1
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Bach K, Dohnálek J, Škerlová J, Kuzmík J, Poláchová E, Stanchev S, Majer P, Fanfrlík J, Pecina A, Řezáč J, Lepšík M, Borshchevskiy V, Polovinkin V, Strisovsky K. Extensive targeting of chemical space at the prime side of ketoamide inhibitors of rhomboid proteases by branched substituents empowers their selectivity and potency. Eur J Med Chem 2024; 275:116606. [PMID: 38901105 DOI: 10.1016/j.ejmech.2024.116606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 06/22/2024]
Abstract
Rhomboid intramembrane serine proteases have been implicated in several pathologies, and emerge as attractive pharmacological target candidates. The most potent and selective rhomboid inhibitors available to date are peptidyl α-ketoamides, but their selectivity for diverse rhomboid proteases and strategies to modulate it in relevant contexts are poorly understood. This gap, together with the lack of suitable in vitro models, hinders ketoamide development for relevant eukaryotic rhomboid enzymes. Here we explore the structure-activity relationship principles of rhomboid inhibiting ketoamides by medicinal chemistry and enzymatic in vitro and in-cell assays with recombinant rhomboid proteases GlpG, human mitochondrial rhomboid PARL and human RHBDL2. We use X-ray crystallography in lipidic cubic phase to understand the binding mode of one of the best ketoamide inhibitors synthesized here containing a branched terminal substituent bound to GlpG. In addition, to extend the interpretation of the co-crystal structure, we use quantum mechanical calculations and quantify the relative importance of interactions along the inhibitor molecule. These combined experimental analyses implicates that more extensive exploration of chemical space at the prime side is unexpectedly powerful for the selectivity of rhomboid inhibiting ketoamides. Together with variations in the peptide sequence at the non-prime side, or its non-peptidic alternatives, this strategy enables targeted tailoring of potent and selective ketoamides towards diverse rhomboid proteases including disease-relevant ones such as PARL and RHBDL2.
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Affiliation(s)
- Kathrin Bach
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic; Department of Molecular Genetics, Faculty of Science, Charles University, Viničná 5, Prague, 128 44, Czech Republic
| | - Jan Dohnálek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic; University of Chemistry and Technology, Technická 5, Prague, 166 28, Czech Republic
| | - Jana Škerlová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Ján Kuzmík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Edita Poláchová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic; First Faculty of Medicine, Charles University, Kateřinská 32, Prague, 121 08, Czech Republic
| | - Stancho Stanchev
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Adam Pecina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic
| | - Valentin Borshchevskiy
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry) Forschungszentrum Jülich 52428 Jülich, Germany
| | - Vitaly Polovinkin
- ELI Beamlines Centre, ELI ERIC, Za Radnicí 835, 252 41, Dolní Břežany, Czech Republic
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague, 160 00, Czech Republic.
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2
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Davies CC, Hu RM, Kamitsuka PJ, Morais GN, de Gonzalez RS, Bustin KA, Matthews ML, Parsons WH. Activity-Based Protein Profiling of RHBDL4 Reveals Proteolysis of the Enzyme and a Distinct Inhibitor Profile. ACS Chem Biol 2024; 19:1674-1682. [PMID: 39041925 DOI: 10.1021/acschembio.4c00273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Rhomboid proteases have fascinated scientists by virtue of their membrane-embedded active sites and proposed involvement in physiological and disease pathways. The human rhomboid protease RHBDL4 has generated particular interest due to its role in endoplasmic reticulum-associated protein degradation and upregulation in several cancers; however, chemical tools for studying this enzyme are currently lacking. Here, we describe the development of an activity-based protein profiling (ABPP) assay for RHBDL4. We have employed this assay to determine that human RHBDL4 undergoes proteolytic processing in cells to produce multiple active proteoforms with truncated C-termini. We have also used this assay to identify chemical scaffolds capable of inhibiting RHBDL4 activity and have observed distinct inhibitor preferences between RHBDL4 and a second human rhomboid protease PARL. Our work demonstrates the power of ABPP technology to characterize active forms of enzymes that might otherwise elude detection and the potential to achieve selective inhibition among the human rhomboid proteases.
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Affiliation(s)
- Cassondra C Davies
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | - Ren-Ming Hu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Paul J Kamitsuka
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | - Gabriel N Morais
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | | | - Katelyn A Bustin
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | - Megan L Matthews
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - William H Parsons
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
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3
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Yang J, Carvalho LAR, Ji S, Chen S, Moreira R, Verhelst SHL. 4-Oxo-β-Lactams as Novel Inhibitors for Rhomboid Proteases. Chembiochem 2023; 24:e202300418. [PMID: 37671979 DOI: 10.1002/cbic.202300418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/10/2023] [Accepted: 09/06/2023] [Indexed: 09/07/2023]
Abstract
Intramembrane serine proteases (rhomboid proteases) are involved in a variety of biological processes and are implicated in several diseases. Here, we report 4-oxo-β-lactams as a novel scaffold for inhibition of rhomboids. We show that they covalently react with the active site and that the covalent bond is sufficiently stable for detection of the covalent rhomboid-lactam complex. 4-Oxo-β-lactams may therefore find future use as both inhibitors and activity-based probes for rhomboid proteases.
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Affiliation(s)
- Jian Yang
- Laboratory of, Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, box 901b, 3000, Leuven, Belgium
| | - Luís A R Carvalho
- Department of Pharmaceutical Sciences and Medicines, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Shanping Ji
- Laboratory of, Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, box 901b, 3000, Leuven, Belgium
| | - Suyuan Chen
- Leibniz Institut für Analytische Wissenschaften - ISAS - e.V, Otto-Hahn Strasse 6b, 44227, Dortmund, Germany
| | - Rui Moreira
- Department of Pharmaceutical Sciences and Medicines, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Steven H L Verhelst
- Laboratory of, Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, box 901b, 3000, Leuven, Belgium
- Leibniz Institut für Analytische Wissenschaften - ISAS - e.V, Otto-Hahn Strasse 6b, 44227, Dortmund, Germany
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4
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Trawally M, Demir-Yazıcı K, İpek Dingis-Birgül S, Kaya K, Akdemir A, Güzel-Akdemir Ö. Dithiocarbamates and dithiocarbonates containing 6-nitrosaccharin scaffold: Synthesis, antimycobacterial activity and in silico target prediction using ensemble docking-based reverse virtual screening. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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5
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Wen W, Cao H, Xu Y, Ren Y, Rao L, Shao X, Chen H, Wu L, Liu J, Su C, Peng C, Huang Y, Wan J. N-Acylamino Saccharin as an Emerging Cysteine-Directed Covalent Warhead and Its Application in the Identification of Novel FBPase Inhibitors toward Glucose Reduction. J Med Chem 2022; 65:9126-9143. [PMID: 35786925 DOI: 10.1021/acs.jmedchem.2c00336] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With a resurgence of covalent drugs, there is an urgent need for the identification of new moieties capable of cysteine bond formation. Herein, we report on the N-acylamino saccharin moieties capable of novel covalent reactions with cysteine. Their utility as alternative electrophilic warheads was demonstrated through the covalent modification of fructose-1,6-bisphosphatase (FBPase), a promising target associated with cancer and type 2 diabetes. The cocrystal structure of title compound W8 bound with FBPase unexpectedly revealed that the N-acylamino saccharin moiety worked as an electrophile warhead that covalently modified the noncatalytic C128 site in FBPase while releasing saccharin, suggesting a previously undiscovered covalent reaction mechanism of saccharin derivatives with cysteine. Treatment of title compound W8 displayed potent inhibition of glucose production in vitro and in vivo. This newly discovered reactive warhead supplements the current repertoire of cysteine covalent modifiers while avoiding some of the limitations generally associated with established moieties.
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Affiliation(s)
- Wuqiang Wen
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Hongxuan Cao
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Yixiang Xu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yanliang Ren
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Li Rao
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Xubo Shao
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Han Chen
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Lixia Wu
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Jiaqi Liu
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Chen Su
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai 201210, China
| | - Yunyuan Huang
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jian Wan
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
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Bohg C, Öster C, Utesch T, Bischoff S, Lange S, Shi C, Sun H, Lange A. A combination of solid-state NMR and MD simulations reveals the binding mode of a rhomboid protease inhibitor. Chem Sci 2021; 12:12754-12762. [PMID: 34703562 PMCID: PMC8494044 DOI: 10.1039/d1sc02146j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 09/01/2021] [Indexed: 11/22/2022] Open
Abstract
Intramembrane proteolysis plays a fundamental role in many biological and pathological processes. Intramembrane proteases thus represent promising pharmacological targets, but few selective inhibitors have been identified. This is in contrast to their soluble counterparts, which are inhibited by many common drugs, and is in part explained by the inherent difficulty to characterize the binding of drug-like molecules to membrane proteins at atomic resolution. Here, we investigated the binding of two different inhibitors to the bacterial rhomboid protease GlpG, an intramembrane protease characterized by a Ser–His catalytic dyad, using solid-state NMR spectroscopy. H/D exchange of deuterated GlpG can reveal the binding position while chemical shift perturbations additionally indicate the allosteric effects of ligand binding. Finally, we determined the exact binding mode of a rhomboid protease-inhibitor using a combination of solid-state NMR and molecular dynamics simulations. We believe this approach can be widely adopted to study the structure and binding of other poorly characterized membrane protein–ligand complexes in a native-like environment and under physiological conditions. Proton-detected solid-state NMR in combination with molecular docking and molecular dynamics (MD) simulations allow the study of rhomboid protease inhibition under native-like conditions.![]()
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Affiliation(s)
- Claudia Bohg
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Carl Öster
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Tillmann Utesch
- Structural Chemistry and Computational Biophysics Group, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Susanne Bischoff
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Sascha Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany .,Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China Huangshan Road 443 Hefei 230027 People's Republic of China
| | - Han Sun
- Structural Chemistry and Computational Biophysics Group, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany .,Institut für Biologie, Humboldt-Universität zu Berlin Invalidenstraße 42 10115 Berlin Germany
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7
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Parsons WH, Rutland NT, Crainic JA, Cardozo JM, Chow AS, Andrews CL, Sheehan BK. Development of succinimide-based inhibitors for the mitochondrial rhomboid protease PARL. Bioorg Med Chem Lett 2021; 49:128290. [PMID: 34311087 DOI: 10.1016/j.bmcl.2021.128290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 01/26/2023]
Abstract
While the biochemistry of rhomboid proteases has been extensively studied since their discovery two decades ago, efforts to define the physiological roles of these enzymes are ongoing and would benefit from chemical probes that can be used to manipulate the functions of these proteins in their native settings. Here, we describe the use of activity-based protein profiling (ABPP) technology to conduct a targeted screen for small-molecule inhibitors of the mitochondrial rhomboid protease PARL, which plays a critical role in regulating mitophagy and cell death. We synthesized a series of succinimide-containing sulfonyl esters and sulfonamides and discovered that these compounds serve as inhibitors of PARL with the most potent sulfonamides having submicromolar affinity for the enzyme. A counterscreen against the bacterial rhomboid protease GlpG demonstrates that several of these compounds display selectivity for PARL over GlpG by as much as two orders of magnitude. Both the sulfonyl ester and sulfonamide scaffolds exhibit reversible binding and are able to engage PARL in mammalian cells. Collectively, our findings provide encouraging precedent for the development of PARL-selective inhibitors and establish N-[(arylsulfonyl)oxy]succinimides and N-arylsulfonylsuccinimides as new molecular scaffolds for inhibiting members of the rhomboid protease family.
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Affiliation(s)
- William H Parsons
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States.
| | - Nicholas T Rutland
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Jennifer A Crainic
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Joaquin M Cardozo
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Alyssa S Chow
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Charlotte L Andrews
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Brendan K Sheehan
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
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8
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Etsè KS, Etsè KD, Nyssen P, Mouithys-Mickalad A. Assessment of anti-inflammatory-like, antioxidant activities and molecular docking of three alkynyl-substituted 3-ylidene-dihydrobenzo[d]isothiazole 1,1-dioxide derivatives. Chem Biol Interact 2021; 344:109513. [PMID: 33974901 DOI: 10.1016/j.cbi.2021.109513] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/12/2021] [Accepted: 05/05/2021] [Indexed: 11/19/2022]
Abstract
The presence of enyne and benzoisothiazole functions in the molecular architecture of compounds 1, 2 and 3 were expected to provide biochemical activities. In the present work, we first examined the molecular surface contact of three alkynyl-substituted 3-ylidenedihydrobenzo[d] isothiazole 1,1-dioxides. The analysis of the Hirshfeld surfaces reveals that only compound 3 exhibited a well-defined red spots, indicating intermolecular interactions identified as S-O⋯H, C-H⋯O and C-O⋯H contacts. Comparative fingerprint histograms of the three compounds show that close pair interactions are dominated by C-H⋯H-C contact. By UV-visible analysis, compound 1 showed the most intense absorbances at 407 and 441 nm, respectively. The radical scavenging activity explored in the DPPH test, shows that only 1 exhibited low anti-radical activity. Furthermore, cellular antioxidant capacity of benzoisothiazoles 1-3 was investigated with PMA-activated HL-60 cells using chemiluminescence and fluorescence techniques in the presence of L-012 and Amplex Red probe, respectively. Results highlight that compound 1 exhibited moderate anti-ROS capacity while compounds 2 and 3 enhanced ROS production. The cytotoxicity test performed on HL-60 cells, using the MTS assay, confirmed the lack of toxicity of the tested benzoisothiazole 1 compared to 2 and 3 which show low cytotoxicity (≤30%). Anti-catalytic activity was evaluated by following the inhibitory potential of the benzoisothiazoles on MPO activity and depicted benzoisothiazoles-MPO interactions by docking. Both SIEFED and docking studies demonstrated an anti-catalytic activity of the tested benzoisothiazoles towards MPO with the best activity for compound 2.
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Affiliation(s)
- Koffi Sénam Etsè
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Quartier Ho^pital B36 Av. Hippocrate 15 B-4000 Liège, Belgium
| | - Kodjo Djidjolé Etsè
- Laboratoire de Physiologie et Biotechnologie Végétales (LPBV), Faculté des Sciences (FDS), Université de Lomé (UL), Lomé, Togo
| | - Pauline Nyssen
- Biomedical Spectroscopy Laboratory, Department of Physics, CESAM, ULiège, Sart-Tilman, B-4000 Liège, Belgium
| | - Ange Mouithys-Mickalad
- Center for Oxygen, Research and Development (CORD) and Center for Interdisciplinary Research on Medicine (CIRM) Institute of Chemistry University of Liège, Sart-Tilman (B.6a), 4000 Liège, Belgium.
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9
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Barniol-Xicota M, Verhelst SHL. Stable and Functional Rhomboid Proteases in Lipid Nanodiscs by Using Diisobutylene/Maleic Acid Copolymers. J Am Chem Soc 2018; 140:14557-14561. [PMID: 30347979 DOI: 10.1021/jacs.8b08441] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Rhomboid proteases form a paradigm for intramembrane proteolysis and have been implicated in several human diseases. However, their study is hampered by difficulties in solubilization and purification. We here report on the use of polymers composed of maleic acid and either diisobutylene or styrene for solubilization of rhomboid proteases in lipid nanodiscs, which proceeds with up to 48% efficiency. We show that the activity of rhomboids in lipid nanodiscs is closer to that in the native membrane than rhomboids in detergent. Moreover, a rhomboid that was proteolytically unstable in detergent turned out to be stable in lipid nanodiscs, underlining the benefit of using these polymer-stabilized nanodiscs. The systems are also compatible with the use of activity-based probes and can be used for small molecule inhibitor screening, allowing several downstream applications.
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Affiliation(s)
- Marta Barniol-Xicota
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine , KU Leuven - University of Leuven , Herestraat 49 box 802 , 3000 Leuven , Belgium
| | - Steven H L Verhelst
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine , KU Leuven - University of Leuven , Herestraat 49 box 802 , 3000 Leuven , Belgium.,AG Chemical Proteomics , Leibniz Institute for Analytical Sciences - ISAS , Otto-Hahn-Str. 6b , 44227 Dortmund , Germany
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10
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The Rhomboid Superfamily: Structural Mechanisms and Chemical Biology Opportunities. Trends Biochem Sci 2018; 43:726-739. [DOI: 10.1016/j.tibs.2018.06.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/08/2018] [Accepted: 06/30/2018] [Indexed: 12/27/2022]
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11
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Goel P, Jumpertz T, Tichá A, Ogorek I, Mikles DC, Hubalek M, Pietrzik CU, Strisovsky K, Schmidt B, Weggen S. Discovery and validation of 2-styryl substituted benzoxazin-4-ones as a novel scaffold for rhomboid protease inhibitors. Bioorg Med Chem Lett 2018; 28:1417-1422. [DOI: 10.1016/j.bmcl.2018.02.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 02/05/2018] [Accepted: 02/08/2018] [Indexed: 11/26/2022]
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