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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Khalily MP, Soydan M. Peptide-based diagnostic and therapeutic agents: Where we are and where we are heading? Chem Biol Drug Des 2023; 101:772-793. [PMID: 36366980 DOI: 10.1111/cbdd.14180] [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: 07/26/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Peptides are increasingly present in all branches of medicine as innovative drugs, imaging agents, theragnostic, and constituent moieties of other sophisticated drugs such as peptide-drug conjugates. Due to new developments in chemical synthesis strategies, computational biology, recombinant technology, and chemical biology, peptide drug development has made a great progress in the last decade. Numerous natural peptides and peptide mimics have been obtained and studied, covering multiple therapeutic areas. Even though peptides have been investigated across the wide therapeutic spectrum, oncology, metabolism, and endocrinology are the most frequent medical indications of them. This review summarizes the current use of and the emerging new opportunities of peptides for diagnosis and treatment of various diseases.
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Affiliation(s)
- Melek P Khalily
- Department of Basic Science and Health, Cannabis Research Institute, Yozgat Bozok University, Yozgat, Turkey
| | - Medine Soydan
- Department of Chemistry, Faculty of Arts and Science, Middle East Technical University, Ankara, Turkey
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3
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Sondag D, Verhoeven S, Löwik DWPM, van Geffen M, Veer CV, van Heerde WL, Boltje TJ, Rutjes FPJT. Activity Sensing of Coagulation and Fibrinolytic Proteases. Chemistry 2022; 29:e202203473. [PMID: 36484562 DOI: 10.1002/chem.202203473] [Citation(s) in RCA: 4] [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] [Received: 11/08/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
The blood coagulation cascade is a complex physiological process involving the action of multiple coupled enzymes, cofactors, and substrates, ultimately leading to clot formation. Serine proteases have a crucial role, and aberrations in their activity can lead to life-threatening bleeding disorders and thrombosis. This review summarizes the essential proteases involved in blood coagulation and fibrinolysis, the endogenous peptide sequences they recognize and hydrolyze, and synthetic peptide probes based on these sequences to measure their activity. The information in this review can contribute to developing novel anticoagulant therapies and specific substrates for point-of-care diagnosis of coagulation pathologies.
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Affiliation(s)
- Daan Sondag
- Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Stijn Verhoeven
- Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Dennis W P M Löwik
- Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Mark van Geffen
- Enzyre BV, Novio Tech Campus, Transistorweg 5-i, 6534 AT, Nijmegen, The Netherlands
| | - Cornelis Van't Veer
- Enzyre BV, Novio Tech Campus, Transistorweg 5-i, 6534 AT, Nijmegen, The Netherlands
| | - Waander L van Heerde
- Enzyre BV, Novio Tech Campus, Transistorweg 5-i, 6534 AT, Nijmegen, The Netherlands.,Department of Haematology, Radboud University Medical Centre, 6525, Nijmegen, The Netherlands.,Haemophilia Treatment Centre Nijmegen Eindhoven Maastricht (HTC-NEM), The Netherlands
| | - Thomas J Boltje
- Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Floris P J T Rutjes
- Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
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Kelly M, Cambray S, McCarthy KA, Wang W, Geisinger E, Ortiz-Marquez J, van Opijnen T, Gao J. Peptide Probes of Colistin Resistance Discovered via Chemically Enhanced Phage Display. ACS Infect Dis 2020; 6:2410-2418. [PMID: 32786283 DOI: 10.1021/acsinfecdis.0c00206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 01/11/2023]
Abstract
Colistin is an antibiotic of last resort used to treat infections caused by multidrug-resistant Gram-negative bacterial pathogens. The recent surge in reported cases of colistin-resistant infections urgently calls for fast and reliable diagnostic methods, which can be used for the facile detection and proper treatment of these challenging infections. A major mechanism of colistin resistance involves phosphoethanolamine (PE) modification of lipopolysaccharide (LPS), the molecular target of colistin. This LPS modification mechanism has been recently reported to be transferrable via a plasmid-carried mcr-1 gene, which is particularly concerning as it may readily confer colistin resistance to a wide array of bacterial pathogens. To develop molecular tools to allow facile detection of colistin resistance, we have herein enlisted a novel phage library that incorporates dynamic covalent warheads to recognize PE modifications on bacterial cells. Screening of this chemically modified phage library against colistin-resistant pathogens revealed a number of peptide probes that readily differentiate colistin-resistant bacterial strains from their colistin-susceptible counterparts. With a fluorophore label, these peptide probes selectively stain colistin-resistant bacteria at sub-to-low micromolar concentrations. The bacterial staining is minimally inhibited by the presence of serum proteins or even blood serum. Mechanistic studies indicate that our peptide probes bind colistin-resistant bacteria primarily by targeting PE-modified lipids. However, some species-specific features of the cell surface can also contribute to the peptides' association to bacterial cells. Further elucidation of such cell surface features may give molecular probes with improved species and strain specificity, which will enable bacterial infection diagnosis with high precision.
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Affiliation(s)
- Michael Kelly
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Samantha Cambray
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Kelly A. McCarthy
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Wenjian Wang
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Edward Geisinger
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Juan Ortiz-Marquez
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Jianmin Gao
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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