1
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Weigert Muñoz A, Zhao W, Sieber SA. Monitoring host-pathogen interactions using chemical proteomics. RSC Chem Biol 2024; 5:73-89. [PMID: 38333198 PMCID: PMC10849124 DOI: 10.1039/d3cb00135k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/09/2023] [Indexed: 02/10/2024] Open
Abstract
With the rapid emergence and the dissemination of microbial resistance to conventional chemotherapy, the shortage of novel antimicrobial drugs has raised a global health threat. As molecular interactions between microbial pathogens and their mammalian hosts are crucial to establish virulence, pathogenicity, and infectivity, a detailed understanding of these interactions has the potential to reveal novel therapeutic targets and treatment strategies. Bidirectional molecular communication between microbes and eukaryotes is essential for both pathogenic and commensal organisms to colonise their host. In particular, several devastating pathogens exploit host signalling to adjust the expression of energetically costly virulent behaviours. Chemical proteomics has emerged as a powerful tool to interrogate the protein interaction partners of small molecules and has been successfully applied to advance host-pathogen communication studies. Here, we present recent significant progress made by this approach and provide a perspective for future studies.
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Affiliation(s)
- Angela Weigert Muñoz
- Center for Functional Protein Assemblies, Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich Ernst-Otto-Fischer-Straße 8 D-85748 Garching Germany
| | - Weining Zhao
- College of Pharmacy, Shenzhen Technology University Shenzhen 518118 China
| | - Stephan A Sieber
- Center for Functional Protein Assemblies, Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich Ernst-Otto-Fischer-Straße 8 D-85748 Garching Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Germany
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2
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Bilgin N, Türkmen VA, Hammami N, Christensen NR, Hintzen JCJ, Mecinović J. Reading and erasing of histone crotonyllysine mimics by the AF9 YEATS domain and SIRT2 deacylase. Bioorg Med Chem 2023; 95:117500. [PMID: 37839329 DOI: 10.1016/j.bmc.2023.117500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023]
Abstract
Lysine acylations on histones and their recognition by chromatin-binding reader domains and removal by histone deacylases function as an important mechanism for eukaryotic gene regulation. Histone lysine crotonylation (Kcr) is an epigenetic mark associated with active transcription, and its installation and removal are dynamically regulated by cellular epigenetic enzymes. Here, we report binding studies and enzyme assays with histone H3K9 peptides bearing simplest Kcr analogs with varying hydrocarbon chain length, bulkiness, rigidity and polarity. We demonstrate that the AF9 YEATS domain displays selectivity for binding of different acylation modifications on histone H3K9 peptides and exhibits preference for bulkier cinnamoylated lysine over crotonylated lysine and its mimics. SIRT2 shows deacylase activity against most of acylated H3K9 peptides bearing different crotonyllysine mimics, however, it displays a poor ability for the removal of cinnamoyl and trifluorocrotonyl groups. These results demonstrate different substrate selectivities of epigenetic proteins acting on crotonyllysine and pave the way for rational design and development of AF9 YEATS and SIRT2 inhibitors for treatment of human diseases, including cancer.
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Affiliation(s)
- Nurgül Bilgin
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Vildan A Türkmen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Nesrin Hammami
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Nadja R Christensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jordi C J Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
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3
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Al-Fakhar MSQ, Bilgin N, Moesgaard L, Witecka A, Drozak J, Kongsted J, Mecinović J. The Role of Trp79 in β-Actin on Histidine Methyltransferase SETD3 Catalysis. Chembiochem 2023; 24:e202300490. [PMID: 37581408 DOI: 10.1002/cbic.202300490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 08/16/2023]
Abstract
Nτ -methylation of His73 in actin by histidine methyltransferase SETD3 plays an important role in stabilising actin filaments in eukaryotes. Mutations in actin and overexpression of SETD3 have been related to human diseases, including cancer. Here, we investigated the importance of Trp79 in β-actin on productive human SETD3 catalysis. Substitution of Trp79 in β-actin peptides by its chemically diverse analogues reveals that the hydrophobic Trp79 binding pocket modulates the catalytic activity of SETD3, and that retaining a bulky and hydrophobic amino acid at position 79 is important for efficient His73 methylation by SETD3. Molecular dynamics simulations show that the Trp79 binding pocket of SETD3 is ideally shaped to accommodate large and hydrophobic Trp79, contributing to the favourable release of water molecules upon binding. Our results demonstrate that the distant Trp79 binding site plays an important role in efficient SETD3 catalysis, contributing to the identification of new SETD3 substrates and the development of chemical probes targeting the biomedically important SETD3.
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Affiliation(s)
- Mays S Q Al-Fakhar
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Nurgül Bilgin
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Laust Moesgaard
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Apolonia Witecka
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Jakub Drozak
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
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4
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Mendez Q, Driscoll HA, Mirando GR, Acca F, Chapados CD, Jones KS, Weiner M, Li X, Ferguson MR. MILKSHAKE Western blot and Sundae ELISA: We all scream for better antibody validation. J Immunol Methods 2023; 521:113540. [PMID: 37597727 PMCID: PMC10568614 DOI: 10.1016/j.jim.2023.113540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Knowing that an antibody's sensitivity and specificity is accurate is crucial for reliable data collection. This certainty is especially difficult to achieve for antibodies (Abs) which bind post-translationally modified proteins. Here we describe two validation methods using surrogate proteins in western blot and ELISA. The first method, which we termed "MILKSHAKE" is a modified maltose binding protein, hence the name, that is enzymatically conjugated to a peptide from the chosen target which is either modified or non-modified at the residue of interest. The surety of the residue's modification status can be used to confirm Ab specificity to the target's post-translational modification (PTM). The second method uses a set of surrogate proteins, which we termed "Sundae". Sundae consists of a set of modified maltose binding proteins with a genetically encoded target sequence, each of which contains a single amino acid substitution at one position of interest. With Sundae, Abs can be evaluated for binding specificities to all twenty amino acids at a single position. Combining MILKSHAKE and Sundae methods, Ab specificity can be determined at a single-residue resolution. These data improve evaluation of commercially available Abs and identify off-target effects for Research-Use-Only and therapeutic Abs.
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Affiliation(s)
- Qiana Mendez
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Holland A Driscoll
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Gregory R Mirando
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Felicity Acca
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Cassandra D Chapados
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Kezzia S Jones
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Michael Weiner
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Xiaofeng Li
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Mary R Ferguson
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
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5
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Brown T, Nguyen T, Zhou B, Zheng YG. Chemical probes and methods for the study of protein arginine methylation. RSC Chem Biol 2023; 4:647-669. [PMID: 37654509 PMCID: PMC10467615 DOI: 10.1039/d3cb00018d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 07/28/2023] [Indexed: 09/02/2023] Open
Abstract
Protein arginine methylation is a widespread post-translational modification (PTM) in eukaryotic cells. This chemical modification in proteins functionally modulates diverse cellular processes from signal transduction, gene expression, and DNA damage repair to RNA splicing. The chemistry of arginine methylation entails the transfer of the methyl group from S-adenosyl-l-methionine (AdoMet, SAM) onto a guanidino nitrogen atom of an arginine residue of a target protein. This reaction is catalyzed by about 10 members of protein arginine methyltransferases (PRMTs). With impacts on a variety of cellular processes, aberrant expression and activity of PRMTs have been shown in many disease conditions. Particularly in oncology, PRMTs are commonly overexpressed in many cancerous tissues and positively correlated with tumor initiation, development and progression. As such, targeting PRMTs is increasingly recognized as an appealing therapeutic strategy for new drug discovery. In the past decade, a great deal of research efforts has been invested in illuminating PRMT functions in diseases and developing chemical probes for the mechanistic study of PRMTs in biological systems. In this review, we provide a brief developmental history of arginine methylation along with some key updates in arginine methylation research, with a particular emphasis on the chemical aspects of arginine methylation. We highlight the research endeavors for the development and application of chemical approaches and chemical tools for the study of functions of PRMTs and arginine methylation in regulating biology and disease.
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Affiliation(s)
- Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Terry Nguyen
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Bo Zhou
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
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6
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Bollmeyer MM, Coleman RE, Majer SH, Ferrao SD, Lancaster KM. Cytochrome P460 Cofactor Maturation Proceeds via Peroxide-Dependent Post-translational Modification. J Am Chem Soc 2023; 145:14404-14416. [PMID: 37338957 PMCID: PMC10431212 DOI: 10.1021/jacs.3c03608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Cytochrome P460s are heme enzymes that oxidize hydroxylamine to nitrous oxide. They bear specialized "heme P460" cofactors that are cross-linked to their host polypeptides by a post-translationally modified lysine residue. Wild-type N. europaea cytochrome P460 may be isolated as a cross-link-deficient proenzyme following anaerobic overexpression in E. coli. When treated with peroxide, this proenzyme undergoes maturation to active enzyme with spectroscopic and catalytic properties that match wild-type cyt P460. This maturation reactivity requires no chaperones─it is intrinsic to the protein. This behavior extends to the broader cytochrome c'β superfamily. Accumulated data reveal key contributions from the secondary coordination sphere that enable selective, complete maturation. Spectroscopic data support the intermediacy of a ferryl species along the maturation pathway.
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Affiliation(s)
- Melissa M. Bollmeyer
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Rachael E. Coleman
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Sean H. Majer
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Silas D. Ferrao
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
| | - Kyle M. Lancaster
- Department of Chemistry and Chemical Biology Cornell University, Baker Laboratory, 162 Sciences Drive, Ithaca, NY 14853, USA
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7
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Bilgin N, Moesgaard L, Rahman MM, Türkmen VA, Kongsted J, Mecinović J. Molecular Recognition of Methacryllysine and Crotonyllysine by the AF9 YEATS Domain. Int J Mol Sci 2023; 24:ijms24087002. [PMID: 37108167 PMCID: PMC10138300 DOI: 10.3390/ijms24087002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Histone lysine methacrylation and crotonylation are epigenetic marks that play important roles in human gene regulation. Here, we explore the molecular recognition of histone H3 peptides possessing methacryllysine and crotonyllysine at positions 18 and 9 (H3K18 and H3K9) by the AF9 YEATS domain. Our binding studies demonstrate that the AF9 YEATS domain displays a higher binding affinity for histones possessing crotonyllysine than the isomeric methacryllysine, indicating that AF9 YEATS distinguishes between the two regioisomers. Molecular dynamics simulations reveal that the crotonyllysine/methacryllysine-mediated desolvation of the AF9 YEATS domain provides an important contribution to the recognition of both epigenetic marks. These results provide important knowledge for the development of AF9 YEATS inhibitors, an area of biomedical interest.
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Affiliation(s)
- Nurgül Bilgin
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Laust Moesgaard
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Mohammad M Rahman
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Vildan A Türkmen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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8
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Peng T, Das T, Ding K, Hang HC. Functional analysis of protein post-translational modifications using genetic codon expansion. Protein Sci 2023; 32:e4618. [PMID: 36883310 PMCID: PMC10031814 DOI: 10.1002/pro.4618] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Post-translational modifications (PTMs) of proteins not only exponentially increase the diversity of proteoforms, but also contribute to dynamically modulating the localization, stability, activity, and interaction of proteins. Understanding the biological consequences and functions of specific PTMs has been challenging for many reasons, including the dynamic nature of many PTMs and the technical limitations to access homogenously modified proteins. The genetic code expansion technology has emerged to provide unique approaches for studying PTMs. Through site-specific incorporation of unnatural amino acids (UAAs) bearing PTMs or their mimics into proteins, genetic code expansion allows the generation of homogenous proteins with site-specific modifications and atomic resolution both in vitro and in vivo. With this technology, various PTMs and mimics have been precisely introduced into proteins. In this review, we summarize the UAAs and approaches that have been recently developed to site-specifically install PTMs and their mimics into proteins for functional studies of PTMs.
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Affiliation(s)
- Tao Peng
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhenChina
- Institute of Chemical Biology, Shenzhen Bay LaboratoryShenzhenChina
| | - Tandrila Das
- Departments of Immunology and Microbiology and ChemistryScripps ResearchLa JollaCaliforniaUSA
| | - Ke Ding
- State Key Laboratory of Chemical OncogenomicsSchool of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhenChina
| | - Howard C. Hang
- Departments of Immunology and Microbiology and ChemistryScripps ResearchLa JollaCaliforniaUSA
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9
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Rehkopf L, Seidel J, Sindlinger J, Wang M, Kirchgäßner S, Schwarzer D. Synthesis of Nε-acetyl-L-homolysine by the Lossen rearrangement and its application for probing deacetylases and binding modules of acetyl-lysine. J Pept Sci 2023; 29:e3462. [PMID: 36416071 DOI: 10.1002/psc.3462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022]
Abstract
Lysine acetylation is a posttranslational protein modification mediating protein-protein interactions by recruitment of bromodomains. Investigations of bromodomains have focused so far on the sequence context of the modification site and acyl-modifications installed at lysine side chains. In contrast, there is only little information about the impact of the lysine residue that carries the modification on bromodomain binding. Here, we report a synthesis strategy for L-acetyl-homolysine from L-2-aminosuberic acid by the Lossen rearrangement. Peptide probes containing acetylated homolysine, lysine, and ornithine were generated and used for probing the binding preferences of four bromodomains from three different families. Tested bromodomains showed distinct binding patterns, and one of them bound acetylated homolysine with similar efficiency as the native substrate containing acetyl-lysine. Deacetylation assays with a bacterial sirtuin showed a strong preference for acetylated lysine, despite a broad specificity for N-acyl modifications.
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Affiliation(s)
- Luisa Rehkopf
- Interfakultäres Institut für Biochemie, Universität Tübingen, Tübingen, Germany
| | - Julian Seidel
- Interfakultäres Institut für Biochemie, Universität Tübingen, Tübingen, Germany.,Institute for Organic and Macromolecular Chemistry, Universität Jena, Jena, Germany
| | - Julia Sindlinger
- Interfakultäres Institut für Biochemie, Universität Tübingen, Tübingen, Germany.,Institute for Inorganic and Analytical Chemistry, Mass Spectrometry Platform, Universität Jena, Jena, Germany
| | - Mary Wang
- Interfakultäres Institut für Biochemie, Universität Tübingen, Tübingen, Germany
| | - Sören Kirchgäßner
- Interfakultäres Institut für Biochemie, Universität Tübingen, Tübingen, Germany
| | - Dirk Schwarzer
- Interfakultäres Institut für Biochemie, Universität Tübingen, Tübingen, Germany
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10
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Kirchgäßner S, Braun MB, Bartlick N, Koç C, Reinkemeier CD, Lemke EA, Stehle T, Schwarzer D. Synthesis, Biochemical Characterization, and Genetic Encoding of a 1,2,4-Triazole Amino Acid as an Acetyllysine Mimic for Bromodomains of the BET Family. Angew Chem Int Ed Engl 2023; 62:e202215460. [PMID: 36585954 DOI: 10.1002/anie.202215460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/23/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
Lysine acetylation is a charge-neutralizing post-translational modification of proteins bound by bromodomains (Brds). A 1,2,4-triazole amino acid (ApmTri) was established as acetyllysine (Kac) mimic recruiting Brds of the BET family in contrast to glutamine commonly used for simulating this modification. Optimization of triazole substituents and side chain spacing allowed BET Brd recruitment to ApmTri-containing peptides with affinities similar to native substrates. Crystal structures of ApmTri-containing peptides in complex with two BET Brds revealed the binding mode which mirrored that of Kac ligands. ApmTri was genetically encoded and recombinant ApmTri-containing proteins co-enriched BRD3(2) from cellular lysates. This interaction was blocked by BET inhibitor JQ1. With genetically encoded ApmTri, biochemistry is now provided with a stable Kac mimic reflecting charge neutralization and Brd recruitment, allowing new investigations into BET proteins in vitro and in vivo.
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Affiliation(s)
- Sören Kirchgäßner
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Michael B Braun
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Natascha Bartlick
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Cengiz Koç
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany.,Current address: Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, The Medical School, Beech Hill Rd, Sheffield, S10 2RX, UK
| | - Christopher D Reinkemeier
- Biocenter, Johannes Gutenberg University Mainz, 55128, Mainz, Germany.,Institute of Molecular Biology Mainz, 55128, Mainz, Germany.,Current address: Department of Biosystems Science and Engineering Basel, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128, Mainz, Germany.,Institute of Molecular Biology Mainz, 55128, Mainz, Germany
| | - Thilo Stehle
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Dirk Schwarzer
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
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11
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Türkmen VA, Hintzen JCJ, Tumber A, Moesgaard L, Salah E, Kongsted J, Schofield CJ, Mecinović J. Substrate selectivity and inhibition of histidine JmjC hydroxylases MINA53 and NO66. RSC Chem Biol 2023; 4:235-243. [PMID: 36908702 PMCID: PMC9994133 DOI: 10.1039/d2cb00182a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/12/2023] [Indexed: 01/15/2023] Open
Abstract
Non-haem Fe(ii) and 2-oxoglutarate (2OG) dependent oxygenases catalyse oxidation of multiple proteins in organisms ranging from bacteria to humans. We describe studies on the substrate selectivity and inhibition of the human ribosomal oxygenases (ROX) MINA53 and NO66, members of the JmjC 2OG oxygenase subfamily, which catalyse C-3 hydroxylation of histidine residues in Rpl27a and Rpl8, respectively. Assays with natural and unnatural histidine analogues incorporated into Rpl peptides provide evidence that MINA53 and NO66 have narrow substrate selectivities compared to some other human JmjC hydroxylases, including factor inhibiting HIF and JMJD6. Notably, the results of inhibition assays with Rpl peptides containing histidine analogues with acyclic side chains, including Asn, Gln and homoGln, suggest the activities of MINA53/NO66, and by implication related 2OG dependent protein hydroxylases/demethylases, might be regulated in vivo by competition with non-oxidised proteins/peptides. The inhibition results also provide avenues for development of inhibitors selective for MINA53 and NO66.
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Affiliation(s)
- Vildan A Türkmen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
| | - Jordi C J Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
| | - Anthony Tumber
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road OX1 3TA Oxford UK
| | - Laust Moesgaard
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
| | - Eidarus Salah
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road OX1 3TA Oxford UK
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
| | - Christopher J Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road OX1 3TA Oxford UK
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
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12
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Van Holsbeeck K, Elsocht M, Ballet S. Propargylamine Amino Acids as Constrained Nε-Substituted Lysine Mimetics. Org Lett 2023; 25:130-133. [PMID: 36546856 DOI: 10.1021/acs.orglett.2c03931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Herein, alkylated propargylamines are reported as constrained lysine mimetics and constructed in a single step using a copper(I)-catalyzed A3-coupling reaction. Using multiple secondary amines, the reaction allowed the generation of a structurally diverse set of N-Fmoc protected amino acid derivatives. In addition, the A3-reaction was applied on solid phase via the assembly of short model tripeptides. Moreover, the internal alkyne moiety allowed further functionalization toward novel 1,4,5-trisubstituted 1,2,3-triazole-based amino acids.
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Affiliation(s)
- Kevin Van Holsbeeck
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Mathias Elsocht
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
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13
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Betlem P, Maas MN, Middelburg J, Pieters BJGE, Mecinović J. Recognition of stapled histone H3K4me3 peptides by epigenetic reader proteins. Chem Commun (Camb) 2022; 58:12196-12199. [DOI: 10.1039/d2cc04294k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Epigenetic reader proteins can display stronger or weaker binding affinities for cyclic histone peptides relative to linear histones, indicating that selectivity of biomolecular recognition can be achieved.
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Affiliation(s)
- Peter Betlem
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Marijn N. Maas
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jim Middelburg
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Bas J. G. E. Pieters
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jasmin Mecinović
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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