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Warminski M, Grab K, Szczepanski K, Spiewla T, Zuberek J, Kowalska J, Jemielity J. Photoactivatable mRNA 5' Cap Analogs for RNA-Protein Crosslinking. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400994. [PMID: 39049186 DOI: 10.1002/advs.202400994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 06/04/2024] [Indexed: 07/27/2024]
Abstract
Chemical modification of messenger RNA (mRNA) has paved the way for advancing mRNA-based therapeutics. The intricate process of mRNA translation in eukaryotes is orchestrated by numerous proteins involved in complex interaction networks. Many of them bind specifically to a unique structure at the mRNA 5'-end, called 5'-cap. Depending on the 5'-terminal sequence and its methylation pattern, different proteins may be involved in the translation initiation and regulation, but a deeper understanding of these mechanisms requires specialized molecular tools to identify natural binders of mRNA 5'-end variants. Here, a series of 8 new synthetic 5'-cap analogs that allow the preparation of RNA molecules with photoreactive tags using a standard in vitro transcription reaction are reported. Two photoreactive tags and four different modification sites are selected to minimize potential interference with cap-protein contacts and to provide complementary properties regarding crosslinking chemistry and molecular interactions. The tailored modification strategy allows for the generation of specific crosslinks with model cap-binding proteins, such as eIF4E and Dcp2. The usefulness of the photoreactive cap analogs is also demonstrated for identifying the cap-binding subunit in a multi-protein complex, which makes them perfect candidates for further development of photoaffinity labeling probes to study more complex mRNA-related processes.
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Affiliation(s)
- Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
| | - Katarzyna Grab
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
- Doctoral School of Exact and Natural Sciences, University of Warsaw, Zwirki i Wigury 93, Warsaw, 02-089, Poland
| | - Kacper Szczepanski
- Doctoral School of Exact and Natural Sciences, University of Warsaw, Zwirki i Wigury 93, Warsaw, 02-089, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, 02-097, Poland
| | - Tomasz Spiewla
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
- Doctoral School of Exact and Natural Sciences, University of Warsaw, Zwirki i Wigury 93, Warsaw, 02-089, Poland
| | - Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, 02-097, Poland
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Sahoo AK, Augusthian PD, Muralitharan I, Vivek-Ananth RP, Kumar K, Kumar G, Ranganathan G, Samal A. In silico identification of potential inhibitors of vital monkeypox virus proteins from FDA approved drugs. Mol Divers 2023; 27:2169-2184. [PMID: 36331784 PMCID: PMC9638297 DOI: 10.1007/s11030-022-10550-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
The World Health Organization (WHO) recently declared the monkeypox outbreak 'A public health emergency of international concern'. The monkeypox virus belongs to the same Orthopoxvirus genus as smallpox. Although smallpox drugs are recommended for use against monkeypox, monkeypox-specific drugs are not yet available. Drug repurposing is a viable and efficient approach in the face of such an outbreak. Therefore, we present a computational drug repurposing study to identify the existing approved drugs which can be potential inhibitors of vital monkeypox virus proteins, thymidylate kinase and D9 decapping enzyme. The target protein structures of the monkeypox virus were modelled using the corresponding protein structures in the vaccinia virus. We identified four potential inhibitors namely, Tipranavir, Cefiderocol, Doxorubicin, and Dolutegravir as candidates for repurposing against monkeypox virus from a library of US FDA approved antiviral and antibiotic drugs using molecular docking and molecular dynamics simulations. The main goal of this in silico study is to identify potential inhibitors against monkeypox virus proteins that can be further experimentally validated for the discovery of novel therapeutic agents against monkeypox disease.
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Affiliation(s)
- Ajaya Kumar Sahoo
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India
| | | | | | - R P Vivek-Ananth
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India
| | - Kishan Kumar
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
| | - Gaurav Kumar
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
| | | | - Areejit Samal
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India.
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India.
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