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Kasperkiewicz P, Kołt S, Janiszewski T, Skowron PM, Krefft D, Brodzik R, Koller KP, Drąg M. Substrate specificity profiling of heat-sensitive serine protease from the fungus Onygena corvina. Biochimie 2024:S0300-9084(24)00161-5. [PMID: 38971457 DOI: 10.1016/j.biochi.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 06/28/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Proteases catalyze hydrolysis of amide bonds within peptides and proteins, therefore they play crucial functions for organism functioning, but also in industry to facilitate numerous processes. Feather-degrading fungus Onygena corvina (O. corvina) is loaded with numerous proteases that can be utilized for variety of applications. The most active species of these enzymes is heat-sensitive serine protease (NHSSP), from O. corvina fungi and due to its potential applications in industry is an alternative to proteinase K. The uniqueness of NHSSP relies on the ability of this enzyme to hydrolyze peptides at neutral to acidic pH values between 5.0 and 8.5, with an optimum of 6.8 and a temperature activity ranging from 15 to 50 °C making NHSSP exceptionally universal enzyme. Thus, we have performed the in-depth characterization of NHSSP substrate specificity by using a positional scanning substrate combinatorial library (PS-SCL). Afterward, we obtained a set of fluorescent substrates hydrolyzed by NHSSP that served as a leading sequence for the first tailored covalent inhibitor of this enzyme, containing a diphenylphosphonate as a warhead and MeOSuc amine protecting group. Our first inhibitor for NHSSP binds potently with target protease and is a tool for future study of this enzyme functions.
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Affiliation(s)
- Paulina Kasperkiewicz
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Sonia Kołt
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Tomasz Janiszewski
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-309, Gdansk, Poland
| | - Daria Krefft
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-309, Gdansk, Poland
| | - Robert Brodzik
- QIAGEN Gdańsk Sp. Z o.o., Trzy Lipy 3/2.58 Street, Gdańsk, Poland
| | - Klaus-Peter Koller
- Institute for Molecular BioScience, University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
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2
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Chykunova Y, Plewka J, Wilk P, Torzyk K, Sienczyk M, Dubin G, Pyrc K. Autoinhibition of suicidal capsid protease from O'nyong'nyong virus. Int J Biol Macromol 2024; 262:130136. [PMID: 38354926 DOI: 10.1016/j.ijbiomac.2024.130136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/10/2024] [Accepted: 02/11/2024] [Indexed: 02/16/2024]
Abstract
Alphaviruses pose a significant threat to public health. Capsid protein encoded in the alphaviral genomes constitutes an interesting therapy target, as it also serves as a protease (CP). Remarkably, it undergoes autoproteolysis, leading to the generation of the C-terminal tryptophan that localizes to the active pocket, deactivating the enzyme. Lack of activity hampers the viral replication cycle, as the virus is not capable of producing the infectious progeny. We investigated the structure and function of the CP encoded in the genome of O'nyong'nyong virus (ONNV), which has instigated outbreaks in Africa. Our research provides a high-resolution crystal structure of the ONNV CP in its active state and evaluates the enzyme's activity. Furthermore, we demonstrated a dose-dependent reduction in ONNV CP proteolytic activity when exposed to indole, suggesting that tryptophan analogs may be a promising basis for developing small molecule inhibitors. It's noteworthy that the capsid protease plays an essential role in virus assembly, binding viral glycoproteins through its glycoprotein-binding hydrophobic pocket. We showed that non-aromatic cyclic compounds like dioxane disrupt this vital interaction. Our findings provide deeper insights into ONNV's biology, and we believe they will prove instrumental in guiding the development of antiviral strategies against arthritogenic alphaviruses.
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Affiliation(s)
- Yuliya Chykunova
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Jacek Plewka
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Piotr Wilk
- Structural Biology Core Facility, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Karolina Torzyk
- Wroclaw University of Science and Technology, Faculty of Chemistry, Division of Medicinal Chemistry and Microbiology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marcin Sienczyk
- Wroclaw University of Science and Technology, Faculty of Chemistry, Division of Medicinal Chemistry and Microbiology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Grzegorz Dubin
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
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3
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Brings S, Mier W, Beijer B, Kliemank E, Herzig S, Szendroedi J, Nawroth PP, Fleming T. Non-cross-linking advanced glycation end products affect prohormone processing. Biochem J 2024; 481:33-44. [PMID: 38112318 DOI: 10.1042/bcj20230321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/01/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
Advanced glycation end products (AGEs) are non-enzymatic post-translational modifications of amino acids and are associated with diabetic complications. One proposed pathomechanism is the impaired processing of AGE-modified proteins or peptides including prohormones. Two approaches were applied to investigate whether substrate modification with AGEs affects the processing of substrates like prohormones to the active hormones. First, we employed solid-phase peptide synthesis to generate unmodified as well as AGE-modified protease substrates. Activity of proteases towards these substrates was quantified. Second, we tested the effect of AGE-modified proinsulin on the processing to insulin. Proteases showed the expected activity towards the unmodified peptide substrates containing arginine or lysine at the C-terminal cleavage site. Indeed, modification with Nε-carboxymethyllysine (CML) or methylglyoxal-hydroimidazolone 1 (MG-H1) affected all proteases tested. Cysteine cathepsins displayed a reduction in activity by ∼50% towards CML and MG-H1 modified substrates. The specific proteases trypsin, proprotein convertases subtilisin-kexins (PCSKs) type proteases, and carboxypeptidase E (CPE) were completely inactive towards modified substrates. Proinsulin incubation with methylglyoxal at physiological concentrations for 24 h resulted in the formation of MG-modified proinsulin. The formation of insulin was reduced by up to 80% in a concentration-dependent manner. Here, we demonstrate the inhibitory effect of substrate-AGE modifications on proteases. The finding that PCSKs and CPE, which are essential for prohormone processing, are inactive towards modified substrates could point to a yet unrecognized pathomechanism resulting from AGE modification relevant for the etiopathogenesis of diabetes and the development of obesity.
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Affiliation(s)
- Sebastian Brings
- Department of Endocrinology, Metabolism and Clinical Chemistry, University Hospital Heidelberg, Heidelberg, Germany
- Department of Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Walter Mier
- Department of Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Barbro Beijer
- Department of Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Elisabeth Kliemank
- Department of Endocrinology, Metabolism and Clinical Chemistry, University Hospital Heidelberg, Heidelberg, Germany
| | - Stephan Herzig
- German Centre of Diabetes Research (DZD), Munich, Germany
- Institute for Diabetes and Cancer IDC Helmholtz Center Munich and Joint Heidelberg-IDC Translational Diabetes Program, Munich, Germany
| | - Julia Szendroedi
- Department of Endocrinology, Metabolism and Clinical Chemistry, University Hospital Heidelberg, Heidelberg, Germany
- German Centre of Diabetes Research (DZD), Munich, Germany
- Institute for Diabetes and Cancer IDC Helmholtz Center Munich and Joint Heidelberg-IDC Translational Diabetes Program, Munich, Germany
- Center for Molecular Biology Heidelberg (ZMBH), Heidelberg, Germany
- Joint Division Molecular Metabolic Control, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter P Nawroth
- Department of Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Fleming
- Department of Endocrinology, Metabolism and Clinical Chemistry, University Hospital Heidelberg, Heidelberg, Germany
- German Centre of Diabetes Research (DZD), Munich, Germany
- Institute for Diabetes and Cancer IDC Helmholtz Center Munich and Joint Heidelberg-IDC Translational Diabetes Program, Munich, Germany
- Center for Molecular Biology Heidelberg (ZMBH), Heidelberg, Germany
- Joint Division Molecular Metabolic Control, German Cancer Research Center (DKFZ), Heidelberg, Germany
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4
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Suleiman M, Almalki FA, Ben Hadda T, Kawsar SMA, Chander S, Murugesan S, Bhat AR, Bogoyavlenskiy A, Jamalis J. Recent Progress in Synthesis, POM Analyses and SAR of Coumarin-Hybrids as Potential Anti-HIV Agents-A Mini Review. Pharmaceuticals (Basel) 2023; 16:1538. [PMID: 38004404 PMCID: PMC10675815 DOI: 10.3390/ph16111538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
The human immunodeficiency virus (HIV) is the primary cause of acquired immune deficiency syndrome (AIDS), one of the deadliest pandemic diseases. Various mechanisms and procedures have been pursued to synthesise several anti-HIV agents, but due to the severe side effects and multidrug resistance spawning from the treatment of HIV/AIDS using highly active retroviral therapy (HAART), it has become imperative to design and synthesise novel anti-HIV agents. Literature has shown that natural sources, particularly the plant kingdom, can release important metabolites that have several biological, mechanistic and structural representations similar to chemically synthesised compounds. Certainly, compounds from natural and ethnomedicinal sources have proven to be effective in the management of HIV/AIDS with low toxicity, fewer side effects and affordability. From plants, fungi and bacteria, coumarin can be obtained, which is a secondary metabolite and is well known for its actions in different stages of the HIV replication cycle: protease, integrase and reverse transcriptase (RT) inhibition, cell membrane fusion and viral host attachment. These, among other reasons, are why coumarin moieties will be the basis of a good building block for the development of potent anti-HIV agents. This review aims to outline the synthetic pathways, structure-activity relationship (SAR) and POM analyses of coumarin hybrids with anti-HIV activity, detailing articles published between 2000 and 2023.
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Affiliation(s)
- Mustapha Suleiman
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia;
- Department of Chemistry, Sokoto State University, Birnin Kebbi Road, Sokoto 852101, Nigeria
| | - Faisal A. Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Mecca 21955, Saudi Arabia; (F.A.A.); (T.B.H.)
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Mecca 21955, Saudi Arabia; (F.A.A.); (T.B.H.)
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, Oujda 60000, Morocco
| | - Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, University of Chittagong, Chittagong 4331, Bangladesh;
| | - Subhash Chander
- Amity Institute of Phytochemistry & Phytomedicine, Amity University Uttar Pradesh, Noida 201313, India;
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Birla Institute of Technology & Science Pilani (BITS Pilani), Pilani Campus, Pilani 333031, India;
| | - Ajmal R. Bhat
- Department of Chemistry, R.T.M. Nagpur University, Nagpur 440033, India;
| | - Andrey Bogoyavlenskiy
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia;
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5
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Modrzycka S, Kołt S, Adams TE, Potoczek S, Huntington JA, Kasperkiewicz P, Drąg M. Fluorescent Activity-Based Probe To Image and Inhibit Factor XIa Activity in Human Plasma. J Med Chem 2023; 66:3785-3797. [PMID: 36898159 PMCID: PMC10041521 DOI: 10.1021/acs.jmedchem.2c00845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Anticoagulation therapy is a mainstay of the treatment of thrombotic disorders; however, conventional anticoagulants trade antithrombotic benefits for bleeding risk. Factor (f) XI deficiency, known as hemophilia C, rarely causes spontaneous bleeding, suggesting that fXI plays a limited role in hemostasis. In contrast, individuals with congenital fXI deficiency display a reduced incidence of ischemic stroke and venous thromboembolism, indicating that fXI plays a role in thrombosis. For these reasons, there is intense interest in pursuing fXI/factor XIa (fXIa) as targets for achieving antithrombotic benefit with reduced bleeding risk. To obtain selective inhibitors of fXIa, we employed libraries of natural and unnatural amino acids to profile fXIa substrate preferences. We developed chemical tools for investigating fXIa activity, such as substrates, inhibitors, and activity-based probes (ABPs). Finally, we demonstrated that our ABP selectively labels fXIa in the human plasma, making this tool suitable for further studies on the role of fXIa in biological samples.
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Affiliation(s)
- Sylwia Modrzycka
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Sonia Kołt
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Ty E Adams
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, U.K
| | - Stanisław Potoczek
- Department of Haematology, Blood Neoplasms, and Bone Marrow Transplantation, Wrocław Medical University, Pasteura 1, 50-367 Wrocław, Poland
| | - James A Huntington
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, U.K
| | - Paulina Kasperkiewicz
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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6
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Groborz KM, Kalinka M, Grzymska J, Kołt S, Snipas SJ, Poręba M. Selective chemical reagents to investigate the role of caspase 6 in apoptosis in acute leukemia T cells. Chem Sci 2023; 14:2289-2302. [PMID: 36873853 PMCID: PMC9977399 DOI: 10.1039/d2sc05827h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/02/2023] [Indexed: 01/04/2023] Open
Abstract
Activated effector caspases 3, 6 and 7 are responsible for cleaving a number of target substrates, leading to the ultimate destruction of cells via apoptosis. The functions of caspases 3 and 7 in apoptosis execution have been widely studied over the years with multiple chemical probes for both of these enzymes. In contrast, caspase 6 seems to be largely neglected when compared to the heavily studied caspases 3 and 7. Therefore, the development of new small-molecule reagents for the selective detection and visualization of caspase 6 activity can improve our understanding of molecular circuits of apoptosis and shed new light on how they intertwine with other types of programmed cell death. In this study, we profiled caspase 6 substrate specificity at the P5 position and discovered that, similar to caspase 2, caspase 6 prefers pentapeptide substrates over tetrapeptides. Based on these data, we developed a set of chemical reagents for caspase 6 investigation, including coumarin-based fluorescent substrates, irreversible inhibitors and selective aggregation-induced emission luminogens (AIEgens). We showed that AIEgens are able to distinguish between caspase 3 and caspase 6 in vitro. Finally, we validated the efficiency and selectivity of the synthesized reagents by monitoring lamin A and PARP cleavage via mass cytometry and western blot analysis. We propose that our reagents may provide new research prospects for single-cell monitoring of caspase 6 activity to reveal its function in programmed cell death pathways.
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Affiliation(s)
- Katarzyna M Groborz
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology Wyb. Wyspiańskiego 27 50-370 Wroclaw Poland
- Genetech Inc. 1 DNA Way South San Francisco CA 94080 USA
| | - Małgorzata Kalinka
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology Wyb. Wyspiańskiego 27 50-370 Wroclaw Poland
| | - Justyna Grzymska
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology Wyb. Wyspiańskiego 27 50-370 Wroclaw Poland
| | - Sonia Kołt
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology Wyb. Wyspiańskiego 27 50-370 Wroclaw Poland
| | - Scott J Snipas
- NCI Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute 10901 North Torrey Pines Road La Jolla CA 92037 USA
| | - Marcin Poręba
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology Wyb. Wyspiańskiego 27 50-370 Wroclaw Poland
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7
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Gladysz R, Malek N, Rut W, Drag M. Investigation of the P1' and P2' sites of IQF substrates and their selectivity toward 20S proteasome subunits. Biol Chem 2023; 404:221-227. [PMID: 36376064 DOI: 10.1515/hsz-2022-0261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/30/2022] [Indexed: 11/16/2022]
Abstract
High levels of expression and activity of the 20S proteasome have been linked to many types of pathologies, including neoplasia, autoimmune disorders, neurodegenerative diseases and many more. Moreover, distinguishing between 20S proteasome catalytic subunits is neglected, although it may provide further insight into the development of pathologies. Several approaches have been developed to detect 20S proteasome activity, one of which is internally quenched fluorescent (IQF) substrates, which currently suffer from low efficiency and sensitivity. Previous reports focused on peptides including natural amino acids; therefore, in this report, we synthesized and analyzed IQF substrates with both natural and unnatural amino acids in the P1' and P2' positions to investigate their influences on selectivity toward 20S proteasome subunits. We found that elongation of the substrate by the P1' and P2' positions increased specificity in comparison to tetrapeptides. Moreover, we were able to obtain IQF substrates for the Ch-L subunit, which was characterized by higher selectivity than formerly used tetrapeptides. These findings may further contribute to the development of novel diagnostic tools for 20S proteasome-dependent disorders.
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Affiliation(s)
- Radoslaw Gladysz
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, ul. Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Natalia Malek
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, ul. Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, ul. Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, ul. Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
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8
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Janiszewski T, Kołt S, Ciastoń I, Vizovisek M, Poręba M, Turk B, Drąg M, Kozieł J, Kasperkiewicz P. Investigation of osteoclast cathepsin K activity in osteoclastogenesis and bone loss using a set of chemical reagents. Cell Chem Biol 2023; 30:159-174.e8. [PMID: 36696904 DOI: 10.1016/j.chembiol.2023.01.001] [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: 05/17/2021] [Revised: 08/28/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023]
Abstract
Cathepsin K (CatK) is a lysosomal cysteine protease whose highest expression is found in osteoclasts, which are the cells responsible for bone resorption. Investigations of the functions and physiological relevance of CatK have often relied on antibody-related techniques, which makes studying its activity patterns a challenging task. Hence, we developed a set of chemical tools for the investigation of CatK activity. We show that our probe is a valuable tool for monitoring the proteolytic activation of CatK during osteoclast formation. Moreover, we demonstrate that our inhibitor of CatK impedes osteoclastogenesis and bone resorption and that CatK is stored in its active form in osteoclasts within their lysosomal compartment and mainly in the ruffled borders of osteoclasts. Given that our probe recognizes active CatK within living cells without exhibiting any observed cytotoxicity in the several models tested, we expect that it would be well suited to theranostic applications in CatK-related diseases.
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Affiliation(s)
- Tomasz Janiszewski
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Sonia Kołt
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Izabela Ciastoń
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Matej Vizovisek
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Marcin Poręba
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, 1000 Ljubljana, Slovenia
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Kozieł
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Paulina Kasperkiewicz
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
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9
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Rut W, Zmudzinski M, Drag M. Design and Synthesis of Ubiquitin-Based Chemical Tools with Unnatural Amino Acids for Selective Detection of Deubiquitinases. Methods Mol Biol 2023; 2591:59-78. [PMID: 36350543 DOI: 10.1007/978-1-0716-2803-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Several chemical approaches have been applied to develop Ub-based substrates and probes selective toward one or a narrow subset of deubiquitinases (DUBs). Since DUBs are highly specific toward ubiquitin and exhibit low activity toward shorter peptides, it is challenging to design truly selective chemical tools to investigate one DUB in biological samples. Incorporating amino acids other than canonical LRG at the P4-P2 positions in the Ub improves DUB activity and selectivity toward Ub derivatives. Here, we describe the protocol for identifying selective peptide sequences using a hybrid combinatorial substrate library (HyCoSuL) approach that can be introduced in the C-terminal motif of Ub. Furthermore, we describe the synthesis protocol of Ub-based probes and substrates containing unnatural amino acids and the application of Ub-based probes to detect DUBs in cell lysates.
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Affiliation(s)
- Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland.
| | - Mikolaj Zmudzinski
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
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10
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Gargantilla M, Persoons L, Kauerová T, del Río N, Daelemans D, Priego EM, Kollar P, Pérez-Pérez MJ. Hybridization Approach to Identify Salicylanilides as Inhibitors of Tubulin Polymerization and Signal Transducers and Activators of Transcription 3 (STAT3). Pharmaceuticals (Basel) 2022; 15:835. [PMID: 35890135 PMCID: PMC9318074 DOI: 10.3390/ph15070835] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 02/06/2023] Open
Abstract
The superimposition of the X-ray complexes of cyclohexanediones (i.e., TUB015), described by our research group, and nocodazole, within the colchicine binding site of tubulin provided an almost perfect overlap of both ligands. This structural information led us to propose hybrids of TUB015 and nocodazole using a salicylanilide core structure. Interestingly, salicylanilides, such as niclosamide, are well-established signal transducers and activators of transcription (STAT3) inhibitors with anticancer properties. Thus, different compounds with this new scaffold have been synthesized with the aim to identify compounds inhibiting tubulin polymerization and/or STAT3 signaling. As a result, we have identified new salicylanilides (6 and 16) that showed significant antiproliferative activity against a panel of cancer cells. Both compounds were able to reduce the levels of p-STAT3Tyr705 without affecting the total expression of STAT3. While compound 6 inhibited tubulin polymerization and arrested the cell cycle of DU145 cells at G2/M, similar to TUB015, compound 16 showed a more potent effect on inhibiting STAT3 phosphorylation and arrested the cell cycle at G1/G0, similar to niclosamide. In both cases, no toxicity towards PBMC cells was detected. Thus, the salicylanilides described here represent a new class of antiproliferative agents affecting tubulin polymerization and/or STAT3 phosphorylation.
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Affiliation(s)
- Marta Gargantilla
- Instituto de Quimica Medica (IQM, CSIC) c/Juan de la Cierva 3, 28006 Madrid, Spain; (M.G.); (N.d.R.); (E.-M.P.)
| | - Leentje Persoons
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium; (L.P.); (D.D.)
| | - Tereza Kauerová
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Masaryk University, Palackeho tr. 1946/1, 612 42 Brno, Czech Republic;
| | - Natalia del Río
- Instituto de Quimica Medica (IQM, CSIC) c/Juan de la Cierva 3, 28006 Madrid, Spain; (M.G.); (N.d.R.); (E.-M.P.)
| | - Dirk Daelemans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium; (L.P.); (D.D.)
| | - Eva-María Priego
- Instituto de Quimica Medica (IQM, CSIC) c/Juan de la Cierva 3, 28006 Madrid, Spain; (M.G.); (N.d.R.); (E.-M.P.)
| | - Peter Kollar
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Masaryk University, Palackeho tr. 1946/1, 612 42 Brno, Czech Republic;
| | - María-Jesús Pérez-Pérez
- Instituto de Quimica Medica (IQM, CSIC) c/Juan de la Cierva 3, 28006 Madrid, Spain; (M.G.); (N.d.R.); (E.-M.P.)
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11
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Modrzycka S, Kołt S, Polderdijk SGI, Adams TE, Potoczek S, Huntington JA, Kasperkiewicz P, Drąg M. Parallel imaging of coagulation pathway proteases activated protein C, thrombin, and factor Xa in human plasma. Chem Sci 2022; 13:6813-6829. [PMID: 35774156 PMCID: PMC9200056 DOI: 10.1039/d2sc01108e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/22/2022] [Indexed: 12/12/2022] Open
Abstract
Activated protein C (APC), thrombin, and factor (f) Xa are vitamin K-dependent serine proteases that are key factors in blood coagulation. Moreover, they play important roles in inflammation, apoptosis, fibrosis, angiogenesis, and viral infections. Abnormal activity of these coagulation factors has been related to multiple conditions, such as bleeding and thrombosis, Alzheimer's disease, sepsis, multiple sclerosis, and COVID-19. The individual activities of APC, thrombin, and fXa in coagulation and in various diseases are difficult to establish since these proteases are related and have similar substrate preferences. Therefore, the development of selective chemical tools that enable imaging and discrimination between coagulation factors in biological samples may provide better insight into their roles in various conditions and potentially aid in the establishment of novel diagnostic tests. In our study, we used a large collection of unnatural amino acids, and this enabled us to extensively explore the binding pockets of the enzymes' active sites. Based on the specificity profiles obtained, we designed highly selective substrates, inhibitors, and fluorescent activity-based probes (ABPs) that were used for fast, direct, and simultaneous detection of APC, thrombin, and fXa in human plasma. Using a collection of natural and unnatural amino acids, we synthesized a set of fluorescent activity-based probes for the fast, direct, and simultaneous detection of coagulation factors in human plasma.![]()
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Affiliation(s)
- Sylwia Modrzycka
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Sonia Kołt
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Stéphanie G I Polderdijk
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge The Keith Peters Building, Hills Road Cambridge CB2 0XY UK
| | - Ty E Adams
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge The Keith Peters Building, Hills Road Cambridge CB2 0XY UK
| | - Stanisław Potoczek
- Department of Haematology, Blood Neoplasms, and Bone Marrow Transplantation, Wrocław Medical University Pasteura 1 50-367 Wrocław Poland
| | - James A Huntington
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge The Keith Peters Building, Hills Road Cambridge CB2 0XY UK
| | - Paulina Kasperkiewicz
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
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12
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HWANG S, ROH E. Synthesis of Geranyloxycoumarin Derivatives under Mild Conditions Using Cs2CO3. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2021. [DOI: 10.18596/jotcsa.996363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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13
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Ponomariov M, Shabat D, Green O. Universal Access to Protease Chemiluminescent Probes through Solid-Phase Synthesis. Bioconjug Chem 2021; 32:2134-2140. [PMID: 34549945 PMCID: PMC8532118 DOI: 10.1021/acs.bioconjchem.1c00384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Indexed: 12/27/2022]
Abstract
Protease chemiluminescent probes exhibit extremely high detection sensitivity for monitoring activity of various proteolytic enzymes. However, their synthesis, performed in solution, involves multiple synthetic and purification steps, thereby generating a major limitation for rapid preparation of such probes with diverse substrate scope. To overcome this limitation, we developed a general solid-phase-synthetic approach to prepare chemiluminescent protease probes, by peptide elongation, performed on an immobilized chemiluminescent enol-ether precursor. The enol-ether precursor is immobilized on a 2-chlorotrityl-chloride resin through an acrylic acid substituent by an acid-labile ester linkage. Next, a stepwise elongation of the peptide is performed using standard Fmoc solid-phase peptide synthesis. After cleavage of the peptide-enol-ether precursor from the resin, by hexafluoro-iso-propanol, a simple oxidation of the enol-ether yields the final chemiluminescent dioxetane protease probe. To validate the applicability of the methodology, two chemiluminescent probes were efficiently prepared by solid-phase synthesis with dipeptidyl substrates designed for activation by aminopeptidase and cathepsin-B proteases. A more complex example was demonstrated by the synthesis of a chemiluminescent probe for detection of PSA, which includes a peptidyl substrate of six amino acids. We anticipate that the described methodology would be useful for rapid preparation of chemiluminescent protease probes with vast and diverse peptidyl substrates.
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Affiliation(s)
- Maria Ponomariov
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Doron Shabat
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Ori Green
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
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14
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Abstract
Cysteine cathepsins are proteases critical in physiopathological processes and show potential as targets or biomarkers for diseases and medical conditions. The 11 members of the cathepsin family are redundant in some cases but remarkably independent of others, demanding the development of both pan-cathepsin targeting tools as well as probes that are selective for specific cathepsins with little off-target activity. This review addresses the diverse design strategies that have been employed to accomplish this tailored selectivity among cysteine cathepsin targets and the imaging modalities incorporated. The power of these diverse tools is contextualized by briefly highlighting the nature of a few prominent cysteine cathepsins, their involvement in select diseases, and the application of cathepsin imaging probes in research spanning basic biochemical studies to clinical applications.
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Affiliation(s)
- Kelton A Schleyer
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1345 Center Dr, Gainesville, FL 32610, USA.
| | - Lina Cui
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1345 Center Dr, Gainesville, FL 32610, USA.
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15
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Evaluation of the effects of phosphorylation of synthetic peptide substrates on their cleavage by caspase-3 and -7. Biochem J 2021; 478:2233-2245. [PMID: 34037204 DOI: 10.1042/bcj20210255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 02/02/2023]
Abstract
Caspases are a family of enzymes that play roles in cell death and inflammation. It has been suggested that in the execution phase of the apoptotic pathway, caspase-3, -6 and -7 are involved. The substrate specificities of two proteases (caspases 3 and 7) are highly similar, which complicates the design of compounds that selectively interact with a single enzyme exclusively. The recognition of residues other than Asp in the P1 position of the substrate by caspase-3/-7 has been reported, promoting interest in the effects of phosphorylation of amino acids in the direct vicinity of the scissile bond. To evaluate conflicting reports on this subject, we synthesized a series of known caspase-3 and -7 substrates and phosphorylated analogs, performed enzyme kinetic assays and mapped the peptide cleavage sites using internally quenched fluorescent peptide substrates. Caspases 3 and 7 will tolerate pSer at the P1 position but only poorly at the P2' position. Our investigation demonstrates the importance of peptide length and composition in interpreting sequence/activity relationships. Based on the results, we conclude that the relationship between caspase-3/-7 and their substrates containing phosphorylated amino acids might depend on the steric conditions and not be directly connected with ionic interactions. Thus, the precise effect of phospho-amino acid residues located in the vicinity of the cleaved bond on the regulation of the substrate specificity of caspases remains difficult to predict. Our observations allow to predict that natural phosphorylated proteins may be cleaved by caspases, but only when extended substrate binding site interactions are satisfied.
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16
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Steuten K, Kim H, Widen JC, Babin BM, Onguka O, Lovell S, Bolgi O, Cerikan B, Neufeldt CJ, Cortese M, Muir RK, Bennett JM, Geiss-Friedlander R, Peters C, Bartenschlager R, Bogyo M. Challenges for Targeting SARS-CoV-2 Proteases as a Therapeutic Strategy for COVID-19. ACS Infect Dis 2021; 7:1457-1468. [PMID: 33570381 PMCID: PMC7901237 DOI: 10.1021/acsinfecdis.0c00815] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Indexed: 12/31/2022]
Abstract
Two proteases produced by the SARS-CoV-2 virus, the main protease and papain-like protease, are essential for viral replication and have become the focus of drug development programs for treatment of COVID-19. We screened a highly focused library of compounds containing covalent warheads designed to target cysteine proteases to identify new lead scaffolds for both Mpro and PLpro proteases. These efforts identified a small number of hits for the Mpro protease and no viable hits for the PLpro protease. Of the Mpro hits identified as inhibitors of the purified recombinant protease, only two compounds inhibited viral infectivity in cellular infection assays. However, we observed a substantial drop in antiviral potency upon expression of TMPRSS2, a transmembrane serine protease that acts in an alternative viral entry pathway to the lysosomal cathepsins. This loss of potency is explained by the fact that our lead Mpro inhibitors are also potent inhibitors of host cell cysteine cathepsins. To determine if this is a general property of Mpro inhibitors, we evaluated several recently reported compounds and found that they are also effective inhibitors of purified human cathepsins L and B and showed similar loss in activity in cells expressing TMPRSS2. Our results highlight the challenges of targeting Mpro and PLpro proteases and demonstrate the need to carefully assess selectivity of SARS-CoV-2 protease inhibitors to prevent clinical advancement of compounds that function through inhibition of a redundant viral entry pathway.
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Affiliation(s)
- Kas Steuten
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Heeyoung Kim
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg partner site, Heidelberg, Germany
| | - John C. Widen
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Brett M. Babin
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Ouma Onguka
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Scott Lovell
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Oguz Bolgi
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Berati Cerikan
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christopher J. Neufeldt
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Ryan K. Muir
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - John M. Bennett
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Ruth Geiss-Friedlander
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Christoph Peters
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
- Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, German
- German Center for Infection Research (DZIF), Heidelberg partner site, Heidelberg, Germany
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
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17
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Nahrjou N, Ghosh A, Tanasova M. Targeting of GLUT5 for Transporter-Mediated Drug-Delivery Is Contingent upon Substrate Hydrophilicity. Int J Mol Sci 2021; 22:ijms22105073. [PMID: 34064801 PMCID: PMC8150966 DOI: 10.3390/ijms22105073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/28/2021] [Accepted: 05/08/2021] [Indexed: 12/14/2022] Open
Abstract
Specific link between high fructose uptake and cancer development and progression highlighted fructose transporters as potential means to achieve GLUT-mediated discrimination between normal and cancer cells. The gained expression of fructose-specific transporter GLUT5 in various cancers offers a possibility for developing cancer-specific imaging and bioactive agents. Herein, we explore the feasibility of delivering a bioactive agent through cancer-relevant fructose-specific transporter GLUT5. We employed specific targeting of GLUT5 by 2,5-anhydro-D-mannitol and investigated several drug conjugates for their ability to induce cancer-specific cytotoxicity. The proof-of-concept analysis was carried out for conjugates of chlorambucil (CLB) in GLUT5-positive breast cancer cells and normal breast cells. The cytotoxicity of conjugates was assessed over 24 h and 48 h, and significant dependence between cancer-selectivity and conjugate size was observed. The differences were found to relate to the loss of GLUT5-mediated uptake upon increased conjugate size and hydrophobicity. The findings provide information on the substrate tolerance of GLUT5 and highlight the importance of maintaining appropriate hydrophilicity for GLUT-mediated delivery.
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Affiliation(s)
- Nazanin Nahrjou
- Chemistry Department, Michigan Technological University, Houghton, MI 49931, USA; (N.N.); (A.G.)
| | - Avik Ghosh
- Chemistry Department, Michigan Technological University, Houghton, MI 49931, USA; (N.N.); (A.G.)
| | - Marina Tanasova
- Chemistry Department, Michigan Technological University, Houghton, MI 49931, USA; (N.N.); (A.G.)
- Health Research Institute, Michigan Technological University, Houghton, MI 49931, USA
- Correspondence:
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18
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Xu Z, Chen Q, Zhang Y, Liang C. Coumarin-based derivatives with potential anti-HIV activity. Fitoterapia 2021; 150:104863. [PMID: 33582266 DOI: 10.1016/j.fitote.2021.104863] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/11/2021] [Accepted: 01/31/2021] [Indexed: 02/06/2023]
Abstract
Acquired immunodeficiency syndrome (AIDS), as a result of human immunodeficiency virus (HIV) infection which leads to severe suppression of immune functions, is an enormous world-wide health threat. The anti-HIV agents are critical for the HIV/AIDS therapy, but the generation of viral mutants and the severe side effects of the anti-HIV agents pose serious hurdles in the treatment of HIV infection, and creat an urgent need to develop novel anti-HIV agents. The plant-derived compounds possess structural and mechanistic diversity, and among them, coumarin-based derivatives have the potential to inhibit different stages in the HIV replication cycle, inclusive of virus-host cell attachment, cell membrane fusion, integration, assembly besides the conventional target like inhibition of the reverse transcriptase, protease, and integrase. Moreover, (+)-calanolide A, a coumarin-based natural product, is a potential anti-HIV agent. Thus, coumarin-based derivatives are useful scaffolds for the development of anti-HIV agents. This review article describes the recent progress in the discovery, structural modification, and structure-activity relationship studies of potent anti-HIV coumarin-based derivatives including natural coumarin compounds, synthetic hybrids, dimers, and other synthetic derivatives covering articles published between 2000 and 2020.
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Affiliation(s)
- Zhi Xu
- Huanghuai University Industry Innovation & Research and Development Institute of Zhumadian, Zhumadian, People's Republic of China.
| | - Qingtai Chen
- Huanghuai University Industry Innovation & Research and Development Institute of Zhumadian, Zhumadian, People's Republic of China
| | - Yan Zhang
- Huanghuai University Industry Innovation & Research and Development Institute of Zhumadian, Zhumadian, People's Republic of China
| | - Changli Liang
- Huanghuai University Industry Innovation & Research and Development Institute of Zhumadian, Zhumadian, People's Republic of China.
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19
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Boyce JH, Dang B, Ary B, Edmondson Q, Craik CS, DeGrado WF, Seiple IB. Platform to Discover Protease-Activated Antibiotics and Application to Siderophore-Antibiotic Conjugates. J Am Chem Soc 2020; 142:21310-21321. [PMID: 33301681 DOI: 10.1021/jacs.0c06987] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Here we present a platform for discovery of protease-activated prodrugs and apply it to antibiotics that target Gram-negative bacteria. Because cleavable linkers for prodrugs had not been developed for bacterial proteases, we used substrate phage to discover substrates for proteases found in the bacterial periplasm. Rather than focusing on a single protease, we used a periplasmic extract of E. coli to find sequences with the greatest susceptibility to the endogenous mixture of periplasmic proteases. Using a fluorescence assay, candidate sequences were evaluated to identify substrates that release native amine-containing payloads. We next designed conjugates consisting of (1) an N-terminal siderophore to facilitate uptake, (2) a protease-cleavable linker, and (3) an amine-containing antibiotic. Using this strategy, we converted daptomycin-which by itself is active only against Gram-positive bacteria-into an antibiotic capable of targeting Gram-negative Acinetobacter species. We similarly demonstrated siderophore-facilitated delivery of oxazolidinone and macrolide antibiotics into a number of Gram-negative species. These results illustrate this platform's utility for development of protease-activated prodrugs, including Trojan horse antibiotics.
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Affiliation(s)
- Jonathan H Boyce
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States.,Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Bobo Dang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China.,Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Beatrice Ary
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Quinn Edmondson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States.,Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Ian B Seiple
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States.,Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
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20
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Maurits E, Degeling CG, Kisselev AF, Florea BI, Overkleeft HS. Structure-Based Design of Fluorogenic Substrates Selective for Human Proteasome Subunits. Chembiochem 2020; 21:3220-3224. [PMID: 32598532 PMCID: PMC7754458 DOI: 10.1002/cbic.202000375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/29/2020] [Indexed: 11/07/2022]
Abstract
Proteasomes are established therapeutic targets for hematological cancers and promising targets for autoimmune diseases. In the past, we have designed and synthesized mechanism-based proteasome inhibitors that are selective for the individual catalytic activities of human constitutive proteasomes and immunoproteasomes: β1c, β1i, β2c, β2i, β5c and β5i. We show here that by taking the oligopeptide recognition element and substituting the electrophile for a fluorogenic leaving group, fluorogenic substrates are obtained that report on the proteasome catalytic activity also targeted by the parent inhibitor. Though not generally applicable (β5c and β2i substrates showing low activity), effective fluorogenic substrates reporting on the individual activity of β1c, β1i, β2c and β5i subunits in Raji (human B cell) lysates and purified 20S proteasome were identified in this manner. Our work thus adds to the expanding proteasome research toolbox through the identification of new and/or more effective subunit-selective fluorogenic substrates.
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Affiliation(s)
- Elmer Maurits
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Christian G. Degeling
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Alexei F. Kisselev
- Department of Drug Discovery and DevelopmentHarrison School of PharmacyAuburn UniversityAuburnAL 36849USA
| | - Bogdan I. Florea
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
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21
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Rut W, Groborz K, Zhang L, Sun X, Zmudzinski M, Pawlik B, Wang X, Jochmans D, Neyts J, Młynarski W, Hilgenfeld R, Drag M. SARS-CoV-2 M pro inhibitors and activity-based probes for patient-sample imaging. Nat Chem Biol 2020; 17:222-228. [PMID: 33093684 DOI: 10.1038/s41589-020-00689-z] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/23/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022]
Abstract
In December 2019, the first cases of infection with a novel coronavirus, SARS-CoV-2, were diagnosed. Currently, there is no effective antiviral treatment for COVID-19. To address this emerging problem, we focused on the SARS-CoV-2 main protease that constitutes one of the most attractive antiviral drug targets. We have synthesized a combinatorial library of fluorogenic substrates with glutamine in the P1 position. We used it to determine the substrate preferences of the SARS-CoV and SARS-CoV-2 main proteases. On the basis of these findings, we designed and synthesized a potent SARS-CoV-2 inhibitor (Ac-Abu-DTyr-Leu-Gln-VS, half-maximal effective concentration of 3.7 µM) and two activity-based probes, for one of which we determined the crystal structure of its complex with the SARS-CoV-2 Mpro. We visualized active SARS-CoV-2 Mpro in nasopharyngeal epithelial cells of patients suffering from COVID-19 infection. The results of our work provide a structural framework for the design of inhibitors as antiviral agents and/or diagnostic tests.
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Affiliation(s)
- Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland.
| | - Katarzyna Groborz
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Linlin Zhang
- Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany.,Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany.,Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, Lübeck, Germany
| | - Mikolaj Zmudzinski
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Bartlomiej Pawlik
- Department of Pediatrics, Oncology & Hematology, Medical University of Lodz, Lodz, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Xinyu Wang
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Dirk Jochmans
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Wojciech Młynarski
- Department of Pediatrics, Oncology & Hematology, Medical University of Lodz, Lodz, Poland
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, Lübeck, Germany.,Center for Brain, Behavior, and Metabolism, University of Lübeck, Lübeck, Germany
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland.
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22
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Rut W, Lv Z, Zmudzinski M, Patchett S, Nayak D, Snipas SJ, El Oualid F, Huang TT, Bekes M, Drag M, Olsen SK. Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti-COVID-19 drug design. SCIENCE ADVANCES 2020; 6:eabd4596. [PMID: 33067239 PMCID: PMC7567588 DOI: 10.1126/sciadv.abd4596] [Citation(s) in RCA: 289] [Impact Index Per Article: 72.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/01/2020] [Indexed: 05/03/2023]
Abstract
Viral papain-like cysteine protease (PLpro, NSP3) is essential for SARS-CoV-2 replication and represents a promising target for the development of antiviral drugs. Here, we used a combinatorial substrate library and performed comprehensive activity profiling of SARS-CoV-2 PLpro. On the scaffold of the best hits from positional scanning, we designed optimal fluorogenic substrates and irreversible inhibitors with a high degree of selectivity for SARS PLpro. We determined crystal structures of two of these inhibitors in complex with SARS-CoV-2 PLpro that reveals their inhibitory mechanisms and provides a molecular basis for the observed substrate specificity profiles. Last, we demonstrate that SARS-CoV-2 PLpro harbors deISGylating activity similar to SARSCoV-1 PLpro but its ability to hydrolyze K48-linked Ub chains is diminished, which our sequence and structure analysis provides a basis for. Together, this work has revealed the molecular rules governing PLpro substrate specificity and provides a framework for development of inhibitors with potential therapeutic value or drug repurposing.
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Affiliation(s)
- Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Zongyang Lv
- Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
- Department of Biochemistry and Structural Biology University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Mikolaj Zmudzinski
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Stephanie Patchett
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Digant Nayak
- Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
- Department of Biochemistry and Structural Biology University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Scott J. Snipas
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | | - Tony T. Huang
- Department of Biochemistry and Structural Biology University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | | | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Shaun K. Olsen
- Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
- Department of Biochemistry and Structural Biology University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
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23
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Poreba M, Groborz KM, Rut W, Pore M, Snipas SJ, Vizovisek M, Turk B, Kuhn P, Drag M, Salvesen GS. Multiplexed Probing of Proteolytic Enzymes Using Mass Cytometry-Compatible Activity-Based Probes. J Am Chem Soc 2020; 142:16704-16715. [PMID: 32870676 PMCID: PMC7595764 DOI: 10.1021/jacs.0c06762] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The subset of the proteome that contains enzymes in their catalytically active form can be interrogated by using probes targeted toward individual specific enzymes. A subset of such enzymes are proteases that are frequently studied with activity-based probes, small inhibitors equipped with a detectable tag, commonly a fluorophore. Due to the spectral overlap of these commonly used fluorophores, multiplex analysis becomes limited. To overcome this, we developed a series of protease-selective lanthanide-labeled probes compatible with mass cytometry giving us the ability to monitor the activity of multiple proteases in parallel. Using these probes, we were able to identify the distribution of four proteases with different active site geometries in three cell lines and peripheral blood mononuclear cells. This provides a framework for the use of mass cytometry for multiplexed enzyme activity detection.
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Affiliation(s)
- Marcin Poreba
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Katarzyna M. Groborz
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Wioletta Rut
- Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Milind Pore
- University of Southern California, USC Michelson Center for Convergent Biosciences, Los Angeles, CA, USA
| | - Scott J. Snipas
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Boris Turk
- Jozef Stefan Institute, Ljubljana, Slovenia
| | - Peter Kuhn
- University of Southern California, USC Michelson Center for Convergent Biosciences, Los Angeles, CA, USA
| | - Marcin Drag
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Guy S. Salvesen
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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24
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Rut W, Zmudzinski M, Snipas SJ, Bekes M, Huang TT, Drag M. Engineered unnatural ubiquitin for optimal detection of deubiquitinating enzymes. Chem Sci 2020; 11:6058-6069. [PMID: 32953009 PMCID: PMC7477763 DOI: 10.1039/d0sc01347a] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/27/2020] [Indexed: 12/15/2022] Open
Abstract
Herein we present a workflow for design and synthesis of novel selective Ub-based tools for DUBs. Selectivity is achieved by incorporation of unnatural amino acids into the Ub C-terminal epitope.
Deubiquitinating enzymes (DUBs) are responsible for removing ubiquitin (Ub) from its protein conjugates. DUBs have been implicated as attractive therapeutic targets in the treatment of viral diseases, neurodegenerative disorders and cancer. The lack of selective chemical tools for the exploration of these enzymes significantly impairs the determination of their roles in both normal and pathological states. Commercially available fluorogenic substrates are based on the C-terminal Ub motif or contain Ub coupled to a fluorophore (Z-LRGG-AMC, Ub-AMC); therefore, these substrates suffer from lack of selectivity. By using a hybrid combinatorial substrate library (HyCoSuL) and a defined P2 library containing a wide variety of nonproteinogenic amino acids, we established a full substrate specificity profile for two DUBs—MERS PLpro and human UCH-L3. Based on these results, we designed and synthesized Ub-based substrates and activity-based probes (ABPs) containing selected unnatural amino acids located in the C-terminal Ub motif. Biochemical analysis and cell lysate experiments confirmed the activity and selectivity of engineered Ub-based substrates and probes. Using this approach, we propose that for any protease that recognizes Ub and Ub-like substrates, a highly active and selective unnatural substrate or probe can be engineered.
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Affiliation(s)
- Wioletta Rut
- Department of Chemical Biology and Bioimaging , Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland . ;
| | - Mikolaj Zmudzinski
- Department of Chemical Biology and Bioimaging , Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland . ;
| | - Scott J Snipas
- Sanford Burnham Prebys Medical Discovery Institute , 10901 North Torrey Pines Road , La Jolla , CA 92037 , USA
| | - Miklos Bekes
- Department of Biochemistry & Molecular Pharmacology , New York University School of Medicine , New York , NY 10016 , USA
| | - Tony T Huang
- Department of Biochemistry & Molecular Pharmacology , New York University School of Medicine , New York , NY 10016 , USA
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging , Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland . ; .,Sanford Burnham Prebys Medical Discovery Institute , 10901 North Torrey Pines Road , La Jolla , CA 92037 , USA
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25
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Janiszewski T, Kołt S, Kaiserman D, Snipas SJ, Li S, Kulbacka J, Saczko J, Bovenschen N, Salvesen G, Drąg M, Bird PI, Kasperkiewicz P. Noninvasive optical detection of granzyme B from natural killer cells with enzyme-activated fluorogenic probes. J Biol Chem 2020; 295:9567-9582. [PMID: 32439802 DOI: 10.1074/jbc.ra120.013204] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/11/2020] [Indexed: 12/31/2022] Open
Abstract
Natural killer (NK) cells are key innate immunity effectors that combat viral infections and control several cancer types. For their immune function, human NK cells rely largely on five different cytotoxic proteases, called granzymes (A/B/H/K/M). Granzyme B (GrB) initiates at least three distinct cell death pathways, but key aspects of its function remain unexplored because selective probes that detect its activity are currently lacking. In this study, we used a set of unnatural amino acids to fully map the substrate preferences of GrB, demonstrating previously unknown GrB substrate preferences. We then used these preferences to design substrate-based inhibitors and a GrB-activatable activity-based fluorogenic probe. We show that our GrB probes do not significantly react with caspases, making them ideal for in-depth analyses of GrB localization and function in cells. Using our quenched fluorescence substrate, we observed GrB within the cytotoxic granules of human YT cells. When used as cytotoxic effectors, YT cells loaded with GrB attacked MDA-MB-231 target cells, and active GrB influenced its target cell-killing efficiency. In summary, we have developed a set of molecular tools for investigating GrB function in NK cells and demonstrate noninvasive visual detection of GrB with an enzyme-activated fluorescent substrate.
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Affiliation(s)
- Tomasz Janiszewski
- Wroclaw University of Science and Technology, Department of Chemical Biology and Bioimaging, Wroclaw, Poland
| | - Sonia Kołt
- Wroclaw University of Science and Technology, Department of Chemical Biology and Bioimaging, Wroclaw, Poland
| | - Dion Kaiserman
- Monash University, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Clayton, VIC, Australia
| | - Scott J Snipas
- Sanford-Burnham Prebys Medical Discovery Institute, NCI-designated Cancer Center, La Jolla, California, USA
| | - Shuang Li
- University Medical Center Utrecht, Department of Pathology, Utrecht, The Netherlands
| | - Julita Kulbacka
- Wroclaw Medical University, Department of Molecular and Cellular Biology, Wroclaw, Poland
| | - Jolanta Saczko
- Wroclaw Medical University, Department of Molecular and Cellular Biology, Wroclaw, Poland
| | - Niels Bovenschen
- University Medical Center Utrecht, Department of Pathology, Utrecht, The Netherlands
| | - Guy Salvesen
- Sanford-Burnham Prebys Medical Discovery Institute, NCI-designated Cancer Center, La Jolla, California, USA
| | - Marcin Drąg
- Wroclaw University of Science and Technology, Department of Chemical Biology and Bioimaging, Wroclaw, Poland.,Sanford-Burnham Prebys Medical Discovery Institute, NCI-designated Cancer Center, La Jolla, California, USA
| | - Phillip I Bird
- Monash University, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Clayton, VIC, Australia
| | - Paulina Kasperkiewicz
- Wroclaw University of Science and Technology, Department of Chemical Biology and Bioimaging, Wroclaw, Poland
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26
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van de Plassche MAT, O’Neill TJ, Seeholzer T, Turk B, Krappmann D, Verhelst SHL. Use of Non-Natural Amino Acids for the Design and Synthesis of a Selective, Cell-Permeable MALT1 Activity-Based Probe. J Med Chem 2020; 63:3996-4004. [DOI: 10.1021/acs.jmedchem.9b01879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Merel A. T. van de Plassche
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven, Herestr. 49, 3000 Leuven, Belgium
| | - Thomas J. O’Neill
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Thomas Seeholzer
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, Sl-1000 Ljubljana, Slovenia
| | - Daniel Krappmann
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Steven H. L. Verhelst
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven, Herestr. 49, 3000 Leuven, Belgium
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
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27
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Rut W, Groborz K, Zhang L, Modrzycka S, Poreba M, Hilgenfeld R, Drag M. Profiling of flaviviral NS2B-NS3 protease specificity provides a structural basis for the development of selective chemical tools that differentiate Dengue from Zika and West Nile viruses. Antiviral Res 2020; 175:104731. [PMID: 32014497 DOI: 10.1016/j.antiviral.2020.104731] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 01/14/2020] [Accepted: 01/30/2020] [Indexed: 12/11/2022]
Abstract
West Nile virus (WNV) and Dengue virus (DENV) are mosquito-borne pathogenic flaviviruses. The NS2B-NS3 proteases found in these viruses are responsible for polyprotein processing and are therefore considered promising medical targets. Another ortholog of these proteases is found in Zika virus (ZIKV). In this work, we applied a combinatorial chemistry approach - Hybrid Combinatorial Substrate Library (HyCoSuL), to compare the substrate specificity profile at the P4-P1 positions of the NS2B-NS3 proteases found in all three viruses. The obtained data demonstrate that Zika and West Nile virus NS2B-NS3 proteases display highly overlapping substrate specificity in all binding pockets, while the Dengue ortholog has slightly different preferences toward natural and unnatural amino acids at the P2 and P4 positions. We used this information to extract specific peptide sequences recognized by the Dengue NS2B-NS3 protease. Next, we applied this knowledge to design a selective substrate and activity-based probe for the Dengue NS2B-NS3 protease. Our work provides a structural framework for the design of inhibitors, which could be used as a lead structure for drug development efforts.
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Affiliation(s)
- Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Katarzyna Groborz
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Linlin Zhang
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany; German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562, Lübeck, Germany
| | - Sylwia Modrzycka
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marcin Poreba
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany; German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562, Lübeck, Germany
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
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28
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Maluch I, Czarna J, Drag M. Applications of Unnatural Amino Acids in Protease Probes. Chem Asian J 2019; 14:4103-4113. [PMID: 31593336 DOI: 10.1002/asia.201901152] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/01/2019] [Indexed: 12/11/2022]
Abstract
Since proteases are involved in a wide range of physiological and disease states, the development of novel tools for imaging proteolytic enzyme activity is attracting increasing interest from scientists. Peptide substrates containing proteinogenic amino acids are often the first line of defining enzyme specificity. This Minireview outlines examples of major recent advances in probing proteases using unnatural amino acid residues, which greatly expands the possibilities for designing substrate probes and inhibitory activity-based probes. This approach already yielded innovative probes that selectively target only one active protease within the group of enzymes exhibiting similar specificity both in cellular assays and in bioimaging research.
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Affiliation(s)
- Izabela Maluch
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw, University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Justyna Czarna
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw, University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw, University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
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29
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Rut W, Nielsen NV, Czarna J, Poreba M, Kanse SM, Drag M. Fluorescent activity-based probe for the selective detection of Factor VII activating protease (FSAP) in human plasma. Thromb Res 2019; 182:124-132. [PMID: 31479940 DOI: 10.1016/j.thromres.2019.08.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/28/2019] [Accepted: 08/17/2019] [Indexed: 12/21/2022]
Abstract
The zymogen form of circulating Factor VII activating protease (FSAP) is activated by histones that are released as a consequence of tissue damage or excessive inflammation. This is likely to have consequences in a number of disease conditions such as stroke, atherosclerosis, liver fibrosis, thrombosis and cancer. To investigate the existence, as well as the concentration of active FSAP (FSAPa) in complex biological systems an active site probe is needed. We used Hybrid Combinatorial Substrate Library (HyCoSuL) to screen for natural and unnatural amino acids that specifically bind to P4-P2 pockets of FSAPa. This information was used to designing a fluorogenic substrate (Ac-Pro-DTyr-Lys-Arg-ACC) as well as an irreversible, fluorogenic activity-based probe Cy5-6-Ahx-Pro-DTyr-Lys-ArgP(OPh)2. In normal human plasma the probe showed very low non-specific reactivity with some plasma proteins but upon activation of pro-FSAP with histones, strong labelling of FSAPa was observed. This labelling could be inhibited by aprotinin and was not found in the plasma of a subject that was homozygous for a polymorphism, which leads to loss of activity, or in plasma that was depleted of FSAP by antibodies. This 2nd generation substrate exhibited 6-fold higher catalytic efficiency than the 1st generation substrate and a much higher selectivity for FSAPa over other plasma proteases. This substrate and probe can be useful to detect and localize FSAPa in normal and pathological tissue and plasma to gain more insight into its functions.
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Affiliation(s)
- Wioletta Rut
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | | | - Justyna Czarna
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marcin Poreba
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland; NCI-designated Cancer Center, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Sandip M Kanse
- Oslo University Hospital and University of Oslo, Norway.
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
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30
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Simultaneous assay for protease activities of hepatitis C virus and human immunodeficiency virus based on fluorescence detection. Sci Rep 2019; 9:9150. [PMID: 31235764 PMCID: PMC6591172 DOI: 10.1038/s41598-019-45711-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/12/2019] [Indexed: 11/18/2022] Open
Abstract
Hepatitis C virus protease (HCV-PR) and human immunodeficiency virus protease (HIV-PR) are important for virus maturation, and thus can be used as potential target molecules for the development of antiviral drugs for the treatment of viral infections. In this study, a novel assay was developed to determine HCV-PR activity. This assay is based on a fluorogenic reaction, in which peptide fragments generated from an acetyl peptide substrate by HCV-PR can be selectively converted into a fluorescent derivative, and quantified by high-performance liquid chromatography (HPLC) with fluorescent detection. Herein, several acetyl-peptides can be used as substrates for HPLC. The application of this assay was further validated by simultaneous detection of HCV-PR and HIV-PR in a reaction mixture. The proposed method can differentiate the enzyme activities of HCV-PR and HIV-PR in a sample using their corresponding substrates. The results suggest that this assay can detect various proteases by employing set of substrate peptides under the same reaction conditions.
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31
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Groborz K, Gonzalez Ramirez ML, Snipas SJ, Salvesen GS, Drąg M, Poręba M. Exploring the prime site in caspases as a novel chemical strategy for understanding the mechanisms of cell death: a proof of concept study on necroptosis in cancer cells. Cell Death Differ 2019; 27:451-465. [PMID: 31209360 DOI: 10.1038/s41418-019-0364-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 05/02/2019] [Accepted: 05/23/2019] [Indexed: 11/09/2022] Open
Abstract
Caspases participate in regulated cell death mechanisms and are divided into apoptotic and proinflammatory caspases. The main problem in identifying the unique role of a particular caspase in the mechanisms of regulated cell death is their overlapping substrate specificity; caspases recognize and hydrolyze similar peptide substrates. Most studies focus on examining the non-prime sites of the caspases, yet there is a need for novel and more precise chemical tools to identify the molecular participants and mechanisms of programmed cell death pathways. Therefore, we developed an innovative chemical approach that examines the prime area of the caspase active sites. This method permits the agile parallel solid-phase synthesis of caspase inhibitors with a high yield and purity. Using synthesized compounds we have shown the similarities and differences in the prime area of the caspase active site and, as a proof of concept, we demonstrated the exclusive role of caspase-8 in necroptosis.
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Affiliation(s)
- Katarzyna Groborz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Monica L Gonzalez Ramirez
- NCI Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Scott J Snipas
- NCI Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Guy S Salvesen
- NCI Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Marcin Drąg
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland. .,NCI Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.
| | - Marcin Poręba
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland. .,NCI Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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32
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Groborz K, Kołt S, Kasperkiewicz P, Drag M. Internally quenched fluorogenic substrates with unnatural amino acids for cathepsin G investigation. Biochimie 2019; 166:103-111. [PMID: 31103725 DOI: 10.1016/j.biochi.2019.05.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 05/14/2019] [Indexed: 02/01/2023]
Abstract
Cathepsin G is one of four members of the neutrophil serine protease family and constitutes an important biological target in various human inflammatory diseases, such as chronic obstructive pulmonary disease, acute respiratory distress syndrome and cystic fibrosis. Many studies have been focused on determining its biological roles, the latest ones concerning its involvement in acute myeloid leukemia, and as such, multiple chemical and biochemical tools were developed to investigate cathepsin G. Nevertheless, most of them lack selectivity or sensitivity and therefore cannot be used in complex systems. Here we present the development of an optimal cathepsin G Internally Quenched Fluorescence (IQF) substrate that incorporates unnatural amino acids causing the increase of its selectivity toward neutrophil elastase and potency in in vitro studies.
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Affiliation(s)
- Katarzyna Groborz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Sonia Kołt
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Paulina Kasperkiewicz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
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33
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Yoo E, Stokes BH, de Jong H, Vanaerschot M, Kumar TRS, Lawrence N, Njoroge M, Garcia A, Van der Westhuyzen R, Momper JD, Ng CL, Fidock DA, Bogyo M. Defining the Determinants of Specificity of Plasmodium Proteasome Inhibitors. J Am Chem Soc 2018; 140:11424-11437. [PMID: 30107725 PMCID: PMC6407133 DOI: 10.1021/jacs.8b06656] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Plasmodium proteasome is an emerging antimalarial target due to its essential role in all the major life cycle stages of the parasite and its contribution to the establishment of resistance to artemisinin (ART)-based therapies. However, because of a similarly essential role for the host proteasome, the key property of any antiproteasome therapeutic is selectivity. Several parasite-specific proteasome inhibitors have recently been reported, however, their selectivity must be improved to enable clinical development. Here we describe screening of diverse libraries of non-natural synthetic fluorogenic substrates to identify determinants at multiple positions on the substrate that produce enhanced selectivity. We find that selection of an optimal electrophilic "warhead" is essential to enable high selectivity that is driven by the peptide binding elements on the inhibitor. We also find that host cell toxicity is dictated by the extent of coinhibition of the human β2 and β5 subunits. Using this information, we identify compounds with over 3 orders of magnitude selectivity for the parasite enzyme. Optimization of the pharmacological properties resulted in molecules that retained high potency and selectivity, were soluble, sufficiently metabolically stable and orally bioavailable. These molecules are highly synergistic with ART and can clear parasites in a mouse model of infection, making them promising leads as antimalarial drugs.
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Affiliation(s)
- Euna Yoo
- Department of Pathology and Stanford University
School of Medicine, Stanford, California 94305, United States
| | - Barbara H. Stokes
- Department of Microbiology and Immunology Columbia
University Medical Center, New York 10032, United States
| | - Hanna de Jong
- Department of Pathology and Stanford University
School of Medicine, Stanford, California 94305, United States
| | - Manu Vanaerschot
- Department of Microbiology and Immunology Columbia
University Medical Center, New York 10032, United States
| | - TRS Kumar
- Department of Microbiology and Immunology Columbia
University Medical Center, New York 10032, United States
| | - Nina Lawrence
- Drug Discovery and Development Centre (H3D),
University of Cape Town, Rondebosch 7701, South Africa
| | - Mathew Njoroge
- Drug Discovery and Development Centre (H3D),
University of Cape Town, Rondebosch 7701, South Africa
| | - Arnold Garcia
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California, San Diego, La Jolla, California 92093, United States
| | | | - Jeremiah D. Momper
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California, San Diego, La Jolla, California 92093, United States
| | - Caroline L. Ng
- Department of Microbiology and Immunology Columbia
University Medical Center, New York 10032, United States
- Department of Pathology and Microbiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - David A. Fidock
- Department of Microbiology and Immunology Columbia
University Medical Center, New York 10032, United States
- Division of Infectious Diseases, Department of
Medicine, Columbia University Medical Center, New York 10032, United States
| | - Matthew Bogyo
- Department of Pathology and Stanford University
School of Medicine, Stanford, California 94305, United States
- Department of Microbiology and Immunology, Stanford
University School of Medicine, Stanford, California 94305, United States
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Rut W, Poręba M, Kasperkiewicz P, Snipas SJ, Drąg M. Selective Substrates and Activity-Based Probes for Imaging of the Human Constitutive 20S Proteasome in Cells and Blood Samples. J Med Chem 2018; 61:5222-5234. [DOI: 10.1021/acs.jmedchem.8b00026] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Wioletta Rut
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marcin Poręba
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
- Program in Cell Death and Survival Networks, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Paulina Kasperkiewicz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
- Program in Cell Death and Survival Networks, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Scott J. Snipas
- Program in Cell Death and Survival Networks, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Marcin Drąg
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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Poreba M, Groborz K, Navarro M, Snipas SJ, Drag M, Salvesen GS. Caspase selective reagents for diagnosing apoptotic mechanisms. Cell Death Differ 2018; 26:229-244. [PMID: 29748600 DOI: 10.1038/s41418-018-0110-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/30/2018] [Accepted: 03/14/2018] [Indexed: 12/21/2022] Open
Abstract
Apical caspases initiate and effector caspases execute apoptosis. Reagents that can distinguish between caspases, particularly apical caspases-8, 9, and 10 are scarce and generally nonspecific. Based upon a previously described large-scale screen of peptide-based caspase substrates termed HyCoSuL, we sought to develop reagents to distinguish between apical caspases in order to reveal their function in apoptotic cell death paradigms. To this end, we selected tetrapeptide-based sequences that deliver optimal substrate selectivity and converted them to inhibitors equipped with a detectable tag (activity-based probes-ABPs). We demonstrate a strong relationship between substrate kinetics and ABP kinetics. To evaluate the utility of selective substrates and ABPs, we examined distinct apoptosis pathways in Jurkat T lymphocyte and MDA-MB-231 breast cancer lines triggered to undergo cell death via extrinsic or intrinsic apoptosis. We report the first highly selective substrate appropriate for quantitation of caspase-8 activity during apoptosis. Converting substrates to ABPs promoted loss-of-activity and selectivity, thus we could not define a single ABP capable of detecting individual apical caspases in complex mixtures. To overcome this, we developed a panel strategy utilizing several caspase-selective ABPs to interrogate apoptosis, revealing the first chemistry-based approach to uncover the participation of caspase-8, but not caspase-9 or -10 in TRAIL-induced extrinsic apoptosis. We propose that using select panels of ABPs can provide information regarding caspase-8 apoptotic signaling more faithfully than can single, generally nonspecific reagents.
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Affiliation(s)
- Marcin Poreba
- NCI Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA. .,Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Katarzyna Groborz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Mario Navarro
- NCI Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Scott J Snipas
- NCI Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Guy S Salvesen
- NCI Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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36
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Catalytic Activity of Sulfated and Phosphated Catalysts towards the Synthesis of Substituted Coumarin. Catalysts 2018. [DOI: 10.3390/catal8010036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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37
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Winter MB, La Greca F, Arastu-Kapur S, Caiazza F, Cimermancic P, Buchholz TJ, Anderl JL, Ravalin M, Bohn MF, Sali A, O'Donoghue AJ, Craik CS. Immunoproteasome functions explained by divergence in cleavage specificity and regulation. eLife 2017; 6:e27364. [PMID: 29182146 PMCID: PMC5705213 DOI: 10.7554/elife.27364] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 11/11/2017] [Indexed: 12/16/2022] Open
Abstract
The immunoproteasome (iP) has been proposed to perform specialized roles in MHC class I antigen presentation, cytokine modulation, and T cell differentiation and has emerged as a promising therapeutic target for autoimmune disorders and cancer. However, divergence in function between the iP and the constitutive proteasome (cP) has been unclear. A global peptide library-based screening strategy revealed that the proteasomes have overlapping but distinct substrate specificities. Differing iP specificity alters the quantity of production of certain MHC I epitopes but does not appear to be preferentially suited for antigen presentation. Furthermore, iP specificity was found to have likely arisen through genetic drift from the ancestral cP. Specificity differences were exploited to develop isoform-selective substrates. Cellular profiling using these substrates revealed that divergence in regulation of the iP balances its relative contribution to proteasome capacity in immune cells, resulting in selective recovery from inhibition. These findings have implications for iP-targeted therapeutic development.
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Affiliation(s)
- Michael B Winter
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
| | - Florencia La Greca
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
| | - Shirin Arastu-Kapur
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
- Onyx PharmaceuticalsInc., an Amgen subsidiarySan FranciscoUnited States
| | - Francesco Caiazza
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
| | - Peter Cimermancic
- Department of Bioengineering and Therapeutic SciencesCalifornia Institute for Quantitative Biosciences, University of California, San FranciscoSan FranciscoUnited States
| | - Tonia J Buchholz
- Onyx PharmaceuticalsInc., an Amgen subsidiarySan FranciscoUnited States
| | - Janet L Anderl
- Onyx PharmaceuticalsInc., an Amgen subsidiarySan FranciscoUnited States
| | - Matthew Ravalin
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
| | - Markus F Bohn
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
| | - Andrej Sali
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
- Department of Bioengineering and Therapeutic SciencesCalifornia Institute for Quantitative Biosciences, University of California, San FranciscoSan FranciscoUnited States
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoSan DiegoUnited States
| | - Charles S Craik
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
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38
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Synthesis of a HyCoSuL peptide substrate library to dissect protease substrate specificity. Nat Protoc 2017; 12:2189-2214. [PMID: 28933778 DOI: 10.1038/nprot.2017.091] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Many biologically and chemically based approaches have been developed to design highly active and selective protease substrates and probes. It is, however, difficult to find substrate sequences that are truly selective for any given protease, as different proteases can demonstrate a great deal of overlap in substrate specificities. In some cases, better enzyme selectivity can be achieved using peptide libraries containing unnatural amino acids such as the hybrid combinatorial substrate library (HyCoSuL), which uses both natural and unnatural amino acids. HyCoSuL is a combinatorial library of tetrapeptides containing amino acid mixtures at the P4-P2 positions, a fixed amino acid at the P1 position, and an ACC (7-amino-4-carbamoylmethylcoumarin) fluorescent tag occupying the P1' position. Once the peptide is recognized and cleaved by a protease, the ACC is released and produces a readable fluorescence signal. Here, we describe the synthesis and screening of HyCoSuL for human caspases and legumain. We also discuss possible modifications and adaptations of this approach that make it a useful tool for developing highly active and selective reagents for a wide variety of proteolytic enzymes. The protocol can be divided into three major parts: (i) solid-phase synthesis of the fluorescence-labeled HyCoSuL, (ii) screening of protease P4-P2 preferences, and (iii) synthesis of the optimized activity probes equipped with an AOMK (acyloxymethyl ketone) reactive group and a biotin label for easy detection. Beginning with the library design, the entire protocol can be completed in 4-8 weeks (HyCoSuL synthesis: 3-5 weeks; HyCoSuL screening per enzyme: 4-8 d; and activity-based probe synthesis: 1-2 weeks).
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39
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Yu H, Zheng J, Yang S, Asiri AM, Alamry KA, Sun M, Zhang K, Wang S, Yang R. Use of a small molecule as an initiator for interchain staudinger reaction: A new ATP sensing platform using product fluorescence. Talanta 2017; 178:282-286. [PMID: 29136823 DOI: 10.1016/j.talanta.2017.09.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/15/2017] [Accepted: 09/17/2017] [Indexed: 10/18/2022]
Abstract
We demonstrated that a small molecule induced interchain Staudinger reaction can be employed for highly selective detection of adenosine triphosphate (ATP), an important energy-storage biomolecule. A designed ATP split aptamer (A1) was first functionalized with a weakly fluorescent coumarin derivative due to an azide group (azido-coumarin). The second DNA strand (A2) was covalently linked with triphenylphosphine, which could selectively and efficiently reduce azido to amino group through the Staudinger reaction. The A2 was then hybridized with a half of another designed longer DNA strand (T1). The second half of T1 was a split aptamer and selectively recognized ATP with A1 to form a sandwich structure. The specific interaction between ATP and the aptamers drew the two functionalized DNA strands (A1 and A2) together to initiate the interchain Staudinger reduction at fmol-nmol concentration level, hence produced fluorescent 7-aminocoumarin which could be used as an indicator for the presence of trace ATP. The reaction process had a concentration dependent manner with ATP in a large concentration range. Such a strategy of interchain Staudinger reaction can be extended to construct biosensors for other small functional molecules on the basis of judiciously designed aptamers.
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Affiliation(s)
- Huan Yu
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China; Department of Materials Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Jing Zheng
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - Sheng Yang
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - Abdullah M Asiri
- NAAM Research Group, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Khalid A Alamry
- NAAM Research Group, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mingtai Sun
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China
| | - Kui Zhang
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China
| | - Suhua Wang
- School of Environment and Chemical Engineering, North China Electric Power University, Beijing 102206, China.
| | - Ronghua Yang
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, PR China.
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40
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Kasperkiewicz P, Altman Y, D'Angelo M, Salvesen GS, Drag M. Toolbox of Fluorescent Probes for Parallel Imaging Reveals Uneven Location of Serine Proteases in Neutrophils. J Am Chem Soc 2017; 139:10115-10125. [PMID: 28672107 DOI: 10.1021/jacs.7b04394] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Neutrophils, the front line defenders against infection, express four serine proteases (NSPs) that play roles in the control of cell-signaling pathways and defense against pathogens and whose imbalance leads to pathological conditions. Dissecting the roles of individual NSPs in humans is problematic because neutrophils are end-stage cells with a short half-life and minimal ongoing protein synthesis. To gain insight into the regulation of NSP activity we have generated a small-molecule chemical toolbox consisting of activity-based probes with different fluorophore-detecting groups with minimal wavelength overlap and highly selective natural and unnatural amino acid recognition sequences. The key feature of these activity-based probes is the ability to use them for simultaneous observation and detection of all four individual NSPs by fluorescence microscopy, a feature never achieved in previous studies. Using these probes we demonstrate uneven distribution of NSPs in neutrophil azurophil granules, such that they seem to be mutually excluded from each other, suggesting the existence of unknown granule-targeting mechanisms.
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Affiliation(s)
- Paulina Kasperkiewicz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.,NCI-designated Cancer Center, Sanford-Burnham Prebys Medical Discovery Institute , La Jolla, California 92037, United States
| | - Yoav Altman
- NCI-designated Cancer Center, Sanford-Burnham Prebys Medical Discovery Institute , La Jolla, California 92037, United States
| | - Maximiliano D'Angelo
- NCI-designated Cancer Center, Sanford-Burnham Prebys Medical Discovery Institute , La Jolla, California 92037, United States
| | - Guy S Salvesen
- NCI-designated Cancer Center, Sanford-Burnham Prebys Medical Discovery Institute , La Jolla, California 92037, United States
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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41
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Rut W, Drag M. Human 20S proteasome activity towards fluorogenic peptides of various chain lengths. Biol Chem 2017; 397:921-6. [PMID: 27176742 DOI: 10.1515/hsz-2016-0176] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 05/03/2016] [Indexed: 11/15/2022]
Abstract
The proteasome is a multicatalytic protease responsible for the degradation of misfolded proteins. We have synthesized fluorogenic substrates in which the peptide chain was systematically elongated from two to six amino acids and evaluated the effect of peptide length on all three catalytic activities of human 20S proteasome. In the cases of five- and six-membered peptides, we have also synthesized libraries of fluorogenic substrates. Kinetic analysis revealed that six-amino-acid substrates are significantly better for chymotrypsin-like and caspase-like activity than shorter peptidic substrates. In the case of trypsin-like activity, a five-amino-acid substrate was optimal.
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42
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Yang L, Hu Z, Luo J, Tang C, Zhang S, Ning W, Dong C, Huang J, Liu X, Zhou HB. Dual functional small molecule fluorescent probes for image-guided estrogen receptor-specific targeting coupled potent antiproliferative potency for breast cancer therapy. Bioorg Med Chem 2017; 25:3531-3539. [DOI: 10.1016/j.bmc.2017.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/21/2017] [Accepted: 05/02/2017] [Indexed: 12/21/2022]
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43
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Silva RN, Oliveira LCG, Parise CB, Oliveira JR, Severino B, Corvino A, di Vaio P, Temussi PA, Caliendo G, Santagada V, Juliano L, Juliano MA. Activity of human kallikrein-related peptidase 6 (KLK6) on substrates containing sequences of basic amino acids. Is it a processing protease? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:558-564. [PMID: 28254587 DOI: 10.1016/j.bbapap.2017.02.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/12/2017] [Accepted: 02/26/2017] [Indexed: 12/25/2022]
Abstract
Human kallikrein 6 (KLK6) is highly expressed in the central nervous system and with elevated level in demyelinating disease. KLK6 has a very restricted specificity for arginine (R) and hydrolyses myelin basic protein, protein activator receptors and human ionotropic glutamate receptor subunits. Here we report a previously unreported activity of KLK6 on peptides containing clusters of basic amino acids, as in synthetic fluorogenic peptidyl-Arg-7-amino-4-carbamoylmethylcoumarin (peptidyl-ACC) peptides and FRET peptides in the format of Abz-peptidyl-Q-EDDnp (where Abz=ortho-aminobenzoic acid and Q-EDDnp=glutaminyl-N-(2,4-dinitrophenyl) ethylenediamine), in which pairs or sequences of basic amino acids (R or K) were introduced. Surprisingly, KLK6 hydrolyzed the fluorogenic peptides Bz-A-R↓R-ACC and Z-R↓R-MCA between the two R groups, resulting in non-fluorescent products. FRET peptides containing furin processing sequences of human MMP-14, nerve growth factor (NGF), Neurotrophin-3 (NT-3) and Neurotrophin-4 (NT-4) were cleaved by KLK6 at the same position expected by furin. Finally, KLK6 cleaved FRET peptides derived from human proenkephalin after the KR, the more frequent basic residues flanking enkephalins in human proenkephalin sequence. This result suggests the ability of KLK6 to release enkephalin from proenkephalin precursors and resembles furin a canonical processing proteolytic enzyme. Molecular models of peptides were built into the KLK6 structure and the marked preference of the cut between the two R of the examined peptides was related to the extended conformation of the substrates.
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Affiliation(s)
- Roberta N Silva
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
| | - Lilian C G Oliveira
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
| | - Carolina B Parise
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
| | - Juliana R Oliveira
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
| | - Beatrice Severino
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano, 49, 80131 Napoli, Italy
| | - Angela Corvino
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano, 49, 80131 Napoli, Italy
| | - Paola di Vaio
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano, 49, 80131 Napoli, Italy
| | - Piero A Temussi
- The Wohl Institute, King's College London, 5 Cutcombe Rd, London SE5 9RT, UK; Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Comp. Univ. Monte Sant'Angelo Via Cintia 21, 80126 Naples, Italy
| | - Giuseppe Caliendo
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano, 49, 80131 Napoli, Italy
| | - Vincenzo Santagada
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano, 49, 80131 Napoli, Italy
| | - Luiz Juliano
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil
| | - Maria A Juliano
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Brazil.
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44
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Łęgowska M, Hamon Y, Wojtysiak A, Grzywa R, Sieńczyk M, Burster T, Korkmaz B, Lesner A. Development of the first internally-quenched fluorescent substrates of human cathepsin C: The application in the enzyme detection in biological samples. Arch Biochem Biophys 2016; 612:91-102. [DOI: 10.1016/j.abb.2016.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/11/2016] [Indexed: 11/26/2022]
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45
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Structure and substrate fingerprint of aminopeptidase P from Plasmodium falciparum. Biochem J 2016; 473:3189-204. [DOI: 10.1042/bcj20160550] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 07/26/2016] [Indexed: 12/18/2022]
Abstract
Malaria is one of the world's most prevalent parasitic diseases, with over 200 million cases annually. Alarmingly, the spread of drug-resistant parasites threatens the effectiveness of current antimalarials and has made the development of novel therapeutic strategies a global health priority. Malaria parasites have a complicated lifecycle, involving an asymptomatic ‘liver stage’ and a symptomatic ‘blood stage’. During the blood stage, the parasites utilise a proteolytic cascade to digest host hemoglobin, which produces free amino acids absolutely necessary for parasite growth and reproduction. The enzymes required for hemoglobin digestion are therefore attractive therapeutic targets. The final step of the cascade is catalyzed by several metalloaminopeptidases, including aminopeptidase P (APP). We developed a novel platform to examine the substrate fingerprint of APP from Plasmodium falciparum (PfAPP) and to show that it can catalyze the removal of any residue immediately prior to a proline. Further, we have determined the crystal structure of PfAPP and present the first examination of the 3D structure of this essential malarial enzyme. Together, these analyses provide insights into potential mechanisms of inhibition that could be used to develop novel antimalarial therapeutics.
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46
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Eto M, Naruse N, Morimoto K, Yamaoka K, Sato K, Tsuji K, Inokuma T, Shigenaga A, Otaka A. Development of an Anilide-Type Scaffold for the Thioester Precursor N-Sulfanylethylcoumarinyl Amide. Org Lett 2016; 18:4416-9. [PMID: 27529363 DOI: 10.1021/acs.orglett.6b02207] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
N-Sulfanylethylcoumarinyl amide (SECmide) peptide, which was initially developed for use in the fluorescence-guided detection of promoters of N-S acyl transfer, was successfully applied to a facile and side reaction-free protocol for N-S acyl-transfer-mediated synthesis of peptide thioesters. Additionally, 4-mercaptobenzylphosphonic acid (MBPA) was proven to be a useful catalyst for the SECmide or N-sulfanylethylanilide (SEAlide)-mediated NCL reaction.
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Affiliation(s)
- Mitsuhiro Eto
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University , Tokushima 770-8505, Japan
| | - Naoto Naruse
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University , Tokushima 770-8505, Japan
| | - Kyohei Morimoto
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University , Tokushima 770-8505, Japan
| | - Kosuke Yamaoka
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University , Tokushima 770-8505, Japan
| | - Kohei Sato
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University , Tokushima 770-8505, Japan
| | - Kohei Tsuji
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University , Tokushima 770-8505, Japan
| | - Tsubasa Inokuma
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University , Tokushima 770-8505, Japan
| | - Akira Shigenaga
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University , Tokushima 770-8505, Japan.,PRESTO, Japan Science and Technology Agency (JST) , Kawaguchi, Saitama 332-0012, Japan
| | - Akira Otaka
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University , Tokushima 770-8505, Japan
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47
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Moradi L, Rabiei K, Belali F. Meglumine sulfate catalyzed solvent-free one-pot synthesis of coumarins under microwave and thermal conditions. SYNTHETIC COMMUN 2016. [DOI: 10.1080/00397911.2016.1201512] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Leila Moradi
- Department of Organic Chemistry, Faculty of Chemistry, University of Kashan, Kashan, Iran
| | - Khadijeh Rabiei
- Department of Chemistry, Faculty of Basic Science, Qom University of Technology, Qom, Iran
| | - Fateme Belali
- Department of Organic Chemistry, Faculty of Chemistry, University of Kashan, Kashan, Iran
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48
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Li YT, Huang YC, Xu Y, Pan M, Li YM. Ubiquitin 7-amino-4-carbamoylmethylcoumarin as an improved fluorogenic substrate for deubiquitinating enzymes. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.05.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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49
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Poreba M, Szalek A, Kasperkiewicz P, Rut W, Salvesen GS, Drag M. Small Molecule Active Site Directed Tools for Studying Human Caspases. Chem Rev 2015; 115:12546-629. [PMID: 26551511 DOI: 10.1021/acs.chemrev.5b00434] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Caspases are proteases of clan CD and were described for the first time more than two decades ago. They play critical roles in the control of regulated cell death pathways including apoptosis and inflammation. Due to their involvement in the development of various diseases like cancer, neurodegenerative diseases, or autoimmune disorders, caspases have been intensively investigated as potential drug targets, both in academic and industrial laboratories. This review presents a thorough, deep, and systematic assessment of all technologies developed over the years for the investigation of caspase activity and specificity using substrates and inhibitors, as well as activity based probes, which in recent years have attracted considerable interest due to their usefulness in the investigation of biological functions of this family of enzymes.
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Affiliation(s)
- Marcin Poreba
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Aleksandra Szalek
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Paulina Kasperkiewicz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Wioletta Rut
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Guy S Salvesen
- Program in Cell Death and Survival Networks, Sanford Burnham Prebys Medical Discovery Institute , La Jolla, California 92037, United States
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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Activity profiling of aminopeptidases in cell lysates using a fluorogenic substrate library. Biochimie 2015; 122:31-7. [PMID: 26449746 DOI: 10.1016/j.biochi.2015.09.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/30/2015] [Indexed: 11/22/2022]
Abstract
Aminopeptidases are exopeptidases that process peptide bonds at the N-terminus of protein substrates, and they are involved in controlling several metabolic pathways. Due to their involvement in diseases such as cancer or rheumatoid arthritis, their presence can also be used as a predictive biomarker. Here, we used a library of fluorogenic substrates containing natural and unnatural amino acids to reliably measure the aminopeptidase N (APN) activity in cell lysates obtained from human, pig and rat kidneys. We compared our results to the substrate specificity profile of isolated APN. Our data strongly support the observation that fluorogenic substrates can be successfully used to identify aminopeptidases and to measure their activity in cell lysates. Moreover, in contrast to assays using single substrates, which can result in overlapping specificity due to cleavage by several aminopeptidases, our library fingerprint can provide information about single enzymes.
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