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] [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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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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3
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Liu X, An T, Yin Z, Zhang W. Palladium-Catalyzed Reductive Double Carbonylation of Nitroarenes with Aryl Halides Using Mo(CO) 6 as a Reductant and Carbonyl Source. Chemistry 2023; 29:e202202880. [PMID: 36177713 DOI: 10.1002/chem.202202880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Indexed: 01/12/2023]
Abstract
A new palladium-catalyzed reductive double carbonylation of nitroarenes with aryl halides for the synthesis of benzoxazin-4-ones has been reported. The key to success was the use of Mo(CO)6 as a reductant and bench-stable solid carbonyl sources. Various aryl iodides, bromides, and trifluoromethanesulfonates are suitable reaction partners and produce corresponding benzoxazin-4-one derivatives in moderate to good yields. Preliminary mechanistic studies indicate that nitrosoarene was first generated as the key intermediate through nitro reduction. Remarkably, this method avoids the use of toxic CO gas and is further applied to the late-stage modification of estrone.
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Affiliation(s)
- Xueling Liu
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University Henan Cancer Hospital, Zhengzhou, 450008, P. R. China
| | - Tongshun An
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, P. R. China
| | - Zhiping Yin
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, P. R. China
| | - Wenzhou Zhang
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University Henan Cancer Hospital, Zhengzhou, 450008, P. R. China
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4
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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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5
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Yang M, Wang J, Lv W, Ba D, Cheng G, Wang L. Synthesis of 2‐Alkenyl‐4
H
‐3,1‐Benzoxazin‐4‐Ones through HFIP‐Mediated Decarboxylative [4+2]‐Annulation of Isatoic Anhydrides with Cyclopropenones under Silver Catalysis. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Mengqi Yang
- School of Medicine Huaqiao University Quanzhou 362021 People's Republic of China
| | - Jixin Wang
- School of Medicine Huaqiao University Quanzhou 362021 People's Republic of China
| | - Weiwei Lv
- College of Materials Science and Engineering Huaqiao University Xiamen 361021 People's Republic of China
| | - Dan Ba
- College of Materials Science and Engineering Huaqiao University Xiamen 361021 People's Republic of China
| | - Guolin Cheng
- College of Materials Science and Engineering Huaqiao University Xiamen 361021 People's Republic of China
| | - Lianhui Wang
- School of Medicine Huaqiao University Quanzhou 362021 People's Republic of China
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6
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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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7
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Yong JY, Vu HM, Li XQ, Gong AJ. Palladium (0)-catalyzed C(sp)-H oxygenation with carboxylic acids. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.130969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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4 H-Benzo[ d][1,3]oxazin-4-ones and Dihydro Analogs from Substituted Anthranilic Acids and Orthoesters. Molecules 2019; 24:molecules24193555. [PMID: 31581424 PMCID: PMC6804250 DOI: 10.3390/molecules24193555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 09/29/2019] [Accepted: 09/29/2019] [Indexed: 01/17/2023] Open
Abstract
A one-pot route to 2-alkyl and 2-aryl-4H-benzo[d][1,3]oxazin-4-ones (also known as 4H-3,1-benzoxazin-4-ones) has been developed and studied. The method involves the reaction of aryl-substituted anthranilic acids with orthoesters in ethanol catalyzed by acetic acid. Additionally, we have also investigated the reaction under microwave conditions. Not all of the substrates were successful in yielding the target heterocycles as some of the reactions failed to undergo the final elimination. This process led to the isolation of (±)-2-alkyl/aryl-2-ethoxy-1,2-dihydro-4H-benzo[d][1,3]oxazin-4-ones. The formation of the dihydro analogs correlated with the electron density on the aromatic ring: Electron-donating groups favored the 4H- benzo[d][1,3]oxazin-4-ones, while electron-withdrawing groups tended to favor the dihydro product. Substituting a pyridine ring for the benzene ring in the substrate acid suppressed the reaction.
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9
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Vu HM, Chen F, Li X. Acetoxylation and Halogenation of 2‐Arylbenzoxazinones via Palladium‐Catalyzed C(sp
2
)‐H Bond Oxidation. ChemistrySelect 2019. [DOI: 10.1002/slct.201902611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Huu Manh Vu
- School of Chemical and Biological EngineeringUniversity of Science and Technology Beijing 30 Xueyuan Road, Haidian District Beijing 100083 PR China
| | - Fei‐Wu Chen
- School of Chemical and Biological EngineeringUniversity of Science and Technology Beijing 30 Xueyuan Road, Haidian District Beijing 100083 PR China
| | - Xu‐Qin Li
- School of Chemical and Biological EngineeringUniversity of Science and Technology Beijing 30 Xueyuan Road, Haidian District Beijing 100083 PR China
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10
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Jiang J, Cai X, Hu Y, Liu X, Chen X, Wang SY, Zhang Y, Zhang S. Thermo-Promoted Reactions of Anthranils with Carboxylic Acids, Amines, Phenols, and Malononitrile under Catalyst-Free Conditions. J Org Chem 2019; 84:2022-2031. [DOI: 10.1021/acs.joc.8b02890] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jing Jiang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren’ai Road, Suzhou, Jiangsu 215123, China
- Jiangsu Key Laboratory for Functional Substances of Chinese of Medicine, College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xin Cai
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren’ai Road, Suzhou, Jiangsu 215123, China
| | - Yanwei Hu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren’ai Road, Suzhou, Jiangsu 215123, China
| | - Xuejun Liu
- Shanghai Fosun Shino Tech Pharmaceutical Co., Ltd., Building 7, No. 1999 ZhangHeng Road, Shanghai, 201203, China
| | - Xiaodong Chen
- Shanghai Fosun Shino Tech Pharmaceutical Co., Ltd., Building 7, No. 1999 ZhangHeng Road, Shanghai, 201203, China
| | - Shun-Yi Wang
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science & Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215123, China
| | - Yinan Zhang
- Jiangsu Key Laboratory for Functional Substances of Chinese of Medicine, College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Shilei Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren’ai Road, Suzhou, Jiangsu 215123, China
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11
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Lang M, Wang J. A carbene-catalyzed tandem isomerization/cyclisation strategy: an efficient assembly of benzoxazinones. Org Chem Front 2019. [DOI: 10.1039/c9qo00094a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An unprecedented example of NHC-catalyzed tandem isomerization/cyclisation is reported to synthesize benzoxazinones.
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Affiliation(s)
- Ming Lang
- School of Pharmaceutical Sciences
- Key Laboratory of Bioorganic Phosphorous Chemistry & Chemical Biology (Ministry of Education)
- Tsinghua University
- Beijing
- China
| | - Jian Wang
- School of Pharmaceutical Sciences
- Key Laboratory of Bioorganic Phosphorous Chemistry & Chemical Biology (Ministry of Education)
- Tsinghua University
- Beijing
- China
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12
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Arutyunova E, Jiang Z, Yang J, Kulepa AN, Young HS, Verhelst S, O’Donoghue AJ, Lemieux MJ. An internally quenched peptide as a new model substrate for rhomboid intramembrane proteases. Biol Chem 2018; 399:1389-1397. [DOI: 10.1515/hsz-2018-0255] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/09/2018] [Indexed: 12/31/2022]
Abstract
AbstractRhomboids are ubiquitous intramembrane serine proteases that cleave transmembrane substrates. Their functions include growth factor signaling, mitochondrial homeostasis, and parasite invasion. A recent study revealed that theEscherichia colirhomboid protease EcGlpG is essential for its extraintestinal pathogenic colonization within the gut. Crystal structures of EcGlpG and theHaemophilus influenzaerhomboid protease HiGlpG have deciphered an active site that is buried within the lipid bilayer but exposed to the aqueous environment via a cavity at the periplasmic face. A lack of physiological transmembrane substrates has hampered progression for understanding their catalytic mechanism and screening inhibitor libraries. To identify a soluble substrate for use in the study of rhomboid proteases, an array of internally quenched peptides were assayed with HiGlpG, EcGlpG and PsAarA fromProvidencia stuartti. One substrate was identified that was cleaved by all three rhomboid proteases, with HiGlpG having the highest cleavage efficiency. Mass spectrometry analysis determined that all enzymes hydrolyze this substrate between norvaline and tryptophan. Kinetic analysis in both detergent and bicellular systems demonstrated that this substrate can be cleaved in solution and in the lipid environment. The substrate was subsequently used to screen a panel of benzoxazin-4-one inhibitors to validate its use in inhibitor discovery.
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13
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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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14
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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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15
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Yang J, Barniol-Xicota M, Nguyen MT, Ticha A, Strisovsky K, Verhelst SH. Benzoxazin-4-ones as novel, easily accessible inhibitors for rhomboid proteases. Bioorg Med Chem Lett 2018; 28:1423-1427. [DOI: 10.1016/j.bmcl.2017.12.056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/21/2017] [Accepted: 12/23/2017] [Indexed: 12/13/2022]
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