1
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Fleuti M, Sanchez-Quirante T, Poštová Slavětínská L, Tloušt'ová E, Tichý M, Gurská S, Džubák P, Hajdúch M, Hocek M. Synthesis and Biological Profiling of Quinolino-Fused 7-Deazapurine Nucleosides. ACS OMEGA 2024; 9:20557-20570. [PMID: 38737052 PMCID: PMC11080019 DOI: 10.1021/acsomega.4c02031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 05/14/2024]
Abstract
A series of quinolino-fused 7-deazapurine (pyrimido[5',4':4,5]pyrrolo[3,2-f]quinoline) ribonucleosides were designed and synthesized. The synthesis of the key 11-chloro-pyrimido[5',4':4,5]pyrrolo[3,2-f]quinoline was based on the Negishi cross-coupling of iodoquinoline with zincated 4,6-dichloropyrimidine followed by azidation and thermal or photochemical cyclization. Vorbrüggen glycosylation of the tetracyclic heterocycle followed by cross-coupling or substitution reactions at position 11 gave the desired set of final nucleosides that showed moderate to weak cytostatic activity and fluorescent properties. The corresponding fused adenosine derivative was converted to the triphosphate and successfully incorporated to RNA using in vitro transcription with T7 RNA polymerase.
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Affiliation(s)
- Marianne Fleuti
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague 2 CZ-12843, Czech Republic
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 CZ-16610, Czech Republic
| | - Tania Sanchez-Quirante
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague 2 CZ-12843, Czech Republic
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 CZ-16610, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 CZ-16610, Czech Republic
| | - Eva Tloušt'ová
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 CZ-16610, Czech Republic
| | - Michal Tichý
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 CZ-16610, Czech Republic
| | - Soňa Gurská
- Institute
of Molecular and Translational Medicine, Palacky University and University
Hospital in Olomouc, Faculty of Medicine and Dentistry, Hněvotínská
5, Olomouc CZ-77515, Czech Republic
| | - Petr Džubák
- Institute
of Molecular and Translational Medicine, Palacky University and University
Hospital in Olomouc, Faculty of Medicine and Dentistry, Hněvotínská
5, Olomouc CZ-77515, Czech Republic
| | - Marián Hajdúch
- Institute
of Molecular and Translational Medicine, Palacky University and University
Hospital in Olomouc, Faculty of Medicine and Dentistry, Hněvotínská
5, Olomouc CZ-77515, Czech Republic
| | - Michal Hocek
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague 2 CZ-12843, Czech Republic
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 CZ-16610, Czech Republic
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2
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Brunderová M, Havlíček V, Matyašovský J, Pohl R, Poštová Slavětínská L, Krömer M, Hocek M. Expedient production of site specifically nucleobase-labelled or hypermodified RNA with engineered thermophilic DNA polymerases. Nat Commun 2024; 15:3054. [PMID: 38594306 PMCID: PMC11004144 DOI: 10.1038/s41467-024-47444-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 03/26/2024] [Indexed: 04/11/2024] Open
Abstract
Innovative approaches to controlled nucleobase-modified RNA synthesis are urgently needed to support RNA biology exploration and to synthesize potential RNA therapeutics. Here we present a strategy for enzymatic construction of nucleobase-modified RNA based on primer-dependent engineered thermophilic DNA polymerases - SFM4-3 and TGK. We demonstrate introduction of one or several different base-modified nucleotides in one strand including hypermodified RNA containing all four modified nucleotides bearing four different substituents, as well as strategy for primer segment removal. We also show facile site-specific or segmented introduction of fluorophores or other functional groups at defined positions in variety of RNA molecules, including structured or long mRNA. Intriguing translation efficacy of single-site modified mRNAs underscores the necessity to study isolated modifications placed at designer positions to disentangle their biological effects and enable development of improved mRNA therapeutics. Our toolbox paves the way for more precise dissecting RNA structures and functions, as well as for construction of diverse types of base-functionalized RNA for therapeutic applications and diagnostics.
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Affiliation(s)
- Mária Brunderová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague, 2, Czech Republic
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Vojtěch Havlíček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague, 2, Czech Republic
| | - Ján Matyašovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
| | - Matouš Krömer
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic.
- The Rosalind Franklin Institute, Harwell Campus, Didcot, Oxfordshire, UK.
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic.
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague, 2, Czech Republic.
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3
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Khatik SY, Roy S, Srivatsan SG. Synthesis and Enzymatic Incorporation of a Dual-App Nucleotide Probe That Reports Antibiotics-Induced Conformational Change in the Bacterial Ribosomal Decoding Site RNA. ACS Chem Biol 2024; 19:687-695. [PMID: 38407057 DOI: 10.1021/acschembio.3c00676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Natural nucleosides are nonfluorescent and do not have intrinsic labels that can be readily utilized for analyzing nucleic acid structure and recognition. In this regard, researchers typically use the so-called "one-label, one-technique" approach to study nucleic acids. However, we envisioned that a responsive dual-app nucleoside system that harnesses the power of two complementing biophysical techniques namely, fluorescence and 19F NMR, will allow the investigation of nucleic acid conformations more comprehensively than before. We recently introduced a nucleoside analogue by tagging trifluoromethyl-benzofuran at the C5 position of 2'-deoxyuridine, which serves as an excellent fluorescent and 19F NMR probe to study G-quadruplex and i-motif structures. Taking forward, here, we report the development of a ribonucleotide version of the dual-app probe to monitor antibiotics-induced conformational changes in RNA. The ribonucleotide analog is derived by conjugating trifluoromethyl-benzofuran at the C5 position of uridine (TFBF-UTP). The analog is efficiently incorporated by T7 RNA polymerase to produce functionalized RNA transcripts. Detailed photophysical and 19F NMR of the nucleoside and nucleotide incorporated into RNA oligonucleotides revealed that the analog is structurally minimally invasive and can be used for probing RNA conformations by fluorescence and 19F NMR techniques. Using the probe, we monitored and estimated aminoglycoside antibiotics binding to the bacterial ribosomal decoding site RNA (A-site, a very important RNA target). While 2-aminopurine, a famous fluorescent nucleic acid probe, fails to detect structurally similar aminoglycoside antibiotics binding to the A-site, our probe reports the binding of different aminoglycosides to the A-site. Taken together, our results demonstrate that TFBF-UTP is a very useful addition to the nucleic acid analysis toolbox and could be used to devise discovery platforms to identify new RNA binders of therapeutic potential.
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Affiliation(s)
- Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Sarupa Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
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4
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Pawlowska R, Graczyk A, Radzikowska-Cieciura E, Wielgus E, Madaj R, Chworos A. Substrate Specificity of T7 RNA Polymerase toward Hypophosphoric Analogues of ATP. ACS OMEGA 2024; 9:9348-9356. [PMID: 38434886 PMCID: PMC10905585 DOI: 10.1021/acsomega.3c08635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/10/2024] [Accepted: 01/29/2024] [Indexed: 03/05/2024]
Abstract
Modified nucleotides are commonly used in molecular biology as substrates or inhibitors for several enzymes but also as tools for the synthesis of modified DNA and RNA fragments. Introduction of modification into RNA, such as phosphorothioate (PS), has been demonstrated to provide higher stability, more effective transport, and enhanced activity of potential therapeutic molecules. Hence, in order to achieve widespread use of RNA molecules in medicine, it is crucial to continuously refine the techniques that enable the effective introduction of modifications into RNA strands. Numerous analogues of nucleotides have been tested for their substrate activity with the T7 RNA polymerase and therefore in the context of their utility for use in in vitro transcription. In the present studies, the substrate preferences of the T7 RNA polymerase toward β,γ-hypophospho-modified ATP derivatives for the synthesis of unmodified RNA and phosphorothioate RNA (PS) are presented. The performed studies revealed the stereoselectivity of this enzyme for α-thio-β,γ-hypo-ATP derivatives, similar to that for α-thio-ATP. Additionally, it is demonstrated herein that hypodiphosphoric acid may inhibit in vitro transcription catalyzed by T7 RNA polymerase.
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Affiliation(s)
- Roza Pawlowska
- Department
of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Anna Graczyk
- Department
of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Ewa Radzikowska-Cieciura
- Department
of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Ewelina Wielgus
- Department
of Structural Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Rafal Madaj
- Department
of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Arkadiusz Chworos
- Department
of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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5
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Bassi T, Hirlinger A, Grayson L, Vantourout J, Toor N. Fluorescent labeling of RNA and DNA on the Hoogsteen edge using sulfinate chemistry. RNA (NEW YORK, N.Y.) 2023; 29:1437-1451. [PMID: 37277186 PMCID: PMC10573292 DOI: 10.1261/rna.079679.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/12/2023] [Indexed: 06/07/2023]
Abstract
We have devised a single pot, low-cost method to add azide groups to unmodified nucleic acids without the need for enzymes or chemically modified nucleoside triphosphates. This involves reacting an azide-containing sulfinate salt with the nucleic acid, leading to replacement of C-H bonds on the nucleobase aromatic rings with C-R, where R is the azide-containing linker derived from the original sulfinate salt. With the addition of azide functional groups, the modified nucleic acid can easily be reacted with any alkyne-labeled compound of interest, including fluorescent dyes as shown in this work. This methodology enables the fluorescent labeling of a wide variety of nucleic acids, including natively folded RNAs, under mild conditions with minimal effects upon biochemical function and ribozyme catalysis. To demonstrate this, we show that a pair of labeled complementary ssDNA oligonucleotides (oligos) can hybridize to form dsDNA, even when labeled with multiple fluorophores per oligo. In addition, we also demonstrate that two different group II introns can splice when prelabeled internally with fluorophores, using our method. Broadly, this demonstrates that sulfinate modification of RNA is compatible with ribozyme function and Watson-Crick pairing, while preserving the labile backbone.
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Affiliation(s)
- Tiziano Bassi
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Anastassia Hirlinger
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Leah Grayson
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Julien Vantourout
- Department of Chemistry, Scripps Research, La Jolla, California 92037, USA
| | - Navtej Toor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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6
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Gao S, Sun Y, Chen X, Zhu C, Liu X, Wang W, Gan L, Lu Y, Schaarschmidt F, Herde M, Witte CP, Chen M. Pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in RNA. Nucleic Acids Res 2023; 51:7451-7464. [PMID: 37334828 PMCID: PMC10415118 DOI: 10.1093/nar/gkad529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 05/31/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023] Open
Abstract
5-Methylated cytosine is a frequent modification in eukaryotic RNA and DNA influencing mRNA stability and gene expression. Here we show that free 5-methylcytidine (5mC) and 5-methyl-2'-deoxycytidine are generated from nucleic acid turnover in Arabidopsis thaliana, and elucidate how these cytidines are degraded, which is unclear in eukaryotes. First CYTIDINE DEAMINASE produces 5-methyluridine (5mU) and thymidine which are subsequently hydrolyzed by NUCLEOSIDE HYDROLASE 1 (NSH1) to thymine and ribose or deoxyribose. Interestingly, far more thymine is generated from RNA than from DNA turnover, and most 5mU is directly released from RNA without a 5mC intermediate, since 5-methylated uridine (m5U) is an abundant RNA modification (m5U/U ∼1%) in Arabidopsis. We show that m5U is introduced mainly by tRNA-SPECIFIC METHYLTRANSFERASE 2A and 2B. Genetic disruption of 5mU degradation in the NSH1 mutant causes m5U to occur in mRNA and results in reduced seedling growth, which is aggravated by external 5mU supplementation, also leading to more m5U in all RNA species. Given the similarities between pyrimidine catabolism in plants, mammals and other eukaryotes, we hypothesize that the removal of 5mU is an important function of pyrimidine degradation in many organisms, which in plants serves to protect RNA from stochastic m5U modification.
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Affiliation(s)
- Shangyu Gao
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Sun
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoguang Chen
- Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Changhua Zhu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoye Liu
- Department of Criminal Science and Technology, Nanjing Forest Police College, Nanjing 210023, China
| | - Wenlei Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lijun Gan
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanwu Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Frank Schaarschmidt
- Department of Biostatistics, Institute of Cell Biology and Biophysics, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Mingjia Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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7
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Yihunie W, Nibret G, Aschale Y. Recent Advances in Messenger Ribonucleic Acid (mRNA) Vaccines and Their Delivery Systems: A Review. Clin Pharmacol 2023; 15:77-98. [PMID: 37554660 PMCID: PMC10405914 DOI: 10.2147/cpaa.s418314] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/28/2023] [Indexed: 08/10/2023] Open
Abstract
Messenger ribonucleic acid (mRNA) was found as the intermediary that transfers genetic information from DNA to ribosomes for protein synthesis in 1961. The emergency use authorization of the two covid-19 mRNA vaccines, BNT162b2 and mRNA-1273, is a significant achievement in the history of vaccine development. Because they are generated in a cell-free environment using the in vitro transcription (IVT) process, mRNA vaccines are risk-free. Moreover, chemical modifications to the mRNA molecule, such as cap structures and changed nucleosides, have proved critical in overcoming immunogenicity concerns, achieving sustained stability, and achieving effective, accurate protein production in vivo. Several vaccine delivery strategies (including protamine, lipid nanoparticles (LNPs), polymers, nanoemulsions, and cell-based administration) were also optimized to load and transport RNA into the cytosol. LNPs, which are composed of a cationic or a pH-dependent ionizable lipid layer, a polyethylene glycol (PEG) component, phospholipids, and cholesterol, are the most advanced systems for delivering mRNA vaccines. Moreover, modifications of the four components that make up the LNPs showed to increase vaccine effectiveness and reduce side effects. Furthermore, the introduction of biodegradable lipids improved LNP biocompatibility. Furthermore, mRNA-based therapies are expected to be effective treatments for a variety of refractory conditions, including infectious diseases, metabolic genetic diseases, cancer, cardiovascular and cerebrovascular diseases. Therefore, the present review aims to provide the scientific community with up-to-date information on mRNA vaccines and their delivery systems.
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Affiliation(s)
- Wubetu Yihunie
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Getinet Nibret
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Yibeltal Aschale
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
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8
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Kang DD, Li H, Dong Y. Advancements of in vitro transcribed mRNA (IVT mRNA) to enable translation into the clinics. Adv Drug Deliv Rev 2023; 199:114961. [PMID: 37321375 PMCID: PMC10264168 DOI: 10.1016/j.addr.2023.114961] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023]
Abstract
The accelerated progress and approval of two mRNA-based vaccines to address the SARS-CoV-2 virus were unprecedented. This record-setting feat was made possible through the solid foundation of research on in vitro transcribed mRNA (IVT mRNA) which could be utilized as a therapeutic modality. Through decades of thorough research to overcome barriers to implementation, mRNA-based vaccines or therapeutics offer many advantages to rapidly address a broad range of applications including infectious diseases, cancers, and gene editing. Here, we describe the advances that have supported the adoption of IVT mRNA in the clinics, including optimization of the IVT mRNA structural components, synthesis, and lastly concluding with different classes of IVT RNA. Continuing interest in driving IVT mRNA technology will enable a safer and more efficacious therapeutic modality to address emerging and existing diseases.
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Affiliation(s)
- Diana D Kang
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Haoyuan Li
- Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Yizhou Dong
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Department of Biomedical Engineering, The Center for Clinical and Translational Science, The Comprehensive Cancer Center; Dorothy M. Davis Heart & Lung Research Institute, Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, United States; Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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9
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Yang H, Eremeeva E, Abramov M, Jacquemyn M, Groaz E, Daelemans D, Herdewijn P. CRISPR-Cas9 recognition of enzymatically synthesized base-modified nucleic acids. Nucleic Acids Res 2023; 51:1501-1511. [PMID: 36611237 PMCID: PMC9976875 DOI: 10.1093/nar/gkac1147] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/09/2022] [Accepted: 11/17/2022] [Indexed: 01/09/2023] Open
Abstract
An enzymatic method has been successfully established enabling the generation of partially base-modified RNA (previously named RZA) constructs, in which all G residues were replaced by isomorphic fluorescent thienoguanosine (thG) analogs, as well as fully modified RZA featuring thG, 5-bromocytosine, 7-deazaadenine and 5-chlorouracil. The transcriptional efficiency of emissive fully modified RZA was found to benefit from the use of various T7 RNA polymerase variants. Moreover, dthG could be incorporated into PCR products by Taq DNA polymerase together with the other three base-modified nucleotides. Notably, the obtained RNA products containing thG as well as thG together with 5-bromocytosine could function as effectively as natural sgRNAs in an in vitro CRISPR-Cas9 cleavage assay. N1-Methylpseudouridine was also demonstrated to be a faithful non-canonical substitute of uridine to direct Cas9 nuclease cleavage when incorporated in sgRNA. The Cas9 inactivation by 7-deazapurines indicated the importance of the 7-nitrogen atom of purines in both sgRNA and PAM site for achieving efficient Cas9 cleavage. Additional aspects of this study are discussed in relation to the significance of sgRNA-protein and PAM--protein interactions that were not highlighted by the Cas9-sgRNA-DNA complex crystal structure. These findings could expand the impact and therapeutic value of CRISPR-Cas9 and other RNA-based technologies.
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Affiliation(s)
- Hui Yang
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Elena Eremeeva
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium.,Queensland University of Technology, Centre for Agriculture and the Bioeconomy, Molecular Engineering Group, George Street 2, 4000 Brisbane, Queensland, Australia
| | - Mikhail Abramov
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Maarten Jacquemyn
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Elisabetta Groaz
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium.,University of Padova, Department of Pharmaceutical and Pharmacological Sciences, Via Marzolo 5, 35131 Padova, Italy
| | - Dirk Daelemans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
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10
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Fleming AM, Burrows CJ. Nanopore sequencing for N1-methylpseudouridine in RNA reveals sequence-dependent discrimination of the modified nucleotide triphosphate during transcription. Nucleic Acids Res 2023; 51:1914-1926. [PMID: 36727474 PMCID: PMC9976907 DOI: 10.1093/nar/gkad044] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/21/2022] [Accepted: 01/16/2023] [Indexed: 02/03/2023] Open
Abstract
Direct RNA sequencing with a commercial nanopore platform was used to sequence RNA containing uridine (U), pseudouridine (Ψ) or N1-methylpseudouridine (m1Ψ) in >100 different 5-nucleotide contexts. The base calling data for Ψ or m1Ψ were similar but different from U allowing their detection. Understanding the nanopore signatures for Ψ and m1Ψ enabled a running start T7 RNA polymerase assay to study the selection of UTP versus ΨTP or m1ΨTP competing mixtures in all possible adjacent sequence contexts. A significant sequence context dependency was observed for T7 RNA polymerase with insertion yields for ΨTP versus UTP spanning a range of 20-65%, and m1ΨTP versus UTP producing variable yields that differ by 15-70%. Experiments with SP6 RNA polymerase, as well as chemically-modified triphosphates and DNA templates provide insight to explain the observations. The SP6 polymerase introduced m1ΨTP when competed with UTP with a smaller window of yields (15-30%) across all sequence contexts studied. These results may aid in future efforts that employ RNA polymerases to make therapeutic mRNAs with sub-stoichiometric amounts of m1Ψ.
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Affiliation(s)
- Aaron M Fleming
- Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA
| | - Cynthia J Burrows
- Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA
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11
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Brunderová M, Krömer M, Vlková M, Hocek M. Chloroacetamide-Modified Nucleotide and RNA for Bioconjugations and Cross-Linking with RNA-Binding Proteins. Angew Chem Int Ed Engl 2023; 62:e202213764. [PMID: 36533569 PMCID: PMC10107093 DOI: 10.1002/anie.202213764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/04/2022] [Accepted: 12/19/2022] [Indexed: 12/23/2022]
Abstract
Reactive RNA probes are useful for studying and identifying RNA-binding proteins. To that end, we designed and synthesized chloroacetamide-linked 7-deaza-ATP which was a good substrate for T7 RNA polymerase in in vitro transcription assay to synthesize reactive RNA probes bearing one or several reactive modifications. Modified RNA probes reacted with thiol-containing molecules as well as with cysteine- or histidine-containing peptides to form stable covalent products. They also reacted selectively with RNA-binding proteins to form cross-linked conjugates in high conversions thanks to proximity effect. Our modified nucleotide and RNA probes are promising tools for applications in RNA (bio)conjugations or RNA proteomics.
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Affiliation(s)
- Mária Brunderová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Matouš Krömer
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Marta Vlková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843, Prague 2, Czech Republic
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12
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Graczyk A, Radzikowska-Cieciura E, Kaczmarek R, Pawlowska R, Chworos A. Modified Nucleotides for Chemical and Enzymatic Synthesis of Therapeutic RNA. Curr Med Chem 2023; 30:1320-1347. [PMID: 36239720 DOI: 10.2174/0929867330666221014111403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022]
Abstract
In recent years, RNA has emerged as a medium with a broad spectrum of therapeutic potential, however, for years, a group of short RNA fragments was studied and considered therapeutic molecules. In nature, RNA plays both functions, with coding and non-coding potential. For RNA, like any other therapeutic, to be used clinically, certain barriers must be crossed. Among them, there are biocompatibility, relatively low toxicity, bioavailability, increased stability, target efficiency and low off-target effects. In the case of RNA, most of these obstacles can be overcome by incorporating modified nucleotides into its structure. This may be achieved by both, in vitro and in vivo biosynthetic methods, as well as chemical synthesis. Some advantages and disadvantages of each approach are summarized here. The wide range of nucleotide analogues has been tested for their utility as monomers for RNA synthesis. Many of them have been successfully implemented, and a lot of pre-clinical and clinical studies involving modified RNA have been carried out. Some of these medications have already been introduced into clinics. After the huge success of RNA-based vaccines that were introduced into widespread use in 2020, and the introduction to the market of some RNA-based drugs, RNA therapeutics containing modified nucleotides appear to be the future of medicine.
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Affiliation(s)
- Anna Graczyk
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Ewa Radzikowska-Cieciura
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Renata Kaczmarek
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Roza Pawlowska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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13
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Vavřina Z, Perlíková P, Milisavljević N, Chevrier F, Smola M, Smith J, Dejmek M, Havlíček V, Buděšínský M, Liboska R, Vaneková L, Brynda J, Boura E, Řezáčová P, Hocek M, Birkuš G. Design, Synthesis, and Biochemical and Biological Evaluation of Novel 7-Deazapurine Cyclic Dinucleotide Analogues as STING Receptor Agonists. J Med Chem 2022; 65:14082-14103. [PMID: 36201304 PMCID: PMC9620234 DOI: 10.1021/acs.jmedchem.2c01305] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Indexed: 11/28/2022]
Abstract
Cyclic dinucleotides (CDNs) are second messengers that activate stimulator of interferon genes (STING). The cGAS-STING pathway plays a promising role in cancer immunotherapy. Here, we describe the synthesis of CDNs containing 7-substituted 7-deazapurine moiety. We used mouse cyclic GMP-AMP synthase and bacterial dinucleotide synthases for the enzymatic synthesis of CDNs. Alternatively, 7-(het)aryl 7-deazapurine CDNs were prepared by Suzuki-Miyaura cross-couplings. New CDNs were tested in biochemical and cell-based assays for their affinity to human STING. Eight CDNs showed better activity than 2'3'-cGAMP, the natural ligand of STING. The effect on cytokine and chemokine induction was also evaluated. The best activities were observed for CDNs bearing large aromatic substituents that point above the CDN molecule. We solved four X-ray structures of complexes of new CDNs with human STING. We observed π-π stacking interactions between the aromatic substituents and Tyr240 that are involved in the stabilization of CDN-STING complexes.
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Affiliation(s)
- Zdeněk Vavřina
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles
University, Hlavova 2030/8, Prague 128 00, Czech Republic
| | - Pavla Perlíková
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Organic Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, Technicka 5, Prague 166 28, Czech Republic
| | - Nemanja Milisavljević
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 00, Czech Republic
| | - Florian Chevrier
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Miroslav Smola
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Joshua Smith
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- First
Faculty of Medicine, Charles University, Katerinska 1660/32, Prague 121 08, Czech Republic
| | - Milan Dejmek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Vojtěch Havlíček
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 00, Czech Republic
| | - Miloš Buděšínský
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Radek Liboska
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Lenka Vaneková
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Cell Biology, Faculty of Science, Charles
University, Vinicna 1594/7, Prague 128 43, Czech Republic
| | - Jiří Brynda
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Evzen Boura
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Pavlína Řezáčová
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Michal Hocek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Gabriel Birkuš
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
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14
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Zhou H, Li Y, Gan Y, Wang R. Total RNA Synthesis and its Covalent Labeling Innovation. Top Curr Chem (Cham) 2022; 380:16. [PMID: 35218412 DOI: 10.1007/s41061-022-00371-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022]
Abstract
RNA plays critical roles in a wide range of physiological processes. For example, it is well known that RNA plays an important role in regulating gene expression, cell proliferation, and differentiation, and many other chemical and biological processes. However, the research community still suffers from limited approaches that can be applied to readily visualize a specific RNA-of-interest (ROI). Several methods can be used to track RNAs; these rely mainly on biological properties, namely, hybridization, aptamer, reporter protein, and protein binding. With respect to covalent approaches, very few cases have been reported. Happily, several new methods for efficient labeling studies of ROIs have been demonstrated successfully in recent years. Additionally, methods employed for the detection of ROIs by RNA modifying enzymes have also proved feasible. Several approaches, namely, phosphoramidite chemistry, in vitro transcription reactions, co-transcription reactions, chemical post-modification, RNA modifying enzymes, ligation, and other methods targeted at RNA labeling have been revealed in the past decades. To illustrate the most recent achievements, this review aims to summarize the most recent research in the field of synthesis of RNAs-of-interest bearing a variety of unnatural nucleosides, the subsequent RNA labeling research via biocompatible ligation, and beyond.
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Affiliation(s)
- Hongling Zhou
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuanyuan Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Youfang Gan
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Rui Wang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Key Laboratory of Natural Product and Resource, Shanghai Institute of Organic Chemistry, Shanghai, 230030, China.
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15
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Depmeier H, Hoffmann E, Bornewasser L, Kath‐Schorr S. Strategies for Covalent Labeling of Long RNAs. Chembiochem 2021; 22:2826-2847. [PMID: 34043861 PMCID: PMC8518768 DOI: 10.1002/cbic.202100161] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/26/2021] [Indexed: 12/17/2022]
Abstract
The introduction of chemical modifications into long RNA molecules at specific positions for visualization, biophysical investigations, diagnostic and therapeutic applications still remains challenging. In this review, we present recent approaches for covalent internal labeling of long RNAs. Topics included are the assembly of large modified RNAs via enzymatic ligation of short synthetic oligonucleotides and synthetic biology approaches preparing site-specifically modified RNAs via in vitro transcription using an expanded genetic alphabet. Moreover, recent approaches to employ deoxyribozymes (DNAzymes) and ribozymes for RNA labeling and RNA methyltransferase based labeling strategies are presented. We discuss the potentials and limits of the individual methods, their applicability for RNAs with several hundred to thousands of nucleotides in length and indicate future directions in the field.
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Affiliation(s)
- Hannah Depmeier
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
| | - Eva Hoffmann
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
| | - Lisa Bornewasser
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
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16
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Jeeva S, Kim KH, Shin CH, Wang BZ, Kang SM. An Update on mRNA-Based Viral Vaccines. Vaccines (Basel) 2021; 9:965. [PMID: 34579202 PMCID: PMC8473183 DOI: 10.3390/vaccines9090965] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 12/23/2022] Open
Abstract
With the success of COVID-19 vaccines, newly created mRNA vaccines against other infectious diseases are beginning to emerge. Here, we review the structural elements required for designing mRNA vaccine constructs for effective in vitro synthetic transcription reactions. The unprecedently speedy development of mRNA vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was enabled with previous innovations in nucleoside modifications during in vitro transcription and lipid nanoparticle delivery materials of mRNA. Recent updates are briefly described in the status of mRNA vaccines against SARS-CoV-2, influenza virus, and other viral pathogens. Unique features of mRNA vaccine platforms and future perspectives are discussed.
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Affiliation(s)
| | | | | | | | - Sang-Moo Kang
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA; (S.J.); (K.-H.K.); (C.H.S.); (B.-Z.W.)
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17
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Kapustina Ž, Jasponė A, Dubovskaja V, Mackevičius G, Lubys A. Enzymatic Synthesis of Chimeric DNA Oligonucleotides by in Vitro Transcription with dTTP, dCTP, dATP, and 2'-Fluoro Modified dGTP. ACS Synth Biol 2021; 10:1625-1632. [PMID: 34110794 DOI: 10.1021/acssynbio.1c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient ways to produce single-stranded DNA are of great interest for diverse applications in molecular biology and nanotechnology. In the present study, we selected T7 RNA polymerase mutants with reduced substrate specificity to employ an in vitro transcription reaction for the synthesis of chimeric DNA oligonucleotides, either individually or in pools. We performed in vitro evolution based on fluorescence-activated droplet sorting and identified mutations V783M, V783L, V689Q, and G555L as novel variants leading to relaxed substrate discrimination. Transcribed chimeric oligonucleotides were tested in PCR, and the quality of amplification products as well as fidelity of oligonucleotide synthesis were assessed by NGS. We concluded that enzymatically produced chimeric DNA transcripts contain significantly fewer deletions and insertions compared to chemically synthesized counterparts and can successfully serve as PCR primers, making the evolved enzymes superior for simple and cheap one-pot synthesis of multiple chimeric DNA oligonucleotides in parallel using a plethora of premixed templates.
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Affiliation(s)
- Žana Kapustina
- UAB Thermo Fisher Scientific Baltics, Research and Development, V. A. Graičiu̅no str. 8, Vilnius 02241, Lithuania
- Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius 10257, Lithuania
| | - Aistė Jasponė
- UAB Thermo Fisher Scientific Baltics, Research and Development, V. A. Graičiu̅no str. 8, Vilnius 02241, Lithuania
| | - Varvara Dubovskaja
- UAB Thermo Fisher Scientific Baltics, Research and Development, V. A. Graičiu̅no str. 8, Vilnius 02241, Lithuania
| | - Gytis Mackevičius
- UAB Thermo Fisher Scientific Baltics, Research and Development, V. A. Graičiu̅no str. 8, Vilnius 02241, Lithuania
| | - Arvydas Lubys
- UAB Thermo Fisher Scientific Baltics, Research and Development, V. A. Graičiu̅no str. 8, Vilnius 02241, Lithuania
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18
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Nance K, Meier JL. Modifications in an Emergency: The Role of N1-Methylpseudouridine in COVID-19 Vaccines. ACS CENTRAL SCIENCE 2021; 7:748-756. [PMID: 34075344 PMCID: PMC8043204 DOI: 10.1021/acscentsci.1c00197] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Indexed: 05/22/2023]
Abstract
The novel coronavirus SARS-CoV-2, the cause of the COVID-19 pandemic, has inspired one of the most efficient vaccine development campaigns in human history. A key aspect of COVID-19 mRNA vaccines is the use of the modified nucleobase N1-methylpseudouridine (m1Ψ) to increase their effectiveness. In this Outlook, we summarize the development and function of m1Ψ in synthetic mRNAs. By demystifying how a novel element within these medicines works, we aim to foster understanding and highlight future opportunities for chemical innovation.
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Affiliation(s)
- Kellie
D. Nance
- Chemical
Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 538 Chandler Street, Frederick, Maryland 21702, United States
| | - Jordan L. Meier
- Chemical
Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 538 Chandler Street, Frederick, Maryland 21702, United States
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19
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Perlíková P, Krajczyk A, Doleželová E, Slapničková M, Milisavljevic N, Slavětínská LP, Tloušt’ová E, Gurská S, Džubák P, Hajdúch M, Zíková A, Hocek M. Synthesis and Antitrypanosomal Activity of 6-Substituted 7-Methyl-7-deazapurine Nucleosides. ACS Infect Dis 2021; 7:917-926. [PMID: 33769794 DOI: 10.1021/acsinfecdis.1c00062] [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] [Indexed: 12/22/2022]
Abstract
Human African Trypanosomiasis caused by Trypanosoma brucei species is one of the most damaging neglected tropical diseases. While the number of newly diagnosed cases per year is record low, there is still high interest in the development of new antitrypanosomal agents in case of resistance to currently used drugs and their combinations, and to replace drugs with serious side effects. We report a series of 7-methyl-7-deazapurine (5-methyl-pyrrolo[2,3-d]pyrimidine) ribonucleosides bearing alkyl, methylsulfanyl, methylamino, or diverse alkoxy groups at position 6 that was prepared through glycosylation of 6-chloro-7-methyl-7-deazapurine followed by nucleophilic substitutions or cross-coupling reactions at position 6 and deprotection. Most of the title nucleosides displayed significant activity against Trypanosoma brucei brucei and T. b. gambiense at submicromolar or nanomolar concentrations and low cytotoxicity and thus represent promising candidates for further development.
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Affiliation(s)
- Pavla Perlíková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Anna Krajczyk
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Eva Doleželová
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
| | - Martina Slapničková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
| | - Nemanja Milisavljevic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Eva Tloušt’ová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Soňa Gurská
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hněvotínská 5, CZ-779 00 Olomouc, Czech Republic
| | - Petr Džubák
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hněvotínská 5, CZ-779 00 Olomouc, Czech Republic
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hněvotínská 5, CZ-779 00 Olomouc, Czech Republic
| | - Alena Zíková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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20
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Englert D, Matveeva R, Sunbul M, Wombacher R, Jäschke A. Aptamer-based proximity labeling guides covalent RNA modification. Chem Commun (Camb) 2021; 57:3480-3483. [PMID: 33688891 DOI: 10.1039/d1cc00786f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe the development of a proximity-induced bio-orthogonal inverse electron demand Diels-Alder reaction that exploits the high-affinity interaction between a dienophile-modified RhoBAST aptamer and its tetramethyl rhodamine methyltetrazine substrate. We applied this concept for covalent RNA labeling in proof-of-principle experiments.
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Affiliation(s)
- Daniel Englert
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany.
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21
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Yang H, Eremeeva E, Abramov M, Herdewijn P. The Network of Replication, Transcription, and Reverse Transcription of a Synthetic Genetic Cassette. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hui Yang
- Medicinal Chemistry Rega Institute for Medical Research KU Leuven Herestraat 49, Box-1041 3000 Leuven Belgium
| | - Elena Eremeeva
- Medicinal Chemistry Rega Institute for Medical Research KU Leuven Herestraat 49, Box-1041 3000 Leuven Belgium
| | - Mikhail Abramov
- Medicinal Chemistry Rega Institute for Medical Research KU Leuven Herestraat 49, Box-1041 3000 Leuven Belgium
| | - Piet Herdewijn
- Medicinal Chemistry Rega Institute for Medical Research KU Leuven Herestraat 49, Box-1041 3000 Leuven Belgium
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22
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Milisavljevic N, Konkolová E, Kozák J, Hodek J, Veselovská L, Sýkorová V, Čížek K, Pohl R, Eyer L, Svoboda P, Růžek D, Weber J, Nencka R, Bouřa E, Hocek M. Antiviral Activity of 7-Substituted 7-Deazapurine Ribonucleosides, Monophosphate Prodrugs, and Triphoshates against Emerging RNA Viruses. ACS Infect Dis 2021; 7:471-478. [PMID: 33395259 DOI: 10.1021/acsinfecdis.0c00829] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A series of 7-deazaadenine ribonucleosides bearing alkyl, alkenyl, alkynyl, aryl, or hetaryl groups at position 7 as well as their 5'-O-triphosphates and two types of monophosphate prodrugs (phosphoramidates and S-acylthioethanol esters) were prepared and tested for antiviral activity against selected RNA viruses (Dengue, Zika, tick-borne encephalitis, West Nile, and SARS-CoV-2). The modified triphosphates inhibited the viral RNA-dependent RNA polymerases at micromolar concentrations through the incorporation of the modified nucleotide and stopping a further extension of the RNA chain. 7-Deazaadenosine nucleosides bearing ethynyl or small hetaryl groups at position 7 showed (sub)micromolar antiviral activities but significant cytotoxicity, whereas the nucleosides bearing bulkier heterocycles were still active but less toxic. Unexpectedly, the monophosphate prodrugs were similarly or less active than the corresponding nucleosides in the in vitro antiviral assays, although the bis(S-acylthioethanol) prodrug 14h was transported to the Huh7 cells and efficiently released the nucleoside monophosphate.
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Affiliation(s)
- Nemanja Milisavljevic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Eva Konkolová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Jaroslav Kozák
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Jan Hodek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Lucia Veselovská
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Karel Čížek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Luděk Eyer
- Department of Virology, Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
| | - Pavel Svoboda
- Department of Virology, Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
- Department of Pharmacology and Pharmacy, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, CZ-61242 Brno, Czech Republic
| | - Daniel Růžek
- Department of Virology, Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Evžen Bouřa
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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23
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Yang H, Eremeeva E, Abramov M, Herdewijn P. The Network of Replication, Transcription, and Reverse Transcription of a Synthetic Genetic Cassette. Angew Chem Int Ed Engl 2020; 60:4175-4182. [PMID: 33142013 DOI: 10.1002/anie.202011887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/27/2020] [Indexed: 11/07/2022]
Abstract
Synthetic nucleic acids, with four non-canonical nucleobases, can function as genetic materials. A comprehensive analysis of PCR amplification, transcription, reverse transcription, and cloning was done to screen for alternative genetic monomers. A small library of six modified nucleobases was selected: the modified 2'-deoxyribonucleoside (dZTPs) and ribonucleoside (rZTPs) triphosphates of 7-deaza-adenine, 5-chlorouracil, 7-deaza-guanine or inosine together with 5-fluorocytosine or 5-bromocytosine. The fragments composed of one to four modified nucleotides (denoted as DZA) have been successfully recognized and transcribed to natural or modified RNA (denoted as RZA) by T7 RNA polymerase. The fully modified RZA fragment could be reverse transcribed and then amplified in the presence of various dZTPs. Noticeably, modified fragments could function as genetic templates in vivo by encoding the 678 base pair gene of a fluorescent protein in bacteria. These results demonstrate the existence of a fully simulated genetic circuit that uses synthetic materials.
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Affiliation(s)
- Hui Yang
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, Box-1041, 3000, Leuven, Belgium
| | - Elena Eremeeva
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, Box-1041, 3000, Leuven, Belgium
| | - Mikhail Abramov
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, Box-1041, 3000, Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, Box-1041, 3000, Leuven, Belgium
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24
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George JT, Srivatsan SG. Bioorthogonal chemistry-based RNA labeling technologies: evolution and current state. Chem Commun (Camb) 2020; 56:12307-12318. [PMID: 33026365 PMCID: PMC7611129 DOI: 10.1039/d0cc05228k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To understand the structure and ensuing function of RNA in various cellular processes, researchers greatly rely on traditional as well as contemporary labeling technologies to devise efficient biochemical and biophysical platforms. In this context, bioorthogonal chemistry based on chemoselective reactions that work under biologically benign conditions has emerged as a state-of-the-art labeling technology for functionalizing biopolymers. Implementation of this technology on sugar, protein, lipid and DNA is fairly well established. However, its use in labeling RNA has posed challenges due to the fragile nature of RNA. In this feature article, we provide an account of bioorthogonal chemistry-based RNA labeling techniques developed in our lab along with a detailed discussion on other technologies put forward recently. In particular, we focus on the development and applications of covalent methods to label RNA by transcription and posttranscription chemo-enzymatic approaches. It is expected that existing as well as new bioorthogonal functionalization methods will immensely advance our understanding of RNA and support the development of RNA-based diagnostic and therapeutic tools.
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Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pune 411008, India.
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25
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Veselovská L, Kudlová N, Gurská S, Lišková B, Medvedíková M, Hodek O, Tloušťová E, Milisavljevic N, Tichý M, Perlíková P, Mertlíková‐Kaiserová H, Trylčová J, Pohl R, Klepetářová B, Džubák P, Hajdúch M, Hocek M. Synthesis and Cytotoxic and Antiviral Activity Profiling of All‐Four Isomeric Series of Pyrido‐Fused 7‐Deazapurine Ribonucleosides. Chemistry 2020; 26:13002-13015. [DOI: 10.1002/chem.202001124] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Lucia Veselovská
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Natálie Kudlová
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry Palacky University and University Hospital in Olomouc Hněvotínská 5 775 15 Olomouc Czech Republic
- Cancer Research Czech Republic Hněvotínská 5 775 15 Olomouc Czech Republic
| | - Soňa Gurská
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry Palacky University and University Hospital in Olomouc Hněvotínská 5 775 15 Olomouc Czech Republic
- Cancer Research Czech Republic Hněvotínská 5 775 15 Olomouc Czech Republic
| | - Barbora Lišková
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry Palacky University and University Hospital in Olomouc Hněvotínská 5 775 15 Olomouc Czech Republic
| | - Martina Medvedíková
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry Palacky University and University Hospital in Olomouc Hněvotínská 5 775 15 Olomouc Czech Republic
| | - Ondřej Hodek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Eva Tloušťová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Nemanja Milisavljevic
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Michal Tichý
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Pavla Perlíková
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Helena Mertlíková‐Kaiserová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Jana Trylčová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Blanka Klepetářová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Petr Džubák
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry Palacky University and University Hospital in Olomouc Hněvotínská 5 775 15 Olomouc Czech Republic
- Cancer Research Czech Republic Hněvotínská 5 775 15 Olomouc Czech Republic
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry Palacky University and University Hospital in Olomouc Hněvotínská 5 775 15 Olomouc Czech Republic
- Cancer Research Czech Republic Hněvotínská 5 775 15 Olomouc Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
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26
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Croce S, Serdjukow S, Carell T, Frischmuth T. Chemoenzymatic Preparation of Functional Click-Labeled Messenger RNA. Chembiochem 2020; 21:1641-1646. [PMID: 31943671 DOI: 10.1002/cbic.201900718] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 12/23/2022]
Abstract
Synthetic mRNAs are promising candidates for a new class of transformative drugs that provide genetic information for patients' cells to develop their own cure. One key advancement to develop so-called druggable mRNAs was the preparation of chemically modified mRNAs, by replacing standard bases with modified bases, such as uridine with pseudouridine, which can ameliorate the immunogenic profile and translation efficiency of the mRNA. Thus the introduction of modified nucleobases was the foundation for the clinical use of such mRNAs. Herein we describe modular and simple methods to chemoenzymatically modify mRNA. Alkyne- and/or azide-modified nucleotides are enzymatically incorporated into mRNA and subsequently conjugated to fluorescent dyes using click chemistry. This allows visualization of the labeled mRNA inside cells. mRNA coding for the enhanced green fluorescent protein (eGFP) was chosen as a model system and the successful expression of eGFP demonstrated that our modified mRNA is accepted by the translation machinery.
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Affiliation(s)
- Stefano Croce
- baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (bei München), Germany
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Sascha Serdjukow
- baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (bei München), Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Thomas Frischmuth
- baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (bei München), Germany
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27
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Shanmugasundaram M, Senthilvelan A, Kore AR. C-5 Substituted Pyrimidine Nucleotides/Nucleosides: Recent Progress in Synthesis, Functionalization, and Applications. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666190809124310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The chemistry of C5 substituted pyrimidine nucleotide serves as a versatile molecular
biology probe for the incorporation of DNA/RNA that has been involved in various
molecular biology applications such as gene expression, chromosome, and mRNA
fluorescence in situ hybridization (FISH) experiment, mutation detection on arrays and
microarrays, in situ RT-PCR, and PCR. In addition to C5 substituted pyrimidine nucleotide,
C5 substituted pyrimidine nucleoside displays a broad spectrum of biological applications
such as antibacterial, antiviral and anticancer activities. This review focusses on
the recent development in the synthesis of aminoallyl pyrimidine nucleotide, aminopropargyl
pyrimidine nucleotide, fluorescent probes containing C5 substituted pyrimidine nucleotide,
2′-deoxycytidine nucleoside containing vinylsulfonamide and acrylamide modification,
C5 alkenyl, C5 alkynyl, and C5 aryl pyrimidine nucleosides through palladium-catalyzed reaction,
pyrimidine nucleoside containing triazole moiety through Click reaction, 5-isoxazol-3-yl-pyrimidine nucleoside,
C5 azide modified pyrimidine nucleoside, 2′-deoxycytidine nucleotide containing photocleavable moiety,
and uridine nucleoside containing germane and their biological applications are outlined.
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Affiliation(s)
- Muthian Shanmugasundaram
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, TX 78744-1832, United States
| | - Annamalai Senthilvelan
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, TX 78744-1832, United States
| | - Anilkumar R. Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, TX 78744-1832, United States
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28
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Leonard P, Kondhare D, Jentgens X, Daniliuc C, Seela F. Nucleobase-Functionalized 5-Aza-7-deazaguanine Ribo- and 2′-Deoxyribonucleosides: Glycosylation, Pd-Assisted Cross-Coupling, and Photophysical Properties. J Org Chem 2019; 84:13313-13328. [DOI: 10.1021/acs.joc.9b01347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Xenia Jentgens
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Constantin Daniliuc
- Institut für Organische Chemie, Universität Münster, Corrensstrasse 40, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
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29
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Hocek M. Enzymatic Synthesis of Base-Functionalized Nucleic Acids for Sensing, Cross-linking, and Modulation of Protein-DNA Binding and Transcription. Acc Chem Res 2019; 52:1730-1737. [PMID: 31181911 DOI: 10.1021/acs.accounts.9b00195] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein-DNA interactions are important in replication, transcription, repair, as well as epigenetic modifications of DNA, which involve methylation and demethylation of DNA resulting in regulation of gene expression. Understanding of these processes and chemical tools for studying and perhaps even modulating them could be of great relevance and importance not only in chemical biology but also in real diagnostics and treatment of diseases. In the past decade, we have been working on development of synthesis of base-modified 2'-deoxyribo- or ribonucleoside triphosphates (dNTPs or NTPs) and their use in enzymatic synthesis of modified nucleic acids using DNA or RNA polymerases. These synthetic and enzymatic methods are briefly summarized with focus on recent development and outlining of scope, limitations, and further challenges. The main focus of this Account is on applications of base-modified nucleic acids in sensing of protein-DNA interactions, in covalent cross-linking to DNA-binding proteins ,and in modulation of protein-DNA binding and transcription. Several environment-sensitive fluorescent nucleotides were incorporated to DNA probes which responded to protein binding by light-up, changing of color, or lifetime of fluorescence. Using a cyclodextrin-peptide transporter, fluorescent nucleotides can be transported through the cell membrane and incorporated to genomic DNA. Several dNTPs bearing reactive groups (i.e., vinylsulfonamide or chloroacetamide) were used for polymerase synthesis of DNA reactive probes which cross-link to Cys, His, or Lys in peptides or proteins. An attractive challenge is to use DNA modifications and bioorthogonal reactions in the major groove of DNA for modulation and switching of protein-DNA interactions. We have systematically explored the influence of major-groove modifications on recognition and cleavage of DNA by restriction endonucleases and constructed simple chemical switches of DNA cleavage. Systematic study of the influence of major-groove modifications on transcription with bacterial RNA polymerases revealed not only that some modified bases are tolerated, but also that the presence of 5-hydroxymethyluracil or -cytosine can even enhance the transcription (350 or 250% compared to native DNA). Based on these results, we have constructed the first chemical switch of transcription based on photocaging of hydroxymethylpyrimidines in DNA by 2-nitrobenzyl protection (transcription off), photochemical deprotection of the DNA (transcription on), and enzymatic phosphorylation (only for 5-hydroxymethyluracil, transcription off). Although it has been so far demonstrated only in vitro, it is the proof-of-principle first step toward chemical epigenetics.
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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30
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Manna S, Srivatsan SG. Synthesis and Enzymatic Incorporation of a Responsive Ribonucleoside Probe That Enables Quantitative Detection of Metallo-Base Pairs. Org Lett 2019; 21:4646-4650. [PMID: 31184159 PMCID: PMC6794643 DOI: 10.1021/acs.orglett.9b01544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Synthesis of a highly
responsive fluorescent ribonucleoside analogue
based on a 5-methoxybenzofuran uracil core, enzymatic incorporation
of its triphosphate substrate into RNA transcripts, and its utility
in the specific detection and estimation of Hg2+-ion-mediated
metallo-base pair formation in DNA–RNA and RNA–RNA duplexes
are described.
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Affiliation(s)
- Sudeshna Manna
- Department of Chemistry , Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road , Pune 411008 , India
| | - Seergazhi G Srivatsan
- Department of Chemistry , Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road , Pune 411008 , India
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31
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Flamme M, McKenzie LK, Sarac I, Hollenstein M. Chemical methods for the modification of RNA. Methods 2019; 161:64-82. [PMID: 30905751 DOI: 10.1016/j.ymeth.2019.03.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
RNA is often considered as being the vector for the transmission of genetic information from DNA to the protein synthesis machinery. However, besides translation RNA participates in a broad variety of fundamental biological roles such as gene expression and regulation, protein synthesis, and even catalysis of chemical reactions. This variety of function combined with intricate three-dimensional structures and the discovery of over 100 chemical modifications in natural RNAs require chemical methods for the modification of RNAs in order to investigate their mechanism, location, and exact biological roles. In addition, numerous RNA-based tools such as ribozymes, aptamers, or therapeutic oligonucleotides require the presence of additional chemical functionalities to strengthen the nucleosidic backbone against degradation or enhance the desired catalytic or binding properties. Herein, the two main methods for the chemical modification of RNA are presented: solid-phase synthesis using phosphoramidite precursors and the enzymatic polymerization of nucleoside triphosphates. The different synthetic and biochemical steps required for each method are carefully described and recent examples of practical applications based on these two methods are discussed.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Luke K McKenzie
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Ivo Sarac
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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32
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Abstract
Attachment of hydrophobic groups to RNA is challenging because of their poor aqueous solubility. One-step acylation of RNA 2'-OH groups in water using a water-soluble imidazole leaving group is described. The effect of the hydrophobic groups on hybridization is reported. Furthermore, propargyl-functionalized RNA is shown to be readily labeled with a fluorophore. Lastly, heptyl-functionalized RNA is found to exhibit the unusual property of solubility in organic solvents.
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Affiliation(s)
- Willem A. Velema
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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