A ligand-based NMR methodology (STI) enabled de novo fragment-based design of inhibitors of the enzyme DXS present in the non-mevalonate pathway in the absence of X-ray co-crystal structures.
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Affiliation(s)
- T. Masini
- Stratingh Institute for Chemistry
- University of Groningen
- NL-9747 AG Groningen, The Netherlands
| | - J. Pilger
- Max-Planck-Institute for Biophysical Chemisty
- 37077 Göttingen, Germany
| | - B. S. Kroezen
- Stratingh Institute for Chemistry
- University of Groningen
- NL-9747 AG Groningen, The Netherlands
| | - B. Illarionov
- Hamburg School of Food Science
- Institute of Food Chemistry
- Hamburg, Germany
| | - P. Lottmann
- Max-Planck-Institute for Biophysical Chemisty
- 37077 Göttingen, Germany
| | - M. Fischer
- Hamburg School of Food Science
- Institute of Food Chemistry
- Hamburg, Germany
| | - C. Griesinger
- Max-Planck-Institute for Biophysical Chemisty
- 37077 Göttingen, Germany
| | - A. K. H. Hirsch
- Stratingh Institute for Chemistry
- University of Groningen
- NL-9747 AG Groningen, The Netherlands
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