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Wojtczak BA, Bednarczyk M, Sikorski PJ, Wojtczak A, Surynt P, Kowalska J, Jemielity J. Synthesis and Evaluation of Diguanosine Cap Analogs Modified at the C8-Position by Suzuki-Miyaura Cross-Coupling: Discovery of 7-Methylguanosine-Based Molecular Rotors. J Org Chem 2023. [PMID: 37209102 DOI: 10.1021/acs.joc.3c00126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Chemical modifications of the mRNA cap structure can enhance the stability, translational properties, and half-life of mRNAs, thereby altering the therapeutic properties of synthetic mRNA. However, cap structure modification is challenging because of the instability of the 5'-5'-triphosphate bridge and N7-methylguanosine. The Suzuki-Miyaura cross-coupling reaction between boronic acid and halogen compound is a mild, convenient, and potentially applicable approach for modifying biomolecules. Herein, we describe two methods to synthesize C8-modified cap structures using the Suzuki-Miyaura cross-coupling reaction. Both methods employed phosphorimidazolide chemistry to form the 5',5'-triphosphate bridge. However, in the first method, the introduction of the modification via the Suzuki-Miyaura cross-coupling reaction at the C8 position occurs postsynthetically, at the dinucleotide level, whereas in the second method, the modification was introduced at the level of the nucleoside 5'-monophosphate, and later, the triphosphate bridge was formed. Both methods were successfully applied to incorporate six different groups (methyl, cyclopropyl, phenyl, 4-dimethylaminophenyl, 4-cyanophenyl, and 1-pyrene) into either the m7G or G moieties of the cap structure. Aromatic substituents at the C8-position of guanosine form a push-pull system that exhibits environment-sensitive fluorescence. We demonstrated that this phenomenon can be harnessed to study the interaction with cap-binding proteins, e.g., eIF4E, DcpS, Nudt16, and snurportin.
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Affiliation(s)
- Blazej A Wojtczak
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
| | - Marcelina Bednarczyk
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093, Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
| | - Anna Wojtczak
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093, Warsaw, Poland
| | - Piotr Surynt
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093, Warsaw, Poland
| | - Joanna Kowalska
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
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2
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Bednarczyk M, Peters JK, Kasprzyk R, Starek J, Warminski M, Spiewla T, Mugridge JS, Gross JD, Jemielity J, Kowalska J. Fluorescence-Based Activity Screening Assay Reveals Small Molecule Inhibitors of Vaccinia Virus mRNA Decapping Enzyme D9. ACS Chem Biol 2022; 17:1460-1471. [PMID: 35576528 PMCID: PMC9207806 DOI: 10.1021/acschembio.2c00049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Vaccinia virus (VACV) represents a family of poxviruses, which possess their own decapping machinery as a part of their strategy to eliminate host mRNAs and evade the innate immune response. D9 is one of the two encoded VACV decapping enzymes that is responsible for cap removal from the 5' end of both host mRNA transcripts and viral double-stranded RNAs. Little is known about the structural requirements for D9 inhibition by small molecules. Here, we identified a minimal D9 substrate and used it to develop a real-time fluorescence assay for inhibitor discovery and characterization. We screened a panel of nucleotide-derived substrate analogues and pharmacologically active candidates to identify several compounds with nano- and low micromolar IC50 values. m7GpppCH2p was the most potent nucleotide inhibitor (IC50 ∼ 0.08 μM), and seliciclib and CP-100356 were the most potent drug-like compounds (IC50 0.57 and 2.7 μM, respectively). The hits identified through screening inhibited D9-catalyzed decapping of 26 nt RNA substrates but were not active toward VACV D10 or human decapping enzyme, Dcp1/2. The inhibition mode for one of the compounds (CP-100356) was elucidated based on the X-ray cocrystal structure, opening the possibility for structure-based design of novel D9 inhibitors and binding probes.
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Affiliation(s)
- Marcelina Bednarczyk
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland
| | - Jessica K. Peters
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland
| | - Jagoda Starek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
| | - Tomasz Spiewla
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
| | - Jeffrey S. Mugridge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - John D. Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
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3
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Kubacka D, Kozarski M, Baranowski MR, Wojcik R, Panecka-Hofman J, Strzelecka D, Basquin J, Jemielity J, Kowalska J. Substrate-Based Design of Cytosolic Nucleotidase IIIB Inhibitors and Structural Insights into Inhibition Mechanism. Pharmaceuticals (Basel) 2022; 15:ph15050554. [PMID: 35631380 PMCID: PMC9144445 DOI: 10.3390/ph15050554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/26/2022] Open
Abstract
Cytosolic nucleotidases (cNs) catalyze dephosphorylation of nucleoside 5’-monophosphates and thereby contribute to the regulation of nucleotide levels in cells. cNs have also been shown to dephosphorylate several therapeutically relevant nucleotide analogues. cN-IIIB has shown in vitro a distinctive activity towards 7-mehtylguanosine monophosphate (m7GMP), which is one key metabolites of mRNA cap. Consequently, it has been proposed that cN-IIIB participates in mRNA cap turnover and prevents undesired accumulation and salvage of m7GMP. Here, we sought to develop molecular tools enabling more advanced studies on the cellular role of cN-IIIB. To that end, we performed substrate and inhibitor property profiling using a library of 41 substrate analogs. The most potent hit compounds (identified among m7GMP analogs) were used as a starting point for structure–activity relationship studies. As a result, we identified several 7-benzylguanosine 5’-monophosphate (Bn7GMP) derivatives as potent, unhydrolyzable cN-IIIB inhibitors. The mechanism of inhibition was elucidated using X-ray crystallography and molecular docking. Finally, we showed that compounds that potently inhibit recombinant cN-IIIB have the ability to inhibit m7GMP decay in cell lysates.
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Affiliation(s)
- Dorota Kubacka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (D.K.); (M.K.); (M.R.B.); (J.P.-H.); (D.S.)
| | - Mateusz Kozarski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (D.K.); (M.K.); (M.R.B.); (J.P.-H.); (D.S.)
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland;
| | - Marek R. Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (D.K.); (M.K.); (M.R.B.); (J.P.-H.); (D.S.)
| | - Radoslaw Wojcik
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland;
| | - Joanna Panecka-Hofman
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (D.K.); (M.K.); (M.R.B.); (J.P.-H.); (D.S.)
| | - Dominika Strzelecka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (D.K.); (M.K.); (M.R.B.); (J.P.-H.); (D.S.)
| | - Jerome Basquin
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany;
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland;
- Correspondence: (J.J.); (J.K.); Tel.: +4822-5543-774
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (D.K.); (M.K.); (M.R.B.); (J.P.-H.); (D.S.)
- Correspondence: (J.J.); (J.K.); Tel.: +4822-5543-774
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4
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Wojcik R, Baranowski MR, Markiewicz L, Kubacka D, Bednarczyk M, Baran N, Wojtczak A, Sikorski PJ, Zuberek J, Kowalska J, Jemielity J. Novel N7-Arylmethyl Substituted Dinucleotide mRNA 5' cap Analogs: Synthesis and Evaluation as Modulators of Translation. Pharmaceutics 2021; 13:pharmaceutics13111941. [PMID: 34834356 PMCID: PMC8623273 DOI: 10.3390/pharmaceutics13111941] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
Dinucleotide analogs of the messenger RNA cap (m7GpppN) are useful research tools and have potential applications as translational inhibitors or reagents for modification of in vitro transcribed mRNAs. It has been previously reported that replacing the methyl group at the N7-position with benzyl (Bn) produces a dinucleotide cap with superior properties. Here, we followed up on this finding by synthesizing 17 novel Bn7GpppG analogs and determining their structure-activity relationship regarding translation and translational inhibition. The compounds were prepared in two steps, including selective N7-alkylation of guanosine 5'-monophosphate by arylmethyl bromide followed by coupling with imidazole-activated GDP, with total yields varying from 22% to 62%. The compounds were then evaluated by determining their affinity for eukaryotic translation initiation factor 4E (eIF4E), testing their susceptibility to decapping pyrophosphatase, DcpS-which is most likely the major cellular enzyme targeting this type of compound-and determining their translation inhibitory properties in vitro. We also synthesized mRNAs capped with the evaluated compounds and tested their translational properties in A549 cells. Our studies identified N7-(4-halogenbenzyl) substituents as promising modifications in the contexts of either mRNA translation or translational inhibition. Finally, to gain more insight into the consequences at the molecular level of N7-benzylation of the mRNA cap, we determined the crystal structures of three compounds with eIF4E.
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Affiliation(s)
- Radoslaw Wojcik
- Centre of New Technologies, University of Warsaw, 02097 Warsaw, Poland; (R.W.); (L.M.); (M.B.); (N.B.); (P.J.S.)
| | - Marek R. Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02093 Warsaw, Poland; (M.R.B.); (D.K.); (A.W.); (J.Z.)
| | - Lukasz Markiewicz
- Centre of New Technologies, University of Warsaw, 02097 Warsaw, Poland; (R.W.); (L.M.); (M.B.); (N.B.); (P.J.S.)
| | - Dorota Kubacka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02093 Warsaw, Poland; (M.R.B.); (D.K.); (A.W.); (J.Z.)
| | - Marcelina Bednarczyk
- Centre of New Technologies, University of Warsaw, 02097 Warsaw, Poland; (R.W.); (L.M.); (M.B.); (N.B.); (P.J.S.)
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02093 Warsaw, Poland; (M.R.B.); (D.K.); (A.W.); (J.Z.)
| | - Natalia Baran
- Centre of New Technologies, University of Warsaw, 02097 Warsaw, Poland; (R.W.); (L.M.); (M.B.); (N.B.); (P.J.S.)
| | - Anna Wojtczak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02093 Warsaw, Poland; (M.R.B.); (D.K.); (A.W.); (J.Z.)
| | - Pawel J. Sikorski
- Centre of New Technologies, University of Warsaw, 02097 Warsaw, Poland; (R.W.); (L.M.); (M.B.); (N.B.); (P.J.S.)
| | - Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02093 Warsaw, Poland; (M.R.B.); (D.K.); (A.W.); (J.Z.)
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02093 Warsaw, Poland; (M.R.B.); (D.K.); (A.W.); (J.Z.)
- Correspondence: (J.K.); (J.J.)
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02097 Warsaw, Poland; (R.W.); (L.M.); (M.B.); (N.B.); (P.J.S.)
- Correspondence: (J.K.); (J.J.)
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5
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Kleczewska N, Sikorski PJ, Warminska Z, Markiewicz L, Kasprzyk R, Baran N, Kwapiszewska K, Karpinska A, Michalski J, Holyst R, Kowalska J, Jemielity J. Cellular delivery of dinucleotides by conjugation with small molecules: targeting translation initiation for anticancer applications. Chem Sci 2021; 12:10242-10251. [PMID: 34377411 PMCID: PMC8336483 DOI: 10.1039/d1sc02143e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/29/2021] [Indexed: 12/15/2022] Open
Abstract
Targeting cap-dependent translation initiation is one of the experimental approaches that could lead to the development of novel anti-cancer therapies. Synthetic dinucleoside 5',5'-triphosphates cap analogs are potent antagonists of eukaryotic translation initiation factor 4E (eIF4E) in vitro and could counteract elevated levels of eIF4E in cancer cells; however, transformation of these compounds into therapeutic agents remains challenging - they do not easily penetrate into cells and are susceptible to enzymatic cleavage. Here, we tested the potential of several small molecule ligands - folic acid, biotin, glucose, and cholesterol - to deliver both hydrolyzable and cleavage-resistant cap analogs into cells. A broad structure-activity relationship (SAR) study using model fluorescent probes and cap-ligand conjugates showed that cholesterol greatly facilitates uptake of cap analogs without disturbing the interactions with eIF4E. The most potent cholesterol conjugate identified showed apoptosis-mediated cytotoxicity towards cancer cells.
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Affiliation(s)
- Natalia Kleczewska
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Zofia Warminska
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Lukasz Markiewicz
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Renata Kasprzyk
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw Banacha 2c 02-097 Warsaw Poland
- Division of Biophysics Institute of Experimental Physics, Faculty of Physics University of Warsaw Pasteura 5 02-093 Warsaw Poland
| | - Natalia Baran
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
- Faculty of Biology University of Warsaw I. Miecznikowa 1 02-096 Warsaw Poland
| | - Karina Kwapiszewska
- Institute of Physical Chemistry Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | - Aneta Karpinska
- Institute of Physical Chemistry Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | - Jaroslaw Michalski
- Institute of Physical Chemistry Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | - Robert Holyst
- Institute of Physical Chemistry Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | - Joanna Kowalska
- Division of Biophysics Institute of Experimental Physics, Faculty of Physics University of Warsaw Pasteura 5 02-093 Warsaw Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
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6
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Evaluation of carboxyfluorescein-labeled 7-methylguanine nucleotides as probes for studying cap-binding proteins by fluorescence anisotropy. Sci Rep 2021; 11:7687. [PMID: 33833335 PMCID: PMC8032668 DOI: 10.1038/s41598-021-87306-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/26/2021] [Indexed: 11/17/2022] Open
Abstract
Fluorescence anisotropy (FA) is a powerful technique for the discovery of protein inhibitors in a high-throughput manner. In this study, we sought to develop new universal FA-based assays for the evaluation of compounds targeting mRNA 5′ cap-binding proteins of therapeutic interest, including eukaryotic translation initiation factor 4E and scavenger decapping enzyme. For this purpose, a library of 19 carboxyfluorescein probes based on 7-methylguanine nucleotides was evaluated as FA probes for these proteins. Optimal probe:protein systems were further investigated in competitive binding experiments and adapted for high-throughput screening. Using a small in-house library of compounds, we verified and confirmed the accuracy of the developed FA assay to study cap-binding protein binders. The applications of the most promising probes were then extended to include evaluation of allosteric inhibitors as well as RNA ligands. From this analysis, we confirmed the utility of the method to study small molecule ligands and evaluate differently 5′ capped RNAs.
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7
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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] [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 Technologies, University of Warsaw, Banacha 2c, 02097, Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02097, Warsaw, Poland
| | - Mateusz Fido
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02093, Warsaw, Poland
| | - Adam Mamot
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02093, Warsaw, Poland
| | - Przemyslaw Wanat
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02093, Warsaw, Poland
| | - Miroslaw Smietanski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02097, Warsaw, Poland
| | - Michal Kopcial
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02097, Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02097, Warsaw, Poland
| | - Victoria H Cowling
- Centre of Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02093, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02097, Warsaw, Poland
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8
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Golojuch S, Kopcial M, Strzelecka D, Kasprzyk R, Baran N, Sikorski PJ, Kowalska J, Jemielity J. Exploring tryptamine conjugates as pronucleotides of phosphate-modified 7-methylguanine nucleotides targeting cap-dependent translation. Bioorg Med Chem 2020; 28:115523. [PMID: 32362385 DOI: 10.1016/j.bmc.2020.115523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/23/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022]
Abstract
Eukaryotic translation initiation factor 4E (eIF4E) is overexpressed in many cancers deregulating translational control of the cell cycle. mRNA 5' cap analogs targeting eIF4E are small molecules with the potential to counteract elevated levels of eIF4E in cancer cells. However, the practical utility of typical cap analogs is limited because of their reduced cell membrane permeability. Transforming the active analogs into their pronucleotide derivatives is a promising approach to overcome this obstacle. 7-Benzylguanosine monophosphate (bn7GMP) is a cap analog that has been successfully transformed into a cell-penetrating pronucleotide by conjugation of the phosphate moiety with tryptamine. In this work, we explored whether a similar strategy is applicable to other cap analogs, particularly phosphate-modified 7-methylguanine nucleotides. We report the synthesis of six new tryptamine conjugates containing N7-methylguanosine mono- and diphosphate and their analogs modified with thiophosphate moiety. These new potential pronucleotides and the expected products of their activation were characterized by biophysical and biochemical methods to determine their affinity towards eIF4E, their ability to inhibit translation in vitro, their susceptibility to enzymatic degradation and their turnover in cell extract. The results suggest that compounds containing the thiophosphate moiety may act as pronucleotides that release low but sustainable concentrations of 7-methylguanosine 5'-phosphorothioate (m7GMPS), which is a translation inhibitor with in vitro potency higher than bn7GMP.
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Affiliation(s)
- Sebastian Golojuch
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland; Faculty of Chemistry, University of Warsaw, L. Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kopcial
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland; Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland; College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Dominika Strzelecka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland; Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland; College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Natalia Baran
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland; Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland.
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland.
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9
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Kopcial M, Wojtczak BA, Kasprzyk R, Kowalska J, Jemielity J. N1-Propargylguanosine Modified mRNA Cap Analogs: Synthesis, Reactivity, and Applications to the Study of Cap-Binding Proteins. Molecules 2019; 24:molecules24101899. [PMID: 31108861 PMCID: PMC6572376 DOI: 10.3390/molecules24101899] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 01/07/2023] Open
Abstract
The mRNA 5′ cap consists of N7-methylguanosine bound by a 5′,5′-triphosphate bridge to the first nucleotide of the transcript. The cap interacts with various specific proteins and participates in all key mRNA-related processes, which may be of therapeutic relevance. There is a growing demand for new biophysical and biochemical methods to study cap–protein interactions and identify the factors which inhibit them. The development of such methods can be aided by the use of properly designed fluorescent molecular probes. Herein, we synthesized a new class of m7Gp3G cap derivatives modified with an alkyne handle at the N1-position of guanosine and, using alkyne-azide cycloaddition, we functionalized them with fluorescent tags to obtain potential probes. The cap derivatives and probes were evaluated in the context of two cap-binding proteins, eukaryotic translation initiation factor (eIF4E) and decapping scavenger (DcpS). Biochemical and biophysical studies revealed that N1-propargyl moiety did not significantly disturb cap–protein interaction. The fluorescent properties of the probes turned out to be in line with microscale thermophoresis (MST)-based binding assays.
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Affiliation(s)
- Michal Kopcial
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland.
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland.
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093 Warsaw, Poland.
| | - Blazej A Wojtczak
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland.
| | - Renata Kasprzyk
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland.
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland.
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093 Warsaw, Poland.
| | - Joanna Kowalska
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093 Warsaw, Poland.
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland.
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