1
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Doud DFR, Woyke T. Novel approaches in function-driven single-cell genomics. FEMS Microbiol Rev 2017; 41:538-548. [PMID: 28591840 PMCID: PMC5812545 DOI: 10.1093/femsre/fux009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/21/2017] [Indexed: 12/27/2022] Open
Abstract
Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology. Function-driven single-cell genomics provides a solution by using a function-based screen to subsample complex microbial communities in a targeted manner for the isolation and genome sequencing of single cells. This enables single-cell sequencing to be focused on cells with specific phenotypic or metabolic characteristics of interest. Recovered genomes are conclusively implicated for both encoding and exhibiting the feature of interest, improving downstream annotation and revealing activity levels within that environment. This emerging approach has already improved our understanding of microbial community functioning and facilitated the experimental analysis of uncharacterized gene product space. Here we provide a comprehensive review of strategies that have been applied for function-driven single-cell genomics and the future directions we envision.
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Affiliation(s)
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
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2
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Konnert L, Lamaty F, Martinez J, Colacino E. Recent Advances in the Synthesis of Hydantoins: The State of the Art of a Valuable Scaffold. Chem Rev 2017. [PMID: 28644621 DOI: 10.1021/acs.chemrev.7b00067] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The review highlights the hydantoin syntheses presented from the point of view of the preparation methods. Novel synthetic routes to various hydantoin structures, the advances brought to the classical methods in the aim of producing more sustainable and environmentally friendly procedures for the preparation of these biomolecules, and a critical comparison of the different synthetic approaches developed in the last twelve years are also described. The review is composed of 95 schemes, 8 figures and 528 references for the last 12 years and includes the description of the hydantoin-based marketed drugs and clinical candidates.
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Affiliation(s)
- Laure Konnert
- Université de Montpellier, Institut des Biomolécules Max Mousseron UMR 5247 CNRS - Universités Montpellier - ENSCM , Place E. Bataillon, Campus Triolet, cc 1703, 34095 Montpellier, France
| | - Frédéric Lamaty
- Université de Montpellier, Institut des Biomolécules Max Mousseron UMR 5247 CNRS - Universités Montpellier - ENSCM , Place E. Bataillon, Campus Triolet, cc 1703, 34095 Montpellier, France
| | - Jean Martinez
- Université de Montpellier, Institut des Biomolécules Max Mousseron UMR 5247 CNRS - Universités Montpellier - ENSCM , Place E. Bataillon, Campus Triolet, cc 1703, 34095 Montpellier, France
| | - Evelina Colacino
- Université de Montpellier, Institut des Biomolécules Max Mousseron UMR 5247 CNRS - Universités Montpellier - ENSCM , Place E. Bataillon, Campus Triolet, cc 1703, 34095 Montpellier, France
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3
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Eleftheriadis N, Thee SA, Zwinderman MRH, Leus NGJ, Dekker FJ. Activity-Based Probes for 15-Lipoxygenase-1. Angew Chem Int Ed Engl 2016; 55:12300-5. [PMID: 27612308 PMCID: PMC5218545 DOI: 10.1002/anie.201606876] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Indexed: 12/12/2022]
Abstract
Human 15-lipoxygenase-1 (15-LOX-1) plays an important role in several inflammatory lung diseases, such as asthma, COPD, and chronic bronchitis, as well as various CNS diseases, such as Alzheimer's disease, Parkinson's disease, and stroke. Activity-based probes of 15-LOX-1 are required to explore the role of this enzyme further and to enable drug discovery. In this study, we developed a 15-LOX-1 activity-based probe for the efficient activity-based labeling of recombinant 15-LOX-1. 15-LOX-1-dependent labeling in cell lysates and tissue samples was also possible. To mimic the natural substrate of the enzyme, we designed activity-based probes that covalently bind to the active enzyme and include a terminal alkene as a chemical reporter for the bioorthogonal linkage of a detectable functionality through an oxidative Heck reaction. The activity-based labeling of 15-LOX-1 should enable the investigation and identification of this enzyme in complex biological samples, thus opening up completely new opportunities for drug discovery.
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Affiliation(s)
- Nikolaos Eleftheriadis
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Stephanie A Thee
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Martijn R H Zwinderman
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Niek G J Leus
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Frank J Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
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4
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Eleftheriadis N, Thee SA, Zwinderman MRH, Leus NGJ, Dekker FJ. Activity-Based Probes for 15-Lipoxygenase-1. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606876] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Nikolaos Eleftheriadis
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Stephanie A. Thee
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Martijn R. H. Zwinderman
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Niek G. J. Leus
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Frank J. Dekker
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
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5
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Stiti N, Chandrasekar B, Strubl L, Mohammed S, Bartels D, van der Hoorn RAL. Nicotinamide Cofactors Suppress Active-Site Labeling of Aldehyde Dehydrogenases. ACS Chem Biol 2016; 11:1578-86. [PMID: 26990764 DOI: 10.1021/acschembio.5b00784] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Active site labeling by (re)activity-based probes is a powerful chemical proteomic tool to globally map active sites in native proteomes without using substrates. Active site labeling is usually taken as a readout for the active state of the enzyme because labeling reflects the availability and reactivity of active sites, which are hallmarks for enzyme activities. Here, we show that this relationship holds tightly, but we also reveal an important exception to this rule. Labeling of Arabidopsis ALDH3H1 with a chloroacetamide probe occurs at the catalytic Cys, and labeling is suppressed upon nitrosylation and oxidation, and upon treatment with other Cys modifiers. These experiments display a consistent and strong correlation between active site labeling and enzymatic activity. Surprisingly, however, labeling is suppressed by the cofactor NAD(+), and this property is shared with other members of the ALDH superfamily and also detected for unrelated GAPDH enzymes with an unrelated hydantoin-based probe in crude extracts of plant cell cultures. Suppression requires cofactor binding to its binding pocket. Labeling is also suppressed by ALDH modulators that bind at the substrate entrance tunnel, confirming that labeling occurs through the substrate-binding cavity. Our data indicate that cofactor binding adjusts the catalytic Cys into a conformation that reduces the reactivity toward chloroacetamide probes.
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Affiliation(s)
- Naim Stiti
- Institute
of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Balakumaran Chandrasekar
- Plant
Chemetics Laboratory, Department of Plant Sciences, University of Oxford, OX1
3RB, Oxford, United Kingdom
- Plant
Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Laura Strubl
- Plant
Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Shabaz Mohammed
- Department
of Biochemistry, University of Oxford, OX1 3QU, Oxford, United Kingdom
| | - Dorothea Bartels
- Institute
of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Renier A. L. van der Hoorn
- Plant
Chemetics Laboratory, Department of Plant Sciences, University of Oxford, OX1
3RB, Oxford, United Kingdom
- Plant
Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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6
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Morimoto K, van der Hoorn RAL. The Increasing Impact of Activity-Based Protein Profiling in Plant Science. PLANT & CELL PHYSIOLOGY 2016; 57:446-61. [PMID: 26872839 DOI: 10.1093/pcp/pcw003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/28/2015] [Indexed: 05/08/2023]
Abstract
The active proteome dictates plant physiology. Yet, active proteins are difficult to predict based on transcript or protein levels, because protein activities are regulated post-translationally in their microenvironments. Over the past 10 years, activity-based protein profiling (ABPP) is increasingly used in plant science. ABPP monitors the activities of hundreds of plant proteins using tagged chemical probes that react with the active site of proteins in a mechanism-dependent manner. Since labeling is covalent and irreversible, labeled proteins can be detected and identified on protein gels and by mass spectrometry using tagged fluorophores and/or biotin. Here, we discuss general concepts, approaches and practical considerations of ABPP, before we summarize the discoveries made using 40 validated probes representing 14 chemotypes that can monitor the active state of >4,500 plant proteins. These discoveries and new opportunities indicate that this emerging functional proteomic technology is a powerful discovery tool that will have an increasing impact on plant science.
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Affiliation(s)
- Kyoko Morimoto
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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7
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Na HN, Yoo YH, Yoon CN, Lee JS. Unbiased proteomic profiling strategy for discovery of bacterial effector proteins reveals that Salmonella protein PheA is a host cell cycle regulator. ACTA ACUST UNITED AC 2015; 22:453-459. [PMID: 25865312 DOI: 10.1016/j.chembiol.2015.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 02/26/2015] [Accepted: 03/03/2015] [Indexed: 11/30/2022]
Abstract
Salmonella utilizes a type III secretion system to inject bacterial effector proteins into the host cell cytosol. Once in the cytosol, these effectors hijack various biochemical pathways to regulate virulence. Despite the importance of effector proteins, especially for understanding host-pathogen interactions, a potentially large number of effectors are yet to be identified. Here, we demonstrate that unbiased chemical proteomic profiling using off-the-shelf fluorescent probes leads to the discovery of a host cell cycle regulator encoded in the Salmonella genome. Our profiling combined with bioinformatic analysis implicates 29 Salmonella as potential effectors. We follow up on the top candidate, chorismate mutase-P/prehenate dehydratase, PheA, and present evidence that PheA is an effector that mimics E2F7 transcription factor of the host cell and promotes G1/S cell cycle arrest. This validates our strategy and opens opportunities for effector identification in the future.
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Affiliation(s)
- Ha-Na Na
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul 136-791, South Korea; Department of Biological Chemistry, University of Science & Technology, 113 Gwahank-ro, Yuseong-gu, Daejeon 305-333, South Korea
| | - Young-Hwa Yoo
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul 136-791, South Korea
| | - Chang No Yoon
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul 136-791, South Korea
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul 136-791, South Korea; Department of Biological Chemistry, University of Science & Technology, 113 Gwahank-ro, Yuseong-gu, Daejeon 305-333, South Korea.
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8
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Šmit BM, Pavlović RZ. Three-step synthetic pathway to fused bicyclic hydantoins involving a selenocyclization step. Tetrahedron 2015. [DOI: 10.1016/j.tet.2014.12.088] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Lee JS, Yoo YH, Yoon CN. Small-molecule probes elucidate global enzyme activity in a proteomic context. BMB Rep 2014; 47:149-57. [PMID: 24499666 PMCID: PMC4163878 DOI: 10.5483/bmbrep.2014.47.3.264] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 12/19/2013] [Accepted: 12/20/2013] [Indexed: 12/05/2022] Open
Abstract
The recent dramatic improvements in high-resolution mass spectrometry (MS) have revolutionized the speed and scope of proteomic studies. Conventional MS-based proteomics methodologies allow global protein profiling based on expression levels. Although these techniques are promising, there are numerous biological activities yet to be unveiled, such as the dynamic regulation of enzyme activity. Chemical proteomics is an emerging field that extends these types proteomic profiling. In particular, activity-based protein profiling (ABPP) utilizes small-molecule probes to monitor enzyme activity directly in living intact subjects. In this mini-review, we summarize the unique roles of smallmolecule probes in proteomics studies and highlight some recent examples in which this principle has been applied. [BMB Reports 2014; 47(3): 149-157]
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Affiliation(s)
- Jun-Seok Lee
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 136-791; University of Science and Technology, Daejeon 305-333, Korea
| | - Young-Hwa Yoo
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 136-791, Korea
| | - Chang No Yoon
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 136-791, Korea
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10
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Dejonghe W, Russinova E. Target identification strategies in plant chemical biology. FRONTIERS IN PLANT SCIENCE 2014; 5:352. [PMID: 25104953 PMCID: PMC4109434 DOI: 10.3389/fpls.2014.00352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/30/2014] [Indexed: 05/03/2023]
Abstract
The current needs to understand gene function in plant biology increasingly require more dynamic and conditional approaches opposed to classic genetic strategies. Gene redundancy and lethality can substantially complicate research, which might be solved by applying a chemical genetics approach. Now understood as the study of small molecules and their effect on biological systems with subsequent target identification, chemical genetics is a fast developing field with a strong history in pharmaceutical research and drug discovery. In plant biology however, chemical genetics is still largely in the starting blocks, with most studies relying on forward genetics and phenotypic analysis for target identification, whereas studies including direct target identification are limited. Here, we provide an overview of recent advances in chemical genetics in plant biology with a focus on target identification. Furthermore, we discuss different strategies for direct target identification and the possibilities and challenges for plant biology.
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Affiliation(s)
- Wim Dejonghe
- Department of Plant Systems Biology, VIBGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
| | - Eugenia Russinova
- Department of Plant Systems Biology, VIBGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- *Correspondence: Eugenia Russinova, Department of Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, VIB-Ghent University, Technologiepark 927, 9052 Ghent, Belgium e-mail:
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11
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Ge J, Zhang CJ, Li L, Chong LM, Wu X, Hao P, Sze SK, Yao SQ. Small molecule probe suitable for in situ profiling and inhibition of protein disulfide isomerase. ACS Chem Biol 2013; 8:2577-85. [PMID: 24070012 DOI: 10.1021/cb4002602] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Proper folding of cellular proteins is assisted by protein disulfide isomerases (PDIs) in the endoplasmic reticulum of mammalian cells. Of the at least 21 PDI family members known in humans, the 57-kDa PDI has been found to be a potential therapeutic target for a variety of human diseases including cancer and neurodegenerative diseases. Consequently, small molecule PDI-targeting inhibitors have been actively pursued in recent years, and thus far, compounds possessing moderate inhibitory activities (IC50 between 0.1 and 100 μM against recombinant PDI) have been discovered. In this article, by using in situ proteome profiling experiments in combination with in vitro PDI enzymatic inhibition assays, we have discovered a phenyl vinyl sulfonate-containing small molecule (P1; shown) as a relatively potent and specific inhibitor of endogenous human PDI in several mammalian cancer cells (e.g., GI50 ∼ 4 μM). It also possesses an IC50 value of 1.7 ± 0.4 μM in an in vitro insulin aggregation assay. Our results indicate P1 is indeed a novel, cell-permeable small molecule PDI inhibitor, and the electrophilic vinyl sulfonate scaffold might serve as a starting point for future development of next-generation PDI inhibitors and probes.
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Affiliation(s)
- Jingyan Ge
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Chong-Jing Zhang
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Lin Li
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Li Min Chong
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Xiaoyuan Wu
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Piliang Hao
- School of Biological
Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Siu Kwan Sze
- School of Biological
Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Shao Q. Yao
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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12
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Su Y, Ge J, Zhu B, Zheng YG, Zhu Q, Yao SQ. Target identification of biologically active small molecules via in situ methods. Curr Opin Chem Biol 2013; 17:768-75. [DOI: 10.1016/j.cbpa.2013.06.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 05/27/2013] [Accepted: 06/02/2013] [Indexed: 12/25/2022]
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13
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Stolze SC, Deu E, Kaschani F, Li N, Florea BI, Richau KH, Colby T, van der Hoorn RAL, Overkleeft HS, Bogyo M, Kaiser M. The antimalarial natural product symplostatin 4 is a nanomolar inhibitor of the food vacuole falcipains. ACTA ACUST UNITED AC 2013; 19:1546-55. [PMID: 23261598 DOI: 10.1016/j.chembiol.2012.09.020] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 09/05/2012] [Accepted: 09/27/2012] [Indexed: 01/10/2023]
Abstract
The marine natural product symplostatin 4 (Sym4) has been recognized as a potent antimalarial agent. However, its mode of action and, in particular, direct targets have to date remained elusive. We report a chemical synthesis of Sym4 and show that Sym4-treatment of P. falciparum-infected red blood cells (RBCs) results in the generation of a swollen food vacuole phenotype and a reduction of parasitemia at nanomolar concentrations. We furthermore demonstrate that Sym4 is a nanomolar inhibitor of the P. falciparum falcipains in infected RBCs, suggesting inhibition of the hemoglobin degradation pathway as Sym4's mode of action. Finally, we reveal a critical influence of the unusual methyl-methoxypyrrolinone (mmp) group of Sym4 for potent inhibition, indicating that Sym4 derivatives with such a mmp moiety might represent viable lead structures for the development of antimalarial falcipain inhibitors.
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Affiliation(s)
- Sara Christina Stolze
- Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
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14
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Misas-Villamil JC, Toenges G, Kolodziejek I, Sadaghiani AM, Kaschani F, Colby T, Bogyo M, van der Hoorn RAL. Activity profiling of vacuolar processing enzymes reveals a role for VPE during oomycete infection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:689-700. [PMID: 23134548 DOI: 10.1111/tpj.12062] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 10/24/2012] [Indexed: 05/23/2023]
Abstract
Vacuolar processing enzymes (VPEs) are important cysteine proteases that are implicated in the maturation of seed storage proteins, and programmed cell death during plant-microbe interactions and development. Here, we introduce a specific, cell-permeable, activity-based probe for VPEs. This probe is highly specific for all four Arabidopsis VPEs, and labeling is activity-dependent, as illustrated by sensitivity for inhibitors, pH and reducing agents. We show that the probe can be used for in vivo imaging and displays multiple active isoforms of VPEs in various tissues and in both monocot and dicot plant species. Thus, VPE activity profiling is a robust, simple and powerful tool for plant research for a wide range of applications. Using VPE activity profiling, we discovered that VPE activity is increased during infection with the oomycete pathogen Hyaloperonospora arabidopsidis (Hpa). The enhanced VPE activity is host-derived and EDS1-independent. Sporulation of Hpa is reduced on vpe mutant plants, demonstrating a role for VPE during compatible interactions that is presumably independent of programmed cell death. Our data indicate that, as an obligate biotroph, Hpa takes advantage of increased VPE activity in the host, e.g. to mediate protein turnover and nutrient release.
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Affiliation(s)
- Johana C Misas-Villamil
- Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
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15
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Park J, Koh M, Park SB. From noncovalent to covalent bonds: a paradigm shift in target protein identification. MOLECULAR BIOSYSTEMS 2013; 9:544-50. [DOI: 10.1039/c2mb25502b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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16
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Honorary Membership of the Gesellschaft Deutscher Chemiker: G. S. Fischer and E. Winterfeldt / Liebig Lectureship: G. Mloston / Innovation Prize in Medicinal/Pharmaceutical Chemistry: C. Ottmann / Raimund Stadler Prize: A. Walther / DuPont Young Professor. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/anie.201207433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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17
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Neue Ehrenmitglieder der Gesellschaft Deutscher Chemiker: G. S. Fischer und E. Winterfeldt / Liebig-Vorlesung: G. Mloston / Innovationspreis in Medizinischer/Pharmazeutischer Chemie: C. Ottmann / Raimund-Stadler-Preis: A. Walther / DuPont-Stipendien für J. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Dhara K, Midya GC, Dash J. A Diversity-Oriented Approach to Spirocyclic and Fused Hydantoins via Olefin Metathesis. J Org Chem 2012; 77:8071-82. [DOI: 10.1021/jo301234r] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Kalyan Dhara
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West
Bengal 741252, India
| | - Ganesh Chandra Midya
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West
Bengal 741252, India
- Department
of Organic Chemistry, Indian Association for the Cultivation of Science,
Jadavpur, Kolkata-700032, India
| | - Jyotirmayee Dash
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West
Bengal 741252, India
- Department
of Organic Chemistry, Indian Association for the Cultivation of Science,
Jadavpur, Kolkata-700032, India
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