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Solari FA, Krahn D, Swieringa F, Verhelst S, Rassaf T, Tasdogan A, Zahedi RP, Lorenz K, Renné T, Heemskerk JWM, Sickmann A. Multi-omics approaches to study platelet mechanisms. Curr Opin Chem Biol 2023; 73:102253. [PMID: 36689818 DOI: 10.1016/j.cbpa.2022.102253] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 08/15/2022] [Revised: 11/17/2022] [Accepted: 11/27/2022] [Indexed: 01/22/2023]
Abstract
Platelets are small anucleate cell fragments (2-4 μm in diameter) in the blood, which play an essential role in thrombosis and hemostasis. Genetic or acquired platelet dysfunctions are linked to bleeding, increased risk of thromboembolic events and cardiovascular diseases. Advanced proteomic approaches may pave the way to a better understanding of the roles of platelets in hemostasis, and pathophysiological processes such as inflammation, metastatic spread and thrombosis. Further insights into the molecular biology of platelets are crucial to aid drug development and identify diagnostic markers of platelet activation. Platelet activation is known to be an extremely rapid process and involves multiple post-translational mechanisms at sub second time scale, including proteolysis and phosphorylation. Multi-omics technologies and biochemical approaches can be exploited to precisely probe and define these posttranslational pathways. Notably, the absence of a nucleus in platelets significantly reduces the number of present proteins, simplifying mass spectrometry-based proteomics and metabolomics approaches.
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Affiliation(s)
- Fiorella A Solari
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44143, Dortmund, Germany
| | - Daniel Krahn
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44143, Dortmund, Germany
| | - Frauke Swieringa
- Synapse Research Institute Maastricht, 6217 KD, Maastricht, the Netherlands
| | - Steven Verhelst
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44143, Dortmund, Germany; Department of Cellular and Molecular Medicine, KU Leuven, University of Leuven, Leuven, Belgium
| | - Tienush Rassaf
- Clinic for Cardiology and Angiology, University Hospital Essen, Essen, Germany
| | - Alpaslan Tasdogan
- Department of Dermatology, University Hospital Essen & German Cancer Consortium, Partner Site, Essen, Germany
| | - Rene P Zahedi
- Department of Internal Medicine, University of Manitoba, Canada
| | - Kristina Lorenz
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44143, Dortmund, Germany; Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Thomas Renné
- Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44143, Dortmund, Germany; Medizinische Fakultät, Ruhr-Universität Bochum, Bochum, Germany; Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, United Kingdom.
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Olson A, Tunér M, Verhelst S. A concise review of glycerol derivatives for use as fuel additives. Heliyon 2023; 9:e13041. [PMID: 36711277 PMCID: PMC9879789 DOI: 10.1016/j.heliyon.2023.e13041] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 01/09/2023] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
Due to renewable fuel mandates worldwide, the increase in biodiesel production has caused an oversupply of low-cost glycerol on the markets, which can negatively affect the sustainability of the biodiesel industry as a whole. In order to avoid that scenario, the transformation of glycerol into value-added products has been investigated, and the production of additives for internal combustion engine fuels is one good example of glycerol valorization. The present work presents a summary of the literature describing the most important chemical pathways through which glycerol can be converted into fuel additives, to be subsequently mixed with either gasoline, biodiesel, or diesel fuel. The focus is on the three major categories, namely glycerol acetals/ketals, ethers, and esters (acetates). Moreover, the effectiveness of the different glycerol-derived compounds is illustrated through several examples from the literature. Finally, a few research gaps on the topic are identified and suggestions for future work are described.
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Ulens C, Bisseling Q, Brams M, Mehregan A, Evans GL, Pasini D, Beard H, Verhelst S, Fish A, van Dorst S, Kambara K, Bertrand D. Molecular Recognition of Neonicotinoid Insecticides by Honeybee Nicotinic Receptors and ACHBP Homologues. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.3171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Arutyunova E, Jiang Z, Yang J, Kulepa AN, Young HS, Verhelst S, O’Donoghue AJ, Lemieux MJ. An internally quenched peptide as a new model substrate for rhomboid intramembrane proteases. Biol Chem 2018; 399:1389-1397. [DOI: 10.1515/hsz-2018-0255] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/09/2018] [Indexed: 12/31/2022]
Abstract
AbstractRhomboids are ubiquitous intramembrane serine proteases that cleave transmembrane substrates. Their functions include growth factor signaling, mitochondrial homeostasis, and parasite invasion. A recent study revealed that theEscherichia colirhomboid protease EcGlpG is essential for its extraintestinal pathogenic colonization within the gut. Crystal structures of EcGlpG and theHaemophilus influenzaerhomboid protease HiGlpG have deciphered an active site that is buried within the lipid bilayer but exposed to the aqueous environment via a cavity at the periplasmic face. A lack of physiological transmembrane substrates has hampered progression for understanding their catalytic mechanism and screening inhibitor libraries. To identify a soluble substrate for use in the study of rhomboid proteases, an array of internally quenched peptides were assayed with HiGlpG, EcGlpG and PsAarA fromProvidencia stuartti. One substrate was identified that was cleaved by all three rhomboid proteases, with HiGlpG having the highest cleavage efficiency. Mass spectrometry analysis determined that all enzymes hydrolyze this substrate between norvaline and tryptophan. Kinetic analysis in both detergent and bicellular systems demonstrated that this substrate can be cleaved in solution and in the lipid environment. The substrate was subsequently used to screen a panel of benzoxazin-4-one inhibitors to validate its use in inhibitor discovery.
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Goel P, Jumpertz T, Mikles DC, Tichá A, Nguyen MTN, Verhelst S, Hubalek M, Johnson DC, Bachovchin DA, Ogorek I, Pietrzik CU, Strisovsky K, Schmidt B, Weggen S. Discovery and Biological Evaluation of Potent and Selective N-Methylene Saccharin-Derived Inhibitors for Rhomboid Intramembrane Proteases. Biochemistry 2017; 56:6713-6725. [PMID: 29185711 DOI: 10.1021/acs.biochem.7b01066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rhomboids are intramembrane serine proteases and belong to the group of structurally and biochemically most comprehensively characterized membrane proteins. They are highly conserved and ubiquitously distributed in all kingdoms of life and function in a wide range of biological processes, including epidermal growth factor signaling, mitochondrial dynamics, and apoptosis. Importantly, rhomboids have been associated with multiple diseases, including Parkinson's disease, type 2 diabetes, and malaria. However, despite a thorough understanding of many structural and functional aspects of rhomboids, potent and selective inhibitors of these intramembrane proteases are still not available. In this study, we describe the computer-based rational design, chemical synthesis, and biological evaluation of novel N-methylene saccharin-based rhomboid protease inhibitors. Saccharin inhibitors displayed inhibitory potency in the submicromolar range, effectiveness against rhomboids both in vitro and in live Escherichia coli cells, and substantially improved selectivity against human serine hydrolases compared to those of previously known rhomboid inhibitors. Consequently, N-methylene saccharins are promising new templates for the development of rhomboid inhibitors, providing novel tools for probing rhomboid functions in physiology and disease.
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Affiliation(s)
- Parul Goel
- Department of Neuropathology, Heinrich-Heine University Duesseldorf , Moorenstrasse 5, 40225 Duesseldorf, Germany.,Clemens Schoepf Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt , Alarich-Weiss-Strasse 4-8, 64287 Darmstadt, Germany
| | - Thorsten Jumpertz
- Department of Neuropathology, Heinrich-Heine University Duesseldorf , Moorenstrasse 5, 40225 Duesseldorf, Germany
| | - David C Mikles
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Anežka Tichá
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Minh T N Nguyen
- Chemical Proteomics Group, Leibnitz Institute for Analytical Sciences (ISAS) e.V. , Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Steven Verhelst
- Chemical Proteomics Group, Leibnitz Institute for Analytical Sciences (ISAS) e.V. , Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.,Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, University of Leuven , Herestraat 49, Box 802, 3000 Leuven, Belgium
| | - Martin Hubalek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Darren C Johnson
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center , 1275 York Avenue, Box 428, New York, New York 10065, United States
| | - Daniel A Bachovchin
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center , 1275 York Avenue, Box 428, New York, New York 10065, United States
| | - Isabella Ogorek
- Department of Neuropathology, Heinrich-Heine University Duesseldorf , Moorenstrasse 5, 40225 Duesseldorf, Germany
| | - Claus U Pietrzik
- Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz , Duesbergweg 6, 55128 Mainz, Germany
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Boris Schmidt
- Clemens Schoepf Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt , Alarich-Weiss-Strasse 4-8, 64287 Darmstadt, Germany
| | - Sascha Weggen
- Department of Neuropathology, Heinrich-Heine University Duesseldorf , Moorenstrasse 5, 40225 Duesseldorf, Germany
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Piloto-Rodríguez R, Melo EA, Goyos-Pérez L, Verhelst S. Conversion of by-products from the vegetable oil industry into biodiesel and its use in internal combustion engines: a review. Braz J Chem Eng 2014. [DOI: 10.1590/0104-6632.20140312s00002763] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Sánchez-Borroto Y, Piloto-Rodriguez R, Errasti M, Sierens R, Verhelst S. Prediction of Cetane Number and Ignition Delay of Biodiesel Using Artificial Neural Networks. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.egypro.2014.10.297] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Vinothkumar KR, Strisovsky K, Andreeva A, Christova Y, Verhelst S, Freeman M. The structural basis for catalysis and substrate specificity of a rhomboid protease. EMBO J 2010; 29:3797-809. [PMID: 20890268 DOI: 10.1038/emboj.2010.243] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 09/06/2010] [Indexed: 12/28/2022] Open
Abstract
Rhomboids are intramembrane proteases that use a catalytic dyad of serine and histidine for proteolysis. They are conserved in both prokaryotes and eukaryotes and regulate cellular processes as diverse as intercellular signalling, parasitic invasion of host cells, and mitochondrial morphology. Their widespread biological significance and consequent medical potential provides a strong incentive to understand the mechanism of these unusual enzymes for identification of specific inhibitors. In this study, we describe the structure of Escherichia coli rhomboid GlpG covalently bound to a mechanism-based isocoumarin inhibitor. We identify the position of the oxyanion hole, and the S₁- and S₂'-binding subsites of GlpG, which are the key determinants of substrate specificity. The inhibitor-bound structure suggests that subtle structural change is sufficient for catalysis, as opposed to large changes proposed from previous structures of unliganded GlpG. Using bound inhibitor as a template, we present a model for substrate binding at the active site and biochemically test its validity. This study provides a foundation for a structural explanation of rhomboid specificity and mechanism, and for inhibitor design.
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Shi GP, Bryant RA, Riese R, Verhelst S, Driessen C, Li Z, Bromme D, Ploegh HL, Chapman HA. Role for cathepsin F in invariant chain processing and major histocompatibility complex class II peptide loading by macrophages. J Exp Med 2000; 191:1177-86. [PMID: 10748235 PMCID: PMC2193169 DOI: 10.1084/jem.191.7.1177] [Citation(s) in RCA: 179] [Impact Index Per Article: 7.5] [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] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The major histocompatibility complex (MHC) class II-associated invariant chain (Ii) regulates intracellular trafficking and peptide loading of MHC class II molecules. Such loading occurs after endosomal degradation of the invariant chain to a approximately 3-kD peptide termed CLIP (class II-associated invariant chain peptide). Cathepsins L and S have both been implicated in degradation of Ii to CLIP in thymus and peripheral lymphoid organs, respectively. However, macrophages from mice deficient in both cathepsins S and L can process Ii and load peptides onto MHC class II dimers normally. Both processes are blocked by a cysteine protease inhibitor, indicating the involvement of an additional Ii-processing enzyme(s). Comparison of cysteine proteases expressed by macrophages with those found in splenocytes and dendritic cells revealed two enzymes expressed exclusively in macrophages, cathepsins Z and F. Recombinant cathepsin Z did not generate CLIP from Ii-MHC class II complexes, whereas cathepsin F was as efficient as cathepsin S in CLIP generation. Inhibition of cathepsin F activity and MHC class II peptide loading by macrophages exhibited similar specificity and activity profiles. These experiments show that cathepsin F, in a subset of antigen presenting cells (APCs), can efficiently degrade Ii. Different APCs can thus use distinct proteases to mediate MHC class II maturation and peptide loading.
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Affiliation(s)
- Guo-Ping Shi
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Harvard Medical School, Boston, Massachusetts 02115
| | - Rebecca A.R. Bryant
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115
| | - Richard Riese
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Harvard Medical School, Boston, Massachusetts 02115
| | - Steven Verhelst
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115
| | - Christoph Driessen
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115
| | - Zhenqiang Li
- Department of Human Genetics, Mount Sinai School of Medicine, New York, New York 10029
| | - Dieter Bromme
- Department of Human Genetics, Mount Sinai School of Medicine, New York, New York 10029
| | - Hidde L. Ploegh
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115
| | - Harold A. Chapman
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Harvard Medical School, Boston, Massachusetts 02115
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Bogyo M, Verhelst S, Bellingard-Dubouchaud V, Toba S, Greenbaum D. Selective targeting of lysosomal cysteine proteases with radiolabeled electrophilic substrate analogs. Chem Biol 2000; 7:27-38. [PMID: 10662686 DOI: 10.1016/s1074-5521(00)00061-2] [Citation(s) in RCA: 179] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND The lysosomal cysteine proteases of the papain family are some of the best studied proteolytic enzymes. Small-molecule inhibitors and fluorogenic substrate mimics have been used to probe the physiological roles of these proteases. A high degree of homology between family members and overlap in substrate specificity have made elucidating individual protease function, expression and activity difficult. RESULTS Using peptide vinyl sulfones and epoxide as templates, we have generated probes that can be tagged with radioactive iodine. The resulting compounds covalently label various cathepsins and several unidentified polypeptides likely to be proteases. MB-074 was found to be a highly selective probe of cathepsin B activity. Probes that labeled several cathepsins were used to examine the specificity and cell permeability of the CA-074 family of inhibitors. Although CA-074 reportedly acts in vivo, we find it is unable to penetrate cells. Esterifying CA-074 resulted in a cell-permeable inhibitor with dramatically reduced activity and specificity for cathepsin B. The probes were also used to monitor protease activity in primary human tumor tissue and cells derived from human placenta. CONCLUSIONS We have generated a highly selective cathepsin B probe and several less specific reagents for the study of cathepsin biology. The reagents have several advantages over commonly used fluorogenic substrates, allowing inhibitor targets to be identified in a pool of total cellular enzymes. We have used the probes to show that cathepsin activity is regulated in tumor tissues and during differentiation of placental-derived cytotrophoblasts to invasive cells required for establishing blood circulation in a developing embryo.
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Affiliation(s)
- M Bogyo
- Departments of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA.
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