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Moliner-Cubel S, Bahamontes-Rosa N, Rodriguez-Alejandre A, Nassau PM, Argyrou A, Bhardwaja A, Buxton RC, Calvo-Vicente D, Mouzon B, McDowell W, Mendoza-Losana A, Gomez-Lorenzo MG. Plasmodium RNA triphosphatase validation as antimalarial target. Int J Parasitol Drugs Drug Resist 2024; 25:100537. [PMID: 38810336 PMCID: PMC11157219 DOI: 10.1016/j.ijpddr.2024.100537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 02/23/2024] [Accepted: 04/04/2024] [Indexed: 05/31/2024]
Abstract
Target-based approaches have traditionally been used in the search for new anti-infective molecules. Target selection process, a critical step in Drug Discovery, identifies targets that are essential to establish or maintain the infection, tractable to be susceptible for inhibition, selective towards their human ortholog and amenable for large scale purification and high throughput screening. The work presented herein validates the Plasmodium falciparum mRNA 5' triphosphatase (PfPRT1), the first enzymatic step to cap parasite nuclear mRNAs, as a candidate target for the development of new antimalarial compounds. mRNA capping is essential to maintain the integrity and stability of the messengers, allowing their translation. PfPRT1 has been identified as a member of the tunnel, metal dependent mRNA 5' triphosphatase family which differs structurally and mechanistically from human metal independent mRNA 5' triphosphatase. In the present study the essentiality of PfPRT1 was confirmed and molecular biology tools and methods for target purification, enzymatic assessment and target engagement were developed, with the goal of running a future high throughput screening to discover PfPRT1 inhibitors.
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Affiliation(s)
- Sonia Moliner-Cubel
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Noemi Bahamontes-Rosa
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Ane Rodriguez-Alejandre
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Pamela M Nassau
- Department of Biological Sciences, GlaxoSmithKline, Stevenage, SG2 7NY, UK
| | - Argyrides Argyrou
- Department of Biological Sciences, GlaxoSmithKline, Stevenage, SG2 7NY, UK
| | - Anshu Bhardwaja
- Department of Biological Sciences, GlaxoSmithKline, Stevenage, SG2 7NY, UK
| | - Rachel C Buxton
- Department of Biological Sciences, GlaxoSmithKline, Stevenage, SG2 7NY, UK
| | - David Calvo-Vicente
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Bernadette Mouzon
- Department of Biological Sciences, GlaxoSmithKline, Stevenage, SG2 7NY, UK
| | - William McDowell
- Department of Biological Sciences, GlaxoSmithKline, Stevenage, SG2 7NY, UK
| | - Alfonso Mendoza-Losana
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Maria G Gomez-Lorenzo
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain.
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Kasprzyk R, Jemielity J. Enzymatic Assays to Explore Viral mRNA Capping Machinery. Chembiochem 2021; 22:3236-3253. [PMID: 34291555 PMCID: PMC8426721 DOI: 10.1002/cbic.202100291] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/21/2021] [Indexed: 12/25/2022]
Abstract
In eukaryotes, mRNA is modified by the addition of the 7-methylguanosine (m7 G) 5' cap to protect mRNA from premature degradation, thereby enhancing translation and enabling differentiation between self (endogenous) and non-self RNAs (e. g., viral ones). Viruses often develop their own mRNA capping pathways to augment the expression of their proteins and escape host innate immune response. Insights into this capping system may provide new ideas for therapeutic interventions and facilitate drug discovery, e. g., against viruses that cause pandemic outbreaks, such as beta-coronaviruses SARS-CoV (2002), MARS-CoV (2012), and the most recent SARS-CoV-2. Thus, proper methods for the screening of large compound libraries are required to identify lead structures that could serve as a basis for rational antiviral drug design. This review summarizes the methods that allow the monitoring of the activity and inhibition of enzymes involved in mRNA capping.
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Affiliation(s)
- Renata Kasprzyk
- Centre of New TechnologiesUniversity of WarsawBanacha 2c02-097WarsawPoland
- College of Inter-Faculty Individual Studies inMathematics and Natural SciencesUniversity of WarsawBanacha 2c02-097WarsawPoland
| | - Jacek Jemielity
- Centre of New TechnologiesUniversity of WarsawBanacha 2c02-097WarsawPoland
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Kasprzyk R, Fido M, Mamot A, Wanat P, Smietanski M, Kopcial M, Cowling VH, Kowalska J, Jemielity J. Direct High-Throughput Screening Assay for mRNA Cap Guanine-N7 Methyltransferase Activity. Chemistry 2020; 26:11266-11275. [PMID: 32259329 PMCID: PMC7262028 DOI: 10.1002/chem.202001036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/01/2020] [Indexed: 12/16/2022]
Abstract
In eukaryotes, mature mRNA is formed through modifications of precursor mRNA, one of which is 5' cap biosynthesis, involving RNA cap guanine-N7 methyltransferase (N7-MTase). N7-MTases are also encoded by some eukaryotic viruses and facilitate their replication. N7-MTase inhibitors have therapeutic potential, but their discovery is difficult because long RNA substrates are usually required for activity. Herein, we report a universal N7-MTase activity assay based on small-molecule fluorescent probes. We synthesized 12 fluorescent substrate analogues (GpppA and GpppG derivatives) varying in the dye type, dye attachment site, and linker length. GpppA labeled with pyrene at the 3'-O position of adenosine acted as an artificial substrate with the properties of a turn-off probe for all three tested N7-MTases (human, parasite, and viral). Using this compound, a N7-MTase inhibitor assay adaptable to high-throughput screening was developed and used to screen synthetic substrate analogues and a commercial library. Several inhibitors with nanomolar activities were identified.
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Affiliation(s)
- Renata Kasprzyk
- Centre of New TechnologiesUniversity of WarsawBanacha 2c02097WarsawPoland
- College of Inter-Faculty Individual Studies in Mathematics and Natural SciencesUniversity of WarsawBanacha 2c02097WarsawPoland
| | - Mateusz Fido
- Division of BiophysicsInstitute of Experimental PhysicsFaculty of PhysicsUniversity of WarsawPasteura 502093WarsawPoland
| | - Adam Mamot
- Division of BiophysicsInstitute of Experimental PhysicsFaculty of PhysicsUniversity of WarsawPasteura 502093WarsawPoland
| | - Przemyslaw Wanat
- Division of BiophysicsInstitute of Experimental PhysicsFaculty of PhysicsUniversity of WarsawPasteura 502093WarsawPoland
| | | | - Michal Kopcial
- Centre of New TechnologiesUniversity of WarsawBanacha 2c02097WarsawPoland
- College of Inter-Faculty Individual Studies in Mathematics and Natural SciencesUniversity of WarsawBanacha 2c02097WarsawPoland
| | - Victoria H. Cowling
- Centre of Gene Regulation and ExpressionSchool of Life SciencesUniversity of DundeeDD1 5EHDundeeUK
| | - Joanna Kowalska
- Division of BiophysicsInstitute of Experimental PhysicsFaculty of PhysicsUniversity of WarsawPasteura 502093WarsawPoland
| | - Jacek Jemielity
- Centre of New TechnologiesUniversity of WarsawBanacha 2c02097WarsawPoland
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Khawaja X, Dunlop J, Kowal D. Scintillation proximity assay in lead discovery. Expert Opin Drug Discov 2013; 3:1267-80. [PMID: 23496165 DOI: 10.1517/17460441.3.11.1267] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Scintillation proximity assay (SPA) is a homogeneous scintillant bead-based platform for the measurement of biological processes and plays an important role in the identification of active chemical entities in drug discovery. OBJECTIVE The design and development of solid-phase SPA approaches are examined and compared with alternative non-radiometric fluorescence-based technologies. METHODS This review provides background on the principle of SPA and its application to biomolecular interactions from a variety of biological sources. CONCLUSION The SPA approach is well suited to the demands of commercial high volume automation and assay miniaturization for target-based high-throughput screening campaigns on synthetic and natural product libraries as well as for benchtop characterization and confirmation studies. In the near future, innovations in the way SPA and fluorescence-based screening strategies are multiplexed will improve our comprehensive understanding of cellular system biology and dramatically advance the lead discovery process for the treatment of complex target-related disorders.
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Affiliation(s)
- Xavier Khawaja
- Depression and Anxiety, Neuroscience Discovery Research, Wyeth Research, Princeton, NJ 08543, USA +1 732 274 4382 ; +1 732 274 4020 ;
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Antczak C, Shum D, Radu C, Seshan VE, Djaballah H. Development and validation of a high-density fluorescence polarization-based assay for the trypanosoma RNA triphosphatase TbCet1. Comb Chem High Throughput Screen 2009; 12:258-68. [PMID: 19275531 DOI: 10.2174/138620709787581729] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
RNA triphosphatases are attractive and mostly unexplored therapeutic targets for the development of broad spectrum antiprotozoal, antiviral and antifungal agents. The use of malachite green as a readout for phosphatases is well characterized and widely employed. However, the reaction depends on high quantities of inorganic phosphate to be generated, which makes this assay not easily amenable to screening in 1536-well format. The overly long reading times required also prohibit its use to screen large chemical libraries. To overcome these limitations, we sought to develop a fluorescence polarization (FP) -based assay for triphosphatases, compatible with miniaturization and fast readouts. For this purpose, we took advantage of the nucleoside triphosphatase activity of this class of enzyme to successfully adapt the Transcreener ADP assay based on the detection of generated ADP by immunocompetition fluorescence polarization to the RNA triphosphatase TbCet1 in 1536-well format. We also tested the performance of this newly developed assay in a pilot screen of 3,000 compounds and we confirmed the activity of the obtained hits. We present and discuss our findings and their importance for the discovery of novel drugs by high throughput screening.
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Affiliation(s)
- Christophe Antczak
- High Throughput Screening Core Facility, Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
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Baker MR, Zarubica T, Wright HT, Rife JP. Scintillation proximity assay for measurement of RNA methylation. Nucleic Acids Res 2009; 37:e32. [PMID: 19181706 PMCID: PMC2651799 DOI: 10.1093/nar/gkn1038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Methylation of RNA by methyltransferases is a phylogenetically ubiquitous post-transcriptional modification that occurs most extensively in transfer RNA (tRNA) and ribosomal RNA (rRNA). Biochemical characterization of RNA methyltransferase enzymes and their methylated product RNA or RNA–protein complexes is usually done by measuring the incorporation of radiolabeled methyl groups into the product over time. This has traditionally required the separation of radiolabeled product from radiolabeled methyl donor through a filter binding assay. We have adapted and optimized a scintillation proximity assay (SPA) to replace the more costly, wasteful and cumbersome filter binding assay and demonstrate its utility in studies of three distinct methyltransferases, RmtA, KsgA and ErmC’. In vitro, RmtA and KsgA methylate different bases in 16S rRNA in 30S ribosomal particles, while ErmC’ most efficiently methylates protein-depleted or protein-free 23S rRNA. This assay does not utilize engineered affinity tags that are often required in SPA, and is capable of detecting either radiolabeled RNA or RNA–protein complex. We show that this method is suitable for quantitating extent of RNA methylation or active RNA methyltransferase, and for testing RNA-methyltransferase inhibitors. This assay can be carried out with techniques routinely used in a typical biochemistry laboratory or could be easily adapted for a high throughput screening format.
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Affiliation(s)
- Matthew R Baker
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298-0133, USA
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