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Genome-scale RNA interference profiling of Trypanosoma brucei cell cycle progression defects. Nat Commun 2022; 13:5326. [PMID: 36088375 PMCID: PMC9464253 DOI: 10.1038/s41467-022-33109-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/31/2022] [Indexed: 11/21/2022] Open
Abstract
Trypanosomatids, which include major pathogens of humans and livestock, are flagellated protozoa for which cell cycle controls and the underlying mechanisms are not completely understood. Here, we describe a genome-wide RNA-interference library screen for cell cycle defects in Trypanosoma brucei. We induced massive parallel knockdown, sorted the perturbed population using high-throughput flow cytometry, deep-sequenced RNAi-targets from each stage and digitally reconstructed cell cycle profiles at a genomic scale; also enabling data visualisation using an online tool ( https://tryp-cycle.pages.dev/ ). Analysis of several hundred genes that impact cell cycle progression reveals >100 flagellar component knockdowns linked to genome endoreduplication, evidence for metabolic control of the G1-S transition, surface antigen regulatory mRNA-binding protein knockdowns linked to G2M accumulation, and a putative nucleoredoxin required for both mitochondrial genome segregation and for mitosis. The outputs provide comprehensive functional genomic evidence for the known and novel machineries, pathways and regulators that coordinate trypanosome cell cycle progression.
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Sáez Conde J, Dean S. Structure, function and druggability of the African trypanosome flagellum. J Cell Physiol 2022; 237:2654-2667. [PMID: 35616248 PMCID: PMC9323424 DOI: 10.1002/jcp.30778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022]
Abstract
African trypanosomes are early branching protists that cause human and animal diseases, termed trypanosomiases. They have been under intensive study for more than 100 years and have contributed significantly to our understanding of eukaryotic biology. The combination of conserved and parasite‐specific features mean that their flagellum has gained particular attention. Here, we discuss the different structural features of the flagellum and their role in transmission and virulence. We highlight the possibilities of targeting flagellar function to cure trypanosome infections and help in the fight to eliminate trypanosomiases.
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Affiliation(s)
- Julia Sáez Conde
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Samuel Dean
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
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3
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Partially Purified Leaf Fractions of Azadirachta indica Inhibit Trypanosome Alternative Oxidase and Exert Antitrypanosomal Effects on Trypanosoma congolense. Acta Parasitol 2022; 67:120-129. [PMID: 34156634 PMCID: PMC8217781 DOI: 10.1007/s11686-021-00437-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/07/2021] [Indexed: 11/29/2022]
Abstract
Introduction Trypanosomiasis is a neglected disease of humans and livestock caused by single-celled flagellated haemo-protozoan parasites belonging to the genus Trypanosoma. Purpose Widespread resistance to trypanocidal drugs creates urgent need for new, more effective drugs with potential to inhibit important trypanosome molecular targets. Methods Nine column chromatographic, partially purified leaf fractions of Azadirachta indica (AIF) were subjected to trypanosome alternative oxidase (TAO) inhibition assay using ubiquinol oxidase assay. The potent TAO inhibitors were evaluated for trypanocidal activities against T. congolense in rat model using in vitro, ex vivo, and in vivo assays. Complete cessation or reduction in parasite motility was scored from 0 (no parasite) to 6 (greater than or equal to 6 × 107 trypanosomes/milliliter of blood), and was used to evaluate the efficacy of in vitro treatments. Results Only AIF1, AIF2, and AIF5 significantly inhibited TAO. AIF1 and AIF5 produced significant, dose-dependent suppression of parasite motility reaching score zero within 1 h with EC50 of 0.005 and 0.004 µg/µL, respectively, while trypanosome-laden blood was still at score six with an EC50 of 44,086 µg/µL. Mice inoculated with the concentrations at scores 0 and 1 (1–2 moribund parasites) at the end of the experiment did not develop parasitaemia. The two fractions significantly (p < 0.05) lowered parasite burden, with the AIF5 exhibiting highest in vivo trypanocidal effects. Packed cell volume was significantly higher in AIF1 (p < 0.05) and AIF5 (p < 0.001) groups compared to DMSO-treated group. Only AIF5 significantly (p < 0.05) lowered malondialdehyde. Conclusion AIF1 and AIF5 offer prospects for the discovery of TAO inhibitor(s).
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Kaur P, Goyal N. Pathogenic role of mitogen activated protein kinases in protozoan parasites. Biochimie 2021; 193:78-89. [PMID: 34706251 DOI: 10.1016/j.biochi.2021.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/29/2021] [Accepted: 10/21/2021] [Indexed: 01/18/2023]
Abstract
Protozoan parasites with complex life cycles have high mortality rates affecting billions of human lives. Available anti-parasitic drugs are inadequate due to variable efficacy, toxicity, poor patient compliance and drug-resistance. Hence, there is an urgent need for the development of safer and better chemotherapeutics. Mitogen Activated Protein Kinases (MAPKs) have drawn much attention as potential drug targets. This review summarizes unique structural and functional features of MAP kinases and their possible role in pathogenesis of obligate intracellular protozoan parasites namely, Leishmania, Trypanosoma, Plasmodium and Toxoplasma. It also provides an overview of available knowledge concerning the target proteins of parasite MAPKs and the need to understand and unravel unknown interaction network(s) of MAPK(s).
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Affiliation(s)
- Pavneet Kaur
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
| | - Neena Goyal
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India.
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5
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Serafim RAM, Elkins JM, Zuercher WJ, Laufer SA, Gehringer M. Chemical Probes for Understudied Kinases: Challenges and Opportunities. J Med Chem 2021; 65:1132-1170. [PMID: 34477374 DOI: 10.1021/acs.jmedchem.1c00980] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over 20 years after the approval of the first-in-class protein kinase inhibitor imatinib, the biological function of a significant fraction of the human kinome remains poorly understood while most research continues to be focused on few well-validated targets. Given the strong genetic evidence for involvement of many kinases in health and disease, the understudied fraction of the kinome holds a large and unexplored potential for future therapies. Specific chemical probes are indispensable tools to interrogate biology enabling proper preclinical validation of novel kinase targets. In this Perspective, we highlight recent case studies illustrating the development of high-quality chemical probes for less-studied kinases and their application in target validation. We spotlight emerging techniques and approaches employed in the generation of chemical probes for protein kinases and beyond and discuss the associated challenges and opportunities.
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Affiliation(s)
- Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Jonathan M Elkins
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - William J Zuercher
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stefan A Laufer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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6
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Zaru R, Onwubiko J, Ribeiro AJM, Cochrane K, Tyzack JD, Muthukrishnan V, Pravda L, Thornton JM, O'Donovan C, Velanker S, Orchard S, Leach A, Martin MJ. The Enzyme Portal: an integrative tool for enzyme information and analysis. FEBS J 2021; 289:5875-5890. [PMID: 34437766 DOI: 10.1111/febs.16168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/10/2021] [Accepted: 08/25/2021] [Indexed: 12/19/2022]
Abstract
Enzymes play essential roles in all life processes and are used extensively in the biomedical and biotechnological fields. However, enzyme-related information is spread across multiple resources making its retrieval time-consuming. In response to this challenge, the Enzyme Portal has been established to facilitate enzyme research, by providing a freely available hub where researchers can easily find and explore enzyme-related information. It integrates relevant enzyme data for a wide range of species from various resources such as UniProtKB, PDBe and ChEMBL. Here, we describe what type of enzyme-related data the Enzyme Portal provides, how the information is organized and, by show-casing two potential use cases, how to access and retrieve it.
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Affiliation(s)
- Rossana Zaru
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Joseph Onwubiko
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Antonio J M Ribeiro
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Keeva Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Jonathan D Tyzack
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Venkatesh Muthukrishnan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Lukas Pravda
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Sameer Velanker
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Andrew Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Maria J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
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Dean S. Basic Biology of Trypanosoma brucei with Reference to the Development of Chemotherapies. Curr Pharm Des 2021; 27:1650-1670. [PMID: 33463458 DOI: 10.2174/1381612827666210119105008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/01/2020] [Accepted: 12/08/2020] [Indexed: 11/22/2022]
Abstract
Trypanosoma brucei are protozoan parasites that cause the lethal human disease African sleeping sickness and the economically devastating disease of cattle, Nagana. African sleeping sickness, also known as Human African Trypanosomiasis (HAT), threatens 65 million people and animal trypanosomiasis makes large areas of farmland unusable. There is no vaccine and licensed therapies against the most severe, late-stage disease are toxic, impractical and ineffective. Trypanosomes are transmitted by tsetse flies, and HAT is therefore predominantly confined to the tsetse fly belt in sub-Saharan Africa. They are exclusively extracellular and they differentiate between at least seven developmental forms that are highly adapted to host and vector niches. In the mammalian (human) host they inhabit the blood, cerebrospinal fluid (late-stage disease), skin, and adipose fat. In the tsetse fly vector they travel from the tsetse midgut to the salivary glands via the ectoperitrophic space and proventriculus. Trypanosomes are evolutionarily divergent compared with most branches of eukaryotic life. Perhaps most famous for their extraordinary mechanisms of monoallelic gene expression and antigenic variation, they have also been investigated because much of their biology is either highly unconventional or extreme. Moreover, in addition to their importance as pathogens, many researchers have been attracted to the field because trypanosomes have some of the most advanced molecular genetic tools and database resources of any model system. The following will cover just some aspects of trypanosome biology and how its divergent biochemistry has been leveraged to develop drugs to treat African sleeping sickness. This is by no means intended to be a comprehensive survey of trypanosome features. Rather, I hope to present trypanosomes as one of the most fascinating and tractable systems to do discovery biology.
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Affiliation(s)
- Samuel Dean
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom
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Singh B, Diaz-Gonzalez R, Ceballos-Perez G, Rojas-Barros DI, Gunaganti N, Gillingwater K, Martinez-Martinez MS, Manzano P, Navarro M, Pollastri MP. Medicinal Chemistry Optimization of a Diaminopurine Chemotype: Toward a Lead for Trypanosoma brucei Inhibitors. J Med Chem 2020; 63:9912-9927. [PMID: 32786222 DOI: 10.1021/acs.jmedchem.0c01017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human African trypanosomiasis (HAT), or sleeping sickness, is caused by the protozoan parasite Trypanosoma brucei and transmitted through the bite of infected tsetse flies. The disease is considered fatal if left untreated. To identify new chemotypes against Trypanosoma brucei, previously we identified 797 potent kinase-targeting inhibitors grouped into 59 clusters plus 53 singleton compounds with at least 100-fold selectivity over HepG2 cells. From this set of hits, a cluster of diaminopurine-derived compounds was identified. Herein, we report our medicinal chemistry investigation involving the exploration of structure-activity and structure-property relationships around one of the high-throughput screening (HTS) hits, N2-(thiophen-3-yl)-N6-(2,2,2-trifluoroethyl)-9H-purine-2,6-diamine (1, NEU-1106). This work led to the identification of a potent lead compound (4aa, NEU-4854) with improved in vitro absorption, distribution, metabolism, and excretion (ADME) properties, which was progressed into proof-of-concept translation of in vitro antiparasitic activity to in vivo efficacy.
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Affiliation(s)
- Baljinder Singh
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Rosario Diaz-Gonzalez
- Instituto de Parasitología y Biomedicina "López-Neyra" Consejo Superior de Investigaciones Científicas (CSIC), Granada 18016, Spain
| | - Gloria Ceballos-Perez
- Instituto de Parasitología y Biomedicina "López-Neyra" Consejo Superior de Investigaciones Científicas (CSIC), Granada 18016, Spain
| | - Domingo I Rojas-Barros
- Instituto de Parasitología y Biomedicina "López-Neyra" Consejo Superior de Investigaciones Científicas (CSIC), Granada 18016, Spain
| | - Naresh Gunaganti
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Kirsten Gillingwater
- Parasite Chemotherapy Unit, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland.,University of Basel, Petersplatz 1, 4001 Basel, Switzerland
| | | | - Pilar Manzano
- Tres Cantos Medicines Development Campus, DDW, GlaxoSmithKline, Tres Cantos 28760, Spain
| | - Miguel Navarro
- Instituto de Parasitología y Biomedicina "López-Neyra" Consejo Superior de Investigaciones Científicas (CSIC), Granada 18016, Spain
| | - Michael P Pollastri
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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9
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Ooi CP, Benz C, Urbaniak MD. Phosphoproteomic analysis of mammalian infective Trypanosoma brucei subjected to heat shock suggests atypical mechanisms for thermotolerance. J Proteomics 2020; 219:103735. [PMID: 32198071 DOI: 10.1016/j.jprot.2020.103735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/11/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
Abstract
The symptoms of African sleeping sickness, caused by the parasite Trypanosoma brucei, can include periods of fever as high as 41 °C which triggers a heat shock response in the parasite. To capture events involved in sensing and responding to heat shock in the mammalian infective form we have conducted a SILAC-based quantitative proteomic and phosphoproteomic analysis of T. brucei cells treated at 41 °C for 1h. Our analysis identified 193 heat shock responsive phosphorylation sites with an average of 5-fold change in abundance, but only 20 heat shock responsive proteins with average of 1.5-fold change. These data indicate that protein abundance does not rapidly respond (≤1 h) to heat shock, and that the changes observed in phosphorylation site abundance are larger and more widespread. The heat shock responsive phosphorylation sites showed enrichment of RNA binding proteins with putative roles in heat shock response included P-body / stress granules and the eukaryotic translation initiation 4F complex. The ZC3H11-MKT1 complex, which stabilises mRNAs of thermotolerance proteins, appears to represent a key signal integration node in the heat shock response. SIGNIFICANCE: We report the first quantitative study of changes in protein and phosphorylation site abundance in response to heat shock in the clinically relevant form of the human parasite Trypanosoma brucei. The identification of heat shock responsive phosphorylation sites on proteins with putative roles in thermotolerance including the ZC3H11-MKT1 complex provides evidence of the role dynamic phosphorylation of RNA binding proteins in co-ordinating heat shock. Temperature changes in the host are a major physiological challenge to parasites and factors conferring tolerance to heat shock constitute overlooked virulence factors. A better understanding of these virulence factors will pave the way for the development of novel drug therapies which selectively target T. brucei.
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Affiliation(s)
- Cher P Ooi
- Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, UK.
| | - Corinna Benz
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK
| | - Michael D Urbaniak
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK.
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Altamura F, Rajesh R, Catta-Preta CMC, Moretti NS, Cestari I. The current drug discovery landscape for trypanosomiasis and leishmaniasis: Challenges and strategies to identify drug targets. Drug Dev Res 2020; 83:225-252. [PMID: 32249457 DOI: 10.1002/ddr.21664] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/05/2020] [Accepted: 03/13/2020] [Indexed: 12/11/2022]
Abstract
Human trypanosomiasis and leishmaniasis are vector-borne neglected tropical diseases caused by infection with the protozoan parasites Trypanosoma spp. and Leishmania spp., respectively. Once restricted to endemic areas, these diseases are now distributed worldwide due to human migration, climate change, and anthropogenic disturbance, causing significant health and economic burden globally. The current chemotherapy used to treat these diseases has limited efficacy, and drug resistance is spreading. Hence, new drugs are urgently needed. Phenotypic compound screenings have prevailed as the leading method to discover new drug candidates against these diseases. However, the publication of the complete genome sequences of multiple strains, advances in the application of CRISPR/Cas9 technology, and in vivo bioluminescence-based imaging have set the stage for advancing target-based drug discovery. This review analyses the limitations of the narrow pool of available drugs presently used for treating these diseases. It describes the current drug-based clinical trials highlighting the most promising leads. Furthermore, the review presents a focused discussion on the most important biological and pharmacological challenges that target-based drug discovery programs must overcome to advance drug candidates. Finally, it examines the advantages and limitations of modern research tools designed to identify and validate essential genes as drug targets, including genomic editing applications and in vivo imaging.
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Affiliation(s)
- Fernando Altamura
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, Quebec, Canada
| | - Rishi Rajesh
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, Quebec, Canada
| | | | - Nilmar S Moretti
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Igor Cestari
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, Quebec, Canada
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Benz C, Urbaniak MD. Organising the cell cycle in the absence of transcriptional control: Dynamic phosphorylation co-ordinates the Trypanosoma brucei cell cycle post-transcriptionally. PLoS Pathog 2019; 15:e1008129. [PMID: 31830130 PMCID: PMC6907760 DOI: 10.1371/journal.ppat.1008129] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/07/2019] [Indexed: 11/18/2022] Open
Abstract
The cell division cycle of the unicellular eukaryote Trypanosome brucei is tightly regulated despite the paucity of transcriptional control that results from the arrangement of genes in polycistronic units and lack of dynamically regulated transcription factors. To identify the contribution of dynamic phosphorylation to T. brucei cell cycle control we have combined cell cycle synchronisation by centrifugal elutriation with quantitative phosphoproteomic analysis. Cell cycle regulated changes in phosphorylation site abundance (917 sites, average 5-fold change) were more widespread and of a larger magnitude than changes in protein abundance (443 proteins, average 2-fold change) and were mostly independent of each other. Hierarchical clustering of co-regulated phosphorylation sites according to their cell cycle profile revealed that a bulk increase in phosphorylation occurs across the cell cycle, with a significant enrichment of known cell cycle regulators and RNA binding proteins (RBPs) within the largest clusters. Cell cycle regulated changes in essential cell cycle kinases are temporally co-ordinated with differential phosphorylation of components of the kinetochore and eukaryotic initiation factors, along with many RBPs not previously linked to the cell cycle such as eight PSP1-C terminal domain containing proteins. The temporal profiles demonstrate the importance of dynamic phosphorylation in co-ordinating progression through the cell cycle, and provide evidence that RBPs play a central role in post-transcriptional regulation of the T. brucei cell cycle. Data are available via ProteomeXchange with identifier PXD013488.
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Affiliation(s)
- Corinna Benz
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Michael D. Urbaniak
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
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Hammarton TC. Who Needs a Contractile Actomyosin Ring? The Plethora of Alternative Ways to Divide a Protozoan Parasite. Front Cell Infect Microbiol 2019; 9:397. [PMID: 31824870 PMCID: PMC6881465 DOI: 10.3389/fcimb.2019.00397] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/06/2019] [Indexed: 01/21/2023] Open
Abstract
Cytokinesis, or the division of the cytoplasm, following the end of mitosis or meiosis, is accomplished in animal cells, fungi, and amoebae, by the constriction of an actomyosin contractile ring, comprising filamentous actin, myosin II, and associated proteins. However, despite this being the best-studied mode of cytokinesis, it is restricted to the Opisthokonta and Amoebozoa, since members of other evolutionary supergroups lack myosin II and must, therefore, employ different mechanisms. In particular, parasitic protozoa, many of which cause significant morbidity and mortality in humans and animals as well as considerable economic losses, employ a wide diversity of mechanisms to divide, few, if any, of which involve myosin II. In some cases, cell division is not only myosin II-independent, but actin-independent too. Mechanisms employed range from primitive mechanical cell rupture (cytofission), to motility- and/or microtubule remodeling-dependent mechanisms, to budding involving the constriction of divergent contractile rings, to hijacking host cell division machinery, with some species able to utilize multiple mechanisms. Here, I review current knowledge of cytokinesis mechanisms and their molecular control in mammalian-infective parasitic protozoa from the Excavata, Alveolata, and Amoebozoa supergroups, highlighting their often-underappreciated diversity and complexity. Billions of people and animals across the world are at risk from these pathogens, for which vaccines and/or optimal treatments are often not available. Exploiting the divergent cell division machinery in these parasites may provide new avenues for the treatment of protozoal disease.
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Affiliation(s)
- Tansy C Hammarton
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
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Namyanja M, Xu ZS, Mugasa CM, Lun ZR, Matovu E, Chen Z, Lubega GW. Preliminary evaluation of a Trypanosoma brucei FG-GAP repeat containing protein of mitochondrial localization. AAS Open Res 2019. [DOI: 10.12688/aasopenres.12986.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Trypanosoma brucei, a causative agent of African Trypanosomiasis, is known to cross the blood brain barrier during the second stage of the disease. It was previously suggested that this parasite crosses the blood brain barrier in a manner similar to that of lymphocytes. This would imply that trypanosomes possess integrins that are required to interact with adhesion molecules located on the blood brain barrier microvascular endothelial cells, as a first step in traversal. To date, no T. brucei integrin has been described. However, one T. brucei putative FG-GAP repeat containing protein (typical of integrins) encoded by the Tb927.11.720 gene, was predicted to be involved in cell-cell/cell-matrix adhesion. Therefore, this study sought to characterize a putative FG-GAP repeat containing protein (FG-GAP RCP) and to determine its cellular localization as a basis for further exploration of its potential role in cell-cell or cell-matrix adhesion. Methods: In this study, we successfully cloned, characterized, expressed and localized this protein using antibodies we produced against its VCBS domain in T. brucei. Results: Contrary to what we initially suspected, our data showed that this protein is localized to the mitochondria but not the plasma membrane. Our data showed that it contains putative calcium binding motifs within the FG-GAP repeats suggesting it could be involved in calcium signaling/binding in the mitochondrion of T. brucei. Conclusion: Based on its localization we conclude that this protein is unlikely to be a trypanosomal integrin and thus that it may not be involved in traversal of the blood brain barrier. However, it could be involved in calcium signaling in the mitochondrion.
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Eberl HC, Werner T, Reinhard FB, Lehmann S, Thomson D, Chen P, Zhang C, Rau C, Muelbaier M, Drewes G, Drewry D, Bantscheff M. Chemical proteomics reveals target selectivity of clinical Jak inhibitors in human primary cells. Sci Rep 2019; 9:14159. [PMID: 31578349 PMCID: PMC6775116 DOI: 10.1038/s41598-019-50335-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022] Open
Abstract
Kinobeads are a set of promiscuous kinase inhibitors immobilized on sepharose beads for the comprehensive enrichment of endogenously expressed protein kinases from cell lines and tissues. These beads enable chemoproteomics profiling of kinase inhibitors of interest in dose-dependent competition studies in combination with quantitative mass spectrometry. We present improved bead matrices that capture more than 350 protein kinases and 15 lipid kinases from human cell lysates, respectively. A multiplexing strategy is suggested that enables determination of apparent dissociation constants in a single mass spectrometry experiment. Miniaturization of the procedure enabled determining the target selectivity of the clinical BCR-ABL inhibitor dasatinib in peripheral blood mononuclear cell (PBMC) lysates from individual donors. Profiling of a set of Jak kinase inhibitors revealed kinase off-targets from nearly all kinase families underpinning the need to profile kinase inhibitors against the kinome. Potently bound off-targets of clinical inhibitors suggest polypharmacology, e.g. through MRCK alpha and beta, which bind to decernotinib with nanomolar affinity.
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Affiliation(s)
- H Christian Eberl
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany.
| | - Thilo Werner
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Friedrich B Reinhard
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Stephanie Lehmann
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Douglas Thomson
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Peiling Chen
- GlaxoSmithKline, Upper Merion, 709 Swedeland Rd #1539, King of Prussia, PA, 19406, United States
| | - Cunyu Zhang
- GlaxoSmithKline, Upper Merion, 709 Swedeland Rd #1539, King of Prussia, PA, 19406, United States
| | - Christina Rau
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Marcel Muelbaier
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Gerard Drewes
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - David Drewry
- GlaxoSmithKline, Research Triangle Park, 5 Moore Drive, North Carolina, 27709, United States.,UNC Eshelman School of Pharmacy, Structural Genomics Consortium, University of North Carolina at Chapel Hill, 120 Mason Farm Rd, Chapel Hill, NC, 27599, United States
| | - Marcus Bantscheff
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany.
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15
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Caffrey CR, El‐Sakkary N, Mäder P, Krieg R, Becker K, Schlitzer M, Drewry DH, Vennerstrom JL, Grevelding CG. Drug Discovery and Development for Schistosomiasis. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/9783527808656.ch8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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16
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Plasmodium Genomics and Genetics: New Insights into Malaria Pathogenesis, Drug Resistance, Epidemiology, and Evolution. Clin Microbiol Rev 2019; 32:32/4/e00019-19. [PMID: 31366610 DOI: 10.1128/cmr.00019-19] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Protozoan Plasmodium parasites are the causative agents of malaria, a deadly disease that continues to afflict hundreds of millions of people every year. Infections with malaria parasites can be asymptomatic, with mild or severe symptoms, or fatal, depending on many factors such as parasite virulence and host immune status. Malaria can be treated with various drugs, with artemisinin-based combination therapies (ACTs) being the first-line choice. Recent advances in genetics and genomics of malaria parasites have contributed greatly to our understanding of parasite population dynamics, transmission, drug responses, and pathogenesis. However, knowledge gaps in parasite biology and host-parasite interactions still remain. Parasites resistant to multiple antimalarial drugs have emerged, while advanced clinical trials have shown partial efficacy for one available vaccine. Here we discuss genetic and genomic studies of Plasmodium biology, host-parasite interactions, population structures, mosquito infectivity, antigenic variation, and targets for treatment and immunization. Knowledge from these studies will advance our understanding of malaria pathogenesis, epidemiology, and evolution and will support work to discover and develop new medicines and vaccines.
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17
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Baker CH, Welburn SC. The Long Wait for a New Drug for Human African Trypanosomiasis. Trends Parasitol 2018; 34:818-827. [DOI: 10.1016/j.pt.2018.08.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 12/22/2022]
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18
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Golkowski M, Perera GK, Vidadala VN, Ojo KK, Van Voorhis WC, Maly DJ, Ong SE. Kinome chemoproteomics characterization of pyrrolo[3,4-c]pyrazoles as potent and selective inhibitors of glycogen synthase kinase 3. Mol Omics 2018; 14:26-36. [PMID: 29725679 DOI: 10.1039/c7mo00006e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Glycogen synthase kinase 3 has evolutionarily conserved roles in cell signaling and metabolism and is a recognized drug target in neurological pathologies, most prominently bipolar disorder. More recently it has been suggested that GSK3 may be a target for the treatment of trypanosomatid parasite infections, e.g. with T. brucei, due to the lethal phenotype observed in parasite GSK3 short RNAi knockdown experiments. Here we investigated the kinome selectivity of a library of pyrrolo[3,4-c]pyrazol inhibitors that were developed against T. brucei GSK3 but that also interact with the human orthologue and other protein kinases. We applied label-free MS-based kinome chemoproteomics profiling with kinobeads to obtain the selectivity profiles of all 39 library members against 217 human protein and lipid kinases. This allowed us to study the structure-activity relationship of the library members as well as the chemical genetic relationships between kinase targets. As a result, we identified a novel and highly selective HsGSK3 inhibitor containing a 2-chloroaniline-substituted squaric acid amide pharmacophore that confers low nanomolar (IC50 = 2.8 nM) and sub-micromolar potency against purified and cellular HsGSK3. The inhibitor will be useful as a new lead for GSK3 inhibitor development and as a chemical genetic probe to study roles of GSK3 in cell signaling.
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Affiliation(s)
- Martin Golkowski
- School of Medicine, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.
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19
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Zíková A, Verner Z, Nenarokova A, Michels PAM, Lukeš J. A paradigm shift: The mitoproteomes of procyclic and bloodstream Trypanosoma brucei are comparably complex. PLoS Pathog 2017; 13:e1006679. [PMID: 29267392 PMCID: PMC5739487 DOI: 10.1371/journal.ppat.1006679] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- * E-mail:
| | - Zdeněk Verner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Anna Nenarokova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Paul A. M. Michels
- Centre for Immunity, Infection and Evolution, The University of Edinburgh, Edinburgh, United Kingdom
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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20
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Characterisation of Casein Kinase 1.1 in Leishmania donovani Using the CRISPR Cas9 Toolkit. BIOMED RESEARCH INTERNATIONAL 2017; 2017:4635605. [PMID: 29333442 PMCID: PMC5733176 DOI: 10.1155/2017/4635605] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/22/2017] [Accepted: 10/12/2017] [Indexed: 02/06/2023]
Abstract
The recent adaptation of CRISPR Cas9 genome editing to Leishmania spp. has opened a new era in deciphering Leishmania biology. The method was recently improved using a PCR-based CRISPR Cas9 approach, which eliminated the need for cloning. This new approach, which allows high-throughput gene deletion, was successfully validated in L. mexicana and L. major. In this study, we validated the toolkit in Leishmania donovani targeting the flagellar protein PF16, confirming that the tagged protein localizes to the flagellum and that null mutants lose their motility. We then used the technique to characterise CK1.1, a member of the casein kinase 1 family, which is involved in the regulation of many cellular processes. We showed that CK1.1 is a low-abundance protein present in promastigotes and in amastigotes. We demonstrated that CK1.1 is not essential for promastigote and axenic amastigote survival or for axenic amastigote differentiation, although it may have a role during stationary phase. Altogether, our data validate the use of PCR-based CRISPR Cas9 toolkit in L. donovani, which will be crucial for genetic modification of hamster-derived, disease-relevant parasites.
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21
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RNAi screening identifies Trypanosoma brucei stress response protein kinases required for survival in the mouse. Sci Rep 2017; 7:6156. [PMID: 28733613 PMCID: PMC5522463 DOI: 10.1038/s41598-017-06501-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/26/2017] [Indexed: 01/05/2023] Open
Abstract
Protein kinases (PKs) are a class of druggable targets in Trypanosoma brucei, the causative agent of Human African Trypanosomiasis (sleeping sickness), yet little is known about which PKs are essential for survival in mammals. A recent kinome-wide RNAi screen with 176 individual bloodstream form Trypanosoma brucei lines identified PKs required for proliferation in culture. In order to assess which PKs are also potential virulence factors essential in vivo, lines were pooled, inoculated into mice, and screened for loss of fitness after 48 h RNAi. The presence of trypanosomes in the bloodstream was assessed using RNAi target sequencing (RITseq) and compared to growth in culture. We identified 49 PKs with a significant loss of fitness in vivo in two independent experiments, and a strong correlation between in vitro and in vivo loss of fitness for the majority. Nine PKs had a more pronounced growth defect in vivo, than in vitro. Amongst these PKs were several with putative functions related to stress responses mediated through the PI3K/TOR or MAPK signaling cascades, which act to protect the parasite from complement-mediated and osmotic lysis. Identification of these virulence-associated PKs provides new insights into T. brucei-host interaction and reveals novel potential protein kinase drug targets.
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22
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Field MC, Horn D, Fairlamb AH, Ferguson MAJ, Gray DW, Read KD, De Rycker M, Torrie LS, Wyatt PG, Wyllie S, Gilbert IH. Anti-trypanosomatid drug discovery: an ongoing challenge and a continuing need. Nat Rev Microbiol 2017; 15:217-231. [PMID: 28239154 PMCID: PMC5582623 DOI: 10.1038/nrmicro.2016.193] [Citation(s) in RCA: 259] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The WHO recognizes human African trypanosomiasis, Chagas disease and the leishmaniases as neglected tropical diseases. These diseases are caused by parasitic trypanosomatids and range in severity from mild and self-curing to near invariably fatal. Public health advances have substantially decreased the effect of these diseases in recent decades but alone will not eliminate them. In this Review, we discuss why new drugs against trypanosomatids are required, approaches that are under investigation to develop new drugs and why the drug discovery pipeline remains essentially unfilled. In addition, we consider the important challenges to drug discovery strategies and the new technologies that can address them. The combination of new drugs, new technologies and public health initiatives is essential for the management, and hopefully eventual elimination, of trypanosomatid diseases from the human population.
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Affiliation(s)
- Mark C Field
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee DD1 5EH, UK
| | - David Horn
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee DD1 5EH, UK
| | - Alan H Fairlamb
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee DD1 5EH, UK
| | - Michael A J Ferguson
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee DD1 5EH, UK
| | - David W Gray
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee DD1 5EH, UK
| | - Kevin D Read
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee DD1 5EH, UK
| | - Manu De Rycker
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee DD1 5EH, UK
| | - Leah S Torrie
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee DD1 5EH, UK
| | - Paul G Wyatt
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee DD1 5EH, UK
| | - Susan Wyllie
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee DD1 5EH, UK
| | - Ian H Gilbert
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee DD1 5EH, UK
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23
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Chen X, Wong YK, Wang J, Zhang J, Lee YM, Shen HM, Lin Q, Hua ZC. Target identification with quantitative activity based protein profiling (ABPP). Proteomics 2016; 17. [PMID: 27723264 DOI: 10.1002/pmic.201600212] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/14/2016] [Accepted: 10/06/2016] [Indexed: 12/20/2022]
Abstract
As many small bioactive molecules fulfill their functions through interacting with protein targets, the identification of such targets is crucial in understanding their mechanisms of action (MOA) and side effects. With technological advancements in target identification, it has become possible to accurately and comprehensively study the MOA and side effects of small molecules. While small molecules with therapeutic potential were derived solely from nature in the past, the remodeling and synthesis of such molecules have now been made possible. Presently, while some small molecules have seen successful application as drugs, the majority remain undeveloped, requiring further understanding of their MOA and side effects to fully tap into their potential. Given the typical promiscuity of many small molecules and the complexity of the cellular proteome, a high-flux and high-accuracy method is necessary. While affinity chromatography approaches combined with MS have had successes in target identification, limitations associated with nonspecific results remain. To overcome these complications, quantitative chemical proteomics approaches have been developed including metabolic labeling, chemical labeling, and label-free methods. These new approaches are adopted in conjunction with activity-based protein profiling (ABPP), allowing for a rapid process and accurate results. This review will briefly introduce the principles involved in ABPP, then summarize current advances in quantitative chemical proteomics approaches as well as illustrate with examples how ABPP coupled with quantitative chemical proteomics has been used to detect the targets of drugs and other bioactive small molecules including natural products.
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Affiliation(s)
- Xiao Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China
| | - Yin Kwan Wong
- Department of Biological Sciences, National University of Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jigang Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China.,Department of Biological Sciences, National University of Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research & Technology (SMART), Singapore
| | - Jianbin Zhang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, P. R., China
| | - Yew-Mun Lee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Han-Ming Shen
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Zi-Chun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China
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24
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Amata E, Xi H, Colmenarejo G, Gonzalez-Diaz R, Cordon-Obras C, Berlanga M, Manzano P, Erath J, Roncal NE, Lee PJ, Leed SE, Rodriguez A, Sciotti RJ, Navarro M, Pollastri MP. Identification of "Preferred" Human Kinase Inhibitors for Sleeping Sickness Lead Discovery. Are Some Kinases Better than Others for Inhibitor Repurposing? ACS Infect Dis 2016; 2:180-186. [PMID: 26998514 PMCID: PMC4791575 DOI: 10.1021/acsinfecdis.5b00136] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Indexed: 01/02/2023]
Abstract
![]()
A kinase-targeting cell-based high-throughput
screen (HTS) against Trypanosoma brucei was recently reported, and this screening set included the Published
Kinase Inhibitor Set (PKIS). From the PKIS was identified 53 compounds
with pEC50 ≥ 6. Utilizing the published data available
for the PKIS, a statistical analysis of these active antiparasitic
compounds was performed, allowing identification of a set of human
kinases having inhibitors that show a high likelihood for blocking T. brucei cellular proliferation in vitro. This observation
was confirmed by testing other established inhibitors of these human
kinases and by mining past screening campaigns at GlaxoSmithKline.
Overall, although the parasite targets of action are not known, inhibitors
of this set of human kinases displayed an enhanced hit rate relative
to a random kinase-targeting HTS campaign, suggesting that repurposing
efforts should focus primarily on inhibitors of these specific human
kinases. We therefore term this statistical analysis-driven approach “preferred lead repurposing”.
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Affiliation(s)
- Emanuele Amata
- Department of Chemistry & Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Hualin Xi
- Computational Sciences Center of Emphasis, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02140, United States
| | - Gonzalo Colmenarejo
- Tres Cantos Medicines Development Campus,
DDW and CIB, GlaxoSmithKline, 28760 Tres Cantos, Spain
| | - Rosario Gonzalez-Diaz
- Instituto de Parasitologı́a
y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Cientı́ficas, 18100 Granada, Spain
| | - Carlos Cordon-Obras
- Instituto de Parasitologı́a
y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Cientı́ficas, 18100 Granada, Spain
| | - Manuela Berlanga
- Tres Cantos Medicines Development Campus,
DDW and CIB, GlaxoSmithKline, 28760 Tres Cantos, Spain
| | - Pilar Manzano
- Tres Cantos Medicines Development Campus,
DDW and CIB, GlaxoSmithKline, 28760 Tres Cantos, Spain
| | - Jessey Erath
- Department of Microbiology, Division of
Parasitology, New York University School of Medicine, 341 East
25th Street New York, New
York 10010, United States
| | - Norma E. Roncal
- Experimental
Therapeutics, Walter Reed Army Institute for Research, 2460 Linden
Lane, Silver Spring, Maryland 20910, United States
| | - Patricia J. Lee
- Experimental
Therapeutics, Walter Reed Army Institute for Research, 2460 Linden
Lane, Silver Spring, Maryland 20910, United States
| | - Susan E. Leed
- Experimental
Therapeutics, Walter Reed Army Institute for Research, 2460 Linden
Lane, Silver Spring, Maryland 20910, United States
| | - Ana Rodriguez
- Department of Microbiology, Division of
Parasitology, New York University School of Medicine, 341 East
25th Street New York, New
York 10010, United States
- Anti-Infectives Screening Core, New York University School of Medicine, New York, New York 10010, United States
| | - Richard J. Sciotti
- Experimental
Therapeutics, Walter Reed Army Institute for Research, 2460 Linden
Lane, Silver Spring, Maryland 20910, United States
| | - Miguel Navarro
- Instituto de Parasitologı́a
y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Cientı́ficas, 18100 Granada, Spain
| | - Michael P. Pollastri
- Department of Chemistry & Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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25
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Gower CM, Thomas JR, Harrington E, Murphy J, Chang MEK, Cornella-Taracido I, Jain RK, Schirle M, Maly DJ. Conversion of a Single Polypharmacological Agent into Selective Bivalent Inhibitors of Intracellular Kinase Activity. ACS Chem Biol 2016; 11:121-31. [PMID: 26505072 DOI: 10.1021/acschembio.5b00847] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Loss-of-function studies are valuable for elucidating kinase function and the validation of new drug targets. While genetic techniques, such as RNAi and genetic knockouts, are highly specific and easy to implement, in many cases post-translational perturbation of kinase activity, specifically pharmacological inhibition, is preferable. However, due to the high degree of structural similarity between kinase active sites and the large size of the kinome, identification of pharmacological agents that are sufficiently selective to probe the function of a specific kinase of interest is challenging, and there is currently no systematic method for accomplishing this goal. Here, we present a modular chemical genetic strategy that uses antibody mimetics as highly selective targeting components of bivalent kinase inhibitors. We demonstrate that it is possible to confer high kinase selectivity to a promiscuous ATP-competitive inhibitor by tethering it to an antibody mimetic fused to the self-labeling protein SNAPtag. With this approach, a potent bivalent inhibitor of the tyrosine kinase Abl was generated. Profiling in complex cell lysates, with competition-based quantitative chemical proteomics, revealed that this bivalent inhibitor possesses greatly enhanced selectivity for its target, BCR-Abl, in K562 cells. Importantly, we show that both components of the bivalent inhibitor can be assembled in K562 cells to block the ability of BCR-Abl to phosphorylate a direct cellular substrate. Finally, we demonstrate the generality of using antibody mimetics as components of bivalent inhibitors by generating a reagent that is selective for the activated state of the serine/threonine kinase ERK2.
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Affiliation(s)
| | - Jason R. Thomas
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Edmund Harrington
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Jason Murphy
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | | | - Ivan Cornella-Taracido
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Rishi K. Jain
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
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26
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Foscolos AS, Papanastasiou I, Foscolos GB, Tsotinis A, Kellici TF, Mavromoustakos T, Taylor MC, Kelly JM. New hydrazones of 5-nitro-2-furaldehyde with adamantanealkanohydrazides: synthesis and in vitro trypanocidal activity. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00035e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A range of hydrazones of 5-nitro-2-furaldehyde with adamantane alkanohydrazides was synthesized and their trypanocidal activity was evaluated.
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Affiliation(s)
- Angeliki-Sofia Foscolos
- School of Health Sciences
- Faculty of Pharmacy
- Department of Pharmaceutical Chemistry
- National and Kapodistrian University of Athens
- 15784 Athens
| | - Ioannis Papanastasiou
- School of Health Sciences
- Faculty of Pharmacy
- Department of Pharmaceutical Chemistry
- National and Kapodistrian University of Athens
- 15784 Athens
| | - George B. Foscolos
- School of Health Sciences
- Faculty of Pharmacy
- Department of Pharmaceutical Chemistry
- National and Kapodistrian University of Athens
- 15784 Athens
| | - Andrew Tsotinis
- School of Health Sciences
- Faculty of Pharmacy
- Department of Pharmaceutical Chemistry
- National and Kapodistrian University of Athens
- 15784 Athens
| | - Tahsin F. Kellici
- Faculty of Chemistry
- Department of Organic Chemistry
- University of Athens
- 15771 Athens
- Greece
| | - Thomas Mavromoustakos
- Faculty of Chemistry
- Department of Organic Chemistry
- University of Athens
- 15771 Athens
- Greece
| | - Martin C. Taylor
- Department of Pathogen Molecular Biology
- London School of Hygiene and Tropical Medicine
- London WC1 E7HT
- UK
| | - John M. Kelly
- Department of Pathogen Molecular Biology
- London School of Hygiene and Tropical Medicine
- London WC1 E7HT
- UK
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27
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Peña I, Pilar Manzano M, Cantizani J, Kessler A, Alonso-Padilla J, Bardera AI, Alvarez E, Colmenarejo G, Cotillo I, Roquero I, de Dios-Anton F, Barroso V, Rodriguez A, Gray DW, Navarro M, Kumar V, Sherstnev A, Drewry DH, Brown JR, Fiandor JM, Julio Martin J. New compound sets identified from high throughput phenotypic screening against three kinetoplastid parasites: an open resource. Sci Rep 2015; 5:8771. [PMID: 25740547 PMCID: PMC4350103 DOI: 10.1038/srep08771] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 01/28/2015] [Indexed: 12/11/2022] Open
Abstract
Using whole-cell phenotypic assays, the GlaxoSmithKline high-throughput screening (HTS) diversity set of 1.8 million compounds was screened against the three kinetoplastids most relevant to human disease, i.e. Leishmania donovani, Trypanosoma cruzi and Trypanosoma brucei. Secondary confirmatory and orthogonal intracellular anti-parasiticidal assays were conducted, and the potential for non-specific cytotoxicity determined. Hit compounds were chemically clustered and triaged for desirable physicochemical properties. The hypothetical biological target space covered by these diversity sets was investigated through bioinformatics methodologies. Consequently, three anti-kinetoplastid chemical boxes of ~200 compounds each were assembled. Functional analyses of these compounds suggest a wide array of potential modes of action against kinetoplastid kinases, proteases and cytochromes as well as potential host–pathogen targets. This is the first published parallel high throughput screening of a pharma compound collection against kinetoplastids. The compound sets are provided as an open resource for future lead discovery programs, and to address important research questions.
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Affiliation(s)
- Imanol Peña
- Molecular Discovery Research, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Spain
| | - M Pilar Manzano
- Diseases of the Developing World (DDW), Tres Cantos Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Spain
| | - Juan Cantizani
- Diseases of the Developing World (DDW), Tres Cantos Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Spain
| | - Albane Kessler
- Diseases of the Developing World (DDW), Tres Cantos Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Spain
| | - Julio Alonso-Padilla
- Department of Microbiology, Division of Parasitology, New York University School of Medicine, New York, NY, USA
| | - Ana I Bardera
- Molecular Discovery Research, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Spain
| | - Emilio Alvarez
- Molecular Discovery Research, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Spain
| | - Gonzalo Colmenarejo
- Molecular Discovery Research, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Spain
| | - Ignacio Cotillo
- Diseases of the Developing World (DDW), Tres Cantos Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Spain
| | - Irene Roquero
- Molecular Discovery Research, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Spain
| | - Francisco de Dios-Anton
- Molecular Discovery Research, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Spain
| | - Vanessa Barroso
- Molecular Discovery Research, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Spain
| | - Ana Rodriguez
- Department of Microbiology, Division of Parasitology, New York University School of Medicine, New York, NY, USA
| | - David W Gray
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | - Miguel Navarro
- Instituto de Parasitología y Biomedicina "López-Neyra" Consejo Superior de Investigaciones Cientificas, Granada, Spain
| | - Vinod Kumar
- Computational Biology, Quantitative Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Alexander Sherstnev
- Computational Biology, Quantitative Sciences, GlaxoSmithKline, Medicines Research Center, Stevenage, Hertfordshire, UK
| | - David H Drewry
- Chemical Sciences, Molecular Discovery Research, GlaxoSmithKline, Research Triangle Park, NC, USA
| | - James R Brown
- Computational Biology, Quantitative Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Jose M Fiandor
- Diseases of the Developing World (DDW), Tres Cantos Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Spain
| | - J Julio Martin
- Molecular Discovery Research, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Spain
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28
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Abstract
Small molecule inhibitors of protein kinases are key tools for signal transduction research and represent a major class of targeted drugs. Recent developments in quantitative proteomics enable an unbiased view on kinase inhibitor selectivity and modes of action in the biological context. While chemical proteomics techniques utilizing quantitative mass spectrometry interrogate both target specificity and affinity in cellular extracts, proteome-wide phosphorylation analyses upon kinase inhibitor treatment identify signal transduction pathway and network regulation in an unbiased manner. Thus, critical information is provided to promote new insights into mechanisms of kinase signaling and their relevance for kinase inhibitor drug discovery.
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Affiliation(s)
- Henrik Daub
- Evotec (München) GmbH, Am Klopferspitz
19a, 82152 Martinsried, Germany
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29
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Abstract
Drug repositioning or repurposing has received much coverage in the scientific literature in recent years and has been responsible for the generation of both new intellectual property and investigational new drug submissions. The literature indicates a significant trend toward the use of computational- or informatics-based methods for generating initial repositioning hypotheses, followed by focused assessment of biological activity in phenotypic assays. Another viable method for drug repositioning is in vitro screening of known drugs or drug-like molecules, initially in disease-relevant phenotypic assays, to identify and validate candidates for repositioning. This approach can use large compound libraries or can focus on subsets of known drugs or drug-like molecules. In this short review, we focus on ways to generate and validate repositioning candidates in disease-related in vitro and phenotypic assays, and we discuss specific examples of this approach as applied to a variety of disease areas. We propose that in vitro screens offer several advantages over biochemical or in vivo methods as a starting point for drug repositioning.
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Affiliation(s)
- Graeme F. Wilkinson
- Emerging Innovations, Innovative Medicines, AstraZeneca, Macclesfield, Cheshire, UK
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30
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Merritt C, Silva L, Tanner AL, Stuart K, Pollastri MP. Kinases as druggable targets in trypanosomatid protozoan parasites. Chem Rev 2014; 114:11280-304. [PMID: 26443079 PMCID: PMC4254031 DOI: 10.1021/cr500197d] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Christopher Merritt
- Seattle
Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109-5219, United States
| | - Lisseth
E. Silva
- Department
of Chemistry & Chemical Biology, Northeastern
University, 417 Egan
Research Center, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Angela L. Tanner
- Department
of Chemistry & Chemical Biology, Northeastern
University, 417 Egan
Research Center, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Kenneth Stuart
- Seattle
Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109-5219, United States
| | - Michael P. Pollastri
- Department
of Chemistry & Chemical Biology, Northeastern
University, 417 Egan
Research Center, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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31
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Urich R, Grimaldi R, Luksch T, Frearson JA, Brenk R, Wyatt PG. The design and synthesis of potent and selective inhibitors of Trypanosoma brucei glycogen synthase kinase 3 for the treatment of human african trypanosomiasis. J Med Chem 2014; 57:7536-49. [PMID: 25198388 PMCID: PMC4175002 DOI: 10.1021/jm500239b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Glycogen synthase kinase 3 (GSK3) is a genetically validated drug target for human African trypanosomiasis (HAT), also called African sleeping sickness. We report the synthesis and biological evaluation of aminopyrazole derivatives as Trypanosoma brucei GSK3 short inhibitors. Low nanomolar inhibitors, which had high selectivity over the off-target human CDK2 and good selectivity over human GSK3β enzyme, have been prepared. These potent kinase inhibitors demonstrated low micromolar levels of inhibition of the Trypanosoma brucei brucei parasite grown in culture.
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Affiliation(s)
- Robert Urich
- Drug Discovery Unit, College of Life Sciences, University of Dundee , Sir James Black Centre, Dow Street, Dundee DD1 5EH, U.K
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32
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Gower CM, Chang MEK, Maly DJ. Bivalent inhibitors of protein kinases. Crit Rev Biochem Mol Biol 2014; 49:102-15. [PMID: 24564382 DOI: 10.3109/10409238.2013.875513] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein kinases are key players in a large number of cellular signaling pathways. Dysregulated kinase activity has been implicated in a number of diseases, and members of this enzyme family are of therapeutic interest. However, due to the fact that most inhibitors interact with the highly conserved ATP-binding sites of kinases, it is a significant challenge to develop pharmacological agents that target only one of the greater than 500 kinases present in humans. A potential solution to this problem is the development of bisubstrate and bivalent kinase inhibitors, in which an active site-directed moiety is tethered to another ligand that targets a location outside of the ATP-binding cleft. Because kinase signaling specificity is modulated by regions outside of the ATP-binding site, strategies that exploit these interactions have the potential to provide reagents with high target selectivity. This review highlights examples of kinase interaction sites that can potentially be exploited by bisubstrate and bivalent inhibitors. Furthermore, an overview of efforts to target these interactions with bisubstrate and bivalent inhibitors is provided. Finally, several examples of the successful application of these reagents in a cellular setting are described.
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Affiliation(s)
- Carrie M Gower
- Department of Chemistry, University of Washington , Seattle, WA , USA
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33
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Regulators of Trypanosoma brucei cell cycle progression and differentiation identified using a kinome-wide RNAi screen. PLoS Pathog 2014; 10:e1003886. [PMID: 24453978 PMCID: PMC3894213 DOI: 10.1371/journal.ppat.1003886] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 12/02/2013] [Indexed: 12/02/2022] Open
Abstract
The African trypanosome, Trypanosoma brucei, maintains an integral link between cell cycle regulation and differentiation during its intricate life cycle. Whilst extensive changes in phosphorylation have been documented between the mammalian bloodstream form and the insect procyclic form, relatively little is known about the parasite's protein kinases (PKs) involved in the control of cellular proliferation and differentiation. To address this, a T. brucei kinome-wide RNAi cell line library was generated, allowing independent inducible knockdown of each of the parasite's 190 predicted protein kinases. Screening of this library using a cell viability assay identified ≥42 PKs that are required for normal bloodstream form proliferation in culture. A secondary screen identified 24 PKs whose RNAi-mediated depletion resulted in a variety of cell cycle defects including in G1/S, kinetoplast replication/segregation, mitosis and cytokinesis, 15 of which are novel cell cycle regulators. A further screen identified for the first time two PKs, named repressor of differentiation kinase (RDK1 and RDK2), depletion of which promoted bloodstream to procyclic form differentiation. RDK1 is a membrane-associated STE11-like PK, whilst RDK2 is a NEK PK that is essential for parasite proliferation. RDK1 acts in conjunction with the PTP1/PIP39 phosphatase cascade to block uncontrolled bloodstream to procyclic form differentiation, whilst RDK2 is a PK whose depletion efficiently induces differentiation in the absence of known triggers. Thus, the RNAi kinome library provides a valuable asset for functional analysis of cell signalling pathways in African trypanosomes as well as drug target identification and validation. The African trypanosome, which is transmitted by the tsetse fly, causes the usually fatal disease Sleeping Sickness in humans and a wasting disease, called Nagana, in livestock in sub-Saharan Africa. There are no vaccines available against the diseases, and various problems are associated with current drug treatments (including toxicity to the patient and parasite drug resistance). Thus, it is important to identify essential parasite proteins that could be targeted by novel drugs. Protein kinases (PKs) are important cell signalling molecules, and are generally considered to have potential as drug targets. Here we report the construction of a library of trypanosome cell lines that allows us to specifically deplete each of the trypanosome's 190 PKs individually and analyse their function. Using this library, we show that ≥42 PKs are essential for proliferation of the mammalian-infective bloodstream form of the parasite (and thus have potential as drug targets), and demonstrate that 24 of these play important roles in coordinating cell division. We also shed light on how the parasite develops during its life cycle as it passes from the mammalian bloodstream form to the tsetse fly gut by identifying the first two PKs that regulate this life cycle developmental step.
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34
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Li J, Yuan J, Cheng KCC, Inglese J, Su XZ. Chemical genomics for studying parasite gene function and interaction. Trends Parasitol 2013; 29:603-11. [PMID: 24215777 DOI: 10.1016/j.pt.2013.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 10/08/2013] [Accepted: 10/08/2013] [Indexed: 12/20/2022]
Abstract
With the development of new technologies in genome sequencing, gene expression profiling, genotyping, and high-throughput screening of chemical compound libraries, small molecules are playing increasingly important roles in studying gene expression regulation, gene-gene interaction, and gene function. Here we briefly review and discuss some recent advancements in drug target identification and phenotype characterization using combinations of high-throughput screening of small-molecule libraries and various genome-wide methods such as whole-genome sequencing, genome-wide association studies (GWAS), and genome-wide expression analysis. These approaches can be used to search for new drugs against parasite infections, to identify drug targets or drug resistance genes, and to infer gene function.
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Affiliation(s)
- Jian Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361005, P.R. China
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35
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Abstract
Owing to the absence of antiparasitic vaccines and the constant threat of drug resistance, the development of novel antiparasitic chemotherapies remains of major importance for disease control. A better understanding of drug transport (uptake and efflux), drug metabolism and the identification of drug targets, and mechanisms of drug resistance would facilitate the development of more effective therapies. Here, we focus on malaria and African trypanosomiasis. We review existing drugs and drug development, emphasizing high-throughput genomic and genetic approaches, which hold great promise for elucidating antiparasitic mechanisms. We describe the approaches and technologies that have been influential for each parasite and develop new ideas for future research directions, including mode-of-action studies for drug target deconvolution.
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Affiliation(s)
- David Horn
- Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Manoj T. Duraisingh
- Harvard School of Public Health, 665 Huntington Avenue, Building 1, Room 715, Boston, Massachusetts 02115, USA
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36
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Nishino M, Choy JW, Gushwa NN, Oses-Prieto JA, Koupparis K, Burlingame AL, Renslo AR, McKerrow JH, Taunton J. Hypothemycin, a fungal natural product, identifies therapeutic targets in Trypanosoma brucei [corrected]. eLife 2013; 2:e00712. [PMID: 23853713 PMCID: PMC3707081 DOI: 10.7554/elife.00712] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 05/28/2013] [Indexed: 12/26/2022] Open
Abstract
Protein kinases are potentially attractive therapeutic targets for neglected parasitic diseases, including African trypanosomiasis caused by the protozoan, Trypanosoma brucei. How to prioritize T. brucei kinases and quantify their intracellular engagement by small-molecule inhibitors remain unsolved problems. Here, we combine chemoproteomics and RNA interference to interrogate trypanosome kinases bearing a Cys-Asp-Xaa-Gly motif (CDXG kinases). We discovered that hypothemycin, a fungal polyketide previously shown to covalently inactivate a subset of human CDXG kinases, kills T. brucei in culture and in infected mice. Quantitative chemoproteomic analysis with a hypothemycin-based probe revealed the relative sensitivity of endogenous CDXG kinases, including TbGSK3short and a previously uncharacterized kinase, TbCLK1. RNAi-mediated knockdown demonstrated that both kinases are essential, but only TbCLK1 is fully engaged by cytotoxic concentrations of hypothemycin in intact cells. Our study identifies TbCLK1 as a therapeutic target for African trypanosomiasis and establishes a new chemoproteomic tool for interrogating CDXG kinases in their native context. DOI:http://dx.doi.org/10.7554/eLife.00712.001 Human African trypanosomiasis—commonly known as sleeping sickness—is a debilitating and potentially fatal tropical disease that is widespread in sub-Saharan Africa. It is caused by the single-celled parasite Trypanosoma brucei, which is transmitted to humans by the bite of the tsetse fly. The infection takes its name from the disruption of the circadian clock that occurs early on in the disorder and leads to sleep disturbances. If left untreated, T. brucei infection leads to coma, organ failure and death. Most of the existing pharmaceutical treatments for sleeping sickness were developed more than 50 years ago. However, they are only weakly absorbed into the bloodstream—meaning that high doses must be used—and they lead to unpleasant side effects. Moreover, the T. brucei parasite is developing resistance to existing drugs, so further research is needed to identify new therapeutic targets. One promising option could be the parasite’s protein kinases. These enzymes, which add phosphate-based chemical groups to proteins, have a key role in regulating protein function and many of them are already being investigated as therapeutic targets for cancers and autoimmune diseases. T. brucei has 182 different kinases, suggesting a wealth of potential new targets. However, many of these are similar to human enzymes, and inhibiting the latter could lead to harmful side effects. Now, Nishino et al. have produced a synthetic version of a microbially derived kinase inhibitor, called hypothemycin, and have shown that it kills T. brucei cells grown in culture. Hypothemycin also killed T. brucei in infected mice, completely curing the infection in one third of animals, although high doses of the drug led to side effects. Using a chemical biology approach and quantitative mass spectrometry, Nishino et al. found that the main target of hypothemycin was a previously unknown kinase that is essential for T. brucei survival. Although hypothemycin itself is probably unsuitable as a treatment due to its lack of specificity, the work of Nishino et al. suggests that its kinase targets deserve further investigation. DOI:http://dx.doi.org/10.7554/eLife.00712.002
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Affiliation(s)
- Mari Nishino
- Tetrad Graduate Program , University of California, San Francisco , San Francisco , United States ; Center for Discovery and Innovation in Parasitic Diseases , University of California, San Francisco , San Francisco , United States
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37
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Abstract
There is an urgent need for the development of new antimalarial drugs with novel modes of actions. The malarial parasite, Plasmodium falciparum, has a relatively small kinome of <100 kinases, with many members exhibiting a high degree of structural divergence from their host counterparts. A number of Plasmodium kinases have recently been shown by reverse genetics to be essential for various parts of the complex parasitic life cycle, and are thus genetically validated as potential targets. Implementation of mass spectrometry-based phosphoproteomics approaches has informed on key phospho-signalling pathways in the parasite. In addition, global phenotypic screens have revealed a large number of putative protein kinase inhibitors with antimalarial potency. Taken together, these investigations point to the Plasmodium kinome as a rich source of potential new targets. In this review, we highlight recent progress made towards this goal.
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38
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Urbaniak MD, Martin DMA, Ferguson MAJ. Global quantitative SILAC phosphoproteomics reveals differential phosphorylation is widespread between the procyclic and bloodstream form lifecycle stages of Trypanosoma brucei. J Proteome Res 2013; 12:2233-44. [PMID: 23485197 PMCID: PMC3646404 DOI: 10.1021/pr400086y] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
We
report a global quantitative phosphoproteomic study of bloodstream
and procyclic form Trypanosoma brucei using SILAC
labeling of each lifecycle stage. Phosphopeptide enrichment by SCX
and TiO2 led to the identification of a total of 10096
phosphorylation sites on 2551 protein groups and quantified the ratios
of 8275 phosphorylation sites between the two lifecycle stages. More
than 9300 of these sites (92%) have not previously been reported.
Model-based gene enrichment analysis identified over representation
of Gene Ontology terms relating to the flagella, protein kinase activity,
and the regulation of gene expression. The quantitative data reveal
that differential protein phosphorylation is widespread between bloodstream
and procyclic form trypanosomes, with significant intraprotein differential
phosphorylation. Despite a lack of dedicated tyrosine kinases, 234
phosphotyrosine residues were identified, and these were 3–4
fold over-represented among site changing >10-fold between the
two lifecycle stages. A significant proportion of the T. brucei kinome was phosphorylated, with evidence that MAPK pathways are
functional in both lifecycle stages. Regulation of gene expression
in T. brucei is exclusively post-transcriptional,
and the extensive phosphorylation of RNA binding proteins observed
may be relevant to the control of mRNA stability in this organism.
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Affiliation(s)
- Michael D Urbaniak
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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39
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Lemeer S, Zörgiebel C, Ruprecht B, Kohl K, Kuster B. Comparing immobilized kinase inhibitors and covalent ATP probes for proteomic profiling of kinase expression and drug selectivity. J Proteome Res 2013; 12:1723-31. [PMID: 23495751 DOI: 10.1021/pr301073j] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Kinases are involved in the regulation of many cellular processes and aberrant kinase signaling has been implicated in human disease. As a consequence, kinases are attractive drug targets. Assessing kinase function and drug selectivity in a more physiological context is challenging and often hampered by the generally low expression level of kinases and the extensive post-translation modification in vivo. Kinase drug selectivity screens by chemical proteomics have gained attention because they allow the profiling of hundreds of kinases against one drug at the same time. Here, we directly compared two such methods, notably, immobilized broad spectrum kinase inhibitors (kinobeads) and active site labeling using desthiobiotin-ATP and -ADP probes. Affinity purification of ∼ 100 kinases by either kinobeads or ATP/ADP probes was readily achieved using 1 mg of cellular protein. Bioinformatic analysis revealed a high degree of complementarity of the two techniques. Kinobeads covered the Tyrosine Kinase family particularly well and ATP probes enriched higher numbers of STE family kinases. A consecutive combination of both enrichment strategies therefore allowed for the coverage of a larger part of the kinome than any one technique alone. While kinobeads are very selective for kinases, the ATP/ADP probes also enriched a large number of other nucleotide binding proteins. Both methods were applied to the selectivity profiling of the small molecular Aurora kinase inhibitor tozasertib in K562 cells. Our data confirmed Aurora A, B, and BCR-ABL as the main targets of tozasertib and identified TNK1, STK2, RPS6KA1, and RPS6KA3 as submicromolar off targets.
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Affiliation(s)
- Simone Lemeer
- Chair of Proteomics and Bioanalytics, Technische Universität München , Emil Erlenmeyer Forum 5, 85354 Freising, Germany
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40
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Lozano-Núñez A, Ikeda KN, Sauer T, de Graffenried CL. An analogue-sensitive approach identifies basal body rotation and flagellum attachment zone elongation as key functions of PLK in Trypanosoma brucei. Mol Biol Cell 2013; 24:1321-33. [PMID: 23447704 PMCID: PMC3639044 DOI: 10.1091/mbc.e12-12-0846] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The Polo-like kinase homologue in Trypanosoma brucei (TbPLK) regulates the assembly of a series of organelles necessary for positioning the parasite's flagellum. An analogue-sensitive strategy is used to acutely and specifically inhibit the kinase with a small molecule, making it possible to identify novel TbPLK functions. Polo-like kinases are important regulators of cell division, playing diverse roles in mitosis and cytoskeletal inheritance. In the parasite Trypanosoma brucei, the single PLK homologue TbPLK is necessary for the assembly of a series of essential organelles that position and adhere the flagellum to the cell surface. Previous work relied on RNA interference or inhibitors of undefined specificity to inhibit TbPLK, both of which have significant experimental limitations. Here we use an analogue-sensitive approach to selectively and acutely inhibit TbPLK. T. brucei cells expressing only analogue-sensitive TbPLK (TbPLKas) grow normally, but upon treatment with inhibitor develop defects in flagellar attachment and cytokinesis. TbPLK cannot migrate effectively when inhibited and remains trapped in the posterior of the cell throughout the cell cycle. Using synchronized cells, we show that active TbPLK is a direct requirement for the assembly and extension of the flagellum attachment zone, which adheres the flagellum to the cell surface, and for the rotation of the duplicated basal bodies, which positions the new flagellum so that it can extend without impinging on the old flagellum. This approach should be applicable to the many kinases found in the T. brucei genome that lack an ascribed function.
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Affiliation(s)
- Ana Lozano-Núñez
- Max F. Perutz Laboratories, Center for Molecular Biology, University of Vienna, 1030 Vienna, Austria
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41
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Koperniku A, Papanastasiou I, Foscolos GB, Tsotinis A, Taylor MC, Kelly JM. Synthesis and trypanocidal action of new adamantane substituted imidazolines. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00081h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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