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Goettig P, Koch NG, Budisa N. Non-Canonical Amino Acids in Analyses of Protease Structure and Function. Int J Mol Sci 2023; 24:14035. [PMID: 37762340 PMCID: PMC10531186 DOI: 10.3390/ijms241814035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.
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Affiliation(s)
- Peter Goettig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
| | - Nikolaj G. Koch
- Biocatalysis Group, Technische Universität Berlin, 10623 Berlin, Germany;
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
| | - Nediljko Budisa
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Gitlin-Domagalska A, Dębowski D, Łęgowska A, Stirnberg M, Okońska J, Gütschow M, Rolka K. Design and chemical syntheses of potent matriptase-2 inhibitors based on trypsin inhibitor SFTI-1 isolated from sunflower seeds. Biopolymers 2017; 108. [DOI: 10.1002/bip.23031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 01/16/2023]
Affiliation(s)
- Agata Gitlin-Domagalska
- Department of Molecular Biochemistry; Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63; Gdansk 80-308 Poland
| | - Dawid Dębowski
- Department of Molecular Biochemistry; Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63; Gdansk 80-308 Poland
| | - Anna Łęgowska
- Department of Molecular Biochemistry; Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63; Gdansk 80-308 Poland
| | - Marit Stirnberg
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4; Bonn 53121 Germany
| | - Joanna Okońska
- Department of Molecular Biochemistry; Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63; Gdansk 80-308 Poland
| | - Michael Gütschow
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4; Bonn 53121 Germany
| | - Krzysztof Rolka
- Department of Molecular Biochemistry; Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63; Gdansk 80-308 Poland
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Kuznetsova SS, Kolesanova EF, Talanova AV, Veselovsky AV. [Prospects for the design of new therapeutically significant protease inhibitors based on knottins and sunflower seed trypsin inhibitor (SFTI 1)]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2016; 62:353-68. [PMID: 27562989 DOI: 10.18097/pbmc20166204353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Plant seed knottins, mainly from the Cucurbitacea family, and sunflower seed trypsin inhibitor (SFTI 1) are the most low-molecular canonical peptide inhibitors of serine proteases. High efficiency of inhibition of various serine proteases, structure rigidity together with the possibility of limited variations of amino acid sequences, high chemical stability, lack of toxic properties, opportunity of production by either chemical synthesis or use of heterologous expression systems make these inhibitors attractive templates for design of new compounds for regulation of therapeutically significant serine protease activities. Hence the design of such compounds represents a prospective research field. The review considers structural characteristics of these inhibitors, their properties, methods of preparation and design of new analogs. Examples of successful employment of natural serine protease inhibitors belonging to knottin family and SFTI 1 as templates for the design of highly specific inhibitors of certain proteases are given.
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Affiliation(s)
| | | | - A V Talanova
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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Fittler H, Avrutina O, Empting M, Kolmar H. Potent inhibitors of human matriptase-1 based on the scaffold of sunflower trypsin inhibitor. J Pept Sci 2014; 20:415-20. [DOI: 10.1002/psc.2629] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/28/2014] [Accepted: 03/03/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Heiko Fittler
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry; Technische Universität Darmstadt; Alarich-Weiss-Straße 4 64287 Darmstadt Germany
| | - Olga Avrutina
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry; Technische Universität Darmstadt; Alarich-Weiss-Straße 4 64287 Darmstadt Germany
| | - Martin Empting
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS); Department Drug Design and Optimization; Campus C2.3 66123 Saarbrücken Germany
| | - Harald Kolmar
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry; Technische Universität Darmstadt; Alarich-Weiss-Straße 4 64287 Darmstadt Germany
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Krzywda S, Jaskolski M, Rolka K, Stawikowski MJ. Structure of a proteolytically resistant analogue of (NLys)5SFTI-1 in complex with trypsin: evidence for the direct participation of the Ser214 carbonyl group in serine protease-mediated proteolysis. ACTA ACUST UNITED AC 2014; 70:668-75. [PMID: 24598736 DOI: 10.1107/s1399004713032252] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/26/2013] [Indexed: 11/11/2022]
Abstract
Peptide-peptoid hybrids are found to be potent inhibitors of serine proteases. These engineered peptidomimetics benefit from both types of units of the biopolymeric structure: the natural inhibitor part serves as a good binding template, while the P1-positioned peptoid component provides complete resistance towards proteolysis. In this report, the mechanism of proteolytic resistance of a P1 peptoid-containing analogue is postulated based on the crystal structure of the (NLys)(5)-modified sunflower trypsin inhibitor SFTI-1 in complex with bovine trypsin solved at 1.29 Å resolution. The structural differences between the (NLys)(5)SFTI-1-trypsin complex and the native SFTI-1-trypsin complex are surprisingly small and reveal the key role of the carbonyl group of the Ser214 residue of the enzyme, which is crucial for binding of the inhibitor and plays a crucial role in proteolysis mediated by serine proteases. The incorporated NLys5 peptoid residue prevents Ser214 from forming a hydrogen bond to the P1 residue, and in turn Gln192 does not form a hydrogen bond to the carbonyl group of the P2 residue. It also increases the distance between the Ser214 carbonyl group and the Ser195 residue, thus preventing proteolysis. The hybrid inhibitor structure reported here provides insight into protein-protein interaction, which can be efficiently and selectively probed with the use of peptoids incorporated within endogenous peptide ligands.
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Affiliation(s)
- Szymon Krzywda
- Department of Chemistry, Adam Mickiewicz University, Grunwaldzka 6, 60-780 Poznan, Poland
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Grunwaldzka 6, 60-780 Poznan, Poland
| | - Krzysztof Rolka
- Faculty of Chemistry, University of Gdansk, Stwosza 63, 80-952 Gdansk, Poland
| | - Maciej J Stawikowski
- Torrey Pines Institute For Molecular Studies, 11350 SW Village Parkway, Port St Lucie, FL 34987, USA
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Lesner A, Karna N, Psurski M, Łęgowska A, Wysocka M, Guzow K, Sieradzan A, Sieńczyk M, Trzonkowski P, Pikuła M, Zieliński M, Kosikowska P, Łukajtis R, Łęgowska M, Dębowski D, Wiczk W, Rolka K. Fluorescent analogs of trypsin inhibitor SFTI-1 isolated from sunflower seeds-synthesis and applications. Biopolymers 2014; 102:124-35. [DOI: 10.1002/bip.22442] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/15/2013] [Accepted: 11/07/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Adam Lesner
- Faculty of Chemistry; Gdansk University; Wita Stwosza 63 80-952 Gdansk Poland
| | - Natalia Karna
- Faculty of Chemistry; Gdansk University; Wita Stwosza 63 80-952 Gdansk Poland
| | - Mateusz Psurski
- Division of Medicinal Chemistry and Microbiology, Department of Chemistry; Wrocław University of Technology; Wybrzeze Wyspianskiego 27 50-370 Wroclaw Poland
- Department of Experimental Oncology; Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences; R. Weigla St. 12 Wroclaw 53-114 Poland
| | - Anna Łęgowska
- Faculty of Chemistry; Gdansk University; Wita Stwosza 63 80-952 Gdansk Poland
| | - Magdalena Wysocka
- Faculty of Chemistry; Gdansk University; Wita Stwosza 63 80-952 Gdansk Poland
| | - Katarzyna Guzow
- Faculty of Chemistry; Gdansk University; Wita Stwosza 63 80-952 Gdansk Poland
| | - Adam Sieradzan
- Faculty of Chemistry; Gdansk University; Wita Stwosza 63 80-952 Gdansk Poland
| | - Marcin Sieńczyk
- Division of Medicinal Chemistry and Microbiology, Department of Chemistry; Wrocław University of Technology; Wybrzeze Wyspianskiego 27 50-370 Wroclaw Poland
| | - Piotr Trzonkowski
- Division of Clinical Immunology and Transplantology; Gdansk Medical University; Sklodowskiej Curie 3A 80-210 Gdansk Poland
| | - Michał Pikuła
- Division of Clinical Immunology and Transplantology; Gdansk Medical University; Sklodowskiej Curie 3A 80-210 Gdansk Poland
| | - Maciej Zieliński
- Division of Clinical Immunology and Transplantology; Gdansk Medical University; Sklodowskiej Curie 3A 80-210 Gdansk Poland
| | - Paulina Kosikowska
- Faculty of Chemistry; Gdansk University; Wita Stwosza 63 80-952 Gdansk Poland
| | - Rałał Łukajtis
- Faculty of Chemistry; Gdansk University; Wita Stwosza 63 80-952 Gdansk Poland
| | - Monika Łęgowska
- Faculty of Chemistry; Gdansk University; Wita Stwosza 63 80-952 Gdansk Poland
| | - Dawid Dębowski
- Faculty of Chemistry; Gdansk University; Wita Stwosza 63 80-952 Gdansk Poland
| | - Wiesław Wiczk
- Faculty of Chemistry; Gdansk University; Wita Stwosza 63 80-952 Gdansk Poland
| | - Krzysztof Rolka
- Faculty of Chemistry; Gdansk University; Wita Stwosza 63 80-952 Gdansk Poland
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Quimbar P, Malik U, Sommerhoff CP, Kaas Q, Chan LY, Huang YH, Grundhuber M, Dunse K, Craik DJ, Anderson MA, Daly NL. High-affinity cyclic peptide matriptase inhibitors. J Biol Chem 2013; 288:13885-96. [PMID: 23548907 DOI: 10.1074/jbc.m113.460030] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Sunflower trypsin inhibitor-1 (SFTI-1) and Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II) are potent protease inhibitors comprising a cyclic backbone. RESULTS Elucidation of structure-activity relationships for SFTI-1 and MCoTI-II was used to design inhibitors with enhanced inhibitory activity. CONCLUSION An analog of MCoTI-II is one of the most potent inhibitors of matriptase. SIGNIFICANCE These results provide a solid basis for the design of selective peptide inhibitors of matriptase with therapeutic potential. The type II transmembrane serine protease matriptase is a key activator of multiple signaling pathways associated with cell proliferation and modification of the extracellular matrix. Deregulated matriptase activity correlates with a number of diseases, including cancer and hence highly selective matriptase inhibitors may have therapeutic potential. The plant-derived cyclic peptide, sunflower trypsin inhibitor-1 (SFTI-1), is a promising drug scaffold with potent matriptase inhibitory activity. In the current study we have analyzed the structure-activity relationships of SFTI-1 and Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II), a structurally divergent trypsin inhibitor from Momordica cochinchinensis that also contains a cyclic backbone. We show that MCoTI-II is a significantly more potent matriptase inhibitor than SFTI-1 and that all alanine mutants of both peptides, generated using positional scanning mutagenesis, have decreased trypsin affinity, whereas several mutations either maintain or result in enhanced matriptase inhibitory activity. These intriguing results were used to design one of the most potent matriptase inhibitors known to date with a 290 pm equilibrium dissociation constant, and provide the first indication on how to modulate affinity for matriptase over trypsin in cyclic peptides. This information might be useful for the design of more selective and therapeutically relevant inhibitors of matriptase.
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Affiliation(s)
- Pedro Quimbar
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
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Zhu S, Qiu Z, Ni T, Zhao X, Yan S, Xing F, Zhao Y, Bai Y, Li M. Dinuclear complexes of copper and zinc with m-xylene/cyclohexane-linked bis-aspartic acids: Synthesis, characterization, dioxygen activation, and catalytic oxidation of nitrobenzene in pure aqueous solution. Dalton Trans 2013; 42:10898-911. [DOI: 10.1039/c3dt50923k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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