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Zellmann F, Schmauk N, Murmann N, Böhm M, Schwenger A, Göbel MW. Quality Control of mRNA Vaccines by Synthetic Ribonucleases: Analysis of the Poly-A-Tail. Chembiochem 2024; 25:e202400347. [PMID: 38742914 DOI: 10.1002/cbic.202400347] [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: 04/17/2024] [Accepted: 05/14/2024] [Indexed: 05/16/2024]
Abstract
The effectivity and safety of mRNA vaccines critically depends on the presence of correct 5' caps and poly-A tails. Due to the high molecular mass of full-size mRNAs, however, the direct analysis by mass spectrometry is hardly possible. Here we describe the use of synthetic ribonucleases to cleave off 5' and 3' terminal fragments which can be further analyzed by HPLC or by LC-MS. Compared to existing methods (e. g. RNase H), the new approach uses robust catalysts, is free of sequence limitations, avoids metal ions and combines fast sample preparation with high precision of the cut.
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Affiliation(s)
- Felix Zellmann
- Analytical Development CureVac SE, Friedrich-Miescher-Str. 15, 72076, Tübingen, Germany
| | - Nina Schmauk
- Analytical Development CureVac SE, Friedrich-Miescher-Str. 15, 72076, Tübingen, Germany
| | - Nina Murmann
- Institut für Organische Chemie und Chemische Biologie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Madeleine Böhm
- Analytical Development CureVac SE, Friedrich-Miescher-Str. 15, 72076, Tübingen, Germany
| | - Alexander Schwenger
- Analytical Development CureVac SE, Friedrich-Miescher-Str. 15, 72076, Tübingen, Germany
| | - Michael W Göbel
- Institut für Organische Chemie und Chemische Biologie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
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Halloy F, Biscans A, Bujold KE, Debacker A, Hill AC, Lacroix A, Luige O, Strömberg R, Sundstrom L, Vogel J, Ghidini A. Innovative developments and emerging technologies in RNA therapeutics. RNA Biol 2022; 19:313-332. [PMID: 35188077 PMCID: PMC8865321 DOI: 10.1080/15476286.2022.2027150] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNA-based therapeutics are emerging as a powerful platform for the treatment of multiple diseases. Currently, the two main categories of nucleic acid therapeutics, antisense oligonucleotides and small interfering RNAs (siRNAs), achieve their therapeutic effect through either gene silencing, splicing modulation or microRNA binding, giving rise to versatile options to target pathogenic gene expression patterns. Moreover, ongoing research seeks to expand the scope of RNA-based drugs to include more complex nucleic acid templates, such as messenger RNA, as exemplified by the first approved mRNA-based vaccine in 2020. The increasing number of approved sequences and ongoing clinical trials has attracted considerable interest in the chemical development of oligonucleotides and nucleic acids as drugs, especially since the FDA approval of the first siRNA drug in 2018. As a result, a variety of innovative approaches is emerging, highlighting the potential of RNA as one of the most prominent therapeutic tools in the drug design and development pipeline. This review seeks to provide a comprehensive summary of current efforts in academia and industry aimed at fully realizing the potential of RNA-based therapeutics. Towards this, we introduce established and emerging RNA-based technologies, with a focus on their potential as biosensors and therapeutics. We then describe their mechanisms of action and their application in different disease contexts, along with the strengths and limitations of each strategy. Since the nucleic acid toolbox is rapidly expanding, we also introduce RNA minimal architectures, RNA/protein cleavers and viral RNA as promising modalities for new therapeutics and discuss future directions for the field.
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Affiliation(s)
- François Halloy
- Department of Paediatrics, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Annabelle Biscans
- Oligonucleotide Chemistry, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Katherine E. Bujold
- Department of Chemistry & Chemical Biology, McMaster University, (Ontario), Canada
| | | | - Alyssa C. Hill
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eth Zürich, Zürich, Switzerland
| | - Aurélie Lacroix
- Sixfold Bioscience, Translation & Innovation Hub, London, UK
| | - Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Linda Sundstrom
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (Hiri), Helmholtz Center for Infection Research (Hzi), Würzburg, Germany
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Alice Ghidini
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
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Luige O, Karalė K, Bose PP, Bollmark M, Tedebark U, Murtola M, Strömberg R. Influence of sequence variation on the RNA cleavage activity of Zn 2+-dimethyl-dppz-PNA-based artificial enzymes. RSC Adv 2022; 12:5398-5406. [PMID: 35425588 PMCID: PMC8981518 DOI: 10.1039/d1ra08319h] [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: 11/12/2021] [Accepted: 01/30/2022] [Indexed: 11/21/2022] Open
Abstract
The development of Zn2+-dependent dimethyl-dppz-PNA conjugates (PNAzymes) as efficient site-specific artificial ribonucleases enables rapid sequence-specific degradation of clinically relevant RNA target sequences, but the significance of the RNA/PNAzyme sequence and structural demands for the identification of novel RNA targets are not fully understood. In the present study, we investigated the influence of sequence variation in the recognition arms of the RNA/PNAzyme complex on the RNA cleavage activity of the artificial enzymes. The base pairs closing the 3-nucleotide bulge region on both sides of the bulge as well as the neighbouring nucleobases were shown to significantly influence the RNA cleavage activity. Elongation of the RNA/PNAzyme complex was shown to be tolerated, although potentially prohibitive for catalytic turnover. The specificity of PNAzyme action was clearly demonstrated by the significantly reduced or absent cleavage activity in complexes containing mismatches. Further investigation into 2- and 4-nucleotide RNA bulges indicated that formation of 3-nucleotide bulges in the target RNA gives the optimal cleavage rates, while some potential off-target cleavage of formed 4-nucleotide bulges of select sequences should be considered.
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Affiliation(s)
- Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet Neo, 141 83 Huddinge Sweden
| | - Kristina Karalė
- Department of Biosciences and Nutrition, Karolinska Institutet Neo, 141 83 Huddinge Sweden
- RISE, Department of Chemical Process and Pharmaceutical Development Forskargatan 18 15136 Södertälje Sweden
| | - Partha Pratim Bose
- Department of Biosciences and Nutrition, Karolinska Institutet Neo, 141 83 Huddinge Sweden
| | - Martin Bollmark
- RISE, Department of Chemical Process and Pharmaceutical Development Forskargatan 18 15136 Södertälje Sweden
| | - Ulf Tedebark
- RISE, Department of Chemical Process and Pharmaceutical Development Forskargatan 18 15136 Södertälje Sweden
| | - Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet Neo, 141 83 Huddinge Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet Neo, 141 83 Huddinge Sweden
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Luige O, Bose PP, Stulz R, Steunenberg P, Brun O, Andersson S, Murtola M, Strömberg R. Zn 2+-Dependent peptide nucleic acid-based artificial ribonucleases with unprecedented efficiency and specificity. Chem Commun (Camb) 2021; 57:10911-10914. [PMID: 34590632 DOI: 10.1039/d1cc04383h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present Zn2+-dependent dimethyl-dipyridophenazine PNA conjugates as efficient RNA cleaving artificial enzymes. These PNAzymes display site-specific RNA cleavage with 10 minute half-lives and cleave clinically relevant RNA models.
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Affiliation(s)
- Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
| | - Partha Pratim Bose
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
| | - Rouven Stulz
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden. .,Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.,DMPK, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Peter Steunenberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
| | - Omar Brun
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
| | - Shalini Andersson
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
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Danneberg F, Westemeier H, Horx P, Zellmann F, Dörr K, Kalden E, Zeiger M, Akpinar A, Berger R, Göbel MW. RNA Hydrolysis by Heterocyclic Amidines and Guanidines: Parameters Affecting Reactivity. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Friederike Danneberg
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Hauke Westemeier
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Germany
| | - Philip Horx
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Germany
| | - Felix Zellmann
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Kathrin Dörr
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Elisabeth Kalden
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Mirco Zeiger
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Abdullah Akpinar
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Robert Berger
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Germany
| | - Michael W. Göbel
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
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Site-Selective Artificial Ribonucleases: Renaissance of Oligonucleotide Conjugates for Irreversible Cleavage of RNA Sequences. Molecules 2021; 26:molecules26061732. [PMID: 33808835 PMCID: PMC8003597 DOI: 10.3390/molecules26061732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022] Open
Abstract
RNA-targeting therapeutics require highly efficient sequence-specific devices capable of RNA irreversible degradation in vivo. The most developed methods of sequence-specific RNA cleavage, such as siRNA or antisense oligonucleotides (ASO), are currently based on recruitment of either intracellular multi-protein complexes or enzymes, leaving alternative approaches (e.g., ribozymes and DNAzymes) far behind. Recently, site-selective artificial ribonucleases combining the oligonucleotide recognition motifs (or their structural analogues) and catalytically active groups in a single molecular scaffold have been proven to be a great competitor to siRNA and ASO. Using the most efficient catalytic groups, utilising both metal ion-dependent (Cu(II)-2,9-dimethylphenanthroline) and metal ion-free (Tris(2-aminobenzimidazole)) on the one hand and PNA as an RNA recognising oligonucleotide on the other, allowed site-selective artificial RNases to be created with half-lives of 0.5-1 h. Artificial RNases based on the catalytic peptide [(ArgLeu)2Gly]2 were able to take progress a step further by demonstrating an ability to cleave miRNA-21 in tumour cells and provide a significant reduction of tumour growth in mice.
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