1
|
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: 3] [Impact Index Per Article: 3.0] [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.
Collapse
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
| |
Collapse
|
2
|
Investigation of in vitro histone H3 glycosylation using H3 tail peptides. Sci Rep 2022; 12:19251. [PMID: 36357422 PMCID: PMC9649660 DOI: 10.1038/s41598-022-21883-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/05/2022] [Indexed: 11/12/2022] Open
Abstract
Posttranslational modifications (PTMs) on histone tails regulate eukaryotic gene expression by impacting the chromatin structure and by modulating interactions with other cellular proteins. One such PTM has been identified as serine and threonine glycosylation, the introduction of the ß-N-acetylglucosamine (GlcNAc) moiety on histone H3 tail at position Ser10 and Thr32. The addition of the ß-O-GlcNAc moiety on serine or threonine residues is facilitated by the O-GlcNAc transferase (OGT), and can be removed by the action of O-GlcNAcase (OGA). Conflicting reports on histone tail GlcNAc modification in vivo prompted us to investigate whether synthetic histone H3 tail peptides in conjunction with other PTMs are substrates for OGT and OGA in vitro. Our enzymatic assays with recombinantly expressed human OGT revealed that the unmodified and PTM-modified histone H3 tails are not substrates for OGT at both sites, Ser10 and Thr32. In addition, full length histone H3 was not a substrate for OGT. Conversely, our work demonstrates that synthetic peptides containing the GlcNAc functionality at Ser10 are substrates for recombinantly expressed human OGA, yielding deglycosylated histone H3 peptides. We also show that the catalytic domains of human histone lysine methyltransferases G9a, GLP and SETD7 and histone lysine acetyltransferases PCAF and GCN5 do somewhat tolerate glycosylated H3Ser10 close to lysine residues that undergo methylation and acetylation reactions, respectively. Overall, this work indicates that GlcNAcylation of histone H3 tail peptide in the presence of OGT does not occur in vitro.
Collapse
|
3
|
Minor structural changes, major functional impacts: posttranslational modifications and drug targets. Arch Pharm Res 2022; 45:693-703. [PMID: 36251238 DOI: 10.1007/s12272-022-01409-y] [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: 10/16/2021] [Accepted: 09/28/2022] [Indexed: 11/27/2022]
Abstract
Posttranslational modifications (PTMs) are essential mechanisms that provide chemical diversity to proteins. The additional functional and structural elements can be introduced to exceed the primary amino acid composition. PTMs impact key biological and physiological processes including cell signaling, metabolism, protein degradation and influences interactions with other macromolecules. However, characterization of the structural and functional signatures of modified proteins has been historically limited. Since defects in PTMs are linked to numerous disorders and diseases, PTMs and their modifying enzymes are considered as potential drug targets. This has fueled new initiatives to determine how PTMs affect protein structure and function. In this review, I summarize some of the major, well-studied protein PTMs and related drug targets. Since PTMs are widely used for therapeutic targets or disease markers, highlighting structural changes after PTM provides new frontiers in understanding the detailed mechanism and related drug developments.
Collapse
|
4
|
Maas MN, Hintzen JCJ, Mecinović J. Probing lysine posttranslational modifications by unnatural amino acids. Chem Commun (Camb) 2022; 58:7216-7231. [PMID: 35678513 DOI: 10.1039/d2cc00708h] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Posttranslational modifications, typically small chemical tags attached on amino acids following protein biosynthesis, have a profound effect on protein structure and function. Numerous chemically and structurally diverse posttranslational modifications, including methylation, acetylation, hydroxylation, and ubiquitination, have been identified and characterised on lysine residues in proteins. In this feature article, we focus on chemical tools that rely on the site-specific incorporation of unnatural amino acids into peptides and proteins to probe posttranslational modifications of lysine. We highlight that simple amino acid mimics enable detailed mechanistic and functional assignment of enzymes that install and remove such modifications, and proteins that specifically recognise lysine posttranslational modifications.
Collapse
Affiliation(s)
- Marijn N Maas
- 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.
| |
Collapse
|
5
|
Hintzen JCJ, Merx J, Maas MN, Langens SGHA, White PB, Boltje TJ, Mecinović J. Amide-derived lysine analogues as substrates and inhibitors of histone lysine methyltransferases and acetyltransferases. Org Biomol Chem 2021; 20:173-181. [PMID: 34877957 DOI: 10.1039/d1ob02191e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Histone lysine methyltransferases and acetyltransferases are two classes of epigenetic enzymes that play pivotal roles in human gene regulation. Although they both recognise and posttranslationally modify lysine residues in histone proteins, their difference in histone peptide-based substrates and inhibitors remains to be firmly established. Here, we have synthesised lysine mimics that posses an amide bond linker in the side chain, incorporated them into histone H3 tail peptides, and examined synthetic histone peptides as substrates and inhibitors for human lysine methyltransferases and acetyltransferases. This work demonstrates that histone lysine methyltransferases G9a and GLP do catalyse methylation of the most similar lysine mimic, whereas they typically do not tolerate more sterically demanding side chains. In contrast, histone lysine acetyltransferases GCN5 and PCAF do not catalyse acetylation of the same panel of lysine analogues. Our results also identify potent H3-based inhibitors of GLP methyltransferase, providing a basis for development of peptidomimetics for targeting KMT enzymes.
Collapse
Affiliation(s)
- Jordi C J Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| | - Jona Merx
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands.
| | - Marijn N Maas
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| | - Sabine G H A Langens
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands.
| | - Paul B White
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands.
| | - Thomas J Boltje
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands.
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| |
Collapse
|
6
|
Hintzen JCJ, Luo Y, Porzberg MRB, White PB, Jian J, Proietti G, Mecinović J. γ-Difluorolysine as a 19F NMR probe for histone lysine methyltransferases and acetyltransferases. Chem Commun (Camb) 2021; 57:6788-6791. [PMID: 34137401 DOI: 10.1039/d1cc02589a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Histone lysine methylation and acetylation are important posttranslational modifications that regulate gene expression in humans. Due to the interplay of these two modifications, new chemical methods to study lysine posttranslational modifications are highly desired. Here, we report the use of γ-difluorolysine as a lysine mimic and 19F NMR probe for examinations of histone methylation and acetylation.
Collapse
Affiliation(s)
- Jordi C J Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark.
| | - Yan Luo
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark. and College of Pharmacy & International Academy of Targeted Therapeutics and Innovation, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Miriam R B Porzberg
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark.
| | - Paul B White
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Jie Jian
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark.
| | - Giordano Proietti
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark.
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark.
| |
Collapse
|
7
|
Pereira BMV, Katakia YT, Majumder S, Thieme K. Unraveling the epigenetic landscape of glomerular cells in kidney disease. J Mol Med (Berl) 2021; 99:785-803. [PMID: 33763722 DOI: 10.1007/s00109-021-02066-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 01/19/2023]
Abstract
Chronic kidney disease (CKD) is a major public health concern and its prevalence and incidence are rising quickly. It is a non-communicable disease primarily caused by diabetes and/or hypertension and is associated with high morbidity and mortality. Despite decades of research efforts, the pathogenesis of CKD remains a puzzle with missing pieces. Understanding the cellular and molecular mechanisms that govern the loss of kidney function is crucial. Abrupt regulation of gene expression in kidney cells is apparent in CKD and shown to be responsible for disease onset and progression. Gene expression regulation extends beyond DNA sequence and involves epigenetic mechanisms including changes in DNA methylation and post-translational modifications of histones, driven by the activity of specific enzymes. Recent advances demonstrate the essential participation of epigenetics in kidney (patho)physiology, as its actions regulate both the integrity of cells but also triggers deleterious signaling pathways. Here, we review the known epigenetic processes regulating the complex filtration unit of the kidney, the glomeruli. The review will elaborate on novel insights into how epigenetics contributes to cell injury in the CKD setting majorly focusing on kidney glomerular cells: the glomerular endothelial cells, the mesangial cells, and the specialized and terminally differentiated podocyte cells.
Collapse
Affiliation(s)
- Beatriz Maria Veloso Pereira
- Laboratório de Bases Celulares e Moleculares da Fisiologia Renal, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biomédicas, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Yash T Katakia
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Pilani, Rajasthan, India
| | - Syamantak Majumder
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Pilani, Rajasthan, India
| | - Karina Thieme
- Laboratório de Bases Celulares e Moleculares da Fisiologia Renal, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biomédicas, Universidade de Sao Paulo, Sao Paulo, SP, Brazil.
| |
Collapse
|
8
|
Proietti G, Wang Y, Punzo C, Mecinović J. Substrate Scope for Human Histone Lysine Acetyltransferase KAT8. Int J Mol Sci 2021; 22:ijms22020846. [PMID: 33467728 PMCID: PMC7830570 DOI: 10.3390/ijms22020846] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/16/2022] Open
Abstract
Biomedically important histone lysine acetyltransferase KAT8 catalyses the acetyl coenzyme A-dependent acetylation of lysine on histone and other proteins. Here, we explore the ability of human KAT8 to catalyse the acetylation of histone H4 peptides possessing lysine and its analogues at position 16 (H4K16). Our synthetic and enzymatic studies on chemically and structurally diverse lysine mimics demonstrate that KAT8 also has a capacity to acetylate selected lysine analogues that possess subtle changes on the side chain and main chain. Overall, this work highlights that KAT8 has a broader substrate scope beyond natural lysine, and contributes to the design of new chemical probes targeting KAT8 and other members of the histone lysine acetyltransferase (KAT) family.
Collapse
Affiliation(s)
- Giordano Proietti
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark; (G.P.); (C.P.)
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands;
| | - Yali Wang
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands;
- Department of Blood Transfusion, Jilin University, 126 Xiantai Street, Changchun 130033, China
| | - Chiara Punzo
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark; (G.P.); (C.P.)
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark; (G.P.); (C.P.)
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands;
- Correspondence:
| |
Collapse
|