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Michenfelder RT, Pashley‐Johnson F, Guschin V, Delafresnaye L, Truong VX, Wagenknecht H, Barner‐Kowollik C. Photochemical Action Plots Map Orthogonal Reactivity in Photochemical Release Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402011. [PMID: 38852174 PMCID: PMC11304248 DOI: 10.1002/advs.202402011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/03/2024] [Indexed: 06/11/2024]
Abstract
The wavelength-by-wavelength resolved photoreactivity of two photo-caged carboxylic acids, i. e. 7-(diethylamino)-coumarin- and 3-perylene-modified substrates, is investigated via photochemical action plots. The observed wavelength-dependent reactivity of the chromophores is contrasted with their absorption profile. The photochemical action plots reveal a remarkable mismatch between the maximum reactivity and the absorbance. Through the action plot data, the study is able to uncover photochemical reactivity maxima at longer and shorter wavelengths, where the molar absorptivity of the chromophores is strongly reduced. Finally, the laser experiments are translated to light emitting diode (LED) irradiation and show efficient visible-light-induced release in a near fully wavelength-orthogonal, sequence-independent fashion (λLED1 = 405 nm, λLED2 = 505 nm) with both chromophores in the same reaction solution. The herein pioneered wavelength orthogonal release systems open an avenue for releasing two different molecular cargos with visible light in a fully orthogonal fashion.
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Affiliation(s)
- Rita T. Michenfelder
- School of Chemistry and PhysicsCentre for Materials ScienceQueensland University of Technology (QUT)2 George StBrisbaneQLD4000Australia
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz‐Haber‐Weg 676131KarlsruheGermany
- Institute of NanotechnologyKarlsruhe Institute of Technology (KIT)Hermann‐von‐Helmholtz‐Platz 176344Eggenstein‐LeopoldshafenGermany
| | - Fred Pashley‐Johnson
- School of Chemistry and PhysicsCentre for Materials ScienceQueensland University of Technology (QUT)2 George StBrisbaneQLD4000Australia
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC) and Laboratory of Organic SynthesisDepartment of Organic and Macromolecular ChemistryFaculty of SciencesGhent UniversityKrijgslaan 281‐S4Ghent9000Belgium
| | - Viktor Guschin
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz‐Haber‐Weg 676131KarlsruheGermany
- Institute of NanotechnologyKarlsruhe Institute of Technology (KIT)Hermann‐von‐Helmholtz‐Platz 176344Eggenstein‐LeopoldshafenGermany
| | - Laura Delafresnaye
- School of Chemistry and PhysicsCentre for Materials ScienceQueensland University of Technology (QUT)2 George StBrisbaneQLD4000Australia
| | - Vinh X. Truong
- Institute of Sustainability for ChemicalsEnergy and Environment (ISCE2)Agency for Science, Technology and Research (A*STAR)1 Pesek Round, Jurong IslandSingapore627833Republic of Singapore
| | - Hans‐Achim Wagenknecht
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz‐Haber‐Weg 676131KarlsruheGermany
| | - Christopher Barner‐Kowollik
- School of Chemistry and PhysicsCentre for Materials ScienceQueensland University of Technology (QUT)2 George StBrisbaneQLD4000Australia
- Institute of NanotechnologyKarlsruhe Institute of Technology (KIT)Hermann‐von‐Helmholtz‐Platz 176344Eggenstein‐LeopoldshafenGermany
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2
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Harisa GI, Faris TM, Sherif AY, Alzhrani RF, Alanazi SA, Kohaf NA, Alanazi FK. Coding Therapeutic Nucleic Acids from Recombinant Proteins to Next-Generation Vaccines: Current Uses, Limitations, and Future Horizons. Mol Biotechnol 2024; 66:1853-1871. [PMID: 37578574 DOI: 10.1007/s12033-023-00821-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023]
Abstract
This study aims to highlight the potential use of cTNAs in therapeutic applications. The COVID-19 pandemic has led to significant use of coding therapeutic nucleic acids (cTNAs) in terms of DNA and mRNA in the development of vaccines. The use of cTNAs resulted in a paradigm shift in the therapeutic field. However, the injection of DNA or mRNA into the human body transforms cells into biological factories to produce the necessary proteins. Despite the success of cTNAs in the production of corona vaccines, they have several limitations such as instability, inability to cross biomembranes, immunogenicity, and the possibility of integration into the human genome. The chemical modification and utilization of smart drug delivery cargoes resolve cTNAs therapeutic problems. The success of cTNAs in corona vaccine production provides perspective for the eradication of influenza viruses, Zika virus, HIV, respiratory syncytial virus, Ebola virus, malaria, and future pandemics by quick vaccine design. Moreover, the progress cTNAs technology is promising for the development of therapy for genetic disease, cancer therapy, and currently incurable diseases.
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Affiliation(s)
- Gamaleldin I Harisa
- Kayyali Chair for Pharmaceutical Industry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia.
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box: 2457, Riyadh, 11451, Saudi Arabia.
- Department of Biochemistry and Molecular Biology, College of Pharmacy, Al-Azhar University, Nasr City, Cairo, Egypt.
| | - Tarek M Faris
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Abdelrahman Y Sherif
- Kayyali Chair for Pharmaceutical Industry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box: 2457, Riyadh, 11451, Saudi Arabia
| | - Riyad F Alzhrani
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box: 2457, Riyadh, 11451, Saudi Arabia
- Nanobiotechnology Research Unit, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Alanazi
- Pharmaceutical Care Services, King Abdulaziz Medical City, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Science Collage of Pharmacy, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Neveen A Kohaf
- Department of Clinical Pharmacy, Faculty of Pharmacy, Al-Azhar University, Cairo, 11651, Egypt
| | - Fars K Alanazi
- Kayyali Chair for Pharmaceutical Industry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box: 2457, Riyadh, 11451, Saudi Arabia
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3
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Warminski M, Grab K, Szczepanski K, Spiewla T, Zuberek J, Kowalska J, Jemielity J. Photoactivatable mRNA 5' Cap Analogs for RNA-Protein Crosslinking. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400994. [PMID: 39049186 DOI: 10.1002/advs.202400994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 06/04/2024] [Indexed: 07/27/2024]
Abstract
Chemical modification of messenger RNA (mRNA) has paved the way for advancing mRNA-based therapeutics. The intricate process of mRNA translation in eukaryotes is orchestrated by numerous proteins involved in complex interaction networks. Many of them bind specifically to a unique structure at the mRNA 5'-end, called 5'-cap. Depending on the 5'-terminal sequence and its methylation pattern, different proteins may be involved in the translation initiation and regulation, but a deeper understanding of these mechanisms requires specialized molecular tools to identify natural binders of mRNA 5'-end variants. Here, a series of 8 new synthetic 5'-cap analogs that allow the preparation of RNA molecules with photoreactive tags using a standard in vitro transcription reaction are reported. Two photoreactive tags and four different modification sites are selected to minimize potential interference with cap-protein contacts and to provide complementary properties regarding crosslinking chemistry and molecular interactions. The tailored modification strategy allows for the generation of specific crosslinks with model cap-binding proteins, such as eIF4E and Dcp2. The usefulness of the photoreactive cap analogs is also demonstrated for identifying the cap-binding subunit in a multi-protein complex, which makes them perfect candidates for further development of photoaffinity labeling probes to study more complex mRNA-related processes.
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Affiliation(s)
- Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
| | - Katarzyna Grab
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
- Doctoral School of Exact and Natural Sciences, University of Warsaw, Zwirki i Wigury 93, Warsaw, 02-089, Poland
| | - Kacper Szczepanski
- Doctoral School of Exact and Natural Sciences, University of Warsaw, Zwirki i Wigury 93, Warsaw, 02-089, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, 02-097, Poland
| | - Tomasz Spiewla
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
- Doctoral School of Exact and Natural Sciences, University of Warsaw, Zwirki i Wigury 93, Warsaw, 02-089, Poland
| | - Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, 02-097, Poland
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Flemmich L, Bereiter R, Micura R. Chemical Synthesis of Modified RNA. Angew Chem Int Ed Engl 2024; 63:e202403063. [PMID: 38529723 DOI: 10.1002/anie.202403063] [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: 02/12/2024] [Revised: 03/16/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Ribonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner-both in vitro and in vivo-are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site-specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid-phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4-acetylcytidine, 5-hydroxymethylcytidine, 3-methylcytidine, 2'-OCF3, and 2'-N3 ribose modifications. We also discuss the all-chemical synthesis of 5'-capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single-molecule FRET studies. Finally, we highlight promising developments in RNA-catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.
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Affiliation(s)
- Laurin Flemmich
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
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5
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Zhao H, Yi D, Li L, Zhao Y, Li M. Modular Weaving DNAzyme in Skeleton of DNA Nanocages for Photoactivatable Catalytic Activity Regulation. Angew Chem Int Ed Engl 2024; 63:e202404064. [PMID: 38517264 DOI: 10.1002/anie.202404064] [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: 02/28/2024] [Indexed: 03/23/2024]
Abstract
DNAzymes exhibit tremendous application potentials in the field of biosensing and gene regulation due to its unique catalytic function. However, spatiotemporally controlled regulation of DNAzyme activity remains a daunting challenge, which may cause nonspecific signal leakage or gene silencing of the catalytic systems. Here, we report a photochemical approach via modular weaving active DNAzyme into the skeleton of tetrahedral DNA nanocages (TDN) for light-triggered on-demand liberation of DNAzyme and thus conditional control of gene regulation activity. We demonstrate that the direct encoding of DNAzyme in TDN could improve the biostability of DNAzyme and ensure the delivery efficiency, comparing with the conventional surface anchoring strategy. Furthermore, the molecular weaving of the DNA nanostructures allows remote control of DNAzyme-mediated gene regulation with high spatiotemporal precision of light. In addition, we demonstrate that the approach is applicable for controlled regulation of the gene editing functions of other functional nucleic acids.
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Affiliation(s)
- Hengzhi Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, 11 ZhongGuanCun BeiYiTiao, Beijing, 100190, China
| | - Deyu Yi
- School of Chemistry and Biological Engineering, Beijing Key Laboratory for Bioengineering and Sensing Technology, University of Science and Technology Beijing, 30 XueYuan Road, Beijing, 100083, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, 11 ZhongGuanCun BeiYiTiao, Beijing, 100190, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, 11 ZhongGuanCun BeiYiTiao, Beijing, 100190, China
| | - Mengyuan Li
- School of Chemistry and Biological Engineering, Beijing Key Laboratory for Bioengineering and Sensing Technology, University of Science and Technology Beijing, 30 XueYuan Road, Beijing, 100083, China
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6
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Bardhan A, Brown W, Albright S, Tsang M, Davidson LA, Deiters A. Direct Activation of Nucleobases with Small Molecules for the Conditional Control of Antisense Function. Angew Chem Int Ed Engl 2024; 63:e202318773. [PMID: 38411401 DOI: 10.1002/anie.202318773] [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: 12/06/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 02/28/2024]
Abstract
Conditionally controlled antisense oligonucleotides provide precise interrogation of gene function at different developmental stages in animal models. Only one example of small molecule-induced activation of antisense function exist. This has been restricted to cyclic caged morpholinos that, based on sequence, can have significant background activity in the absence of the trigger. Here, we provide a new approach using azido-caged nucleobases that are site-specifically introduced into antisense morpholinos. The caging group design is a simple azidomethylene (Azm) group that, despite its very small size, efficiently blocks Watson-Crick base pairing in a programmable fashion. Furthermore, it undergoes facile decaging via Staudinger reduction when exposed to a small molecule phosphine, generating the native antisense oligonucleotide under conditions compatible with biological environments. We demonstrated small molecule-induced gene knockdown in mammalian cells, zebrafish embryos, and frog embryos. We validated the general applicability of this approach by targeting three different genes.
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Affiliation(s)
- Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Wes Brown
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Savannah Albright
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Michael Tsang
- Department of Cell Biology, Center for Integrative Organ Systems., University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Lance A Davidson
- Department of Bioengineering, Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
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7
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Su K, Vázquez O. Enlightening epigenetics: optochemical tools illuminate the path. Trends Biochem Sci 2024; 49:290-304. [PMID: 38350805 DOI: 10.1016/j.tibs.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/20/2023] [Accepted: 01/10/2024] [Indexed: 02/15/2024]
Abstract
Optochemical tools have become potent instruments for understanding biological processes at the molecular level, and the past decade has witnessed their use in epigenetics and epitranscriptomics (also known as RNA epigenetics) for deciphering gene expression regulation. By using photoresponsive molecules such as photoswitches and photocages, researchers can achieve precise control over when and where specific events occur. Therefore, these are invaluable for studying both histone and nucleotide modifications and exploring disease-related mechanisms. We systematically report and assess current examples in the field, and identify open challenges and future directions. These outstanding proof-of-concept investigations will inspire other chemical biologists to participate in these emerging fields given the potential of photochromic molecules in research and biomedicine.
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Affiliation(s)
- Kaijun Su
- Department of Chemistry, University of Marburg, Marburg D-35043, Germany
| | - Olalla Vázquez
- Department of Chemistry, University of Marburg, Marburg D-35043, Germany; Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg D-35043, Germany.
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8
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Weissenboeck F, Klöcker N, Špaček P, Hüwel S, Rentmeister A. Stabilized 5' Cap Analogue for Optochemical Activation of mRNA Translation. ACS OMEGA 2024; 9:12810-12816. [PMID: 38524462 PMCID: PMC10955689 DOI: 10.1021/acsomega.3c08505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/02/2024] [Accepted: 01/19/2024] [Indexed: 03/26/2024]
Abstract
The 5' cap is a distinguishing feature of transcripts made by polymerase II and characterized by an N7-methylated guanosine (m7G) linked to the first transcribed nucleotide by a 5'-5' triphosphate bridge. It stabilizes eukaryotic mRNAs and plays a crucial role in translation initiation. Its importance in mRNA processing, translation, and turnover makes the 5' cap a privileged structure for engineering by non-natural modifications. A photocleavable group at the 5' cap of guanosine was recently used to mute translation of exogenous mRNAs. Its removal by light enabled direct control of protein production at the posttranscriptional level. Modifications in the triphosphate bridge impede degradation by specific decapping enzymes and maintain translation. Here, we combined 5' cap modifications at different positions and investigated how they impact 5' cap-dependent processes in distinct manners. We synthesized 5' cap analogues with a photocleavable group at the N2-position of m7G in addition to a medronate in the triphosphate bridge to obtain a photoactivatable 5' cap analogue featuring a methylene group between the β and γ phosphates. The resulting Medronate-FlashCap transiently or permanently impeded distinct crucial interactions of the 5' cap required for translation and degradation. We show that the Medronate-FlashCap is compatible with in vitro transcription to generate muted mRNA and that light can be used to activate translation in cells. After light-induced removal of the photocleavable group, the Medronate-FlashCap remained stable against degradation by the decapping enzyme DcpS. The additional methylene group renders the 5' cap resistant to DcpS, while maintaining the interaction with cap-binding proteins.
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Affiliation(s)
| | - Nils Klöcker
- Institute of Biochemistry, University of Münster, Münster 48149, Germany
| | - Petr Špaček
- Institute of Biochemistry, University of Münster, Münster 48149, Germany
| | - Sabine Hüwel
- Institute of Biochemistry, University of Münster, Münster 48149, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, University of Münster, Münster 48149, Germany
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9
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Bollu A, Schepers H, Klöcker N, Erguven M, Lawrence-Dörner AM, Rentmeister A. Visible Light Activates Coumarin-Caged mRNA for Cytoplasmic Cap Methylation in Cells. Chemistry 2024; 30:e202303174. [PMID: 37883670 DOI: 10.1002/chem.202303174] [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: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 10/28/2023]
Abstract
Protein synthesis is important and regulated by various mechanisms in the cell. Translation initiation in eukaryotes starts at the 5' cap and is the most complex of the three phases of mRNA translation. It requires methylation of the N7 position of the terminal guanosine (m7 G). The canonical capping occurs in the nucleus, however, cytoplasmic recapping has been discovered. It functions in switching mRNAs between translating and non-translating states, but the individual steps are difficult to dissect. We targeted cytoplasmic cap methylation as the ultimate step of cytoplasmic recapping. We present an N7G photocaged 5' cap that can be activated for cytoplasmic methylation by visible light. We report chemical and chemo-enzymatic synthesis of this 5' cap with 7-(diethylamino)-4-methyl-coumarin (DEACM) at the N7G and validate that it is not bound by translation initiation factor 4E (eIF4E). We demonstrate incorporation into mRNA, the release of unmethylated cap analog and enzymatic remethylation to functional cap 0 after irradiation at 450 nm. In cells, irradiation triggers translation of mRNAs with the N7G photocaged 5' cap via cytoplasmic cap methylation.
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Affiliation(s)
- Amarnath Bollu
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Helena Schepers
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Mehmet Erguven
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
- Cells in Motion Interfaculty Centre, University of Münster, Waldeyerstraße 15, 48149, Münster, Germany
| | - Ann-Marie Lawrence-Dörner
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
- Cells in Motion Interfaculty Centre, University of Münster, Waldeyerstraße 15, 48149, Münster, Germany
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10
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Perenkov AD, Sergeeva AD, Vedunova MV, Krysko DV. In Vitro Transcribed RNA-Based Platform Vaccines: Past, Present, and Future. Vaccines (Basel) 2023; 11:1600. [PMID: 37897003 PMCID: PMC10610676 DOI: 10.3390/vaccines11101600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
mRNA was discovered in 1961, but it was not used as a vaccine until after three decades. Recently, the development of mRNA vaccine technology gained great impetus from the pursuit of vaccines against COVID-19. To improve the properties of RNA vaccines, and primarily their circulation time, self-amplifying mRNA and trans-amplifying mRNA were developed. A separate branch of mRNA technology is circular RNA vaccines, which were developed with the discovery of the possibility of translation on their protein matrix. Circular RNA has several advantages over mRNA vaccines and is considered a fairly promising platform, as is trans-amplifying mRNA. This review presents an overview of the mRNA platform and a critical discussion of the more modern self-amplifying mRNA, trans-amplifying mRNA, and circular RNA platforms created on its basis. Finally, the main features, advantages, and disadvantages of each of the presented mRNA platforms are discussed. This discussion will facilitate the decision-making process in selecting the most appropriate platform for creating RNA vaccines against cancer or viral diseases.
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Affiliation(s)
- Alexey D Perenkov
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
| | - Alena D Sergeeva
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
| | - Maria V Vedunova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
| | - Dmitri V Krysko
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
- Cell Death Investigation and Therapy (CDIT) Laboratory, Anatomy and Embryology Unit, Department of Human Structure and Repair, Faculty of Medicine and Health Science, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent, 9000 Ghent, Belgium
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11
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Cornelissen NV, Mineikaitė R, Erguven M, Muthmann N, Peters A, Bartels A, Rentmeister A. Post-synthetic benzylation of the mRNA 5' cap via enzymatic cascade reactions. Chem Sci 2023; 14:10962-10970. [PMID: 37829022 PMCID: PMC10566477 DOI: 10.1039/d3sc03822j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 08/28/2023] [Indexed: 10/14/2023] Open
Abstract
mRNAs are emerging modalities for vaccination and protein replacement therapy. Increasing the amount of protein produced by stabilizing the transcript or enhancing translation without eliciting a strong immune response are major steps towards overcoming the present limitations and improving their therapeutic potential. The 5' cap is a hallmark of mRNAs and non-natural modifications can alter the properties of the entire transcript selectively. Here, we developed a versatile enzymatic cascade for regioselective benzylation of various biomolecules and applied it for post-synthetic modification of mRNA at the 5' cap to demonstrate its potential. Starting from six synthetic methionine analogues bearing (hetero-)benzyl groups, S-adenosyl-l-methionine analogues are formed and utilized for N7G-cap modification of mRNAs. This post-synthetic enzymatic modification exclusively modifies mRNAs at the terminal N7G, producing mRNAs with functional 5' caps. It avoids the wrong orientation of the 5' cap-a problem in common co-transcriptional capping. In the case of the 4-chlorobenzyl group, protein production was increased to 139% during in vitro translation and to 128-150% in four different cell lines. This 5' cap modification did not activate cytosolic pathogen recognition receptors TLR3, TLR7 or TLR8 significantly more than control mRNAs, underlining its potential to contribute to the development of future mRNA therapeutics.
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Affiliation(s)
- N V Cornelissen
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
| | - R Mineikaitė
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
| | - M Erguven
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
- University of Münster, Cells in Motion Interfaculty Centre Waldeyerstr. 15 48149 Münster Germany
| | - N Muthmann
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
| | - A Peters
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
| | - A Bartels
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
| | - A Rentmeister
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
- University of Münster, Cells in Motion Interfaculty Centre Waldeyerstr. 15 48149 Münster Germany
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12
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Gehringer M, Pape F, Méndez M, Barbie P, Unzue Lopez A, Lefranc J, Klingler FM, Hessler G, Langer T, Diamanti E, Schiedel M. Back in Person: Frontiers in Medicinal Chemistry 2023. ChemMedChem 2023; 18:e202300344. [PMID: 37485831 DOI: 10.1002/cmdc.202300344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/12/2023] [Indexed: 07/25/2023]
Abstract
The Frontiers in Medicinal Chemistry (FiMC) is the largest international Medicinal Chemistry conference in the German speaking area and took place from April 3rd to 5th 2023 in Vienna (Austria). Fortunately, after being cancelled in 2020 and two years (2021-2022) of entirely virtual meetings, due to the COVID-19 pandemic, the FiMC could be held in a face-to-face format again. Organized by the Division of Medicinal Chemistry of the German Chemical Society (GDCh), the Division of Pharmaceutical and Medicinal Chemistry of the German Pharmaceutical Society (DPhG), together with the Division of Medicinal Chemistry of the Austrian Chemical Society (GÖCH), the Austrian Pharmaceutical Society (ÖPhG), and a local organization committee from the University of Vienna headed by Thierry Langer, the meeting brought together 260 participants from 21 countries. The program included 38 lectures by leading scientists from industry and academia as well as early career investigators. Moreover, 102 posters were presented in two highly interactive poster sessions.
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Affiliation(s)
- Matthias Gehringer
- Institute of Pharmaceutical Sciences, Pharmaceutical/Medicinal Chemistry Department, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Felix Pape
- NUVISAN Innovation Campus Berlin, NUVISAN ICB GmbH, Muellerstraße 178, 13353, Berlin, Germany
| | - María Méndez
- Sanofi R&D, Integrated Drug Discovery, Industriepark Höchst, Bldg. G838, 65926, Frankfurt am Main, Germany
| | - Philipp Barbie
- Bayer AG, R&D, Pharmaceuticals, Laboratory IV, Bldg. S106, 231, 13342, Berlin, Germany
| | - Andrea Unzue Lopez
- Merck Healthcare KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | - Julien Lefranc
- Merck Healthcare KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | | | - Gerhard Hessler
- Sanofi R&D, Integrated Drug Discovery, Industriepark Höchst, Bldg. G877, 65926, Frankfurt am Main, Germany
| | - Thierry Langer
- Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria
| | - Eleonora Diamanti
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Matthias Schiedel
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstraße 55, 38106, Braunschweig, Germany
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13
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Lāce I, Bazzi S, Uranga J, Schirmacher A, Diederichsen U, Mata RA, Simeth NA. Modulating Secondary Structure Motifs Through Photo-Labile Peptide Staples. Chembiochem 2023; 24:e202300270. [PMID: 37216330 DOI: 10.1002/cbic.202300270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 05/24/2023]
Abstract
Peptide-protein interactions (PPIs) are facilitated by the well-defined three-dimensional structure of bioactive peptides, interesting compounds for the development of new therapeutic agents. Their secondary structure and thus their propensity to engage in PPIs can be influenced by the introduction of peptide staples on the side chains. In particular, light-controlled staples based on azobenzene photoswitches and their structural influence on helical peptides have been studied extensively. In contrast, photolabile staples bearing photocages as a structural key motif, have mainly been used to block supramolecular interactions. Their influence on the secondary structure of the target peptide is under-investigated. Thus, in this study we use a combination of spectroscopic techniques and in silico simulations to systematically study a series of helical peptides with varying length of the photo-labile staple to obtain a detailed insight into the structure-property relationship in such photoresponsive biomolecules.
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Affiliation(s)
- Ilze Lāce
- Institute for Organic and Biomolecular Chemistry, Department of Chemistry, University of Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
| | - Sophia Bazzi
- Institute for Physical Chemistry, Department of Chemistry, University of Göttingen, Tammannstr. 6, 37077, Göttingen, Germany
| | - Jon Uranga
- Institute for Physical Chemistry, Department of Chemistry, University of Göttingen, Tammannstr. 6, 37077, Göttingen, Germany
| | - Anastasiya Schirmacher
- Institute for Organic and Biomolecular Chemistry, Department of Chemistry, University of Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
| | - Ulf Diederichsen
- Institute for Organic and Biomolecular Chemistry, Department of Chemistry, University of Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
| | - Ricardo A Mata
- Institute for Physical Chemistry, Department of Chemistry, University of Göttingen, Tammannstr. 6, 37077, Göttingen, Germany
| | - Nadja A Simeth
- Institute for Organic and Biomolecular Chemistry, Department of Chemistry, University of Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Universitätsmedizin Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
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14
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Yu F, Li X, Zhao J, Zhao Y, Li L. Photoactivated DNA Assembly and Disassembly for On-Demand Activation and Termination of cGAS-STING Signaling. Angew Chem Int Ed Engl 2023; 62:e202305837. [PMID: 37365782 DOI: 10.1002/anie.202305837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/14/2023] [Accepted: 06/26/2023] [Indexed: 06/28/2023]
Abstract
Despite significant progress in DNA self-assembly for interfacing with biology, spatiotemporally controlled regulation of biological process via in situ dynamic DNA assembly remains an outstanding challenge. Here, we report an optically triggered DNA assembly and disassembly strategy that enables on-demand activation and termination of the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signaling pathway. In the design, an activatable DNA hairpin is engineered with a photocleavable group at defined site to modulate its self-assembly activity. Light activation induces the configurational switching and consequent self-assembly of the DNA hairpins to form long linear double-stranded structures, allowing to stimulate cGAS protein to synthesize 2',3'-cyclic-GMP-AMP (cGAMP) for STING stimulation. Furthermore, by endowing the pre-assembled DNA scaffold with a built-in photolysis feature, we demonstrate that the cGAS-STING stimulation can be efficiently terminated through remote photo-triggering, providing for the first time a route to control the temporal "dose" on-demand for such a stimulation. We envision that this regulation strategy will benefit and inspire both fundamental research and therapeutic applications regarding the cGAS-STING pathway.
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Affiliation(s)
- Fangzhi Yu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, 100190, Beijing, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiangfei Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, 100190, Beijing, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jian Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, 100190, Beijing, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, 100190, Beijing, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, 100190, Beijing, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, 100049, Beijing, China
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15
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Janosko C, Shade O, Courtney TM, Horst TJ, Liu M, Khare SD, Deiters A. Genetic Encoding of Arylazopyrazole Phenylalanine for Optical Control of Translation. ACS OMEGA 2023; 8:26590-26596. [PMID: 37521667 PMCID: PMC10373180 DOI: 10.1021/acsomega.3c03512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023]
Abstract
An arylazopyrazole was explored for its use as an enhanced photoswitchable amino acid in genetic code expansion. This new unnatural amino acid was successfully incorporated into proteins in both bacterial and mammalian cells. While photocontrol of translation required pulsed irradiations, complete selectivity for the trans-configuration by the pyrrolysyl tRNA synthetase was observed, demonstrating expression of a gene of interest selectively controlled via light exposure.
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Affiliation(s)
- Chasity
P. Janosko
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Olivia Shade
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Taylor M. Courtney
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Trevor J. Horst
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Melinda Liu
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Sagar D. Khare
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Alexander Deiters
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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16
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Inagaki M, Abe N, Li Z, Nakashima Y, Acharyya S, Ogawa K, Kawaguchi D, Hiraoka H, Banno A, Meng Z, Tada M, Ishida T, Lyu P, Kokubo K, Murase H, Hashiya F, Kimura Y, Uchida S, Abe H. Cap analogs with a hydrophobic photocleavable tag enable facile purification of fully capped mRNA with various cap structures. Nat Commun 2023; 14:2657. [PMID: 37169757 PMCID: PMC10175277 DOI: 10.1038/s41467-023-38244-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/21/2023] [Indexed: 05/13/2023] Open
Abstract
Starting with the clinical application of two vaccines in 2020, mRNA therapeutics are currently being investigated for a variety of applications. Removing immunogenic uncapped mRNA from transcribed mRNA is critical in mRNA research and clinical applications. Commonly used capping methods provide maximum capping efficiency of around 80-90% for widely used Cap-0- and Cap-1-type mRNAs. However, uncapped and capped mRNA possesses almost identical physicochemical properties, posing challenges to their physical separation. In this work, we develop hydrophobic photocaged tag-modified cap analogs, which separate capped mRNA from uncapped mRNA by reversed-phase high-performance liquid chromatography. Subsequent photo-irradiation recovers footprint-free native capped mRNA. This approach provides 100% capping efficiency even in Cap-2-type mRNA with versatility applicable to 650 nt and 4,247 nt mRNA. We find that the Cap-2-type mRNA shows up to 3- to 4-fold higher translation activity in cultured cells and animals than the Cap-1-type mRNA prepared by the standard capping method.
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Affiliation(s)
- Masahito Inagaki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Naoko Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Zhenmin Li
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Yuko Nakashima
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Susit Acharyya
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Kazuya Ogawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Daisuke Kawaguchi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Haruka Hiraoka
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Ayaka Banno
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Zheyu Meng
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Mizuki Tada
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Tatsuma Ishida
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Pingxue Lyu
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Kengo Kokubo
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Hirotaka Murase
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Yasuaki Kimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Satoshi Uchida
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.
- CREST, Japan Science and Technology Agency, 7, Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan.
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.
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17
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Kozarski M, Drazkowska K, Bednarczyk M, Warminski M, Jemielity J, Kowalska J. Towards superior mRNA caps accessible by click chemistry: synthesis and translational properties of triazole-bearing oligonucleotide cap analogs. RSC Adv 2023; 13:12809-12824. [PMID: 37114020 PMCID: PMC10126820 DOI: 10.1039/d3ra00026e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/01/2023] [Indexed: 04/29/2023] Open
Abstract
Messenger RNA (mRNA)-based gene delivery is a powerful strategy for the development of vaccines and therapeutics. Consequently, approaches that enable efficient synthesis of mRNAs with high purity and biological activity are in demand. Chemically modified 7-methylguanosine (m7G) 5' caps can augment the translational properties of mRNA; however, efficient synthesis of structurally complex caps, especially on a large scale, is challenging. Previously, we proposed a new strategy to assemble dinucleotide mRNA caps by replacing the traditional pyrophosphate bond formation by copper-catalyzed azide-alkyne cycloaddition (CuAAC). Here, we used CuAAC to synthesize 12 novel triazole-containing tri- and tetranucleotide cap analogs with the aim of exploring the chemical space around the first transcribed nucleotide in mRNA and overcoming some of the limitations previously reported for the triazole-containing dinucleotide analogs. We evaluated the efficiency of incorporation into RNA for these analogs and their influence on the translational properties of in vitro transcribed (IVT) mRNAs in rabbit reticulocyte lysate and JAWS II cultured cells. The incorporation of the triazole moiety within the 5',5'-oligophosphate of trinucleotide cap produced compounds that were well incorporated into RNA by T7 polymerase while replacing the 5',3'-phosphodiester bond with triazole impaired incorporation and translation efficiency, despite a neutral effect on the interaction with the translation initiation factor eIF4E. One of the compounds (m7Gppp-tr-C2H4pAmpG), had translational activity and other biochemical properties comparable to natural cap 1 structure, thus being a promising mRNA capping reagent for potential in cellulo and in vivo applications in the field of mRNA-based therapeutics.
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Affiliation(s)
- Mateusz Kozarski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw Pasteura 5 02-093 Warsaw Poland
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Karolina Drazkowska
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Marcelina Bednarczyk
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw Pasteura 5 02-093 Warsaw Poland
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Marcin Warminski
- 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
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw Pasteura 5 02-093 Warsaw Poland
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18
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Liu Y, Shi Y, Yu L, Wu Z, Jiang JH. Reversible Acylation of RNA Enables Activatable Biosensing. Anal Chem 2023; 95:6490-6495. [PMID: 37053522 DOI: 10.1021/acs.analchem.3c00723] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
There is a high demand to develop chemical tools to control the property and function of RNA. Current methods mainly rely on ultraviolet light-based caging strategies, which may cause phototoxicity in live cell-based experiments. We herein report an endogenous stimulus-responsive RNA acylation approach by introducing boronate ester (BE) groups to 2'-hydroxyls through postsynthetic modification. Treatment with hydrogen peroxide (H2O2) yields a phenol derivative which undergoes a 1,6-eliminaton for the traceless release of 2'-hydroxyl. We demonstrated that the acylation of crRNA enabled conditional regulation of CRISPR/Cas13a activity for activatable detection of target RNA. We also showed that the highly specific acylation of the single RNA in 8-17 DNAzyme allowed reversible control of the catalytic activity of DNAzyme, which was further applied to the cell-selective imaging of metal ions in cancer cells. Thus, our strategy provides a simple, general, and cell-selective method to control RNA activity, affording great potential in the construction of activatable RNA sensors and pre-RNA medicines.
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Affiliation(s)
- Yining Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yang Shi
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lanxing Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Zhenkun Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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19
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Bollu A, Klöcker N, Špaček P, P Weissenboeck F, Hüwel S, Rentmeister A. Light-Activated Translation of Different mRNAs in Cells via Wavelength-Dependent Photouncaging. Angew Chem Int Ed Engl 2023; 62:e202209975. [PMID: 36417319 PMCID: PMC10107135 DOI: 10.1002/anie.202209975] [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: 07/07/2022] [Revised: 11/20/2022] [Accepted: 11/23/2022] [Indexed: 11/24/2022]
Abstract
The 5' cap is a hallmark of eukaryotic mRNA involved in the initiation of translation. Its modification with a single photo-cleavable group can bring translation of mRNA under the control of light. However, UV irradiation causes cell stress and downregulation of translation. Furthermore, complex processes often involve timed expression of more than one gene. The approach would thus greatly benefit from the ability to photo-cleave by blue light and to control more than one mRNA at a time. We report the synthesis of a 5' cap modified with a 7-(diethylamino)coumarin (CouCap) and adapted conditions for in vitro transcription. Translation of the resulting CouCap-mRNA is muted in vitro and in mammalian cells, and can be initiated by irradiation with 450 nm. The native cap is restored and no non-natural residues nor sequence alterations remain in the mRNA. Multiplexing for two different mRNAs was achieved by combining cap analogs with coumarin- and ortho-nitrobenzyl-based photo-cleavable groups.
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Affiliation(s)
- Amarnath Bollu
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Petr Špaček
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Florian P Weissenboeck
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Sabine Hüwel
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
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20
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Klöcker N, Anhäuser L, Rentmeister A. Enzymatic Modification of the 5' Cap with Photocleavable ONB-Derivatives Using GlaTgs V34A. Chembiochem 2023; 24:e202200522. [PMID: 36408753 PMCID: PMC10108117 DOI: 10.1002/cbic.202200522] [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: 09/09/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/22/2022]
Abstract
The 5' cap of mRNA plays a critical role in mRNA processing, quality control and turnover. Enzymatic availability of the 5' cap governs translation and could be a tool to investigate cell fate decisions and protein functions or develop protein replacement therapies. We have previously reported on the chemical synthesis of 5' cap analogues with photocleavable groups for this purpose. However, the synthesis is complex and post-synthetic enzymatic installation may make the technique more applicable to biological researchers. Common 5' cap analogues, like the cap 0, are commercially available and routinely used for in vitro transcription. Here, we report a facile enzymatic approach to attach photocleavable groups site-specifically to the N2 position of m7 G of the 5' cap. By expanding the substrate scope of the methyltransferase variant GlaTgs V34A and using synthetic co-substrate analogues, we could enzymatically photocage the 5' cap and recover it after irradiation.
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Affiliation(s)
- Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, Münster, Germany
| | - Lea Anhäuser
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, Münster, Germany
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21
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Dittmar M, Weissenböck FP, Rentmeister A. Lichtgesteuerte Translation von mRNA in Eukaryoten. BIOSPEKTRUM : ZEITSCHRIFT DER GESELLSCHAFT FUR BIOLOGISHE CHEMIE (GBCH) UND DER VEREINIGUNG FUR ALLGEMEINE UND ANGEWANDTE MIKROBIOLOGIE (VAAM) 2023; 29:31-34. [PMID: 36845577 PMCID: PMC9942070 DOI: 10.1007/s12268-023-1881-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Messenger RNA (mRNA) shows great potential for medical applications, as recently demonstrated by the mRNA-based vaccines against the coronavirus. In addition, it has long been used for ectopic gene expression in cells and model organisms. While numerous methodologies are available for controlling gene expression at the level of transcription, approaches to control translation are scarce. Here we review strategies for direct light-mediated activation of mRNA translation via photocleavable groups and their potential to achieve spatial and temporal control of protein production.
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Affiliation(s)
- Maria Dittmar
- Institut für Biochemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, D-48149 Münster, Deutschland
| | - Florian Peter Weissenböck
- Institut für Biochemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, D-48149 Münster, Deutschland
| | - Andrea Rentmeister
- Institut für Biochemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, D-48149 Münster, Deutschland
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22
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Xiong H, Xu Y, Kim B, Rha H, Zhang B, Li M, Yang GF, Kim JS. Photo-controllable biochemistry: Exploiting the photocages in phototherapeutic window. Chem 2022. [DOI: 10.1016/j.chempr.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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Feng Z, Ducos B, Scerbo P, Aujard I, Jullien L, Bensimon D. The Development and Application of Opto-Chemical Tools in the Zebrafish. Molecules 2022; 27:molecules27196231. [PMID: 36234767 PMCID: PMC9572478 DOI: 10.3390/molecules27196231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
The zebrafish is one of the most widely adopted animal models in both basic and translational research. This popularity of the zebrafish results from several advantages such as a high degree of similarity to the human genome, the ease of genetic and chemical perturbations, external fertilization with high fecundity, transparent and fast-developing embryos, and relatively low cost-effective maintenance. In particular, body translucency is a unique feature of zebrafish that is not adequately obtained with other vertebrate organisms. The animal’s distinctive optical clarity and small size therefore make it a successful model for optical modulation and observation. Furthermore, the convenience of microinjection and high embryonic permeability readily allow for efficient delivery of large and small molecules into live animals. Finally, the numerous number of siblings obtained from a single pair of animals offers large replicates and improved statistical analysis of the results. In this review, we describe the development of opto-chemical tools based on various strategies that control biological activities with unprecedented spatiotemporal resolution. We also discuss the reported applications of these tools in zebrafish and highlight the current challenges and future possibilities of opto-chemical approaches, particularly at the single cell level.
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Affiliation(s)
- Zhiping Feng
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
- Correspondence: (Z.F.); (D.B.)
| | - Bertrand Ducos
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- High Throughput qPCR Core Facility, Ecole Normale Supérieure, Paris Sciences Letters University, 46 Rue d’Ulm, 75005 Paris, France
| | - Pierluigi Scerbo
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Inovarion, 75005 Paris, France
| | - Isabelle Aujard
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - Ludovic Jullien
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - David Bensimon
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Correspondence: (Z.F.); (D.B.)
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Flamme M, Katkevica D, Pajuste K, Katkevics M, Sabat N, Hanlon S, Marzuoli I, Püntener K, Sladojevich F, Hollenstein M. Benzoyl and pivaloyl as efficient protecting groups for controlled enzymatic synthesis of DNA and XNA oligonucleotides. ASIAN J ORG CHEM 2022. [DOI: 10.1002/ajoc.202200384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marie Flamme
- Institut Pasteur Structrual Biology and Chemistry FRANCE
| | - Dace Katkevica
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Chemistry LATVIA
| | - Karlis Pajuste
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Chemistry LATVIA
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Chemistry LATVIA
| | - Nazarii Sabat
- Institut Pasteur Structural Biology and Chemistry FRANCE
| | - Steven Hanlon
- Hoffmann-La Roche Ltd Synthetic Molecules Technical Development SWITZERLAND
| | - Irene Marzuoli
- Hoffmann-La Roche Ltd Synthetic Molecules Technical Development SWITZERLAND
| | - Kurt Püntener
- Hoffmann-La Roche Ltd Synthetic Molecules Technical Development SWITZERLAND
| | | | - Marcel Hollenstein
- Institut Pasteur Department of Structural Biology and Chemistry 28 Rue du Dr. Roux 75015 Paris FRANCE
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