1
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Serwanja J, Wieland AC, Haubenhofer A, Brandstetter H, Schönauer E. A conserved strategy to attack collagen: The activator domain in bacterial collagenases unwinds triple-helical collagen. Proc Natl Acad Sci U S A 2024; 121:e2321002121. [PMID: 38593072 PMCID: PMC11032491 DOI: 10.1073/pnas.2321002121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/14/2024] [Indexed: 04/11/2024] Open
Abstract
Bacterial collagenases are important virulence factors, secreted by several pathogenic Clostridium, Bacillus, Spirochaetes, and Vibrio species. Yet, the mechanism by which these enzymes cleave collagen is not well understood. Based on biochemical and mutational studies we reveal that collagenase G (ColG) from Hathewaya histolytica recognizes and processes collagen substrates differently depending on their nature (fibrillar vs. soluble collagen); distinct dynamic interactions between the activator and peptidase domain are required based on the substrate type. Using biochemical and circular dichroism studies, we identify the presumed noncatalytic activator domain as the single-domain triple helicase that unwinds collagen locally, transiently, and reversibly.
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Affiliation(s)
- Jamil Serwanja
- Department of Biosciences and Medical Biology, Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
- Center for Tumor Biology and Immunology (CTBI), Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
| | - Alexander C. Wieland
- Department of Biosciences and Medical Biology, Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
- Center for Tumor Biology and Immunology (CTBI), Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
| | - Astrid Haubenhofer
- Department of Biosciences and Medical Biology, Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
- Center for Tumor Biology and Immunology (CTBI), Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
| | - Hans Brandstetter
- Department of Biosciences and Medical Biology, Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
- Center for Tumor Biology and Immunology (CTBI), Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
| | - Esther Schönauer
- Department of Biosciences and Medical Biology, Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
- Center for Tumor Biology and Immunology (CTBI), Paris-Lodron University of Salzburg, SalzburgA-5020, Austria
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2
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Lange RW, Bloch K, Heindl MR, Wollenhaupt J, Weiss MS, Brandstetter H, Klebe G, Falcone FH, Böttcher-Friebertshäuser E, Dahms SO, Steinmetzer T. Fragment-Based Design, Synthesis, and Characterization of Aminoisoindole-Derived Furin Inhibitors. ChemMedChem 2024:e202400057. [PMID: 38385828 DOI: 10.1002/cmdc.202400057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 02/23/2024]
Abstract
A 1H-isoindol-3-amine was identified as suitable P1 group for the proprotein convertase furin using a crystallographic screening with a set of 20 fragments known to occupy the S1 pocket of trypsin-like serine proteases. Its binding mode is very similar to that observed for the P1 group of benzamidine-derived peptidic furin inhibitors suggesting an aminomethyl substitution of this fragment to obtain a couplable P1 residue for the synthesis of substrate-analogue furin inhibitors. The obtained inhibitors possess a slightly improved picomolar inhibitory potency compared to their benzamidine-derived analogues. The crystal structures of two inhibitors in complex with furin revealed that the new P1 group is perfectly suited for incorporation in peptidic furin inhibitors. Selected inhibitors were tested for antiviral activity against respiratory syncytial virus (RSV) and a furin-dependent influenza A virus (SC35M/H7N7) in A549 human lung cells and demonstrated an efficient inhibition of virus activation and replication at low micromolar or even submicromolar concentrations. First results suggest that the Mas-related G-protein coupled receptor GPCR-X2 could be a potential off-target for certain benzamidine-derived furin inhibitors.
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Affiliation(s)
- Roman W Lange
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6-10, D-35032, Marburg, Germany Phone
| | - Konstantin Bloch
- Institute of Virology, Philipps University, Hans-Meerwein-Str. 2, Marburg, Germany
| | - Miriam Ruth Heindl
- Institute of Virology, Philipps University, Hans-Meerwein-Str. 2, Marburg, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, 12489, Berlin, Germany
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, 12489, Berlin, Germany
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, Billrothstrasse 11, A-5020, Salzburg, Austria Phone
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6-10, D-35032, Marburg, Germany Phone
| | - Franco H Falcone
- Institute of Parasitology, BFS, Justus Liebig University, 35392, Giessen, Germany
| | | | - Sven O Dahms
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6-10, D-35032, Marburg, Germany Phone
- Department of Biosciences, University of Salzburg, Billrothstrasse 11, A-5020, Salzburg, Austria Phone
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6-10, D-35032, Marburg, Germany Phone
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3
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Konstantinović J, Kany AM, Alhayek A, Abdelsamie AS, Sikandar A, Voos K, Yao Y, Andreas A, Shafiei R, Loretz B, Schönauer E, Bals R, Brandstetter H, Hartmann RW, Ducho C, Lehr CM, Beisswenger C, Müller R, Rox K, Haupenthal J, Hirsch AK. Inhibitors of the Elastase LasB for the Treatment of Pseudomonas aeruginosa Lung Infections. ACS Cent Sci 2023; 9:2205-2215. [PMID: 38161367 PMCID: PMC10755728 DOI: 10.1021/acscentsci.3c01102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Indexed: 01/03/2024]
Abstract
Infections caused by the Gram-negative pathogen Pseudomonas aeruginosa are emerging worldwide as a major threat to human health. Conventional antibiotic monotherapy suffers from rapid resistance development, underlining urgent need for novel treatment concepts. Here, we report on a nontraditional approach to combat P. aeruginosa-derived infections by targeting its main virulence factor, the elastase LasB. We discovered a new chemical class of phosphonates with an outstanding in vitro ADMET and PK profile, auspicious activity both in vitro and in vivo. We established the mode of action through a cocrystal structure of our lead compound with LasB and in several in vitro and ex vivo models. The proof of concept of a combination of our pathoblocker with levofloxacin in a murine neutropenic lung infection model and the reduction of LasB protein levels in blood as a proof of target engagement demonstrate the great potential for use as an adjunctive treatment of lung infections in humans.
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Affiliation(s)
- Jelena Konstantinović
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Andreas M. Kany
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Alaa Alhayek
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Ahmed S. Abdelsamie
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department
of Chemistry of Natural and Microbial Products, Institute of Pharmaceutical and Drug Industries Research, National
Research Centre, El-Buhouth Street, Dokki, Cairo 12622, Egypt
| | - Asfandyar Sikandar
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Katrin Voos
- Department
of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken 66123, Germany
| | - Yiwen Yao
- Department
of Internal Medicine V − Pulmonology, Allergology and Critical
Care Medicine, Saarland University, Homburg 66421, Germany
| | - Anastasia Andreas
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Roya Shafiei
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Saarland
University, Department of Pharmacy, Saarbrücken 66123, Germany
| | - Brigitta Loretz
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Esther Schönauer
- Department
of Biosciences and Medical Biology, Division of Structural Biology, University of Salzburg, Salzburg 5020, Austria
| | - Robert Bals
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department
of Internal Medicine V − Pulmonology, Allergology and Critical
Care Medicine, Saarland University, Homburg 66421, Germany
| | - Hans Brandstetter
- Department
of Biosciences and Medical Biology, Division of Structural Biology, University of Salzburg, Salzburg 5020, Austria
| | - Rolf W. Hartmann
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Saarland
University, Department of Pharmacy, Saarbrücken 66123, Germany
| | - Christian Ducho
- Department
of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken 66123, Germany
| | - Claus-Michael Lehr
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Saarland
University, Department of Pharmacy, Saarbrücken 66123, Germany
| | - Christoph Beisswenger
- Department
of Internal Medicine V − Pulmonology, Allergology and Critical
Care Medicine, Saarland University, Homburg 66421, Germany
| | - Rolf Müller
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Saarland
University, Department of Pharmacy, Saarbrücken 66123, Germany
- Helmholtz
International Lab for Anti-infectives, Saarbrücken 66123, Germany
| | - Katharina Rox
- Department
of Chemical Biology (CBIO), Helmholtz Centre
for Infection Research (HZI), Braunschweig 38124, Germany
- Deutsches
Zentrum für Infektionsforschung (DZIF) e.V., Braunschweig 38124, Germany
| | - Jörg Haupenthal
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Anna K.H. Hirsch
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Saarland
University, Department of Pharmacy, Saarbrücken 66123, Germany
- Helmholtz
International Lab for Anti-infectives, Saarbrücken 66123, Germany
- Deutsches
Zentrum für Infektionsforschung (DZIF) e.V., Braunschweig 38124, Germany
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4
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Santos N, Brandstetter H, Dall E. Arabidopsis thaliana Phytocystatin 6 Forms Functional Oligomer and Amyloid Fibril States. Biochemistry 2023; 62:3420-3429. [PMID: 37989209 PMCID: PMC10702442 DOI: 10.1021/acs.biochem.3c00530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023]
Abstract
Cystatins encode a high functional variability not only because of their ability to inhibit different classes of proteases but also because of their propensity to form oligomers and amyloid fibrils. Phytocystatins, essential regulators of protease activity in plants, specifically inhibit papain-like cysteine proteases (PLCPs) and legumains through two distinct cystatin domains. Mammalian cystatins can form amyloid fibrils; however, the potential for amyloid fibril formation of phytocystatins remains unknown. In this study, we demonstrate that Arabidopsis thaliana phytocystatin 6 (AtCYT6) exists as a mixture of monomeric, dimeric, and oligomeric forms in solution. Noncovalent oligomerization was facilitated by the N-terminal cystatin domain, while covalent dimerization occurred through disulfide bond formation in the interdomain linker. The noncovalent dimeric form of AtCYT6 retained activity against its target proteases, papain and legumain, albeit with reduced inhibitory potency. Additionally, we observed the formation of amyloid fibrils by AtCYT6 under acidic pH conditions and upon heating. The amyloidogenic potential could be attributed to the AtCYT6's N-terminal domain (AtCYT6-NTD). Importantly, AtCYT6 amyloid fibrils harbored inhibitory activities against both papain and legumain. These findings shed light on the oligomerization and amyloidogenic behavior of AtCYT6, expanding our understanding of phytocystatin biology and its potential functional implications for plant protease regulation.
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Affiliation(s)
- Naiá
P. Santos
- Department of Biosciences and Medical
Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Hans Brandstetter
- Department of Biosciences and Medical
Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Elfriede Dall
- Department of Biosciences and Medical
Biology, University of Salzburg, 5020 Salzburg, Austria
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5
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Santos NP, Soh WT, Demir F, Tenhaken R, Briza P, Huesgen PF, Brandstetter H, Dall E. Phytocystatin 6 is a context-dependent, tight-binding inhibitor of Arabidopsis thaliana legumain isoform β. Plant J 2023; 116:1681-1695. [PMID: 37688791 PMCID: PMC10952133 DOI: 10.1111/tpj.16458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/11/2023]
Abstract
Plant legumains are crucial for processing seed storage proteins and are critical regulators of plant programmed cell death. Although research on legumains boosted recently, little is known about their activity regulation. In our study, we used pull-down experiments to identify AtCYT6 as a natural inhibitor of legumain isoform β (AtLEGβ) in Arabidopsis thaliana. Biochemical analysis revealed that AtCYT6 inhibits both AtLEGβ and papain-like cysteine proteases through two separate cystatin domains. The N-terminal domain inhibits papain-like proteases, while the C-terminal domain inhibits AtLEGβ. Furthermore, we showed that AtCYT6 interacts with legumain in a substrate-like manner, facilitated by a conserved asparagine residue in its reactive center loop. Complex formation was additionally stabilized by charged exosite interactions, contributing to pH-dependent inhibition. Processing of AtCYT6 by AtLEGβ suggests a context-specific regulatory mechanism with implications for plant physiology, development, and programmed cell death. These findings enhance our understanding of AtLEGβ regulation and its broader physiological significance.
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Affiliation(s)
- Naiá P. Santos
- Department of Biosciences and Medical BiologyUniversity of Salzburg5020SalzburgAustria
| | - Wai Tuck Soh
- Department of Biosciences and Medical BiologyUniversity of Salzburg5020SalzburgAustria
- Present address:
Max Planck Institute for Multidisciplinary SciencesD‐37077GöttingenGermany
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics52428JülichZEA‐3, Forschungszentrum JülichGermany
- Present address:
Department of BiomedicineAarhus University8000Aarhus CDenmark
| | - Raimund Tenhaken
- Department of Environment and BiodiversityUniversity of Salzburg5020SalzburgAustria
| | - Peter Briza
- Department of Biosciences and Medical BiologyUniversity of Salzburg5020SalzburgAustria
| | - Pitter F. Huesgen
- Central Institute for Engineering, Electronics and Analytics52428JülichZEA‐3, Forschungszentrum JülichGermany
- CECADMedical Faculty and University Hospital, University of Cologne50931CologneGermany
- Institute for Biochemistry, Faculty of Mathematics and Natural SciencesUniversity of Cologne50674CologneGermany
| | - Hans Brandstetter
- Department of Biosciences and Medical BiologyUniversity of Salzburg5020SalzburgAustria
| | - Elfriede Dall
- Department of Biosciences and Medical BiologyUniversity of Salzburg5020SalzburgAustria
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6
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Serwanja J, Brandstetter H, Schönauer E. Quantitative cross-linking via engineered cysteines to study inter-domain interactions in bacterial collagenases. STAR Protoc 2023; 4:102519. [PMID: 37605531 PMCID: PMC10458335 DOI: 10.1016/j.xpro.2023.102519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/23/2023] Open
Abstract
Inter-domain movements act as important activity modulators in multi-domain proteins. Here, we present a protocol for inter-domain cross-linking via engineered cysteines. Using collagenase G (ColG) from Hathewaya histolytica as a model, we describe steps for the design, expression, purification, and cross-linking of the target protein. We detail a system to monitor the progress of the cross-linking reaction and to confirm the structural integrity of the purified cross-linked proteins. We anticipate this protocol to be readily adaptable to other multi-domain enzymes. For complete details on the use and execution of this protocol, please refer to Serwanja et al.1.
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Affiliation(s)
- Jamil Serwanja
- Department of Biosciences and Medical Biology, Paris Lodron University of Salzburg, Salzburg 5020, Austria
| | - Hans Brandstetter
- Department of Biosciences and Medical Biology, Paris Lodron University of Salzburg, Salzburg 5020, Austria
| | - Esther Schönauer
- Department of Biosciences and Medical Biology, Paris Lodron University of Salzburg, Salzburg 5020, Austria.
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7
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Holzner C, Böttinger K, Blöchl C, Huber CG, Dahms SO, Dall E, Brandstetter H. Legumain Functions as a Transient TrkB Sheddase. Int J Mol Sci 2023; 24:ijms24065394. [PMID: 36982466 PMCID: PMC10049731 DOI: 10.3390/ijms24065394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
While primarily found in endo-lysosomal compartments, the cysteine protease legumain can also translocate to the cell surface if stabilized by the interaction with the RGD-dependent integrin receptor αVβ3. Previously, it has been shown that legumain expression is inversely related to BDNF-TrkB activity. Here we show that legumain can conversely act on TrkB-BDNF by processing the C-terminal linker region of the TrkB ectodomain in vitro. Importantly, when in complex with BDNF, TrkB was not cleaved by legumain. Legumain-processed TrkB was still able to bind BDNF, suggesting a potential scavenger function of soluble TrkB towards BDNF. The work thus presents another mechanistic link explaining the reciprocal TrkB signaling and δ-secretase activity of legumain, with relevance for neurodegeneration.
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8
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Elamin T, Brandstetter H, Dall E. Legumain Activity Is Controlled by Extended Active Site Residues and Substrate Conformation. Int J Mol Sci 2022; 23:12548. [PMID: 36293424 PMCID: PMC9604545 DOI: 10.3390/ijms232012548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Legumain is a lysosomal cysteine protease with strict specificity for cleaving after asparagine residues. By sequence comparison, legumain belongs to MEROPS clan CD of the cysteine proteases, which indicates its structural and mechanistic relation to caspases. Contrasting caspases, legumain harbors a pH-dependent ligase activity in addition to the protease activity. Although we already have a significant body of knowledge on the catalytic activities of legumain, many mechanistic details are still elusive. In this study, we provide evidence that extended active site residues and substrate conformation are steering legumain activities. Biochemical experiments and bioinformatics analysis showed that the catalytic Cys189 and His148 residues are regulated by sterically close Glu190, Ser215 and Asn42 residues. While Glu190 serves as an activity brake, Ser215 and Asn42 have a favorable effect on legumain protease activity. Mutagenesis studies using caspase-9 as model enzyme additionally showed that a similar Glu190 activity brake is also implemented in the caspases. Furthermore, we show that the substrate's conformational flexibility determines whether it will be hydrolyzed or ligated by legumain. The functional understanding of the extended active site residues and of substrate prerequisites will allow us to engineer proteases with increased enzymatic activity and better ligase substrates, with relevance for biotechnological applications.
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Affiliation(s)
| | | | - Elfriede Dall
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
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9
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Alhayek A, Abdelsamie AS, Schönauer E, Camberlein V, Hutterer E, Posselt G, Serwanja J, Blöchl C, Huber CG, Haupenthal J, Brandstetter H, Wessler S, Hirsch AKH. Discovery and Characterization of Synthesized and FDA-Approved Inhibitors of Clostridial and Bacillary Collagenases. J Med Chem 2022; 65:12933-12955. [PMID: 36154055 PMCID: PMC9574867 DOI: 10.1021/acs.jmedchem.2c00785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Indexed: 12/04/2022]
Abstract
In view of the worldwide antimicrobial resistance (AMR) threat, new bacterial targets and anti-infective agents are needed. Since important roles in bacterial pathogenesis have been demonstrated for the collagenase H and G (ColH and ColG) from Clostridium histolyticum, collagenase Q1 and A (ColQ1 and ColA) from Bacillus cereus represent attractive antivirulence targets. Furthermore, repurposing FDA-approved drugs may assist to tackle the AMR crisis and was addressed in this work. Here, we report on the discovery of two potent and chemically stable bacterial collagenase inhibitors: synthesized and FDA-approved diphosphonates and hydroxamates. Both classes showed high in vitro activity against the clostridial and bacillary collagenases. The potent diphosphonates reduced B. cereus-mediated detachment and death of cells and Galleria mellonella larvae. The hydroxamates were also tested in a similar manner; they did not have an effect in infection models. This might be due to their fast binding kinetics to bacterial collagenases.
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Affiliation(s)
- Alaa Alhayek
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
- Department
of Pharmacy, Saarland University, Campus Building C2. 3, 66123 Saarbrücken, Germany
| | - Ahmed S. Abdelsamie
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
- Department
of Chemistry of Natural and Microbial Products, Institute of Pharmaceutical and Drug Industries Research, National
Research Centre, El-Buhouth
St., Dokki, 12622 Cairo, Egypt
| | - Esther Schönauer
- Department
of Biosciences and Medical Biology, University
of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Virgyl Camberlein
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Evelyn Hutterer
- Department
of Biosciences and Medical Biology, University
of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Gernot Posselt
- Department
of Biosciences and Medical Biology, University
of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Jamil Serwanja
- Department
of Biosciences and Medical Biology, University
of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Constantin Blöchl
- Department
of Biosciences and Medical Biology, University
of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Christian G. Huber
- Department
of Biosciences and Medical Biology, University
of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Jörg Haupenthal
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Hans Brandstetter
- Department
of Biosciences and Medical Biology, University
of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Silja Wessler
- Department
of Biosciences and Medical Biology, University
of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Anna K. H. Hirsch
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
- Department
of Pharmacy, Saarland University, Campus Building C2. 3, 66123 Saarbrücken, Germany
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10
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Hoppe IJ, Prommegger B, Uhl A, Lohrig U, Huber CG, Brandstetter H. The Fluorescent Enzyme Cascade Detects Low Abundance Protein Modifications Suitable for the Assembly of Functionally Annotated Modificatome Databases. Chembiochem 2022; 23:e202200399. [PMID: 35920326 DOI: 10.1002/cbic.202200399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/27/2022] [Indexed: 01/07/2023]
Abstract
Pathophysiological functions of proteins critically depend on both their chemical composition, including post-translational modifications, and their three-dimensional structure, commonly referred to as structure-activity relationship. Current analytical methods, like capillary electrophoresis or mass spectrometry, suffer from limitations, such as the detection of unexpected modifications at low abundance and their insensitivity to conformational changes. Building on previous enzyme-based analytical methods, we here introduce a fluorescence-based enzyme cascade (fEC), which can detect diverse chemical and conformational variations in protein samples and assemble them into digital databases. Together with complementary analytical methods an automated fEC analysis established unique modification-function relationships, which can be expanded to a proteome-wide scale, i. e. a functionally annotated modificatome. The fEC offers diverse applications, including hypersensitive biomarker detection in complex samples.
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Affiliation(s)
- Isabel J Hoppe
- Department of Biosciences and Medical Biology and Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
| | - Bernhard Prommegger
- Department of Artificial Intelligence and Human Interfaces, University of Salzburg, Jakob Haringer Str. 2, A-5020, Salzburg, Austria
| | - Andreas Uhl
- Department of Artificial Intelligence and Human Interfaces, University of Salzburg, Jakob Haringer Str. 2, A-5020, Salzburg, Austria
| | - Urs Lohrig
- Technical Development Biosimilars, Global Drug Development, Novartis, Sandoz GmbH, Biochemiestr. 10, A-6250, Kundl, Austria
| | - Christian G Huber
- Department of Biosciences and Medical Biology and Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
| | - Hans Brandstetter
- Department of Biosciences and Medical Biology and Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
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11
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Elamin T, Santos NP, Briza P, Brandstetter H, Dall E. Structural and functional studies of legumain-mycocypin complexes revealed a competitive, exosite-regulated mode of interaction. J Biol Chem 2022; 298:102502. [PMID: 36116553 PMCID: PMC9579014 DOI: 10.1016/j.jbc.2022.102502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 12/01/2022] Open
Abstract
Under pathophysiologic conditions such as Alzheimer’s disease and cancer, the endolysosomal cysteine protease legumain was found to translocate to the cytosol, the nucleus, and the extracellular space. These noncanonical localizations demand for a tight regulation of legumain activity, which is in part conferred by protein inhibitors. While there is a significant body of knowledge on the interaction of human legumain with endogenous cystatins, only little is known on its regulation by fungal mycocypins. Mycocypins are characterized by (i) versatile, plastic surface loops allowing them to inhibit different classes of enzymes and (ii) a high resistance toward extremes of pH and temperature. These properties make mycocypins attractive starting points for biotechnological and medical applications. In this study, we show that mycocypins utilize an adaptable reactive center loop to target the active site of legumain in a substrate-like manner. The interaction was further stabilized by variable, isoform-specific exosites, converting the substrate recognition into inhibition. Additionally, we found that selected mycocypins were capable of covalent complex formation with legumain by forming a disulfide bond to the active site cysteine. Furthermore, our inhibition studies with other clan CD proteases suggested that mycocypins may serve as broad-spectrum inhibitors of clan CD proteases. Our studies uncovered the potential of mycocypins as a new scaffold for drug development, providing the basis for the design of specific legumain inhibitors.
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Affiliation(s)
- Tasneem Elamin
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Naiá P Santos
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Peter Briza
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Hans Brandstetter
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Elfriede Dall
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria.
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12
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Kaya C, Walter I, Alhayek A, Shafiei R, Jézéquel G, Andreas A, Konstantinović J, Schönauer E, Sikandar A, Haupenthal J, Müller R, Brandstetter H, Hartmann RW, Hirsch AK. Structure-Based Design of α-Substituted Mercaptoacetamides as Inhibitors of the Virulence Factor LasB from Pseudomonas aeruginosa. ACS Infect Dis 2022; 8:1010-1021. [PMID: 35451824 PMCID: PMC9112332 DOI: 10.1021/acsinfecdis.1c00628] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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Antivirulence therapy
has become a widely applicable method for
fighting infections caused by multidrug-resistant bacteria. Among
the many virulence factors produced by the Gram-negative bacterium Pseudomonas aeruginosa, elastase (LasB) stands out
as an important target as it plays a pivotal role in the invasion
of the host tissue and evasion of the immune response. In this work,
we explored the recently reported LasB inhibitor class of α-benzyl-N-aryl mercaptoacetamides by exploiting the crystal structure
of one of the compounds. Our exploration yielded inhibitors that maintained
inhibitory activity, selectivity, and increased hydrophilicity. These
inhibitors were found to reduce the pathogenicity of the bacteria
and to maintain the integrity of lung and skin cells in the diseased
state. Furthermore, two most promising compounds increased the survival
rate of Galleria mellonella larvae
treated with P. aeruginosa culture
supernatant.
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Affiliation(s)
- Cansu Kaya
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Isabell Walter
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Alaa Alhayek
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Roya Shafiei
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Gwenaëlle Jézéquel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Anastasia Andreas
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Jelena Konstantinović
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Esther Schönauer
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Straße, 34, 5020 Salzburg, Austria
| | - Asfandyar Sikandar
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Campus E 8.1, 66123 Saarbrücken, Germany
| | - Hans Brandstetter
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Straße, 34, 5020 Salzburg, Austria
| | - Rolf W. Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Anna K.H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Campus E 8.1, 66123 Saarbrücken, Germany
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13
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Dahms SO, Schnapp G, Winter M, Büttner FH, Schlepütz M, Gnamm C, Pautsch A, Brandstetter H. Dichlorophenylpyridine-Based Molecules Inhibit Furin through an Induced-Fit Mechanism. ACS Chem Biol 2022; 17:816-821. [PMID: 35377598 PMCID: PMC9016704 DOI: 10.1021/acschembio.2c00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
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Inhibitors of the
proprotein convertase furin might serve as broad-spectrum
antiviral therapeutics. High cellular potency and antiviral activity
against acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have
been reported for (3,5-dichlorophenyl)pyridine-derived furin inhibitors.
Here we characterized the binding mechanism of this inhibitor class
using structural, biophysical, and biochemical methods. We established
a MALDI-TOF-MS-based furin activity assay, determined IC50 values, and solved X-ray structures of (3,5-dichlorophenyl)pyridine-derived
compounds in complex with furin. The inhibitors induced a substantial
conformational rearrangement of the active-site cleft by exposing
a central buried tryptophan residue. These changes formed an extended
hydrophobic surface patch where the 3,5-dichlorophenyl moiety of the
inhibitors was inserted into a newly formed binding pocket. Consistent
with these structural rearrangements, we observed slow off-rate binding
kinetics and strong structural stabilization in surface plasmon resonance
and differential scanning fluorimetry experiments, respectively. The
discovered furin conformation offers new opportunities for structure-based
drug discovery.
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Affiliation(s)
- Sven O. Dahms
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Straße 34, A-5020 Salzburg, Austria
| | - Gisela Schnapp
- Department of Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH& Co KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Martin Winter
- Department of Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH& Co KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Frank H. Büttner
- Department of Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH& Co KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Marco Schlepütz
- Department of I&R Research, R&D Project Management and Development Strategies, Boehringer Ingelheim Pharma GmbH& Co KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Christian Gnamm
- Department of Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH& Co KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Alexander Pautsch
- Department of Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH& Co KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Hans Brandstetter
- Department of Biosciences and Medical Biology, University of Salzburg, Hellbrunner Straße 34, A-5020 Salzburg, Austria
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14
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Alhayek A, Khan ES, Schönauer E, Däinghaus T, Shafiei R, Voos K, Han MKL, Ducho C, Posselt G, Wessler S, Brandstetter H, Haupenthal J, del Campo A, Hirsch AKH. Inhibition of Collagenase Q1 of
Bacillus cereus
as a Novel Antivirulence Strategy for the Treatment of Skin‐Wound Infections. Advanced Therapeutics 2022; 5:2100222. [PMID: 35310821 PMCID: PMC7612511 DOI: 10.1002/adtp.202100222] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Despite the progress in surgical techniques and antibiotic prophylaxis, opportunistic wound infections with Bacillus cereus remain a public health problem. Secreted toxins are one of the main factors contributing to B. cereus pathogenicity. A promising strategy to treat such infections is to target these toxins and not the bacteria. Although the exoenzymes produced by B. cereus are thoroughly investigated, little is known about the role of B. cereus collagenases in wound infections. In this report, the collagenolytic activity of secreted collagenases (Col) is characterized in the B. cereus culture supernatant (csn) and its isolated recombinantly produced ColQ1 is characterized. The data reveals that ColQ1 causes damage on dermal collagen (COL). This results in gaps in the tissue, which might facilitate the spread of bacteria. The importance of B. cereus collagenases is also demonstrated in disease promotion using two inhibitors. Compound 2 shows high efficacy in peptidolytic, gelatinolytic, and COL degradation assays. It also preserves the fibrillar COLs in skin tissue challenged with ColQ1, as well as the viability of skin cells treated with B. cereus csn. A Galleria mellonella model highlights the significance of collagenase inhibition in vivo.
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Affiliation(s)
- Alaa Alhayek
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) 38124 Saarbrücken Germany
- Department of Pharmacy Saarland University, Saarbrücken Campus Campus E8.1 66123 Saarbrücken Germany
| | - Essak S. Khan
- Leibniz Institute for New Materials (INM) Saarland University Campus D2 2 66123 Saarbrücken Germany
| | - Esther Schönauer
- Department of Biosciences and Medical Biology Hellbrunner Str. 34 University of Salzburg Salzburg 5020 Austria
| | - Tobias Däinghaus
- Leibniz Institute for New Materials (INM) Saarland University Campus D2 2 66123 Saarbrücken Germany
| | - Roya Shafiei
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) 38124 Saarbrücken Germany
| | - Katrin Voos
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Mitchell K. L. Han
- Leibniz Institute for New Materials (INM) Saarland University Campus D2 2 66123 Saarbrücken Germany
| | - Christian Ducho
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Gernot Posselt
- Department of Biosciences and Medical Biology Hellbrunner Str. 34 University of Salzburg Salzburg 5020 Austria
| | - Silja Wessler
- Department of Biosciences and Medical Biology Hellbrunner Str. 34 University of Salzburg Salzburg 5020 Austria
| | - Hans Brandstetter
- Department of Biosciences and Medical Biology Hellbrunner Str. 34 University of Salzburg Salzburg 5020 Austria
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) 38124 Saarbrücken Germany
| | - Aránzazu del Campo
- Leibniz Institute for New Materials (INM) Saarland University Campus D2 2 66123 Saarbrücken Germany
- Chemistry Department Saarland University 66123 Saarbrücken Germany
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) 38124 Saarbrücken Germany
- Department of Pharmacy Saarland University, Saarbrücken Campus Campus E8.1 66123 Saarbrücken Germany
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15
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Dall E, Licht A, Brandstetter H. Production of Functional Plant Legumain Proteases Using the Leishmania tarentolae Expression System. Methods Mol Biol 2022; 2447:35-51. [PMID: 35583771 DOI: 10.1007/978-1-0716-2079-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant proteases of the legumain-type are key players in many processes along the plant life cycle. In particular, legumains are especially important in plant programmed cell death and the processing and maturation of seed storage proteins within the vacuole. Plant legumains are therefore synonymously called vacuolar processing enzymes (VPEs). Because of their dual protease and cyclase activities, plant legumains are of great interest to biotechnological applications, e.g., for the development of cyclic peptides for drug design. Despite this high interest by the scientific community, the recombinant expression of plant legumains proved challenging due to several posttranslational modifications, including (1) the formation of structurally critical disulfide bonds, (2) activation via pH-dependent proteolytic processing, and (3) stabilization by varying degrees of glycosylation. Recently we could show that LEXSY is a robust expression system for the production of plant legumains. Here we provide a general protocol for the recombinant expression of plant legumains in Leishmania cells. We further included detailed procedures for legumain purification, activation and subsequent activity assays and additionally note specific considerations with regard to isoform specific activation intermediates. This protocol serves as a universal strategy for different legumain isoforms from different source organisms.
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Affiliation(s)
- Elfriede Dall
- Department of Biosciences, University of Salzburg, Salzburg, Austria.
| | | | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, Salzburg, Austria
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16
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Mills-Goodlet R, Johnson L, Hoppe IJ, Regl C, Geppert M, Schenck M, Huber S, Hauser M, Ferreira F, Hüsing N, Huber CG, Brandstetter H, Duschl A, Himly M. The nanotopography of SiO 2 particles impacts the selectivity and 3D fold of bound allergens. Nanoscale 2021; 13:20508-20520. [PMID: 34854455 PMCID: PMC8675021 DOI: 10.1039/d1nr05958k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
A detailed description of the changes that occur during the formation of protein corona represents a fundamental question in nanoscience, given that it not only impacts the behaviour of nanoparticles but also affects the bound proteins. Relevant questions include whether proteins selectively bind particles, whether a specific orientation is preferred for binding, and whether particle binding leads to a modulation of their 3D fold. For allergens, it is important to answer these questions given that all these effects can modify the allergenic response of atopic individuals. These potential impacts on the bound allergen are closely related to the specific properties of the involved nanoparticles. One important property influencing the formation of protein corona is the nanotopography of the particles. Herein, we studied the effect of nanoparticle porosity on allergen binding using mesoporous and non-porous SiO2 NPs. We investigated (i) the selectivity of allergen binding from a mixture such as crude pollen extract, (ii) whether allergen binding results in a preferred orientation, (iii) the influence of binding on the conformation of the allergen, and (iv) how the binding affects the allergenic response. Nanotopography was found to play a major role in the formation of protein corona, impacting the physicochemical and biological properties of the NP-bound allergen. The porosity of the surface of the SiO2 nanoparticles resulted in a higher binding capacity with pronounced selectivity for (preferentially) binding the major birch pollen allergen Bet v 1. Furthermore, the binding of Bet v 1 to the mesoporous rather than the non-porous SiO2 nanoparticles influenced the 3D fold of the protein, resulting in at least partial unfolding. Consequently, this conformational change influenced the allergenic response, as observed by mediator release assays employing the sera of patients and immune effector cells. For an in-depth understanding of the bio-nano interactions, the properties of the particles need to be considered not only regarding the identity and morphology of the material, but also their nanotopography, given that porosity may greatly influence the structure, and hence the biological behaviour of the bound proteins. Thus, thorough structural investigations upon the formation of protein corona are important when considering immunological outcomes, as particle binding can influence the allergenic response elicited by the bound allergen.
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Affiliation(s)
| | - Litty Johnson
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
| | - Isabel J Hoppe
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, Paris Lodron University of Salzburg, Austria
| | - Christof Regl
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
| | - Mark Geppert
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
| | - Milena Schenck
- Dept. Chemistry and Physics of Materials, Paris Lodron University of Salzburg, Austria
| | - Sara Huber
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
| | - Michael Hauser
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
| | - Fátima Ferreira
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
| | - Nicola Hüsing
- Dept. Chemistry and Physics of Materials, Paris Lodron University of Salzburg, Austria
| | - Christian G Huber
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, Paris Lodron University of Salzburg, Austria
| | - Hans Brandstetter
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, Paris Lodron University of Salzburg, Austria
| | - Albert Duschl
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
| | - Martin Himly
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
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17
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Johnson L, Aglas L, Soh WT, Geppert M, Hofer S, Hofstätter N, Briza P, Ferreira F, Weiss R, Brandstetter H, Duschl A, Himly M. Structural Alterations of Antigens at the Material Interface: An Early Decision Toolbox Facilitating Safe-by-Design Nanovaccine Development. Int J Mol Sci 2021; 22:10895. [PMID: 34639235 PMCID: PMC8509464 DOI: 10.3390/ijms221910895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/18/2022] Open
Abstract
Nanomaterials have found extensive interest in the development of novel vaccines, as adjuvants and/or carriers in vaccination platforms. Conjugation of protein antigens at the particle surface by non-covalent adsorption is the most widely used approach in licensed particulate vaccines. Hence, it is essential to understand proteins' structural integrity at the material interface in order to develop safe-by-design nanovaccines. In this study, we utilized two model proteins, the wild-type allergen Bet v 1 and its hypoallergenic fold variant (BM4), to compare SiO2 nanoparticles with Alhydrogel® as particulate systems. A set of biophysical and functional assays including circular dichroism spectroscopy and proteolytic degradation was used to examine the antigens' structural integrity at the material interface. Conjugation of both biomolecules to the particulate systems decreased their proteolytic stability. However, we observed qualitative and quantitative differences in antigen processing concomitant with differences in their fold stability. These changes further led to an alteration in IgE epitope recognition. Here, we propose a toolbox of biophysical and functional in vitro assays for the suitability assessment of nanomaterials in the early stages of vaccine development. These tools will aid in safe-by-design innovations and allow fine-tuning the properties of nanoparticle candidates to shape a specific immune response.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Martin Himly
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria; (L.J.); (L.A.); (W.T.S.); (M.G.); (S.H.); (N.H.); (P.B.); (F.F.); (R.W.); (H.B.); (A.D.)
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18
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Dall E, Stanojlovic V, Demir F, Briza P, Dahms SO, Huesgen PF, Cabrele C, Brandstetter H. The Peptide Ligase Activity of Human Legumain Depends on Fold Stabilization and Balanced Substrate Affinities. ACS Catal 2021; 11:11885-11896. [PMID: 34621593 PMCID: PMC8491156 DOI: 10.1021/acscatal.1c02057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/30/2021] [Indexed: 12/11/2022]
Abstract
Protein modification by enzymatic breaking and forming of peptide bonds significantly expands the repertoire of genetically encoded protein sequences. The dual protease-ligase legumain exerts the two opposing activities within a single protein scaffold. Primarily localized to the endolysosomal system, legumain represents a key enzyme in the generation of antigenic peptides for subsequent presentation on the MHCII complex. Here we show that human legumain catalyzes the ligation and cyclization of linear peptides at near-neutral pH conditions, where legumain is intrinsically unstable. Conformational stabilization significantly enhanced legumain's ligase activity, which further benefited from engineering the prime substrate recognition sites for improved affinity. Additionally, we provide evidence that specific legumain activation states allow for differential regulation of its activities. Together these results set the basis for engineering legumain proteases and ligases with applications in biotechnology and drug development.
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Affiliation(s)
- Elfriede Dall
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Vesna Stanojlovic
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Peter Briza
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Sven O. Dahms
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Pitter F. Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, 52428 Jülich, Germany
- CECAD, Medical Faculty and University Hospital, University of Cologne, 50931 Cologne, Germany
- Institute for Biochemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, 50674 Cologne, Germany
| | - Chiara Cabrele
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
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19
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Abstract
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The pro-protein convertase
furin is a highly specific serine protease
involved in the proteolytic maturation of many proteins in the secretory
pathway. It also activates surface proteins of many viruses including
the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
Furin inhibitors effectively suppress viral replication and thus are
promising antiviral therapeutics with broad application potential.
Polybasic substrate-like ligands typically trigger conformational
changes shifting furin’s active site cleft from the OFF-state
to the ON-state. Here, we solved the X-ray structures of furin in
complex with four different arginine mimetic compounds with reduced
basicity. These guanylhydrazone-based inhibitor complexes showed for
the first time an active site-directed binding mode to furin’s
OFF-state conformation. The compounds undergo unique interactions
within the S1 pocket, largely different compared to substrate-like
ligands. A second binding site was identified at the S4/S5 pocket
of furin. Crystallography-based titration experiments confirmed the
S1 site as the primary binding pocket. We also tested the proprotein
convertases PC5/6 and PC7 for inhibition by guanylhydrazones and found
an up to 7-fold lower potency for PC7. Interestingly, the observed
differences in the Ki values correlated
with the sequence conservation of the PCs at the allosteric sodium
binding site. Therefore, OFF-state-specific targeting of furin can
serve as a valuable strategy for structure-based development of PC-selective
small-molecule inhibitors.
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Affiliation(s)
- Sven O. Dahms
- Department of Biosciences, University of Salzburg, Hellbrunnerstraße 34, A-5020 Salzburg, Austria
| | - Tanja Haider
- Department of Biosciences, University of Salzburg, Hellbrunnerstraße 34, A-5020 Salzburg, Austria
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Torsten Steinmetzer
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, Hellbrunnerstraße 34, A-5020 Salzburg, Austria
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20
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Vadivel K, Schmidt AE, Cascio D, Padmanabhan K, Krishnaswamy S, Brandstetter H, Bajaj SP. Structure of human factor VIIa-soluble tissue factor with calcium, magnesium and rubidium. Acta Crystallogr D Struct Biol 2021; 77:809-819. [PMID: 34076594 PMCID: PMC8171065 DOI: 10.1107/s2059798321003922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 04/12/2021] [Indexed: 11/10/2022] Open
Abstract
Coagulation factor VIIa (FVIIa) consists of a γ-carboxyglutamic acid (GLA) domain, two epidermal growth factor-like (EGF) domains and a protease domain. FVIIa binds three Mg2+ ions and four Ca2+ ions in the GLA domain, one Ca2+ ion in the EGF1 domain and one Ca2+ ion in the protease domain. Further, FVIIa contains an Na+ site in the protease domain. Since Na+ and water share the same number of electrons, Na+ sites in proteins are difficult to distinguish from waters in X-ray structures. Here, to verify the Na+ site in FVIIa, the structure of the FVIIa-soluble tissue factor (TF) complex was solved at 1.8 Å resolution containing Mg2+, Ca2+ and Rb+ ions. In this structure, Rb+ replaced two Ca2+ sites in the GLA domain and occupied three non-metal sites in the protease domain. However, Rb+ was not detected at the expected Na+ site. In kinetic experiments, Na+ increased the amidolytic activity of FVIIa towards the synthetic substrate S-2288 (H-D-Ile-Pro-Arg-p-nitroanilide) by ∼20-fold; however, in the presence of Ca2+, Na+ had a negligible effect. Ca2+ increased the hydrolytic activity of FVIIa towards S-2288 by ∼60-fold in the absence of Na+ and by ∼82-fold in the presence of Na+. In molecular-dynamics simulations, Na+ stabilized the two Na+-binding loops (the 184-loop and 220-loop) and the TF-binding region spanning residues 163-180. Ca2+ stabilized the Ca2+-binding loop (the 70-loop) and Na+-binding loops but not the TF-binding region. Na+ and Ca2+ together stabilized both the Na+-binding and Ca2+-binding loops and the TF-binding region. Previously, Rb+ has been used to define the Na+ site in thrombin; however, it was unsuccessful in detecting the Na+ site in FVIIa. A conceivable explanation for this observation is provided.
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Affiliation(s)
- Kanagasabai Vadivel
- Department of Orthopaedic Surgery, University of California, Los Angeles, CA 90095, USA
| | - Amy E. Schmidt
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Duilio Cascio
- DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | | | - Sriram Krishnaswamy
- Division of Hematology, The Children’s Hospital of Philadelphia University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - S. Paul Bajaj
- Department of Orthopaedic Surgery, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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21
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Voos K, Schönauer E, Alhayek A, Haupenthal J, Andreas A, Müller R, Hartmann RW, Brandstetter H, Hirsch AKH, Ducho C. Front Cover: Phosphonate as a Stable Zinc‐Binding Group for “Pathoblocker” Inhibitors of Clostridial Collagenase H (ColH) (ChemMedChem 8/2021). ChemMedChem 2021. [DOI: 10.1002/cmdc.202100229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Katrin Voos
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Esther Schönauer
- Department of Biosciences and Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization Division of Structural Biology University of Salzburg Billrothstrasse 11 5020 Salzburg Austria
| | - Alaa Alhayek
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
- Department of Pharmacy Saarland University Campus E8 1 66123 Saarbrücken Germany
| | - Jörg Haupenthal
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
| | - Anastasia Andreas
- Department of Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
- Department of Pharmacy Saarland University Campus E8 1 66123 Saarbrücken Germany
| | - Rolf Müller
- Department of Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
- Department of Pharmacy Saarland University Campus E8 1 66123 Saarbrücken Germany
| | - Rolf W. Hartmann
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
- Department of Pharmacy Saarland University Campus E8 1 66123 Saarbrücken Germany
| | - Hans Brandstetter
- Department of Biosciences and Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization Division of Structural Biology University of Salzburg Billrothstrasse 11 5020 Salzburg Austria
| | - Anna K. H. Hirsch
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
- Department of Pharmacy Saarland University Campus E8 1 66123 Saarbrücken Germany
| | - Christian Ducho
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
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22
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Voos K, Schönauer E, Alhayek A, Haupenthal J, Andreas A, Müller R, Hartmann RW, Brandstetter H, Hirsch AKH, Ducho C. Phosphonate as a Stable Zinc-Binding Group for "Pathoblocker" Inhibitors of Clostridial Collagenase H (ColH). ChemMedChem 2021; 16:1257-1267. [PMID: 33506625 PMCID: PMC8251769 DOI: 10.1002/cmdc.202000994] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Indexed: 01/05/2023]
Abstract
Microbial infections are a significant threat to public health, and resistance is on the rise, so new antibiotics with novel modes of action are urgently needed. The extracellular zinc metalloprotease collagenase H (ColH) from Clostridium histolyticum is a virulence factor that catalyses tissue damage, leading to improved host invasion and colonisation. Besides the major role of ColH in pathogenicity, its extracellular localisation makes it a highly attractive target for the development of new antivirulence agents. Previously, we had found that a highly selective and potent thiol prodrug (with a hydrolytically cleavable thiocarbamate unit) provided efficient ColH inhibition. We now report the synthesis and biological evaluation of a range of zinc-binding group (ZBG) variants of this thiol-derived inhibitor, with the mercapto unit being replaced by other zinc ligands. Among these, an analogue with a phosphonate motif as ZBG showed promising activity against ColH, an improved selectivity profile, and significantly higher stability than the thiol reference compound, thus making it an attractive candidate for future drug development.
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Affiliation(s)
- Katrin Voos
- Department of PharmacyPharmaceutical and Medicinal ChemistrySaarland UniversityCampus C2 366123SaarbrückenGermany
| | - Esther Schönauer
- Department of Biosciences andChristian Doppler Laboratory for Innovative Tools for Biosimilar CharacterizationDivision of Structural BiologyUniversity of SalzburgBillrothstrasse 115020SalzburgAustria
| | - Alaa Alhayek
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus E8 166123SaarbrückenGermany
| | - Jörg Haupenthal
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
| | - Anastasia Andreas
- Department of Microbial Natural ProductsHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus E8 166123SaarbrückenGermany
| | - Rolf Müller
- Department of Microbial Natural ProductsHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus E8 166123SaarbrückenGermany
| | - Rolf W. Hartmann
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus E8 166123SaarbrückenGermany
| | - Hans Brandstetter
- Department of Biosciences andChristian Doppler Laboratory for Innovative Tools for Biosimilar CharacterizationDivision of Structural BiologyUniversity of SalzburgBillrothstrasse 115020SalzburgAustria
| | - Anna K. H. Hirsch
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus E8 166123SaarbrückenGermany
| | - Christian Ducho
- Department of PharmacyPharmaceutical and Medicinal ChemistrySaarland UniversityCampus C2 366123SaarbrückenGermany
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23
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Lam van TV, Heindl MR, Schlutt C, Böttcher-Friebertshäuser E, Bartenschlager R, Klebe G, Brandstetter H, Dahms SO, Steinmetzer T. The Basicity Makes the Difference: Improved Canavanine-Derived Inhibitors of the Proprotein Convertase Furin. ACS Med Chem Lett 2021; 12:426-432. [PMID: 33732412 PMCID: PMC7957917 DOI: 10.1021/acsmedchemlett.0c00651] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/05/2021] [Indexed: 12/17/2022] Open
Abstract
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Furin activates numerous
viral glycoproteins, and its inhibition
prevents virus replication and spread. Through the replacement of
arginine by the less basic canavanine, new inhibitors targeting furin
in the trans-Golgi network were developed. These inhibitors exert
potent antiviral activity in cell culture with much lower toxicity
than arginine-derived analogues, most likely due to their reduced
protonation in the blood circulation. Thus, despite its important
physiological functions, furin might be a suitable antiviral drug
target.
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Affiliation(s)
- Thuy Van Lam van
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032 Marburg, Germany
| | - Miriam Ruth Heindl
- Institute of Virology, Philipps University, Hans-Meerwein-Strasse 2, 35043 Marburg, Germany
| | - Christine Schlutt
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032 Marburg, Germany
| | | | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University and German Center for Infection Research, Heidelberg Partner Site, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032 Marburg, Germany
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Sven O. Dahms
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032 Marburg, Germany
- Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032 Marburg, Germany
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24
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Eckhard U, Blöchl C, Jenkins BGL, Mansfield MJ, Huber CG, Doxey AC, Brandstetter H. Identification and characterization of the proteolytic flagellin from the common freshwater bacterium Hylemonella gracilis. Sci Rep 2020; 10:19052. [PMID: 33149258 PMCID: PMC7643111 DOI: 10.1038/s41598-020-76010-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/22/2020] [Indexed: 12/14/2022] Open
Abstract
Flagellins are the protein components of bacterial flagella and assemble in up to 20,000 copies to form extracellular flagellar filaments. An unusual family of flagellins was recently discovered that contains a unique metalloprotease domain within its surface-exposed hypervariable region. To date, these proteolytic flagellins (also termed flagellinolysins) have only been characterized in the Gram-positive organism Clostridium haemolyticum, where flagellinolysin was shown to be proteolytically active and capable of cleaving extracellular protein substrates. The biological function of flagellinolysin and its activity in other organisms, however, remain unclear. Here, using molecular biochemistry and proteomics, we have performed an initial characterization of a novel flagellinolysin identified from Hylemonella gracilis, a Gram-negative organism originally isolated from pond water. We demonstrate that H. gracilis flagellinolysin (HgrFlaMP) is an active calcium-dependent zinc metallopeptidase and characterize its cleavage specificity profile using both trypsin and GluC-derived peptide libraries and protein substrates. Based on high-throughput degradomic assays, HgrFlaMP cleaved 784 unique peptides and displayed a cleavage site specificity similar to flagellinolysin from C. haemolyticum. Additionally, by using a set of six protein substrates, we identified 206 protein-embedded cleavage sites, further refining the substrate preference of HgrFlaMP, which is dominated by large hydrophobic amino acids in P1', and small hydrophobic or medium-sized polar residues on the amino-terminal side of the scissile bond. Intriguingly, recombinant HgrFlaMP was also capable of cleaving full-length flagellins from another species, suggesting its potential involvement in interbacterial interactions. Our study reports the first experimentally characterized proteolytic flagellin in a Gram-negative organism, and provides new insights into flagellum-mediated enzymatic activity.
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Affiliation(s)
- Ulrich Eckhard
- Department of Biosciences, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria. .,Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Baldiri Reixac, 15-21, 08028, Barcelona, Catalonia, Spain.
| | - Constantin Blöchl
- Department of Biosciences, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria
| | - Benjamin G L Jenkins
- Department of Biology, University of Waterloo, 200 University Ave. West, Waterloo, ON, N2L 3G1, Canada
| | - Michael J Mansfield
- Department of Biology, University of Waterloo, 200 University Ave. West, Waterloo, ON, N2L 3G1, Canada.,Genomics and Regulatory Sytems Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Christian G Huber
- Department of Biosciences, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, 200 University Ave. West, Waterloo, ON, N2L 3G1, Canada.
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria
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25
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Dall E, Zauner FB, Soh WT, Demir F, Dahms SO, Cabrele C, Huesgen PF, Brandstetter H. Structural and functional studies of Arabidopsis thaliana legumain beta reveal isoform specific mechanisms of activation and substrate recognition. J Biol Chem 2020; 295:13047-13064. [PMID: 32719006 PMCID: PMC7489914 DOI: 10.1074/jbc.ra120.014478] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/14/2020] [Indexed: 01/19/2023] Open
Abstract
The vacuolar cysteine protease legumain plays important functions in seed maturation and plant programmed cell death. Because of their dual protease and ligase activity, plant legumains have become of particular biotechnological interest, e.g. for the synthesis of cyclic peptides for drug design or for protein engineering. However, the molecular mechanisms behind their dual protease and ligase activities are still poorly understood, limiting their applications. Here, we present the crystal structure of Arabidopsis thaliana legumain isoform β (AtLEGβ) in its zymogen state. Combining structural and biochemical experiments, we show for the first time that plant legumains encode distinct, isoform-specific activation mechanisms. Whereas the autocatalytic activation of isoform γ (AtLEGγ) is controlled by the latency-conferring dimer state, the activation of the monomeric AtLEGβ is concentration independent. Additionally, in AtLEGβ the plant-characteristic two-chain intermediate state is stabilized by hydrophobic rather than ionic interactions, as in AtLEGγ, resulting in significantly different pH stability profiles. The crystal structure of AtLEGβ revealed unrestricted nonprime substrate binding pockets, consistent with the broad substrate specificity, as determined by degradomic assays. Further to its protease activity, we show that AtLEGβ exhibits a true peptide ligase activity. Whereas cleavage-dependent transpeptidase activity has been reported for other plant legumains, AtLEGβ is the first example of a plant legumain capable of linking free termini. The discovery of these isoform-specific differences will allow us to identify and rationally design efficient ligases with application in biotechnology and drug development.
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Affiliation(s)
- Elfriede Dall
- Department of Biosciences, University of Salzburg, Salzburg, Austria.
| | - Florian B Zauner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Wai Tuck Soh
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Sven O Dahms
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Chiara Cabrele
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany; CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany; Institute for Biochemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, Salzburg, Austria.
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26
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Konstantinović J, Yahiaoui S, Alhayek A, Haupenthal J, Schönauer E, Andreas A, Kany AM, Müller R, Koehnke J, Berger FK, Bischoff M, Hartmann RW, Brandstetter H, Hirsch AKH. N-Aryl-3-mercaptosuccinimides as Antivirulence Agents Targeting Pseudomonas aeruginosa Elastase and Clostridium Collagenases. J Med Chem 2020; 63:8359-8368. [PMID: 32470298 PMCID: PMC7429951 DOI: 10.1021/acs.jmedchem.0c00584] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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In light of the global
antimicrobial-resistance crisis, there is
an urgent need for novel bacterial targets and antibiotics with novel
modes of action. It has been shown that Pseudomonas aeruginosa elastase (LasB) and Clostridium histolyticum (Hathewaya histolytica) collagenase (ColH) play a significant
role in the infection process and thereby represent promising antivirulence
targets. Here, we report novel N-aryl-3-mercaptosuccinimide
inhibitors that target both LasB and ColH, displaying potent activities in vitro and high selectivity for the bacterial over human
metalloproteases. Additionally, the inhibitors demonstrate no signs
of cytotoxicity against selected human cell lines and in a zebrafish
embryo toxicity model. Furthermore, the most active ColH inhibitor
shows a significant reduction of collagen degradation in an ex vivo pig-skin model.
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Affiliation(s)
- Jelena Konstantinović
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Samir Yahiaoui
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Alaa Alhayek
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Jörg Haupenthal
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Esther Schönauer
- Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020 Salzburg, Austria
| | - Anastasia Andreas
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Andreas M Kany
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany.,Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Jesko Koehnke
- Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Fabian K Berger
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421 Homburg/Saar, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421 Homburg/Saar, Germany
| | - Rolf W Hartmann
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020 Salzburg, Austria
| | - Anna K H Hirsch
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
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27
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Aglas L, Soh WT, Kraiem A, Wenger M, Brandstetter H, Ferreira F. Ligand Binding of PR-10 Proteins with a Particular Focus on the Bet v 1 Allergen Family. Curr Allergy Asthma Rep 2020; 20:25. [PMID: 32430735 PMCID: PMC7237532 DOI: 10.1007/s11882-020-00918-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Purpose of Review Pathogenesis-related class 10 (PR-10) proteins are highly conserved plant proteins, which are induced in response to abiotic and biotic stress factors. To date, no unique biological function could be assigned to them. Rather a more general role of PR-10 in plant development and defense mechanisms has been proposed. In addition, some PR-10 proteins act as allergens by triggering allergic symptoms in sensitized individuals. Regardless of the diversity of reported activities, all PR-10 proteins share a common fold characterized by a solvent-accessible hydrophobic cavity, which serves as a binding site for a myriad of small-molecule ligands, mostly phytohormones and flavonoids. Recent Findings Most of available data relate to the ligand binding activity of allergenic PR-10, particularly for those belonging to Bet v 1 family of allergens. Bet v 1 and its homologues were shown to bind flavonoids with high affinity, but the specificity appears to differ between homologues from different species. The flavonoid Q3O-(Glc)-Gal was shown to specifically bind to hazelnut Cor a 1 but not to Bet v 1. Similarly, Q3OS bound only to the major isoform Bet v 1.0101 and not to other closely related isoforms. In contrast, Bet v 1 and hazelnut Cor a 1 showed very similar binding behavior towards other flavonoids such as quercetin, genistein, apigenin, daidzein, and resveratrol. Summary Recent research findings highlighted the importance of more precise knowledge of ligand binding for understanding the functional diversification of PR-10 proteins.
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Affiliation(s)
- Lorenz Aglas
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
| | - Wai Tuck Soh
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria.,Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Amin Kraiem
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
| | - Mario Wenger
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
| | - Fatima Ferreira
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria.
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Soh WT, Demir F, Dall E, Perrar A, Dahms SO, Kuppusamy M, Brandstetter H, Huesgen PF. ExteNDing Proteome Coverage with Legumain as a Highly Specific Digestion Protease. Anal Chem 2020; 92:2961-2971. [PMID: 31951383 PMCID: PMC7075662 DOI: 10.1021/acs.analchem.9b03604] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Bottom-up
mass spectrometry-based proteomics utilizes proteolytic
enzymes with well characterized specificities to generate peptides
amenable for identification by high-throughput tandem mass spectrometry.
Trypsin, which cuts specifically after the basic residues lysine and
arginine, is the predominant enzyme used for proteome digestion, although
proteases with alternative specificities are required to detect sequences
that are not accessible after tryptic digest. Here, we show that the
human cysteine protease legumain exhibits a strict substrate specificity
for cleavage after asparagine and aspartic acid residues during in-solution
digestions of proteomes extracted from Escherichia
coli, mouse embryonic fibroblast cell cultures, and Arabidopsis thaliana leaves. Generating peptides
highly complementary in sequence, yet similar in their biophysical
properties, legumain (as compared to trypsin or GluC) enabled complementary
proteome and protein sequence coverage. Importantly, legumain further
enabled the identification and enrichment of protein N-termini not
accessible in GluC- or trypsin-digested samples. Legumain cannot cleave
after glycosylated Asn residues, which enabled the robust identification
and orthogonal validation of N-glycosylation sites based on alternating
sequential sample treatments with legumain and PNGaseF and vice versa.
Taken together, we demonstrate that legumain is a practical, efficient
protease for extending the proteome and sequence coverage achieved
with trypsin, with unique possibilities for the characterization of
post-translational modification sites.
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Affiliation(s)
- Wai Tuck Soh
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3 , Forschungszentrum Jülich , 52428 Jülich , Germany
| | - Elfriede Dall
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria
| | - Andreas Perrar
- Central Institute for Engineering, Electronics and Analytics, ZEA-3 , Forschungszentrum Jülich , 52428 Jülich , Germany
| | - Sven O Dahms
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria
| | - Maithreyan Kuppusamy
- Central Institute for Engineering, Electronics and Analytics, ZEA-3 , Forschungszentrum Jülich , 52428 Jülich , Germany
| | - Hans Brandstetter
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3 , Forschungszentrum Jülich , 52428 Jülich , Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, Medical Faculty and University Hospital , University of Cologne , 50931 Cologne , Germany.,Institute for Biochemistry, Faculty of Mathematics and Natural Sciences , University of Cologne , 50674 Cologne , Germany
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Soh WT, Aglas L, Mueller GA, Gilles S, Weiss R, Scheiblhofer S, Huber S, Scheidt T, Thompson PM, Briza P, London RE, Traidl‐Hoffmann C, Cabrele C, Brandstetter H, Ferreira F. Multiple roles of Bet v 1 ligands in allergen stabilization and modulation of endosomal protease activity. Allergy 2019; 74:2382-2393. [PMID: 31230350 PMCID: PMC6910946 DOI: 10.1111/all.13948] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 04/30/2019] [Indexed: 12/21/2022]
Abstract
Background Over 100 million people worldwide suffer from birch pollen allergy. Bet v 1 has been identified as the major birch pollen allergen. However, the molecular mechanisms of birch allergic sensitization, including the roles of Bet v 1 and other components of the birch pollen extract, remain incompletely understood. Here, we examined how known birch pollen–derived molecules influence the endolysosomal processing of Bet v 1, thereby shaping its allergenicity. Methods We analyzed the biochemical and immunological interaction of ligands with Bet v 1. We then investigated the proteolytic processing of Bet v 1 by endosomal extracts in the presence and absence of ligands, followed by a detailed kinetic analysis of Bet v 1 processing by individual endolysosomal proteases as well as the T‐cell epitope presentation in BMDCs. Results We identified E1 phytoprostanes as novel Bet v 1 ligands. Pollen‐derived ligands enhanced the proteolytic resistance of Bet v 1, affecting degradation kinetics and preferential cleavage sites of the endolysosomal proteases cathepsin S and legumain. E1 phytoprostanes exhibited a dual role by stabilizing Bet v 1 and inhibiting cathepsin protease activity. Conclusion Bet v 1 can serve as a transporter of pollen‐derived, bioactive compounds. When carried to the endolysosome, such compounds can modulate the proteolytic activity, including its processing by cysteine cathepsins. We unveil a paradigm shift from an allergen‐centered view to a more systemic view that includes the host endolysosomal enzymes.
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Affiliation(s)
- Wai Tuck Soh
- Department of Biosciences University of Salzburg Salzburg Austria
| | - Lorenz Aglas
- Department of Biosciences University of Salzburg Salzburg Austria
| | - Geoffrey A. Mueller
- Department of Health and Human Services, Genome Integrity and Structural Biology Laboratory National Institute of Environmental Health Sciences, National Institutes of Health Research Triangle Park North Carolina
| | - Stefanie Gilles
- Institute of Environmental Medicine UNIKA‐T, Technical University Munich and Helmholtz Zentrum München Augsburg Germany
- Christine‐Kühne‐Center for Allergy Research and Education (CK CARE) Davos Switzerland
| | - Richard Weiss
- Department of Biosciences University of Salzburg Salzburg Austria
| | | | - Sara Huber
- Department of Biosciences University of Salzburg Salzburg Austria
| | - Tamara Scheidt
- Department of Biosciences University of Salzburg Salzburg Austria
| | - Peter M. Thompson
- Department of Health and Human Services, Genome Integrity and Structural Biology Laboratory National Institute of Environmental Health Sciences, National Institutes of Health Research Triangle Park North Carolina
| | - Peter Briza
- Department of Biosciences University of Salzburg Salzburg Austria
| | - Robert E. London
- Department of Health and Human Services, Genome Integrity and Structural Biology Laboratory National Institute of Environmental Health Sciences, National Institutes of Health Research Triangle Park North Carolina
| | - Claudia Traidl‐Hoffmann
- Institute of Environmental Medicine UNIKA‐T, Technical University Munich and Helmholtz Zentrum München Augsburg Germany
- Christine‐Kühne‐Center for Allergy Research and Education (CK CARE) Davos Switzerland
| | - Chiara Cabrele
- Department of Biosciences University of Salzburg Salzburg Austria
| | | | - Fatima Ferreira
- Department of Biosciences University of Salzburg Salzburg Austria
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30
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Wildner S, Griessner I, Stemeseder T, Regl C, Soh WT, Stock LG, Völker T, Alessandri C, Mari A, Huber CG, Stutz H, Brandstetter H, Gadermaier G. Boiling down the cysteine-stabilized LTP fold - loss of structural and immunological integrity of allergenic Art v 3 and Pru p 3 as a consequence of irreversible lanthionine formation. Mol Immunol 2019; 116:140-150. [DOI: 10.1016/j.molimm.2019.10.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 01/27/2023]
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Abstract
Trypsin and chymotrypsin-like serine proteases from family S1 (clan PA) constitute the largest protease group in humans and more generally in vertebrates. The prototypes chymotrypsin, trypsin and elastase represent simple digestive proteases in the gut, where they cleave nearly any protein. Multidomain trypsin-like proteases are key players in the tightly controlled blood coagulation and complement systems, as well as related proteases that are secreted from diverse immune cells. Some serine proteases are expressed in nearly all tissues and fluids of the human body, such as the human kallikreins and kallikrein-related peptidases with specialization for often unique substrates and accurate timing of activity. HtrA and membrane-anchored serine proteases fulfill important physiological tasks with emerging roles in cancer. The high diversity of all family members, which share the tandem β-barrel architecture of the chymotrypsin-fold in the catalytic domain, is conferred by the large differences of eight surface loops, surrounding the active site. The length of these loops alters with insertions and deletions, resulting in remarkably different three-dimensional arrangements. In addition, metal binding sites for Na+, Ca2+ and Zn2+ serve as regulatory elements, as do N-glycosylation sites. Depending on the individual tasks of the protease, the surface loops determine substrate specificity, control the turnover and allow regulation of activation, activity and degradation by other proteins, which are often serine proteases themselves. Most intriguingly, in some serine proteases, the surface loops interact as allosteric network, partially tuned by protein co-factors. Knowledge of these subtle and complicated molecular motions may allow nowadays for new and specific pharmaceutical or medical approaches.
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Affiliation(s)
- Peter Goettig
- Division of Structural Biology, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria.
| | - Hans Brandstetter
- Division of Structural Biology, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
| | - Viktor Magdolen
- Clinical Research Unit, Department of Obstetrics and Gynecology, School of Medicine, Technical University of Munich, Ismaninger Strasse 22, 81675, München, Germany
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32
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Fang H, Zögg T, Brandstetter H. Maturation of coagulation factor IX during Xase formation as deduced using factor VIII-derived peptides. FEBS Open Bio 2019; 9:1370-1378. [PMID: 31077577 PMCID: PMC6668378 DOI: 10.1002/2211-5463.12653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/08/2019] [Accepted: 05/10/2019] [Indexed: 11/08/2022] Open
Abstract
Blood coagulation involves extrinsic and intrinsic pathways, which merge at the activation step of blood coagulation factor X to factor Xa. This step is catalysed by the extrinsic or intrinsic Xase, which consists of a complex of factor VIIa and its cofactor tissue factor or factor IXa (FIXa) and its cofactor coagulation factor VIIIa (FVIIIa). Upon complex formation with FVIIIa, FIXa is conformationally activated to the Xase complex. However, the mechanistic understanding of this molecular recognition is limited. Here, we examined FVIIIa‐FIXa binding in the context of FIXa's activation status. Given the complexity and the labile nature of FVIIIa, we decided to employ two FVIII‐derived peptides (558‐loop, a2 peptide) to model the cofactor binding of FIX(a) using biosensor chip technology. These two FVIII peptides are known to mediate the key interactions between FVIIIa and FIXa. We found both of these cofactor mimetics as well as full‐length FVIIIa bind more tightly to zymogenic FIX than to proteolytically activated FIXa. Consequently and surprisingly, we observed that the catalytically inactive FIX zymogen can outcompete the activated FIXa from the complex with FVIIIa, resulting in an inactive, zymogenic Xase complex. By contrast, the thrombophilic Padua mutant FIXa‐R170 in complex with the protein–substrate analogue BPTI bound tighter to FVIIIa than to the zymogen form FIX‐R170L, suggesting that the active Xase complex preferentially forms in the Padua variant. Together, these results provide a mechanistic basis for the thrombophilic nature of the FIX‐R170L mutant and suggest the existence of a newly discovered safety measure within the coagulation cascade.
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Affiliation(s)
- Han Fang
- Department of BiosciencesUniversity of SalzburgAustria
| | - Thomas Zögg
- Department of BiosciencesUniversity of SalzburgAustria
- VIB‐VUB Center for Structural BiologyBrusselsBelgium
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33
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Pereira GAN, da Silva EB, Braga SFP, Leite PG, Martins LC, Vieira RP, Soh WT, Villela FS, Costa FMR, Ray D, de Andrade SF, Brandstetter H, Oliveira RB, Caffrey CR, Machado FS, Ferreira RS. Discovery and characterization of trypanocidal cysteine protease inhibitors from the 'malaria box'. Eur J Med Chem 2019; 179:765-778. [PMID: 31284086 DOI: 10.1016/j.ejmech.2019.06.062] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 02/04/2023]
Abstract
Chagas disease, Human African Trypanosomiasis, and schistosomiasis are neglected parasitic diseases for which new treatments are urgently needed. To identify new chemical leads, we screened the 400 compounds of the Open Access Malaria Box against the cysteine proteases, cruzain (Trypanosoma cruzi), rhodesain (Trypanosoma brucei) and SmCB1 (Schistosoma mansoni), which are therapeutic targets for these diseases. Whereas just three hits were observed for SmCB1, 70 compounds inhibited cruzain or rhodesain by at least 50% at 5 μM. Among those, 15 commercially available compounds were selected for confirmatory assays, given their potency, time-dependent inhibition profile and reported activity against parasites. Additional assays led to the confirmation of four novel classes of cruzain and rhodesain inhibitors, with potency in the low-to mid-micromolar range against enzymes and T. cruzi. Assays against mammalian cathepsins S and B revealed inhibitor selectivity for parasitic proteases. For the two competitive inhibitors identified (compounds 7 and 12), their binding mode was predicted by docking, providing a basis for structure-based optimization efforts. Compound 12 also acted directly against the trypomastigote and the intracellular amastigote forms of T. cruzi at 3 μM. Therefore, through a combination of experimental and computational approaches, we report promising hits for optimization in the development of new trypanocidal drugs.
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Affiliation(s)
- Glaécia A N Pereira
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil; CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, Brazil
| | - Elany B da Silva
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Saulo F P Braga
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil; CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, Brazil
| | - Paulo Gaio Leite
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Luan C Martins
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Rafael P Vieira
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil; CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, Brazil
| | - Wai Tuck Soh
- Structural Biology Group By Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Filipe S Villela
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Francielly M R Costa
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Debalina Ray
- University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA
| | - Saulo F de Andrade
- Pharmaceutical Synthesis Group (PHARSG), Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, Brazil
| | - Hans Brandstetter
- Structural Biology Group By Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Renata B Oliveira
- Faculdade de Farmácia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Conor R Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Fabiana S Machado
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Rafaela S Ferreira
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil.
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34
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Barbosa da Silva E, Dall E, Briza P, Brandstetter H, Ferreira RS. Cruzain structures: apocruzain and cruzain bound to S-methyl thiomethanesulfonate and implications for drug design. Acta Crystallogr F Struct Biol Commun 2019; 75:419-427. [PMID: 31204688 PMCID: PMC6572096 DOI: 10.1107/s2053230x19006320] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/03/2019] [Indexed: 11/10/2022] Open
Abstract
Chagas disease, which is caused by Trypanosoma cruzi, affects more than six million people worldwide. Cruzain is the major cysteine protease involved in the survival of this parasite. Here, the expression, purification and crystallization of this enzyme are reported. The cruzain crystals diffracted to 1.2 Å resolution, yielding two novel cruzain structures: apocruzain and cruzain bound to the reversible covalent inhibitor S-methyl thiomethanesulfonate. Mass-spectrometric experiments confirmed the presence of a methylthiol group attached to the catalytic cysteine. Comparison of these structures with previously published structures indicates the rigidity of the cruzain structure. These results provide further structural information about the enzyme and may help in new in silico studies to identify or optimize novel prototypes of cruzain inhibitors.
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Affiliation(s)
- Elany Barbosa da Silva
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Elfriede Dall
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Peter Briza
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Rafaela Salgado Ferreira
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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35
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Schilling O, Biniossek ML, Mayer B, Elsässer B, Brandstetter H, Goettig P, Stenman UH, Koistinen H. Specificity profiling of human trypsin-isoenzymes. Biol Chem 2019; 399:997-1007. [PMID: 29883318 DOI: 10.1515/hsz-2018-0107] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/05/2018] [Indexed: 01/18/2023]
Abstract
In humans, three different trypsin-isoenzymes have been described. Of these, trypsin-3 appears to be functionally different from the others. In order to systematically study the specificity of the trypsin-isoenzymes, we utilized proteome-derived peptide libraries and quantitative proteomics. We found similar specificity profiles dominated by the well-characterized preference for cleavage after lysine and arginine. Especially, trypsin-1 slightly favored lysine over arginine in this position, while trypsin-3 did not discriminate between them. In the P1' position, which is the residue C-terminal to the cleavage site, we noticed a subtle enrichment of alanine and glycine for all three trypsins and for trypsin-3 there were additional minor P1' and P2' preferences for threonine and aspartic acid, respectively. These findings were confirmed by FRET peptide substrates showing different susceptibility to cleavage by different trypsins. The preference of trypsin-3 for aspartic acid in P2' is explained by salt bridge formation with the unique Arg193. This salt bridge enables and stabilizes a canonical oxyanion conformation by the amides of Ser195 and Arg193, thus manifesting a selective substrate-assisted catalysis. As trypsin-3 has been proposed to be a therapeutic target and marker for cancers, our results may aid the development of specific inhibitors for cancer therapy and diagnostic probes.
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Affiliation(s)
- Oliver Schilling
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Martin L Biniossek
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
| | - Bettina Mayer
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
| | - Brigitta Elsässer
- Department of Biosciences, University of Salzburg, Billrothstr. 11, A-5020 Salzburg, Austria
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, Billrothstr. 11, A-5020 Salzburg, Austria
| | - Peter Goettig
- Department of Biosciences, University of Salzburg, Billrothstr. 11, A-5020 Salzburg, Austria
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Central Hospital, Haartmaninkatu 8, FI-00290 Helsinki, Finland
| | - Hannu Koistinen
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Central Hospital, Haartmaninkatu 8, FI-00290 Helsinki, Finland
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36
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Dahms SO, Demir F, Huesgen PF, Thorn K, Brandstetter H. Sirtilins - the new old members of the vitamin K-dependent coagulation factor family. J Thromb Haemost 2019; 17:470-481. [PMID: 30644641 PMCID: PMC6850207 DOI: 10.1111/jth.14384] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Indexed: 12/04/2022]
Abstract
Essentials Blood coagulation is driven by vitamin K (VK)-dependent proteases. We have identified and characterized 'sirtilin' as an additional VK-dependent protease. Sirtilins emerged early in the evolution of the coagulation system of vertebrates. Ubiquitous occurrence might indicate an important functional role of sirtilins. SUMMARY: Background Vitamin K (VK)-dependent proteases are major players in blood coagulation, including both the initiation and the regulation of the cascade. Five different members of this protease family have been described, comprising the following coagulation factors: factor VII, FIX, FX, protein C (PC), and prothrombin (FII). FVII, FIX, FX and PC share a typical domain architecture, with an N-terminal γ-carboxyglutamate (Gla) domain, two epidermal growth factor-like (EGF) domains, and a C-terminal trypsin-like serine protease (SP) domain. Objectives We have identified uncharacterized proteins in snake genomes showing the typical Gla-EGF1-EGF2-SP domain architecture but relatively low sequence conservation compared to known VK-dependent proteases. On the basis of sequence analysis, we hypothesized that these proteins are functional members of the VK-dependent protease family. Methods/results Using phylogenetic analyses, we confirmed the so-called 'sirtilins' as an additional VK-dependent protease class. These proteases were found in several vertebrates, including jawless fish, cartilaginous fish, bony fish, reptiles, birds, and marsupials, but not in other mammals. The recombinant zymogen form of Thamnophis sirtalis sirtilin was produced by in vitro renaturation, and was activated with human activated FXI. The activated form of sirtilin proteolytically cleaved peptide and protein substrates, including prothrombin. Mass spectrometry-based substrate profiling of sirtilin revealed a narrower sequence specificity than those of FIX and FX. Conclusions The ubiquitous occurrence of sirtilins in many vertebrate classes might indicate an important functional role. Understanding the detailed functions of sirtilins might contribute to a deeper understanding of the evolution and function of the vertebrate coagulation system.
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Affiliation(s)
- Sven O. Dahms
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Fatih Demir
- ZEA‐3 AnalyticsCentral Institute for Engineering, Electronics and AnalyticsForschungszentrum JülichJülichGermany
| | - Pitter F. Huesgen
- ZEA‐3 AnalyticsCentral Institute for Engineering, Electronics and AnalyticsForschungszentrum JülichJülichGermany
| | - Karina Thorn
- Haemophilia ResearchNovo Nordisk A/SMåløvDenmark
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Guo S, Briza P, Magdolen V, Brandstetter H, Goettig P. Activation and activity of glycosylated KLKs 3, 4 and 11. Biol Chem 2018; 399:1009-1022. [DOI: 10.1515/hsz-2018-0148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/21/2018] [Indexed: 01/10/2023]
Abstract
Abstract
Human kallikrein-related peptidases 3, 4, 11, and KLK2, the activator of KLK3/PSA, belong to the prostatic group of the KLKs, whose major physiological function is semen liquefaction during the fertilization process. Notably, these KLKs are upregulated in prostate cancer and are used as clinical biomarkers or have been proposed as therapeutic targets. However, this potential awaits a detailed characterization of these proteases. In order to study glycosylated prostatic KLKs resembling the natural proteases, we used Leishmania (LEXSY) and HEK293 cells for secretory expression. Both systems allowed the subsequent purification of soluble pro-KLK zymogens with correct propeptides and of the mature forms. Periodic acid-Schiff reaction, enzymatic deglycosylation assays, and mass spectrometry confirmed the glycosylation of these KLKs. Activation of glycosylated pro-KLKs 4 and 11 turned out to be most efficient by glycosylated KLK2 and KLK4, respectively. By comparing the glycosylated prostatic KLKs with their non-glycosylated counterparts from Escherichia coli, it was observed that the N-glycans stabilize the KLK proteases and change their activation profiles and their enzymatic activity to some extent. The functional role of glycosylation in prostate-specific KLKs could pave the way to a deeper understanding of their biology and to medical applications.
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Bode W, Brandstetter H, Mather T, Stubbs MT. Comparative Analysis of Haemostatic Proteinases: Structural Aspects of Thrombin, Factor Xa, Factor IXa and Protein C. Thromb Haemost 2018. [DOI: 10.1055/s-0038-1657577] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Wolfram Bode
- Max-Planck-lnstitut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried bei München, Germany
| | - Hans Brandstetter
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Timothy Mather
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation and Howard Hughes Medical Institute, Oklahoma City, OK, USA
| | - Milton T Stubbs
- lnstitut für Pharmazeutische Chemie der Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
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39
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Dall E, Hollerweger JC, Dahms SO, Cui H, Häussermann K, Brandstetter H. Structural and functional analysis of cystatin E reveals enzymologically relevant dimer and amyloid fibril states. J Biol Chem 2018; 293:13151-13165. [PMID: 29967063 PMCID: PMC6109925 DOI: 10.1074/jbc.ra118.002154] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/26/2018] [Indexed: 12/26/2022] Open
Abstract
Protein activity is often regulated by altering the oligomerization state. One mechanism of multimerization involves domain swapping, wherein proteins exchange parts of their structures and thereby form long-lived dimers or multimers. Domain swapping has been specifically observed in amyloidogenic proteins, for example the cystatin superfamily of cysteine protease inhibitors. Cystatins are twin-headed inhibitors, simultaneously targeting the lysosomal cathepsins and legumain, with important roles in cancer progression and Alzheimer's disease. Although cystatin E is the most potent legumain inhibitor identified so far, nothing is known about its propensity to oligomerize. In this study, we show that conformational destabilization of cystatin E leads to the formation of a domain-swapped dimer with increased conformational stability. This dimer was active as a legumain inhibitor by forming a trimeric complex. By contrast, the binding sites toward papain-like proteases were buried within the cystatin E dimer. We also showed that the dimers could further convert to amyloid fibrils. Unexpectedly, cystatin E amyloid fibrils contained functional protein, which inhibited both legumain and papain-like enzymes. Fibril formation was further regulated by glycosylation. We speculate that cystatin amyloid fibrils might serve as a binding platform to stabilize the pH-sensitive legumain and cathepsins in the extracellular environment, contributing to their physiological and pathological functions.
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Affiliation(s)
- Elfriede Dall
- From the Department of Biosciences, University of Salzburg, A-5020 Salzburg, Austria and
| | - Julia C Hollerweger
- From the Department of Biosciences, University of Salzburg, A-5020 Salzburg, Austria and
| | - Sven O Dahms
- From the Department of Biosciences, University of Salzburg, A-5020 Salzburg, Austria and
| | - Haissi Cui
- the Center for Integrated Protein Science Munich, Technical University of Munich, D-85748 Munich, Germany
| | - Katharina Häussermann
- the Center for Integrated Protein Science Munich, Technical University of Munich, D-85748 Munich, Germany
| | - Hans Brandstetter
- From the Department of Biosciences, University of Salzburg, A-5020 Salzburg, Austria and
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40
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Hollerweger JC, Hoppe IJ, Regl C, Stock LG, Huber CG, Lohrig U, Stutz H, Brandstetter H. Analytical Cascades of Enzymes for Sensitive Detection of Structural Variations in Protein Samples. Anal Chem 2018; 90:5055-5065. [PMID: 29582994 DOI: 10.1021/acs.analchem.7b04874] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein function critically depends on structure. However, current analytical tools to monitor consistent higher-order structure with high sensitivity, as for instance required in the development of biopharmaceuticals, are limited. To complement existing assays, we present the analytical cascade of enzymes (ACE), a method based on enzymatic modifications of target proteins, which serve to exponentially amplify structural differences between them. The method enables conformational and chemical fingerprinting of closely related proteins, allowing for the sensitive detection of heterogeneities in protein preparations with high precision. Using this method, we detect protein variants differing in conformation only, as well as structural changes induced by diverse covalent modifications. Additionally, we employ this method to identify the nature of structural variants. Moreover, the ACE method should help to address the limited reproducibility in fundamental research, which partly relates to sample heterogeneities.
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Affiliation(s)
- Julia C Hollerweger
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , 5020 Salzburg , Austria
| | - Isabel J Hoppe
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , 5020 Salzburg , Austria
| | - Christof Regl
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , 5020 Salzburg , Austria
| | - Lorenz G Stock
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , 5020 Salzburg , Austria
| | - Christian G Huber
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , 5020 Salzburg , Austria
| | - Urs Lohrig
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , 5020 Salzburg , Austria.,Physical and Chemical Characterization Biosimilars , Sandoz GmbH , A-6250 Kundl , Austria
| | - Hanno Stutz
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , 5020 Salzburg , Austria
| | - Hans Brandstetter
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , 5020 Salzburg , Austria
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41
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Zauner FB, Elsässer B, Dall E, Cabrele C, Brandstetter H. Structural analyses of Arabidopsis thaliana legumain γ reveal differential recognition and processing of proteolysis and ligation substrates. J Biol Chem 2018; 293:8934-8946. [PMID: 29628443 PMCID: PMC5995516 DOI: 10.1074/jbc.m117.817031] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 02/18/2018] [Indexed: 11/06/2022] Open
Abstract
Legumain is a dual-function protease-peptide ligase whose activities are of great interest to researchers studying plant physiology and to biotechnological applications. However, the molecular mechanisms determining the specificities for proteolysis and ligation are unclear because structural information on the substrate recognition by a fully activated plant legumain is unavailable. Here, we present the X-ray structure of Arabidopsis thaliana legumain isoform γ (AtLEGγ) in complex with the covalent peptidic Ac-YVAD chloromethyl ketone (CMK) inhibitor targeting the catalytic cysteine. Mapping of the specificity pockets preceding the substrate-cleavage site explained the known substrate preference. The comparison of inhibited and free AtLEGγ structures disclosed a substrate-induced disorder-order transition with synergistic rearrangements in the substrate-recognition sites. Docking and in vitro studies with an AtLEGγ ligase substrate, sunflower trypsin inhibitor (SFTI), revealed a canonical, protease substrate-like binding to the active site-binding pockets preceding and following the cleavage site. We found the interaction of the second residue after the scissile bond, P2'-S2', to be critical for deciding on proteolysis versus cyclization. cis-trans-Isomerization of the cyclic peptide product triggered its release from the AtLEGγ active site and prevented inadvertent cleavage. The presented integrative mechanisms of proteolysis and ligation (transpeptidation) explain the interdependence of legumain and its preferred substrates and provide a rational framework for engineering optimized proteases, ligases, and substrates.
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Affiliation(s)
- Florian B Zauner
- From the Department of Biosciences, University of Salzburg, Salzburg 5020, Austria
| | - Brigitta Elsässer
- From the Department of Biosciences, University of Salzburg, Salzburg 5020, Austria
| | - Elfriede Dall
- From the Department of Biosciences, University of Salzburg, Salzburg 5020, Austria
| | - Chiara Cabrele
- From the Department of Biosciences, University of Salzburg, Salzburg 5020, Austria
| | - Hans Brandstetter
- From the Department of Biosciences, University of Salzburg, Salzburg 5020, Austria
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42
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Zauner FB, Dall E, Regl C, Grassi L, Huber CG, Cabrele C, Brandstetter H. Crystal Structure of Plant Legumain Reveals a Unique Two-Chain State with pH-Dependent Activity Regulation. Plant Cell 2018; 30:686-699. [PMID: 29453229 PMCID: PMC5894848 DOI: 10.1105/tpc.17.00963] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/13/2018] [Accepted: 02/13/2018] [Indexed: 05/10/2023]
Abstract
The vacuolar cysteine protease legumain can cleave and selectively rebuild peptide bonds, thereby vastly expanding the sequential repertoire of biomolecules. In this context, plant legumains have recently attracted particular interest. Furthermore, legumains have important roles in many physiological processes, including programmed cell death. Their efficient peptide bond ligase activity has gained tremendous interest in the design of cyclic peptides for drug design. However, the mechanistic understanding of these dual activities is incomplete and partly conflicting. Here, we present the crystal structure of a plant legumain, Arabidopsis thaliana isoform-γ (AtLEGγ). Employing a conserved legumain fold, the plant legumain AtLEGγ revealed unique mechanisms of autoactivation, including a plant-specific two-chain activation state, which remains conformationally stable at neutral pH, which is a prerequisite for full ligase activity and survival in different cell compartments. The charge distribution around the α6-helix mediates the pH-dependent dimerization and serves as a gatekeeper for the active site, thus regulating its protease and ligase activity.
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Affiliation(s)
- Florian B Zauner
- Department of Molecular Biology and Christian Doppler Laboratory for Biosimilar Research, University of Salzburg, A-5020 Salzburg, Austria
| | - Elfriede Dall
- Department of Molecular Biology and Christian Doppler Laboratory for Biosimilar Research, University of Salzburg, A-5020 Salzburg, Austria
| | - Christof Regl
- Department of Molecular Biology and Christian Doppler Laboratory for Biosimilar Research, University of Salzburg, A-5020 Salzburg, Austria
| | - Luigi Grassi
- Department of Molecular Biology and Christian Doppler Laboratory for Biosimilar Research, University of Salzburg, A-5020 Salzburg, Austria
| | - Christian G Huber
- Department of Molecular Biology and Christian Doppler Laboratory for Biosimilar Research, University of Salzburg, A-5020 Salzburg, Austria
| | - Chiara Cabrele
- Department of Molecular Biology and Christian Doppler Laboratory for Biosimilar Research, University of Salzburg, A-5020 Salzburg, Austria
| | - Hans Brandstetter
- Department of Molecular Biology and Christian Doppler Laboratory for Biosimilar Research, University of Salzburg, A-5020 Salzburg, Austria
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43
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Schinagl A, Kerschbaumer RJ, Sabarth N, Douillard P, Scholz P, Voelkel D, Hollerweger JC, Goettig P, Brandstetter H, Scheiflinger F, Thiele M. Role of the Cysteine 81 Residue of Macrophage Migration Inhibitory Factor as a Molecular Redox Switch. Biochemistry 2018; 57:1523-1532. [PMID: 29412660 DOI: 10.1021/acs.biochem.7b01156] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Macrophage migration inhibitory factor (MIF) is a pro-inflammatory and tumor-promoting cytokine that occurs in two redox-dependent immunologically distinct conformational isoforms. The disease-related structural isoform of MIF (oxMIF) can be specifically and predominantly detected in the circulation of patients with inflammatory diseases and in tumor tissue, whereas the ubiquitously expressed isoform of MIF (redMIF) is abundantly expressed in healthy and diseased subjects. In this article, we report that cysteine 81 within MIF serves as a "switch cysteine" for the conversion of redMIF to oxMIF. Modulating cysteine 81 by thiol reactive agents leads to significant structural rearrangements of the protein, resulting in a decreased β-sheet content and an increased random coil content, but maintaining the trimeric quaternary structure. This conformational change in the MIF molecule enables binding of oxMIF-specific antibodies BaxB01 and BaxM159, which showed beneficial activity in animal models of inflammation and cancer. Crystal structure analysis of the MIF-derived EPCALCS peptide, bound in its oxMIF-like conformation by the Fab fragment of BaxB01, revealed that this peptide adopts a curved conformation, making the central thiol protein oxidoreductase motif competent to undergo disulfide shuffling. We conclude that redMIF might reflect a latent zymogenic form of MIF, and formation of oxMIF leads to a physiologically relevant, i.e., enzymatically active, state.
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Affiliation(s)
- Alexander Schinagl
- Baxalta Innovations GmbH , Uferstrasse 15 , 2304 Orth an der Donau , Austria
| | | | - Nicolas Sabarth
- Baxalta Innovations GmbH , Uferstrasse 15 , 2304 Orth an der Donau , Austria
| | - Patrice Douillard
- Baxalta Innovations GmbH , Uferstrasse 15 , 2304 Orth an der Donau , Austria
| | - Peter Scholz
- Baxalta Innovations GmbH , Uferstrasse 15 , 2304 Orth an der Donau , Austria
| | - Dirk Voelkel
- Baxalta Innovations GmbH , Uferstrasse 15 , 2304 Orth an der Donau , Austria
| | - Julia C Hollerweger
- Division of Structural Biology and Bioinformatics , University of Salzburg , Billrothstrasse 11 , 5020 Salzburg , Austria
| | - Peter Goettig
- Division of Structural Biology and Bioinformatics , University of Salzburg , Billrothstrasse 11 , 5020 Salzburg , Austria
| | - Hans Brandstetter
- Division of Structural Biology and Bioinformatics , University of Salzburg , Billrothstrasse 11 , 5020 Salzburg , Austria
| | | | - Michael Thiele
- Baxalta Innovations GmbH , Uferstrasse 15 , 2304 Orth an der Donau , Austria
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44
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Soh WT, Briza P, Dall E, Asam C, Schubert M, Huber S, Aglas L, Bohle B, Ferreira F, Brandstetter H. Two Distinct Conformations in Bet v 2 Determine Its Proteolytic Resistance to Cathepsin S. Int J Mol Sci 2017; 18:ijms18102156. [PMID: 29035299 PMCID: PMC5666837 DOI: 10.3390/ijms18102156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/04/2017] [Accepted: 10/11/2017] [Indexed: 12/17/2022] Open
Abstract
Birch pollen allergy affects more than 20% of the European allergic population. On a molecular level, birch pollen allergy can be linked to the two dominant allergens Bet v 1 and Bet v 2. Bet v 2 belongs to the profilin family, which is abundant in the plant kingdom. Importantly, the homologous plant profilins have a conserved cysteine motif with a currently unknown functional relevance. In particular, it is unknown whether the motif is relevant for disulfide formation and to what extent it would affect the profilins’ structural, functional and immunological properties. Here we present crystal structures of Bet v 2 in the reduced and the oxidized state, i.e., without and with a disulfide bridge. Despite overall structural similarity, the two structures distinctly differ at their termini which are stabilized to each other in the oxidized, i.e., disulfide-linked state. These structural differences translate into differences in their proteolytic resistance. Whereas the oxidized Bet v 2 is rather resistant towards the endolysosomal protease cathepsin S, it is rapidly degraded in the reduced form. By contrast, both Bet v 2 forms exhibit similar immunological properties as evidenced by their binding to IgE antibodies from birch pollen allergic patients and by their ability to trigger histamine release in a humanized rat basophilic leukemia cells (RBL) assay, independent of the presence or absence of the disulfide bridge. Taken together our findings suggest that the oxidized Bet v 2 conformation should be the relevant species, with a much longer retention time to trigger immune responses.
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Affiliation(s)
- Wai Tuck Soh
- Department of Molecular Biology, University of Salzburg, Salzburg 5020, Austria.
| | - Peter Briza
- Department of Molecular Biology, University of Salzburg, Salzburg 5020, Austria.
| | - Elfriede Dall
- Department of Molecular Biology, University of Salzburg, Salzburg 5020, Austria.
| | - Claudia Asam
- Department of Molecular Biology, University of Salzburg, Salzburg 5020, Austria.
| | - Mario Schubert
- Department of Molecular Biology, University of Salzburg, Salzburg 5020, Austria.
| | - Sara Huber
- Department of Molecular Biology, University of Salzburg, Salzburg 5020, Austria.
| | - Lorenz Aglas
- Department of Molecular Biology, University of Salzburg, Salzburg 5020, Austria.
| | - Barbara Bohle
- Department of Pathophysiology, Medical University of Vienna, Vienna 1090, Austria.
| | - Fatima Ferreira
- Department of Molecular Biology, University of Salzburg, Salzburg 5020, Austria.
| | - Hans Brandstetter
- Department of Molecular Biology, University of Salzburg, Salzburg 5020, Austria.
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45
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Elsässer B, Zauner FB, Messner J, Soh WT, Dall E, Brandstetter H. Distinct Roles of Catalytic Cysteine and Histidine in the Protease and Ligase Mechanisms of Human Legumain As Revealed by DFT-Based QM/MM Simulations. ACS Catal 2017; 7:5585-5593. [PMID: 28932620 PMCID: PMC5600538 DOI: 10.1021/acscatal.7b01505] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/10/2017] [Indexed: 11/30/2022]
Abstract
![]()
The cysteine protease enzyme legumain hydrolyzes peptide bonds
with high specificity after asparagine and under more acidic conditions
after aspartic acid [BakerE. N.1980, 141, 441−4847003158; BakerE. N.; 1977, 111, 207–210859183; DrenthJ.; 1976, 15, 3731–3738952885; MenardR.; 1994, 137; PolgarL.1978, 88, 513–521689035; StorerA. C.; 1994, 244, 486–5007845227. Remarkably,
legumain additionally exhibits ligase activity that prevails at pH
> 5.5. The atomic reaction mechanisms including their pH dependence
are only partly understood. Here we present a density functional theory
(DFT)-based quantum mechanics/molecular mechanics (QM/MM) study of
the detailed reaction mechanism of both activities for human legumain
in solution. Contrasting the situation in other papain-like proteases,
our calculations reveal that the active site Cys189 must be present
in the protonated state for a productive nucleophilic attack and simultaneous
rupture of the scissile peptide bond, consistent with the experimental
pH profile of legumain-catalyzed cleavages. The resulting thioester
intermediate (INT1) is converted by water attack on the thioester
into a second intermediate, a diol (INT2), which is released by proton
abstraction by Cys189. Surprisingly, we found that ligation is not
the exact reverse of the proteolysis but can proceed via two distinct
routes. Whereas the transpeptidation route involves aminolysis of
the thioester (INT1), at pH 6 a cysteine-independent, histidine-assisted
ligation route was found. Given legumain’s important roles
in immunity, cancer, and neurodegenerative diseases, our findings
open up possibilities for targeted drug design in these fields.
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Affiliation(s)
- Brigitta Elsässer
- Department
of Molecular Biology, University of Salzburg, Billrothstrasse 11, A-5020 Salzburg, Austria
| | - Florian B. Zauner
- Department
of Molecular Biology, University of Salzburg, Billrothstrasse 11, A-5020 Salzburg, Austria
| | - Johann Messner
- Information
Management, University of Linz, Alternberger Strasse 69, A-4040 Linz, Austria
| | - Wai Tuck Soh
- Department
of Molecular Biology, University of Salzburg, Billrothstrasse 11, A-5020 Salzburg, Austria
| | - Elfriede Dall
- Department
of Molecular Biology, University of Salzburg, Billrothstrasse 11, A-5020 Salzburg, Austria
| | - Hans Brandstetter
- Department
of Molecular Biology, University of Salzburg, Billrothstrasse 11, A-5020 Salzburg, Austria
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46
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Schönauer E, Kany AM, Haupenthal J, Hüsecken K, Hoppe IJ, Voos K, Yahiaoui S, Elsässer B, Ducho C, Brandstetter H, Hartmann RW. Discovery of a Potent Inhibitor Class with High Selectivity toward Clostridial Collagenases. J Am Chem Soc 2017; 139:12696-12703. [PMID: 28820255 PMCID: PMC5607459 DOI: 10.1021/jacs.7b06935] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Secreted virulence
factors like bacterial collagenases are conceptually
attractive targets for fighting microbial infections. However, previous
attempts to develop potent compounds against these metalloproteases
failed to achieve selectivity against human matrix metalloproteinases
(MMPs). Using a surface plasmon resonance-based screening complemented
with enzyme inhibition assays, we discovered an N-aryl mercaptoacetamide-based inhibitor scaffold that showed
sub-micromolar affinities toward collagenase H (ColH) from the human
pathogen Clostridium histolyticum. Moreover, these
inhibitors also efficiently blocked the homologous bacterial collagenases,
ColG from C. histolyticum, ColT from C. tetani, and ColQ1 from the Bacillus cereus strain Q1,
while showing negligible activity toward human MMPs-1, -2, -3, -7,
-8, and -14. The most active compound displayed a more than 1000-fold
selectivity over human MMPs. This selectivity can be rationalized
by the crystal structure of ColH with this compound, revealing a distinct
non-primed binding mode to the active site. The non-primed binding
mode presented here paves the way for the development of selective
broad-spectrum bacterial collagenase inhibitors with potential therapeutic
application in humans.
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Affiliation(s)
- Esther Schönauer
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Andreas M Kany
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany
| | - Jörg Haupenthal
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany
| | - Kristina Hüsecken
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany
| | - Isabel J Hoppe
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Katrin Voos
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University , Campus C2.3, 66123 Saarbrücken, Germany
| | - Samir Yahiaoui
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany
| | - Brigitta Elsässer
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University , Campus C2.3, 66123 Saarbrücken, Germany
| | - Hans Brandstetter
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Rolf W Hartmann
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University , Campus C2.3, 66123 Saarbrücken, Germany
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47
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Debela M, Magdolen V, Bode W, Brandstetter H, Goettig P. Structural basis for the Zn2+ inhibition of the zymogen-like kallikrein-related peptidase 10. Biol Chem 2017; 397:1251-1264. [PMID: 27611765 PMCID: PMC5551965 DOI: 10.1515/hsz-2016-0205] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 09/04/2016] [Indexed: 12/18/2022]
Abstract
Although kallikrein-related peptidase 10 (KLK10) is expressed in a variety of human tissues and body fluids, knowledge of its physiological functions is fragmentary. Similarly, the pathophysiology of KLK10 in cancer is not well understood. In some cancer types, a role as tumor suppressor has been suggested, while in others elevated expression is associated with poor patient prognosis. Active human KLK10 exhibits a unique, three residue longer N-terminus with respect to other serine proteases and an extended 99-loop nearly as long as in tissue kallikrein KLK1. Crystal structures of recombinant ligand-free KLK10 and a Zn2+ bound form explain to some extent the mixed trypsin- and chymotrypsin-like substrate specificity. Zn2+-inhibition of KLK10 appears to be based on a unique mechanism, which involves direct binding and blocking of the catalytic triad. Since the disordered N-terminus and several loops adopt a zymogen-like conformation, the active protease conformation is very likely induced by interaction with the substrate, in particular at the S1 subsite and at the unusual Ser193 as part of the oxyanion hole. The KLK10 structures indicate that the N-terminus, the nearby 75-, 148-, and the 99-loops are connected in an allosteric network, which is present in other trypsin-like serine proteases with several variations.
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Affiliation(s)
| | - Viktor Magdolen
- Klinische Forschergruppe der Frauenklinik, Klinikum rechts der Isar der TU München, Ismaninger Str. 22, D-81675 München, Germany
| | - Wolfram Bode
- Max-Planck-Institut für Biochemie, Proteinase Research Group, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Hans Brandstetter
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, A-5020 Salzburg, Austria
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48
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Zhang Z, Obianyo O, Dall E, Du Y, Fu H, Liu X, Kang SS, Song M, Yu SP, Cabrele C, Schubert M, Li X, Wang JZ, Brandstetter H, Ye K. Inhibition of delta-secretase improves cognitive functions in mouse models of Alzheimer's disease. Nat Commun 2017; 8:14740. [PMID: 28345579 PMCID: PMC5378956 DOI: 10.1038/ncomms14740] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 01/26/2017] [Indexed: 12/21/2022] Open
Abstract
δ-secretase, also known as asparagine endopeptidase (AEP) or legumain, is a lysosomal cysteine protease that cleaves both amyloid precursor protein (APP) and tau, mediating the amyloid-β and tau pathology in Alzheimer's disease (AD). Here we report the therapeutic effect of an orally bioactive and brain permeable δ-secretase inhibitor in mouse models of AD. We performed a high-throughput screen and identified a non-toxic and selective δ-secretase inhibitor, termed compound 11, that specifically blocks δ-secretase but not other related cysteine proteases. Co-crystal structure analysis revealed a dual active site-directed and allosteric inhibition mode of this compound class. Chronic treatment of tau P301S and 5XFAD transgenic mice with this inhibitor reduces tau and APP cleavage, ameliorates synapse loss and augments long-term potentiation, resulting in protection of memory. Therefore, these findings demonstrate that this δ-secretase inhibitor may be an effective clinical therapeutic agent towards AD.
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Affiliation(s)
- Zhentao Zhang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Obiamaka Obianyo
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Elfriede Dall
- Department of Molecular Biology, University of Salzburg, Salzburg A-5020, Austria
| | - Yuhong Du
- Department of Pharmacology, Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Haian Fu
- Department of Pharmacology, Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Xia Liu
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Seong Su Kang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Mingke Song
- Department of Anesthesiology Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Shan-Ping Yu
- Department of Anesthesiology Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Chiara Cabrele
- Department of Molecular Biology, University of Salzburg, Salzburg A-5020, Austria
| | - Mario Schubert
- Department of Molecular Biology, University of Salzburg, Salzburg A-5020, Austria
| | - Xiaoguang Li
- Pathophysiology Department, School of Basic Medicine and the Collaborative Innovation Center for Brain Science, Key Laboratory of Ministry of Education of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jian-Zhi Wang
- Pathophysiology Department, School of Basic Medicine and the Collaborative Innovation Center for Brain Science, Key Laboratory of Ministry of Education of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Co-innovation Center of Neuroregeneration, Nantong 226001, China
| | - Hans Brandstetter
- Department of Molecular Biology, University of Salzburg, Salzburg A-5020, Austria
| | - Keqiang Ye
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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49
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Braga SFP, Martins LC, da Silva EB, Sales Júnior PA, Murta SMF, Romanha AJ, Soh WT, Brandstetter H, Ferreira RS, de Oliveira RB. Synthesis and biological evaluation of potential inhibitors of the cysteine proteases cruzain and rhodesain designed by molecular simplification. Bioorg Med Chem 2017; 25:1889-1900. [DOI: 10.1016/j.bmc.2017.02.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 01/31/2017] [Accepted: 02/06/2017] [Indexed: 10/20/2022]
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50
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Stemeseder T, Freier R, Wildner S, Fuchs JE, Briza P, Lang R, Batanero E, Lidholm J, Liedl KR, Campo P, Hawranek T, Villalba M, Brandstetter H, Ferreira F, Gadermaier G. Crystal structure of Pla l 1 reveals both structural similarity and allergenic divergence within the Ole e 1-like protein family. J Allergy Clin Immunol 2016; 140:277-280. [PMID: 27965108 DOI: 10.1016/j.jaci.2016.10.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 09/16/2016] [Accepted: 10/05/2016] [Indexed: 10/20/2022]
Affiliation(s)
- Teresa Stemeseder
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Regina Freier
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Sabrina Wildner
- Christian Doppler Laboratory for Biosimilar Characterization, University of Salzburg, Salzburg, Austria
| | - Julian E Fuchs
- Institute of General, Inorganic, and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Peter Briza
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Roland Lang
- Paracelsus Medical University Salzburg, Department of Dermatology, Salzburg, Austria
| | - Eva Batanero
- Departamento Bioquímica y Biología Molecular I, Universidad Complutense, Madrid, Spain
| | | | - Klaus R Liedl
- Institute of General, Inorganic, and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Paloma Campo
- Allergy Unit, Instituto de Investigación Biomédica de Málaga, Regional University Hospital of Malaga, Malaga, Spain
| | - Thomas Hawranek
- Paracelsus Medical University Salzburg, Department of Dermatology, Salzburg, Austria
| | - Mayte Villalba
- Departamento Bioquímica y Biología Molecular I, Universidad Complutense, Madrid, Spain
| | - Hans Brandstetter
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Biosimilar Characterization, University of Salzburg, Salzburg, Austria
| | - Fatima Ferreira
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Gabriele Gadermaier
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Biosimilar Characterization, University of Salzburg, Salzburg, Austria.
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