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Mohd S, Oder A, Specker E, Neuenschwander M, Von Kries JP, Daumke O. Identification of drug-like molecules targeting the ATPase activity of dynamin-like EHD4. PLoS One 2024; 19:e0302704. [PMID: 39074100 DOI: 10.1371/journal.pone.0302704] [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: 04/09/2024] [Accepted: 07/13/2024] [Indexed: 07/31/2024] Open
Abstract
Eps15 (epidermal growth factor receptor pathway substrate 15) homology domain-containing proteins (EHDs) comprise a family of eukaryotic dynamin-related ATPases that participate in various endocytic membrane trafficking pathways. Dysregulation of EHDs function has been implicated in various diseases, including cancer. The lack of small molecule inhibitors which acutely target individual EHD members has hampered progress in dissecting their detailed cellular membrane trafficking pathways and their function during disease. Here, we established a Malachite green-based assay compatible with high throughput screening to monitor the liposome-stimulated ATPase of EHD4. In this way, we identified a drug-like molecule that inhibited EHD4's liposome-stimulated ATPase activity. Structure activity relationship (SAR) studies indicated sites of preferred substitutions for more potent inhibitor synthesis. Moreover, the assay optimization in this work can be applied to other dynamin family members showing a weak and liposome-dependent nucleotide hydrolysis activity.
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Affiliation(s)
- Saif Mohd
- Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Andreas Oder
- Screening Unit, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Edgar Specker
- Screening Unit, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Martin Neuenschwander
- Screening Unit, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Jens Peter Von Kries
- Screening Unit, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Oliver Daumke
- Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
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2
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Gorenflos López JL, Dornan GL, Boback N, Neuenschwander M, Oder A, Kemnitz-Hassanin K, Schmieder P, Specker E, Asikoglu HC, Oberdanner C, Seyffarth C, von Kries JP, Lauster D, Hinderlich S, Hackenberger CPR. Small Molecules Targeting Human UDP-GlcNAc 2-Epimerase. Chembiochem 2023; 24:e202300555. [PMID: 37769151 DOI: 10.1002/cbic.202300555] [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: 08/08/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023]
Abstract
Uridine diphosphate N-acetylglucosamine 2-epimerase (GNE) is a key enzyme in the sialic acid biosynthesis pathway. Sialic acids are primarily terminal carbohydrates on glycans and play fundamental roles in health and disease. In search of effective GNE inhibitors not based on a carbohydrate scaffold, we performed a high-throughput screening campaign of 68,640 drug-like small molecules against recombinant GNE using a UDP detection assay. We validated nine of the primary actives with an orthogonal real-time NMR assay and verified their IC50 values in the low micromolar to nanomolar range manually. Stability and solubility studies revealed three compounds for further evaluation. Thermal shift assays, analytical size exclusion, and interferometric scattering microscopy demonstrated that the GNE inhibitors acted on the oligomeric state of the protein. Finally, hydrogen-deuterium exchange mass spectrometry (HDX-MS) revealed which sections of GNE were shifted upon the addition of the inhibitors. In summary, we have identified three small molecules as GNE inhibitors with high potency in vitro, which serve as promising candidates to modulate sialic acid biosynthesis in more complex systems.
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Affiliation(s)
- Jacob L Gorenflos López
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
- Humboldt Universität zu Berlin, Department Chemie, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - Gillian L Dornan
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Nico Boback
- Freie Universität Berlin, Institut für Pharmazie, Biopharmazeutika, Kelchstr. 31, 12169, Berlin, Germany
| | - Martin Neuenschwander
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Andreas Oder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Kristin Kemnitz-Hassanin
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Edgar Specker
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Hatice Ceyda Asikoglu
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
- Berliner Hochschule für Technik (BHT), Seestrasse 64, 13347, Berlin, Germany
| | | | - Carola Seyffarth
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Jens Peter von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Daniel Lauster
- Freie Universität Berlin, Institut für Pharmazie, Biopharmazeutika, Kelchstr. 31, 12169, Berlin, Germany
| | - Stephan Hinderlich
- Berliner Hochschule für Technik (BHT), Seestrasse 64, 13347, Berlin, Germany
| | - Christian P R Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125, Berlin, Germany
- Humboldt Universität zu Berlin, Department Chemie, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
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Lloyd MD, Yevglevskis M, Nathubhai A, James TD, Threadgill MD, Woodman TJ. Racemases and epimerases operating through a 1,1-proton transfer mechanism: reactivity, mechanism and inhibition. Chem Soc Rev 2021; 50:5952-5984. [PMID: 34027955 PMCID: PMC8142540 DOI: 10.1039/d0cs00540a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Racemases and epimerases catalyse changes in the stereochemical configurations of chiral centres and are of interest as model enzymes and as biotechnological tools. They also occupy pivotal positions within metabolic pathways and, hence, many of them are important drug targets. This review summarises the catalytic mechanisms of PLP-dependent, enolase family and cofactor-independent racemases and epimerases operating by a deprotonation/reprotonation (1,1-proton transfer) mechanism and methods for measuring their catalytic activity. Strategies for inhibiting these enzymes are reviewed, as are specific examples of inhibitors. Rational design of inhibitors based on substrates has been extensively explored but there is considerable scope for development of transition-state mimics and covalent inhibitors and for the identification of inhibitors by high-throughput, fragment and virtual screening approaches. The increasing availability of enzyme structures obtained using X-ray crystallography will facilitate development of inhibitors by rational design and fragment screening, whilst protein models will facilitate development of transition-state mimics.
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Affiliation(s)
- Matthew D Lloyd
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
| | - Maksims Yevglevskis
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and CatSci Ltd., CBTC2, Capital Business Park, Wentloog, Cardiff CF3 2PX, UK
| | - Amit Nathubhai
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and University of Sunderland, School of Pharmacy & Pharmaceutical Sciences, Sciences Complex, Sunderland SR1 3SD, UK
| | - Tony D James
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK and School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, People's Republic of China
| | - Michael D Threadgill
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth SY23 3BY, UK
| | - Timothy J Woodman
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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Poier N, Hochstöger J, Hackenberg S, Scherzad A, Bregenzer M, Schopper D, Kleinsasser N. Effects of Zinc Oxide Nanoparticles in HUVEC: Cyto- and Genotoxicity and Functional Impairment After Long-Term and Repetitive Exposure in vitro. Int J Nanomedicine 2020; 15:4441-4452. [PMID: 32606688 PMCID: PMC7319515 DOI: 10.2147/ijn.s246797] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/17/2020] [Indexed: 12/13/2022] Open
Abstract
Purpose The present study focuses on threshold levels for cytotoxicity after long-term and repetitive exposure for HUVEC as a model for the specific microvascular endothelial system. Furthermore, possible genotoxic effects and functional impairment caused by ZnO NPs in HUVEC are elucidated. Methods Thresholds for cytotoxic effects are determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and Annexin V assay. To demonstrate DNA damage, single-cell microgel electrophoresis (comet) assay is performed after exposure to sub-cytotoxic concentrations of ZnO NPs. The proliferation assay, dot blot assay and capillary tube formation assay are also carried out to analyze functional impairment. Results NPs showed to be spherical in shape with an average size of 45–55 nm. Long-term exposure as well as repetitive exposure with ZnO NPs exceeding 25 µg/mL lead to decreased viability in HUVEC. In addition, DNA damage was indicated by the comet assay after long-term and repetitive exposure. Twenty-four hours after long-term exposure, the proliferation assay does not show any difference between negative control and exposed cells. Forty-eight hours after exposure, HUVEC show an inverse concentration-related ability to proliferate. The dot blot assay provides evidence that ZnO NPs lead to a decreased release of VEGF, while capillary tube formation assay shows restriction in the ability of HUVEC to build tubes and meshes as a first step in angiogenesis. Conclusion Sub-cytotoxic concentrations of ZnO NPs lead to DNA damage and functional impairment in HUVEC. Based on these data, ZnO NPs may affect neo-angiogenesis. Further investigation based on tissue cultures is required to elucidate the impact of ZnO NPs on human cell systems.
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Affiliation(s)
- Nikolaus Poier
- Department of Otorhinolaryngology, Head and Neck Surgery, Kepler University Hospital, Linz 4021, Austria.,Medical Faculty, Johannes Kepler University Linz, Linz 4040, Austria
| | - Johannes Hochstöger
- Department of Otorhinolaryngology, Head and Neck Surgery, Kepler University Hospital, Linz 4021, Austria.,Medical Faculty, Johannes Kepler University Linz, Linz 4040, Austria
| | - Stephan Hackenberg
- Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University of Wuerzburg, Würzburg 97080, Germany
| | - Agmal Scherzad
- Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University of Wuerzburg, Würzburg 97080, Germany
| | - Maximilian Bregenzer
- Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University of Wuerzburg, Würzburg 97080, Germany
| | - Dominik Schopper
- Department of Otorhinolaryngology, Head and Neck Surgery, Kepler University Hospital, Linz 4021, Austria.,Medical Faculty, Johannes Kepler University Linz, Linz 4040, Austria
| | - Norbert Kleinsasser
- Department of Otorhinolaryngology, Head and Neck Surgery, Kepler University Hospital, Linz 4021, Austria.,Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University of Wuerzburg, Würzburg 97080, Germany
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Sialic acid as a target for the development of novel antiangiogenic strategies. Future Med Chem 2018; 10:2835-2854. [PMID: 30539670 DOI: 10.4155/fmc-2018-0298] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Sialic acid is associated with glycoproteins and gangliosides of eukaryotic cells. It regulates various molecular interactions, being implicated in inflammation and cancer, where its expression is regulated by sialyltransferases and sialidases. Angiogenesis, the formation of new capillaries, takes place during inflammation and cancer, and represents the outcome of several interactions occurring at the endothelial surface among angiogenic growth factors, inhibitors, receptors, gangliosides and cell-adhesion molecules. Here, we elaborate on the evidences that many structures involved in angiogenesis are sialylated and that their interactions depend on sialic acid with implications in angiogenesis itself, inflammation and cancer. We also discuss the possibility to exploit sialic acid as a target for the development of novel antiangiogenic drugs.
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Abstract
Sialic acids are cytoprotectors, mainly localized on the surface of cell membranes with multiple and outstanding cell biological functions. The history of their structural analysis, occurrence, and functions is fascinating and described in this review. Reports from different researchers on apparently similar substances from a variety of biological materials led to the identification of a 9-carbon monosaccharide, which in 1957 was designated "sialic acid." The most frequently occurring member of the sialic acid family is N-acetylneuraminic acid, followed by N-glycolylneuraminic acid and O-acetylated derivatives, and up to now over about 80 neuraminic acid derivatives have been described. They appeared first in the animal kingdom, ranging from echinoderms up to higher animals, in many microorganisms, and are also expressed in insects, but are absent in higher plants. Sialic acids are masks and ligands and play as such dual roles in biology. Their involvement in immunology and tumor biology, as well as in hereditary diseases, cannot be underestimated. N-Glycolylneuraminic acid is very special, as this sugar cannot be expressed by humans, but is a xenoantigen with pathogenetic potential. Sialidases (neuraminidases), which liberate sialic acids from cellular compounds, had been known from very early on from studies with influenza viruses. Sialyltransferases, which are responsible for the sialylation of glycans and elongation of polysialic acids, are studied because of their significance in development and, for instance, in cancer. As more information about the functions in health and disease is acquired, the use of sialic acids in the treatment of diseases is also envisaged.
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Affiliation(s)
- Roland Schauer
- Biochemisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
| | - Johannis P Kamerling
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
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The benefits of in silico modeling to identify possible small-molecule drugs and their off-target interactions. Future Med Chem 2018; 10:423-432. [PMID: 29380627 DOI: 10.4155/fmc-2017-0151] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The research into the use of small molecules as drugs continues to be a key driver in the development of molecular databases, computer-aided drug design software and collaborative platforms. The evolution of computational approaches is driven by the essential criteria that a drug molecule has to fulfill, from the affinity to targets to minimal side effects while having adequate absorption, distribution, metabolism, and excretion (ADME) properties. A combination of ligand- and structure-based drug development approaches is already used to obtain consensus predictions of small molecule activities and their off-target interactions. Further integration of these methods into easy-to-use workflows informed by systems biology could realize the full potential of available data in the drug discovery and reduce the attrition of drug candidates.
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